diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..2d87f8c --- /dev/null +++ b/.gitignore @@ -0,0 +1,164 @@ +.vscode/ + +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +share/python-wheels/ +*.egg-info/ +.installed.cfg +*.egg +MANIFEST + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.nox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*.cover +*.py,cover +.hypothesis/ +.pytest_cache/ +cover/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py +db.sqlite3 +db.sqlite3-journal + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +.pybuilder/ +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# IPython +profile_default/ +ipython_config.py + +# pyenv +# For a library or package, you might want to ignore these files since the code is +# intended to run in multiple environments; otherwise, check them in: +# .python-version + +# pipenv +# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. +# However, in case of collaboration, if having platform-specific dependencies or dependencies +# having no cross-platform support, pipenv may install dependencies that don't work, or not +# install all needed dependencies. +#Pipfile.lock + +# poetry +# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control. +# This is especially recommended for binary packages to ensure reproducibility, and is more +# commonly ignored for libraries. +# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control +#poetry.lock + +# pdm +# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control. +#pdm.lock +# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it +# in version control. +# https://pdm.fming.dev/#use-with-ide +.pdm.toml + +# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm +__pypackages__/ + +# Celery stuff +celerybeat-schedule +celerybeat.pid + +# SageMath parsed files +*.sage.py + +# Environments +.env +.venv +env/ +venv/ +ENV/ +env.bak/ +venv.bak/ + +# Spyder project settings +.spyderproject +.spyproject + +# Rope project settings +.ropeproject + +# mkdocs documentation +/site + +# mypy +.mypy_cache/ +.dmypy.json +dmypy.json + +# Pyre type checker +.pyre/ + +# pytype static type analyzer +.pytype/ + +# Cython debug symbols +cython_debug/ + +# PyCharm +# JetBrains specific template is maintained in a separate JetBrains.gitignore that can +# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore +# and can be added to the global gitignore or merged into this file. For a more nuclear +# option (not recommended) you can uncomment the following to ignore the entire idea folder. +#.idea/ + +nb/ diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000..0e5ae1d --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,21 @@ +repos: + - repo: https://github.com/pre-commit/pre-commit-hooks + rev: v4.4.0 + hooks: + - id: check-yaml + args: ["--unsafe"] + - id: end-of-file-fixer + - id: trailing-whitespace + exclude: docs/img/ + - repo: https://github.com/psf/black + rev: 23.3.0 + hooks: + - id: black + args: ["-l", "120"] + exclude: quantdb/ingest.py + - repo: https://github.com/PyCQA/isort + rev: 5.12.0 + hooks: + - id: isort + name: isort (python) + args: ["-m", "3", "--tc"] diff --git a/README.md b/README.md new file mode 100644 index 0000000..0824a0a --- /dev/null +++ b/README.md @@ -0,0 +1,18 @@ +## Configuration Files + +Email tom.h.gillespie@gmail.com for the configuration files to be stored in the following locations: + + - .pgpass # database passwords + - config.yaml # database metadata + +### Linux & MacOS .pgpass location + +`~/.pgpass` + +### Linux config.yaml location + +`~/.config/quantdb/config.yaml` + +### MacOS config.yaml location + +`~/Library/Application\ Support/quantdb/config.yaml` diff --git a/README.pdf b/README.pdf new file mode 100644 index 0000000..3c1924b Binary files /dev/null and b/README.pdf differ diff --git a/data-curation/CadaverVNMorphology_OutputMetrics.ipynb b/data-curation/CadaverVNMorphology_OutputMetrics.ipynb new file mode 100644 index 0000000..a6227bb --- /dev/null +++ b/data-curation/CadaverVNMorphology_OutputMetrics.ipynb @@ -0,0 +1,518 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 25, + "metadata": {}, + "outputs": [], + "source": [ + "from typing import Any\n", + "\n", + "import scipy.io\n", + "import pandas as pd\n", + "import numpy\n", + "\n", + "\n", + "def explode_single_element_lists(\n", + " data: list[Any] | numpy.ndarray[Any, Any]\n", + ") -> list[Any] | Any:\n", + " \"\"\"Explode lists from data only if they contain a single element.\n", + "\n", + " Parameters\n", + " ----------\n", + " data : list | numpy.ndarray\n", + " list or numpy array; can be fed to pandas DataFrame.map\n", + "\n", + " Returns\n", + " -------\n", + " list | Any\n", + " list of multiple elements or single element\n", + " \"\"\"\n", + " if isinstance(data, numpy.ndarray):\n", + " data = data.tolist()\n", + " if isinstance(data, list) and len(data) == 1:\n", + " data = data[0]\n", + " if isinstance(data, list) and len(data) == 1:\n", + " data = explode_single_element_lists(data)\n", + " return data\n", + "\n", + "\n", + "mat_file_path = \"../data/CadaverVNMorphology_OutputMetrics.mat\"\n", + "data_c = scipy.io.loadmat(mat_file_path)\n", + "\n", + "\n", + "dfs: list[pd.DataFrame] = []\n", + "for key in data_c.keys():\n", + " if \"__\" in key:\n", + " continue\n", + " data = data_c[key]\n", + " df = pd.DataFrame(data).map(explode_single_element_lists)\n", + " df.index = [key] # type: ignore\n", + " dfs.append(df)\n", + "\n", + "df = pd.concat(dfs)\n", + "df.index.name = \"\"\n", + "df.to_csv(\"../data/CadaverVNMorphology_OutputMetrics.csv\", index=True)" + ] + }, + { + "cell_type": "code", + "execution_count": 27, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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"size": 324421154, "fileExtension": "jpx"}]}} diff --git a/ingest-tab-from-file_v2.ipynb b/ingest-tab-from-file_v2.ipynb new file mode 100644 index 0000000..d480366 --- /dev/null +++ b/ingest-tab-from-file_v2.ipynb @@ -0,0 +1,1050 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [], + "source": [ + "# compenency query is for fasc diam, nerv diam, and lateriality" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "RelationshipDirection.MANYTOONE\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "/Users/tmsincomb/Dropbox (Personal)/repos/quantitative-db/quantdb/ingest_tabular/models.py:1487: SAWarning: relationship 'ObjDescCat.values_cat' will copy column obj_desc_cat.desc_cat to column values_cat.desc_cat, which conflicts with relationship(s): 'DescriptorsCat.values_cat' (copies descriptors_cat.id to values_cat.desc_cat). If this is not the intention, consider if these relationships should be linked with back_populates, or if viewonly=True should be applied to one or more if they are read-only. For the less common case that foreign key constraints are partially overlapping, the orm.foreign() annotation can be used to isolate the columns that should be written towards. To silence this warning, add the parameter 'overlaps=\"values_cat\"' to the 'ObjDescCat.values_cat' relationship. (Background on this warning at: https://sqlalche.me/e/20/qzyx) (This warning originated from the `configure_mappers()` process, which was invoked automatically in response to a user-initiated operation.)\n", + " for relationship_prop in cls.__mapper__.relationships:\n", + "/Users/tmsincomb/Dropbox (Personal)/repos/quantitative-db/quantdb/ingest_tabular/models.py:1487: SAWarning: relationship 'ValuesCat.descriptors_cat' will copy column descriptors_cat.id to column values_cat.desc_cat, which conflicts with relationship(s): 'ObjDescCat.values_cat' (copies obj_desc_cat.desc_cat to values_cat.desc_cat). If this is not the intention, consider if these relationships should be linked with back_populates, or if viewonly=True should be applied to one or more if they are read-only. For the less common case that foreign key constraints are partially overlapping, the orm.foreign() annotation can be used to isolate the columns that should be written towards. To silence this warning, add the parameter 'overlaps=\"values_cat\"' to the 'ValuesCat.descriptors_cat' relationship. (Background on this warning at: https://sqlalche.me/e/20/qzyx) (This warning originated from the `configure_mappers()` process, which was invoked automatically in response to a user-initiated operation.)\n", + " for relationship_prop in cls.__mapper__.relationships:\n", + "/Users/tmsincomb/Dropbox (Personal)/repos/quantitative-db/quantdb/ingest_tabular/models.py:1487: SAWarning: relationship 'ValuesCat.obj_desc_cat' will copy column obj_desc_cat.desc_cat to column values_cat.desc_cat, which conflicts with relationship(s): 'DescriptorsCat.values_cat' (copies descriptors_cat.id to values_cat.desc_cat), 'ValuesCat.descriptors_cat' (copies descriptors_cat.id to values_cat.desc_cat). If this is not the intention, consider if these relationships should be linked with back_populates, or if viewonly=True should be applied to one or more if they are read-only. For the less common case that foreign key constraints are partially overlapping, the orm.foreign() annotation can be used to isolate the columns that should be written towards. To silence this warning, add the parameter 'overlaps=\"descriptors_cat,values_cat\"' to the 'ValuesCat.obj_desc_cat' relationship. (Background on this warning at: https://sqlalche.me/e/20/qzyx) (This warning originated from the `configure_mappers()` process, which was invoked automatically in response to a user-initiated operation.)\n", + " for relationship_prop in cls.__mapper__.relationships:\n", + "/Users/tmsincomb/Dropbox (Personal)/repos/quantitative-db/quantdb/ingest_tabular/models.py:1487: SAWarning: relationship 'ValuesCat.obj_desc_inst' will copy column obj_desc_inst.object to column values_cat.object, which conflicts with relationship(s): 'ObjDescCat.values_cat' (copies obj_desc_cat.object to values_cat.object), 'ValuesCat.obj_desc_cat' (copies obj_desc_cat.object to values_cat.object). If this is not the intention, consider if these relationships should be linked with back_populates, or if viewonly=True should be applied to one or more if they are read-only. For the less common case that foreign key constraints are partially overlapping, the orm.foreign() annotation can be used to isolate the columns that should be written towards. To silence this warning, add the parameter 'overlaps=\"obj_desc_cat,values_cat\"' to the 'ValuesCat.obj_desc_inst' relationship. (Background on this warning at: https://sqlalche.me/e/20/qzyx) (This warning originated from the `configure_mappers()` process, which was invoked automatically in response to a user-initiated operation.)\n", + " for relationship_prop in cls.__mapper__.relationships:\n", + "/Users/tmsincomb/Dropbox (Personal)/repos/quantitative-db/quantdb/ingest_tabular/models.py:1487: SAWarning: relationship 'ValuesCat.obj_desc_inst' will copy column obj_desc_inst.desc_inst to column values_cat.desc_inst, which conflicts with relationship(s): 'ValuesCat.descriptors_inst' (copies descriptors_inst.id to values_cat.desc_inst). If this is not the intention, consider if these relationships should be linked with back_populates, or if viewonly=True should be applied to one or more if they are read-only. For the less common case that foreign key constraints are partially overlapping, the orm.foreign() annotation can be used to isolate the columns that should be written towards. To silence this warning, add the parameter 'overlaps=\"descriptors_inst\"' to the 'ValuesCat.obj_desc_inst' relationship. (Background on this warning at: https://sqlalche.me/e/20/qzyx) (This warning originated from the `configure_mappers()` process, which was invoked automatically in response to a user-initiated operation.)\n", + " for relationship_prop in cls.__mapper__.relationships:\n", + "/Users/tmsincomb/Dropbox (Personal)/repos/quantitative-db/quantdb/ingest_tabular/models.py:1487: SAWarning: relationship 'ValuesCat.objects' will copy column objects.id to column values_cat.object, which conflicts with relationship(s): 'ObjDescCat.values_cat' (copies obj_desc_cat.object to values_cat.object), 'ValuesCat.obj_desc_cat' (copies obj_desc_cat.object to values_cat.object), 'ValuesCat.obj_desc_inst' (copies obj_desc_inst.object to values_cat.object). If this is not the intention, consider if these relationships should be linked with back_populates, or if viewonly=True should be applied to one or more if they are read-only. For the less common case that foreign key constraints are partially overlapping, the orm.foreign() annotation can be used to isolate the columns that should be written towards. To silence this warning, add the parameter 'overlaps=\"obj_desc_cat,obj_desc_inst,values_cat\"' to the 'ValuesCat.objects' relationship. (Background on this warning at: https://sqlalche.me/e/20/qzyx) (This warning originated from the `configure_mappers()` process, which was invoked automatically in response to a user-initiated operation.)\n", + " for relationship_prop in cls.__mapper__.relationships:\n" + ] + }, + { + "data": { + "text/plain": [ + "" + ] + }, + "execution_count": 2, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "import pandas as pdfdsadaasdfd\n", + "import uuid\n", + "\n", + "from sqlalchemy import inspect\n", + "from sqlalchemy.orm import Session\n", + "from sqlalchemy.inspection import inspect\n", + "from sqlalchemy.exc import IntegrityError\n", + "\n", + "from quantdb.ingest import Queries, InternalIds\n", + "from quantdb.client import get_session\n", + "from sqlalchemy.sql.elements import ClauseElement\n", + "from quantdb.ingest_tabular.models import (\n", + " # Ingest,\n", + " # Unit,\n", + " Objects,\n", + " Units,\n", + " Addresses,\n", + " Aspects,\n", + " DescriptorsInst,\n", + " DescriptorsQuant,\n", + " ObjDescInst,\n", + " ObjDescQuant,\n", + " ValuesInst,\n", + " ValuesQuant,\n", + ")\n", + "\n", + "session = get_session(echo=False)\n", + "\n", + "object_ = Objects(\n", + " id=\"55c5b69c-test-4881-a105-e4048af26fa5\",\n", + " id_type=\"dataset\",\n", + " id_file=None,\n", + " id_internal=None,\n", + ")\n", + "\n", + "# ingest = Ingest(session=session)\n", + "unit = Units(\n", + " label=\"test\",\n", + " iri=\"https://uri.interlex.org/tgbugs/uris/readable/quantdb/units/test\",\n", + ")\n", + "\n", + "aspect = Aspects(\n", + " label=\"diameter-test\",\n", + " description=None,\n", + " iri=\"http://uri.interlex.org/tgbugs/uris/readable/aspect/diameter-test\",\n", + ")\n", + "\n", + "desc_inst = DescriptorsInst(\n", + " label=\"nerve-volume-test\",\n", + " iri=\"https://uri.interlex.org/tgbugs/uris/readable/quantdb/classes/nerve/volume-test\",\n", + " description=None,\n", + ")\n", + "\n", + "desc_quant = DescriptorsQuant(\n", + " shape=\"scalar\",\n", + " label=\"nerve-volume-test3\",\n", + " aggregation_type=\"instance\",\n", + " description=None,\n", + " curator_note=None,\n", + " aspects=aspect,\n", + ")\n", + "\n", + "print(list(desc_quant.__mapper__.relationships)[0].direction)\n", + "getattr(desc_quant, \"aspects\", [])" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [], + "source": [ + "def object_as_dict(obj):\n", + " return {\n", + " c.key: getattr(obj, c.key)\n", + " for c in inspect(obj).mapper.column_attrs\n", + " if getattr(obj, c.key)\n", + " }\n", + "\n", + "\n", + "def get_or_create(session, obj, back_populate=None):\n", + " model = obj.__class__\n", + " data = object_as_dict(obj)\n", + " instance = session.query(model).filter_by(**data).one_or_none()\n", + " if instance:\n", + " return instance\n", + " else:\n", + " params = {\n", + " k: v for k, v in data.items() if not isinstance(v, ClauseElement)\n", + " }\n", + " instance = model(**params)\n", + " try:\n", + " session.add(instance)\n", + " session.commit()\n", + " if back_populate:\n", + " for attr, value in back_populate.items():\n", + " setattr(instance, attr, value)\n", + " session.commit()\n", + " except Exception:\n", + " session.rollback()\n", + " instance = session.query(model).filter_by(**data).one()\n", + " return instance\n", + " else:\n", + " return instance\n", + "\n", + "\n", + "def back_populate_tables(db: Session, obj) -> object:\n", + " \"\"\"\n", + " Recursively back-populates objects in the database,\n", + " retrieving existing objects instead of failing on duplicates.\n", + " Iterates through all relationships of the object for both\n", + " initial population and recursive calls.\n", + " Includes a complete rollback if any commit fails.\n", + " Filters by all primary key columns of the object.\n", + " Handles cases where the child object is not a valid ORM instance.\n", + "\n", + " Args:\n", + " db: The database session.\n", + " obj: The ORM model object.\n", + "\n", + " Returns:\n", + " The ORM model object, with its related objects back-populated.\n", + " \"\"\"\n", + "\n", + " mapper = obj.__mapper__ # Get the mapper for the object\n", + " print(obj)\n", + " try:\n", + " # Iterate through all relationships of the object\n", + " for relationship_prop in mapper.relationships:\n", + " if (\n", + " relationship_prop.direction.name == \"MANYTOONE\"\n", + " or relationship_prop.direction.name == \"MANYTOMANY\"\n", + " ):\n", + " parent = getattr(obj, relationship_prop.key)\n", + " if parent:\n", + " filter_criteria = object_as_dict(parent)\n", + " existing_obj = (\n", + " db.query(type(parent))\n", + " .filter_by(**filter_criteria)\n", + " .first()\n", + " )\n", + " if existing_obj:\n", + " for key, value in object_as_dict(existing_obj).items():\n", + " if hasattr(parent, key):\n", + " setattr(parent, key, value)\n", + " print(\"populated\", object_as_dict(parent))\n", + " setattr(obj, relationship_prop.key, parent)\n", + " # db.add(parent)\n", + " # db.commit()\n", + " back_populate_tables(db, parent)\n", + "\n", + " print(\"object\", type(obj))\n", + " filter_criteria = object_as_dict(obj)\n", + " print(\"filter using\", filter_criteria)\n", + " existing_obj = db.query(type(obj)).filter_by(**filter_criteria).first()\n", + " print(\"is existing?\", existing_obj)\n", + " if not existing_obj:\n", + " db.merge(obj)\n", + " db.flush()\n", + " db.commit()\n", + " # db.refresh(obj)\n", + " print(\"after commit\", object_as_dict(obj))\n", + " else:\n", + " for key, value in object_as_dict(existing_obj).items():\n", + " if hasattr(obj, key):\n", + " setattr(obj, key, value)\n", + " print(\"after update\", object_as_dict(existing_obj))\n", + "\n", + " except IntegrityError as e:\n", + " db.rollback() # Rollback the transaction in case of an error\n", + " print(f\"Error during commit: {e}\")\n", + " raise # Re-raise the exception to indicate failure\n", + "\n", + " return obj # Return the object with its related objects back-populated" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [], + "source": [ + "# Params\n", + "object = Objects(\n", + " id=\"N:dataset:99a9a99a-a5b8-4881-a105-e4048af26fa5\",\n", + " id_type=\"dataset\",\n", + " id_file=None,\n", + " id_internal=None,\n", + ")\n", + "\n", + "# back_populate_tables(session, object)" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [], + "source": [ + "# Domain\n", + "unit = Units(\n", + " label=\"test\",\n", + " iri=\"https://uri.interlex.org/tgbugs/uris/readable/quantdb/units/test\",\n", + ")\n", + "\n", + "aspect = Aspects(\n", + " label=\"diameter-test-backpop4\",\n", + " description=None,\n", + " iri=\"http://uri.interlex.org/tgbugs/uris/readable/aspect/diameter-test-backpop4\",\n", + ")\n", + "\n", + "desc_inst = DescriptorsInst(\n", + " label=\"nerve-volume-test\",\n", + " iri=\"https://uri.interlex.org/tgbugs/uris/readable/quantdb/classes/nerve/volume-test\",\n", + " description=None,\n", + ")\n", + "\n", + "desc_quant = DescriptorsQuant(\n", + " shape=\"scalar\",\n", + " label=\"nerve-volume-test8\",\n", + " aggregation_type=\"instance\",\n", + " description=None,\n", + " curator_note=None,\n", + " aspects=aspect,\n", + " descriptors_inst=desc_inst,\n", + ")\n", + "\n", + "\n", + "# getattr(desc_quant, \"aspects\")\n", + "# list(desc_quant.aspects.__mapper__.relationships)\n", + "# back_populate_tables(session, desc_quant)\n", + "# print(\"here\", aspect.id)\n", + "# print(\"here\", desc_quant.aspects)" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\n", + "populated {'id': 2, 'addr_type': 'constant', 'value_type': 'single', 'addr_field': 'literally this value right here'}\n", + "\n", + "object \n", + "filter using {'id': 2, 'addr_type': 'constant', 'value_type': 'single', 'addr_field': 'literally this value right here'}\n", + "is existing? \n", + "after update {'id': 2, 'addr_type': 'constant', 'value_type': 'single', 'addr_field': 'literally this value right here'}\n", + "populated {'id': 34, 'label': 'nerve-volume-test', 'iri': 'https://uri.interlex.org/tgbugs/uris/readable/quantdb/classes/nerve/volume-test'}\n", + "\n", + "object \n", + "filter using {'id': 34, 'label': 'nerve-volume-test', 'iri': 'https://uri.interlex.org/tgbugs/uris/readable/quantdb/classes/nerve/volume-test'}\n", + "is existing? \n", + "after update {'id': 34, 'label': 'nerve-volume-test', 'iri': 'https://uri.interlex.org/tgbugs/uris/readable/quantdb/classes/nerve/volume-test'}\n", + "populated {'id': UUID('99a9a99a-a5b8-4881-a105-e4048af26fa5'), 'id_type': 'dataset'}\n", + "\n", + "object \n", + "filter using {'id': UUID('99a9a99a-a5b8-4881-a105-e4048af26fa5'), 'id_type': 'dataset'}\n", + "is existing? \n", + "after update {'id': UUID('99a9a99a-a5b8-4881-a105-e4048af26fa5'), 'id_type': 'dataset'}\n", + "object \n", + "filter using {'object': UUID('99a9a99a-a5b8-4881-a105-e4048af26fa5'), 'desc_inst': 34}\n", + "is existing? \n", + "after update {'object': UUID('99a9a99a-a5b8-4881-a105-e4048af26fa5'), 'desc_inst': 34, 'addr_field': 33}\n", + "\n", + "populated {'id': 2, 'addr_type': 'constant', 'value_type': 'single', 'addr_field': 'literally this value right here'}\n", + "\n", + "object \n", + "filter using {'id': 2, 'addr_type': 'constant', 'value_type': 'single', 'addr_field': 'literally this value right here'}\n", + "is existing? \n", + "after update {'id': 2, 'addr_type': 'constant', 'value_type': 'single', 'addr_field': 'literally this value right here'}\n", + "populated {'id': 34, 'shape': 'scalar', 'label': 'nerve-volume-test8', 'aggregation_type': 'instance', 'aspect': 29, 'domain': 34}\n", + "\n", + "populated {'id': 29, 'label': 'diameter-test-backpop4', 'iri': 'http://uri.interlex.org/tgbugs/uris/readable/aspect/diameter-test-backpop4'}\n", + "\n", + "object \n", + "filter using {'id': 29, 'label': 'diameter-test-backpop4', 'iri': 'http://uri.interlex.org/tgbugs/uris/readable/aspect/diameter-test-backpop4'}\n", + "is existing? \n", + "after update {'id': 29, 'label': 'diameter-test-backpop4', 'iri': 'http://uri.interlex.org/tgbugs/uris/readable/aspect/diameter-test-backpop4'}\n", + "populated {'id': 34, 'label': 'nerve-volume-test', 'iri': 'https://uri.interlex.org/tgbugs/uris/readable/quantdb/classes/nerve/volume-test'}\n", + "\n", + "object \n", + "filter using {'id': 34, 'label': 'nerve-volume-test', 'iri': 'https://uri.interlex.org/tgbugs/uris/readable/quantdb/classes/nerve/volume-test'}\n", + "is existing? \n", + "after update {'id': 34, 'label': 'nerve-volume-test', 'iri': 'https://uri.interlex.org/tgbugs/uris/readable/quantdb/classes/nerve/volume-test'}\n", + "object \n", + "filter using {'id': 34, 'shape': 'scalar', 'label': 'nerve-volume-test8', 'aggregation_type': 'instance', 'aspect': 29, 'domain': 34}\n", + "is existing? \n", + "after update {'id': 34, 'shape': 'scalar', 'label': 'nerve-volume-test8', 'aggregation_type': 'instance', 'aspect': 29, 'domain': 34}\n", + "populated {'id': UUID('99a9a99a-a5b8-4881-a105-e4048af26fa5'), 'id_type': 'dataset'}\n", + "\n", + "object \n", + "filter using {'id': UUID('99a9a99a-a5b8-4881-a105-e4048af26fa5'), 'id_type': 'dataset'}\n", + "is existing? \n", + "after update {'id': UUID('99a9a99a-a5b8-4881-a105-e4048af26fa5'), 'id_type': 'dataset'}\n", + "object \n", + "filter using {'object': UUID('99a9a99a-a5b8-4881-a105-e4048af26fa5'), 'desc_quant': 34}\n", + "is existing? \n", + "after update {'object': UUID('99a9a99a-a5b8-4881-a105-e4048af26fa5'), 'desc_quant': 34, 'addr_field': 33}\n" + ] + }, + { + "data": { + "text/plain": [ + "" + ] + }, + "execution_count": 6, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# Objects\n", + "\n", + "address = Addresses(\n", + " addr_type=\"constant\",\n", + " value_type=\"single\",\n", + ")\n", + "\n", + "obj_desc_inst = ObjDescInst(\n", + " objects=object,\n", + " descriptors_inst=desc_inst,\n", + " addresses_field=address,\n", + ")\n", + "\n", + "obj_desc_quant = ObjDescQuant(\n", + " objects=object,\n", + " descriptors_quant=desc_quant,\n", + " addresses_field=address,\n", + ")\n", + "\n", + "back_populate_tables(session, obj_desc_inst)\n", + "back_populate_tables(session, obj_desc_quant)" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\n", + "populated {'id': 34, 'label': 'nerve-volume-test', 'iri': 'https://uri.interlex.org/tgbugs/uris/readable/quantdb/classes/nerve/volume-test'}\n", + "\n", + "object \n", + "filter using {'id': 34, 'label': 'nerve-volume-test', 'iri': 'https://uri.interlex.org/tgbugs/uris/readable/quantdb/classes/nerve/volume-test'}\n", + "is existing? \n", + "after update {'id': 34, 'label': 'nerve-volume-test', 'iri': 'https://uri.interlex.org/tgbugs/uris/readable/quantdb/classes/nerve/volume-test'}\n", + "populated {'id': 34, 'shape': 'scalar', 'label': 'nerve-volume-test8', 'aggregation_type': 'instance', 'aspect': 29, 'domain': 34}\n", + "\n", + "populated {'id': 29, 'label': 'diameter-test-backpop4', 'iri': 'http://uri.interlex.org/tgbugs/uris/readable/aspect/diameter-test-backpop4'}\n", + "\n", + "object \n", + "filter using {'id': 29, 'label': 'diameter-test-backpop4', 'iri': 'http://uri.interlex.org/tgbugs/uris/readable/aspect/diameter-test-backpop4'}\n", + "is existing? \n", + "after update {'id': 29, 'label': 'diameter-test-backpop4', 'iri': 'http://uri.interlex.org/tgbugs/uris/readable/aspect/diameter-test-backpop4'}\n", + "populated {'id': 34, 'label': 'nerve-volume-test', 'iri': 'https://uri.interlex.org/tgbugs/uris/readable/quantdb/classes/nerve/volume-test'}\n", + "\n", + "object \n", + "filter using {'id': 34, 'label': 'nerve-volume-test', 'iri': 'https://uri.interlex.org/tgbugs/uris/readable/quantdb/classes/nerve/volume-test'}\n", + "is existing? \n", + "after update {'id': 34, 'label': 'nerve-volume-test', 'iri': 'https://uri.interlex.org/tgbugs/uris/readable/quantdb/classes/nerve/volume-test'}\n", + "object \n", + "filter using {'id': 34, 'shape': 'scalar', 'label': 'nerve-volume-test8', 'aggregation_type': 'instance', 'aspect': 29, 'domain': 34}\n", + "is existing? \n", + "after update {'id': 34, 'shape': 'scalar', 'label': 'nerve-volume-test8', 'aggregation_type': 'instance', 'aspect': 29, 'domain': 34}\n", + "populated {'id': 227, 'type': 'sample', 'id_sub': 'sub-test', 'desc_inst': 34, 'dataset': UUID('99a9a99a-a5b8-4881-a105-e4048af26fa5'), 'id_formal': 'sam-l-seg-c7-A-level-test', 'id_sam': 'sam-l-seg-c7-A-level-test'}\n", + "\n", + "populated {'id': UUID('99a9a99a-a5b8-4881-a105-e4048af26fa5'), 'id_type': 'dataset'}\n", + "\n", + "object \n", + "filter using {'id': UUID('99a9a99a-a5b8-4881-a105-e4048af26fa5'), 'id_type': 'dataset'}\n", + "is existing? \n", + "after update {'id': UUID('99a9a99a-a5b8-4881-a105-e4048af26fa5'), 'id_type': 'dataset'}\n", + "object \n", + "filter using {'id': 227, 'type': 'sample', 'id_sub': 'sub-test', 'desc_inst': 34, 'dataset': UUID('99a9a99a-a5b8-4881-a105-e4048af26fa5'), 'id_formal': 'sam-l-seg-c7-A-level-test', 'id_sam': 'sam-l-seg-c7-A-level-test'}\n", + "is existing? \n", + "after update {'id': 227, 'type': 'sample', 'id_sub': 'sub-test', 'desc_inst': 34, 'dataset': UUID('99a9a99a-a5b8-4881-a105-e4048af26fa5'), 'id_formal': 'sam-l-seg-c7-A-level-test', 'id_sam': 'sam-l-seg-c7-A-level-test'}\n", + "populated {'id': UUID('99a9a99a-a5b8-4881-a105-e4048af26fa5'), 'id_type': 'dataset'}\n", + "\n", + "object \n", + "filter using {'id': UUID('99a9a99a-a5b8-4881-a105-e4048af26fa5'), 'id_type': 'dataset'}\n", + "is existing? \n", + "after update {'id': UUID('99a9a99a-a5b8-4881-a105-e4048af26fa5'), 'id_type': 'dataset'}\n", + "object \n", + "filter using {'value': 0.5, 'object': UUID('99a9a99a-a5b8-4881-a105-e4048af26fa5'), 'desc_inst': 34, 'desc_quant': 34, 'value_blob': {'key1': 'value1'}, 'instance': 227}\n", + "is existing? \n", + "after update {'id': 651, 'value': Decimal('0.5'), 'object': UUID('99a9a99a-a5b8-4881-a105-e4048af26fa5'), 'desc_inst': 34, 'desc_quant': 34, 'value_blob': {'key1': 'value1'}, 'instance': 227}\n" + ] + } + ], + "source": [ + "# Value\n", + "values_inst = ValuesInst(\n", + " type=\"sample\",\n", + " id_sub=\"sub-test\",\n", + " id_formal=\"sam-l-seg-c7-A-level-test\",\n", + " local_identifier=None,\n", + " id_sam=\"sam-l-seg-c7-A-level-test\",\n", + " # descriptors_inst=desc_inst,\n", + " # dataset=object.id,\n", + " objects=object,\n", + ")\n", + "values_quant = ValuesQuant(\n", + " value=0.5,\n", + " objects=object,\n", + " orig_value=None,\n", + " orig_units=None,\n", + " descriptors_inst=desc_inst,\n", + " descriptors_quant=desc_quant,\n", + " values_inst=values_inst,\n", + " value_blob={\"key1\": \"value1\"},\n", + ")\n", + "\n", + "with session.no_autoflush:\n", + " back_populate_tables(session, values_quant)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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NFascdFasc_umdNerve_umlateralitylevelsexsub_samthkperi_umid_sub
115[437.21394287682614, 258.82574913412543, 307.9...2546.924091677267LCMC50-2[24.794722747116708, 27.92527295706188, 17.016...sub-C50-2
25[120.12238286446609, 243.86502700380925, 322.2...2019.0831006899302LCMC53-2[23.91547828345668, 15.931285254737446, 29.499...sub-C53-2
38[365.4037755654016, 284.53752037921583, 53.536...1615.1166896226846LCMC54-3[19.700748058232335, 28.26263525939993, 9.6459...sub-C54-3
41657.18271130567971025.5346591258096LCMC55-3[26.020421901161313, 46.18048430372056, 13.711...sub-C55-3
57[455.24233996428916, 509.9466847724346, 287.73...1838.3739820401397LCMC57-36.81653463390343sub-C57-3
\n", + "
" + ], + "text/plain": [ + " NFasc dFasc_um \\\n", + "1 15 [437.21394287682614, 258.82574913412543, 307.9... \n", + "2 5 [120.12238286446609, 243.86502700380925, 322.2... \n", + "3 8 [365.4037755654016, 284.53752037921583, 53.536... \n", + "4 1 657.1827113056797 \n", + "5 7 [455.24233996428916, 509.9466847724346, 287.73... \n", + "\n", + " dNerve_um laterality level sex sub_sam \\\n", + "1 2546.924091677267 L C M C50-2 \n", + "2 2019.0831006899302 L C M C53-2 \n", + "3 1615.1166896226846 L C M C54-3 \n", + "4 1025.5346591258096 L C M C55-3 \n", + "5 1838.3739820401397 L C M C57-3 \n", + "\n", + " thkperi_um id_sub \n", + "1 [24.794722747116708, 27.92527295706188, 17.016... sub-C50-2 \n", + "2 [23.91547828345668, 15.931285254737446, 29.499... sub-C53-2 \n", + "3 [19.700748058232335, 28.26263525939993, 9.6459... sub-C54-3 \n", + "4 [26.020421901161313, 46.18048430372056, 13.711... sub-C55-3 \n", + "5 6.81653463390343 sub-C57-3 " + ] + }, + "execution_count": 8, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# ingest.insert_objects(\n", + "# objects=[\n", + "# Objects(id=\"55c5b69c-a5b8-4881-a105-e4048af26fa5\", id_type=\"dataset\"),\n", + "# ]\n", + "# )\n", + "import pandas as pd\n", + "\n", + "df = pd.read_csv(\"data/CadaverVNMorphology_OutputMetrics.csv\", index_col=0)\n", + "df = df.T.reset_index(drop=True)\n", + "df[\"id_sub\"] = \"sub-\" + df.sub_sam\n", + "df.index = df.index + 1\n", + "df.head()" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": {}, + "outputs": [], + "source": [ + "df.id_sub = \"sub-\" + df.sub_sam" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\n", + "populated {'id': 2, 'addr_type': 'constant', 'value_type': 'single', 'addr_field': 'literally this value right here'}\n", + "\n", + "object \n", + "filter using {'id': 2, 'addr_type': 'constant', 'value_type': 'single', 'addr_field': 'literally this value right here'}\n", + "is existing? \n", + "after update {'id': 2, 'addr_type': 'constant', 'value_type': 'single', 'addr_field': 'literally this value right here'}\n", + "populated {'id': 22, 'label': 'fascicle', 'iri': 'https://uri.interlex.org/tgbugs/uris/readable/quantdb/classes/fascicle'}\n", + "\n", + "object \n", + "filter using {'id': 22, 'label': 'fascicle', 'iri': 'https://uri.interlex.org/tgbugs/uris/readable/quantdb/classes/fascicle'}\n", + "is existing? \n", + "after update {'id': 22, 'label': 'fascicle', 'iri': 'https://uri.interlex.org/tgbugs/uris/readable/quantdb/classes/fascicle'}\n", + "populated {'id': UUID('55c5b69c-a5b8-4881-a105-e4048af26fa5'), 'id_type': 'dataset'}\n", + "\n", + "object \n", + "filter using {'id': UUID('55c5b69c-a5b8-4881-a105-e4048af26fa5'), 'id_type': 'dataset'}\n", + "is existing? \n", + "after update {'id': UUID('55c5b69c-a5b8-4881-a105-e4048af26fa5'), 'id_type': 'dataset'}\n", + "object \n", + "filter using {'object': UUID('55c5b69c-a5b8-4881-a105-e4048af26fa5'), 'desc_inst': 22}\n", + "is existing? \n", + "after update {'object': UUID('55c5b69c-a5b8-4881-a105-e4048af26fa5'), 'desc_inst': 22, 'addr_field': 2}\n", + "\n", + "populated {'id': 2, 'addr_type': 'constant', 'value_type': 'single', 'addr_field': 'literally this value right here'}\n", + "\n", + "object \n", + "filter using {'id': 2, 'addr_type': 'constant', 'value_type': 'single', 'addr_field': 'literally this value right here'}\n", + "is existing? \n", + "after update {'id': 2, 'addr_type': 'constant', 'value_type': 'single', 'addr_field': 'literally this value right here'}\n", + "populated {'id': 35, 'shape': 'scalar', 'label': 'count of fascicles', 'aggregation_type': 'instance', 'aspect': 34, 'domain': 22}\n", + "\n", + "populated {'id': 34, 'label': 'count', 'iri': 'http://uri.interlex.org/tgbugs/uris/readable/aspect/count'}\n", + "\n", + "object \n", + "filter using {'id': 34, 'label': 'count', 'iri': 'http://uri.interlex.org/tgbugs/uris/readable/aspect/count'}\n", + "is existing? \n", + "after update {'id': 34, 'label': 'count', 'iri': 'http://uri.interlex.org/tgbugs/uris/readable/aspect/count'}\n", + "populated {'id': 22, 'label': 'fascicle', 'iri': 'https://uri.interlex.org/tgbugs/uris/readable/quantdb/classes/fascicle'}\n", + "\n", + "object \n", + "filter using {'id': 22, 'label': 'fascicle', 'iri': 'https://uri.interlex.org/tgbugs/uris/readable/quantdb/classes/fascicle'}\n", + "is existing? \n", + "after update {'id': 22, 'label': 'fascicle', 'iri': 'https://uri.interlex.org/tgbugs/uris/readable/quantdb/classes/fascicle'}\n", + "object \n", + "filter using {'id': 35, 'shape': 'scalar', 'label': 'count of fascicles', 'aggregation_type': 'instance', 'aspect': 34, 'domain': 22}\n", + "is existing? \n", + "after update {'id': 35, 'shape': 'scalar', 'label': 'count of fascicles', 'aggregation_type': 'instance', 'aspect': 34, 'domain': 22}\n", + "populated {'id': UUID('55c5b69c-a5b8-4881-a105-e4048af26fa5'), 'id_type': 'dataset'}\n", + "\n", + "object \n", + "filter using {'id': UUID('55c5b69c-a5b8-4881-a105-e4048af26fa5'), 'id_type': 'dataset'}\n", + "is existing? \n", + "after update {'id': UUID('55c5b69c-a5b8-4881-a105-e4048af26fa5'), 'id_type': 'dataset'}\n", + "object \n", + "filter using {'object': UUID('55c5b69c-a5b8-4881-a105-e4048af26fa5'), 'desc_quant': 35}\n", + "is existing? \n", + "after update {'object': UUID('55c5b69c-a5b8-4881-a105-e4048af26fa5'), 'desc_quant': 35, 'addr_field': 2}\n", + "\n", + "populated {'id': 22, 'label': 'fascicle', 'iri': 'https://uri.interlex.org/tgbugs/uris/readable/quantdb/classes/fascicle'}\n", + "\n", + "object \n", + "filter using {'id': 22, 'label': 'fascicle', 'iri': 'https://uri.interlex.org/tgbugs/uris/readable/quantdb/classes/fascicle'}\n", + "is existing? \n", + "after update {'id': 22, 'label': 'fascicle', 'iri': 'https://uri.interlex.org/tgbugs/uris/readable/quantdb/classes/fascicle'}\n", + "populated {'id': 35, 'shape': 'scalar', 'label': 'count of fascicles', 'aggregation_type': 'instance', 'aspect': 34, 'domain': 22}\n", + "\n", + "populated {'id': 34, 'label': 'count', 'iri': 'http://uri.interlex.org/tgbugs/uris/readable/aspect/count'}\n", + "\n", + "object \n", + "filter using {'id': 34, 'label': 'count', 'iri': 'http://uri.interlex.org/tgbugs/uris/readable/aspect/count'}\n", + "is existing? \n", + "after update {'id': 34, 'label': 'count', 'iri': 'http://uri.interlex.org/tgbugs/uris/readable/aspect/count'}\n", + "populated {'id': 22, 'label': 'fascicle', 'iri': 'https://uri.interlex.org/tgbugs/uris/readable/quantdb/classes/fascicle'}\n", + "\n", + "object \n", + "filter using {'id': 22, 'label': 'fascicle', 'iri': 'https://uri.interlex.org/tgbugs/uris/readable/quantdb/classes/fascicle'}\n", + "is existing? \n", + "after update {'id': 22, 'label': 'fascicle', 'iri': 'https://uri.interlex.org/tgbugs/uris/readable/quantdb/classes/fascicle'}\n", + "object \n", + "filter using {'id': 35, 'shape': 'scalar', 'label': 'count of fascicles', 'aggregation_type': 'instance', 'aspect': 34, 'domain': 22}\n", + "is existing? \n", + "after update {'id': 35, 'shape': 'scalar', 'label': 'count of fascicles', 'aggregation_type': 'instance', 'aspect': 34, 'domain': 22}\n", + "populated {'id': 297, 'type': 'subject', 'id_sub': 'sub-C50-2', 'dataset': UUID('55c5b69c-a5b8-4881-a105-e4048af26fa5'), 'id_formal': 'sub-C50-2'}\n", + "\n", + "populated {'id': UUID('55c5b69c-a5b8-4881-a105-e4048af26fa5'), 'id_type': 'dataset'}\n", + "\n", + "object \n", + "filter using {'id': UUID('55c5b69c-a5b8-4881-a105-e4048af26fa5'), 'id_type': 'dataset'}\n", + "is existing? \n", + "after update {'id': UUID('55c5b69c-a5b8-4881-a105-e4048af26fa5'), 'id_type': 'dataset'}\n", + "object \n", + "filter using {'id': 297, 'type': 'subject', 'id_sub': 'sub-C50-2', 'dataset': UUID('55c5b69c-a5b8-4881-a105-e4048af26fa5'), 'id_formal': 'sub-C50-2'}\n", + "is existing? \n", + "after update {'id': 297, 'type': 'subject', 'id_sub': 'sub-C50-2', 'dataset': UUID('55c5b69c-a5b8-4881-a105-e4048af26fa5'), 'id_formal': 'sub-C50-2'}\n", + "populated {'id': UUID('55c5b69c-a5b8-4881-a105-e4048af26fa5'), 'id_type': 'dataset'}\n", + "\n", + "object \n", + "filter using {'id': UUID('55c5b69c-a5b8-4881-a105-e4048af26fa5'), 'id_type': 'dataset'}\n", + "is existing? \n", + "after update {'id': UUID('55c5b69c-a5b8-4881-a105-e4048af26fa5'), 'id_type': 'dataset'}\n", + "object \n", + "filter using {'value': 15, 'object': UUID('55c5b69c-a5b8-4881-a105-e4048af26fa5'), 'desc_inst': 22, 'desc_quant': 35, 'value_blob': '15', 'instance': 297}\n", + "is existing? None\n" + ] + }, + { + "ename": "AssertionError", + "evalue": "Dependency rule on column 'descriptors_quant.id' tried to blank-out primary key column 'obj_desc_quant.desc_quant' on instance ''", + "output_type": "error", + "traceback": [ + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mAssertionError\u001b[0m Traceback (most recent call last)", + "Cell \u001b[0;32mIn[10], line 91\u001b[0m\n\u001b[1;32m 78\u001b[0m session\u001b[38;5;241m.\u001b[39mcommit()\n\u001b[1;32m 80\u001b[0m values_quant \u001b[38;5;241m=\u001b[39m ValuesQuant(\n\u001b[1;32m 81\u001b[0m value\u001b[38;5;241m=\u001b[39m\u001b[38;5;28mint\u001b[39m(row[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mNFasc\u001b[39m\u001b[38;5;124m\"\u001b[39m]),\n\u001b[1;32m 82\u001b[0m objects\u001b[38;5;241m=\u001b[39m\u001b[38;5;28mobject\u001b[39m,\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 88\u001b[0m value_blob\u001b[38;5;241m=\u001b[39mrow[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mNFasc\u001b[39m\u001b[38;5;124m\"\u001b[39m],\n\u001b[1;32m 89\u001b[0m )\n\u001b[0;32m---> 91\u001b[0m \u001b[43mback_populate_tables\u001b[49m\u001b[43m(\u001b[49m\u001b[43msession\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mvalues_quant\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 92\u001b[0m \u001b[38;5;66;03m# # values to iterate through\u001b[39;00m\n\u001b[1;32m 93\u001b[0m \u001b[38;5;66;03m# values_inst = ValuesInst(\u001b[39;00m\n\u001b[1;32m 94\u001b[0m \u001b[38;5;66;03m# type=\"sample\",\u001b[39;00m\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 113\u001b[0m \n\u001b[1;32m 114\u001b[0m \u001b[38;5;66;03m# back_populate_tables(session, values_quant)\u001b[39;00m\n", + "Cell \u001b[0;32mIn[3], line 87\u001b[0m, in \u001b[0;36mback_populate_tables\u001b[0;34m(db, obj)\u001b[0m\n\u001b[1;32m 85\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m existing_obj:\n\u001b[1;32m 86\u001b[0m db\u001b[38;5;241m.\u001b[39mmerge(obj)\n\u001b[0;32m---> 87\u001b[0m \u001b[43mdb\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mflush\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 88\u001b[0m db\u001b[38;5;241m.\u001b[39mcommit()\n\u001b[1;32m 89\u001b[0m \u001b[38;5;66;03m# db.refresh(obj)\u001b[39;00m\n", + "File \u001b[0;32m~/miniforge3/envs/quantdb/lib/python3.12/site-packages/sqlalchemy/orm/session.py:4352\u001b[0m, in \u001b[0;36mSession.flush\u001b[0;34m(self, objects)\u001b[0m\n\u001b[1;32m 4350\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[1;32m 4351\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_flushing \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mTrue\u001b[39;00m\n\u001b[0;32m-> 4352\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_flush\u001b[49m\u001b[43m(\u001b[49m\u001b[43mobjects\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 4353\u001b[0m \u001b[38;5;28;01mfinally\u001b[39;00m:\n\u001b[1;32m 4354\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_flushing \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mFalse\u001b[39;00m\n", + "File \u001b[0;32m~/miniforge3/envs/quantdb/lib/python3.12/site-packages/sqlalchemy/orm/session.py:4487\u001b[0m, in \u001b[0;36mSession._flush\u001b[0;34m(self, objects)\u001b[0m\n\u001b[1;32m 4484\u001b[0m transaction\u001b[38;5;241m.\u001b[39mcommit()\n\u001b[1;32m 4486\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m:\n\u001b[0;32m-> 4487\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;28;43;01mwith\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[43mutil\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msafe_reraise\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\u001b[43m:\u001b[49m\n\u001b[1;32m 4488\u001b[0m \u001b[43m \u001b[49m\u001b[43mtransaction\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mrollback\u001b[49m\u001b[43m(\u001b[49m\u001b[43m_capture_exception\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mTrue\u001b[39;49;00m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/miniforge3/envs/quantdb/lib/python3.12/site-packages/sqlalchemy/util/langhelpers.py:146\u001b[0m, in \u001b[0;36msafe_reraise.__exit__\u001b[0;34m(self, type_, value, traceback)\u001b[0m\n\u001b[1;32m 144\u001b[0m \u001b[38;5;28;01massert\u001b[39;00m exc_value \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m\n\u001b[1;32m 145\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_exc_info \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m \u001b[38;5;66;03m# remove potential circular references\u001b[39;00m\n\u001b[0;32m--> 146\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m exc_value\u001b[38;5;241m.\u001b[39mwith_traceback(exc_tb)\n\u001b[1;32m 147\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 148\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_exc_info \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m \u001b[38;5;66;03m# remove potential circular references\u001b[39;00m\n", + "File \u001b[0;32m~/miniforge3/envs/quantdb/lib/python3.12/site-packages/sqlalchemy/orm/session.py:4448\u001b[0m, in \u001b[0;36mSession._flush\u001b[0;34m(self, objects)\u001b[0m\n\u001b[1;32m 4446\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_warn_on_events \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mTrue\u001b[39;00m\n\u001b[1;32m 4447\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m-> 4448\u001b[0m \u001b[43mflush_context\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mexecute\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 4449\u001b[0m \u001b[38;5;28;01mfinally\u001b[39;00m:\n\u001b[1;32m 4450\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_warn_on_events \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mFalse\u001b[39;00m\n", + "File \u001b[0;32m~/miniforge3/envs/quantdb/lib/python3.12/site-packages/sqlalchemy/orm/unitofwork.py:466\u001b[0m, in \u001b[0;36mUOWTransaction.execute\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 464\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 465\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m rec \u001b[38;5;129;01min\u001b[39;00m topological\u001b[38;5;241m.\u001b[39msort(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mdependencies, postsort_actions):\n\u001b[0;32m--> 466\u001b[0m \u001b[43mrec\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mexecute\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/miniforge3/envs/quantdb/lib/python3.12/site-packages/sqlalchemy/orm/unitofwork.py:591\u001b[0m, in \u001b[0;36mProcessAll.execute\u001b[0;34m(self, uow)\u001b[0m\n\u001b[1;32m 589\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mdependency_processor\u001b[38;5;241m.\u001b[39mprocess_deletes(uow, states)\n\u001b[1;32m 590\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m--> 591\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mdependency_processor\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mprocess_saves\u001b[49m\u001b[43m(\u001b[49m\u001b[43muow\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mstates\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/miniforge3/envs/quantdb/lib/python3.12/site-packages/sqlalchemy/orm/dependency.py:604\u001b[0m, in \u001b[0;36mOneToManyDP.process_saves\u001b[0;34m(self, uowcommit, states)\u001b[0m\n\u001b[1;32m 598\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m child \u001b[38;5;129;01min\u001b[39;00m history\u001b[38;5;241m.\u001b[39mdeleted:\n\u001b[1;32m 599\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m (\n\u001b[1;32m 600\u001b[0m should_null_fks\n\u001b[1;32m 601\u001b[0m \u001b[38;5;129;01mand\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mcascade\u001b[38;5;241m.\u001b[39mdelete_orphan\n\u001b[1;32m 602\u001b[0m \u001b[38;5;129;01mand\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mhasparent(child)\n\u001b[1;32m 603\u001b[0m ):\n\u001b[0;32m--> 604\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_synchronize\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 605\u001b[0m \u001b[43m \u001b[49m\u001b[43mstate\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mchild\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mNone\u001b[39;49;00m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mTrue\u001b[39;49;00m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43muowcommit\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mFalse\u001b[39;49;00m\n\u001b[1;32m 606\u001b[0m \u001b[43m \u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 608\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_pks_changed(uowcommit, state):\n\u001b[1;32m 609\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m child \u001b[38;5;129;01min\u001b[39;00m history\u001b[38;5;241m.\u001b[39munchanged:\n", + "File \u001b[0;32m~/miniforge3/envs/quantdb/lib/python3.12/site-packages/sqlalchemy/orm/dependency.py:625\u001b[0m, in \u001b[0;36mOneToManyDP._synchronize\u001b[0;34m(self, state, child, associationrow, clearkeys, uowcommit, pks_changed)\u001b[0m\n\u001b[1;32m 623\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m\n\u001b[1;32m 624\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m clearkeys:\n\u001b[0;32m--> 625\u001b[0m \u001b[43msync\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mclear\u001b[49m\u001b[43m(\u001b[49m\u001b[43mdest\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mmapper\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mprop\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msynchronize_pairs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 626\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 627\u001b[0m sync\u001b[38;5;241m.\u001b[39mpopulate(\n\u001b[1;32m 628\u001b[0m source,\n\u001b[1;32m 629\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mparent,\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 634\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mpassive_updates \u001b[38;5;129;01mand\u001b[39;00m pks_changed,\n\u001b[1;32m 635\u001b[0m )\n", + "File \u001b[0;32m~/miniforge3/envs/quantdb/lib/python3.12/site-packages/sqlalchemy/orm/sync.py:88\u001b[0m, in \u001b[0;36mclear\u001b[0;34m(dest, dest_mapper, synchronize_pairs)\u001b[0m\n\u001b[1;32m 82\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m l, r \u001b[38;5;129;01min\u001b[39;00m synchronize_pairs:\n\u001b[1;32m 83\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m (\n\u001b[1;32m 84\u001b[0m r\u001b[38;5;241m.\u001b[39mprimary_key\n\u001b[1;32m 85\u001b[0m \u001b[38;5;129;01mand\u001b[39;00m dest_mapper\u001b[38;5;241m.\u001b[39m_get_state_attr_by_column(dest, dest\u001b[38;5;241m.\u001b[39mdict, r)\n\u001b[1;32m 86\u001b[0m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;129;01min\u001b[39;00m orm_util\u001b[38;5;241m.\u001b[39m_none_set\n\u001b[1;32m 87\u001b[0m ):\n\u001b[0;32m---> 88\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mAssertionError\u001b[39;00m(\n\u001b[1;32m 89\u001b[0m \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mDependency rule on column \u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;132;01m{\u001b[39;00ml\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124m \u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 90\u001b[0m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mtried to blank-out primary key \u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 91\u001b[0m \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mcolumn \u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mr\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124m on instance \u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;132;01m{\u001b[39;00morm_util\u001b[38;5;241m.\u001b[39mstate_str(dest)\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 92\u001b[0m )\n\u001b[1;32m 93\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[1;32m 94\u001b[0m dest_mapper\u001b[38;5;241m.\u001b[39m_set_state_attr_by_column(dest, dest\u001b[38;5;241m.\u001b[39mdict, r, \u001b[38;5;28;01mNone\u001b[39;00m)\n", + "\u001b[0;31mAssertionError\u001b[0m: Dependency rule on column 'descriptors_quant.id' tried to blank-out primary key column 'obj_desc_quant.desc_quant' on instance ''" + ] + } + ], + "source": [ + "# number of fascicles\n", + "\n", + "# Dataset\n", + "object = Objects(\n", + " id=\"N:dataset:55c5b69c-a5b8-4881-a105-e4048af26fa5\",\n", + " id_type=\"dataset\",\n", + " id_file=None,\n", + " id_internal=None,\n", + ")\n", + "\n", + "# Domain\n", + "unit = Units(\n", + " label=\"unitless\",\n", + " # iri=\"https://uri.interlex.org/tgbugs/uris/readable/quantdb/units/micrometer\",\n", + ")\n", + "aspect = Aspects(\n", + " label=\"count\",\n", + " description=None,\n", + " iri=\"http://uri.interlex.org/tgbugs/uris/readable/aspect/count\",\n", + ")\n", + "# focus of measurement\n", + "desc_inst = DescriptorsInst(\n", + " label=\"fascicle\",\n", + " # iri=\"https://uri.interlex.org/tgbugs/uris/readable/quantdb/classes/nerve/volume-test\",\n", + " # description=None,\n", + ")\n", + "# how to calculate unit\n", + "desc_quant = DescriptorsQuant(\n", + " shape=\"scalar\",\n", + " label=\"count of fascicles\",\n", + " aggregation_type=\"instance\",\n", + " description=None,\n", + " curator_note=None,\n", + " aspects=aspect,\n", + " descriptors_inst=desc_inst,\n", + ")\n", + "\n", + "# Objects\n", + "address = Addresses(\n", + " addr_type=\"constant\",\n", + " value_type=\"single\",\n", + ")\n", + "obj_desc_inst = ObjDescInst(\n", + " objects=object,\n", + " descriptors_inst=desc_inst,\n", + " addresses_field=address,\n", + ")\n", + "obj_desc_quant = ObjDescQuant(\n", + " objects=object,\n", + " descriptors_quant=desc_quant,\n", + " addresses_field=address,\n", + ")\n", + "\n", + "back_populate_tables(session, obj_desc_inst)\n", + "back_populate_tables(session, obj_desc_quant)\n", + "\n", + "from sqlalchemy.orm.exc import NoResultFound\n", + "\n", + "for i, row in df.iterrows():\n", + " try:\n", + " # Check if the entry already exists\n", + " existing_values_inst = (\n", + " session.query(ValuesInst)\n", + " .filter_by(id_sub=row.id_sub, id_formal=row.id_sub, objects=object)\n", + " .one()\n", + " )\n", + " values_inst = existing_values_inst\n", + " except NoResultFound:\n", + " # If not found, create a new entry\n", + " values_inst = ValuesInst(\n", + " type=\"subject\",\n", + " id_sub=row.id_sub,\n", + " id_formal=row.id_sub,\n", + " local_identifier=None,\n", + " objects=object,\n", + " )\n", + " session.add(values_inst)\n", + " session.commit()\n", + "\n", + " values_quant = ValuesQuant(\n", + " value=int(row[\"NFasc\"]),\n", + " objects=object,\n", + " orig_value=None,\n", + " orig_units=None,\n", + " descriptors_inst=desc_inst,\n", + " descriptors_quant=desc_quant,\n", + " values_inst=values_inst,\n", + " value_blob=row[\"NFasc\"],\n", + " )\n", + "\n", + " back_populate_tables(session, values_quant)\n", + "# # values to iterate through\n", + "# values_inst = ValuesInst(\n", + "# type=\"sample\",\n", + "# id_sub=\"sub-\",\n", + "# id_formal=\"\",\n", + "# local_identifier=None,\n", + "# id_sam=\"\",\n", + "# # descriptors_inst=desc_inst,\n", + "# # dataset=object.id,\n", + "# objects=object,\n", + "# )\n", + "# values_quant = ValuesQuant(\n", + "# value=0.5,\n", + "# objects=object,\n", + "# orig_value=None,\n", + "# orig_units=None,\n", + "# descriptors_inst=desc_inst,\n", + "# descriptors_quant=desc_quant,\n", + "# values_inst=values_inst,\n", + "# value_blob={\"key1\": \"value1\"},\n", + "# )\n", + "\n", + "# back_populate_tables(session, values_quant)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# NFac\n", + "\n", + "# Dataset\n", + "object = Objects(\n", + " id=\"N:dataset:55c5b69c-a5b8-4881-a105-e4048af26fa5\",\n", + " id_type=\"dataset\",\n", + " id_file=None,\n", + " id_internal=None,\n", + ")\n", + "\n", + "# Domain\n", + "unit = Units(\n", + " label=\"unitless\",\n", + " # iri=\"https://uri.interlex.org/tgbugs/uris/readable/quantdb/units/micrometer\",\n", + ")\n", + "aspect = Aspects(\n", + " label=\"count\",\n", + " description=None,\n", + " iri=\"http://uri.interlex.org/tgbugs/uris/readable/aspect/count\",\n", + ")\n", + "# focus of measurement\n", + "desc_inst = DescriptorsInst(\n", + " label=\"fascicle\",\n", + " # iri=\"https://uri.interlex.org/tgbugs/uris/readable/quantdb/classes/nerve/volume-test\",\n", + " # description=None,\n", + ")\n", + "# how to calculate unit\n", + "desc_quant = DescriptorsQuant(\n", + " shape=\"scalar\",\n", + " label=\"count of fascicles\",\n", + " aggregation_type=\"instance\",\n", + " description=None,\n", + " curator_note=None,\n", + " aspects=aspect,\n", + " descriptors_inst=desc_inst,\n", + ")\n", + "\n", + "# Objects\n", + "address = Addresses(\n", + " addr_type=\"constant\",\n", + " value_type=\"single\",\n", + ")\n", + "obj_desc_inst = ObjDescInst(\n", + " objects=object,\n", + " descriptors_inst=desc_inst,\n", + " addresses_field=address,\n", + ")\n", + "obj_desc_quant = ObjDescQuant(\n", + " objects=object,\n", + " descriptors_quant=desc_quant,\n", + " addresses_field=address,\n", + ")\n", + "\n", + "back_populate_tables(session, obj_desc_inst)\n", + "back_populate_tables(session, obj_desc_quant)\n", + "\n", + "from sqlalchemy.orm.exc import NoResultFound\n", + "\n", + "for i, row in df.iterrows():\n", + " try:\n", + " # Check if the entry already exists\n", + " existing_values_inst = (\n", + " session.query(ValuesInst)\n", + " .filter_by(id_sub=row.id_sub, id_formal=row.id_sub, objects=object)\n", + " .one()\n", + " )\n", + " values_inst = existing_values_inst\n", + " except NoResultFound:\n", + " # If not found, create a new entry\n", + " values_inst = ValuesInst(\n", + " type=\"subject\",\n", + " id_sub=row.id_sub,\n", + " id_formal=row.id_sub,\n", + " local_identifier=None,\n", + " objects=object,\n", + " )\n", + " session.add(values_inst)\n", + " session.commit()\n", + "\n", + " values_quant = ValuesQuant(\n", + " value=int(row[\"NFasc\"]),\n", + " objects=object,\n", + " orig_value=None,\n", + " orig_units=None,\n", + " descriptors_inst=desc_inst,\n", + " descriptors_quant=desc_quant,\n", + " values_inst=values_inst,\n", + " value_blob=row[\"NFasc\"],\n", + " )\n", + "\n", + " back_populate_tables(session, values_quant)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# dream ingest" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# ingest.insert_descriptors_quant(\n", + "# descriptor_quants=[\n", + "# DescriptorQuant(\n", + "# label=\"fascicle cross section diameter um min\",\n", + "# domain=26, # \"fiber-cross-section\" # TODO: label to ID\n", + "# aspect=5, # \"diameter\", # TODO: label to ID\n", + "# unit=4, # pixel\", # TODO: label to ID\n", + "# aggregation_type=\"min\",\n", + "# ),\n", + "# ]\n", + "# )\n", + "\n", + "# # dream ingest\n", + "# csv = pd.read_csv(\"data/CadaverVNMorphology_OutputMetrics.csv\", index_col=0)\n", + "# ingest.insert_descriptors_quant(**csv.to_dict(orient=\"records\"))" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "quantdb", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.12.2" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/ingest-tab-from-penn_v1.ipynb b/ingest-tab-from-penn_v1.ipynb new file mode 100644 index 0000000..bb80351 --- /dev/null +++ b/ingest-tab-from-penn_v1.ipynb @@ -0,0 +1,1236 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 38, + "metadata": {}, + "outputs": [], + "source": [ + "from quantdb.ingest_tabular.pennsieve_client import PennsieveClient\n", + "\n", + "penncli = PennsieveClient()" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# From Pennsieve directly" + ] + }, + { + "cell_type": "code", + "execution_count": 62, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{'nodeId': 'N:package:cc6c1783-4eb4-4a0a-b723-247827ebeb4e',\n", + " 'fileName': 'naveen_paper_B733_T7L_A_LEVEL_3_fascicles.csv',\n", + " 'packageName': 'naveen_paper_B733_T7L_A_LEVEL_3_fascicles.csv',\n", + " 'path': ['derivative', 'sam-l', 'sam-l-seg-t7', 'sam-l-seg-t7-LEVEL_3'],\n", + " 'url': 'https://prd-sparc-storage-use1.s3.amazonaws.com/O367/D3090/be5e20cb-86e2-41ea-a72f-e29d61354c96/cc6c1783-4eb4-4a0a-b723-247827ebeb4e?response-content-disposition=attachment%3B%20filename%3D%22naveen_paper_B733_T7L_A_LEVEL_3_fascicles.csv%22&X-Amz-Security-Token=IQoJb3JpZ2luX2VjEH8aCXVzLWVhc3QtMSJHMEUCIAPch%2BauQrPQv21R0RXeIldFPBezXJBak%2FnCmQ%2F317bTAiEA%2Fk%2B653R0GVTYYy3RlaE5nnPR3oEjUkHPZ%2FzfzNWZFCAqigQIp%2F%2F%2F%2F%2F%2F%2F%2F%2F%2F%2FARADGgw3NDA0NjMzMzcxNzciDN3ESJWEi1SigEZhZireA4etY0qpkpsnV%2FLZKvXvfmPzVQZ%2F96LEJUqCnAEttICbb%2BmKLcIqKm4AvjziRHltIQmsmeFHLazhcNzCZ%2Bhgz1o%2BuhDFeFWimy3UNxwKGXn6g0sc5sCMytJBXKKL8Omq5tSDpVVn7quipiIlZbM1S0nLed6LNZ4ScNHhSA%2Fues8byTAHTBZXV3OUML9AFrAcggwvoxdwCM28G4lS%2B0vY4vM0%2BT84%2BKhwiGAEjiSNuVJzgG7%2BVCywWoFxxrw9G0ckZznZb7h%2BzMyhg9Z7HmgfIAIQfLxXTD1%2FG0FfyQ0%2BpNd2CPhSbpkfIkN8LjGbjtAA1qIVcnZJpAWoFObmAnPBSPBggrb86Ugrt7QfqC9kRoxwLlUECmfMPSE9yRZrMFmm63vRMWCcJPsgTB3pQYVOWorUZTLCkeZvtI6MhwEJzqbalDE%2FRCWrQhmQhZUYTqFhaDdcGEXEUWHnkZ%2FNhez7WSGev2GjIgw1URhhAXxQfjmvUQ2gXAo24ihLhvytqug6zQwgJ5jyy9EacQCXdtHbQzrG%2FWrBk6VPYaN%2FSov4LFk6FPWgx9lO3Q249ksJmKh7JjsMSppUe9vh5Jf%2Bnnp%2BjvUrHzK5Orv00RVnl7oDmBsZBK6uSAi7bskk%2FZfRKH0w5uuLtwY6pQEAZsm%2BeoKoUxJqPoB3ZKFCiludpY4TuNPFOF8%2FJYyIjR%2FVV0VEIfDmKH5YJef8KvQI7vEVsxq6oFW2iPhLXNiHf8GAR0AUSv0bDRC1QU0S0royAOv5CyambGBJSFIVXLmKSoHIgyUrl5X7EshnOe648LLvWaSbyJHa2%2F6orbvd2dHyO9%2FjfrOJYRP%2BNrZlclRi48R3bRz9Ub93MHDNhqsefPmlndM%3D&X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Date=20240912T142530Z&X-Amz-SignedHeaders=host&X-Amz-Expires=10800&X-Amz-Credential=ASIA2YZYN33M3LYCBBHW%2F20240912%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Signature=7512d6c9dc110c72f1ef35f9978edbb4057cdb5903729d270849db99ad895825',\n", + " 'size': 26289}" + ] + }, + "execution_count": 62, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# penncli = PennsieveClient()\n", + "did = \"N:dataset:aa43eda8-b29a-4c25-9840-ecbd57598afc\"\n", + "manifest = penncli.get_dataset_manifest(did)\n", + "\n", + "\n", + "def pull_files(id_or_name: str, pattern: str | None = None) -> list[str]:\n", + " \"\"\"Export a dataset to a directory\n", + "\n", + " Parameters\n", + " ----------\n", + " id_or_name : str\n", + " Dataset ID or name\n", + " output_dir : Path | str\n", + " Output directory\n", + " verbose : bool, optional\n", + " Prints filename being downloaded, by default True\n", + " \"\"\"\n", + " files = []\n", + " url = \"https://api.pennsieve.io/packages/download-manifest\"\n", + " # output_dir = Path(output_dir) / id_or_name\n", + " # Pull dataset for root children IDs\n", + " dataset = penncli.get_dataset(id_or_name)\n", + " for child in dataset[\"children\"]:\n", + " payload = {\"nodeIds\": [child[\"content\"][\"nodeId\"]]}\n", + " # Pull tree for 1 child at a time since prebuilt s3 links only last a couple hours\n", + " # If all children are pulled at once, the links will expire before all files are downloaded if over 200GBs\n", + " # resp = penncli._post(url, payload=payload)\n", + " # try:\n", + " # manifest = resp.json()\n", + " # except:\n", + " # print(payload)\n", + " # print(resp.text)\n", + " # continue\n", + " manifest = penncli.get_child_manifest(\n", + " node_id=child[\"content\"][\"nodeId\"]\n", + " )\n", + " for filemeta in manifest[\"data\"]:\n", + " # filemeta[\"\"] = manifest[\"datasetId\"]\n", + " if Path(filemeta[\"fileName\"]).suffix in [\".csv\"]:\n", + " files.append(filemeta)\n", + " return dataset, files\n", + "\n", + "\n", + "dataset, files = pull_files(did)\n", + "fascicle_files = [v for v in files if \"fascicles\" in v[\"fileName\"].lower()]\n", + "file = fascicle_files[-1]\n", + "file" + ] + }, + { + "cell_type": "code", + "execution_count": 63, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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fasciclearealongest_diametershortest_diametereff_diamc_estimate_navc_estimate_nfnfibers_w_c_estimate_navnfibers_w_c_estimate_nfnfibers_all...epi_distepi_dist_invnerve_based_areanerve_based_perimeternerve_based_eff_diamperinerium_verticesperinerium_vertices_pxnerve_based_shortest_diameterhull_contrshull_contr_areas
01601840.629341907.000466846.340808875.37836901650246132111521115...515.9310.000477860.1984084.885780.020[[3127.5 113.4 ]\\n [3160.35 113.4 ]\\n [3192...[[20850 756]\\n [21069 756]\\n [21280 826]...630.464[ 0. 5. 10. 15. 20. 25. 30. 35. 40. ...[3.38965189e+06 3.29847812e+06 3.20848098e+06 ...
12151657.783648566.334306329.680645439.42768201300154828482848...274.845241.087163417.7361544.309456.147[[1488.15 480.75]\\n [1504.8 485.55]\\n [1521...[[ 9921 3205]\\n [10032 3237]\\n [10143 3262]...350.905[ 0. 5. 10. 15. 20. 25. 30. 35. 40. ...[1.08945157e+06 1.03852465e+06 9.88700989e+05 ...
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5 rows × 49 columns

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" + ], + "text/plain": [ + " fascicle area longest_diameter shortest_diameter eff_diam \\\n", + "0 1 601840.629341 907.000466 846.340808 875.378369 \n", + "1 2 151657.783648 566.334306 329.680645 439.427682 \n", + "2 3 42956.807122 253.176413 208.473851 233.868137 \n", + "3 4 19745.681094 177.272006 131.860742 158.559080 \n", + "4 5 72513.774721 370.254924 237.445074 303.854250 \n", + "\n", + " c_estimate_nav c_estimate_nf nfibers_w_c_estimate_nav \\\n", + "0 0 16502 4613 \n", + "1 0 1300 1548 \n", + "2 0 239 289 \n", + "3 0 108 120 \n", + "4 0 630 695 \n", + "\n", + " nfibers_w_c_estimate_nf nfibers_all ... epi_dist epi_dist_inv \\\n", + "0 21115 21115 ... 515.931 0.000 \n", + "1 2848 2848 ... 274.845 241.087 \n", + "2 528 528 ... 239.555 276.376 \n", + "3 228 228 ... 394.411 121.521 \n", + "4 1325 1325 ... 432.613 83.318 \n", + "\n", + " nerve_based_area nerve_based_perimeter nerve_based_eff_diam \\\n", + "0 477860.198 4084.885 780.020 \n", + "1 163417.736 1544.309 456.147 \n", + "2 51265.699 894.344 255.487 \n", + "3 24790.376 657.547 177.663 \n", + "4 81804.589 1104.140 322.733 \n", + "\n", + " perinerium_vertices \\\n", + "0 [[3127.5 113.4 ]\\n [3160.35 113.4 ]\\n [3192... \n", + "1 [[1488.15 480.75]\\n [1504.8 485.55]\\n [1521... \n", + "2 [[605.55 361.5 ]\\n [614.85 361.5 ]\\n [624.3 3... \n", + "3 [[728.1 470.85]\\n [734.7 469.2 ]\\n [741. 4... \n", + "4 [[1107. 441.45]\\n [1115.55 446.4 ]\\n [1119... \n", + "\n", + " perinerium_vertices_px \\\n", + "0 [[20850 756]\\n [21069 756]\\n [21280 826]... \n", + "1 [[ 9921 3205]\\n [10032 3237]\\n [10143 3262]... \n", + "2 [[4037 2410]\\n [4099 2410]\\n [4162 2410]\\n [42... \n", + "3 [[4854 3139]\\n [4898 3128]\\n [4940 3123]\\n [49... \n", + "4 [[7380 2943]\\n [7437 2976]\\n [7462 3032]\\n [75... \n", + "\n", + " nerve_based_shortest_diameter \\\n", + "0 630.464 \n", + "1 350.905 \n", + "2 215.234 \n", + "3 138.983 \n", + "4 250.218 \n", + "\n", + " hull_contrs \\\n", + "0 [ 0. 5. 10. 15. 20. 25. 30. 35. 40. ... \n", + "1 [ 0. 5. 10. 15. 20. 25. 30. 35. 40. ... \n", + "2 [ 0. 5. 10. 15. 20. 25. 30. 35. 40. ... \n", + "3 [ 0. 5. 10. 15. 20. 25. 30. 35. 40. 45. 50. 5... \n", + "4 [ 0. 5. 10. 15. 20. 25. 30. 35. 40. ... \n", + "\n", + " hull_contr_areas \n", + "0 [3.38965189e+06 3.29847812e+06 3.20848098e+06 ... \n", + "1 [1.08945157e+06 1.03852465e+06 9.88700989e+05 ... \n", + "2 [3.41771325e+05 3.12657208e+05 2.84935875e+05 ... \n", + "3 [165269.175 144192.08666671 124780.433718... \n", + "4 [545363.925 509233.56034859 474385.219163... \n", + "\n", + "[5 rows x 49 columns]" + ] + }, + "execution_count": 63, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "import pandas as pd\n", + "\n", + "df = pd.read_csv(file[\"url\"])\n", + "if \"Unnamed: 0\" in df.columns:\n", + " df = df.drop(columns=[\"Unnamed: 0\"])\n", + "df.head(1)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# From a file source" + ] + }, + { + "cell_type": "code", + "execution_count": 43, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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\n", + "\n", + "[8 rows x 54 columns]" + ] + }, + "execution_count": 43, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "pd.read_csv(\"data/CadaverVNMorphology_OutputMetrics.csv\")" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "metadata": {}, + "outputs": [], + "source": [ + "from quantdb.config import auth\n", + "from sqlalchemy import create_engine\n", + "from quantdb.utils import dbUri, isoformat, log\n", + "from sqlalchemy.sql import text as sql_text\n", + "from sqlalchemy.orm import Session\n", + "\n", + "# pull in the db connection info\n", + "dbkwargs = {\n", + " k: auth.get(f\"db-{k}\") for k in (\"user\", \"host\", \"port\", \"database\")\n", + "} # TODO integrate with cli options\n", + "# custom user variable needed\n", + "dbkwargs[\"dbuser\"] = dbkwargs.pop(\"user\")\n", + "# create connection env with DB\n", + "engine = create_engine(dbUri(**dbkwargs))\n", + "# bool: echo me\n", + "engine.echo = True\n", + "# use connection env as unique session\n", + "session = Session(engine)\n", + "\n", + "\n", + "class Queries:\n", + " def __init__(self, session):\n", + " self.session = session\n", + "\n", + " def address_from_fadd_type_fadd(self, fadd_type, fadd):\n", + " # FIXME multi etc.\n", + " res = [\n", + " i\n", + " for i, in self.session.execute(\n", + " sql_text(\n", + " \"select * from address_from_fadd_type_fadd(:fadd_type, :fadd)\"\n", + " ),\n", + " dict(fadd_type=fadd_type, fadd=fadd),\n", + " )\n", + " ]\n", + " if res:\n", + " return res[0]\n", + "\n", + " def desc_inst_from_label(self, label):\n", + " # FIXME multi etc.\n", + " res = [\n", + " i\n", + " for i, in self.session.execute(\n", + " sql_text(\"select * from desc_inst_from_label(:label)\"),\n", + " dict(label=label),\n", + " )\n", + " ]\n", + " if res:\n", + " return res[0]\n", + "\n", + " def desc_quant_from_label(self, label):\n", + " # FIXME multi etc.\n", + " res = [\n", + " i\n", + " for i, in self.session.execute(\n", + " sql_text(\"select * from desc_quant_from_label(:label)\"),\n", + " dict(label=label),\n", + " )\n", + " ]\n", + " if res:\n", + " return res[0]\n", + "\n", + " def desc_cat_from_label_domain_label(self, label, domain_label):\n", + " # FIXME multi etc.\n", + " res = [\n", + " i\n", + " for i, in self.session.execute(\n", + " sql_text(\n", + " \"select * from desc_cat_from_label_domain_label(:label, :domain_label)\"\n", + " ),\n", + " dict(label=label, domain_label=domain_label),\n", + " )\n", + " ]\n", + " if res:\n", + " return res[0]\n", + "\n", + " def cterm_from_label(self, label):\n", + " # FIXME multi etc.\n", + " res = [\n", + " i\n", + " for i, in self.session.execute(\n", + " sql_text(\"select * from cterm_from_label(:label)\"),\n", + " dict(label=label),\n", + " )\n", + " ]\n", + " if res:\n", + " return res[0]\n", + "\n", + " def insts_from_dataset_ids(self, dataset, ids):\n", + " return list(\n", + " self.session.execute(\n", + " sql_text(\n", + " \"select * from insts_from_dataset_ids(:dataset, :ids)\"\n", + " ),\n", + " dict(dataset=dataset, ids=ids),\n", + " )\n", + " )\n", + "\n", + "\n", + "class InternalIds:\n", + " def set_desc_quant_from_label(self, label: str, desctriptor: str):\n", + " self.__setattr__(label, desctriptor)\n", + "\n", + " def __init__(self, queries) -> None:\n", + "\n", + " q = queries\n", + " self._q = queries\n", + "\n", + " self.addr_suid = q.address_from_fadd_type_fadd(\n", + " \"tabular-header\", \"id_sub\"\n", + " )\n", + " self.addr_said = q.address_from_fadd_type_fadd(\n", + " \"tabular-header\", \"id_sam\"\n", + " )\n", + " self.addr_spec = q.address_from_fadd_type_fadd(\n", + " \"tabular-header\", \"species\"\n", + " )\n", + " self.addr_saty = q.address_from_fadd_type_fadd(\n", + " \"tabular-header\", \"sample_type\"\n", + " )\n", + " self.addr_faid = q.address_from_fadd_type_fadd(\n", + " \"tabular-header\", \"fascicle\"\n", + " ) # for REVA ft\n", + "\n", + " self.addr_tmod = q.address_from_fadd_type_fadd(\n", + " \"tabular-header\", \"modality\"\n", + " )\n", + " # addr_trai = address_from_fadd_type_fadd('tabular-header', 'raw_anat_index')\n", + " # addr_tnai = address_from_fadd_type_fadd('tabular-header', 'norm_anat_index')\n", + " # addr_context = address_from_fadd_type_fadd('context', '#/path-metadata/{index of match remote_id}/dataset_relative_path') # XXX this doesn't do what we want, I think what we really would want in these contexts are objects_internal that reference the file system state for a given updated snapshot, that is the real \"object\" that corresponds to the path-metadata.json that we are working from\n", + "\n", + " # addr_jpmod = address_from_fadd_type_fadd('json-path-with-types', '#/#int/modality')\n", + " # addr_jprai = address_from_fadd_type_fadd('json-path-with-types', '#/#int/anat_index')\n", + " # addr_jpnai = address_from_fadd_type_fadd('json-path-with-types', '#/#int/norm_anat_index')\n", + "\n", + " self.addr_jpdrp = q.address_from_fadd_type_fadd(\n", + " \"json-path-with-types\",\n", + " \"#/path-metadata/data/#int/dataset_relative_path\",\n", + " )\n", + "\n", + " # XXX these are more accurate if opaque\n", + " self.addr_jpmod = q.address_from_fadd_type_fadd(\n", + " \"json-path-with-types\",\n", + " \"#/path-metadata/data/#int/dataset_relative_path#derive-modality\",\n", + " )\n", + " # addr_jprai = address_from_fadd_type_fadd('json-path-with-types', '#/path-metadata/data/#int/dataset_relative_path#derive-raw-anat-index')\n", + " self.addr_jpnai = q.address_from_fadd_type_fadd(\n", + " \"json-path-with-types\",\n", + " \"#/path-metadata/data/#int/dataset_relative_path#derive-norm-anat-index-v1\",\n", + " )\n", + " self.addr_jpnain = q.address_from_fadd_type_fadd(\n", + " \"json-path-with-types\",\n", + " \"#/path-metadata/data/#int/dataset_relative_path#derive-norm-anat-index-v1-min\",\n", + " )\n", + " self.addr_jpnaix = q.address_from_fadd_type_fadd(\n", + " \"json-path-with-types\",\n", + " \"#/path-metadata/data/#int/dataset_relative_path#derive-norm-anat-index-v1-max\",\n", + " )\n", + " self.addr_jpsuid = q.address_from_fadd_type_fadd(\n", + " \"json-path-with-types\",\n", + " \"#/path-metadata/data/#int/dataset_relative_path#derive-subject-id\",\n", + " )\n", + " self.addr_jpsaid = q.address_from_fadd_type_fadd(\n", + " \"json-path-with-types\",\n", + " \"#/path-metadata/data/#int/dataset_relative_path#derive-sample-id\",\n", + " )\n", + "\n", + " self.addr_jpspec = q.address_from_fadd_type_fadd(\n", + " \"json-path-with-types\", \"#/local/tom-made-it-up/species\"\n", + " )\n", + " self.addr_jpsaty = q.address_from_fadd_type_fadd(\n", + " \"json-path-with-types\", \"#/local/tom-made-it-up/sample_type\"\n", + " )\n", + "\n", + " # future version when we actually have the metadata files\n", + " # addr_jpmod = address_from_fadd_type_fadd('json-path-with-types', '#/curation-export/manifest/#int/modality')\n", + " # addr_jprai = address_from_fadd_type_fadd('json-path-with-types', '#/curation-export/samples/#int/raw_anat_index')\n", + " # addr_jpnai = address_from_fadd_type_fadd('json-path-with-types', '#/curation-export/samples/#int/norm_anat_index')\n", + " # addr_jpsuid = address_from_fadd_type_fadd('json-path-with-types', '#/curation-export/subjects/#int/id_sub')\n", + " # addr_jpsaid = address_from_fadd_type_fadd('json-path-with-types', '#/curation-export/samples/#int/id_sam')\n", + "\n", + " self.addr_const_null = q.address_from_fadd_type_fadd(\"constant\", None)\n", + "\n", + " # qd_rai = desc_quant_from_label('reva ft sample anatomical location distance index raw')\n", + " self.qd_nai = q.desc_quant_from_label(\n", + " \"reva ft sample anatomical location distance index normalized v1\"\n", + " )\n", + " self.qd_nain = q.desc_quant_from_label(\n", + " \"reva ft sample anatomical location distance index normalized v1 min\"\n", + " )\n", + " self.qd_naix = q.desc_quant_from_label(\n", + " \"reva ft sample anatomical location distance index normalized v1 max\"\n", + " )\n", + "\n", + " self.cd_mod = q.desc_cat_from_label_domain_label(\n", + " \"hasDataAboutItModality\", None\n", + " )\n", + " self.cd_bot = q.desc_cat_from_label_domain_label(\n", + " \"bottom\", None\n", + " ) # we just need something we can reference that points to null so we can have a refernce to all the objects\n", + "\n", + " self.id_human = q.desc_inst_from_label(\"human\")\n", + " self.id_nerve = q.desc_inst_from_label(\"nerve\")\n", + " self.id_nerve_volume = q.desc_inst_from_label(\"nerve-volume\")\n", + " self.luid = {\n", + " \"human\": self.id_human,\n", + " \"nerve\": self.id_nerve,\n", + " \"nerve-volume\": self.id_nerve_volume,\n", + " }\n", + "\n", + " self.ct_mod = q.cterm_from_label(\"microct\") # lol ct ct\n", + " self.ct_hack = q.cterm_from_label(\"hack-associate-some-value\")\n", + " self.luct = {\n", + " \"ct-hack\": self.ct_hack,\n", + " \"microct\": self.ct_mod,\n", + " }" + ] + }, + { + "cell_type": "code", + "execution_count": 21, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "Units(label='mm', iri='http://qudt.org/vocab/unit/MM')" + ] + }, + "execution_count": 21, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "Units(\"mm\", \"http://qudt.org/vocab/unit/MM\")" + ] + }, + { + "cell_type": "code", + "execution_count": 71, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "2024-09-12 07:32:03,543 INFO sqlalchemy.engine.Engine BEGIN (implicit)\n", + "2024-09-12 07:32:03,544 INFO sqlalchemy.engine.Engine INSERT INTO units (label, iri) VALUES (%(label)s, %(iri)s)\n", + "2024-09-12 07:32:03,544 INFO sqlalchemy.engine.Engine [cached since 5593s ago] {'label': 'pixel', 'iri': 'http://uri.interlex.org/tgbugs/uris/readable/aspect/unit/pixel'}\n", + "Error: (psycopg2.errors.UniqueViolation) duplicate key value violates unique constraint \"units_label_key\"\n", + "DETAIL: Key (label)=(pixel) already exists.\n", + "\n", + "[SQL: INSERT INTO units (label, iri) VALUES (%(label)s, %(iri)s)]\n", + "[parameters: {'label': 'pixel', 'iri': 'http://uri.interlex.org/tgbugs/uris/readable/aspect/unit/pixel'}]\n", + "(Background on this error at: https://sqlalche.me/e/20/gkpj)\n", + "2024-09-12 07:32:03,636 INFO sqlalchemy.engine.Engine ROLLBACK\n", + "2024-09-12 07:32:03,681 INFO sqlalchemy.engine.Engine BEGIN (implicit)\n", + "2024-09-12 07:32:03,681 INFO sqlalchemy.engine.Engine INSERT INTO objects (id, id_type) VALUES (%(id)s, %(id_type)s) ON CONFLICT DO NOTHING\n", + "2024-09-12 07:32:03,681 INFO sqlalchemy.engine.Engine [cached since 252.6s ago] {'id': 'aa43eda8-b29a-4c25-9840-ecbd57598afc', 'id_type': 'dataset'}\n", + "2024-09-12 07:32:03,773 INFO sqlalchemy.engine.Engine COMMIT\n" + ] + } + ], + "source": [ + "from dataclasses import dataclass, asdict\n", + "import typing\n", + "from typing import ClassVar, Dict, Protocol, Any\n", + "\n", + "type UUID = str\n", + "\n", + "\n", + "class Dataclass(Protocol):\n", + " __dataclass_fields__: ClassVar[Dict[str, Any]]\n", + "\n", + "\n", + "@dataclass\n", + "class Unit:\n", + " __table__ = \"units\"\n", + " label: str\n", + " iri: str\n", + "\n", + "\n", + "@dataclass\n", + "class Objects:\n", + " __table__ = \"objects\"\n", + " id: UUID\n", + " id_type: str\n", + " id_file: int | None = None\n", + " id_internal: UUID | None = None\n", + "\n", + "\n", + "@dataclass\n", + "class DescriptorQuant:\n", + " __table__ = \"descriptors_quant\"\n", + " label: str\n", + " aggregation_type: str\n", + " unit: str | None = None\n", + " aspect: int | None = None\n", + " domain: str | None = None\n", + " description: str | None = None\n", + " curator_note: str | None = None\n", + " shape: str = \"scalar\"\n", + "\n", + "\n", + "class Ingest:\n", + "\n", + " def __init__(self, session: Session):\n", + " self.session = session\n", + "\n", + " def execute_insert(\n", + " self, query: str, dataclasses: typing.Sequence[Dataclass]\n", + " ) -> None:\n", + " \"\"\"Execute a query with dataclasses as parameters\n", + "\n", + " Parameters\n", + " ----------\n", + " query : str\n", + " sql query string\n", + " dataclasses : typing.Sequence[Dataclass]\n", + " a list of SQL table dataclasses to be inserted\n", + " \"\"\"\n", + " statement = sql_text(query)\n", + " params = [asdict(dataclass) for dataclass in dataclasses]\n", + " try:\n", + " self.session.execute(statement=statement, params=params)\n", + " self.session.commit()\n", + " except Exception as e:\n", + " print(f\"Error: {e}\")\n", + " self.session.rollback()\n", + "\n", + " def insert_units(self, units: typing.Sequence[Unit]) -> None:\n", + " query = r\"INSERT INTO units (label, iri) VALUES (:label, :iri)\"\n", + " self.execute_insert(query=query, dataclasses=units)\n", + "\n", + " def insert_objects(self, objects: typing.Sequence[Objects]) -> None:\n", + " query = r\"INSERT INTO objects (id, id_type) VALUES (:id, :id_type) ON CONFLICT DO NOTHING\"\n", + " self.execute_insert(query=query, dataclasses=objects)\n", + "\n", + " def insert_descriptors_quant(\n", + " self, descriptor_quants: typing.Sequence[DescriptorQuant]\n", + " ) -> None:\n", + " query = r\"INSERT INTO descriptors_quant (label, domain, aspect, unit, aggregation_type) VALUES (:label, :domain, :aspect, :unit, :aggregation_type)\"\n", + " self.execute_insert(query=query, dataclasses=descriptor_quants)\n", + "\n", + "\n", + "ingest = Ingest(session=session)\n", + "\n", + "ingest.insert_units(\n", + " units=[\n", + " Unit(\n", + " label=\"pixel\",\n", + " iri=\"http://uri.interlex.org/tgbugs/uris/readable/aspect/unit/pixel\",\n", + " ),\n", + " ]\n", + ")\n", + "\n", + "ingest.insert_objects(\n", + " objects=[\n", + " Objects(id=dataset[\"content\"][\"id\"].split(\":\")[-1], id_type=\"dataset\"),\n", + " ]\n", + ")\n", + "\n", + "ingest.insert_descriptors_quant(\n", + " descriptor_quants=[\n", + " DescriptorQuant(\n", + " label=\"fascicle cross section diameter um min\",\n", + " domain=26, # \"fiber-cross-section\" # TODO: label to ID\n", + " aspect=5, # \"diameter\", # TODO: label to ID\n", + " unit=4, # pixel\", # TODO: label to ID\n", + " aggregation_type=\"min\",\n", + " ),\n", + " ]\n", + ")" + ] + }, + { + "cell_type": "code", + "execution_count": 66, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "'N:dataset:aa43eda8-b29a-4c25-9840-ecbd57598afc'" + ] + }, + "execution_count": 66, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "dataset[\"content\"][\"id\"]" + ] + }, + { + "cell_type": "code", + "execution_count": 54, + "metadata": {}, + "outputs": [ + { + "ename": "IndentationError", + "evalue": "expected an indented block after function definition on line 32 (4174477168.py, line 36)", + "output_type": "error", + "traceback": [ + "\u001b[0;36m Cell \u001b[0;32mIn[54], line 36\u001b[0;36m\u001b[0m\n\u001b[0;31m Ingests(dataset).extract()\u001b[0m\n\u001b[0m ^\u001b[0m\n\u001b[0;31mIndentationError\u001b[0m\u001b[0;31m:\u001b[0m expected an indented block after function definition on line 32\n" + ] + } + ], + "source": [ + "# wrap columns\n", + "q = Queries(session)\n", + "i = InternalIds(q)\n", + "\n", + "# updated_transitive,\n", + "# values_objects,\n", + "# values_dataset_object,\n", + "# make_values_instances,\n", + "# make_values_parents,\n", + "# make_void,\n", + "# make_vocd,\n", + "# make_voqd,\n", + "# make_values_cat,\n", + "# make_values_quant,\n", + "\n", + "\n", + "class Ingests:\n", + " \"\"\"Create ingest objects for a dataset using Pennsieive direct\"\"\"\n", + "\n", + " def __init__(self, dataset: str) -> None:\n", + " self.dataset = dataset\n", + "\n", + " def extract(self):\n", + " return (self.updated_transitive(), self.values_objects())\n", + "\n", + " def updated_transitive(self):\n", + " \"\"\"Last updated Timestamp\"\"\"\n", + " return max(\n", + " [v[\"content\"][\"updatedAt\"] for v in self.dataset[\"children\"]]\n", + " )\n", + " \n", + " def values_objects(self):\n", + " \n", + " \n", + "Ingests(dataset).extract()" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "quantdb", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.12.2" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/ingest.ipynb b/ingest.ipynb new file mode 100644 index 0000000..38c2ce8 --- /dev/null +++ b/ingest.ipynb @@ -0,0 +1,1102 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# f001" + ] + }, + { + "cell_type": "code", + "execution_count": 61, + "metadata": {}, + "outputs": [], + "source": [ + "penncli = PennsieveClient()" + ] + }, + { + "cell_type": "code", + "execution_count": 45, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "'2024-06-29T22:46:50.374403Z'" + ] + }, + "execution_count": 45, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "max([v[\"content\"][\"updatedAt\"] for v in penncli.get_dataset(did)[\"children\"]])" + ] + }, + { + "cell_type": "code", + "execution_count": 62, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{'nodeId': 'N:package:cc6c1783-4eb4-4a0a-b723-247827ebeb4e',\n", + " 'fileName': 'naveen_paper_B733_T7L_A_LEVEL_3_fascicles.csv',\n", + " 'packageName': 'naveen_paper_B733_T7L_A_LEVEL_3_fascicles.csv',\n", + " 'path': ['derivative', 'sam-l', 'sam-l-seg-t7', 'sam-l-seg-t7-LEVEL_3'],\n", + " 'url': 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+ " 'size': 26289}" + ] + }, + "execution_count": 62, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# penncli = PennsieveClient()\n", + "did = \"N:dataset:aa43eda8-b29a-4c25-9840-ecbd57598afc\"\n", + "manifest = penncli.get_dataset_manifest(did)\n", + "manifest\n", + "\n", + "\n", + "def pull_files(id_or_name: str, pattern: str | None = None) -> list[str]:\n", + " \"\"\"Export a dataset to a directory\n", + "\n", + " Parameters\n", + " ----------\n", + " id_or_name : str\n", + " Dataset ID or name\n", + " output_dir : Path | str\n", + " Output directory\n", + " verbose : bool, optional\n", + " Prints filename being downloaded, by default True\n", + " \"\"\"\n", + " files = []\n", + " url = \"https://api.pennsieve.io/packages/download-manifest\"\n", + " # output_dir = Path(output_dir) / id_or_name\n", + " # Pull dataset for root children IDs\n", + " dataset = penncli.get_dataset(id_or_name)\n", + " for child in dataset[\"children\"]:\n", + " payload = {\"nodeIds\": [child[\"content\"][\"nodeId\"]]}\n", + " # Pull tree for 1 child at a time since prebuilt s3 links only last a couple hours\n", + " # If all children are pulled at once, the links will expire before all files are downloaded if over 200GBs\n", + " # resp = penncli._post(url, payload=payload)\n", + " # try:\n", + " # manifest = resp.json()\n", + " # except:\n", + " # print(payload)\n", + " # print(resp.text)\n", + " # continue\n", + " manifest = penncli.get_child_manifest(\n", + " node_id=child[\"content\"][\"nodeId\"]\n", + " )\n", + " for filemeta in manifest[\"data\"]:\n", + " # filemeta[\"\"] = manifest[\"datasetId\"]\n", + " if Path(filemeta[\"fileName\"]).suffix in [\".csv\"]:\n", + " files.append(filemeta)\n", + " return dataset, files\n", + "\n", + "\n", + "dataset, files = pull_files(did)\n", + "fascicle_files = [v for v in files if \"fascicles\" in v[\"fileName\"].lower()]\n", + "file = fascicle_files[-1]\n", + "file" + ] + }, + { + "cell_type": "code", + "execution_count": 63, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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fasciclearealongest_diametershortest_diametereff_diamc_estimate_navc_estimate_nfnfibers_w_c_estimate_navnfibers_w_c_estimate_nfnfibers_all...epi_distepi_dist_invnerve_based_areanerve_based_perimeternerve_based_eff_diamperinerium_verticesperinerium_vertices_pxnerve_based_shortest_diameterhull_contrshull_contr_areas
01601840.629341907.000466846.340808875.37836901650246132111521115...515.9310.000477860.1984084.885780.020[[3127.5 113.4 ]\\n [3160.35 113.4 ]\\n [3192...[[20850 756]\\n [21069 756]\\n [21280 826]...630.464[ 0. 5. 10. 15. 20. 25. 30. 35. 40. ...[3.38965189e+06 3.29847812e+06 3.20848098e+06 ...
12151657.783648566.334306329.680645439.42768201300154828482848...274.845241.087163417.7361544.309456.147[[1488.15 480.75]\\n [1504.8 485.55]\\n [1521...[[ 9921 3205]\\n [10032 3237]\\n [10143 3262]...350.905[ 0. 5. 10. 15. 20. 25. 30. 35. 40. ...[1.08945157e+06 1.03852465e+06 9.88700989e+05 ...
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4572513.774721370.254924237.445074303.854250063069513251325...432.61383.31881804.5891104.140322.733[[1107. 441.45]\\n [1115.55 446.4 ]\\n [1119...[[7380 2943]\\n [7437 2976]\\n [7462 3032]\\n [75...250.218[ 0. 5. 10. 15. 20. 25. 30. 35. 40. ...[545363.925 509233.56034859 474385.219163...
\n", + "

5 rows × 49 columns

\n", + "
" + ], + "text/plain": [ + " fascicle area longest_diameter shortest_diameter eff_diam \\\n", + "0 1 601840.629341 907.000466 846.340808 875.378369 \n", + "1 2 151657.783648 566.334306 329.680645 439.427682 \n", + "2 3 42956.807122 253.176413 208.473851 233.868137 \n", + "3 4 19745.681094 177.272006 131.860742 158.559080 \n", + "4 5 72513.774721 370.254924 237.445074 303.854250 \n", + "\n", + " c_estimate_nav c_estimate_nf nfibers_w_c_estimate_nav \\\n", + "0 0 16502 4613 \n", + "1 0 1300 1548 \n", + "2 0 239 289 \n", + "3 0 108 120 \n", + "4 0 630 695 \n", + "\n", + " nfibers_w_c_estimate_nf nfibers_all ... epi_dist epi_dist_inv \\\n", + "0 21115 21115 ... 515.931 0.000 \n", + "1 2848 2848 ... 274.845 241.087 \n", + "2 528 528 ... 239.555 276.376 \n", + "3 228 228 ... 394.411 121.521 \n", + "4 1325 1325 ... 432.613 83.318 \n", + "\n", + " nerve_based_area nerve_based_perimeter nerve_based_eff_diam \\\n", + "0 477860.198 4084.885 780.020 \n", + "1 163417.736 1544.309 456.147 \n", + "2 51265.699 894.344 255.487 \n", + "3 24790.376 657.547 177.663 \n", + "4 81804.589 1104.140 322.733 \n", + "\n", + " perinerium_vertices \\\n", + "0 [[3127.5 113.4 ]\\n [3160.35 113.4 ]\\n [3192... \n", + "1 [[1488.15 480.75]\\n [1504.8 485.55]\\n [1521... \n", + "2 [[605.55 361.5 ]\\n [614.85 361.5 ]\\n [624.3 3... \n", + "3 [[728.1 470.85]\\n [734.7 469.2 ]\\n [741. 4... \n", + "4 [[1107. 441.45]\\n [1115.55 446.4 ]\\n [1119... \n", + "\n", + " perinerium_vertices_px \\\n", + "0 [[20850 756]\\n [21069 756]\\n [21280 826]... \n", + "1 [[ 9921 3205]\\n [10032 3237]\\n [10143 3262]... \n", + "2 [[4037 2410]\\n [4099 2410]\\n [4162 2410]\\n [42... \n", + "3 [[4854 3139]\\n [4898 3128]\\n [4940 3123]\\n [49... \n", + "4 [[7380 2943]\\n [7437 2976]\\n [7462 3032]\\n [75... \n", + "\n", + " nerve_based_shortest_diameter \\\n", + "0 630.464 \n", + "1 350.905 \n", + "2 215.234 \n", + "3 138.983 \n", + "4 250.218 \n", + "\n", + " hull_contrs \\\n", + "0 [ 0. 5. 10. 15. 20. 25. 30. 35. 40. ... \n", + "1 [ 0. 5. 10. 15. 20. 25. 30. 35. 40. ... \n", + "2 [ 0. 5. 10. 15. 20. 25. 30. 35. 40. ... \n", + "3 [ 0. 5. 10. 15. 20. 25. 30. 35. 40. 45. 50. 5... \n", + "4 [ 0. 5. 10. 15. 20. 25. 30. 35. 40. ... \n", + "\n", + " hull_contr_areas \n", + "0 [3.38965189e+06 3.29847812e+06 3.20848098e+06 ... \n", + "1 [1.08945157e+06 1.03852465e+06 9.88700989e+05 ... \n", + "2 [3.41771325e+05 3.12657208e+05 2.84935875e+05 ... \n", + "3 [165269.175 144192.08666671 124780.433718... \n", + "4 [545363.925 509233.56034859 474385.219163... \n", + "\n", + "[5 rows x 49 columns]" + ] + }, + "execution_count": 63, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "import pandas as pd\n", + "\n", + "df = pd.read_csv(file[\"url\"])\n", + "if \"Unnamed: 0\" in df.columns:\n", + " df = df.drop(columns=[\"Unnamed: 0\"])\n", + "df.head()" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "metadata": {}, + "outputs": [], + "source": [ + "from quantdb.config import auth\n", + "from sqlalchemy import create_engine\n", + "from quantdb.utils import dbUri, isoformat, log\n", + "from sqlalchemy.sql import text as sql_text\n", + "from sqlalchemy.orm import Session\n", + "\n", + "# pull in the db connection info\n", + "dbkwargs = {\n", + " k: auth.get(f\"db-{k}\") for k in (\"user\", \"host\", \"port\", \"database\")\n", + "} # TODO integrate with cli options\n", + "# custom user variable needed\n", + "dbkwargs[\"dbuser\"] = dbkwargs.pop(\"user\")\n", + "# create connection env with DB\n", + "engine = create_engine(dbUri(**dbkwargs))\n", + "# bool: echo me\n", + "engine.echo = True\n", + "# use connection env as unique session\n", + "session = Session(engine)\n", + "\n", + "\n", + "class Queries:\n", + " def __init__(self, session):\n", + " self.session = session\n", + "\n", + " def address_from_fadd_type_fadd(self, fadd_type, fadd):\n", + " # FIXME multi etc.\n", + " res = [\n", + " i\n", + " for i, in self.session.execute(\n", + " sql_text(\n", + " \"select * from address_from_fadd_type_fadd(:fadd_type, :fadd)\"\n", + " ),\n", + " dict(fadd_type=fadd_type, fadd=fadd),\n", + " )\n", + " ]\n", + " if res:\n", + " return res[0]\n", + "\n", + " def desc_inst_from_label(self, label):\n", + " # FIXME multi etc.\n", + " res = [\n", + " i\n", + " for i, in self.session.execute(\n", + " sql_text(\"select * from desc_inst_from_label(:label)\"),\n", + " dict(label=label),\n", + " )\n", + " ]\n", + " if res:\n", + " return res[0]\n", + "\n", + " def desc_quant_from_label(self, label):\n", + " # FIXME multi etc.\n", + " res = [\n", + " i\n", + " for i, in self.session.execute(\n", + " sql_text(\"select * from desc_quant_from_label(:label)\"),\n", + " dict(label=label),\n", + " )\n", + " ]\n", + " if res:\n", + " return res[0]\n", + "\n", + " def desc_cat_from_label_domain_label(self, label, domain_label):\n", + " # FIXME multi etc.\n", + " res = [\n", + " i\n", + " for i, in self.session.execute(\n", + " sql_text(\n", + " \"select * from desc_cat_from_label_domain_label(:label, :domain_label)\"\n", + " ),\n", + " dict(label=label, domain_label=domain_label),\n", + " )\n", + " ]\n", + " if res:\n", + " return res[0]\n", + "\n", + " def cterm_from_label(self, label):\n", + " # FIXME multi etc.\n", + " res = [\n", + " i\n", + " for i, in self.session.execute(\n", + " sql_text(\"select * from cterm_from_label(:label)\"),\n", + " dict(label=label),\n", + " )\n", + " ]\n", + " if res:\n", + " return res[0]\n", + "\n", + " def insts_from_dataset_ids(self, dataset, ids):\n", + " return list(\n", + " self.session.execute(\n", + " sql_text(\n", + " \"select * from insts_from_dataset_ids(:dataset, :ids)\"\n", + " ),\n", + " dict(dataset=dataset, ids=ids),\n", + " )\n", + " )\n", + "\n", + "\n", + "class InternalIds:\n", + " def set_desc_quant_from_label(self, label: str, desctriptor: str):\n", + " self.__setattr__(label, desctriptor)\n", + "\n", + " def __init__(self, queries) -> None:\n", + "\n", + " q = queries\n", + " self._q = queries\n", + "\n", + " self.addr_suid = q.address_from_fadd_type_fadd(\n", + " \"tabular-header\", \"id_sub\"\n", + " )\n", + " self.addr_said = q.address_from_fadd_type_fadd(\n", + " \"tabular-header\", \"id_sam\"\n", + " )\n", + " self.addr_spec = q.address_from_fadd_type_fadd(\n", + " \"tabular-header\", \"species\"\n", + " )\n", + " self.addr_saty = q.address_from_fadd_type_fadd(\n", + " \"tabular-header\", \"sample_type\"\n", + " )\n", + " self.addr_faid = q.address_from_fadd_type_fadd(\n", + " \"tabular-header\", \"fascicle\"\n", + " ) # for REVA ft\n", + "\n", + " self.addr_tmod = q.address_from_fadd_type_fadd(\n", + " \"tabular-header\", \"modality\"\n", + " )\n", + " # addr_trai = address_from_fadd_type_fadd('tabular-header', 'raw_anat_index')\n", + " # addr_tnai = address_from_fadd_type_fadd('tabular-header', 'norm_anat_index')\n", + " # addr_context = address_from_fadd_type_fadd('context', '#/path-metadata/{index of match remote_id}/dataset_relative_path') # XXX this doesn't do what we want, I think what we really would want in these contexts are objects_internal that reference the file system state for a given updated snapshot, that is the real \"object\" that corresponds to the path-metadata.json that we are working from\n", + "\n", + " # addr_jpmod = address_from_fadd_type_fadd('json-path-with-types', '#/#int/modality')\n", + " # addr_jprai = address_from_fadd_type_fadd('json-path-with-types', '#/#int/anat_index')\n", + " # addr_jpnai = address_from_fadd_type_fadd('json-path-with-types', '#/#int/norm_anat_index')\n", + "\n", + " self.addr_jpdrp = q.address_from_fadd_type_fadd(\n", + " \"json-path-with-types\",\n", + " \"#/path-metadata/data/#int/dataset_relative_path\",\n", + " )\n", + "\n", + " # XXX these are more accurate if opaque\n", + " self.addr_jpmod = q.address_from_fadd_type_fadd(\n", + " \"json-path-with-types\",\n", + " \"#/path-metadata/data/#int/dataset_relative_path#derive-modality\",\n", + " )\n", + " # addr_jprai = address_from_fadd_type_fadd('json-path-with-types', '#/path-metadata/data/#int/dataset_relative_path#derive-raw-anat-index')\n", + " self.addr_jpnai = q.address_from_fadd_type_fadd(\n", + " \"json-path-with-types\",\n", + " \"#/path-metadata/data/#int/dataset_relative_path#derive-norm-anat-index-v1\",\n", + " )\n", + " self.addr_jpnain = q.address_from_fadd_type_fadd(\n", + " \"json-path-with-types\",\n", + " \"#/path-metadata/data/#int/dataset_relative_path#derive-norm-anat-index-v1-min\",\n", + " )\n", + " self.addr_jpnaix = q.address_from_fadd_type_fadd(\n", + " \"json-path-with-types\",\n", + " \"#/path-metadata/data/#int/dataset_relative_path#derive-norm-anat-index-v1-max\",\n", + " )\n", + " self.addr_jpsuid = q.address_from_fadd_type_fadd(\n", + " \"json-path-with-types\",\n", + " \"#/path-metadata/data/#int/dataset_relative_path#derive-subject-id\",\n", + " )\n", + " self.addr_jpsaid = q.address_from_fadd_type_fadd(\n", + " \"json-path-with-types\",\n", + " \"#/path-metadata/data/#int/dataset_relative_path#derive-sample-id\",\n", + " )\n", + "\n", + " self.addr_jpspec = q.address_from_fadd_type_fadd(\n", + " \"json-path-with-types\", \"#/local/tom-made-it-up/species\"\n", + " )\n", + " self.addr_jpsaty = q.address_from_fadd_type_fadd(\n", + " \"json-path-with-types\", \"#/local/tom-made-it-up/sample_type\"\n", + " )\n", + "\n", + " # future version when we actually have the metadata files\n", + " # addr_jpmod = address_from_fadd_type_fadd('json-path-with-types', '#/curation-export/manifest/#int/modality')\n", + " # addr_jprai = address_from_fadd_type_fadd('json-path-with-types', '#/curation-export/samples/#int/raw_anat_index')\n", + " # addr_jpnai = address_from_fadd_type_fadd('json-path-with-types', '#/curation-export/samples/#int/norm_anat_index')\n", + " # addr_jpsuid = address_from_fadd_type_fadd('json-path-with-types', '#/curation-export/subjects/#int/id_sub')\n", + " # addr_jpsaid = address_from_fadd_type_fadd('json-path-with-types', '#/curation-export/samples/#int/id_sam')\n", + "\n", + " self.addr_const_null = q.address_from_fadd_type_fadd(\"constant\", None)\n", + "\n", + " # qd_rai = desc_quant_from_label('reva ft sample anatomical location distance index raw')\n", + " self.qd_nai = q.desc_quant_from_label(\n", + " \"reva ft sample anatomical location distance index normalized v1\"\n", + " )\n", + " self.qd_nain = q.desc_quant_from_label(\n", + " \"reva ft sample anatomical location distance index normalized v1 min\"\n", + " )\n", + " self.qd_naix = q.desc_quant_from_label(\n", + " \"reva ft sample anatomical location distance index normalized v1 max\"\n", + " )\n", + "\n", + " self.cd_mod = q.desc_cat_from_label_domain_label(\n", + " \"hasDataAboutItModality\", None\n", + " )\n", + " self.cd_bot = q.desc_cat_from_label_domain_label(\n", + " \"bottom\", None\n", + " ) # we just need something we can reference that points to null so we can have a refernce to all the objects\n", + "\n", + " self.id_human = q.desc_inst_from_label(\"human\")\n", + " self.id_nerve = q.desc_inst_from_label(\"nerve\")\n", + " self.id_nerve_volume = q.desc_inst_from_label(\"nerve-volume\")\n", + " self.luid = {\n", + " \"human\": self.id_human,\n", + " \"nerve\": self.id_nerve,\n", + " \"nerve-volume\": self.id_nerve_volume,\n", + " }\n", + "\n", + " self.ct_mod = q.cterm_from_label(\"microct\") # lol ct ct\n", + " self.ct_hack = q.cterm_from_label(\"hack-associate-some-value\")\n", + " self.luct = {\n", + " \"ct-hack\": self.ct_hack,\n", + " \"microct\": self.ct_mod,\n", + " }" + ] + }, + { + "cell_type": "code", + "execution_count": 21, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "Units(label='mm', iri='http://qudt.org/vocab/unit/MM')" + ] + }, + "execution_count": 21, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "Units(\"mm\", \"http://qudt.org/vocab/unit/MM\")" + ] + }, + { + "cell_type": "code", + "execution_count": 71, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "2024-09-12 07:32:03,543 INFO sqlalchemy.engine.Engine BEGIN (implicit)\n", + "2024-09-12 07:32:03,544 INFO sqlalchemy.engine.Engine INSERT INTO units (label, iri) VALUES (%(label)s, %(iri)s)\n", + "2024-09-12 07:32:03,544 INFO sqlalchemy.engine.Engine [cached since 5593s ago] {'label': 'pixel', 'iri': 'http://uri.interlex.org/tgbugs/uris/readable/aspect/unit/pixel'}\n", + "Error: (psycopg2.errors.UniqueViolation) duplicate key value violates unique constraint \"units_label_key\"\n", + "DETAIL: Key (label)=(pixel) already exists.\n", + "\n", + "[SQL: INSERT INTO units (label, iri) VALUES (%(label)s, %(iri)s)]\n", + "[parameters: {'label': 'pixel', 'iri': 'http://uri.interlex.org/tgbugs/uris/readable/aspect/unit/pixel'}]\n", + "(Background on this error at: https://sqlalche.me/e/20/gkpj)\n", + "2024-09-12 07:32:03,636 INFO sqlalchemy.engine.Engine ROLLBACK\n", + "2024-09-12 07:32:03,681 INFO sqlalchemy.engine.Engine BEGIN (implicit)\n", + "2024-09-12 07:32:03,681 INFO sqlalchemy.engine.Engine INSERT INTO objects (id, id_type) VALUES (%(id)s, %(id_type)s) ON CONFLICT DO NOTHING\n", + "2024-09-12 07:32:03,681 INFO sqlalchemy.engine.Engine [cached since 252.6s ago] {'id': 'aa43eda8-b29a-4c25-9840-ecbd57598afc', 'id_type': 'dataset'}\n", + "2024-09-12 07:32:03,773 INFO sqlalchemy.engine.Engine COMMIT\n" + ] + } + ], + "source": [ + "from dataclasses import dataclass, asdict\n", + "import typing\n", + "from typing import ClassVar, Dict, Protocol, Any\n", + "\n", + "type UUID = str\n", + "\n", + "\n", + "class Dataclass(Protocol):\n", + " __dataclass_fields__: ClassVar[Dict[str, Any]]\n", + "\n", + "\n", + "@dataclass\n", + "class Unit:\n", + " __table__ = \"units\"\n", + " label: str\n", + " iri: str\n", + "\n", + "\n", + "@dataclass\n", + "class Objects:\n", + " __table__ = \"objects\"\n", + " id: UUID\n", + " id_type: str\n", + " id_file: int | None = None\n", + " id_internal: UUID | None = None\n", + "\n", + "\n", + "@dataclass\n", + "class DescriptorQuant:\n", + " __table__ = \"descriptors_quant\"\n", + " label: str\n", + " iri: str\n", + "\n", + "\n", + "class Ingest:\n", + "\n", + " def __init__(self, session: Session):\n", + " self.session = session\n", + "\n", + " def execute_insert(\n", + " self, query: str, dataclasses: typing.Sequence[Dataclass]\n", + " ) -> None:\n", + " \"\"\"Execute a query with dataclasses as parameters\n", + "\n", + " Parameters\n", + " ----------\n", + " query : str\n", + " sql query string\n", + " dataclasses : typing.Sequence[Dataclass]\n", + " a list of SQL table dataclasses to be inserted\n", + " \"\"\"\n", + " statement = sql_text(query)\n", + " params = [asdict(dataclass) for dataclass in dataclasses]\n", + " try:\n", + " self.session.execute(statement=statement, params=params)\n", + " self.session.commit()\n", + " except Exception as e:\n", + " print(f\"Error: {e}\")\n", + " self.session.rollback()\n", + "\n", + " def insert_units(self, units: typing.Sequence[Unit]) -> None:\n", + " query = r\"INSERT INTO units (label, iri) VALUES (:label, :iri)\"\n", + " self.execute_insert(query=query, dataclasses=units)\n", + "\n", + " def insert_objects(self, objects: typing.Sequence[Objects]) -> None:\n", + " query = r\"INSERT INTO objects (id, id_type) VALUES (:id, :id_type) ON CONFLICT DO NOTHING\"\n", + " self.execute_insert(query=query, dataclasses=objects)\n", + "\n", + " def insert_descriptors_quant(\n", + " self, descriptors: typing.Sequence[DescriptorQuant]\n", + " ) -> None:\n", + " query = (\n", + " r\"INSERT INTO descriptors_quant (label, iri) VALUES (:label, :iri)\"\n", + " )\n", + " self.execute_insert(query=query, dataclasses=descriptors)\n", + "\n", + "\n", + "ingest = Ingest(session=session)\n", + "\n", + "ingest.insert_units(\n", + " units=[\n", + " Unit(\n", + " label=\"pixel\",\n", + " iri=\"http://uri.interlex.org/tgbugs/uris/readable/aspect/unit/pixel\",\n", + " ),\n", + " ]\n", + ")\n", + "\n", + "ingest.insert_objects(\n", + " objects=[\n", + " Objects(id=dataset[\"content\"][\"id\"].split(\":\")[-1], id_type=\"dataset\"),\n", + " ]\n", + ")" + ] + }, + { + "cell_type": "code", + "execution_count": 66, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "'N:dataset:aa43eda8-b29a-4c25-9840-ecbd57598afc'" + ] + }, + "execution_count": 66, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "dataset[\"content\"][\"id\"]" + ] + }, + { + "cell_type": "code", + "execution_count": 54, + "metadata": {}, + "outputs": [ + { + "ename": "IndentationError", + "evalue": "expected an indented block after function definition on line 32 (4174477168.py, line 36)", + "output_type": "error", + "traceback": [ + "\u001b[0;36m Cell \u001b[0;32mIn[54], line 36\u001b[0;36m\u001b[0m\n\u001b[0;31m Ingests(dataset).extract()\u001b[0m\n\u001b[0m ^\u001b[0m\n\u001b[0;31mIndentationError\u001b[0m\u001b[0;31m:\u001b[0m expected an indented block after function definition on line 32\n" + ] + } + ], + "source": [ + "# wrap columns\n", + "q = Queries(session)\n", + "i = InternalIds(q)\n", + "\n", + "# updated_transitive,\n", + "# values_objects,\n", + "# values_dataset_object,\n", + "# make_values_instances,\n", + "# make_values_parents,\n", + "# make_void,\n", + "# make_vocd,\n", + "# make_voqd,\n", + "# make_values_cat,\n", + "# make_values_quant,\n", + "\n", + "\n", + "class Ingests:\n", + " \"\"\"Create ingest objects for a dataset using Pennsieive direct\"\"\"\n", + "\n", + " def __init__(self, dataset: str) -> None:\n", + " self.dataset = dataset\n", + "\n", + " def extract(self):\n", + " return (self.updated_transitive(), self.values_objects())\n", + "\n", + " def updated_transitive(self):\n", + " \"\"\"Last updated Timestamp\"\"\"\n", + " return max(\n", + " [v[\"content\"][\"updatedAt\"] for v in self.dataset[\"children\"]]\n", + " )\n", + " \n", + " def values_objects(self):\n", + " \n", + " \n", + "Ingests(dataset).extract()" + ] + }, + { + "cell_type": "code", + "execution_count": 60, + "metadata": {}, + "outputs": [], + "source": [ + "from __future__ import annotations\n", + "from functools import cache\n", + "from pathlib import Path\n", + "from pydantic import BaseSettings, BaseModel\n", + "import boto3\n", + "from botocore.client import BaseClient\n", + "import requests\n", + "from typing import Tuple, List, Any\n", + "\n", + "\n", + "class PennsieveModel(BaseSettings):\n", + " PENNSIEVE_API_TOKEN: str\n", + " PENNSIEVE_API_SECRET: str\n", + " auth_url: str = \"https://api.pennsieve.io/authentication/cognito-config\"\n", + " private_dataset_url: str = \"https://api.pennsieve.io/datasets/\"\n", + " public_dataset_url: str = \"https://api.pennsieve.io/discover/datasets\"\n", + "\n", + " class Config: # type: ignore\n", + "\n", + " env_file = Path.home() / \".scicrunch/credentials/pennsieve\"\n", + " fields = {\n", + " \"PENNSIEVE_API_TOKEN\": {\"env\": \"PENNSIEVE_API_TOKEN\"},\n", + " \"PENNSIEVE_API_SECRET\": {\"env\": \"PENNSIEVE_API_SECRET\"},\n", + " }\n", + "\n", + "\n", + "class Settings(BaseSettings):\n", + " pennsieve: PennsieveModel = PennsieveModel()\n", + "\n", + "\n", + "class PennsieveClient:\n", + " def __init__(self):\n", + " settings = Settings().pennsieve\n", + " self.public_dataset_url = settings.public_dataset_url\n", + " self.private_dataset_url = settings.private_dataset_url\n", + " self.auth_url = settings.auth_url\n", + " self.api_key = self.__aws_bot_login(\n", + " token=settings.PENNSIEVE_API_TOKEN,\n", + " secret=settings.PENNSIEVE_API_SECRET,\n", + " )\n", + " self.headers = {\n", + " \"Authorization\": f\"Bearer {self.api_key}\",\n", + " \"accept\": \"*/*\",\n", + " }\n", + " self.session = requests.Session()\n", + "\n", + " def __reauth(self) -> None:\n", + " settings = Settings().pennsieve\n", + " self.api_key = self.__aws_bot_login(\n", + " token=settings.PENNSIEVE_API_TOKEN,\n", + " secret=settings.PENNSIEVE_API_SECRET,\n", + " )\n", + " self.headers = {\n", + " \"Authorization\": f\"Bearer {self.api_key}\",\n", + " \"accept\": \"*/*\",\n", + " }\n", + "\n", + " def __aws_bot_login(self, token: str, secret: str) -> str:\n", + " \"\"\"Awful AWS bot login for real API key using token + secrets\"\"\"\n", + " r = requests.get(self.auth_url)\n", + " r.raise_for_status()\n", + " cognito_app_client_id = r.json()[\"tokenPool\"][\"appClientId\"]\n", + " cognito_region = r.json()[\"region\"]\n", + " cognito_idp_client: BaseClient = boto3.client( # type: ignore\n", + " \"cognito-idp\",\n", + " region_name=cognito_region,\n", + " aws_access_key_id=\"\",\n", + " aws_secret_access_key=\"\",\n", + " )\n", + " login_response = cognito_idp_client.initiate_auth( # type: ignore\n", + " AuthFlow=\"USER_PASSWORD_AUTH\",\n", + " AuthParameters={\"USERNAME\": token, \"PASSWORD\": secret},\n", + " ClientId=cognito_app_client_id,\n", + " )\n", + " api_key: str = login_response[\"AuthenticationResult\"][\"AccessToken\"]\n", + " return api_key\n", + "\n", + " def __get(\n", + " self,\n", + " url: str,\n", + " params: dict[str, Any] | None = None,\n", + " ) -> requests.Response:\n", + " \"\"\"\n", + " Get request to endpoint with params\n", + "\n", + " Parameters\n", + " ----------\n", + " endpoint : URL\n", + " API endpoint to hit\n", + " params : dict, optional\n", + " API options, by default None\n", + "\n", + " Returns\n", + " -------\n", + " dict\n", + " API json response\n", + " \"\"\"\n", + " response = requests.get(url, headers=self.headers, params=params)\n", + " response.raise_for_status()\n", + " return response\n", + "\n", + " def _post(\n", + " self,\n", + " url: str,\n", + " data: dict[str, Any] | None = None,\n", + " payload: dict[str, Any] | None = None,\n", + " ) -> requests.Response:\n", + " \"\"\"\n", + " Post request to endpoint with data or json payload\n", + "\n", + " Parameters\n", + " ----------\n", + " endpoint : URL\n", + " API endpoint to hit\n", + " data : dict, optional\n", + " API contents, by default None\n", + " json : dict, optional\n", + " API contents, by default None\n", + "\n", + " Returns\n", + " -------\n", + " dict\n", + " API json response\n", + " \"\"\"\n", + " response = self.session.post(\n", + " url, data=data, json=payload, headers=self.headers\n", + " )\n", + " # Pennsieve API is unstable, only fail on 500s\n", + " if response.status_code >= 400:\n", + " print(response.text)\n", + " self.__reauth()\n", + " response = self.session.post(\n", + " url, data=data, json=payload, headers=self.headers\n", + " )\n", + " response.raise_for_status()\n", + " return response\n", + "\n", + " @staticmethod\n", + " def create_path(path: Path) -> None:\n", + " try:\n", + " path.mkdir(parents=True, exist_ok=False)\n", + " except FileExistsError:\n", + " pass\n", + "\n", + " def get_user(self):\n", + " return self.__get(\"https://api.pennsieve.io/user/\").json()\n", + "\n", + " @cache\n", + " def get_dataset(self, id_or_name: str) -> dict[str, Any]:\n", + " return self.__get(\n", + " f\"https://api.pennsieve.io/datasets/{id_or_name}\"\n", + " ).json()\n", + "\n", + " def get_dataset_packages(self, id_or_name: str) -> dict[str, Any]:\n", + " return self.__get(\n", + " f\"https://api.pennsieve.io/datasets/{id_or_name}/packages\"\n", + " ).json()[\"packages\"]\n", + "\n", + " @cache\n", + " def get_dataset_manifest(self, id_or_name: str) -> dict[str, Any]:\n", + " url = \"https://api.pennsieve.io/packages/download-manifest\"\n", + " dataset = self.get_dataset(id_or_name)\n", + " payload = {\n", + " \"nodeIds\": [\n", + " child[\"content\"][\"nodeId\"] for child in dataset[\"children\"]\n", + " ]\n", + " }\n", + " dataset[\"files\"] = self._post(url, payload=payload).json()\n", + " return dataset\n", + "\n", + " @cache\n", + " def get_child_manifest(self, node_id: str) -> dict[str, Any]:\n", + " url = \"https://api.pennsieve.io/packages/download-manifest\"\n", + " payload = {\"nodeIds\": [node_id]}\n", + " resp = self._post(url, payload=payload)\n", + " return resp.json()\n", + "\n", + " def export_dataset(\n", + " self, id_or_name: str, output_dir: Path | str, verbose: bool = True\n", + " ) -> None:\n", + " \"\"\"Export a dataset to a directory\n", + "\n", + " Parameters\n", + " ----------\n", + " id_or_name : str\n", + " Dataset ID or name\n", + " output_dir : Path | str\n", + " Output directory\n", + " verbose : bool, optional\n", + " Prints filename being downloaded, by default True\n", + " \"\"\"\n", + " url = \"https://api.pennsieve.io/packages/download-manifest\"\n", + " output_dir = Path(output_dir) / id_or_name\n", + " # Pull dataset for root children IDs\n", + " dataset = self.get_dataset(id_or_name)\n", + " for child in dataset[\"children\"]:\n", + " payload = {\"nodeIds\": [child[\"content\"][\"nodeId\"]]}\n", + " # Pull tree for 1 child at a time since prebuilt s3 links only last a couple hours\n", + " # If all children are pulled at once, the links will expire before all files are downloaded if over 200GBs\n", + " manifest = self._post(url, payload=payload).json()\n", + " for filemeta in manifest[\"data\"]:\n", + " parents_path = output_dir / \"/\".join(filemeta[\"path\"])\n", + " # Create nested parent directories if they don\"t exist\n", + " self.create_path(parents_path)\n", + " file_path = parents_path / filemeta[\"fileName\"]\n", + " if verbose:\n", + " print(f\"downloading path: {file_path}\")\n", + " url = filemeta[\"url\"]\n", + " # If file already exists, skip if it is stopped in the middle of downloading\n", + " # TODO: query file for checksum; very slow but will garuntee no partial downloads\n", + " if file_path.exists():\n", + " continue\n", + " # Stream download to file\n", + " with requests.get(url, stream=True) as r:\n", + " r.raise_for_status()\n", + " with open(file_path, \"wb\") as f:\n", + " for chunk in r.iter_content(chunk_size=8192):\n", + " f.write(chunk)\n", + "\n", + " def _private_datasets(self):\n", + " \"\"\"Get Private dataset for it\"s N:# ID\n", + "\n", + " Notes\n", + " -----\n", + " There is no known limiter at the moment. Expect all results and be conservative.\n", + " \"\"\"\n", + " return self.__get(self.private_dataset_url).json()\n", + "\n", + " def _public_datasets(\n", + " self, limit: int = 1, offset: int = 0, asc: bool = False\n", + " ) -> list[dict[str, Any]]:\n", + " \"\"\"Everything about the dataset except the N:# id itself\"\"\"\n", + " params = {\n", + " \"limit\": limit,\n", + " \"offset\": offset,\n", + " \"orderBy\": \"date\",\n", + " \"orderDirection\": \"asc\" if asc else \"desc\",\n", + " }\n", + " return self.__get(self.public_dataset_url, params=params).json()[\n", + " \"datasets\"\n", + " ]\n", + "\n", + " def get_datasets(self) -> List[dict[str, Any]]:\n", + " \"\"\"\n", + " Get all complete datasets\n", + " \"\"\"\n", + " # Private API endpoint Needs to be normalized via content key\n", + " intId_id = {\n", + " d[\"content\"][\"intId\"]: d[\"content\"][\"id\"]\n", + " for d in self._private_datasets()\n", + " }\n", + " datasets = self._public_datasets(limit=100000)\n", + " for dataset in datasets:\n", + " dataset[\"dataset_id\"] = intId_id.get(dataset[\"sourceDatasetId\"])\n", + " return datasets\n", + "\n", + " def get_partial_hash(self) -> Tuple[int, int, int | None]:\n", + " \"\"\"Get latest dataset id & version to see if anything new from pennsieve is worth pulling\"\"\"\n", + " latest_dataset = self._public_datasets()[0]\n", + " partial_hash = (\n", + " latest_dataset[\"sourceDatasetId\"],\n", + " latest_dataset[\"version\"],\n", + " latest_dataset[\"revision\"],\n", + " )\n", + " return partial_hash" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "quantdb", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.12.2" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/out.py b/out.py new file mode 100644 index 0000000..b5fb74a --- /dev/null +++ b/out.py @@ -0,0 +1,1033 @@ +from typing import List, Optional + +from sqlalchemy import ( + CheckConstraint, + Column, + DateTime, + Enum, + ForeignKeyConstraint, + Identity, + Index, + Integer, + Numeric, + PrimaryKeyConstraint, + String, + Table, + Text, + UniqueConstraint, + Uuid, + text, +) +from sqlalchemy.dialects.postgresql import JSONB +from sqlalchemy.orm import Mapped, declarative_base, mapped_column, relationship +from sqlalchemy.orm.base import Mapped + +Base = declarative_base() +metadata = Base.metadata + + +class Addresses(Base): + __tablename__ = "addresses" + __table_args__ = ( + PrimaryKeyConstraint("id", name="addresses_pkey"), + UniqueConstraint( + "addr_type", + "addr_field", + "value_type", + name="addresses_addr_type_addr_field_value_type_key", + ), + ) + + id = mapped_column( + Integer, + Identity( + start=1, + increment=1, + minvalue=1, + maxvalue=2147483647, + cycle=False, + cache=1, + ), + ) + addr_type = mapped_column( + Enum( + "constant", + "tabular-header", + "tabular-alt-header", + "workbook-sheet-tabular-header", + "workbook-sheet-tabular-alt-header", + "json-path-with-types", + "file-system-extracted", + "arbitrary-function", + name="address_type", + ) + ) + value_type = mapped_column( + Enum("single", "multi", name="field_value_type"), + server_default=text("'single'::field_value_type"), + ) + addr_field = mapped_column(Text) + curator_note = mapped_column(Text) + + obj_desc_inst: Mapped[List["ObjDescInst"]] = relationship( + "ObjDescInst", + uselist=True, + foreign_keys="[ObjDescInst.addr_desc_inst]", + back_populates="addresses", + ) + obj_desc_inst_: Mapped[List["ObjDescInst"]] = relationship( + "ObjDescInst", + uselist=True, + foreign_keys="[ObjDescInst.addr_field]", + back_populates="addresses_", + ) + obj_desc_cat: Mapped[List["ObjDescCat"]] = relationship( + "ObjDescCat", + uselist=True, + foreign_keys="[ObjDescCat.addr_desc_inst]", + back_populates="addresses", + ) + obj_desc_cat_: Mapped[List["ObjDescCat"]] = relationship( + "ObjDescCat", + uselist=True, + foreign_keys="[ObjDescCat.addr_field]", + back_populates="addresses_", + ) + obj_desc_quant: Mapped[List["ObjDescQuant"]] = relationship( + "ObjDescQuant", + uselist=True, + foreign_keys="[ObjDescQuant.addr_aspect]", + back_populates="addresses", + ) + obj_desc_quant_: Mapped[List["ObjDescQuant"]] = relationship( + "ObjDescQuant", + uselist=True, + foreign_keys="[ObjDescQuant.addr_desc_inst]", + back_populates="addresses_", + ) + obj_desc_quant1: Mapped[List["ObjDescQuant"]] = relationship( + "ObjDescQuant", + uselist=True, + foreign_keys="[ObjDescQuant.addr_field]", + back_populates="addresses1", + ) + obj_desc_quant2: Mapped[List["ObjDescQuant"]] = relationship( + "ObjDescQuant", + uselist=True, + foreign_keys="[ObjDescQuant.addr_unit]", + back_populates="addresses2", + ) + + +class Aspects(Base): + __tablename__ = "aspects" + __table_args__ = ( + PrimaryKeyConstraint("id", name="aspects_pkey"), + UniqueConstraint("iri", name="aspects_iri_key"), + UniqueConstraint("label", name="aspects_label_key"), + ) + + id = mapped_column( + Integer, + Identity( + start=1, + increment=1, + minvalue=1, + maxvalue=2147483647, + cycle=False, + cache=1, + ), + ) + label = mapped_column(Text, nullable=False) + iri = mapped_column(Text, nullable=False) + description = mapped_column(Text) + + aspects: Mapped["Aspects"] = relationship( + "Aspects", + secondary="aspect_parent", + primaryjoin=lambda: Aspects.id == t_aspect_parent.c.id, + secondaryjoin=lambda: Aspects.id == t_aspect_parent.c.parent, + back_populates="aspects_", + ) + aspects_: Mapped["Aspects"] = relationship( + "Aspects", + secondary="aspect_parent", + primaryjoin=lambda: Aspects.id == t_aspect_parent.c.parent, + secondaryjoin=lambda: Aspects.id == t_aspect_parent.c.id, + back_populates="aspects", + ) + descriptors_quant: Mapped[List["DescriptorsQuant"]] = relationship( + "DescriptorsQuant", uselist=True, back_populates="aspects" + ) + + +class ControlledTerms(Base): + __tablename__ = "controlled_terms" + __table_args__ = ( + PrimaryKeyConstraint("id", name="controlled_terms_pkey"), + UniqueConstraint("iri", name="controlled_terms_iri_key"), + UniqueConstraint("label", name="controlled_terms_label_key"), + ) + + id = mapped_column( + Integer, + Identity( + start=1, + increment=1, + minvalue=1, + maxvalue=2147483647, + cycle=False, + cache=1, + ), + ) + label = mapped_column(Text, nullable=False) + iri = mapped_column(Text, nullable=False) + + values_cat: Mapped[List["ValuesCat"]] = relationship( + "ValuesCat", uselist=True, back_populates="controlled_terms" + ) + + +class DescriptorsInst(Base): + __tablename__ = "descriptors_inst" + __table_args__ = ( + PrimaryKeyConstraint("id", name="descriptors_inst_pkey"), + UniqueConstraint("iri", name="descriptors_inst_iri_key"), + UniqueConstraint("label", name="descriptors_inst_label_key"), + ) + + id = mapped_column( + Integer, + Identity( + start=1, + increment=1, + minvalue=1, + maxvalue=2147483647, + cycle=False, + cache=1, + ), + ) + label = mapped_column(Text, nullable=False) + iri = mapped_column(Text, nullable=False) + description = mapped_column(Text) + + descriptors_inst: Mapped["DescriptorsInst"] = relationship( + "DescriptorsInst", + secondary="class_parent", + primaryjoin=lambda: DescriptorsInst.id == t_class_parent.c.id, + secondaryjoin=lambda: DescriptorsInst.id == t_class_parent.c.parent, + back_populates="descriptors_inst_", + ) + descriptors_inst_: Mapped["DescriptorsInst"] = relationship( + "DescriptorsInst", + secondary="class_parent", + primaryjoin=lambda: DescriptorsInst.id == t_class_parent.c.parent, + secondaryjoin=lambda: DescriptorsInst.id == t_class_parent.c.id, + back_populates="descriptors_inst", + ) + descriptors_cat: Mapped[List["DescriptorsCat"]] = relationship( + "DescriptorsCat", uselist=True, back_populates="descriptors_inst" + ) + descriptors_quant: Mapped[List["DescriptorsQuant"]] = relationship( + "DescriptorsQuant", uselist=True, back_populates="descriptors_inst" + ) + obj_desc_inst: Mapped[List["ObjDescInst"]] = relationship( + "ObjDescInst", uselist=True, back_populates="descriptors_inst" + ) + values_inst: Mapped[List["ValuesInst"]] = relationship( + "ValuesInst", uselist=True, back_populates="descriptors_inst" + ) + values_cat: Mapped[List["ValuesCat"]] = relationship( + "ValuesCat", uselist=True, back_populates="descriptors_inst" + ) + values_quant: Mapped[List["ValuesQuant"]] = relationship( + "ValuesQuant", uselist=True, back_populates="descriptors_inst" + ) + + +class Objects(Base): + __tablename__ = "objects" + __table_args__ = ( + CheckConstraint( + "id_type <> 'package'::remote_id_type OR id_file IS NOT NULL", + name="constraint_objects_remote_id_type_id_package", + ), + CheckConstraint( + "id_type <> 'quantdb'::remote_id_type OR id_internal IS NOT NULL AND id = id_internal", + name="constraint_objects_remote_id_type_id_internal", + ), + ForeignKeyConstraint( + ["id_internal"], + ["objects_internal.id"], + name="objects_id_internal_fkey", + ), + PrimaryKeyConstraint("id", name="objects_pkey"), + Index("idx_objects_id_internal", "id_internal"), + ) + + id = mapped_column(Uuid) + id_type = mapped_column( + Enum( + "organization", + "dataset", + "collection", + "package", + "quantdb", + name="remote_id_type", + ), + nullable=False, + ) + id_file = mapped_column(Integer) + id_internal = mapped_column(Uuid) + + objects_internal: Mapped[Optional["ObjectsInternal"]] = relationship( + "ObjectsInternal", foreign_keys=[id_internal], back_populates="objects" + ) + objects: Mapped["Objects"] = relationship( + "Objects", + secondary="dataset_object", + primaryjoin=lambda: Objects.id == t_dataset_object.c.dataset, + secondaryjoin=lambda: Objects.id == t_dataset_object.c.object, + back_populates="objects_", + ) + objects_: Mapped["Objects"] = relationship( + "Objects", + secondary="dataset_object", + primaryjoin=lambda: Objects.id == t_dataset_object.c.object, + secondaryjoin=lambda: Objects.id == t_dataset_object.c.dataset, + back_populates="objects", + ) + objects_internal_: Mapped[List["ObjectsInternal"]] = relationship( + "ObjectsInternal", + uselist=True, + foreign_keys="[ObjectsInternal.dataset]", + back_populates="objects_", + ) + obj_desc_inst: Mapped[List["ObjDescInst"]] = relationship( + "ObjDescInst", uselist=True, back_populates="objects" + ) + values_inst: Mapped[List["ValuesInst"]] = relationship( + "ValuesInst", uselist=True, back_populates="objects" + ) + obj_desc_cat: Mapped[List["ObjDescCat"]] = relationship( + "ObjDescCat", uselist=True, back_populates="objects" + ) + obj_desc_quant: Mapped[List["ObjDescQuant"]] = relationship( + "ObjDescQuant", uselist=True, back_populates="objects" + ) + values_cat: Mapped[List["ValuesCat"]] = relationship( + "ValuesCat", uselist=True, back_populates="objects" + ) + values_quant: Mapped[List["ValuesQuant"]] = relationship( + "ValuesQuant", uselist=True, back_populates="objects" + ) + + +class ObjectsInternal(Base): + __tablename__ = "objects_internal" + __table_args__ = ( + CheckConstraint( + "type <> 'path-metadata'::oi_type OR updated_transitive IS NOT NULL AND dataset IS NOT NULL", + name="constraint_objects_internal_type_updated_transitive", + ), + ForeignKeyConstraint( + ["dataset"], ["objects.id"], name="constraint_oi_dataset_fk" + ), + PrimaryKeyConstraint("id", name="objects_internal_pkey"), + UniqueConstraint( + "dataset", + "updated_transitive", + name="objects_internal_dataset_updated_transitive_key", + ), + ) + + id = mapped_column(Uuid, server_default=text("gen_random_uuid()")) + type = mapped_column( + Enum("path-metadata", "other", name="oi_type"), + server_default=text("'other'::oi_type"), + ) + dataset = mapped_column(Uuid) + updated_transitive = mapped_column(DateTime) + label = mapped_column(Text) + curator_note = mapped_column(Text) + + objects: Mapped[List["Objects"]] = relationship( + "Objects", + uselist=True, + foreign_keys="[Objects.id_internal]", + back_populates="objects_internal", + ) + objects_: Mapped[Optional["Objects"]] = relationship( + "Objects", foreign_keys=[dataset], back_populates="objects_internal_" + ) + + +class Units(Base): + __tablename__ = "units" + __table_args__ = ( + PrimaryKeyConstraint("id", name="units_pkey"), + UniqueConstraint("iri", name="units_iri_key"), + UniqueConstraint("label", name="units_label_key"), + ) + + id = mapped_column( + Integer, + Identity( + start=1, + increment=1, + minvalue=1, + maxvalue=2147483647, + cycle=False, + cache=1, + ), + ) + label = mapped_column(Text, nullable=False) + iri = mapped_column(Text, nullable=False) + + descriptors_quant: Mapped[List["DescriptorsQuant"]] = relationship( + "DescriptorsQuant", uselist=True, back_populates="units" + ) + + +t_aspect_parent = Table( + "aspect_parent", + metadata, + Column("id", Integer, nullable=False), + Column("parent", Integer, nullable=False), + ForeignKeyConstraint(["id"], ["aspects.id"], name="aspect_parent_id_fkey"), + ForeignKeyConstraint( + ["parent"], ["aspects.id"], name="aspect_parent_parent_fkey" + ), + PrimaryKeyConstraint("id", "parent", name="aspect_parent_pkey"), +) + + +t_class_parent = Table( + "class_parent", + metadata, + Column("id", Integer, nullable=False), + Column("parent", Integer, nullable=False), + ForeignKeyConstraint( + ["id"], ["descriptors_inst.id"], name="class_parent_id_fkey" + ), + ForeignKeyConstraint( + ["parent"], ["descriptors_inst.id"], name="class_parent_parent_fkey" + ), + PrimaryKeyConstraint("id", "parent", name="class_parent_pkey"), +) + + +t_dataset_object = Table( + "dataset_object", + metadata, + Column("dataset", Uuid, nullable=False), + Column("object", Uuid, nullable=False), + ForeignKeyConstraint( + ["dataset"], ["objects.id"], name="dataset_object_dataset_fkey" + ), + ForeignKeyConstraint( + ["object"], ["objects.id"], name="dataset_object_object_fkey" + ), + PrimaryKeyConstraint("dataset", "object", name="dataset_object_pkey"), +) + + +class DescriptorsCat(Base): + __tablename__ = "descriptors_cat" + __table_args__ = ( + ForeignKeyConstraint( + ["domain"], + ["descriptors_inst.id"], + name="descriptors_cat_domain_fkey", + ), + PrimaryKeyConstraint("id", name="descriptors_cat_pkey"), + UniqueConstraint( + "domain", + "range", + "label", + name="descriptors_cat_domain_range_label_key", + ), + ) + + id = mapped_column( + Integer, + Identity( + start=1, + increment=1, + minvalue=1, + maxvalue=2147483647, + cycle=False, + cache=1, + ), + ) + domain = mapped_column(Integer) + range = mapped_column(Enum("open", "controlled", name="cat_range_type")) + label = mapped_column(Text) + description = mapped_column(Text) + curator_note = mapped_column(Text) + + descriptors_inst: Mapped[Optional["DescriptorsInst"]] = relationship( + "DescriptorsInst", back_populates="descriptors_cat" + ) + obj_desc_cat: Mapped[List["ObjDescCat"]] = relationship( + "ObjDescCat", uselist=True, back_populates="descriptors_cat" + ) + values_cat: Mapped[List["ValuesCat"]] = relationship( + "ValuesCat", uselist=True, back_populates="descriptors_cat" + ) + + +class DescriptorsQuant(Base): + __tablename__ = "descriptors_quant" + __table_args__ = ( + ForeignKeyConstraint( + ["aspect"], ["aspects.id"], name="descriptors_quant_aspect_fkey" + ), + ForeignKeyConstraint( + ["domain"], + ["descriptors_inst.id"], + name="descriptors_quant_domain_fkey", + ), + ForeignKeyConstraint( + ["unit"], ["units.id"], name="descriptors_quant_unit_fkey" + ), + PrimaryKeyConstraint("id", name="descriptors_quant_pkey"), + UniqueConstraint("label", name="descriptors_quant_label_key"), + UniqueConstraint( + "unit", + "aspect", + "domain", + "shape", + "aggregation_type", + name="descriptors_quant_unit_aspect_domain_shape_aggregation_type_key", + ), + ) + + id = mapped_column( + Integer, + Identity( + start=1, + increment=1, + minvalue=1, + maxvalue=2147483647, + cycle=False, + cache=1, + ), + ) + shape = mapped_column( + Enum("scalar", name="quant_shape"), + nullable=False, + server_default=text("'scalar'::quant_shape"), + ) + label = mapped_column(Text, nullable=False) + aggregation_type = mapped_column( + Enum( + "instance", + "function", + "summary", + "mean", + "media", + "mode", + "sum", + "min", + "max", + name="quant_agg_type", + ), + nullable=False, + server_default=text("'instance'::quant_agg_type"), + ) + unit = mapped_column(Integer) + aspect = mapped_column(Integer) + domain = mapped_column(Integer) + description = mapped_column(Text) + curator_note = mapped_column(Text) + + aspects: Mapped[Optional["Aspects"]] = relationship( + "Aspects", back_populates="descriptors_quant" + ) + descriptors_inst: Mapped[Optional["DescriptorsInst"]] = relationship( + "DescriptorsInst", back_populates="descriptors_quant" + ) + units: Mapped[Optional["Units"]] = relationship( + "Units", back_populates="descriptors_quant" + ) + obj_desc_quant: Mapped[List["ObjDescQuant"]] = relationship( + "ObjDescQuant", uselist=True, back_populates="descriptors_quant" + ) + values_quant: Mapped[List["ValuesQuant"]] = relationship( + "ValuesQuant", uselist=True, back_populates="descriptors_quant" + ) + + +class ObjDescInst(Base): + __tablename__ = "obj_desc_inst" + __table_args__ = ( + ForeignKeyConstraint( + ["addr_desc_inst"], + ["addresses.id"], + name="obj_desc_inst_addr_desc_inst_fkey", + ), + ForeignKeyConstraint( + ["addr_field"], + ["addresses.id"], + name="obj_desc_inst_addr_field_fkey", + ), + ForeignKeyConstraint( + ["desc_inst"], + ["descriptors_inst.id"], + name="obj_desc_inst_desc_inst_fkey", + ), + ForeignKeyConstraint( + ["object"], ["objects.id"], name="obj_desc_inst_object_fkey" + ), + PrimaryKeyConstraint("object", "desc_inst", name="obj_desc_inst_pkey"), + ) + + object = mapped_column(Uuid, nullable=False) + desc_inst = mapped_column(Integer, nullable=False) + addr_field = mapped_column(Integer, nullable=False) + addr_desc_inst = mapped_column(Integer) + expect = mapped_column(Integer) + + addresses: Mapped[Optional["Addresses"]] = relationship( + "Addresses", + foreign_keys=[addr_desc_inst], + back_populates="obj_desc_inst", + ) + addresses_: Mapped["Addresses"] = relationship( + "Addresses", foreign_keys=[addr_field], back_populates="obj_desc_inst_" + ) + descriptors_inst: Mapped["DescriptorsInst"] = relationship( + "DescriptorsInst", back_populates="obj_desc_inst" + ) + objects: Mapped["Objects"] = relationship( + "Objects", back_populates="obj_desc_inst" + ) + values_cat: Mapped[List["ValuesCat"]] = relationship( + "ValuesCat", uselist=True, back_populates="obj_desc_inst" + ) + values_quant: Mapped[List["ValuesQuant"]] = relationship( + "ValuesQuant", uselist=True, back_populates="obj_desc_inst" + ) + + +class ValuesInst(Base): + __tablename__ = "values_inst" + __table_args__ = ( + CheckConstraint( + "id_sam ~ '^sam-'::text", name="values_inst_id_sam_check" + ), + CheckConstraint( + "id_sub ~ '^sub-'::text", name="values_inst_id_sub_check" + ), + CheckConstraint( + "type <> 'below'::instance_type OR id_sub IS NOT NULL OR id_sam IS NOT NULL", + name="constraint_values_inst_type_below", + ), + CheckConstraint( + "type <> 'sample'::instance_type OR id_sam IS NOT NULL AND id_sam = id_formal", + name="constraint_values_inst_type_id_sam", + ), + CheckConstraint( + "type <> 'subject'::instance_type OR id_sub = id_formal AND id_sam IS NULL", + name="constraint_values_inst_type_id_sub", + ), + CheckConstraint( + "type = 'below'::instance_type AND NOT id_formal ~ '^(sub|sam)-'::text OR type = 'subject'::instance_type AND id_formal ~ '^sub-'::text OR type = 'sample'::instance_type AND id_formal ~ '^sam-'::text", + name="constraint_values_inst_type_id_formal", + ), + ForeignKeyConstraint( + ["dataset"], ["objects.id"], name="values_inst_dataset_fkey" + ), + ForeignKeyConstraint( + ["desc_inst"], + ["descriptors_inst.id"], + name="values_inst_desc_inst_fkey", + ), + PrimaryKeyConstraint("id", name="values_inst_pkey"), + UniqueConstraint( + "dataset", "id_formal", name="values_inst_dataset_id_formal_key" + ), + Index("idx_values_inst_dataset", "dataset"), + Index("idx_values_inst_dataset_id_formal", "dataset", "id_formal"), + Index("idx_values_inst_dataset_id_sam", "dataset", "id_sam"), + Index("idx_values_inst_dataset_id_sub", "dataset", "id_sub"), + Index("idx_values_inst_desc_inst", "desc_inst"), + Index("idx_values_inst_id_formal", "id_formal"), + Index("idx_values_inst_id_sam", "id_sam"), + Index("idx_values_inst_id_sub", "id_sub"), + ) + + id = mapped_column( + Integer, + Identity( + start=1, + increment=1, + minvalue=1, + maxvalue=2147483647, + cycle=False, + cache=1, + ), + ) + type = mapped_column( + Enum("subject", "sample", "below", name="instance_type"), nullable=False + ) + id_sub = mapped_column(Text, nullable=False) + desc_inst = mapped_column(Integer) + dataset = mapped_column(Uuid) + id_formal = mapped_column(Text) + local_identifier = mapped_column(Text) + id_sam = mapped_column(Text) + + objects: Mapped[Optional["Objects"]] = relationship( + "Objects", back_populates="values_inst" + ) + descriptors_inst: Mapped[Optional["DescriptorsInst"]] = relationship( + "DescriptorsInst", back_populates="values_inst" + ) + values_inst: Mapped["ValuesInst"] = relationship( + "ValuesInst", + secondary="equiv_inst", + primaryjoin=lambda: ValuesInst.id == t_equiv_inst.c.left_thing, + secondaryjoin=lambda: ValuesInst.id == t_equiv_inst.c.right_thing, + back_populates="values_inst_", + ) + values_inst_: Mapped["ValuesInst"] = relationship( + "ValuesInst", + secondary="equiv_inst", + primaryjoin=lambda: ValuesInst.id == t_equiv_inst.c.right_thing, + secondaryjoin=lambda: ValuesInst.id == t_equiv_inst.c.left_thing, + back_populates="values_inst", + ) + values_inst1: Mapped["ValuesInst"] = relationship( + "ValuesInst", + secondary="instance_parent", + primaryjoin=lambda: ValuesInst.id == t_instance_parent.c.id, + secondaryjoin=lambda: ValuesInst.id == t_instance_parent.c.parent, + back_populates="values_inst2", + ) + values_inst2: Mapped["ValuesInst"] = relationship( + "ValuesInst", + secondary="instance_parent", + primaryjoin=lambda: ValuesInst.id == t_instance_parent.c.parent, + secondaryjoin=lambda: ValuesInst.id == t_instance_parent.c.id, + back_populates="values_inst1", + ) + values_cat: Mapped[List["ValuesCat"]] = relationship( + "ValuesCat", uselist=True, back_populates="values_inst" + ) + values_quant: Mapped[List["ValuesQuant"]] = relationship( + "ValuesQuant", uselist=True, back_populates="values_inst" + ) + + +t_equiv_inst = Table( + "equiv_inst", + metadata, + Column("left_thing", Integer, nullable=False), + Column("right_thing", Integer, nullable=False), + CheckConstraint("left_thing <> right_thing", name="sse_no_self"), + ForeignKeyConstraint( + ["left_thing"], ["values_inst.id"], name="equiv_inst_left_thing_fkey" + ), + ForeignKeyConstraint( + ["right_thing"], ["values_inst.id"], name="equiv_inst_right_thing_fkey" + ), + PrimaryKeyConstraint("left_thing", "right_thing", name="equiv_inst_pkey"), +) + + +t_instance_parent = Table( + "instance_parent", + metadata, + Column("id", Integer, nullable=False), + Column("parent", Integer, nullable=False), + ForeignKeyConstraint( + ["id"], ["values_inst.id"], name="instance_parent_id_fkey" + ), + ForeignKeyConstraint( + ["parent"], ["values_inst.id"], name="instance_parent_parent_fkey" + ), + PrimaryKeyConstraint("id", "parent", name="instance_parent_pkey"), +) + + +class ObjDescCat(Base): + __tablename__ = "obj_desc_cat" + __table_args__ = ( + ForeignKeyConstraint( + ["addr_desc_inst"], + ["addresses.id"], + name="obj_desc_cat_addr_desc_inst_fkey", + ), + ForeignKeyConstraint( + ["addr_field"], + ["addresses.id"], + name="obj_desc_cat_addr_field_fkey", + ), + ForeignKeyConstraint( + ["desc_cat"], + ["descriptors_cat.id"], + name="obj_desc_cat_desc_cat_fkey", + ), + ForeignKeyConstraint( + ["object"], ["objects.id"], name="obj_desc_cat_object_fkey" + ), + PrimaryKeyConstraint("object", "desc_cat", name="obj_desc_cat_pkey"), + ) + + object = mapped_column(Uuid, nullable=False) + desc_cat = mapped_column(Integer, nullable=False) + addr_field = mapped_column(Integer, nullable=False) + addr_desc_inst = mapped_column(Integer) + expect = mapped_column(Integer) + + addresses: Mapped[Optional["Addresses"]] = relationship( + "Addresses", + foreign_keys=[addr_desc_inst], + back_populates="obj_desc_cat", + ) + addresses_: Mapped["Addresses"] = relationship( + "Addresses", foreign_keys=[addr_field], back_populates="obj_desc_cat_" + ) + descriptors_cat: Mapped["DescriptorsCat"] = relationship( + "DescriptorsCat", back_populates="obj_desc_cat" + ) + objects: Mapped["Objects"] = relationship( + "Objects", back_populates="obj_desc_cat" + ) + values_cat: Mapped[List["ValuesCat"]] = relationship( + "ValuesCat", uselist=True, back_populates="obj_desc_cat" + ) + + +class ObjDescQuant(Base): + __tablename__ = "obj_desc_quant" + __table_args__ = ( + ForeignKeyConstraint( + ["addr_aspect"], + ["addresses.id"], + name="obj_desc_quant_addr_aspect_fkey", + ), + ForeignKeyConstraint( + ["addr_desc_inst"], + ["addresses.id"], + name="obj_desc_quant_addr_desc_inst_fkey", + ), + ForeignKeyConstraint( + ["addr_field"], + ["addresses.id"], + name="obj_desc_quant_addr_field_fkey", + ), + ForeignKeyConstraint( + ["addr_unit"], + ["addresses.id"], + name="obj_desc_quant_addr_unit_fkey", + ), + ForeignKeyConstraint( + ["desc_quant"], + ["descriptors_quant.id"], + name="obj_desc_quant_desc_quant_fkey", + ), + ForeignKeyConstraint( + ["object"], ["objects.id"], name="obj_desc_quant_object_fkey" + ), + PrimaryKeyConstraint( + "object", "desc_quant", name="obj_desc_quant_pkey" + ), + ) + + object = mapped_column(Uuid, nullable=False) + desc_quant = mapped_column(Integer, nullable=False) + addr_field = mapped_column(Integer, nullable=False) + addr_unit = mapped_column(Integer) + addr_aspect = mapped_column(Integer) + addr_desc_inst = mapped_column(Integer) + expect = mapped_column(Integer) + + addresses: Mapped[Optional["Addresses"]] = relationship( + "Addresses", foreign_keys=[addr_aspect], back_populates="obj_desc_quant" + ) + addresses_: Mapped[Optional["Addresses"]] = relationship( + "Addresses", + foreign_keys=[addr_desc_inst], + back_populates="obj_desc_quant_", + ) + addresses1: Mapped["Addresses"] = relationship( + "Addresses", foreign_keys=[addr_field], back_populates="obj_desc_quant1" + ) + addresses2: Mapped[Optional["Addresses"]] = relationship( + "Addresses", foreign_keys=[addr_unit], back_populates="obj_desc_quant2" + ) + descriptors_quant: Mapped["DescriptorsQuant"] = relationship( + "DescriptorsQuant", back_populates="obj_desc_quant" + ) + objects: Mapped["Objects"] = relationship( + "Objects", back_populates="obj_desc_quant" + ) + values_quant: Mapped[List["ValuesQuant"]] = relationship( + "ValuesQuant", uselist=True, back_populates="obj_desc_quant" + ) + + +class ValuesCat(Base): + __tablename__ = "values_cat" + __table_args__ = ( + CheckConstraint( + "value_open IS NOT NULL OR value_controlled IS NOT NULL", + name="constraint_values_cat_some_value", + ), + ForeignKeyConstraint( + ["desc_cat"], + ["descriptors_cat.id"], + name="values_cat_desc_cat_fkey", + ), + ForeignKeyConstraint( + ["desc_inst"], + ["descriptors_inst.id"], + name="values_cat_desc_inst_fkey", + ), + ForeignKeyConstraint( + ["instance"], ["values_inst.id"], name="values_cat_instance_fkey" + ), + ForeignKeyConstraint( + ["object", "desc_cat"], + ["obj_desc_cat.object", "obj_desc_cat.desc_cat"], + name="values_cat_object_desc_cat_fkey", + ), + ForeignKeyConstraint( + ["object", "desc_inst"], + ["obj_desc_inst.object", "obj_desc_inst.desc_inst"], + name="values_cat_object_desc_inst_fkey", + ), + ForeignKeyConstraint( + ["object"], ["objects.id"], name="values_cat_object_fkey" + ), + ForeignKeyConstraint( + ["value_controlled"], + ["controlled_terms.id"], + name="values_cat_value_controlled_fkey", + ), + PrimaryKeyConstraint("id", name="values_cat_pkey"), + Index("idx_values_cat_desc_cat", "desc_cat"), + Index("idx_values_cat_desc_inst", "desc_inst"), + Index("idx_values_cat_instance", "instance"), + Index("idx_values_cat_object", "object"), + Index("idx_values_cat_value_controlled", "value_controlled"), + ) + + id = mapped_column( + Integer, + Identity( + start=1, + increment=1, + minvalue=1, + maxvalue=2147483647, + cycle=False, + cache=1, + ), + ) + object = mapped_column(Uuid, nullable=False) + desc_inst = mapped_column(Integer, nullable=False) + desc_cat = mapped_column(Integer, nullable=False) + value_open = mapped_column(Text) + value_controlled = mapped_column(Integer) + instance = mapped_column(Integer) + + descriptors_cat: Mapped["DescriptorsCat"] = relationship( + "DescriptorsCat", back_populates="values_cat" + ) + descriptors_inst: Mapped["DescriptorsInst"] = relationship( + "DescriptorsInst", back_populates="values_cat" + ) + values_inst: Mapped[Optional["ValuesInst"]] = relationship( + "ValuesInst", back_populates="values_cat" + ) + obj_desc_cat: Mapped["ObjDescCat"] = relationship( + "ObjDescCat", back_populates="values_cat" + ) + obj_desc_inst: Mapped["ObjDescInst"] = relationship( + "ObjDescInst", back_populates="values_cat" + ) + objects: Mapped["Objects"] = relationship( + "Objects", back_populates="values_cat" + ) + controlled_terms: Mapped[Optional["ControlledTerms"]] = relationship( + "ControlledTerms", back_populates="values_cat" + ) + + +class ValuesQuant(Base): + __tablename__ = "values_quant" + __table_args__ = ( + ForeignKeyConstraint( + ["desc_inst"], + ["descriptors_inst.id"], + name="values_quant_desc_inst_fkey", + ), + ForeignKeyConstraint( + ["desc_quant"], + ["descriptors_quant.id"], + name="values_quant_desc_quant_fkey", + ), + ForeignKeyConstraint( + ["instance"], ["values_inst.id"], name="values_quant_instance_fkey" + ), + ForeignKeyConstraint( + ["object", "desc_inst"], + ["obj_desc_inst.object", "obj_desc_inst.desc_inst"], + name="values_quant_object_desc_inst_fkey", + ), + ForeignKeyConstraint( + ["object", "desc_quant"], + ["obj_desc_quant.object", "obj_desc_quant.desc_quant"], + name="values_quant_object_desc_quant_fkey", + ), + ForeignKeyConstraint( + ["object"], ["objects.id"], name="values_quant_object_fkey" + ), + PrimaryKeyConstraint("id", name="values_quant_pkey"), + Index("idx_values_quant_desc_inst", "desc_inst"), + Index("idx_values_quant_desc_quant", "desc_quant"), + Index("idx_values_quant_instance", "instance"), + Index("idx_values_quant_object", "object"), + ) + + id = mapped_column( + Integer, + Identity( + start=1, + increment=1, + minvalue=1, + maxvalue=2147483647, + cycle=False, + cache=1, + ), + ) + value = mapped_column(Numeric, nullable=False) + object = mapped_column(Uuid, nullable=False) + desc_inst = mapped_column(Integer, nullable=False) + desc_quant = mapped_column(Integer, nullable=False) + value_blob = mapped_column(JSONB, nullable=False) + instance = mapped_column(Integer) + orig_value = mapped_column(String) + orig_units = mapped_column(String) + + descriptors_inst: Mapped["DescriptorsInst"] = relationship( + "DescriptorsInst", back_populates="values_quant" + ) + descriptors_quant: Mapped["DescriptorsQuant"] = relationship( + "DescriptorsQuant", back_populates="values_quant" + ) + values_inst: Mapped[Optional["ValuesInst"]] = relationship( + "ValuesInst", back_populates="values_quant" + ) + obj_desc_inst: Mapped["ObjDescInst"] = relationship( + "ObjDescInst", back_populates="values_quant" + ) + obj_desc_quant: Mapped["ObjDescQuant"] = relationship( + "ObjDescQuant", back_populates="values_quant" + ) + objects: Mapped["Objects"] = relationship( + "Objects", back_populates="values_quant" + ) diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..8c43395 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,29 @@ +[build-system] +requires = ["hatchling"] +build-backend = "hatchling.build" + +[project] +dependencies = [ + "sqlalchemy ~= 2.0.29", + "pydantic ~= 1.10", + "fastapi ~= 0.110.1", + "uvicorn ~= 0.29.0", + "flask ~= 3.0.3", + "Flask-SQLAlchemy ~= 3.1.1", + "orthauth ~= 0.0.18", + "cython", + "psycopg2-binary", + "sparcur", +] +name = "quantdb" +version = "0.1.0" +description = "Quantitative DB" +readme = "README.md" +packages = [{ include = "quantdb" }] +requires-python = ">=3.10" + +# [project.scripts] +# quantdb-fastapi = "uvicorn quantdb.main:app --reload" + +[project.optional-dependencies] +dev = ["pytest ~= 8.1.1", "pre-commit ~= 3.7.0"] diff --git a/quantdb/__init__.py b/quantdb/__init__.py index e69de29..9d48db4 100644 --- a/quantdb/__init__.py +++ b/quantdb/__init__.py @@ -0,0 +1 @@ +from __future__ import annotations diff --git a/quantdb/api.py b/quantdb/api.py index 2785fc2..16ff278 100644 --- a/quantdb/api.py +++ b/quantdb/api.py @@ -1,16 +1,33 @@ +import copy import json import uuid -import copy -from decimal import Decimal from datetime import datetime +from decimal import Decimal +from functools import lru_cache +from typing import Any, Dict, Generator, Literal, Optional + +from fastapi import ( + Depends, + FastAPI, + File, + HTTPException, + Query, + Request, + UploadFile, +) +from fastapi.security import OAuth2PasswordBearer from flask import Flask, request +from sqlalchemy import text +from sqlalchemy.orm import Session # type: ignore from sqlalchemy.sql import text as sql_text -from quantdb.utils import log, dbUri, isoformat -from quantdb.config import auth -from quantdb import exceptions as exc +from quantdb import exceptions as exc +from quantdb.config import Settings, auth +from quantdb.mysql_app.database import SessionLocal +from quantdb.utils import dbUri, isoformat, log -log = log.getChild('api') +log = log.getChild("api") +fastapi_app = FastAPI() class JEncode(json.JSONEncoder): @@ -27,32 +44,77 @@ def default(self, obj): url_sql_where = ( # TODO arity spec here - # dupes overwrite params but that is ok, this way we get the correct table alias for both cases - ('object', 'object', 'cv.object = any(:object)', 'cat'), # XXX should not use this outside values/ unless we left outer due to intersect ? - ('object', 'object', 'qv.object = any(:object)', 'quant'), # XXX should not use this outside values/ unless we left outer due to intersect ? + ( + "object", + "object", + "cv.object = any(:object)", + "cat", + ), # XXX should not use this outside values/ unless we left outer due to intersect ? + ( + "object", + "object", + "qv.object = any(:object)", + "quant", + ), # XXX should not use this outside values/ unless we left outer due to intersect ? + ("desc-inst", "desc_inst", "idin.label = any(:desc_inst)", "both"), + ("dataset", "dataset", "im.dataset = :dataset", "both"), + ("inst", "inst", "im.id_formal = any(:inst)", "both"), + ("subject", "subject", "im.id_sub = any(:subject)", "both"), + ("sample", "sample", "im.id_sam = any(:sample)", "both"), + ("desc-cat", "desc_cat", "cd.label = any(:desc_cat)", "cat"), + ("value-cat", "value_cat", "ct.label = any(:value_cat)", "cat"), + ( + "value-cat-open", + "value_cat_open", + "cv.value_open = any(:value_cat_open)", + "cat", + ), + ("unit", "unit", "u.label = any(:unit)", "quant"), + ("aspect", "aspect", "ain.label = any(:aspect)", "quant"), + ("agg-type", "agg_type", "qd.aggregation_type = :agg_type", "quant"), + # TODO shape + ("value-quant", "value_quant", "qv.value = :value_quant", "quant"), + ( + "value-quant-margin", + "value_quant_margin", + "qv.value <= :value_quant + :value_quant_margin AND qv.value >= :value_quant - :value_quant_margin", + "quant", + ), + ( + "value-quant-min", + "value_quant_min", + "qv.value >= :value_quant_min", + "quant", + ), + ( + "value-quant-max", + "value_quant_max", + "qv.value <= :value_quant_max", + "quant", + ), +) - ('desc-inst', 'desc_inst', 'idin.label = any(:desc_inst)', 'both'), - ('dataset', 'dataset', 'im.dataset = :dataset', 'both'), - ('inst', 'inst', 'im.id_formal = any(:inst)', 'both'), - ('subject', 'subject', 'im.id_sub = any(:subject)', 'both'), - ('sample', 'sample', 'im.id_sam = any(:sample)', 'both'), - ('desc-cat', 'desc_cat', 'cd.label = any(:desc_cat)', 'cat'), +@lru_cache() +def get_settings(): + """ + Get settings from mongodb - alternative for test and production credientials - ('value-cat', 'value_cat', 'ct.label = any(:value_cat)', 'cat'), - ('value-cat-open', 'value_cat_open', 'cv.value_open = any(:value_cat_open)', 'cat'), + Returns + ------- + Settings + pydantic BaseSettings model with MongoDB credentials + """ + return Settings() - ('unit', 'unit', 'u.label = any(:unit)', 'quant'), - ('aspect', 'aspect', 'ain.label = any(:aspect)', 'quant'), - ('agg-type', 'agg_type', 'qd.aggregation_type = :agg_type', 'quant'), - # TODO shape - ('value-quant', 'value_quant', 'qv.value = :value_quant', 'quant'), - ('value-quant-margin', 'value_quant_margin', 'qv.value <= :value_quant + :value_quant_margin AND qv.value >= :value_quant - :value_quant_margin', 'quant'), - ('value-quant-min', 'value_quant_min', 'qv.value >= :value_quant_min', 'quant'), - ('value-quant-max', 'value_quant_max', 'qv.value <= :value_quant_max', 'quant'), -) +def get_mysql_db() -> Generator[Session, Any, None]: + db = SessionLocal() + try: + yield db + finally: + db.close() def get_where(kwargs): @@ -62,146 +124,140 @@ def get_where(kwargs): for u, s, w, t in url_sql_where: if u in kwargs and kwargs[u]: params[s] = kwargs[u] - if t == 'cat': + if t == "cat": _where_cat.append(w) - elif t == 'quant': + elif t == "quant": # do not include value-quant if value-quant-margin is provided - if (u == 'value-quant' and - 'value-quant-margin' in kwargs and - kwargs['value-quant-margin']): + if u == "value-quant" and "value-quant-margin" in kwargs and kwargs["value-quant-margin"]: continue else: _where_quant.append(w) - elif t == 'both': + elif t == "both": _where_cat.append(w) _where_quant.append(w) else: - raise ValueError('wat') + raise ValueError("wat") - where_cat = ' AND '.join(_where_cat) - where_quant = ' AND '.join(_where_quant) - log.log(9, f'\nwhere-quant\n{where_quant}\nwhere-quant') + where_cat = " AND ".join(_where_cat) + where_quant = " AND ".join(_where_quant) + log.log(9, f"\nwhere-quant\n{where_quant}\nwhere-quant") return where_cat, where_quant, params def main_query(endpoint, kwargs): ep_select = { #'instances': 'im.dataset, im.id_formal, im.id_sam, im.id_sub, id.label', - 'values/inst': ( - 'im.dataset, ' - 'im.id_formal AS inst, ' - 'im.id_sam AS sample, ' - 'im.id_sub AS subject, ' - 'id.label AS desc_inst' + "values/inst": ( + "im.dataset, " + "im.id_formal AS inst, " + "im.id_sam AS sample, " + "im.id_sub AS subject, " + "id.label AS desc_inst" ), - 'objects': ( # TODO probably some path metadata file type, etc. too - 'im.dataset, ' - 'o.id, ' - 'o.id_type, ' - 'oi.updated_transitive' + "objects": ( # TODO probably some path metadata file type, etc. too + "im.dataset, " "o.id, " "o.id_type, " "oi.updated_transitive" ), - 'values/cat': ( - 'im.dataset, ' - 'im.id_formal AS inst, ' - 'id.label AS desc_inst, ' - 'cdid.label AS domain, ' - 'cd.range, ' - 'cd.label AS desc_cat, ' - 'cv.value_open, ' - 'ct.label AS value_controlled' # TODO and where did it come from TODO iri + "values/cat": ( + "im.dataset, " + "im.id_formal AS inst, " + "id.label AS desc_inst, " + "cdid.label AS domain, " + "cd.range, " + "cd.label AS desc_cat, " + "cv.value_open, " + "ct.label AS value_controlled" # TODO and where did it come from TODO iri ), # TODO will want/need to return the shape of the value for these as well since that will be needed to correctly interpret the contents of the value field in the future - 'values/quant': ( - 'im.dataset, ' - 'im.id_formal AS inst, ' - 'id.label AS desc_inst, ' - 'qd.aggregation_type AS agg_type, ' - 'a.label AS aspect, ' - 'u.label AS unit, qv.value' # TODO and where did it come from + "values/quant": ( + "im.dataset, " + "im.id_formal AS inst, " + "id.label AS desc_inst, " + "qd.aggregation_type AS agg_type, " + "a.label AS aspect, " + "u.label AS unit, qv.value" # TODO and where did it come from ), - 'values/cat-quant': ( + "values/cat-quant": ( ( "'value-cat' AS type, " - 'im.dataset, ' - 'im.id_formal AS inst, ' - 'id.label AS desc_inst, ' - 'cdid.label AS domain, ' - 'cd.range, ' - 'NULL::quant_agg_type as agg_type, ' # have to annoate the nulls because distinct causes type inference to fail ??? - 'cd.label AS pred_or_asp, ' - 'cv.value_open AS vo_or_unit, ' - 'ct.label AS value_controlled, ' - 'NULL::numeric AS value') - , ( + "im.dataset, " + "im.id_formal AS inst, " + "id.label AS desc_inst, " + "cdid.label AS domain, " + "cd.range, " + "NULL::quant_agg_type as agg_type, " # have to annoate the nulls because distinct causes type inference to fail ??? + "cd.label AS pred_or_asp, " + "cv.value_open AS vo_or_unit, " + "ct.label AS value_controlled, " + "NULL::numeric AS value" + ), + ( "'value-quant' AS type, im.dataset, " - 'im.id_formal AS inst, id.label AS desc_inst, ' - 'NULL AS domain, ' - 'NULL::cat_range_type AS range, ' - 'qd.aggregation_type AS agg_type, ' - 'a.label AS aspect, ' - 'u.label AS unit, ' - 'NULL AS vc, qv.value' - )), - 'desc/inst': ( - 'id.iri, ' - 'id.label, ' - 'idpar.label as subclassof ' - ), - 'desc/cat': ( - 'cd.label, ' - 'cdid.label AS domain, ' - 'cd.range, ' - 'cd.description ' - ), - 'desc/quant': ( - 'qd.label, ' - 'id.label AS domain, ' - 'qd.shape, ' - 'qd.aggregation_type as agg_type, ' - 'a.label AS aspect, ' - 'u.label AS unit, ' - 'qd.description ' + "im.id_formal AS inst, id.label AS desc_inst, " + "NULL AS domain, " + "NULL::cat_range_type AS range, " + "qd.aggregation_type AS agg_type, " + "a.label AS aspect, " + "u.label AS unit, " + "NULL AS vc, qv.value" + ), ), - 'terms': ( - 'ct.iri, ' - 'ct.label ' - ), - 'units': ( - 'u.iri, ' - 'u.label ' - ), - 'aspects': ( - 'a.iri, ' - 'a.label, ' - 'aspar.label as subclassof ' + "desc/inst": ("id.iri, " "id.label, " "idpar.label as subclassof "), + "desc/cat": ("cd.label, " "cdid.label AS domain, " "cd.range, " "cd.description "), + "desc/quant": ( + "qd.label, " + "id.label AS domain, " + "qd.shape, " + "qd.aggregation_type as agg_type, " + "a.label AS aspect, " + "u.label AS unit, " + "qd.description " ), + "terms": ("ct.iri, " "ct.label "), + "units": ("u.iri, " "u.label "), + "aspects": ("a.iri, " "a.label, " "aspar.label as subclassof "), }[endpoint] # FIXME move extra and select out and pass then in in as arguments ? or retain control here? - def gkw(k): return k in kwargs and kwargs[k] + def gkw(k): + return k in kwargs and kwargs[k] class sn: # select needs - objects = endpoint == 'objects' - desc_inst = endpoint not in ('objects', 'terms', 'units', 'aspects',) - desc_cat = endpoint in ('values/cat', 'values/cat-quant', 'desc/cat') - value_cat = endpoint in ('values/cat', 'values/cat-quant', 'terms') - aspect = endpoint in ('values/quant', 'values/cat-quant', 'desc/quant', 'aspects') - unit = endpoint in ('values/quant', 'values/cat-quant', 'desc/quant', 'units') - agg_type = endpoint in ('values/quant', 'values/cat-quant') - desc_quant = (aspect or unit or agg_type) - parent_aspect = endpoint == 'aspects' - parent_desc_inst = endpoint == 'desc/inst' + objects = endpoint == "objects" + desc_inst = endpoint not in ( + "objects", + "terms", + "units", + "aspects", + ) + desc_cat = endpoint in ("values/cat", "values/cat-quant", "desc/cat") + value_cat = endpoint in ("values/cat", "values/cat-quant", "terms") + aspect = endpoint in ( + "values/quant", + "values/cat-quant", + "desc/quant", + "aspects", + ) + unit = endpoint in ( + "values/quant", + "values/cat-quant", + "desc/quant", + "units", + ) + agg_type = endpoint in ("values/quant", "values/cat-quant") + desc_quant = aspect or unit or agg_type + parent_aspect = endpoint == "aspects" + parent_desc_inst = endpoint == "desc/inst" class kw: # keywords - prov = gkw('prov') - source_only = gkw('source-only') - desc_inst = gkw('desc-inst') - desc_cat = gkw('desc-cat') - value_cat = gkw('value-cat') - aspect = gkw('aspect') - unit = gkw('unit') - agg_type = gkw('agg-type') - desc_quant = (aspect or unit or agg_type) + prov = gkw("prov") + source_only = gkw("source-only") + desc_inst = gkw("desc-inst") + desc_cat = gkw("desc-cat") + value_cat = gkw("value-cat") + aspect = gkw("aspect") + unit = gkw("unit") + agg_type = gkw("agg-type") + desc_quant = aspect or unit or agg_type q_par_desc_inst = """ JOIN descriptors_inst AS idstart ON idstart.id = {join_to}.desc_inst @@ -241,7 +297,8 @@ class kw: # keywords adc.addr_type as prov_value_addr_type, adc.addr_field as prov_value_addr_field, adc.value_type as prov_value_type -""" + (""", +""" + ( + """, NULL::address_type as prov_unit_addr_type, NULL as prov_unit_addr_field, NULL::field_value_type as prov_unit_type, @@ -249,7 +306,10 @@ class kw: # keywords NULL::address_type as prov_aspect_addr_type, NULL as prov_aspect_addr_field, NULL::field_value_type as prov_aspect_type -""" if sn.unit or endpoint == 'values/inst' else '') +""" + if sn.unit or endpoint == "values/inst" + else "" + ) s_prov_q = """ adq.addr_type as prov_value_addr_type, @@ -283,132 +343,211 @@ class kw: # keywords LEFT OUTER JOIN addresses AS ada ON ada.id = odq.addr_aspect """ - maybe_distinct = 'DISTINCT ' if ( - endpoint.startswith('desc/') or - endpoint in ('terms', 'units', 'aspects') or - (sn.objects or kw.prov) and not kw.source_only) else '' + maybe_distinct = ( + "DISTINCT " + if ( + endpoint.startswith("desc/") + or endpoint in ("terms", "units", "aspects") + or (sn.objects or kw.prov) + and not kw.source_only + ) + else "" + ) ep_select_cat, ep_select_quant = ep_select if isinstance(ep_select, tuple) else (ep_select, ep_select) - select_cat = f'SELECT {maybe_distinct}{ep_select_cat}' + ( - (s_prov_objs + s_prov_i + ((',\n' + s_prov_c) if endpoint != 'values/inst' else '')) if kw.prov else '') - select_quant = f'SELECT {maybe_distinct}{ep_select_quant}' + ( - (s_prov_objs + s_prov_i + ((',\n' + s_prov_q) if endpoint != 'values/inst' else '')) if kw.prov else '') + select_cat = f"SELECT {maybe_distinct}{ep_select_cat}" + ( + (s_prov_objs + s_prov_i + ((",\n" + s_prov_c) if endpoint != "values/inst" else "")) if kw.prov else "" + ) + select_quant = f"SELECT {maybe_distinct}{ep_select_quant}" + ( + (s_prov_objs + s_prov_i + ((",\n" + s_prov_q) if endpoint != "values/inst" else "")) if kw.prov else "" + ) _where_cat, _where_quant, params = get_where(kwargs) - where_cat = f'WHERE {_where_cat}' if _where_cat else '' - where_quant = f'WHERE {_where_quant}' if _where_quant else '' + where_cat = f"WHERE {_where_cat}" if _where_cat else "" + where_quant = f"WHERE {_where_quant}" if _where_quant else "" # FIXME even trying to be smart here about which joins to pull just papers over the underlying perf issue # shaves about 140ms off but the underlying issue remains - q_cat = '\n'.join(( - 'FROM values_cat AS cv', - '\n'.join(( - 'JOIN descriptors_inst AS idin', - 'CROSS JOIN LATERAL get_child_closed_desc_inst(idin.id) AS idc ON cv.desc_inst = idc.child -- FIXME', - )) if kw.desc_inst else '', - (q_par_desc_inst.format(join_to='cv') if sn.parent_desc_inst else - 'JOIN descriptors_inst AS id ON cv.desc_inst = id.id' - ) if sn.desc_inst or kw.desc_inst else '', # FIXME handle parents case - 'JOIN values_inst AS im ON cv.instance = im.id', - '\n'.join(( - 'JOIN descriptors_cat AS cd ON cv.desc_cat = cd.id', - 'LEFT OUTER JOIN descriptors_inst AS cdid ON cd.domain = cdid.id -- XXX TODO mismach', - )) if sn.desc_cat or kw.desc_cat else '', - 'LEFT OUTER JOIN controlled_terms AS ct ON cv.value_controlled = ct.id' if sn.value_cat or kw.value_cat else '', - (('\n' - 'JOIN objects AS o ON cv.object = o.id\n' - 'LEFT OUTER JOIN objects_internal AS oi\n' - 'ON oi.id = o.id\n') - if kw.source_only else - ('\n' # have to use LEFT OUTER because object might have only one of cat or quant - 'LEFT OUTER JOIN values_quant AS qv ON qv.instance = im.id\n' - 'JOIN objects AS o ON cv.object = o.id OR qv.object = o.id\n' - 'LEFT OUTER JOIN objects_internal AS oi\n' - 'ON oi.id = o.id\n') - ) if sn.objects or kw.prov else '', - (q_prov_i + q_prov_c) if kw.prov else '', - )) - - q_quant = '\n'.join(( - 'FROM values_quant AS qv', - '\n'.join(( - 'JOIN descriptors_inst AS idin', - 'CROSS JOIN LATERAL get_child_closed_desc_inst(idin.id) AS idc ON qv.desc_inst = idc.child -- FIXME', - )) if kw.desc_inst else '', - (q_par_desc_inst.format(join_to='qv') if sn.parent_desc_inst else - 'JOIN descriptors_inst AS id ON qv.desc_inst = id.id' - ) if sn.desc_inst or kw.desc_inst else '', # FIXME handle parents case - 'JOIN values_inst AS im ON qv.instance = im.id', - 'JOIN descriptors_quant AS qd ON qv.desc_quant = qd.id' if ( - sn.desc_quant or kw.desc_quant) else '', - '\n'.join(( - 'JOIN aspects AS ain', - 'CROSS JOIN LATERAL get_child_closed_aspect(ain.id) AS ac ON qd.aspect = ac.child', - 'JOIN aspects AS a ON ac.child = a.id', - )) if kw.aspect else ( - (q_par_aspect if sn.parent_aspect else - 'JOIN aspects AS a ON qd.aspect = a.id' - ) if sn.aspect else ''), # FIXME handle parents case - 'LEFT OUTER JOIN units AS u ON qd.unit = u.id' if sn.unit or kw.unit else '', - (('\n' - 'JOIN objects AS o ON qv.object = o.id\n' - 'LEFT OUTER JOIN objects_internal AS oi ON oi.id = o.id\n') - if kw.source_only else - ('\n' # have to use LEFT OUTER because object might have only one of cat or quant - 'LEFT OUTER JOIN values_cat AS cv ON cv.instance = im.id\n' - 'JOIN objects AS o ON qv.object = o.id OR cv.object = o.id\n' - 'LEFT OUTER JOIN objects_internal AS oi ON oi.id = o.id\n') - ) if sn.objects or kw.prov else '', - (q_prov_i + q_prov_q) if kw.prov else '', - )) - - sw_cat = f'{select_cat}\n{q_cat}\n{where_cat}' # XXX yes this can be malformed in some cases - sw_quant = f'{select_quant}\n{q_quant}\n{where_quant}' # XXX yes this can be malformed in some cases - if endpoint in ('values/cat', 'terms', 'desc/cat'): + q_cat = "\n".join( + ( + "FROM values_cat AS cv", + ( + "\n".join( + ( + "JOIN descriptors_inst AS idin", + "CROSS JOIN LATERAL get_child_closed_desc_inst(idin.id) AS idc ON cv.desc_inst = idc.child -- FIXME", + ) + ) + if kw.desc_inst + else "" + ), + ( + ( + q_par_desc_inst.format(join_to="cv") + if sn.parent_desc_inst + else "JOIN descriptors_inst AS id ON cv.desc_inst = id.id" + ) + if sn.desc_inst or kw.desc_inst + else "" + ), # FIXME handle parents case + "JOIN values_inst AS im ON cv.instance = im.id", + ( + "\n".join( + ( + "JOIN descriptors_cat AS cd ON cv.desc_cat = cd.id", + "LEFT OUTER JOIN descriptors_inst AS cdid ON cd.domain = cdid.id -- XXX TODO mismach", + ) + ) + if sn.desc_cat or kw.desc_cat + else "" + ), + ( + "LEFT OUTER JOIN controlled_terms AS ct ON cv.value_controlled = ct.id" + if sn.value_cat or kw.value_cat + else "" + ), + ( + ( + ( + "\n" + "JOIN objects AS o ON cv.object = o.id\n" + "LEFT OUTER JOIN objects_internal AS oi\n" + "ON oi.id = o.id\n" + ) + if kw.source_only + else ( + "\n" # have to use LEFT OUTER because object might have only one of cat or quant + "LEFT OUTER JOIN values_quant AS qv ON qv.instance = im.id\n" + "JOIN objects AS o ON cv.object = o.id OR qv.object = o.id\n" + "LEFT OUTER JOIN objects_internal AS oi\n" + "ON oi.id = o.id\n" + ) + ) + if sn.objects or kw.prov + else "" + ), + (q_prov_i + q_prov_c) if kw.prov else "", + ) + ) + + q_quant = "\n".join( + ( + "FROM values_quant AS qv", + ( + "\n".join( + ( + "JOIN descriptors_inst AS idin", + "CROSS JOIN LATERAL get_child_closed_desc_inst(idin.id) AS idc ON qv.desc_inst = idc.child -- FIXME", + ) + ) + if kw.desc_inst + else "" + ), + ( + ( + q_par_desc_inst.format(join_to="qv") + if sn.parent_desc_inst + else "JOIN descriptors_inst AS id ON qv.desc_inst = id.id" + ) + if sn.desc_inst or kw.desc_inst + else "" + ), # FIXME handle parents case + "JOIN values_inst AS im ON qv.instance = im.id", + ("JOIN descriptors_quant AS qd ON qv.desc_quant = qd.id" if (sn.desc_quant or kw.desc_quant) else ""), + ( + "\n".join( + ( + "JOIN aspects AS ain", + "CROSS JOIN LATERAL get_child_closed_aspect(ain.id) AS ac ON qd.aspect = ac.child", + "JOIN aspects AS a ON ac.child = a.id", + ) + ) + if kw.aspect + else ( + (q_par_aspect if sn.parent_aspect else "JOIN aspects AS a ON qd.aspect = a.id") if sn.aspect else "" + ) + ), # FIXME handle parents case + ("LEFT OUTER JOIN units AS u ON qd.unit = u.id" if sn.unit or kw.unit else ""), + ( + ( + ( + "\n" + "JOIN objects AS o ON qv.object = o.id\n" + "LEFT OUTER JOIN objects_internal AS oi ON oi.id = o.id\n" + ) + if kw.source_only + else ( + "\n" # have to use LEFT OUTER because object might have only one of cat or quant + "LEFT OUTER JOIN values_cat AS cv ON cv.instance = im.id\n" + "JOIN objects AS o ON qv.object = o.id OR cv.object = o.id\n" + "LEFT OUTER JOIN objects_internal AS oi ON oi.id = o.id\n" + ) + ) + if sn.objects or kw.prov + else "" + ), + (q_prov_i + q_prov_q) if kw.prov else "", + ) + ) + + sw_cat = f"{select_cat}\n{q_cat}\n{where_cat}" # XXX yes this can be malformed in some cases + sw_quant = f"{select_quant}\n{q_quant}\n{where_quant}" # XXX yes this can be malformed in some cases + if endpoint in ("values/cat", "terms", "desc/cat"): query = sw_cat - elif endpoint in ('values/quant', 'units', 'aspects', 'desc/quant'): # FIXME TODO make it possible to cross query terms, units, aspects + elif endpoint in ( + "values/quant", + "units", + "aspects", + "desc/quant", + ): # FIXME TODO make it possible to cross query terms, units, aspects query = sw_quant else: - operator = 'UNION' if 'union-cat-quant' in kwargs and kwargs['union-cat-quant'] else 'INTERSECT' - query = f'{sw_cat}\n{operator}\n{sw_quant}' + operator = "UNION" if "union-cat-quant" in kwargs and kwargs["union-cat-quant"] else "INTERSECT" + query = f"{sw_cat}\n{operator}\n{sw_quant}" - log.log(9, '\n' + query) + log.log(9, "\n" + query) return query, params def to_json(record_type, res, prov=False): rows = list(res) if rows: - if record_type == 'object': - result = [{k: v for k, v in r._asdict().items() if k != 'id'} - # do not leak internal ids because the might change and are not meaningful - if r.id_type == 'quantdb' else - {k: v for k, v in r._asdict().items() if k != 'updated_transitive'} - for r in rows] - elif record_type is None and 'type' in rows[0]._fields: - rem_cat = 'value', 'agg_type' + if record_type == "object": + result = [ + ( + {k: v for k, v in r._asdict().items() if k != "id"} + # do not leak internal ids because the might change and are not meaningful + if r.id_type == "quantdb" + else {k: v for k, v in r._asdict().items() if k != "updated_transitive"} + ) + for r in rows + ] + elif record_type is None and "type" in rows[0]._fields: + rem_cat = "value", "agg_type" + def type_fields_cat(k): - if k == 'pred_or_asp': - return 'desc_cat' - elif k == 'vo_or_unit': - return 'value_open' + if k == "pred_or_asp": + return "desc_cat" + elif k == "vo_or_unit": + return "value_open" else: return k - rem_quant = 'domain', 'range', 'value_controlled' + rem_quant = "domain", "range", "value_controlled" + def type_fields_quant(k): - if k == 'pred_or_asp': - return 'aspect' - elif k == 'vo_or_unit': - return 'unit' + if k == "pred_or_asp": + return "aspect" + elif k == "vo_or_unit": + return "unit" else: return k def prow(r): - if r.type == 'value-cat': + if r.type == "value-cat": rem, type_fields = rem_cat, type_fields_cat - elif r.type == 'value-quant': + elif r.type == "value-quant": rem, type_fields = rem_quant, type_fields_quant else: - raise NotImplementedError(f'wat {r.type}') + raise NotImplementedError(f"wat {r.type}") return {type_fields(k): v for k, v in r._asdict().items() if k not in rem} @@ -418,35 +557,40 @@ def prow(r): for r in result: if record_type is not None: - r['type'] = record_type + r["type"] = record_type - for cull_none in ('subclassof',): + for cull_none in ("subclassof",): if cull_none in r and r[cull_none] is None: r.pop(cull_none) if prov: + def pop_prefix(d, prefix): - usc = prefix.count('_') - return {k.split('_', 1 + usc)[-1]:v for k in list(d) if k.startswith(prefix + '_') and (v := d.pop(k)) is not None} + usc = prefix.count("_") + return { + k.split("_", 1 + usc)[-1]: v + for k in list(d) + if k.startswith(prefix + "_") and (v := d.pop(k)) is not None + } for r in result: - provs = pop_prefix(r, 'prov') - if 'source_id_type' in provs and provs['source_id_type'] == 'quantdb': - provs.pop('source_id', None) # don't leak internal ids + provs = pop_prefix(r, "prov") + if "source_id_type" in provs and provs["source_id_type"] == "quantdb": + provs.pop("source_id", None) # don't leak internal ids else: - provs.pop('source_updated_transitive', None) # always None in this case + provs.pop("source_updated_transitive", None) # always None in this case - for prefix in ('desc_inst', 'inst', 'value', 'value', 'source'): + for prefix in ("desc_inst", "inst", "value", "value", "source"): d = pop_prefix(provs, prefix) if d: - d['type'] = 'address' if prefix != 'source' else 'object' + d["type"] = "address" if prefix != "source" else "object" provs[prefix] = d - provs['type'] = 'prov' - r['prov'] = provs + provs["type"] = "prov" + r["prov"] = provs out = result - #breakpoint() + # breakpoint() else: out = [] @@ -461,60 +605,51 @@ def wrap_out(endpoint, kwargs, out): parameters = {k: v for k, v in kwargs.items() if v} n_records = len(out) blob = { - 'type': 'quantdb-query-result', - 'endpoint': endpoint, - 'parameters': parameters, - 'records': n_records, - 'result': out, + "type": "quantdb-query-result", + "endpoint": endpoint, + "parameters": parameters, + "records": n_records, + "result": out, } return blob args_default = { - 'object': [], - 'updated-transitive': None, # TODO needed to query for some internal - + "object": [], + "updated-transitive": None, # TODO needed to query for some internal ## inst - 'desc-inst': [], # aka class - + "desc-inst": [], # aka class # value-inst - 'dataset': None, - 'inst': [], - 'subject': [], - 'sample': [], - 'include-equivalent': False, - + "dataset": None, + "inst": [], + "subject": [], + "sample": [], + "include-equivalent": False, ## cat - 'desc-cat': [], # aka predicate - - 'value-cat': [], - 'value-cat-open': [], - + "desc-cat": [], # aka predicate + "value-cat": [], + "value-cat-open": [], ## quant # desc-quant - 'unit': [], - 'aspect': [], - 'agg-type': None, + "unit": [], + "aspect": [], + "agg-type": None, # TODO shape - - 'value-quant': None, - 'value-quant-margin': None, - 'value-quant-min': None, - 'value-quant-max': None, - - 'limit': 100, + "value-quant": None, + "value-quant-margin": None, + "value-quant-min": None, + "value-quant-max": None, + "limit": 500, #'operator': 'INTERSECT', # XXX ... - 'union-cat-quant': False, # by default we intersect but sometimes you want the union instead e.g. if object is passed - 'source-only': False, - 'include-unused': False, - 'prov': False, - + "union-cat-quant": False, # by default we intersect but sometimes you want the union instead e.g. if object is passed + "source-only": False, + "include-unused": False, + "prov": False, #'cat-value': [], #'class': [], #'predicate': None, #'object': None, #'filter': [], - #'quant-value': None, #'quant-margin': None, #'quant-min': None, @@ -522,66 +657,81 @@ def wrap_out(endpoint, kwargs, out): } -def getArgs(request, endpoint, dev=False): +app = FastAPI() + + +def getArgs(request: Request, endpoint: str, dev: bool = False) -> Dict[str, Any]: default = copy.deepcopy(args_default) + # TODO: temporary fix to allow flask and fastapi to work together + try: + args = request.query_params + except Exception as e: + args = request.args + if dev: - default['return-query'] = False + default["return-query"] = False # modify defaults by endpoint - if endpoint != 'objects': - default.pop('source-only') + if endpoint != "objects": + default.pop("source-only") - if not (endpoint.startswith('desc/') or endpoint in ('terms', 'units', 'aspects')): - default.pop('include-unused') + if not (endpoint.startswith("desc/") or endpoint in ("terms", "units", "aspects")): + default.pop("include-unused") else: # prevent filtering on the thing we are trying to query - if endpoint == 'terms': - default.pop('value-cat') - elif endpoint == 'units': - default.pop('unit') - elif endpoint == 'aspects': - default.pop('aspect') - elif endpoint == 'desc/inst': - default.pop('desc-inst') - elif endpoint == 'desc/cat': - default.pop('desc-cat') - - if not endpoint.startswith('values/'): - default.pop('prov') - elif endpoint == 'values/cat': - [default.pop(k) for k in list(default) if k.startswith('value-quant') or k in ('unit', 'aspect', 'agg-type')] - elif endpoint == 'values/quant': - [default.pop(k) for k in list(default) if k in ('desc-cat', 'value-cat', 'value-cat-open')] - - extras = set(request.args) - set(default) + if endpoint == "terms": + default.pop("value-cat") + elif endpoint == "units": + default.pop("unit") + elif endpoint == "aspects": + default.pop("aspect") + elif endpoint == "desc/inst": + default.pop("desc-inst") + elif endpoint == "desc/cat": + default.pop("desc-cat") + + if not endpoint.startswith("values/"): + default.pop("prov") + elif endpoint == "values/cat": + [default.pop(k) for k in list(default) if k.startswith("value-quant") or k in ("unit", "aspect", "agg-type")] + elif endpoint == "values/quant": + [default.pop(k) for k in list(default) if k in ("desc-cat", "value-cat", "value-cat-open")] + + extras = set(args) - set(default) if extras: # FIXME raise this as a 401, TODO need error types for this - nl = '\n' - raise exc.UnknownArg(f'unknown args: {nl.join(extras)}') + nl = "\n" + raise exc.UnknownArg(f"unknown args: {nl.join(extras)}") def convert(k, d): - if k in request.args: + if k in args: # arity is determined here - if k in ('dataset', 'include-equivalent', 'union-cat-quant', 'include-unused', 'agg-type') or k.startswith('value-quant'): - v = request.args[k] - if k in ('dataset',): + if k in ( + "dataset", + "include-equivalent", + "union-cat-quant", + "include-unused", + "agg-type", + ) or k.startswith("value-quant"): + v = args[k] + if k in ("dataset",): v = uuid.UUID(v) else: - v = request.args.getlist(k) - if k in ('object',): + v = args.getlist(k) + if k in ("object",): v = [uuid.UUID(_) for _ in v] # caste to uuid to simplify sqlalchemy type mapping else: return d - if k in ('include-equivalent', 'union-cat-quant', 'include-unused'): - if v.lower() == 'true': + if k in ("include-equivalent", "union-cat-quant", "include-unused"): + if v.lower() == "true": return True - elif v.lower() == 'false': + elif v.lower() == "false": return False else: raise TypeError(f'Expected a bool, got "{v}" instead.') - elif k.startswith('value-quant') or k in ('limit',): + elif k.startswith("value-quant") or k in ("limit",): try: return float(v) except ValueError as e: @@ -589,34 +739,35 @@ def convert(k, d): else: return v - out = {k:convert(k, v) for k, v in default.items()} + out = {k: convert(k, v) for k, v in default.items()} return out -def make_app(db=None, name='quantdb-api-server', dev=False): +def make_app(db=None, name="quantdb-api-server", dev=False): app = Flask(name) - kwargs = {k:auth.get(f'db-{k}') # TODO integrate with cli options - for k in ('user', 'host', 'port', 'database')} - kwargs['dbuser'] = kwargs.pop('user') - app.config['SQLALCHEMY_DATABASE_URI'] = dbUri(**kwargs) # use os.environ.update - app.config['SQLALCHEMY_TRACK_MODIFICATIONS'] = False + app.config["SQLALCHEMY_DATABASE_URI"] = get_settings().SQLALCHEMY_DATABASE_URI + app.config["SQLALCHEMY_TRACK_MODIFICATIONS"] = False db.init_app(app) session = db.session - bp = '/api/1/' + bp = "/api/1/" def default_flow(endpoint, record_type, query_fun, json_fun, alt_query_fun=None): try: kwargs = getArgs(request, endpoint, dev=dev) except exc.UnknownArg as e: - return json.dumps({'error': e.args[0], 'http_response_status': 422}), 422 + return ( + json.dumps({"error": e.args[0], "http_response_status": 422}), + 422, + ) except Exception as e: breakpoint() raise e - def gkw(k): return k in kwargs and kwargs[k] + def gkw(k): + return k in kwargs and kwargs[k] - if gkw('include-unused'): + if gkw("include-unused"): query_fun = alt_query_fun # FIXME record_type is actually determined entirely in query_fun right now @@ -626,7 +777,7 @@ def gkw(k): return k in kwargs and kwargs[k] breakpoint() raise e - if gkw('return-query'): + if gkw("return-query"): return query try: @@ -636,137 +787,389 @@ def gkw(k): return k in kwargs and kwargs[k] raise e try: - out = json_fun(record_type, res, prov=('prov' in kwargs and kwargs['prov'])) - resp = json.dumps(wrap_out(endpoint, kwargs, out), cls=JEncode), 200, {'Content-Type': 'application/json'} + out = json_fun(record_type, res, prov=("prov" in kwargs and kwargs["prov"])) + resp = ( + json.dumps(wrap_out(endpoint, kwargs, out), cls=JEncode), + 200, + {"Content-Type": "application/json"}, + ) except Exception as e: breakpoint() raise e return resp - @app.route(f'{bp}/objects') + @app.route(f"{bp}/test") + def route_test_check(): + "objects with derived values that match all criteria" + return "testing-api" + + @app.route(f"{bp}/objects") def route_1_objects(): "objects with derived values that match all criteria" - return default_flow('objects', 'object', main_query, to_json) + return default_flow("objects", "object", main_query, to_json) - @app.route(f'{bp}/desc/inst') - @app.route(f'{bp}/descriptors/inst') - @app.route(f'{bp}/classes') + @app.route(f"{bp}/desc/inst") + @app.route(f"{bp}/descriptors/inst") + @app.route(f"{bp}/classes") def route_1_desc_inst(): def query(endpoint, kwargs): - return ('SELECT ' - - 'id.iri, ' - 'id.label, ' - 'idpar.label as subclassof' - + return ( + ( + "SELECT " + "id.iri, " + "id.label, " + "idpar.label as subclassof" """ FROM descriptors_inst AS id LEFT OUTER JOIN class_parent AS ip ON ip.id = id.id LEFT OUTER JOIN descriptors_inst AS idpar ON idpar.id = ip.parent -"""), {} +""" + ), + {}, + ) - return default_flow('desc/inst', 'desc-inst', main_query, to_json, alt_query_fun=query) + return default_flow("desc/inst", "desc-inst", main_query, to_json, alt_query_fun=query) - @app.route(f'{bp}/desc/cat') - @app.route(f'{bp}/descriptors/cat') - @app.route(f'{bp}/predicates') + @app.route(f"{bp}/desc/cat") + @app.route(f"{bp}/descriptors/cat") + @app.route(f"{bp}/predicates") def route_1_desc_cat(): def query(endpoint, kwargs): - return ('select ' - - 'cd.label, ' - 'cdid.label AS domain, ' - 'cd.range, ' - 'cd.description ' - - 'from descriptors_cat as cd ' - 'left outer join descriptors_inst as cdid on cdid.id = cd.domain' - ), {} - - return default_flow('desc/cat', 'desc-cat', main_query, to_json, alt_query_fun=query) # TODO likely need different args e.g. to filter by desc_inst - - @app.route(f'{bp}/desc/quant') - @app.route(f'{bp}/descriptors/quant') + return ( + "select " + "cd.label, " + "cdid.label AS domain, " + "cd.range, " + "cd.description " + "from descriptors_cat as cd " + "left outer join descriptors_inst as cdid on cdid.id = cd.domain" + ), {} + + return default_flow( + "desc/cat", "desc-cat", main_query, to_json, alt_query_fun=query + ) # TODO likely need different args e.g. to filter by desc_inst + + @app.route(f"{bp}/desc/quant") + @app.route(f"{bp}/descriptors/quant") def route_1_desc_quant(): def query(endpoint, kwargs): - return ('select ' - - 'qd.label, ' - 'id.label AS domain, ' - 'qd.shape, ' - 'qd.aggregation_type as agg_type, ' - 'a.label AS aspect, ' - 'u.label AS unit, ' - 'qd.description ' - - 'from descriptors_quant as qd ' - 'left outer join descriptors_inst as id on id.id = qd.domain ' - 'left outer join units as u on u.id = qd.unit ' - 'join aspects as a on a.id = qd.aspect' - ), {} - - return default_flow('desc/quant', 'desc-quant', main_query, to_json, alt_query_fun=query) # TODO likely need different args e.g. to filter by desc_inst - - @app.route(f'{bp}/values/inst') - @app.route(f'{bp}/instances') + return ( + "select " + "qd.label, " + "id.label AS domain, " + "qd.shape, " + "qd.aggregation_type as agg_type, " + "a.label AS aspect, " + "u.label AS unit, " + "qd.description " + "from descriptors_quant as qd " + "left outer join descriptors_inst as id on id.id = qd.domain " + "left outer join units as u on u.id = qd.unit " + "join aspects as a on a.id = qd.aspect" + ), {} + + return default_flow( + "desc/quant", "desc-quant", main_query, to_json, alt_query_fun=query + ) # TODO likely need different args e.g. to filter by desc_inst + + @app.route(f"{bp}/values/inst") + @app.route(f"{bp}/instances") def route_1_val_inst(): "instances associated with values that match all critiera" - return default_flow('values/inst', 'instance', main_query, to_json) + return default_flow("values/inst", "instance", main_query, to_json) - @app.route(f'{bp}/values') - @app.route(f'{bp}/values/cat-quant') + @app.route(f"{bp}/values") + @app.route(f"{bp}/values/cat-quant") def route_1_val_cat_quant(): - return default_flow('values/cat-quant', None, main_query, to_json) + return default_flow("values/cat-quant", None, main_query, to_json) - @app.route(f'{bp}/values/cat') + @app.route(f"{bp}/values/cat") def route_1_val_cat(): - return default_flow('values/cat', 'value-cat', main_query, to_json) + return default_flow("values/cat", "value-cat", main_query, to_json) - @app.route(f'{bp}/values/quant') + @app.route(f"{bp}/values/quant") def route_1_val_quant(): - return default_flow('values/quant', 'value-quant', main_query, to_json) + return default_flow("values/quant", "value-quant", main_query, to_json) - @app.route(f'{bp}/terms') - @app.route(f'{bp}/controlled-terms') + @app.route(f"{bp}/terms") + @app.route(f"{bp}/controlled-terms") def route_1_cterms(): def query(endpoint, kwargs): - return ('select ' + return ("select " "ct.iri, " "ct.label " "from controlled_terms as ct"), {} - 'ct.iri, ' - 'ct.label ' + return default_flow("terms", "term", main_query, to_json, alt_query_fun=query) - 'from controlled_terms as ct'), {} - - return default_flow('terms', 'term', main_query, to_json, alt_query_fun=query) - - @app.route(f'{bp}/units') + @app.route(f"{bp}/units") def route_1_units(): def query(endpoint, kwargs): - return ('select ' - - 'u.iri, ' - 'u.label ' + return ("select " "u.iri, " "u.label " "from units as u"), {} - 'from units as u'), {} + return default_flow("units", "unit", main_query, to_json, alt_query_fun=query) - return default_flow('units', 'unit', main_query, to_json, alt_query_fun=query) - - @app.route(f'{bp}/aspects') + @app.route(f"{bp}/aspects") def route_1_aspects(): def query(endpoint, kwargs): - return ('SELECT ' - - 'a.iri, ' - 'a.label, ' - 'aspar.label AS subclassof ' - + return ( + ( + "SELECT " + "a.iri, " + "a.label, " + "aspar.label AS subclassof " """ FROM aspects AS a LEFT OUTER JOIN aspect_parent AS ap ON ap.id = a.id LEFT OUTER JOIN aspects AS aspar ON aspar.id = ap.parent -"""), {} +""" + ), + {}, + ) - return default_flow('aspects', 'aspect', main_query, to_json, alt_query_fun=query) + return default_flow("aspects", "aspect", main_query, to_json, alt_query_fun=query) return app + + +def default_flow_fastapi( + request, + session, + endpoint, + record_type, + query_fun, + json_fun, + alt_query_fun=None, +): + try: + kwargs = getArgs(request, endpoint) + except exc.UnknownArg as e: + return ( + json.dumps({"error": e.args[0], "http_response_status": 422}), + 422, + ) + except Exception as e: + # breakpoint() + raise e + + def gkw(k): + return k in kwargs and kwargs[k] + + if gkw("include-unused"): + query_fun = alt_query_fun + + # FIXME record_type is actually determined entirely in query_fun right now + try: + query, params = query_fun(endpoint, kwargs) + except Exception as e: + # breakpoint() + raise e + + if gkw("return-query"): + return query + + try: + res = session.execute(sql_text(query), params) + except Exception as e: + # breakpoint() + raise e + + try: + out = json_fun(record_type, res, prov=("prov" in kwargs and kwargs["prov"])) + resp = ( + json.dumps(wrap_out(endpoint, kwargs, out), cls=JEncode), + 200, + {"Content-Type": "application/json"}, + ) + except Exception as e: + # breakpoint() + raise e + + return resp + + +@fastapi_app.get( + "/test", + status_code=200, +) +def get_test( + mysql_db: Session = Depends(get_mysql_db), # type: ignore +) -> Any: + return "testing-api" + + +# @fastapi_app.get( +# "/objects", +# status_code=200, +# ) +# def get_objects( +# request: Request, +# session: Session = Depends(get_mysql_db), # type: ignore +# ) -> Any: +# """objects with derived values that match all criteria""" +# resp, status_code, header = default_flow_fastapi( +# request, session, "objects", "object", main_query, to_json +# ) +# result = json.loads(resp) # fastapi does not like json strings +# return result + + +@fastapi_app.get( + "/objects", + status_code=200, +) +def get_objects( + request: Request, + session: Session = Depends(get_mysql_db), # type: ignore +) -> Any: + query = text( + """ +SELECT * FROM objects +""" + ) + result = session.execute(query) + data = result.mappings().all() + return data + + +@fastapi_app.get( + "/obj/desc/cat", + status_code=200, +) +def get_obj_desc_cat( + request: Request, + session: Session = Depends(get_mysql_db), # type: ignore +) -> Any: + query = text( + """ +SELECT * FROM obj_desc_cat +""" + ) + result = session.execute(query) + data = result.mappings().all() + return data + + +@fastapi_app.get( + "/descriptors/cat", + status_code=200, +) +def get_descriptors_cat( + request: Request, + session: Session = Depends(get_mysql_db), # type: ignore +) -> Any: + query = text( + """ +SELECT * FROM descriptors_cat +""" + ) + result = session.execute(query) + data = result.mappings().all() + return data + + +@fastapi_app.get( + "/values/cat", + status_code=200, +) +def get_values_cat( + request: Request, + session: Session = Depends(get_mysql_db), # type: ignore +) -> Any: + query = text( + """ +SELECT * FROM values_cat +""" + ) + result = session.execute(query) + data = result.mappings().all() + return data + + +@fastapi_app.get( + "/units", + status_code=200, +) +def get_units( + request: Request, + session: Session = Depends(get_mysql_db), # type: ignore +) -> Any: + query = text( + """ +SELECT * FROM units +""" + ) + result = session.execute(query) + data = result.mappings().all() + return data + + +@fastapi_app.get( + "/descriptors/quant", + status_code=200, +) +def get_descriptors_quant( + request: Request, + session: Session = Depends(get_mysql_db), # type: ignore +) -> Any: + query = text( + """ +SELECT * FROM descriptors_quant +""" + ) + result = session.execute(query) + data = result.mappings().all() + return data + + +@fastapi_app.get( + "/descriptors/inst", + status_code=200, +) +def get_descriptors_inst( + request: Request, + session: Session = Depends(get_mysql_db), # type: ignore +) -> Any: + query = text( + """ +SELECT * FROM descriptors_inst +""" + ) + result = session.execute(query) + data = result.mappings().all() + return data + + +@fastapi_app.get( + "/aspects", + status_code=200, +) +def get_aspects( + request: Request, + session: Session = Depends(get_mysql_db), # type: ignore +) -> Any: + query = text( + """ +SELECT * FROM aspects +""" + ) + result = session.execute(query) + data = result.mappings().all() + return data + + +@fastapi_app.get( + "/table/{name}/", + status_code=200, +) +def get_aspects( + name: str, + request: Request, + session: Session = Depends(get_mysql_db), # type: ignore +) -> Any: + query = text( + f""" +SELECT * FROM {name} +""" + ) + result = session.execute(query) + data = result.mappings().all() + return data diff --git a/quantdb/api_server.py b/quantdb/api_server.py index 28f7228..0d5c8c3 100644 --- a/quantdb/api_server.py +++ b/quantdb/api_server.py @@ -1,12 +1,13 @@ -from quantdb.utils import setPS1 -from quantdb.api import make_app from flask_sqlalchemy import SQLAlchemy +from quantdb.api import make_app +from quantdb.utils import setPS1 + setPS1(__file__) db = SQLAlchemy() app = make_app(db=db) -if __name__ == '__main__': - app.run(host='localhost', port=8989, threaded=True) +if __name__ == "__main__": + app.run(host="localhost", port=8989, threaded=True) diff --git a/quantdb/auth-config.py b/quantdb/auth-config.py index 796f45d..3b430a3 100644 --- a/quantdb/auth-config.py +++ b/quantdb/auth-config.py @@ -1,33 +1,27 @@ -{'config-search-paths': ['{:user-config-path}/quantdb/config.yaml',], - 'auth-variables': { - # test-db - 'test-db-user': { - 'default': 'quantdb-test-user', - 'environment-variables': 'QUANTDB_TEST_DB_USER'}, - 'test-db-host': { - 'default': 'localhost', - 'environment-variables': 'QUANTDB_TEST_DB_HOST'}, - 'test-db-port': { - 'default': 5432, - 'environment-variables': 'QUANTDB_TEST_DB_PORT'}, - 'test-db-database': { - # we DO set a default database for testing - # so that it is present for reference - 'default': 'quantdb_test', - 'environment-variables': 'QUANTDB_TEST_DB_DATABASE QUANTDB_TEST_DATABASE',}, - # db - 'db-user': { - 'default': 'quantdb-user', - 'environment-variables': 'QUANTDB_DB_USER'}, - 'db-host': { - 'default': 'localhost', - 'environment-variables': 'QUANTDB_DB_HOST'}, - 'db-port': { - 'default': 5432, - 'environment-variables': 'QUANTDB_DB_PORT'}, - 'db-database': { - # we don't set a default here to prevent - # accidental operations on a default db - 'default': None, - 'environment-variables': 'QUANTDB_DB_DATABASE QUANTDB_DATABASE',}, - }} +{ + "config-search-paths": [ + "{:user-config-path}/quantdb/config.yaml", + ], + "auth-variables": { + # test-db + "test-db-user": {"default": "quantdb-test-user", "environment-variables": "QUANTDB_TEST_DB_USER"}, + "test-db-host": {"default": "localhost", "environment-variables": "QUANTDB_TEST_DB_HOST"}, + "test-db-port": {"default": 5432, "environment-variables": "QUANTDB_TEST_DB_PORT"}, + "test-db-database": { + # we DO set a default database for testing + # so that it is present for reference + "default": "quantdb_test", + "environment-variables": "QUANTDB_TEST_DB_DATABASE QUANTDB_TEST_DATABASE", + }, + # db + "db-user": {"default": "quantdb-user", "environment-variables": "QUANTDB_DB_USER"}, + "db-host": {"default": "localhost", "environment-variables": "QUANTDB_DB_HOST"}, + "db-port": {"default": 5432, "environment-variables": "QUANTDB_DB_PORT"}, + "db-database": { + # we don't set a default here to prevent + # accidental operations on a default db + "default": None, + "environment-variables": "QUANTDB_DB_DATABASE QUANTDB_DATABASE", + }, + }, +} diff --git a/quantdb/client.py b/quantdb/client.py new file mode 100644 index 0000000..05f3373 --- /dev/null +++ b/quantdb/client.py @@ -0,0 +1,22 @@ +from sqlalchemy import create_engine +from sqlalchemy.orm import Session + +from quantdb.config import auth +from quantdb.utils import dbUri + + +def get_session(echo: bool = True) -> Session: + # pull in the db connection info + dbkwargs = { + k: auth.get(f"db-{k}") for k in ("user", "host", "port", "database") + } # TODO integrate with cli options + # custom user variable needed + dbkwargs["dbuser"] = dbkwargs.pop("user") + dbkwargs["dbuser"] = "quantdb-test-admin" + # create connection env with DB + engine = create_engine(dbUri(**dbkwargs)) # type: ignore + # bool: echo me + engine.echo = echo + # use connection env as unique session + session = Session(engine) + return session diff --git a/quantdb/config.py b/quantdb/config.py index aa2a831..024821d 100644 --- a/quantdb/config.py +++ b/quantdb/config.py @@ -1,2 +1,16 @@ +from dataclasses import dataclass + import orthauth as oa -auth = oa.configure_here('auth-config.py', __name__) + +from quantdb.utils import dbUri + +auth = oa.configure_here("auth-config.py", __name__) + + +@dataclass +class Settings: + """Settings for the app.""" + + db_params = {k: auth.get(f"db-{k}") for k in ("user", "host", "port", "database")} + db_params["dbuser"] = db_params.pop("user") + SQLALCHEMY_DATABASE_URI = dbUri(**db_params) diff --git a/quantdb/exceptions.py b/quantdb/exceptions.py index 6210d55..ac996ce 100644 --- a/quantdb/exceptions.py +++ b/quantdb/exceptions.py @@ -1,6 +1,6 @@ class QuantdbError(Exception): - """ base """ + """base""" class UnknownArg(QuantdbError): - """ url query parameter unknown """ + """url query parameter unknown""" diff --git a/quantdb/ingest.py b/quantdb/ingest.py index 1fc839a..350f89f 100644 --- a/quantdb/ingest.py +++ b/quantdb/ingest.py @@ -1,28 +1,30 @@ -import sys import json import pathlib +import sys from collections import defaultdict + import requests +from sparcur import objects as sparcur_objects # register pathmeta type +# FIXME sparcur dependencies, or keep ingest separate +from sparcur.utils import fromJson from sqlalchemy import create_engine -from sqlalchemy.orm import Session -from sqlalchemy.sql import text as sql_text from sqlalchemy.dialects.postgresql import JSONB +from sqlalchemy.orm import Session from sqlalchemy.sql import bindparam -# FIXME sparcur dependencies, or keep ingest separate -from sparcur.utils import fromJson -from sparcur import objects as sparcur_objects # register pathmeta type -from quantdb.utils import log, dbUri, isoformat +from sqlalchemy.sql import text as sql_text -######### start database interaction section +from quantdb.utils import dbUri, isoformat, log +######### start database interaction section -log = log.getChild('ingest') +log = log.getChild("ingest") try: - if get_ipython().__class__.__name__ == 'ZMQInteractiveShell': + if get_ipython().__class__.__name__ == "ZMQInteractiveShell": import sys # FIXME hack that should be in jupyter-repl env or something - sys.breakpointhook = lambda : None + + sys.breakpointhook = lambda: None except NameError: pass @@ -30,7 +32,7 @@ # from interlex.core import getName class getName: class MyBool: - """ python is dumb """ + """python is dumb""" def __init__(self): self.counter = -1 @@ -38,10 +40,19 @@ def __init__(self): def valueCheck(self, value): if isinstance(value, dict): - value = hash(frozenset((k, self.valueCheck(v) - if isinstance(v, list) or isinstance(v, dict) - else v) - for k, v in value.items())) + value = hash( + frozenset( + ( + k, + ( + self.valueCheck(v) + if isinstance(v, list) or isinstance(v, dict) + else v + ), + ) + for k, v in value.items() + ) + ) elif isinstance(value, list): value = tuple(self.valueCheck(e) for e in value) elif isinstance(value, bool): @@ -59,7 +70,7 @@ def __call__(self, value, type=None): return self.value_to_name[value] else: self.counter += 1 - name = 'v' + str(self.counter) + name = "v" + str(self.counter) if type is None: self.value_to_name[value] = name @@ -70,11 +81,15 @@ def __call__(self, value, type=None): # from interlex.core import makeParamsValues -def makeParamsValues(*value_sets, constants=tuple(), types=tuple(), row_types=tuple()): +def makeParamsValues( + *value_sets, constants=tuple(), types=tuple(), row_types=tuple() +): # TODO variable sized records and # common value names - if constants and not all(':' in c for c in constants): - raise ValueError(f'All constants must pass variables in via params {constants}') + if constants and not all(":" in c for c in constants): + raise ValueError( + f"All constants must pass variables in via params {constants}" + ) getname = getName() @@ -90,14 +105,27 @@ def makeParamsValues(*value_sets, constants=tuple(), types=tuple(), row_types=tu # proto_params doesn't need to be a dict # values will be reduced when we create params as a dict if row_types: - proto_params = [(tuple(getname(value, type=t) for value, t in zip(row, row_types)), row) for row in values] + proto_params = [ + ( + tuple( + getname(value, type=t) + for value, t in zip(row, row_types) + ), + row, + ) + for row in values + ] else: - proto_params = [(tuple(getname(value) for value in row), row) for row in values] - - values_template = ', '.join('(' + ', '.join(constants + - tuple(':' + name - for name in names)) + ')' - for names, _ in proto_params) + proto_params = [ + (tuple(getname(value) for value in row), row) for row in values + ] + + values_template = ", ".join( + "(" + + ", ".join(constants + tuple(":" + name for name in names)) + + ")" + for names, _ in proto_params + ) yield values_template if row_types: _done = set() @@ -115,7 +143,6 @@ def makeParamsValues(*value_sets, constants=tuple(), types=tuple(), row_types=tu if maybe_type is not None: bindparams.append(bindparam(name, type_=maybe_type)) - yield params if types or row_types: yield bindparams # TODO not sure if there are dupes here @@ -133,24 +160,24 @@ def makeParamsValues(*value_sets, constants=tuple(), types=tuple(), row_types=tu a abdominal """ sam_ordering = { - 'l': 0, # left - 'r': 0, # right - 'c': 0, # cardiac safe to keep at zero since the c index usually come after t - 'a': 1, # anterior abdominal - 'p': 1, # posterior abdominal + "l": 0, # left + "r": 0, # right + "c": 0, # cardiac safe to keep at zero since the c index usually come after t + "a": 1, # anterior abdominal + "p": 1, # posterior abdominal } seg_ordering = { - 'c': 0, # cervical - 't': 1, # thoracic - 'a': 2, # abdominal + "c": 0, # cervical + "t": 1, # thoracic + "a": 2, # abdominal } def anat_index(sample): # count the number of distinct values less than a given integer - # create the map + # create the map - sam, sam_id, seg, seg_id = sample.split('-') + sam, sam_id, seg, seg_id = sample.split("-") # FIXME bad becase left and right are unstable and we don't care about this, we just want relative to max possible # don't do this with sort sam_ind = sam_ordering[sam_id] @@ -160,22 +187,24 @@ def anat_index(sample): seg_ind = v break else: - if sam_id == 'c': - #print('c sample', sample) - #rest = int(''.join(_ for _ in seg_id if _.isdigit())) + if sam_id == "c": + # print('c sample', sample) + # rest = int(''.join(_ for _ in seg_id if _.isdigit())) rest = int(seg_id[:-1]) suffix = int(seg_id[-1].encode().hex()) return sam_ind, 0, rest, suffix else: - msg = f'unknown seg {sample}' + msg = f"unknown seg {sample}" print(msg) # FIXME TODO logging - #raise ValueError(msg) - #return int(f'{sam_ind}000') + # raise ValueError(msg) + # return int(f'{sam_ind}000') return sam_ind, 0, 0, 0 - rest = int(seg_id[len(prefix):]) # FIXME this convention is not always followed + rest = int( + seg_id[len(prefix) :] + ) # FIXME this convention is not always followed comps = sam_ind, seg_ind, rest, 0 - #return int(f'{sam_ind}{seg_ind}{rest:0>2d}') + # return int(f'{sam_ind}{seg_ind}{rest:0>2d}') return comps @@ -183,15 +212,18 @@ def pps(path_structure): if len(path_structure) == 6: # FIXME utter hack top, subject, sam_1, segment, modality, file = path_structure - p1 = sam_1, subject # child, parent to match db convention wasDerivedFrom + p1 = ( + sam_1, + subject, + ) # child, parent to match db convention wasDerivedFrom p2 = segment, sam_1 return { - 'parents': (p1, p2), - 'subject': subject, - 'sample': segment, - 'modality': modality, + "parents": (p1, p2), + "subject": subject, + "sample": segment, + "modality": modality, # note that because we do not convert to a single value we cannot include raw_anat_index in the qdb but that's ok - 'raw_anat_index_v1': anat_index(segment), + "raw_anat_index_v1": anat_index(segment), } else: raise NotImplementedError(path_structure) @@ -199,147 +231,255 @@ def pps(path_structure): def ext(j): out = {} - out['dataset'] = j['dataset_id'] - out['object'] = j['remote_id'] - out['file_id'] = j['file_id'] if 'file_id' in j else int(j['uri_api'].rsplit('/')[-1]) # XXX old pathmeta schema that didn't include file id - ps = pathlib.Path(j['dataset_relative_path']).parts - [p for p in ps if p.startswith('sub-') or p.startswith('sam-')] + out["dataset"] = j["dataset_id"] + out["object"] = j["remote_id"] + out["file_id"] = ( + j["file_id"] if "file_id" in j else int(j["uri_api"].rsplit("/")[-1]) + ) # XXX old pathmeta schema that didn't include file id + ps = pathlib.Path(j["dataset_relative_path"]).parts + [p for p in ps if p.startswith("sub-") or p.startswith("sam-")] out.update(pps(ps)) return out class Queries: - def __init__(self, session): self.session = session def address_from_fadd_type_fadd(self, fadd_type, fadd): # FIXME multi etc. - res = [i for i, in self.session.execute(sql_text("select * from address_from_fadd_type_fadd(:fadd_type, :fadd)"), dict(fadd_type=fadd_type, fadd=fadd))] + res = [ + i + for i, in self.session.execute( + sql_text( + "select * from address_from_fadd_type_fadd(:fadd_type, :fadd)" + ), + dict(fadd_type=fadd_type, fadd=fadd), + ) + ] if res: return res[0] - def desc_inst_from_label(self, label): # FIXME multi etc. - res = [i for i, in self.session.execute(sql_text("select * from desc_inst_from_label(:label)"), dict(label=label))] + res = [ + i + for i, in self.session.execute( + sql_text("select * from desc_inst_from_label(:label)"), + dict(label=label), + ) + ] if res: return res[0] - def desc_quant_from_label(self, label): # FIXME multi etc. - res = [i for i, in self.session.execute(sql_text("select * from desc_quant_from_label(:label)"), dict(label=label))] + res = [ + i + for i, in self.session.execute( + sql_text("select * from desc_quant_from_label(:label)"), + dict(label=label), + ) + ] if res: return res[0] - def desc_cat_from_label_domain_label(self, label, domain_label): # FIXME multi etc. - res = [i for i, in self.session.execute(sql_text("select * from desc_cat_from_label_domain_label(:label, :domain_label)"), - dict(label=label, domain_label=domain_label))] + res = [ + i + for i, in self.session.execute( + sql_text( + "select * from desc_cat_from_label_domain_label(:label, :domain_label)" + ), + dict(label=label, domain_label=domain_label), + ) + ] if res: return res[0] - def cterm_from_label(self, label): # FIXME multi etc. - res = [i for i, in self.session.execute(sql_text("select * from cterm_from_label(:label)"), dict(label=label))] + res = [ + i + for i, in self.session.execute( + sql_text("select * from cterm_from_label(:label)"), + dict(label=label), + ) + ] if res: return res[0] - def insts_from_dataset_ids(self, dataset, ids): - return list(self.session.execute(sql_text("select * from insts_from_dataset_ids(:dataset, :ids)"), dict(dataset=dataset, ids=ids))) + return list( + self.session.execute( + sql_text( + "select * from insts_from_dataset_ids(:dataset, :ids)" + ), + dict(dataset=dataset, ids=ids), + ) + ) class InternalIds: - def __init__(self, queries): - q = queries - self._q = queries - - self.addr_suid = q.address_from_fadd_type_fadd('tabular-header', 'id_sub') - self.addr_said = q.address_from_fadd_type_fadd('tabular-header', 'id_sam') - self.addr_spec = q.address_from_fadd_type_fadd('tabular-header', 'species') - self.addr_saty = q.address_from_fadd_type_fadd('tabular-header', 'sample_type') + def set_desc_quant_from_label(self, label: str, desctriptor: str): + self.__setattr__(label, desctriptor) - self.addr_tmod = q.address_from_fadd_type_fadd('tabular-header', 'modality') - #addr_trai = address_from_fadd_type_fadd('tabular-header', 'raw_anat_index') - #addr_tnai = address_from_fadd_type_fadd('tabular-header', 'norm_anat_index') - #addr_context = address_from_fadd_type_fadd('context', '#/path-metadata/{index of match remote_id}/dataset_relative_path') # XXX this doesn't do what we want, I think what we really would want in these contexts are objects_internal that reference the file system state for a given updated snapshot, that is the real "object" that corresponds to the path-metadata.json that we are working from + def __init__(self, queries) -> None: - #addr_jpmod = address_from_fadd_type_fadd('json-path-with-types', '#/#int/modality') - #addr_jprai = address_from_fadd_type_fadd('json-path-with-types', '#/#int/anat_index') - #addr_jpnai = address_from_fadd_type_fadd('json-path-with-types', '#/#int/norm_anat_index') + q = queries + self._q = queries - self.addr_jpdrp = q.address_from_fadd_type_fadd('json-path-with-types', '#/path-metadata/data/#int/dataset_relative_path') + self.addr_suid = q.address_from_fadd_type_fadd( + "tabular-header", "id_sub" + ) + self.addr_said = q.address_from_fadd_type_fadd( + "tabular-header", "id_sam" + ) + self.addr_spec = q.address_from_fadd_type_fadd( + "tabular-header", "species" + ) + self.addr_saty = q.address_from_fadd_type_fadd( + "tabular-header", "sample_type" + ) + self.addr_faid = q.address_from_fadd_type_fadd( + "tabular-header", "fascicle" + ) # for REVA ft + + self.addr_tmod = q.address_from_fadd_type_fadd( + "tabular-header", "modality" + ) + # addr_trai = address_from_fadd_type_fadd('tabular-header', 'raw_anat_index') + # addr_tnai = address_from_fadd_type_fadd('tabular-header', 'norm_anat_index') + # addr_context = address_from_fadd_type_fadd('context', '#/path-metadata/{index of match remote_id}/dataset_relative_path') # XXX this doesn't do what we want, I think what we really would want in these contexts are objects_internal that reference the file system state for a given updated snapshot, that is the real "object" that corresponds to the path-metadata.json that we are working from + + # addr_jpmod = address_from_fadd_type_fadd('json-path-with-types', '#/#int/modality') + # addr_jprai = address_from_fadd_type_fadd('json-path-with-types', '#/#int/anat_index') + # addr_jpnai = address_from_fadd_type_fadd('json-path-with-types', '#/#int/norm_anat_index') + + self.addr_jpdrp = q.address_from_fadd_type_fadd( + "json-path-with-types", + "#/path-metadata/data/#int/dataset_relative_path", + ) # XXX these are more accurate if opaque - self.addr_jpmod = q.address_from_fadd_type_fadd('json-path-with-types', '#/path-metadata/data/#int/dataset_relative_path#derive-modality') - #addr_jprai = address_from_fadd_type_fadd('json-path-with-types', '#/path-metadata/data/#int/dataset_relative_path#derive-raw-anat-index') - self.addr_jpnai = q.address_from_fadd_type_fadd('json-path-with-types', '#/path-metadata/data/#int/dataset_relative_path#derive-norm-anat-index-v1') - self.addr_jpnain = q.address_from_fadd_type_fadd('json-path-with-types', '#/path-metadata/data/#int/dataset_relative_path#derive-norm-anat-index-v1-min') - self.addr_jpnaix = q.address_from_fadd_type_fadd('json-path-with-types', '#/path-metadata/data/#int/dataset_relative_path#derive-norm-anat-index-v1-max') - self.addr_jpsuid = q.address_from_fadd_type_fadd('json-path-with-types', '#/path-metadata/data/#int/dataset_relative_path#derive-subject-id') - self.addr_jpsaid = q.address_from_fadd_type_fadd('json-path-with-types', '#/path-metadata/data/#int/dataset_relative_path#derive-sample-id') - - self.addr_jpspec = q.address_from_fadd_type_fadd('json-path-with-types', '#/local/tom-made-it-up/species') - self.addr_jpsaty = q.address_from_fadd_type_fadd('json-path-with-types', '#/local/tom-made-it-up/sample_type') + self.addr_jpmod = q.address_from_fadd_type_fadd( + "json-path-with-types", + "#/path-metadata/data/#int/dataset_relative_path#derive-modality", + ) + # addr_jprai = address_from_fadd_type_fadd('json-path-with-types', '#/path-metadata/data/#int/dataset_relative_path#derive-raw-anat-index') + self.addr_jpnai = q.address_from_fadd_type_fadd( + "json-path-with-types", + "#/path-metadata/data/#int/dataset_relative_path#derive-norm-anat-index-v1", + ) + self.addr_jpnain = q.address_from_fadd_type_fadd( + "json-path-with-types", + "#/path-metadata/data/#int/dataset_relative_path#derive-norm-anat-index-v1-min", + ) + self.addr_jpnaix = q.address_from_fadd_type_fadd( + "json-path-with-types", + "#/path-metadata/data/#int/dataset_relative_path#derive-norm-anat-index-v1-max", + ) + self.addr_jpsuid = q.address_from_fadd_type_fadd( + "json-path-with-types", + "#/path-metadata/data/#int/dataset_relative_path#derive-subject-id", + ) + self.addr_jpsaid = q.address_from_fadd_type_fadd( + "json-path-with-types", + "#/path-metadata/data/#int/dataset_relative_path#derive-sample-id", + ) + + self.addr_jpspec = q.address_from_fadd_type_fadd( + "json-path-with-types", "#/local/tom-made-it-up/species" + ) + self.addr_jpsaty = q.address_from_fadd_type_fadd( + "json-path-with-types", "#/local/tom-made-it-up/sample_type" + ) # future version when we actually have the metadata files - #addr_jpmod = address_from_fadd_type_fadd('json-path-with-types', '#/curation-export/manifest/#int/modality') - #addr_jprai = address_from_fadd_type_fadd('json-path-with-types', '#/curation-export/samples/#int/raw_anat_index') - #addr_jpnai = address_from_fadd_type_fadd('json-path-with-types', '#/curation-export/samples/#int/norm_anat_index') - #addr_jpsuid = address_from_fadd_type_fadd('json-path-with-types', '#/curation-export/subjects/#int/id_sub') - #addr_jpsaid = address_from_fadd_type_fadd('json-path-with-types', '#/curation-export/samples/#int/id_sam') - - self.addr_const_null = q.address_from_fadd_type_fadd('constant', None) - - #qd_rai = desc_quant_from_label('reva ft sample anatomical location distance index raw') - self.qd_nai = q.desc_quant_from_label('reva ft sample anatomical location distance index normalized v1') - self.qd_nain = q.desc_quant_from_label('reva ft sample anatomical location distance index normalized v1 min') - self.qd_naix = q.desc_quant_from_label('reva ft sample anatomical location distance index normalized v1 max') - - self.cd_mod = q.desc_cat_from_label_domain_label('hasDataAboutItModality', None) - self.cd_bot = q.desc_cat_from_label_domain_label('bottom', None) # we just need something we can reference that points to null so we can have a refernce to all the objects - - self.id_human = q.desc_inst_from_label('human') - self.id_nerve = q.desc_inst_from_label('nerve') - self.id_nerve_volume = q.desc_inst_from_label('nerve-volume') + # addr_jpmod = address_from_fadd_type_fadd('json-path-with-types', '#/curation-export/manifest/#int/modality') + # addr_jprai = address_from_fadd_type_fadd('json-path-with-types', '#/curation-export/samples/#int/raw_anat_index') + # addr_jpnai = address_from_fadd_type_fadd('json-path-with-types', '#/curation-export/samples/#int/norm_anat_index') + # addr_jpsuid = address_from_fadd_type_fadd('json-path-with-types', '#/curation-export/subjects/#int/id_sub') + # addr_jpsaid = address_from_fadd_type_fadd('json-path-with-types', '#/curation-export/samples/#int/id_sam') + + self.addr_const_null = q.address_from_fadd_type_fadd("constant", None) + + # qd_rai = desc_quant_from_label('reva ft sample anatomical location distance index raw') + self.qd_nai = q.desc_quant_from_label( + "reva ft sample anatomical location distance index normalized v1" + ) + self.qd_nain = q.desc_quant_from_label( + "reva ft sample anatomical location distance index normalized v1 min" + ) + self.qd_naix = q.desc_quant_from_label( + "reva ft sample anatomical location distance index normalized v1 max" + ) + + self.cd_mod = q.desc_cat_from_label_domain_label( + "hasDataAboutItModality", None + ) + self.cd_bot = q.desc_cat_from_label_domain_label( + "bottom", None + ) # we just need something we can reference that points to null so we can have a refernce to all the objects + + self.id_human = q.desc_inst_from_label("human") + self.id_nerve = q.desc_inst_from_label("nerve") + self.id_nerve_volume = q.desc_inst_from_label("nerve-volume") self.luid = { - 'human': self.id_human, - 'nerve': self.id_nerve, - 'nerve-volume': self.id_nerve_volume, + "human": self.id_human, + "nerve": self.id_nerve, + "nerve-volume": self.id_nerve_volume, } - self.ct_mod = q.cterm_from_label('microct') # lol ct ct - self.ct_hack = q.cterm_from_label('hack-associate-some-value') + self.ct_mod = q.cterm_from_label("microct") # lol ct ct + self.ct_hack = q.cterm_from_label("hack-associate-some-value") self.luct = { - 'ct-hack': self.ct_hack, - 'microct': self.ct_mod, + "ct-hack": self.ct_hack, + "microct": self.ct_mod, } + # Fascicles + # F + class Inserts: # TODO pass -def ingest(dataset_uuid, extract_fun, session, commit=False, dev=False, values_args=None): - """ generic ingest workflow - this_dataset_updated_uuid might not be needed in future, - add a kwarg to control it maybe? +def ingest( + dataset_uuid, + extract_fun, + session, + commit=False, + dev=False, + values_args: list | None = None, +): + """generic ingest workflow + this_dataset_updated_uuid might not be needed in future, + add a kwarg to control it maybe? """ - ocdn = ' ON CONFLICT DO NOTHING' if dev else '' + ocdn = " ON CONFLICT DO NOTHING" if dev else "" if extract_fun is None and values_args is None: - raise TypeError('need one of extract_fun or values_args') - - (updated_transitive, values_objects, values_dataset_object, - make_values_instances, make_values_parents, - make_void, make_vocd, make_voqd, make_values_cat, make_values_quant - ) = extract_fun(dataset_uuid) if values_args is None else values_args + raise TypeError("need one of extract_fun or values_args") + + ( + updated_transitive, + values_objects, + values_dataset_object, + make_values_instances, + make_values_parents, + make_void, + make_vocd, + make_voqd, + make_values_cat, + make_values_quant, + ) = ( + extract_fun(dataset_uuid) if values_args is None else values_args + ) q = Queries(session) i = InternalIds(q) @@ -348,13 +488,23 @@ def ingest(dataset_uuid, extract_fun, session, commit=False, dev=False, values_a values_instances = make_values_instances(i) res0 = session.execute( - sql_text('INSERT INTO objects (id, id_type) VALUES (:id, :id_type) ON CONFLICT DO NOTHING'), - dict(id=dataset_uuid, id_type='dataset')) + sql_text( + "INSERT INTO objects (id, id_type) VALUES (:id, :id_type) ON CONFLICT DO NOTHING" + ), + dict(id=dataset_uuid, id_type="dataset"), + ) # oh dear https://stackoverflow.com/questions/34708509/how-to-use-returning-with-on-conflict-in-postgresql res1 = session.execute( - sql_text("WITH ins AS (INSERT INTO objects_internal (type, dataset, updated_transitive, label) VALUES ('path-metadata', :dataset, :updated_transitive, :label) ON CONFLICT DO NOTHING RETURNING id) SELECT id FROM ins UNION ALL SELECT id FROM objects_internal WHERE type = 'path-metadata' AND dataset = :dataset AND updated_transitive = :updated_transitive"), # TODO see whether we actually need union all here or whether union by itself is sufficient - dict(dataset=dataset_uuid, updated_transitive=updated_transitive, label=f'test-load-for-f001 {isoformat(updated_transitive)}')) + sql_text( + "WITH ins AS (INSERT INTO objects_internal (type, dataset, updated_transitive, label) VALUES ('path-metadata', :dataset, :updated_transitive, :label) ON CONFLICT DO NOTHING RETURNING id) SELECT id FROM ins UNION ALL SELECT id FROM objects_internal WHERE type = 'path-metadata' AND dataset = :dataset AND updated_transitive = :updated_transitive" + ), # TODO see whether we actually need union all here or whether union by itself is sufficient + dict( + dataset=dataset_uuid, + updated_transitive=updated_transitive, + label=f"test-load-for-f001 {isoformat(updated_transitive)}", + ), + ) # it is better to use this approach for all top down information # just assume that it is coming from some combination of the metadata files and the file system @@ -365,47 +515,93 @@ def ingest(dataset_uuid, extract_fun, session, commit=False, dev=False, values_a voqd = make_voqd(this_dataset_updated_uuid, i) res1_1 = session.execute( - sql_text('INSERT INTO objects (id, id_type, id_internal) VALUES (:id, :id_type, :id) ON CONFLICT DO NOTHING'), # FIXME bad ocdn here - dict(id=this_dataset_updated_uuid, id_type='quantdb')) + sql_text( + "INSERT INTO objects (id, id_type, id_internal) VALUES (:id, :id_type, :id) ON CONFLICT DO NOTHING" + ), # FIXME bad ocdn here + dict(id=this_dataset_updated_uuid, id_type="quantdb"), + ) vt, params = makeParamsValues(values_objects) - session.execute(sql_text(f'INSERT INTO objects (id, id_type, id_file) VALUES {vt}{ocdn}'), params) + session.execute( + sql_text( + f"INSERT INTO objects (id, id_type, id_file) VALUES {vt}{ocdn}" + ), + params, + ) vt, params = makeParamsValues(values_dataset_object) - session.execute(sql_text(f'INSERT INTO dataset_object (dataset, object) VALUES {vt}{ocdn}'), params) + session.execute( + sql_text( + f"INSERT INTO dataset_object (dataset, object) VALUES {vt}{ocdn}" + ), + params, + ) vt, params = makeParamsValues(values_instances) - session.execute(sql_text(f'INSERT INTO values_inst (dataset, id_formal, type, desc_inst, id_sub, id_sam) VALUES {vt}{ocdn}'), params) + session.execute( + sql_text( + f"INSERT INTO values_inst (dataset, id_formal, type, desc_inst, id_sub, id_sam) VALUES {vt}{ocdn}" + ), + params, + ) # inserts that depend on instances having already been inserted - ilt = q.insts_from_dataset_ids(dataset_uuid, [f for d, f, *rest in values_instances]) + ilt = q.insts_from_dataset_ids( + dataset_uuid, [f for d, f, *rest in values_instances] + ) luinst = {(str(dataset), id_formal): id for id, dataset, id_formal in ilt} values_parents = make_values_parents(luinst) values_cv = make_values_cat(this_dataset_updated_uuid, i, luinst) values_qv = make_values_quant(this_dataset_updated_uuid, i, luinst) vt, params = makeParamsValues(values_parents) - session.execute(sql_text(f'INSERT INTO instance_parent VALUES {vt}{ocdn}'), params) + session.execute( + sql_text(f"INSERT INTO instance_parent VALUES {vt}{ocdn}"), params + ) vt, params = makeParamsValues(void) - session.execute(sql_text(f'INSERT INTO obj_desc_inst (object, desc_inst, addr_field, addr_desc_inst) VALUES {vt}{ocdn}'), params) + session.execute( + sql_text( + f"INSERT INTO obj_desc_inst (object, desc_inst, addr_field, addr_desc_inst) VALUES {vt}{ocdn}" + ), + params, + ) vt, params = makeParamsValues(vocd) - session.execute(sql_text(f'INSERT INTO obj_desc_cat (object, desc_cat, addr_field) VALUES {vt}{ocdn}'), params) + session.execute( + sql_text( + f"INSERT INTO obj_desc_cat (object, desc_cat, addr_field) VALUES {vt}{ocdn}" + ), + params, + ) vt, params = makeParamsValues(voqd) - session.execute(sql_text(f'INSERT INTO obj_desc_quant (object, desc_quant, addr_field) VALUES {vt}{ocdn}'), params) + session.execute( + sql_text( + f"INSERT INTO obj_desc_quant (object, desc_quant, addr_field) VALUES {vt}{ocdn}" + ), + params, + ) vt, params = makeParamsValues(values_cv) - session.execute(sql_text(f'INSERT INTO values_cat (value_open, value_controlled, object, desc_inst, desc_cat, instance) VALUES {vt}{ocdn}'), params) + session.execute( + sql_text( + f"INSERT INTO values_cat (value_open, value_controlled, object, desc_inst, desc_cat, instance) VALUES {vt}{ocdn}" + ), + params, + ) vt, params, bindparams = makeParamsValues( # FIXME LOL the types spec here is atrocious ... but it does work ... # XXX and barring the unfortunate case, which we have now encountered where # now fixed in the local impl - values_qv, row_types=(None, None, None, None, None, JSONB)) + values_qv, + row_types=(None, None, None, None, None, JSONB), + ) - t = sql_text(f'INSERT INTO values_quant (value, object, desc_inst, desc_quant, instance, value_blob) VALUES {vt}{ocdn}') + t = sql_text( + f"INSERT INTO values_quant (value, object, desc_inst, desc_quant, instance, value_blob) VALUES {vt}{ocdn}" + ) tin = t.bindparams(*bindparams) session.execute(tin, params) @@ -413,13 +609,218 @@ def ingest(dataset_uuid, extract_fun, session, commit=False, dev=False, values_a session.commit() +def sample_id_from_package_uuid(package_uuid): + raise NotImplementedError("TODO") + return sample_id + + +def sub_id_from_sam_id(sample_id): + raise NotImplementedError("TODO") + return subject_id + + +def rows_from_package_uuid(package_uuid): + raise NotImplementedError("TODO") + return rows + + +def map_addresses(table_header, package_addresses): + raise NotImplementedError("TODO") + return defined_columns + + +def extract_reva_ft_tabular( + dataset_uuid: str, package_uuid: str, package_addresses: str, sample_id=None +): + # TODO: Troy + # worst case derivtive files might need a manual assertion linking to sample + sample_id = sample_id_from_package_uuid( + package_uuid + ) # look a the file hierarchy and find the sample + subject_id = sub_id_from_sam_id(sample_id) + rows = rows_from_package_uuid(package_uuid) + instances = [] + values = [] + defined_columns = map_addresses(rows[0], package_addresses) + for row in rows[1:]: + subthing_id = row[1] # change to "fascicle" + # might need another factor when coming from microct virtual sections if it is not in the spreadsheet + formal_id = sample_id + subthing_id + instances.append( + { + "dataset": dataset_uuid, + "id_formal": formal_id, + "type": "below", + "desc_inst": "fascicle-cross-section", + "id_sub": subject_id, + "id_sam": sample_id, + } + ) + # for column_name, column_index in defined_columns: + + # TODO return the make functions that match those produced by extract_fun in ingest + # return ( + # updated_transitive, + # values_objects, + # values_dataset_object, + # make_values_instances, + # make_values_parents, + # make_void, + # make_vocd, + # make_voqd, + # make_values_cat, + # make_values_quant, + # ) + + +def make_descriptors_etc_reva_ft_tabular(): + # the things we need to insert as part of the specification of the schema for the files we are ingesting + + # aspect + need_aspects = [ + "area", + "diameter", + ] + + # unit + units = [ + "um", + "pixel", + ] + + # quantitative descriptors + need_qd = [ + "fascicle cross section diameter um", + "fascicle cross section diameter um min", + "fascicle cross section diameter um max", + # TODO: add more here + ] + + q = Queries(session) + i = InternalIds(q) + + # TODO properly query to find existing or add new quantitative descriptors + # query descriptors? + + # OR put them in inserts.sql + # insert descripters? + + # addresses + column_name_qd_mapping = [ + # ('fascicle'), # covered in the values_inst + ("area", i.area), + ( + "longest_diameter", + i.longest_diameter, + ), # TODO: fascicle cross section diameter unit max + ( + "shortest_diameter", + i.shortest_diameter, + ), # fascicle cross section diameter unit min + ("eff_diam", i.fcsdu), # TODO: effective diameter + ( + "c_estimate_nav", + i.c_estimate_nav, + ), # TODO: c estimate nerve area volume + ("c_estimate_nf", i.c_estimate_nf), # TODO: c estimate nerve fascicle + ( + "nfibers_w_c_estimate_nav", + i.nfibers_w_c_estimate_nav, + ), # TODO: number of fibers with c estimate nerve area volume + ( + "nfibers_w_c_estimate_nf", + i.nfibers_w_c_estimate_nf, + ), # TODO: number of fibers with c estimate nerve fascicle + ("nfibers_all", i.nfibers_all), # number of fibers all + ("n_a_alpha", i.n_a_alpha), # TODO: TODO: number of fibers alpha + ("n_a_beta", i.n_a_beta), # TODO: BUG: number of fibers beta + ("n_a_gamma", i.n_a_gamma), # TODO: BUG: number of fibers gamma + ("n_a_delta", i.n_a_delta), # TODO: BUG: number of fibers delta + ("n_b", i.n_b), # TODO: number of fibers b + ( + "n_unmyel_nf", + i.n_unmyel_nf, + ), # TODO: number of unmyelinated neral filimant + ("n_nav", i.n_nav), # TODO: number of nerve axon volume + ("n_chat", i.n_chat), # TODO: number cholen acetal transferase + ( + "n_myelinated", + i.n_myelinated, + ), # TODO: number of myelinated nerve fibers + ("area_a_alpha", i.area_a_alpha), # TODO: area of fibers alpha + ("area_a_beta", i.area_a_beta), # TODO: area of fibers beta + ("area_a_gamma", i.area_a_gamma), # TODO: area of fibers gamma + ("area_a_delta", i.area_a_delta), # TODO: area of fibers delta + ("area_b", i.area_b), # TODO: area of fibers b + ( + "area_unmyel_nf", + i.area_unmyel_nf, + ), # TODO: area of unmyelinated nerve fibers + ("area_nav", i.area_nav), # TODO: area of nerve axon volume + ("area_chat", i.area_chat), # TODO: TODO: area of chat + ( + "area_myelinated", + i.area_myelinated, + ), # TODO: area of myelinated nerve fibers + ("chat_available", i.chat_available), # TODO: chat available + ("nav_available", i.nav_available), # TODO: nerve axon volume available + ("x_pix", i.x_pix), # TODO: x pixel; microns + ("y_pix", i.y_pix), # TODO: y pixel + ("x_um", i.x_um), # TODO: x um + ("y_um", i.y_um), # TODO: y um + ("x_cent", i.x_cent), # TODO: x center + ("y_cent", i.y_cent), # TODO: y center + ("rho", i.rho), # TODO: rho; microns + ("rho_pix", i.rho_pix), # TODO: rho pixel + ("phi", i.phi), # TODO: phi + ("epi_dist", i.epi_dist), # TODO: epineurium distance + ("epi_dist_inv", i.epi_dist_inv), # TODO: epineurium distance inverse + ("nerve_based_area", i.nerve_based_area), # TODO: nerve based area + ( + "nerve_based_perimeter", + i.nerve_based_perimeter, + ), # TODO: nerve based perimeter + ( + "nerve_based_eff_diam", + i.nerve_based_eff_diam, + ), # TODO: nerve based effective diameter + ( + "perinerium_vertices", + i.perinerium_vertices, + ), # TODO: perinerium vertices + ( + "perinerium_vertices_px", + i.perinerium_vertices_px, + ), # TODO: perinerium vertices pixel + ( + "nerve_based_shortest_diameter", + i.nerve_based_shortest_diameter, + ), # TODO: nerve based shortest diameter + ("hull_contrs", i.hull_contrs), # TODO: hull contours + ("hull_contr_areas", i.hull_contr_areas), # TODO: hull contour areas + ] + addresses = [ + ("tabular-header", name) + for name, qd in column_name_qd_mapping + if qd is not None + ] + # TODO do the inserts + + def extract_reva_ft(dataset_uuid, source_local=False, visualize=False): if source_local: - with open(pathlib.Path(f'~/.local/share/sparcur/export/datasets/{dataset_uuid}/LATEST/path-metadata.json').expanduser(), 'rt') as f: + with open( + pathlib.Path( + f"~/.local/share/sparcur/export/datasets/{dataset_uuid}/LATEST/path-metadata.json" + ).expanduser(), + "rt", + ) as f: blob = json.load(f) else: - resp = requests.get(f'https://cassava.ucsd.edu/sparc/datasets/{dataset_uuid}/LATEST/path-metadata.json') + resp = requests.get( + f"https://cassava.ucsd.edu/sparc/datasets/{dataset_uuid}/LATEST/path-metadata.json" + ) try: blob = resp.json() @@ -427,117 +828,160 @@ def extract_reva_ft(dataset_uuid, source_local=False, visualize=False): breakpoint() raise e - for j in blob['data']: - j['type'] = 'pathmeta' + for j in blob["data"]: + j["type"] = "pathmeta" ir = fromJson(blob) - updated_transitive = max([i['timestamp_updated'] for i in ir['data'][1:]]) # 1: to skip the dataset object itself - - jpx = [r for r in ir['data'] if 'mimetype' in r and r['mimetype'] == 'image/jpx'] - + updated_transitive = max( + [i["timestamp_updated"] for i in ir["data"][1:]] + ) # 1: to skip the dataset object itself + jpx = [ + r + for r in ir["data"] + if "mimetype" in r and r["mimetype"] == "image/jpx" + ] exts = [ext(j) for j in jpx] - #hrm = sorted(exts, key=lambda j: j['raw_anat_index']) - #max_rai = max([e['raw_anat_index'] for e in exts]) - #import math - #log_max_rai = math.log10(max_rai) + # hrm = sorted(exts, key=lambda j: j['raw_anat_index']) + # max_rai = max([e['raw_anat_index'] for e in exts]) + # import math + # log_max_rai = math.log10(max_rai) # normalize the index by mapping distinct values to the integers - nondist = sorted([e['raw_anat_index_v1'] for e in exts]) - lin_distinct = {v:i for i, v in enumerate(sorted(set([e['raw_anat_index_v1'] for e in exts])))} + nondist = sorted([e["raw_anat_index_v1"] for e in exts]) + lin_distinct = { + v: i + for i, v in enumerate( + sorted(set([e["raw_anat_index_v1"] for e in exts])) + ) + } max_distinct = len(lin_distinct) mdp1 = max_distinct + 0.1 # to simplify adding overlap dd = defaultdict(list) for e in exts: - #e['norm_anat_index'] = math.log10(e['raw_anat_index']) / log_max_rai - pos = lin_distinct[e['raw_anat_index_v1']] - e['norm_anat_index_v1'] = (pos + 0.55) / mdp1 - e['norm_anat_index_v1_min'] = pos / mdp1 - e['norm_anat_index_v1_max'] = (pos + 1.1) / mdp1 # ensure there is overlap between section for purposes of testing + # e['norm_anat_index'] = math.log10(e['raw_anat_index']) / log_max_rai + pos = lin_distinct[e["raw_anat_index_v1"]] + e["norm_anat_index_v1"] = (pos + 0.55) / mdp1 + e["norm_anat_index_v1_min"] = pos / mdp1 + e["norm_anat_index_v1_max"] = ( + pos + 1.1 + ) / mdp1 # ensure there is overlap between section for purposes of testing # TODO norm_anat_index_min # TODO norm_anat_index_max - dd[e['dataset'], e['sample']].append(e) + dd[e["dataset"], e["sample"]].append(e) inst_obj_index = dict(dd) - max_nai = max([e['norm_anat_index_v1'] for e in exts]) - min_nain = min([e['norm_anat_index_v1_min'] for e in exts]) - max_naix = max([e['norm_anat_index_v1_max'] for e in exts]) + max_nai = max([e["norm_anat_index_v1"] for e in exts]) + min_nain = min([e["norm_anat_index_v1_min"] for e in exts]) + max_naix = max([e["norm_anat_index_v1_max"] for e in exts]) if visualize: x = list(range(len(exts))) - #ry = sorted([e['raw_anat_index'] for e in exts]) - ny = sorted([e['norm_anat_index_v1'] for e in exts]) - nyn = sorted([e['norm_anat_index_v1_min'] for e in exts]) - nyx = sorted([e['norm_anat_index_v1_max'] for e in exts]) + # ry = sorted([e['raw_anat_index'] for e in exts]) + ny = sorted([e["norm_anat_index_v1"] for e in exts]) + nyn = sorted([e["norm_anat_index_v1_min"] for e in exts]) + nyx = sorted([e["norm_anat_index_v1_max"] for e in exts]) nnx = list(zip(nyn, nyx)) import pylab as plt import seaborn - #plt.figure() - #seaborn.scatterplot(x=x, y=ry) + + # plt.figure() + # seaborn.scatterplot(x=x, y=ry) plt.figure() - #end = 10 + # end = 10 end = len(x) seaborn.scatterplot(x=x[:end], y=ny[:end]) seaborn.scatterplot(x=x[:end], y=nyn[:end]) seaborn.scatterplot(x=x[:end], y=nyx[:end]) - datasets = {i.uuid: {'id_type': i.type} - for e in exts - if (i := e['dataset']) - } + datasets = { + i.uuid: {"id_type": i.type} for e in exts if (i := e["dataset"]) + } - packages = {i.uuid: { - 'id_type': i.type, - 'id_file': e['file_id'], + packages = { + i.uuid: { + "id_type": i.type, + "id_file": e["file_id"], + } + for e in exts + if (i := e["object"]) } - for e in exts - if (i := e['object']) - } objects = {**datasets, **packages} - dataset_object = list(set((d.uuid, o.uuid) for e in exts - if (d := e['dataset']) and (o := e['object']) - )) - - subjects = {k: {'type': 'subject', - 'desc_inst': 'human', - 'id_sub': k[1], - } for k in sorted(set((e['dataset'], e['subject']) for e in exts))} - segments = {k[:2]: {'type': 'sample', # FIXME vs below ??? - 'desc_inst': 'nerve-volume', # FIXME should this be nerve-segment and then we use nerve-volume for the 1:1 with files? - 'id_sub': k[-1], - 'id_sam': k[1], - } for k in sorted(set((e['dataset'], e['sample'], e['subject']) for e in exts))} - parents = sorted(set((e['dataset'],) + p for e in exts for p in e['parents'])) - sam_other = {p[:2]:{'type': 'sample', 'desc_inst': 'nerve', 'id_sub': p[-1], 'id_sam': p[1]} for p in parents if p[:2] not in segments} + dataset_object = list( + set( + (d.uuid, o.uuid) + for e in exts + if (d := e["dataset"]) and (o := e["object"]) + ) + ) + + subjects = { + k: { + "type": "subject", + "desc_inst": "human", + "id_sub": k[1], + } + for k in sorted(set((e["dataset"], e["subject"]) for e in exts)) + } + segments = { + k[:2]: { + "type": "sample", # FIXME vs below ??? + "desc_inst": "nerve-volume", # FIXME should this be nerve-segment and then we use nerve-volume for the 1:1 with files? + "id_sub": k[-1], + "id_sam": k[1], + } + for k in sorted( + set((e["dataset"], e["sample"], e["subject"]) for e in exts) + ) + } + parents = sorted( + set((e["dataset"],) + p for e in exts for p in e["parents"]) + ) + sam_other = { + p[:2]: { + "type": "sample", + "desc_inst": "nerve", + "id_sub": p[-1], + "id_sam": p[1], + } + for p in parents + if p[:2] not in segments + } samples = {**segments, **sam_other} instances = {**subjects, **samples} values_objects = [ - (i, o['id_type'], o['id_file'] if 'id_file' in o else None) + (i, o["id_type"], o["id_file"] if "id_file" in o else None) for i, o in objects.items() - if o['id_type'] != 'dataset' # already did it above + if o["id_type"] != "dataset" # already did it above ] values_dataset_object = dataset_object def make_values_instances(i): values_instances = [ - (d.uuid, f, inst['type'], i.luid[inst['desc_inst']], - inst['id_sub'] if 'id_sub' in inst else None, - inst['id_sam'] if 'id_sam' in inst else None, + ( + d.uuid, + f, + inst["type"], + i.luid[inst["desc_inst"]], + inst["id_sub"] if "id_sub" in inst else None, + inst["id_sam"] if "id_sam" in inst else None, ) - for (d, f), inst in instances.items()] + for (d, f), inst in instances.items() + ] return values_instances def make_values_parents(luinst): - """ need the lookup for instances """ + """need the lookup for instances""" values_parents = [ (luinst[d.uuid, child], luinst[d.uuid, parent]) - for d, child, parent in parents] + for d, child, parent in parents + ] return values_parents # XXX REMINDER an object descriptor pair can be associated with an arbitrary number of measured instances @@ -548,20 +992,40 @@ def make_values_parents(luinst): # XXX the external source is part of the issue I think def make_void(this_dataset_updated_uuid, i): void = [ # FIXME this is rather annoying because you have to list all expected types in advance, but I guess that is what we want - - (this_dataset_updated_uuid, i.id_human, i.addr_jpsuid, i.addr_jpspec), - (this_dataset_updated_uuid, i.id_nerve, i.addr_jpsaid, i.addr_jpsaty), - (this_dataset_updated_uuid, i.id_nerve_volume, i.addr_jpsaid, i.addr_jpsaty), - + ( + this_dataset_updated_uuid, + i.id_human, + i.addr_jpsuid, + i.addr_jpspec, + ), + ( + this_dataset_updated_uuid, + i.id_nerve, + i.addr_jpsaid, + i.addr_jpsaty, + ), + ( + this_dataset_updated_uuid, + i.id_nerve_volume, + i.addr_jpsaid, + i.addr_jpsaty, + ), # FIXME what about manifests? those link metadata as an extra hop ... everything meta related needs to come from combined object metadata ??? # that would certainly make more sense than the nonsense that is going on here, it would simplify the referencing for all the topdown # information that we have but it sort of obscures sources, however this _is_ contextual info ... sigh # XXX the other option would just be to just put the darned files in the instance measured table :/ because we do have data about them # annoying :/ - - #+ [(i, 'nerve-volume', addr_context) for i in packages] - ] + [(o, i.id_nerve_volume, i.addr_const_null, None) # XXX FIXME this is the only way I can think to do this right now ? - for o, b in objects.items() if b['id_type'] == 'package'] + # + [(i, 'nerve-volume', addr_context) for i in packages] + ] + [ + ( + o, + i.id_nerve_volume, + i.addr_const_null, + None, + ) # XXX FIXME this is the only way I can think to do this right now ? + for o, b in objects.items() + if b["id_type"] == "package" + ] return void @@ -570,8 +1034,15 @@ def make_vocd(this_dataset_updated_uuid, i): # FIXME this reveals that there are cases where we may not have void for a single file or that the id comes from context and is not embedded # figuring out how to turn that around is going to take a bit of thinking (this_dataset_updated_uuid, i.cd_mod, i.addr_jpmod), - ] + [(o, i.cd_bot, i.addr_const_null) # XXX FIXME this is the only way I can think to do this right now ? - for o, b in objects.items() if b['id_type'] == 'package'] + ] + [ + ( + o, + i.cd_bot, + i.addr_const_null, + ) # XXX FIXME this is the only way I can think to do this right now ? + for o, b in objects.items() + if b["id_type"] == "package" + ] return vocd @@ -579,35 +1050,38 @@ def make_voqd(this_dataset_updated_uuid, i): voqd = [ # FIXME this isn't quite right, we should just do it to the segments and pretend it is from the samples file I think? # FIXME addr_aspect and addr_unit are ... implicit, there is no conditional dispatch but the choice of the constant quantative descriptor comes from ... tgbugs? or what? I think we just leave it as null because it is a constant across all fields, but maybe we just use constant null? but why bother in that case? (this_dataset_updated_uuid, i.qd_nai, i.addr_jpnai), - (this_dataset_updated_uuid, i.qd_nain, i.addr_jpnain), # XXX FIXME is this really an aggregation type in this case? I guess it technically if the sample space is over all the points inside the segment or something + ( + this_dataset_updated_uuid, + i.qd_nain, + i.addr_jpnain, + ), # XXX FIXME is this really an aggregation type in this case? I guess it technically if the sample space is over all the points inside the segment or something (this_dataset_updated_uuid, i.qd_naix, i.addr_jpnaix), ] return voqd def make_values_cat(this_dataset_updated_uuid, i, luinst): - #obj_index = {e['object']: e for e in exts} + # obj_index = {e['object']: e for e in exts} values_cv = [ # value_open, value_controlled, object, desc_inst, desc_cat - (e[k], - i.luct[e[k]], - this_dataset_updated_uuid, - #e['object'].uuid, # FIXME still not right this comes from the updated latest - i.id_nerve_volume, - cd, # if we mess this up the fk ok obj_desc_cat will catch it :) - luinst[e['dataset'].uuid, e['sample']], # get us the instance + ( + e[k], + i.luct[e[k]], + this_dataset_updated_uuid, + # e['object'].uuid, # FIXME still not right this comes from the updated latest + i.id_nerve_volume, + cd, # if we mess this up the fk ok obj_desc_cat will catch it :) + luinst[e["dataset"].uuid, e["sample"]], # get us the instance ) for e in exts - for k, cd in ( - ('modality', i.cd_mod), - ) - + for k, cd in (("modality", i.cd_mod),) ] + [ - (None, - i.ct_hack, - e['object'].uuid, - i.id_nerve_volume, - i.cd_bot, # if we mess this up the fk ok obj_desc_cat will catch it :) - luinst[e['dataset'].uuid, e['sample']], # get us the instance + ( + None, + i.ct_hack, + e["object"].uuid, + i.id_nerve_volume, + i.cd_bot, # if we mess this up the fk ok obj_desc_cat will catch it :) + luinst[e["dataset"].uuid, e["sample"]], # get us the instance ) for e in exts ] @@ -616,78 +1090,155 @@ def make_values_cat(this_dataset_updated_uuid, i, luinst): def make_values_quant(this_dataset_updated_uuid, i, luinst): values_qv = [ # value, object, desc_inst, desc_quant, inst, value_blob - (e[k], - #e['object'].uuid, # FIXME TODO we could fill this here but we choose to use this_dataset_updated_uuid instead I think - this_dataset_updated_uuid, - i.id_nerve_volume, - qd, # if we mess this up the fk ok obj_desc_cat will catch it :) - luinst[e['dataset'].uuid, e['sample']], # get us the instance - e[k], + ( + e[k], + # e['object'].uuid, # FIXME TODO we could fill this here but we choose to use this_dataset_updated_uuid instead I think + this_dataset_updated_uuid, + i.id_nerve_volume, + qd, # if we mess this up the fk ok obj_desc_cat will catch it :) + luinst[e["dataset"].uuid, e["sample"]], # get us the instance + e[k], ) for e in exts for k, qd in ( - #('raw_anat_index', qd_rai), # XXX this is a bad place to store object -> field -> qd mappings also risks mismatch on address - ('norm_anat_index_v1', i.qd_nai), - ('norm_anat_index_v1_min', i.qd_nain), - ('norm_anat_index_v1_max', i.qd_naix), + # ('raw_anat_index', qd_rai), # XXX this is a bad place to store object -> field -> qd mappings also risks mismatch on address + ("norm_anat_index_v1", i.qd_nai), + ("norm_anat_index_v1_min", i.qd_nain), + ("norm_anat_index_v1_max", i.qd_naix), ) ] return values_qv - return (updated_transitive, values_objects, values_dataset_object, - make_values_instances, make_values_parents, - make_void, make_vocd, make_voqd, - make_values_cat, make_values_quant, - ) + return ( + updated_transitive, + values_objects, + values_dataset_object, + make_values_instances, + make_values_parents, + make_void, + make_vocd, + make_voqd, + make_values_cat, + make_values_quant, + ) # this is where things get annoying with needing selects on instance measured -def ingest_reva_ft_all(session, source_local=False, do_insert=True, batch=False, commit=False, dev=False): - +def ingest_reva_ft_all( + session: Session, # type: ignore + source_local: bool = False, + do_insert: bool = True, + batch: bool = False, + commit: bool = False, + dev: bool = False, +) -> None: + """ + Ingest all REVA datasets + + Parameters + ---------- + session : Session + connection to DB using engine env + do_insert : bool, optional + insert the data, by default True + batch : bool, optional + batch the inserts, by default False + commit : bool, optional + commit the transaction, by default False + dev : bool, optional + dev mode, by default False + """ dataset_uuids = ( - 'aa43eda8-b29a-4c25-9840-ecbd57598afc', # f001 + "aa43eda8-b29a-4c25-9840-ecbd57598afc", # f001 # the rest have uuid1 issues :/ all in the undefined folder it seems, might be able to fix with a reupload - 'bc4cc558-727c-4691-ae6d-498b57a10085', # f002 # XXX has a uuid1 so breaking in prod right now have to push the new pipelines - 'ec6ad74e-7b59-409b-8fc7-a304319b6faf', # f003 # also uuid1 issue - 'a8b2bdc7-54df-46a3-810e-83cdf33cfc3a', # f004 - '04a5fed9-7ba6-4292-b1a6-9cab5c38895f', # f005 + "bc4cc558-727c-4691-ae6d-498b57a10085", # f002 # XXX has a uuid1 so breaking in prod right now have to push the new pipelines + "ec6ad74e-7b59-409b-8fc7-a304319b6faf", # f003 # also uuid1 issue + "a8b2bdc7-54df-46a3-810e-83cdf33cfc3a", # f004 + "04a5fed9-7ba6-4292-b1a6-9cab5c38895f", # f005 ) batched = [] for dataset_uuid in dataset_uuids: if do_insert and not batch: - ingest(dataset_uuid, extract_reva_ft, session, source_local=source_local, commit=commit, dev=dev) + ingest( + dataset_uuid=dataset_uuid, + extract_fun=extract_reva_ft, + session=session, # type: ignore + # source_local=source_local, + commit=commit, + dev=dev, + ) else: # FIXME make it possible to stage everything and then batch the inserts - values_args = extract_reva_ft(dataset_uuid, source_local=source_local) + values_args = extract_reva_ft( + dataset_uuid, source_local=source_local + ) if batch: batched.append((dataset_uuid, values_args)) if do_insert and batch: for duuid, vargs in batched: - ingest(duuid, None, session, commit=commit, dev=dev, values_args=vargs) + ingest( + duuid, None, session, commit=commit, dev=dev, values_args=vargs + ) def main(source_local=False, commit=False, echo=True): + """Run generic REVA ingest + + WARNING: will be changes to dynamic source other than REVA in future. + + Parameters + ---------- + source_local : bool, optional + nothing yet, by default False + commit : bool, optional + dry run if false; real ingest if true, by default False + echo : bool, optional + TODO: not clear look at alchemy docs, by default True + + Raises + ------ + e + _description_ + """ from quantdb.config import auth - dbkwargs = {k:auth.get(f'db-{k}') # TODO integrate with cli options - for k in ('user', 'host', 'port', 'database')} - dbkwargs['dbuser'] = dbkwargs.pop('user') + + # pull in the db connection info + dbkwargs = { + k: auth.get(f"db-{k}") for k in ("user", "host", "port", "database") + } # TODO integrate with cli options + # custom user variable needed + dbkwargs["dbuser"] = dbkwargs.pop("user") + # create connection env with DB engine = create_engine(dbUri(**dbkwargs)) + # bool: echo me engine.echo = echo + # use connection env as unique session session = Session(engine) + # try to ingest reva facular tubular all try: - ingest_reva_ft_all(session, source_local=source_local, do_insert=True, batch=True, commit=commit, dev=True) + ingest_reva_ft_all( + session=session, # type: ignore + # source_local=source_local=source_local, + do_insert=True, + batch=True, + commit=commit, + dev=True, + ) + # failed: undue DB request, close connection, and remove connection env. except Exception as e: session.rollback() session.close() engine.dispose() raise e + # rm alloc memory in GIL for connection session.close() + # rm alloc memory in GIL for connection env engine.dispose() -if __name__ == '__main__': +if __name__ == "__main__": main() diff --git a/quantdb/ingest_tabular/ingest_api.py b/quantdb/ingest_tabular/ingest_api.py new file mode 100644 index 0000000..589720a --- /dev/null +++ b/quantdb/ingest_tabular/ingest_api.py @@ -0,0 +1,128 @@ +import typing +from dataclasses import asdict, dataclass +from typing import Any, AnyStr, ClassVar, Dict, Protocol + +from sqlalchemy import Column, ForeignKey, Integer, String +from sqlalchemy.orm import Session, declarative_base +from sqlalchemy.sql import text + +Base = declarative_base() + + +class UUID(str): + pass + + +class Dataclass(Protocol): + __dataclass_fields__: ClassVar[Dict[str, Any]] + + +@dataclass +class Unit: + __table__ = "units" + id = Column(Integer, primary_key=True) + label = Column(String, nullable=True) + iri = Column(String) + + +@dataclass +class Objects: + __table__ = "objects" + id: UUID + id_type: str + id_file: int | None = None + id_internal: UUID | None = None + + +@dataclass +class DescriptorQuant: + __table__ = "descriptors_quant" + label: str + aggregation_type: str + unit: str | None = None + aspect: int | None = None + domain: str | None = None + description: str | None = None + curator_note: str | None = None + shape: str = "scalar" + + +@dataclass +class ValuesQuant: + __table__ = "values_quant" + value: float + object: UUID + desc_inst: int + desc_quant: int + value_blob: float + instance: int | None = None + orig_value: str | None = None + orig_units: str | None = None + + +@dataclass +class DescriptorInst: + __table__ = "descriptors_inst" + label: str + description: str | None = None + iri: str | None = None + + +class ObjDescQuant: + __table__ = "obj_desc_quant" + object: UUID + desc_inst: int + desc_quant: int + + +class Ingest: + def __init__(self, session: Session): + self.session = session + + def execute_insert(self, query: str, dataclasses: typing.Sequence[Dataclass]) -> None: + """Execute a query with dataclasses as parameters + + Parameters + ---------- + query : str + sql query string + dataclasses : typing.Sequence[Dataclass] + a list of SQL table dataclasses to be inserted + """ + statement = text(query) + params = [asdict(dataclass) for dataclass in dataclasses] + try: + result = self.session.execute(statement=statement, params=params) + self.session.commit() + return result + except Exception as e: + print(f"Error: {e}") + self.session.rollback() + + def insert_units(self, units: typing.Sequence[Unit]) -> None: + query = r"INSERT INTO units (label, iri) VALUES (:label, :iri)" + self.execute_insert(query=query, dataclasses=units) + + def insert_objects(self, objects: typing.Sequence[Objects]) -> None: + query = r"INSERT INTO objects (id, id_type) VALUES (:id, :id_type) ON CONFLICT DO NOTHING" + self.execute_insert(query=query, dataclasses=objects) + + def insert_descriptors_quant(self, descriptor_quants: typing.Sequence[DescriptorQuant]) -> None: + query = r"INSERT INTO descriptors_quant (label, domain, aspect, unit, aggregation_type) VALUES (:label, :domain, :aspect, :unit, :aggregation_type)" + self.execute_insert(query=query, dataclasses=descriptor_quants) + + def insert_values_quant( + self, + values_quant: typing.Sequence[ValuesQuant], + ): + pass + + +# ingest.insert_units( +# units=[ +# Unit( +# label="pixel", +# iri="http://uri.interlex.org/tgbugs/uris/readable/aspect/unit/pixel", +# ), +# ] +# ) diff --git a/quantdb/ingest_tabular/ingest_tabular_fascicles.py b/quantdb/ingest_tabular/ingest_tabular_fascicles.py new file mode 100644 index 0000000..e69de29 diff --git a/quantdb/ingest_tabular/ingest_tabular_fibers.py b/quantdb/ingest_tabular/ingest_tabular_fibers.py new file mode 100644 index 0000000..e69de29 diff --git a/quantdb/ingest_tabular/ingest_tabular_morphology.py b/quantdb/ingest_tabular/ingest_tabular_morphology.py new file mode 100644 index 0000000..e69de29 diff --git a/quantdb/ingest_tabular/models.py b/quantdb/ingest_tabular/models.py new file mode 100644 index 0000000..945c9a4 --- /dev/null +++ b/quantdb/ingest_tabular/models.py @@ -0,0 +1,1494 @@ +from typing import List, Optional +import uuid + +from sqlalchemy import ( + CheckConstraint, + Column, + DateTime, + Enum, + ForeignKey, + ForeignKeyConstraint, + Identity, + Index, + Integer, + Numeric, + PrimaryKeyConstraint, + String, + Table, + Text, + UniqueConstraint, + Uuid, + text, +) +from sqlalchemy.dialects.postgresql import JSONB +from sqlalchemy.orm import ( + Mapped, + declarative_base, + foreign, + mapped_column, + relationship, + validates, +) +from sqlalchemy.orm.base import Mapped +from sqlalchemy import event + +Base = declarative_base() +metadata = Base.metadata + + +class Addresses(Base): + """Addresses of data + + Parameters + ---------- + id : int + Unique identifier for the address. + addr_type : str, optional + Type of address. + value_type : str, optional + Type of value. + addr_field : str, optional + Address field. + curator_note : str, optional + Curator note. + + Example + ------- + #/path-metadata/data/#int/dataset_relative_path + """ + + __tablename__ = "addresses" + __table_args__ = ( + PrimaryKeyConstraint("id", name="addresses_pkey"), + UniqueConstraint( + "addr_type", + "addr_field", + "value_type", + name="addresses_addr_type_addr_field_value_type_key", + ), + ) + + id = mapped_column( + Integer, + Identity( + start=1, + increment=1, + minvalue=1, + maxvalue=2147483647, + cycle=False, + cache=1, + ), + ) + addr_type = mapped_column( + Enum( + "constant", + "tabular-header", + "tabular-alt-header", + "workbook-sheet-tabular-header", + "workbook-sheet-tabular-alt-header", + "json-path-with-types", + "file-system-extracted", + "arbitrary-function", + name="address_type", + ) + ) + value_type = mapped_column( + Enum("single", "multi", name="field_value_type"), + server_default=text("'single'::field_value_type"), + ) + addr_field = mapped_column(Text) + curator_note = mapped_column(Text) + + obj_desc_inst: Mapped[List["ObjDescInst"]] = relationship( + "ObjDescInst", + uselist=True, + foreign_keys="[ObjDescInst.addr_desc_inst]", + back_populates="addresses", + viewonly=True, + cascade="all, delete-orphan", + ) + obj_desc_inst_: Mapped[List["ObjDescInst"]] = relationship( + "ObjDescInst", + uselist=True, + foreign_keys="[ObjDescInst.addr_field]", + back_populates="addresses_field", + viewonly=True, + cascade="all, delete-orphan", + ) + obj_desc_cat: Mapped[List["ObjDescCat"]] = relationship( + "ObjDescCat", + uselist=True, + foreign_keys="[ObjDescCat.addr_desc_inst]", + back_populates="addresses", + viewonly=True, + cascade="all, delete-orphan", + ) + obj_desc_cat_: Mapped[List["ObjDescCat"]] = relationship( + "ObjDescCat", + uselist=True, + foreign_keys="[ObjDescCat.addr_field]", + back_populates="addresses_", + viewonly=True, + cascade="all, delete-orphan", + ) + obj_desc_quant: Mapped[List["ObjDescQuant"]] = relationship( + "ObjDescQuant", + uselist=True, + foreign_keys="[ObjDescQuant.addr_aspect]", + back_populates="addresses_aspect", + viewonly=True, + cascade="all, delete-orphan", + ) + obj_desc_quant_: Mapped[List["ObjDescQuant"]] = relationship( + "ObjDescQuant", + uselist=True, + foreign_keys="[ObjDescQuant.addr_desc_inst]", + back_populates="addresses", + viewonly=True, + cascade="all, delete-orphan", + ) + obj_desc_quant1: Mapped[List["ObjDescQuant"]] = relationship( + "ObjDescQuant", + uselist=True, + foreign_keys="[ObjDescQuant.addr_field]", + back_populates="addresses_field", + viewonly=True, + cascade="all, delete-orphan", + ) + obj_desc_quant2: Mapped[List["ObjDescQuant"]] = relationship( + "ObjDescQuant", + uselist=True, + foreign_keys="[ObjDescQuant.addr_unit]", + back_populates="addresses_unit", + viewonly=True, + cascade="all, delete-orphan", + ) + + +class Aspects(Base): + """Aspects of data + + Parameters + ---------- + id : int + Unique identifier for the aspect. + label : str + Label of the aspect. + iri : str + IRI of the aspect. + description : str, optional + Description of the aspect. + + Example + ------- + label: "distance" + iri: "http://uri.interlex.org/tgbugs/uris/readable/aspect/distance" + """ + + __tablename__ = "aspects" + __table_args__ = ( + PrimaryKeyConstraint("id", name="aspects_pkey"), + UniqueConstraint("iri", name="aspects_iri_key"), + UniqueConstraint("label", name="aspects_label_key"), + ) + + id = mapped_column( + Integer, + Identity( + start=1, + increment=1, + minvalue=1, + maxvalue=2147483647, + cycle=False, + cache=1, + ), + ) + label = mapped_column(Text, nullable=False) + iri = mapped_column(Text, nullable=False) + description = mapped_column(Text) + + # aspects: Mapped["Aspects"] = relationship( + # "Aspects", + # secondary="aspect_parent", + # primaryjoin=lambda: Aspects.id == t_aspect_parent.c.id, + # secondaryjoin=lambda: Aspects.id == t_aspect_parent.c.parent, + # back_populates="aspects_", + # ) + # aspects_: Mapped["Aspects"] = relationship( + # "Aspects", + # secondary="aspect_parent", + # primaryjoin=lambda: Aspects.id == t_aspect_parent.c.parent, + # secondaryjoin=lambda: Aspects.id == t_aspect_parent.c.id, + # back_populates="aspects", + # ) + descriptors_quant: Mapped[List["DescriptorsQuant"]] = relationship( + "DescriptorsQuant", + uselist=True, + back_populates="aspects", + viewonly=True, + cascade="all, delete-orphan", + ) + + +class ControlledTerms(Base): + """Controlled terms + + Parameters + ---------- + id : int + Unique identifier for the controlled term. + label : str + Label of the controlled term. + iri : str + IRI of the controlled term. + """ + + __tablename__ = "controlled_terms" + __table_args__ = ( + PrimaryKeyConstraint("id", name="controlled_terms_pkey"), + UniqueConstraint("iri", name="controlled_terms_iri_key"), + UniqueConstraint("label", name="controlled_terms_label_key"), + ) + + id = mapped_column( + Integer, + Identity( + start=1, + increment=1, + minvalue=1, + maxvalue=2147483647, + cycle=False, + cache=1, + ), + ) + label = mapped_column(Text, nullable=False) + iri = mapped_column(Text, nullable=False) + + values_cat: Mapped[List["ValuesCat"]] = relationship( + "ValuesCat", uselist=True, back_populates="controlled_terms" + ) + + +class DescriptorsInst(Base): + """Descriptors Instance + + Parameters + ---------- + id : int + Unique identifier for the descriptor. + label : str + Label of the descriptor. + iri : str + IRI of the descriptor. + description : str, optional + Description of the descriptor. + + """ + + __tablename__ = "descriptors_inst" + __table_args__ = ( + PrimaryKeyConstraint("id", name="descriptors_inst_pkey"), + UniqueConstraint("iri", name="descriptors_inst_iri_key"), + UniqueConstraint("label", name="descriptors_inst_label_key"), + ) + + id = mapped_column( + Integer, + Identity( + start=1, + increment=1, + minvalue=1, + maxvalue=2147483647, + cycle=False, + cache=1, + ), + ) + label = mapped_column(Text, nullable=False) + iri = mapped_column(Text, nullable=False) + description = mapped_column(Text) + + # descriptors_inst: Mapped["DescriptorsInst"] = relationship( + # "DescriptorsInst", + # secondary="class_parent", + # primaryjoin=lambda: DescriptorsInst.id == t_class_parent.c.id, + # secondaryjoin=lambda: DescriptorsInst.id == t_class_parent.c.parent, + # back_populates="descriptors_inst_", + # ) + # descriptors_inst_: Mapped["DescriptorsInst"] = relationship( + # "DescriptorsInst", + # secondary="class_parent", + # primaryjoin=lambda: DescriptorsInst.id == t_class_parent.c.parent, + # secondaryjoin=lambda: DescriptorsInst.id == t_class_parent.c.id, + # back_populates="descriptors_inst", + # ) + descriptors_cat: Mapped[List["DescriptorsCat"]] = relationship( + "DescriptorsCat", uselist=True, back_populates="descriptors_inst" + ) + descriptors_quant: Mapped[List["DescriptorsQuant"]] = relationship( + "DescriptorsQuant", + uselist=True, + back_populates="descriptors_inst", + viewonly=True, + cascade="all, delete-orphan", + ) + obj_desc_inst: Mapped[List["ObjDescInst"]] = relationship( + "ObjDescInst", + uselist=True, + back_populates="descriptors_inst", + viewonly=True, + cascade="all, delete-orphan", + ) + values_inst: Mapped[List["ValuesInst"]] = relationship( + "ValuesInst", + uselist=True, + back_populates="descriptors_inst", + viewonly=True, + cascade="all, delete-orphan", + ) + values_cat: Mapped[List["ValuesCat"]] = relationship( + "ValuesCat", + uselist=True, + back_populates="descriptors_inst", + viewonly=True, + cascade="all, delete-orphan", + ) + values_quant: Mapped[List["ValuesQuant"]] = relationship( + "ValuesQuant", + uselist=True, + back_populates="descriptors_inst", + viewonly=True, + cascade="all, delete-orphan", + ) + + +class Objects(Base): + """ + Represents an object in the database with various relationships and constraints. + + Attributes + ---------- + id : Uuid + Unique identifier for the object. + id_type : Enum + Type of the remote ID, can be one of 'organization', 'dataset', 'collection', 'package', or 'quantdb'. + id_file : Integer + Identifier for the file associated with the object. + id_internal : Uuid + Internal identifier for the object. + + Relationships + ------------- + objects : Mapped["Objects"] + Relationship to other objects through the 'dataset_object' table. + objects_ : Mapped["Objects"] + Reverse relationship to other objects through the 'dataset_object' table. + obj_desc_inst : Mapped[List["ObjDescInst"]] + Relationship to object description instances. + values_inst : Mapped[List["ValuesInst"]] + Relationship to value instances. + obj_desc_cat : Mapped[List["ObjDescCat"]] + Relationship to object description categories. + obj_desc_quant : Mapped[List["ObjDescQuant"]] + Relationship to object description quantities. + values_cat : Mapped[List["ValuesCat"]] + Relationship to value categories. + values_quant : Mapped[List["ValuesQuant"]] + Relationship to value quantities. + + Constraints + ----------- + __table_args__ : tuple + Contains various constraints and indexes for the table: + - CheckConstraint to ensure 'id_file' is not NULL if 'id_type' is 'package'. + - CheckConstraint to ensure 'id_internal' is not NULL and 'id' equals 'id_internal' if 'id_type' is 'quantdb'. + - PrimaryKeyConstraint on 'id'. + - Index on 'id_internal'. + """ + + __tablename__ = "objects" + __table_args__ = ( + # CheckConstraint( + # "id_type <> 'package'::remote_id_type OR id_file IS NOT NULL", + # name="constraint_objects_remote_id_type_id_package", + # ), + # CheckConstraint( + # "id_type <> 'quantdb'::remote_id_type OR id_internal IS NOT NULL AND id = id_internal", + # name="constraint_objects_remote_id_type_id_internal", + # ), + # ForeignKeyConstraint( + # ["id_internal"], + # ["objects_internal.id"], + # name="objects_id_internal_fkey", + # ), + PrimaryKeyConstraint("id", name="objects_pkey"), + Index("idx_objects_id_internal", "id_internal"), + ) + + id = mapped_column(Uuid) + id_type = mapped_column( + Enum( + "organization", + "dataset", + "collection", + "package", + "quantdb", + name="remote_id_type", + ), + nullable=False, + ) + id_file = mapped_column(Integer, nullable=True) + id_internal = mapped_column(Uuid, nullable=True) + + # objects_internal: Mapped[Optional["ObjectsInternal"]] = relationship( + # "ObjectsInternal", foreign_keys=[id_internal], back_populates="objects" + # ) + # objects: Mapped["Objects"] = relationship( + # "Objects", + # secondary="dataset_object", + # primaryjoin=lambda: Objects.id == t_dataset_object.c.dataset, + # secondaryjoin=lambda: Objects.id == t_dataset_object.c.object, + # back_populates="objects_", + # ) + # objects_: Mapped["Objects"] = relationship( + # "Objects", + # secondary="dataset_object", + # primaryjoin=lambda: Objects.id == t_dataset_object.c.object, + # secondaryjoin=lambda: Objects.id == t_dataset_object.c.dataset, + # back_populates="objects", + # ) + # objects_internal_: Mapped[List["ObjectsInternal"]] = relationship( + # "ObjectsInternal", + # uselist=True, + # foreign_keys="[ObjectsInternal.dataset]", + # back_populates="objects_", + # ) + obj_desc_inst: Mapped[List["ObjDescInst"]] = relationship( + "ObjDescInst", + uselist=True, + back_populates="objects", + viewonly=True, + cascade="all, delete-orphan", + ) + obj_desc_cat: Mapped[List["ObjDescCat"]] = relationship( + "ObjDescCat", + uselist=True, + back_populates="objects", + viewonly=True, + cascade="all, delete-orphan", + ) + obj_desc_quant: Mapped[List["ObjDescQuant"]] = relationship( + "ObjDescQuant", + uselist=True, + back_populates="objects", + viewonly=True, + cascade="all, delete-orphan", + ) + values_inst: Mapped[List["ValuesInst"]] = relationship( + "ValuesInst", + uselist=True, + back_populates="objects", + viewonly=True, + cascade="all, delete-orphan", + ) + values_cat: Mapped[List["ValuesCat"]] = relationship( + "ValuesCat", + uselist=True, + back_populates="objects", + viewonly=True, + cascade="all, delete-orphan", + ) + values_quant: Mapped[List["ValuesQuant"]] = relationship( + "ValuesQuant", + uselist=True, + back_populates="objects", + viewonly=True, + cascade="all, delete-orphan", + ) + + def __repr__(self): + return f"" + + @staticmethod + def preprocess_id(id_value: str) -> str: + """ + Preprocess the id to remove 'N:dataset:' if it exists. + + Parameters + ---------- + id_value : str + The original id value. + + Returns + ------- + str + The preprocessed id value. + """ + if isinstance(id_value, str): + if id_value.startswith("N:dataset:"): + return id_value.replace("N:dataset:", "") + # if isinstance(id_value, str): + # id_value = uuid.UUID(id_value) + return id_value + + @validates("id") + def validate_id(self, key: str, id_value: str) -> str: + """ + Validate and preprocess the id before storing it. + + Parameters + ---------- + key : str + The key being validated. + id_value : str + The original id value. + + Returns + ------- + str + The preprocessed id value. + """ + return self.preprocess_id(id_value) + + +# class ObjectsInternal(Base): +# __tablename__ = "objects_internal" +# __table_args__ = ( +# CheckConstraint( +# "type <> 'path-metadata'::oi_type OR updated_transitive IS NOT NULL AND dataset IS NOT NULL", +# name="constraint_objects_internal_type_updated_transitive", +# ), +# ForeignKeyConstraint( +# ["dataset"], ["objects.id"], name="constraint_oi_dataset_fk" +# ), +# PrimaryKeyConstraint("id", name="objects_internal_pkey"), +# UniqueConstraint( +# "dataset", +# "updated_transitive", +# name="objects_internal_dataset_updated_transitive_key", +# ), +# ) + +# id = mapped_column(Uuid, server_default=text("gen_random_uuid()")) +# type = mapped_column( +# Enum("path-metadata", "other", name="oi_type"), +# server_default=text("'other'::oi_type"), +# ) +# dataset = mapped_column(Uuid) +# updated_transitive = mapped_column(DateTime) +# label = mapped_column(Text) +# curator_note = mapped_column(Text) + +# BUG: cycles! +# objects: Mapped[List["Objects"]] = relationship( +# "Objects", +# uselist=True, +# foreign_keys="[Objects.id_internal]", +# back_populates="objects_internal", +# ) +# objects_: Mapped[Optional["Objects"]] = relationship( +# "Objects", foreign_keys=[dataset], back_populates="objects_internal_" +# ) + + +class Units(Base): + __tablename__ = "units" + __table_args__ = ( + PrimaryKeyConstraint("id", name="units_pkey"), + UniqueConstraint("iri", name="units_iri_key"), + UniqueConstraint("label", name="units_label_key"), + ) + + id = mapped_column( + Integer, + Identity( + start=1, + increment=1, + minvalue=1, + maxvalue=2147483647, + cycle=False, + cache=1, + ), + primary_key=True, + ) + label = mapped_column(Text, nullable=False) + iri = mapped_column(Text, nullable=False) + + descriptors_quant: Mapped[List["DescriptorsQuant"]] = relationship( + "DescriptorsQuant", uselist=True, back_populates="units" + ) + + +t_aspect_parent = Table( + "aspect_parent", + metadata, + Column("id", Integer, nullable=False), + Column("parent", Integer, nullable=False), + ForeignKeyConstraint(["id"], ["aspects.id"], name="aspect_parent_id_fkey"), + ForeignKeyConstraint( + ["parent"], ["aspects.id"], name="aspect_parent_parent_fkey" + ), + PrimaryKeyConstraint("id", "parent", name="aspect_parent_pkey"), +) + + +t_class_parent = Table( + "class_parent", + metadata, + Column("id", Integer, nullable=False), + Column("parent", Integer, nullable=False), + ForeignKeyConstraint( + ["id"], ["descriptors_inst.id"], name="class_parent_id_fkey" + ), + ForeignKeyConstraint( + ["parent"], ["descriptors_inst.id"], name="class_parent_parent_fkey" + ), + PrimaryKeyConstraint("id", "parent", name="class_parent_pkey"), +) + + +t_dataset_object = Table( + "dataset_object", + metadata, + Column("dataset", Uuid, nullable=False), + Column("object", Uuid, nullable=False), + ForeignKeyConstraint( + ["dataset"], ["objects.id"], name="dataset_object_dataset_fkey" + ), + ForeignKeyConstraint( + ["object"], ["objects.id"], name="dataset_object_object_fkey" + ), + PrimaryKeyConstraint("dataset", "object", name="dataset_object_pkey"), +) + + +class DescriptorsCat(Base): + __tablename__ = "descriptors_cat" + __table_args__ = ( + ForeignKeyConstraint( + ["domain"], + ["descriptors_inst.id"], + name="descriptors_cat_domain_fkey", + ), + PrimaryKeyConstraint("id", name="descriptors_cat_pkey"), + UniqueConstraint( + "domain", + "range", + "label", + name="descriptors_cat_domain_range_label_key", + ), + ) + + id = mapped_column( + Integer, + Identity( + start=1, + increment=1, + minvalue=1, + maxvalue=2147483647, + cycle=False, + cache=1, + ), + ) + domain = mapped_column(Integer) + range = mapped_column(Enum("open", "controlled", name="cat_range_type")) + label = mapped_column(Text) + description = mapped_column(Text) + curator_note = mapped_column(Text) + + descriptors_inst: Mapped[Optional["DescriptorsInst"]] = relationship( + "DescriptorsInst", back_populates="descriptors_cat" + ) + obj_desc_cat: Mapped[List["ObjDescCat"]] = relationship( + "ObjDescCat", uselist=True, back_populates="descriptors_cat" + ) + values_cat: Mapped[List["ValuesCat"]] = relationship( + "ValuesCat", uselist=True, back_populates="descriptors_cat" + ) + + +class DescriptorsQuant(Base): + """ + DescriptorsQuant model representing quantitative descriptors. + Attributes + ---------- + id : int + Primary key of the descriptor. + shape : str + Shape of the descriptor, default is 'scalar'. + label : str + Label of the descriptor. + aggregation_type : str + Type of aggregation, default is 'instance'. + unit : int + Foreign key referencing the unit. + aspect : int + Foreign key referencing the aspect. + domain : int + Foreign key referencing the domain. + description : str + Description of the descriptor. + curator_note : str + Notes from the curator. + Relationships + ------------- + aspects : Optional[Aspects] + Relationship to the Aspects model. + descriptors_inst : Optional[DescriptorsInst] + Relationship to the DescriptorsInst model. + units : Optional[Units] + Relationship to the Units model. + obj_desc_quant : List[ObjDescQuant] + Relationship to the ObjDescQuant model. + values_quant : List[ValuesQuant] + Relationship to the ValuesQuant model. + """ + + __tablename__ = "descriptors_quant" + __table_args__ = ( + ForeignKeyConstraint( + ["aspect"], ["aspects.id"], name="descriptors_quant_aspect_fkey" + ), + ForeignKeyConstraint( + ["domain"], + ["descriptors_inst.id"], + name="descriptors_quant_domain_fkey", + ), + ForeignKeyConstraint( + ["unit"], ["units.id"], name="descriptors_quant_unit_fkey" + ), + PrimaryKeyConstraint("id", name="descriptors_quant_pkey"), + UniqueConstraint("label", name="descriptors_quant_label_key"), + UniqueConstraint( + "unit", + "aspect", + "domain", + "shape", + "aggregation_type", + name="descriptors_quant_unit_aspect_domain_shape_aggregation_type_key", + ), + ) + + id = mapped_column( + Integer, + Identity( + start=1, + increment=1, + minvalue=1, + maxvalue=2147483647, + cycle=False, + cache=1, + ), + ) + shape = mapped_column( + Enum("scalar", name="quant_shape"), + nullable=False, + server_default=text("'scalar'::quant_shape"), + ) + label = mapped_column(Text, nullable=False) + aggregation_type = mapped_column( + Enum( + "instance", + "function", + "summary", + "mean", + "media", + "mode", + "sum", + "min", + "max", + name="quant_agg_type", + ), + nullable=False, + server_default=text("'instance'::quant_agg_type"), + ) + unit = mapped_column(Integer) + aspect = mapped_column(Integer, ForeignKey("aspects.id")) + domain = mapped_column(Integer) + description = mapped_column(Text) + curator_note = mapped_column(Text) + + aspects: Mapped[Optional["Aspects"]] = relationship( + "Aspects", back_populates="descriptors_quant" + ) + descriptors_inst: Mapped[Optional["DescriptorsInst"]] = relationship( + "DescriptorsInst", back_populates="descriptors_quant" + ) + units: Mapped[Optional["Units"]] = relationship( + "Units", back_populates="descriptors_quant" + ) + obj_desc_quant: Mapped[List["ObjDescQuant"]] = relationship( + "ObjDescQuant", uselist=True, back_populates="descriptors_quant" + ) + values_quant: Mapped[List["ValuesQuant"]] = relationship( + "ValuesQuant", uselist=True, back_populates="descriptors_quant" + ) + + +class ObjDescInst(Base): + __tablename__ = "obj_desc_inst" + __table_args__ = ( + ForeignKeyConstraint( + ["addr_desc_inst"], + ["addresses.id"], + name="obj_desc_inst_addr_desc_inst_fkey", + ), + ForeignKeyConstraint( + ["addr_field"], + ["addresses.id"], + name="obj_desc_inst_addr_field_fkey", + ), + ForeignKeyConstraint( + ["desc_inst"], + ["descriptors_inst.id"], + name="obj_desc_inst_desc_inst_fkey", + ), + ForeignKeyConstraint( + ["object"], ["objects.id"], name="obj_desc_inst_object_fkey" + ), + PrimaryKeyConstraint("object", "desc_inst", name="obj_desc_inst_pkey"), + ) + + object = mapped_column(Uuid, nullable=False) + desc_inst = mapped_column(Integer, nullable=False) + addr_field = mapped_column(Integer, nullable=False) + addr_desc_inst = mapped_column(Integer) + expect = mapped_column(Integer) + + addresses: Mapped[Optional["Addresses"]] = relationship( + "Addresses", + foreign_keys=[addr_desc_inst], + back_populates="obj_desc_inst", + ) + addresses_field: Mapped["Addresses"] = relationship( + "Addresses", foreign_keys=[addr_field], back_populates="obj_desc_inst_" + ) + descriptors_inst: Mapped["DescriptorsInst"] = relationship( + "DescriptorsInst", back_populates="obj_desc_inst" + ) + objects: Mapped["Objects"] = relationship( + "Objects", + back_populates="obj_desc_inst", + viewonly=True, + cascade="all, delete-orphan", + ) + values_cat: Mapped[List["ValuesCat"]] = relationship( + "ValuesCat", + uselist=True, + back_populates="obj_desc_inst", + viewonly=True, + cascade="all, delete-orphan", + ) + values_quant: Mapped[List["ValuesQuant"]] = relationship( + "ValuesQuant", + uselist=True, + back_populates="obj_desc_inst", + viewonly=True, + cascade="all, delete-orphan", + ) + + +class ValuesInst(Base): + """ + Represents an instance of values in the database. + + Attributes + ---------- + id : int + The primary key of the values instance. + type : str + The type of the instance, which can be 'subject', 'sample', or 'below'. + id_sub : str + The subject identifier. + desc_inst : int + The descriptor instance identifier. + dataset : UUID + The dataset identifier. + id_formal : str + The formal identifier. + local_identifier : str + The local identifier. + id_sam : str + The sample identifier. + objects : Optional[Objects] + The related objects. + descriptors_inst : Optional[DescriptorsInst] + The related descriptor instances. + values_inst : ValuesInst + The related values instances through the 'equiv_inst' table. + values_inst_ : ValuesInst + The related values instances through the 'equiv_inst' table. + values_inst1 : ValuesInst + The related values instances through the 'instance_parent' table. + values_inst2 : ValuesInst + The related values instances through the 'instance_parent' table. + values_cat : List[ValuesCat] + The related categorical values. + values_quant : List[ValuesQuant] + The related quantitative values. + + Relationships + ------------- + objects : relationship + Relationship to the Objects table. + descriptors_inst : relationship + Relationship to the DescriptorsInst table. + values_inst : relationship + Self-referential relationship through the 'equiv_inst' table (left to right). + values_inst_ : relationship + Self-referential relationship through the 'equiv_inst' table (right to left). + values_inst1 : relationship + Self-referential relationship through the 'instance_parent' table (id to parent). + values_inst2 : relationship + Self-referential relationship through the 'instance_parent' table (parent to id). + values_cat : relationship + Relationship to the ValuesCat table. + values_quant : relationship + Relationship to the ValuesQuant table. + """ + + __tablename__ = "values_inst" + __table_args__ = ( + CheckConstraint( + "id_sam ~ '^sam-'::text", name="values_inst_id_sam_check" + ), + CheckConstraint( + "id_sub ~ '^sub-'::text", name="values_inst_id_sub_check" + ), + CheckConstraint( + "type <> 'below'::instance_type OR id_sub IS NOT NULL OR id_sam IS NOT NULL", + name="constraint_values_inst_type_below", + ), + CheckConstraint( + "type <> 'sample'::instance_type OR id_sam IS NOT NULL AND id_sam = id_formal", + name="constraint_values_inst_type_id_sam", + ), + CheckConstraint( + "type <> 'subject'::instance_type OR id_sub = id_formal AND id_sam IS NULL", + name="constraint_values_inst_type_id_sub", + ), + CheckConstraint( + "type = 'below'::instance_type AND NOT id_formal ~ '^(sub|sam)-'::text OR type = 'subject'::instance_type AND id_formal ~ '^sub-'::text OR type = 'sample'::instance_type AND id_formal ~ '^sam-'::text", + name="constraint_values_inst_type_id_formal", + ), + ForeignKeyConstraint( + ["dataset"], ["objects.id"], name="values_inst_dataset_fkey" + ), + ForeignKeyConstraint( + ["desc_inst"], + ["descriptors_inst.id"], + name="values_inst_desc_inst_fkey", + ), + PrimaryKeyConstraint("id", name="values_inst_pkey"), + UniqueConstraint( + "dataset", "id_formal", name="values_inst_dataset_id_formal_key" + ), + Index("idx_values_inst_dataset", "dataset"), + Index("idx_values_inst_dataset_id_formal", "dataset", "id_formal"), + Index("idx_values_inst_dataset_id_sam", "dataset", "id_sam"), + Index("idx_values_inst_dataset_id_sub", "dataset", "id_sub"), + Index("idx_values_inst_desc_inst", "desc_inst"), + Index("idx_values_inst_id_formal", "id_formal"), + Index("idx_values_inst_id_sam", "id_sam"), + Index("idx_values_inst_id_sub", "id_sub"), + ) + + id = mapped_column( + Integer, + Identity( + start=1, + increment=1, + minvalue=1, + maxvalue=2147483647, + cycle=False, + cache=1, + ), + ) + type = mapped_column( + Enum("subject", "sample", "below", name="instance_type"), nullable=False + ) + id_sub = mapped_column(Text, nullable=False) + desc_inst = mapped_column(Integer) + dataset = mapped_column(Uuid, ForeignKey("objects.id")) + id_formal = mapped_column(Text) + local_identifier = mapped_column(Text) + id_sam = mapped_column(Text) + + objects: Mapped[Optional["Objects"]] = relationship( + "Objects", + back_populates="values_inst", + viewonly=True, + cascade="all, delete-orphan", + ) + descriptors_inst: Mapped[Optional["DescriptorsInst"]] = relationship( + "DescriptorsInst", back_populates="values_inst" + ) + # values_inst: Mapped["ValuesInst"] = relationship( + # "ValuesInst", + # secondary="equiv_inst", + # primaryjoin=lambda: ValuesInst.id == t_equiv_inst.c.left_thing, + # secondaryjoin=lambda: ValuesInst.id == t_equiv_inst.c.right_thing, + # back_populates="values_inst_", + # ) + # values_inst_: Mapped["ValuesInst"] = relationship( + # "ValuesInst", + # secondary="equiv_inst", + # primaryjoin=lambda: ValuesInst.id == t_equiv_inst.c.right_thing, + # secondaryjoin=lambda: ValuesInst.id == t_equiv_inst.c.left_thing, + # back_populates="values_inst", + # ) + # values_inst1: Mapped["ValuesInst"] = relationship( + # "ValuesInst", + # secondary="instance_parent", + # primaryjoin=lambda: ValuesInst.id == t_instance_parent.c.id, + # secondaryjoin=lambda: ValuesInst.id == t_instance_parent.c.parent, + # back_populates="values_inst2", + # ) + # values_inst2: Mapped["ValuesInst"] = relationship( + # "ValuesInst", + # secondary="instance_parent", + # primaryjoin=lambda: ValuesInst.id == t_instance_parent.c.parent, + # secondaryjoin=lambda: ValuesInst.id == t_instance_parent.c.id, + # back_populates="values_inst1", + # ) + values_cat: Mapped[List["ValuesCat"]] = relationship( + "ValuesCat", uselist=True, back_populates="values_inst" + ) + values_quant: Mapped[List["ValuesQuant"]] = relationship( + "ValuesQuant", + uselist=True, + back_populates="values_inst", + viewonly=True, + cascade="all, delete-orphan", + ) + + +t_equiv_inst = Table( + "equiv_inst", + metadata, + Column("left_thing", Integer, nullable=False), + Column("right_thing", Integer, nullable=False), + CheckConstraint("left_thing <> right_thing", name="sse_no_self"), + ForeignKeyConstraint( + ["left_thing"], ["values_inst.id"], name="equiv_inst_left_thing_fkey" + ), + ForeignKeyConstraint( + ["right_thing"], ["values_inst.id"], name="equiv_inst_right_thing_fkey" + ), + PrimaryKeyConstraint("left_thing", "right_thing", name="equiv_inst_pkey"), +) + + +t_instance_parent = Table( + "instance_parent", + metadata, + Column("id", Integer, nullable=False), + Column("parent", Integer, nullable=False), + ForeignKeyConstraint( + ["id"], ["values_inst.id"], name="instance_parent_id_fkey" + ), + ForeignKeyConstraint( + ["parent"], ["values_inst.id"], name="instance_parent_parent_fkey" + ), + PrimaryKeyConstraint("id", "parent", name="instance_parent_pkey"), +) + + +class ObjDescCat(Base): + __tablename__ = "obj_desc_cat" + __table_args__ = ( + ForeignKeyConstraint( + ["addr_desc_inst"], + ["addresses.id"], + name="obj_desc_cat_addr_desc_inst_fkey", + ), + ForeignKeyConstraint( + ["addr_field"], + ["addresses.id"], + name="obj_desc_cat_addr_field_fkey", + ), + ForeignKeyConstraint( + ["desc_cat"], + ["descriptors_cat.id"], + name="obj_desc_cat_desc_cat_fkey", + ), + ForeignKeyConstraint( + ["object"], ["objects.id"], name="obj_desc_cat_object_fkey" + ), + PrimaryKeyConstraint("object", "desc_cat", name="obj_desc_cat_pkey"), + ) + + object = mapped_column(Uuid, nullable=False) + desc_cat = mapped_column(Integer, nullable=False) + addr_field = mapped_column(Integer, nullable=False) + addr_desc_inst = mapped_column(Integer) + expect = mapped_column(Integer) + + addresses: Mapped[Optional["Addresses"]] = relationship( + "Addresses", + foreign_keys=[addr_desc_inst], + back_populates="obj_desc_cat", + ) + addresses_: Mapped["Addresses"] = relationship( + "Addresses", foreign_keys=[addr_field], back_populates="obj_desc_cat_" + ) + descriptors_cat: Mapped["DescriptorsCat"] = relationship( + "DescriptorsCat", back_populates="obj_desc_cat" + ) + objects: Mapped["Objects"] = relationship( + "Objects", back_populates="obj_desc_cat" + ) + values_cat: Mapped[List["ValuesCat"]] = relationship( + "ValuesCat", uselist=True, back_populates="obj_desc_cat" + ) + + +class ObjDescQuant(Base): + __tablename__ = "obj_desc_quant" + __table_args__ = ( + ForeignKeyConstraint( + ["addr_aspect"], + ["addresses.id"], + name="obj_desc_quant_addr_aspect_fkey", + ), + ForeignKeyConstraint( + ["addr_desc_inst"], + ["addresses.id"], + name="obj_desc_quant_addr_desc_inst_fkey", + ), + ForeignKeyConstraint( + ["addr_field"], + ["addresses.id"], + name="obj_desc_quant_addr_field_fkey", + ), + ForeignKeyConstraint( + ["addr_unit"], + ["addresses.id"], + name="obj_desc_quant_addr_unit_fkey", + ), + ForeignKeyConstraint( + ["desc_quant"], + ["descriptors_quant.id"], + name="obj_desc_quant_desc_quant_fkey", + ), + ForeignKeyConstraint( + ["object"], ["objects.id"], name="obj_desc_quant_object_fkey" + ), + PrimaryKeyConstraint( + "object", "desc_quant", name="obj_desc_quant_pkey" + ), + ) + + object = mapped_column(Uuid, nullable=False) + desc_quant = mapped_column(Integer, nullable=False) + addr_field = mapped_column(Integer, nullable=False) + addr_unit = mapped_column(Integer) + addr_aspect = mapped_column(Integer) + addr_desc_inst = mapped_column(Integer) + expect = mapped_column(Integer) + + addresses: Mapped[Optional["Addresses"]] = relationship( + "Addresses", + foreign_keys=[addr_desc_inst], + back_populates="obj_desc_quant_", + ) + addresses_aspect: Mapped[Optional["Addresses"]] = relationship( + "Addresses", foreign_keys=[addr_aspect], back_populates="obj_desc_quant" + ) + addresses_field: Mapped["Addresses"] = relationship( + "Addresses", foreign_keys=[addr_field], back_populates="obj_desc_quant1" + ) + addresses_unit: Mapped[Optional["Addresses"]] = relationship( + "Addresses", foreign_keys=[addr_unit], back_populates="obj_desc_quant2" + ) + descriptors_quant: Mapped["DescriptorsQuant"] = relationship( + "DescriptorsQuant", back_populates="obj_desc_quant" + ) + objects: Mapped["Objects"] = relationship( + "Objects", + back_populates="obj_desc_quant", + viewonly=True, + cascade="all, delete-orphan", + ) + values_quant: Mapped[List["ValuesQuant"]] = relationship( + "ValuesQuant", + uselist=True, + back_populates="obj_desc_quant", + viewonly=True, + cascade="all, delete-orphan", + ) + + +class ValuesCat(Base): + __tablename__ = "values_cat" + __table_args__ = ( + CheckConstraint( + "value_open IS NOT NULL OR value_controlled IS NOT NULL", + name="constraint_values_cat_some_value", + ), + ForeignKeyConstraint( + ["desc_cat"], + ["descriptors_cat.id"], + name="values_cat_desc_cat_fkey", + ), + ForeignKeyConstraint( + ["desc_inst"], + ["descriptors_inst.id"], + name="values_cat_desc_inst_fkey", + ), + ForeignKeyConstraint( + ["instance"], ["values_inst.id"], name="values_cat_instance_fkey" + ), + ForeignKeyConstraint( + ["object", "desc_cat"], + ["obj_desc_cat.object", "obj_desc_cat.desc_cat"], + name="values_cat_object_desc_cat_fkey", + ), + ForeignKeyConstraint( + ["object", "desc_inst"], + ["obj_desc_inst.object", "obj_desc_inst.desc_inst"], + name="values_cat_object_desc_inst_fkey", + ), + ForeignKeyConstraint( + ["object"], ["objects.id"], name="values_cat_object_fkey" + ), + ForeignKeyConstraint( + ["value_controlled"], + ["controlled_terms.id"], + name="values_cat_value_controlled_fkey", + ), + PrimaryKeyConstraint("id", name="values_cat_pkey"), + Index("idx_values_cat_desc_cat", "desc_cat"), + Index("idx_values_cat_desc_inst", "desc_inst"), + Index("idx_values_cat_instance", "instance"), + Index("idx_values_cat_object", "object"), + Index("idx_values_cat_value_controlled", "value_controlled"), + ) + + id = mapped_column( + Integer, + Identity( + start=1, + increment=1, + minvalue=1, + maxvalue=2147483647, + cycle=False, + cache=1, + ), + ) + object = mapped_column(Uuid, nullable=False) + desc_inst = mapped_column(Integer, nullable=False) + desc_cat = mapped_column(Integer, nullable=False) + value_open = mapped_column(Text) + value_controlled = mapped_column(Integer) + instance = mapped_column(Integer) + + descriptors_cat: Mapped["DescriptorsCat"] = relationship( + "DescriptorsCat", back_populates="values_cat" + ) + descriptors_inst: Mapped["DescriptorsInst"] = relationship( + "DescriptorsInst", back_populates="values_cat" + ) + values_inst: Mapped[Optional["ValuesInst"]] = relationship( + "ValuesInst", back_populates="values_cat" + ) + obj_desc_cat: Mapped["ObjDescCat"] = relationship( + "ObjDescCat", back_populates="values_cat" + ) + obj_desc_inst: Mapped["ObjDescInst"] = relationship( + "ObjDescInst", back_populates="values_cat" + ) + objects: Mapped["Objects"] = relationship( + "Objects", back_populates="values_cat" + ) + controlled_terms: Mapped[Optional["ControlledTerms"]] = relationship( + "ControlledTerms", back_populates="values_cat" + ) + + +class ValuesQuant(Base): + __tablename__ = "values_quant" + __table_args__ = ( + ForeignKeyConstraint( + ["desc_inst"], + ["descriptors_inst.id"], + name="values_quant_desc_inst_fkey", + ), + ForeignKeyConstraint( + ["desc_quant"], + ["descriptors_quant.id"], + name="values_quant_desc_quant_fkey", + ), + ForeignKeyConstraint( + ["instance"], ["values_inst.id"], name="values_quant_instance_fkey" + ), + ForeignKeyConstraint( + ["object", "desc_inst"], + ["obj_desc_inst.object", "obj_desc_inst.desc_inst"], + name="values_quant_object_desc_inst_fkey", + ), + ForeignKeyConstraint( + ["object", "desc_quant"], + ["obj_desc_quant.object", "obj_desc_quant.desc_quant"], + name="values_quant_object_desc_quant_fkey", + ), + ForeignKeyConstraint( + ["object"], ["objects.id"], name="values_quant_object_fkey" + ), + PrimaryKeyConstraint("id", name="values_quant_pkey"), + Index("idx_values_quant_desc_inst", "desc_inst"), + Index("idx_values_quant_desc_quant", "desc_quant"), + Index("idx_values_quant_instance", "instance"), + Index("idx_values_quant_object", "object"), + ) + + id = mapped_column( + Integer, + Identity( + start=1, + increment=1, + minvalue=1, + maxvalue=2147483647, + cycle=False, + cache=1, + ), + ) + value = mapped_column(Numeric, nullable=False) + object = mapped_column(Uuid, ForeignKey("objects.id"), nullable=False) + desc_inst = mapped_column(Integer, nullable=False) + desc_quant = mapped_column(Integer, nullable=False) + value_blob = mapped_column(JSONB, nullable=False) + instance = mapped_column(Integer) + orig_value = mapped_column(String) + orig_units = mapped_column(String) + + descriptors_inst: Mapped["DescriptorsInst"] = relationship( + "DescriptorsInst", back_populates="values_quant" + ) + descriptors_quant: Mapped["DescriptorsQuant"] = relationship( + "DescriptorsQuant", back_populates="values_quant" + ) + values_inst: Mapped[Optional["ValuesInst"]] = relationship( + "ValuesInst", back_populates="values_quant" + ) + obj_desc_inst: Mapped["ObjDescInst"] = relationship( + "ObjDescInst", + back_populates="values_quant", + viewonly=True, + cascade="all, delete-orphan", + ) + obj_desc_quant: Mapped["ObjDescQuant"] = relationship( + "ObjDescQuant", + back_populates="values_quant", + viewonly=True, + cascade="all, delete-orphan", + ) + objects: Mapped["Objects"] = relationship( + "Objects", + back_populates="values_quant", + viewonly=True, + cascade="all, delete-orphan", + ) + + @staticmethod + def update_desc_inst( + target: "ValuesQuant", value, oldvalue, initiator + ) -> None: + """ + Automatically update desc_inst when descriptors_inst parent is updated. + """ + if target.descriptors_inst: + target.desc_inst = target.descriptors_inst.id + + @staticmethod + def register_listeners() -> None: + """ + Register event listeners for the ValuesQuant model. + """ + event.listen( + ValuesQuant.descriptors_inst, "set", ValuesQuant.update_desc_inst + ) + + +# @event.listens_for(ValuesQuant.descriptors_inst, "set") +# def set_desc_inst_from_descriptor(target, value, oldvalue, initiator): +# print(target, value, oldvalue, initiator) +# if value is not None: +# target.desc_inst = value.id + + +def update_all_children(target, value, oldvalue, initiator): + # Loop through all relationships of the target (parent) object + for relationship_prop in target.__mapper__.relationships: + related_objects = getattr(target, relationship_prop.key) + + # If there are related objects, update their attributes + if related_objects is not None: + # Handle single and multiple relationships + related_objects = ( + related_objects + if isinstance(related_objects, list) + else [related_objects] + ) + for related_obj in related_objects: + # Update attributes on related objects as needed + # For demonstration, we'll update an attribute based on parent_value + if hasattr(related_obj, "child_value"): + related_obj.child_value = ( + f"Updated from parent_value: {value}" + ) + if hasattr(related_obj, "other_child_value"): + related_obj.other_child_value = ( + f"Updated from parent_value: {value}" + ) + + +# # Attach the listener to all attributes on the Parent model +# for column in ValuesQuant.__table__.columns: +# event.listen(getattr(ValuesQuant, column.name), "set", update_all_children) + + +# @event.listens_for(ValuesQuant.descriptors_inst, "set") +# def update_desc_inst(target, value, oldvalue, initiator): +# if value is not None: +# target.desc_inst = value.id + + +# Helper function to find the foreign key field associated with a relationship +def get_foreign_key_field(model, relationship_key): + """Get the local foreign key field name for a given relationship key in the model.""" + for constraint in model.__table__.constraints: + if isinstance(constraint, ForeignKeyConstraint): + for element in constraint.elements: + # Match the local column to the relationship key + if element.column.table.name == relationship_key: + return element.parent.name + return None + + +# General listener function for updating foreign keys dynamically +def update_foreign_key(target, value, oldvalue, initiator): + if value is not None: + # Use the initiator key to find the appropriate foreign key field + relationship_key = ( + initiator.key + ) # Use initiator.key to get the relationship name + foreign_key_field = get_foreign_key_field( + target.__class__, relationship_key + ) + + # Set the foreign key field if it exists on the target + if foreign_key_field and hasattr(target, foreign_key_field): + setattr(target, foreign_key_field, value.id) + + +# Function to attach the listener to all relationships in a given model +def add_dynamic_listeners(base): + for cls in base.__subclasses__(): + for relationship_prop in cls.__mapper__.relationships: + event.listen( + getattr(cls, relationship_prop.key), "set", update_foreign_key + ) + + +# Attach listeners to all models in the Base +add_dynamic_listeners(Base) diff --git a/quantdb/ingest_tabular/pennsieve_client.py b/quantdb/ingest_tabular/pennsieve_client.py new file mode 100644 index 0000000..6fd61db --- /dev/null +++ b/quantdb/ingest_tabular/pennsieve_client.py @@ -0,0 +1,245 @@ +from __future__ import annotations + +from functools import cache +from pathlib import Path +from typing import Any, List, Tuple + +import boto3 +import requests +from botocore.client import BaseClient +from pydantic import BaseSettings + + +class PennsieveModel(BaseSettings): + PENNSIEVE_API_TOKEN: str + PENNSIEVE_API_SECRET: str + auth_url: str = "https://api.pennsieve.io/authentication/cognito-config" + private_dataset_url: str = "https://api.pennsieve.io/datasets/" + public_dataset_url: str = "https://api.pennsieve.io/discover/datasets" + + class Config: # type: ignore + env_file = Path.home() / ".scicrunch/credentials/pennsieve" + fields = { + "PENNSIEVE_API_TOKEN": {"env": "PENNSIEVE_API_TOKEN"}, + "PENNSIEVE_API_SECRET": {"env": "PENNSIEVE_API_SECRET"}, + } + + +class Settings(BaseSettings): + pennsieve: PennsieveModel = PennsieveModel() + + +class PennsieveClient: + def __init__(self): + settings = Settings().pennsieve + self.public_dataset_url = settings.public_dataset_url + self.private_dataset_url = settings.private_dataset_url + self.auth_url = settings.auth_url + self.api_key = self.__aws_bot_login( + token=settings.PENNSIEVE_API_TOKEN, + secret=settings.PENNSIEVE_API_SECRET, + ) + self.headers = { + "Authorization": f"Bearer {self.api_key}", + "accept": "*/*", + } + self.session = requests.Session() + + def __reauth(self) -> None: + settings = Settings().pennsieve + self.api_key = self.__aws_bot_login( + token=settings.PENNSIEVE_API_TOKEN, + secret=settings.PENNSIEVE_API_SECRET, + ) + self.headers = { + "Authorization": f"Bearer {self.api_key}", + "accept": "*/*", + } + + def __aws_bot_login(self, token: str, secret: str) -> str: + """Awful AWS bot login for real API key using token + secrets""" + r = requests.get(self.auth_url) + r.raise_for_status() + cognito_app_client_id = r.json()["tokenPool"]["appClientId"] + cognito_region = r.json()["region"] + cognito_idp_client: BaseClient = boto3.client( # type: ignore + "cognito-idp", + region_name=cognito_region, + aws_access_key_id="", + aws_secret_access_key="", + ) + login_response = cognito_idp_client.initiate_auth( # type: ignore + AuthFlow="USER_PASSWORD_AUTH", + AuthParameters={"USERNAME": token, "PASSWORD": secret}, + ClientId=cognito_app_client_id, + ) + api_key: str = login_response["AuthenticationResult"]["AccessToken"] + return api_key + + def __get( + self, + url: str, + params: dict[str, Any] | None = None, + ) -> requests.Response: + """ + Get request to endpoint with params + + Parameters + ---------- + endpoint : URL + API endpoint to hit + params : dict, optional + API options, by default None + + Returns + ------- + dict + API json response + """ + response = requests.get(url, headers=self.headers, params=params) + response.raise_for_status() + return response + + def _post( + self, + url: str, + data: dict[str, Any] | None = None, + payload: dict[str, Any] | None = None, + ) -> requests.Response: + """ + Post request to endpoint with data or json payload + + Parameters + ---------- + endpoint : URL + API endpoint to hit + data : dict, optional + API contents, by default None + json : dict, optional + API contents, by default None + + Returns + ------- + dict + API json response + """ + response = self.session.post(url, data=data, json=payload, headers=self.headers) + # Pennsieve API is unstable, only fail on 500s + if response.status_code >= 400: + print(response.text) + self.__reauth() + response = self.session.post(url, data=data, json=payload, headers=self.headers) + response.raise_for_status() + return response + + @staticmethod + def create_path(path: Path) -> None: + try: + path.mkdir(parents=True, exist_ok=False) + except FileExistsError: + pass + + def get_user(self): + return self.__get("https://api.pennsieve.io/user/").json() + + @cache + def get_dataset(self, id_or_name: str) -> dict[str, Any]: + return self.__get(f"https://api.pennsieve.io/datasets/{id_or_name}").json() + + def get_dataset_packages(self, id_or_name: str) -> dict[str, Any]: + return self.__get(f"https://api.pennsieve.io/datasets/{id_or_name}/packages").json()["packages"] + + @cache + def get_dataset_manifest(self, id_or_name: str) -> dict[str, Any]: + url = "https://api.pennsieve.io/packages/download-manifest" + dataset = self.get_dataset(id_or_name) + payload = {"nodeIds": [child["content"]["nodeId"] for child in dataset["children"]]} + dataset["files"] = self._post(url, payload=payload).json() + return dataset + + @cache + def get_child_manifest(self, node_id: str) -> dict[str, Any]: + url = "https://api.pennsieve.io/packages/download-manifest" + payload = {"nodeIds": [node_id]} + resp = self._post(url, payload=payload) + return resp.json() + + def export_dataset(self, id_or_name: str, output_dir: Path | str, verbose: bool = True) -> None: + """Export a dataset to a directory + + Parameters + ---------- + id_or_name : str + Dataset ID or name + output_dir : Path | str + Output directory + verbose : bool, optional + Prints filename being downloaded, by default True + """ + url = "https://api.pennsieve.io/packages/download-manifest" + output_dir = Path(output_dir) / id_or_name + # Pull dataset for root children IDs + dataset = self.get_dataset(id_or_name) + for child in dataset["children"]: + payload = {"nodeIds": [child["content"]["nodeId"]]} + # Pull tree for 1 child at a time since prebuilt s3 links only last a couple hours + # If all children are pulled at once, the links will expire before all files are downloaded if over 200GBs + manifest = self._post(url, payload=payload).json() + for filemeta in manifest["data"]: + parents_path = output_dir / "/".join(filemeta["path"]) + # Create nested parent directories if they don"t exist + self.create_path(parents_path) + file_path = parents_path / filemeta["fileName"] + if verbose: + print(f"downloading path: {file_path}") + url = filemeta["url"] + # If file already exists, skip if it is stopped in the middle of downloading + # TODO: query file for checksum; very slow but will garuntee no partial downloads + if file_path.exists(): + continue + # Stream download to file + with requests.get(url, stream=True) as r: + r.raise_for_status() + with open(file_path, "wb") as f: + for chunk in r.iter_content(chunk_size=8192): + f.write(chunk) + + def _private_datasets(self): + """Get Private dataset for it"s N:# ID + + Notes + ----- + There is no known limiter at the moment. Expect all results and be conservative. + """ + return self.__get(self.private_dataset_url).json() + + def _public_datasets(self, limit: int = 1, offset: int = 0, asc: bool = False) -> list[dict[str, Any]]: + """Everything about the dataset except the N:# id itself""" + params = { + "limit": limit, + "offset": offset, + "orderBy": "date", + "orderDirection": "asc" if asc else "desc", + } + return self.__get(self.public_dataset_url, params=params).json()["datasets"] + + def get_datasets(self) -> List[dict[str, Any]]: + """ + Get all complete datasets + """ + # Private API endpoint Needs to be normalized via content key + intId_id = {d["content"]["intId"]: d["content"]["id"] for d in self._private_datasets()} + datasets = self._public_datasets(limit=100000) + for dataset in datasets: + dataset["dataset_id"] = intId_id.get(dataset["sourceDatasetId"]) + return datasets + + def get_partial_hash(self) -> Tuple[int, int, int | None]: + """Get latest dataset id & version to see if anything new from pennsieve is worth pulling""" + latest_dataset = self._public_datasets()[0] + partial_hash = ( + latest_dataset["sourceDatasetId"], + latest_dataset["version"], + latest_dataset["revision"], + ) + return partial_hash diff --git a/quantdb/main.py b/quantdb/main.py index ffa04a8..deb5246 100644 --- a/quantdb/main.py +++ b/quantdb/main.py @@ -1,11 +1,13 @@ from fastapi import FastAPI from fastapi.middleware.wsgi import WSGIMiddleware + from quantdb.api_server import app as flask_app app = FastAPI() -app.mount('/', WSGIMiddleware(flask_app)) +app.mount("/", WSGIMiddleware(flask_app)) if __name__ == "__main__": import uvicorn - uvicorn.run("quantdb.main:app", host='127.0.0.1', port=8990, reload=True) + + uvicorn.run("quantdb.main:app", host="127.0.0.1", port=8990, reload=True) diff --git a/quantdb/mysql_app/__init__.py b/quantdb/mysql_app/__init__.py new file mode 100644 index 0000000..07ed76d --- /dev/null +++ b/quantdb/mysql_app/__init__.py @@ -0,0 +1,5 @@ +# from __future__ import annotations + +# from . import database + +# __all__ = ["database"] diff --git a/quantdb/mysql_app/config.py b/quantdb/mysql_app/config.py new file mode 100644 index 0000000..024821d --- /dev/null +++ b/quantdb/mysql_app/config.py @@ -0,0 +1,16 @@ +from dataclasses import dataclass + +import orthauth as oa + +from quantdb.utils import dbUri + +auth = oa.configure_here("auth-config.py", __name__) + + +@dataclass +class Settings: + """Settings for the app.""" + + db_params = {k: auth.get(f"db-{k}") for k in ("user", "host", "port", "database")} + db_params["dbuser"] = db_params.pop("user") + SQLALCHEMY_DATABASE_URI = dbUri(**db_params) diff --git a/quantdb/mysql_app/crud/descriptors_quant.py b/quantdb/mysql_app/crud/descriptors_quant.py new file mode 100644 index 0000000..3c2c114 --- /dev/null +++ b/quantdb/mysql_app/crud/descriptors_quant.py @@ -0,0 +1,168 @@ +import logging +from typing import Any, List + +from sqlalchemy.orm import Session + +from quantdb.client import get_session +from quantdb.ingest_tabular.models import DescriptorsQuant + +logger = logging.getLogger(__name__) +session = get_session() + + +# Create a new DescriptorsQuant record +def create_descriptors_quant( + db_session: Session, **kwargs: Any +) -> DescriptorsQuant: + """ + Create a new DescriptorsQuant record in the database if it does not already exist. + + Parameters + ---------- + session : Session + The SQLAlchemy session to use for database operations. + **kwargs : dict[str, Any] + Keyword arguments representing the fields and values for the DescriptorsQuant record. + + Returns + ------- + DescriptorsQuant + The newly created DescriptorsQuant record, or the existing record if it already exists. + + Notes + ----- + This function checks for the existence of a record based on the provided fields and values. + If a matching record is found, it is returned. Otherwise, a new record is created, added to + the session, and committed to the database. + """ + # Check if the record already exists based on unique constraints or identifying fields + existing_record = ( + db_session.query(DescriptorsQuant).filter_by(**kwargs).first() + ) + if existing_record: + logger.info("Record already exists: %s", existing_record) + return existing_record + + # Create a new record if it doesn't exist + new_descriptor = DescriptorsQuant(**kwargs) + db_session.add(new_descriptor) + db_session.commit() + return new_descriptor + + +# Read DescriptorsQuant records +def read_descriptors_quant( + db_session: Session, record_id: int | None = None, **filters: dict[str, Any] +) -> Any | None | List[DescriptorsQuant]: + """ + Retrieve descriptors from the database. + This function queries the DescriptorsQuant table in the database using the provided SQLAlchemy session. + It can retrieve a specific record by its ID or filter records based on additional criteria. + + Parameters + ---------- + session : Session + The SQLAlchemy session to use for the query. + record_id : int, optional + The ID of the specific record to retrieve. Defaults to None. + **filters : dict, optional + Additional keyword arguments to filter the query. + + Returns + ------- + DescriptorsQuant or list of DescriptorsQuant + The retrieved record if `record_id` is provided, + a list of records if filters are provided, or all records if no filters are applied. + """ + query = db_session.query(DescriptorsQuant) + if record_id: + return query.get(record_id) + if filters: + return query.filter_by(**filters).all() + return query.all() + + +# Update a DescriptorsQuant record +def update_descriptors_quant( + db_session: Session, record_id: int, **kwargs: dict[str, Any] +) -> None | DescriptorsQuant: + """ + Update a DescriptorsQuant record with the given record_id and kwargs. + + Parameters + ---------- + session : Session + SQLAlchemy session object. + record_id : int + ID of the record to update. + kwargs : dict + Fields to update in the record. + + Returns + ------- + DescriptorsQuant + The updated record or None if not found. + """ + record = db_session.query(DescriptorsQuant).get(record_id) + if not record: + print(f"Record with id {record_id} not found") + return None + for key, value in kwargs.items(): + setattr(record, key, value) + print(f"Updated record: {record}") + session.commit() + return record + + +# Delete a DescriptorsQuant record +def delete_descriptors_quant(db_session: Session, record_id: int) -> None | Any: + """ + Deletes a DescriptorsQuant record from the database. + + Parameters + ---------- + session : Session + The SQLAlchemy session to use for the database operation. + record_id : int + The ID of the DescriptorsQuant record to delete. + + Returns + ------- + None or Any + Returns None if the record does not exist, otherwise returns the deleted record. + """ + record = session.query(DescriptorsQuant).get(record_id) + if not record: + return None + db_session.delete(record) + db_session.commit() + return record + + +# Example usage +if __name__ == "__main__": + # Create a new record + new_record = create_descriptors_quant( + session, + label="Example Label", + shape="scalar", + aggregation_type="instance", + unit=1, + aspect=1, + domain=1, + ) + print(f"Created: {new_record}") + + # Read records + records = read_descriptors_quant(session) + print(f"Read: {records}") + + # Update a record + updated_record = update_descriptors_quant( + session, new_record.id, label="Updated Label" + ) + print(f"Updated: {updated_record}") + + # # Delete a record + # deleted_record = delete_descriptors_quant(session, new_record.id) + # print(f"Deleted: {deleted_record}") diff --git a/quantdb/mysql_app/crud/objects.py b/quantdb/mysql_app/crud/objects.py new file mode 100644 index 0000000..c5189b6 --- /dev/null +++ b/quantdb/mysql_app/crud/objects.py @@ -0,0 +1,74 @@ +import logging +from typing import Any, List + +from sqlalchemy.orm import Session + +from quantdb.client import get_session +from quantdb.ingest_tabular.models import Objects + +logger = logging.getLogger(__name__) +session = get_session() + + +# Create a new Objects record +def create_object(session: Session, **kwargs): + new_record = Objects(**kwargs) + session.add(new_record) + session.commit() + return new_record + + +# Read Objects records +def read_objects(session: Session, record_id=None, **filters): + query = session.query(Objects) + if record_id: + return query.get(record_id) + if filters: + return query.filter_by(**filters).all() + return query.all() + + +# Update an Objects record +def update_object(session: Session, record_id, **kwargs): + record = session.query(Objects).get(record_id) + if not record: + return None + for key, value in kwargs.items(): + setattr(record, key, value) + session.commit() + return record + + +# Delete an Objects record +def delete_object(session: Session, record_id): + record = session.query(Objects).get(record_id) + if not record: + return None + session.delete(record) + session.commit() + return record + + +# Example usage +if __name__ == "__main__": + # Create a new record + new_record = create_object( + session, + id="some-uuid", + id_type="dataset", + id_file=123, + id_internal="another-uuid", + ) + print(f"Created: {new_record}") + + # Read records + records = read_objects(session) + print(f"Read: {records}") + + # Update a record + updated_record = update_object(session, new_record.id, id_file=456) + print(f"Updated: {updated_record}") + + # Delete a record + deleted_record = delete_object(session, new_record.id) + print(f"Deleted: {deleted_record}") diff --git a/quantdb/mysql_app/crud/values_quant.py b/quantdb/mysql_app/crud/values_quant.py new file mode 100644 index 0000000..c40126b --- /dev/null +++ b/quantdb/mysql_app/crud/values_quant.py @@ -0,0 +1,261 @@ +import decimal +import logging +import uuid +from typing import Any, List + +from sqlalchemy import Uuid +from sqlalchemy.orm import Session, class_mapper + +from quantdb.client import get_session +from quantdb.ingest_tabular.models import ( + DescriptorsInst, + DescriptorsQuant, + ObjDescInst, + ObjDescQuant, + Objects, + ValuesInst, + ValuesQuant, +) + +logger = logging.getLogger(__name__) +session = get_session() + + +def model_to_dict(instance) -> None | dict[str, Any]: + """ + Convert a SQLAlchemy model instance to a dictionary. + """ + if not instance: + return None + + # Get the class mapper + mapper = class_mapper(instance.__class__) # type: ignore + + # Extract column names and their values + columns = [column.key for column in mapper.columns] + instance_dict = {column: getattr(instance, column) for column in columns} # type: ignore + + return instance_dict + + +def create_value_quant( + db: Session, + value: decimal.Decimal, + object: str | uuid.UUID, + desc_quant: int | str | DescriptorsQuant, + desc_inst: int | str | DescriptorsInst, + value_blob: None | dict[str, Any] = None, + instance: None | int = None, + orig_value: None | str = None, + orig_units: None | str = None, +) -> ValuesQuant: + """ + Creates a new value record in the database. + + Parameters + ---------- + db : Session + The database session. + value : decimal.Decimal + The numeric value associated with the entry. + object : uuid.UUID + The UUID of the related object. + desc_inst : int, optional + The foreign key referencing `descriptors_inst.id` (default is None). + desc_quant : int + The foreign key referencing `descriptors_quant.id`. + value_blob : dict, optional + Additional value data as a JSONB object (default is None). + instance : int, optional + The foreign key referencing `values_inst.id` (default is None). + orig_value : str, optional + The original value as a string (default is None). + orig_units : str, optional + The original units of the value (default is None). + + Returns + ------- + ValuesQuant + The newly created ValuesQuant object. + """ + # Check if the object exists, if not create it + logger.debug("Checking if object exists in the database.") + object_record = db.query(Objects).filter(Objects.id == object).first() + if not object_record: + logger.info(f"Object with id {object} not found. Creating new object.") + object_record = Objects(id=object) + db.add(object_record) + db.commit() + db.refresh(object_record) + logger.info(f"Created new object with id {object_record.id}") + + if desc_inst is None: + logger.debug("desc_inst not provided. Attempting to find matching DescriptorsInst.") + # Propagate DescriptorsInst if desc_inst was not given + desc_inst_record = db.query(DescriptorsInst).filter(DescriptorsInst.object == object).first() + if desc_inst_record: + desc_inst = desc_inst_record.id + logger.info(f"Found matching DescriptorsInst with id {desc_inst}") + else: + logger.error("desc_inst is required if no matching DescriptorsInst found for the given object.") + raise ValueError("desc_inst is required if no matching DescriptorsInst found for the given object.") + + logger.debug("Creating new ValuesQuant record.") + new_value_quant = ValuesQuant( + value=value, + object=object, + desc_inst=desc_inst, + desc_quant=desc_quant, + value_blob=value_blob, + instance=instance, + orig_value=orig_value, + orig_units=orig_units, + ) + db.add(new_value_quant) + db.commit() + db.refresh(new_value_quant) + logger.info(f"Created new ValuesQuant record with id {new_value_quant.id}") + return new_value_quant + + +def get_value_quant_by_id(db: Session, value_quant_id: int): + """ + Retrieves a value record by its ID. + + Parameters + ---------- + db : Session + The database session. + value_quant_id : int + The ID of the value to retrieve. + + Returns + ------- + ValuesQuant or None + The ValuesQuant object if found, otherwise None. + """ + return db.query(ValuesQuant).filter(ValuesQuant.id == value_quant_id).first() + + +def get_all_value_quants(db: Session): + """ + Retrieves all value records. + + Parameters + ---------- + db : Session + The database session. + + Returns + ------- + list of ValuesQuant + A list of all ValuesQuant objects. + """ + return db.query(ValuesQuant).all() + + +def update_value_quant( + db: Session, + value_quant_id: int, + value: decimal.Decimal = None, + value_blob: dict = None, + instance: int = None, + orig_value: str = None, + orig_units: str = None, +): + """ + Updates an existing value record. + + Parameters + ---------- + db : Session + The database session. + value_quant_id : int + The ID of the value to update. + value : decimal.Decimal, optional + The updated numeric value (default is None). + value_blob : dict, optional + The updated additional value data as a JSONB object (default is None). + instance : int, optional + The updated foreign key referencing `values_inst.id` (default is None). + orig_value : str, optional + The updated original value as a string (default is None). + orig_units : str, optional + The updated original units of the value (default is None). + + Returns + ------- + ValuesQuant or None + The updated ValuesQuant object if found, otherwise None. + """ + value_quant = get_value_quant_by_id(db, value_quant_id) + if value_quant: + if value is not None: + value_quant.value = value + if value_blob is not None: + value_quant.value_blob = value_blob + if instance is not None: + value_quant.instance = instance + if orig_value is not None: + value_quant.orig_value = orig_value + if orig_units is not None: + value_quant.orig_units = orig_units + db.commit() + db.refresh(value_quant) + return value_quant + + +def delete_value_quant(db: Session, value_quant_id: int): + """ + Deletes a value record. + + Parameters + ---------- + db : Session + The database session. + value_quant_id : int + The ID of the value to delete. + + Returns + ------- + bool + True if the value was deleted, False otherwise. + """ + value_quant = get_value_quant_by_id(db, value_quant_id) + if value_quant: + db.delete(value_quant) + db.commit() + return True + return False + + +if __name__ == "__main__": + # Create a new value record + new_value_quant = create_value_quant( + db=session, + value=decimal.Decimal("123.45"), + object=uuid.UUID("38215e04-e8ab-4a55-8291-46839f96ed1b"), + desc_inst=15, # Ensure this is a valid foreign key reference + desc_quant=2, # Ensure this is a valid foreign key reference + value_blob={"additional_info": "some extra data"}, + orig_value="123.45", + orig_units="meters", + ) + + # Get a value record by ID + # value_quant = get_value_quant_by_id(session, 1) + # print(model_to_dict(value_quant)) + + # Get all value records + # all_value_quants = get_all_value_quants(db) + + # # Update a value record + # updated_value_quant = update_value_quant( + # db=db, + # value_quant_id=1, + # value=456.78, + # value_blob={"additional_info": "updated extra data"} + # ) + + # # Delete a value record + # was_deleted = delete_value_quant(db, 1) diff --git a/quantdb/mysql_app/database.py b/quantdb/mysql_app/database.py new file mode 100644 index 0000000..27d51bd --- /dev/null +++ b/quantdb/mysql_app/database.py @@ -0,0 +1,17 @@ +from __future__ import annotations + +from typing import Any + +from sqlalchemy import create_engine +from sqlalchemy.ext.declarative import declarative_base +from sqlalchemy.orm import sessionmaker + +from quantdb.config import Settings + +# TODO: get new setting env setup first +SQLALCHEMY_DATABASE_URL = Settings().SQLALCHEMY_DATABASE_URI + +engine = create_engine(SQLALCHEMY_DATABASE_URL) +SessionLocal = sessionmaker(autocommit=False, autoflush=False, bind=engine) + +Base: Any = declarative_base() diff --git a/quantdb/router.py b/quantdb/router.py new file mode 100644 index 0000000..4ef2147 --- /dev/null +++ b/quantdb/router.py @@ -0,0 +1,27 @@ +from typing import Literal + +import uvicorn +from fastapi import FastAPI +from fastapi.middleware.wsgi import WSGIMiddleware + +from quantdb.api_server import app as quantdb_flask_app + +app = FastAPI() +app.mount("/quantdb", WSGIMiddleware(quantdb_flask_app)) + + +# Root URL +@app.get("/") +def index() -> Literal["Hello"]: + return "Hello" + + +# Using FastAPI instance +@app.get("/url-list") +def get_all_urls(): + url_list = [{"path": route.path, "name": route.name} for route in app.routes] + return url_list + + +if __name__ == "__main__": + uvicorn.run("router:app", host="localhost", port=8000, reload=True) diff --git a/quantdb/source_map/morphology.csv b/quantdb/source_map/morphology.csv new file mode 100644 index 0000000..9897c7a --- /dev/null +++ b/quantdb/source_map/morphology.csv @@ -0,0 +1 @@ +n_b, 'number of bars: 100000', 'desc' \ No newline at end of file diff --git a/quantdb/utils.py b/quantdb/utils.py index 169a5c1..7619e64 100644 --- a/quantdb/utils.py +++ b/quantdb/utils.py @@ -1,6 +1,6 @@ +import logging import os import sys -import logging from datetime import datetime @@ -12,46 +12,39 @@ def makeSimpleLogger(name, level=logging.INFO): logger.setLevel(level) ch = logging.StreamHandler() # FileHander goes to disk - fmt = ('[%(asctime)s] - %(levelname)8s - ' - '%(name)14s - ' - '%(filename)16s:%(lineno)-4d - ' - '%(message)s') + fmt = "[%(asctime)s] - %(levelname)8s - " "%(name)14s - " "%(filename)16s:%(lineno)-4d - " "%(message)s" formatter = logging.Formatter(fmt) ch.setFormatter(formatter) logger.addHandler(ch) return logger -log = makeSimpleLogger('quantdb') -logd = log.getChild('data') +log = makeSimpleLogger("quantdb") +logd = log.getChild("data") # from pyontutils.utils_fast import setPS1 def setPS1(script__file__): try: - text = 'Running ' + os.path.basename(script__file__) - os.sys.stdout.write('\x1b]2;{}\x07\n'.format(text)) + text = "Running " + os.path.basename(script__file__) + os.sys.stdout.write("\x1b]2;{}\x07\n".format(text)) except AttributeError as e: log.exception(e) def dbUri(dbuser, host, port, database): - if hasattr(sys, 'pypy_version_info'): - dialect = 'psycopg2cffi' + if hasattr(sys, "pypy_version_info"): + dialect = "psycopg2cffi" else: - dialect = 'psycopg2' - return f'postgresql+{dialect}://{dbuser}@{host}:{port}/{database}' + dialect = "psycopg2" + return f"postgresql+{dialect}://{dbuser}@{host}:{port}/{database}" # from pyontutils.utils_fast import isoformat -def isoformat(datetime_instance, timespec='auto'): +def isoformat(datetime_instance, timespec="auto"): kwargs = {} if isinstance(datetime_instance, datetime): # don't pass timespec if type is not date not datetime - kwargs['timespec'] = timespec - - return (datetime_instance - .isoformat(**kwargs) - .replace('.', ',') - .replace('+00:00', 'Z')) + kwargs["timespec"] = timespec + return datetime_instance.isoformat(**kwargs).replace(".", ",").replace("+00:00", "Z") diff --git a/sql/postgres.sql b/sql/postgres.sql index dbbe6ce..f556ff3 100644 --- a/sql/postgres.sql +++ b/sql/postgres.sql @@ -35,4 +35,3 @@ ALTER ROLE "quantdb-test-admin" SET search_path = quantdb, public; ALTER ROLE "quantdb-test-user" SET search_path = quantdb, public; ALTER ROLE "quantdb-admin" SET search_path = quantdb, public; ALTER ROLE "quantdb-user" SET search_path = quantdb, public; - diff --git a/sql/tables.sql b/sql/tables.sql index c8a1e6c..16eef0e 100644 --- a/sql/tables.sql +++ b/sql/tables.sql @@ -478,7 +478,7 @@ CREATE TYPE prov_type AS ENUM ( ); create table provenance( --- +-- id integer GENERATED BY DEFAULT AS IDENTITY PRIMARY KEY, type prov_type, -- this control the interpretation of the field source field_name text, -- XXX no longer has meaning since we are using obj_desc_quant diff --git a/test/test_api.py b/test/test_api.py index 0453fa1..669cee2 100644 --- a/test/test_api.py +++ b/test/test_api.py @@ -1,9 +1,23 @@ import json import pprint + +import pytest +from fastapi import FastAPI +from fastapi.middleware.wsgi import WSGIMiddleware +from fastapi.testclient import TestClient from flask_sqlalchemy import SQLAlchemy + from quantdb.api import make_app from quantdb.utils import log +db = SQLAlchemy() +quantdb_flask_app = make_app(db=db, dev=True) + +# TODO: middleware to mount the flask app for now +app = FastAPI() +app.mount("/quantdb", WSGIMiddleware(quantdb_flask_app)) +client = TestClient(app) + def test(): db = SQLAlchemy() @@ -11,101 +25,82 @@ def test(): client = app.test_client() runner = app.test_cli_runner() - dataset_uuid = 'aa43eda8-b29a-4c25-9840-ecbd57598afc' - some_object = '414886a9-9ec7-447e-b4d8-3ae42fda93b7' # XXX FAKE - actual_package_uuid = '15bcbcd5-b054-40ef-9b5c-6a260d441621' - base = 'http://localhost:8989/api/1/' + dataset_uuid = "aa43eda8-b29a-4c25-9840-ecbd57598afc" + some_object = "414886a9-9ec7-447e-b4d8-3ae42fda93b7" # XXX FAKE + actual_package_uuid = "15bcbcd5-b054-40ef-9b5c-6a260d441621" + base = "http://localhost:8000/quantdb/api/1/" urls = ( - f'{base}values/inst', - f'{base}values/inst?dataset={dataset_uuid}', - f'{base}values/inst?dataset={dataset_uuid}&union-cat-quant=true', - f'{base}values/inst?dataset={dataset_uuid}&aspect=distance&aspect=time', - f'{base}values/inst?dataset={dataset_uuid}&aspect=distance&value-quant-min=0.5', - f'{base}values/inst?desc-inst=nerve-volume', - - f'{base}objects?dataset={dataset_uuid}', - f'{base}objects?dataset={dataset_uuid}&aspect=distance', - f'{base}objects?dataset={dataset_uuid}&aspect=distance&value-quant-min=0.5', # expect nothing - f'{base}objects?dataset={dataset_uuid}&aspect=distance&value-quant-min=0.5&union-cat-quant=true', - - f'{base}objects?dataset={dataset_uuid}&subject=sub-f001', - f'{base}objects?subject=sub-f001', - f'{base}objects?subject=sub-f001&union-cat-quant=true', - f'{base}objects?subject=sub-f001&subject=sub-f002&subject=sub-f003&subject=sub-f004&subject=sub-f005', - f'{base}objects?subject=sub-f001&subject=sub-f002&subject=sub-f003&subject=sub-f004&subject=sub-f005&union-cat-quant=true', - f'{base}objects?subject=sub-f001&desc-cat=none&value-quant-min=0.5&union-cat-quant=true', - f'{base}objects?subject=sub-f001&desc-cat=none&aspect=distance&value-quant-min=0.5&union-cat-quant=true', - f'{base}objects?subject=sub-f001&aspect=distance&value-quant-min=0.5&union-cat-quant=true', - f'{base}objects?aspect=distance&value-quant-min=0.5&union-cat-quant=true', - f'{base}objects?desc-cat=none&aspect=distance&value-quant-min=0.5&union-cat-quant=true', - f'{base}objects?desc-cat=none&aspect=distance&value-quant-min=0.5', - f'{base}objects?aspect=distance&value-quant-min=0.5', - f'{base}objects?aspect=distance&value-quant-min=0.5&source-only=true', - f'{base}objects?desc-inst=nerve-volume&aspect=distance&value-quant-min=0.5&source-only=true', - + f"{base}values/inst", + f"{base}values/inst?dataset={dataset_uuid}", + f"{base}values/inst?dataset={dataset_uuid}&union-cat-quant=true", + f"{base}values/inst?dataset={dataset_uuid}&aspect=distance&aspect=time", + f"{base}values/inst?dataset={dataset_uuid}&aspect=distance&value-quant-min=0.5", + f"{base}values/inst?desc-inst=nerve-volume", + f"{base}objects?dataset={dataset_uuid}", + f"{base}objects?dataset={dataset_uuid}&aspect=distance", + f"{base}objects?dataset={dataset_uuid}&aspect=distance&value-quant-min=0.5", # expect nothing + f"{base}objects?dataset={dataset_uuid}&aspect=distance&value-quant-min=0.5&union-cat-quant=true", + f"{base}objects?dataset={dataset_uuid}&subject=sub-f001", + f"{base}objects?subject=sub-f001", + f"{base}objects?subject=sub-f001&union-cat-quant=true", + f"{base}objects?subject=sub-f001&subject=sub-f002&subject=sub-f003&subject=sub-f004&subject=sub-f005", + f"{base}objects?subject=sub-f001&subject=sub-f002&subject=sub-f003&subject=sub-f004&subject=sub-f005&union-cat-quant=true", + f"{base}objects?subject=sub-f001&desc-cat=none&value-quant-min=0.5&union-cat-quant=true", + f"{base}objects?subject=sub-f001&desc-cat=none&aspect=distance&value-quant-min=0.5&union-cat-quant=true", + f"{base}objects?subject=sub-f001&aspect=distance&value-quant-min=0.5&union-cat-quant=true", + f"{base}objects?aspect=distance&value-quant-min=0.5&union-cat-quant=true", + f"{base}objects?desc-cat=none&aspect=distance&value-quant-min=0.5&union-cat-quant=true", + f"{base}objects?desc-cat=none&aspect=distance&value-quant-min=0.5", + f"{base}objects?aspect=distance&value-quant-min=0.5", + f"{base}objects?aspect=distance&value-quant-min=0.5&source-only=true", + f"{base}objects?desc-inst=nerve-volume&aspect=distance&value-quant-min=0.5&source-only=true", # values-quant - f'{base}values/quant?dataset={dataset_uuid}&aspect=distance', - f'{base}values/quant?object={actual_package_uuid}&aspect=distance', - f'{base}values/quant?aspect=distance', - f'{base}values/quant?aspect=distance-via-reva-ft-sample-id-normalized-v1', - f'{base}values/quant?aspect=distance-via-reva-ft-sample-id-normalized-v1&agg-type=instance', - f'{base}values/quant?aspect=distance-via-reva-ft-sample-id-normalized-v1&value-quant-min=0.4&value-quant-max=0.7', - + f"{base}values/quant?dataset={dataset_uuid}&aspect=distance", + f"{base}values/quant?object={actual_package_uuid}&aspect=distance", + f"{base}values/quant?aspect=distance", + f"{base}values/quant?aspect=distance-via-reva-ft-sample-id-normalized-v1", + f"{base}values/quant?aspect=distance-via-reva-ft-sample-id-normalized-v1&agg-type=instance", + f"{base}values/quant?aspect=distance-via-reva-ft-sample-id-normalized-v1&value-quant-min=0.4&value-quant-max=0.7", # values-cat - f'{base}values/cat?object={actual_package_uuid}', - f'{base}values/cat?object={actual_package_uuid}&union-cat-quant=true', # shouldn't need it in this case - - f'{base}values/cat-quant?object={actual_package_uuid}', - f'{base}values/cat-quant?object={actual_package_uuid}&union-cat-quant=true', - + f"{base}values/cat?object={actual_package_uuid}", + f"{base}values/cat?object={actual_package_uuid}&union-cat-quant=true", # shouldn't need it in this case + f"{base}values/cat-quant?object={actual_package_uuid}", + f"{base}values/cat-quant?object={actual_package_uuid}&union-cat-quant=true", # values-cat-quant - f'{base}values?dataset={dataset_uuid}&aspect=distance&value-quant-min=0.5', - f'{base}values?dataset={dataset_uuid}&aspect=distance&value-quant-min=0.5&union-cat-quant=true', - - f'{base}values?object={actual_package_uuid}', - f'{base}values?object={actual_package_uuid}&union-cat-quant=true', - - f'{base}values/inst?object={actual_package_uuid}', - f'{base}values/inst?object={actual_package_uuid}&union-cat-quant=true', - + f"{base}values?dataset={dataset_uuid}&aspect=distance&value-quant-min=0.5", + f"{base}values?dataset={dataset_uuid}&aspect=distance&value-quant-min=0.5&union-cat-quant=true", + f"{base}values?object={actual_package_uuid}", + f"{base}values?object={actual_package_uuid}&union-cat-quant=true", + f"{base}values/inst?object={actual_package_uuid}", + f"{base}values/inst?object={actual_package_uuid}&union-cat-quant=true", # prov - f'{base}values/inst?prov=true', - - f'{base}values/quant?aspect=distance&prov=true', - - f'{base}values/cat?object={actual_package_uuid}', - f'{base}values/cat?object={actual_package_uuid}&prov=true', # FIXME somehow this has a 3x increase in records, and non-distinct - - f'{base}values/cat-quant?object={actual_package_uuid}&union-cat-quant=true', - f'{base}values/cat-quant?object={actual_package_uuid}&union-cat-quant=true&prov=true', - - f'{base}values/cat-quant', - f'{base}values/cat-quant?prov=true', - - f'{base}values/cat-quant?union-cat-quant=true', - f'{base}values/cat-quant?union-cat-quant=true&prov=true', - + f"{base}values/inst?prov=true", + f"{base}values/quant?aspect=distance&prov=true", + f"{base}values/cat?object={actual_package_uuid}", + f"{base}values/cat?object={actual_package_uuid}&prov=true", # FIXME somehow this has a 3x increase in records, and non-distinct + f"{base}values/cat-quant?object={actual_package_uuid}&union-cat-quant=true", + f"{base}values/cat-quant?object={actual_package_uuid}&union-cat-quant=true&prov=true", + f"{base}values/cat-quant", + f"{base}values/cat-quant?prov=true", + f"{base}values/cat-quant?union-cat-quant=true", + f"{base}values/cat-quant?union-cat-quant=true&prov=true", # desc - f'{base}desc/inst', - f'{base}desc/cat', - f'{base}desc/quant', - - f'{base}desc/inst?include-unused=true', - f'{base}desc/cat?include-unused=true', - f'{base}desc/quant?include-unused=true', - + f"{base}desc/inst", + f"{base}desc/cat", + f"{base}desc/quant", + f"{base}desc/inst?include-unused=true", + f"{base}desc/cat?include-unused=true", + f"{base}desc/quant?include-unused=true", # descriptor values - f'{base}terms', - f'{base}aspects', - f'{base}units', - - f'{base}terms?include-unused=true', - f'{base}aspects?include-unused=true', - f'{base}units?include-unused=true', + f"{base}terms", + f"{base}aspects", + f"{base}units", + f"{base}terms?include-unused=true", + f"{base}aspects?include-unused=true", + f"{base}units?include-unused=true", # TODO maybe shapes here as well? - ) - #log.setLevel(9) + # log.setLevel(9) resps = [] for url in urls: log.debug(url) @@ -117,8 +112,89 @@ def test(): pprint.pprint(resps, width=120) # (i := 6, resps[i], urls[i]) - #q = client.get(f'{base}values/quant?dataset={dataset_uuid}&aspect=distance&return-query=true').data.decode() - #q = client.get(f'{base}values/cat?object={actual_package_uuid}&prov=true&return-query=true').data.decode() - #print(q) + # q = client.get(f'{base}values/quant?dataset={dataset_uuid}&aspect=distance&return-query=true').data.decode() + # q = client.get(f'{base}values/cat?object={actual_package_uuid}&prov=true&return-query=true').data.decode() + # print(q) breakpoint() + +@pytest.mark.parametrize( + "url", + [ + "http://localhost:8000/quantdb/api/1/values/inst", + "http://localhost:8000/quantdb/api/1/values/inst?dataset=aa43eda8-b29a-4c25-9840-ecbd57598afc", + "http://localhost:8000/quantdb/api/1/values/inst?dataset=aa43eda8-b29a-4c25-9840-ecbd57598afc&union-cat-quant=true", + "http://localhost:8000/quantdb/api/1/values/inst?dataset=aa43eda8-b29a-4c25-9840-ecbd57598afc&aspect=distance&aspect=time", + "http://localhost:8000/quantdb/api/1/values/inst?dataset=aa43eda8-b29a-4c25-9840-ecbd57598afc&aspect=distance&value-quant-min=0.5", + "http://localhost:8000/quantdb/api/1/values/inst?desc-inst=nerve-volume", + "http://localhost:8000/quantdb/api/1/objects?dataset=aa43eda8-b29a-4c25-9840-ecbd57598afc", + "http://localhost:8000/quantdb/api/1/objects?dataset=aa43eda8-b29a-4c25-9840-ecbd57598afc&aspect=distance", + "http://localhost:8000/quantdb/api/1/objects?dataset=aa43eda8-b29a-4c25-9840-ecbd57598afc&aspect=distance&value-quant-min=0.5", + "http://localhost:8000/quantdb/api/1/objects?dataset=aa43eda8-b29a-4c25-9840-ecbd57598afc&aspect=distance&value-quant-min=0.5&union-cat-quant=true", + "http://localhost:8000/quantdb/api/1/objects?dataset=aa43eda8-b29a-4c25-9840-ecbd57598afc&subject=sub-f001", + "http://localhost:8000/quantdb/api/1/objects?subject=sub-f001", + "http://localhost:8000/quantdb/api/1/objects?subject=sub-f001&union-cat-quant=true", + "http://localhost:8000/quantdb/api/1/objects?subject=sub-f001&subject=sub-f002&subject=sub-f003&subject=sub-f004&subject=sub-f005", + "http://localhost:8000/quantdb/api/1/objects?subject=sub-f001&subject=sub-f002&subject=sub-f003&subject=sub-f004&subject=sub-f005&union-cat-quant=true", + "http://localhost:8000/quantdb/api/1/objects?subject=sub-f001&desc-cat=none&value-quant-min=0.5&union-cat-quant=true", + "http://localhost:8000/quantdb/api/1/objects?subject=sub-f001&desc-cat=none&aspect=distance&value-quant-min=0.5&union-cat-quant=true", + "http://localhost:8000/quantdb/api/1/objects?subject=sub-f001&aspect=distance&value-quant-min=0.5&union-cat-quant=true", + "http://localhost:8000/quantdb/api/1/objects?aspect=distance&value-quant-min=0.5&union-cat-quant=true", + "http://localhost:8000/quantdb/api/1/objects?desc-cat=none&aspect=distance&value-quant-min=0.5&union-cat-quant=true", + "http://localhost:8000/quantdb/api/1/objects?desc-cat=none&aspect=distance&value-quant-min=0.5", + "http://localhost:8000/quantdb/api/1/objects?aspect=distance&value-quant-min=0.5", + "http://localhost:8000/quantdb/api/1/objects?aspect=distance&value-quant-min=0.5&source-only=true", + "http://localhost:8000/quantdb/api/1/objects?desc-inst=nerve-volume&aspect=distance&value-quant-min=0.5&source-only=true", + "http://localhost:8000/quantdb/api/1/values/quant?dataset=aa43eda8-b29a-4c25-9840-ecbd57598afc&aspect=distance", + "http://localhost:8000/quantdb/api/1/values/quant?object=15bcbcd5-b054-40ef-9b5c-6a260d441621&aspect=distance", + "http://localhost:8000/quantdb/api/1/values/quant?aspect=distance", + "http://localhost:8000/quantdb/api/1/values/quant?aspect=distance-via-reva-ft-sample-id-normalized-v1", + "http://localhost:8000/quantdb/api/1/values/quant?aspect=distance-via-reva-ft-sample-id-normalized-v1&agg-type=instance", + "http://localhost:8000/quantdb/api/1/values/quant?aspect=distance-via-reva-ft-sample-id-normalized-v1&value-quant-min=0.4&value-quant-max=0.7", + "http://localhost:8000/quantdb/api/1/values/cat?object=15bcbcd5-b054-40ef-9b5c-6a260d441621", + "http://localhost:8000/quantdb/api/1/values/cat?object=15bcbcd5-b054-40ef-9b5c-6a260d441621&union-cat-quant=true", + "http://localhost:8000/quantdb/api/1/values/cat-quant?object=15bcbcd5-b054-40ef-9b5c-6a260d441621", + "http://localhost:8000/quantdb/api/1/values/cat-quant?object=15bcbcd5-b054-40ef-9b5c-6a260d441621&union-cat-quant=true", + "http://localhost:8000/quantdb/api/1/values?dataset=aa43eda8-b29a-4c25-9840-ecbd57598afc&aspect=distance&value-quant-min=0.5", + "http://localhost:8000/quantdb/api/1/values?dataset=aa43eda8-b29a-4c25-9840-ecbd57598afc&aspect=distance&value-quant-min=0.5&union-cat-quant=true", + "http://localhost:8000/quantdb/api/1/values?object=15bcbcd5-b054-40ef-9b5c-6a260d441621", + "http://localhost:8000/quantdb/api/1/values?object=15bcbcd5-b054-40ef-9b5c-6a260d441621&union-cat-quant=true", + "http://localhost:8000/quantdb/api/1/values/inst?object=15bcbcd5-b054-40ef-9b5c-6a260d441621", + "http://localhost:8000/quantdb/api/1/values/inst?object=15bcbcd5-b054-40ef-9b5c-6a260d441621&union-cat-quant=true", + "http://localhost:8000/quantdb/api/1/values/inst?prov=true", + "http://localhost:8000/quantdb/api/1/values/quant?aspect=distance&prov=true", + "http://localhost:8000/quantdb/api/1/values/cat?object=15bcbcd5-b054-40ef-9b5c-6a260d441621", + "http://localhost:8000/quantdb/api/1/values/cat?object=15bcbcd5-b054-40ef-9b5c-6a260d441621&prov=true", + "http://localhost:8000/quantdb/api/1/values/cat-quant?object=15bcbcd5-b054-40ef-9b5c-6a260d441621&union-cat-quant=true", + "http://localhost:8000/quantdb/api/1/values/cat-quant?object=15bcbcd5-b054-40ef-9b5c-6a260d441621&union-cat-quant=true&prov=true", + "http://localhost:8000/quantdb/api/1/values/cat-quant", + "http://localhost:8000/quantdb/api/1/values/cat-quant?prov=true", + "http://localhost:8000/quantdb/api/1/values/cat-quant?union-cat-quant=true", + "http://localhost:8000/quantdb/api/1/values/cat-quant?union-cat-quant=true&prov=true", + "http://localhost:8000/quantdb/api/1/desc/inst", + "http://localhost:8000/quantdb/api/1/desc/cat", + "http://localhost:8000/quantdb/api/1/desc/quant", + "http://localhost:8000/quantdb/api/1/desc/inst?include-unused=true", + "http://localhost:8000/quantdb/api/1/desc/cat?include-unused=true", + "http://localhost:8000/quantdb/api/1/desc/quant?include-unused=true", + "http://localhost:8000/quantdb/api/1/terms", + "http://localhost:8000/quantdb/api/1/aspects", + "http://localhost:8000/quantdb/api/1/units", + "http://localhost:8000/quantdb/api/1/terms?include-unused=true", + "http://localhost:8000/quantdb/api/1/aspects?include-unused=true", + "http://localhost:8000/quantdb/api/1/units?include-unused=true", + ], +) +def test_urls(url: str) -> None: + """Test all urls if they return a valid response. + + Parameters + ---------- + url : str + complete url to test + """ + resp = client.get(url) + assert resp.status_code < 400 + data = resp.json() + assert isinstance(data, dict) + # pprint.pprint(data, width=120)