diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
deleted file mode 100644
index 46d590b..0000000
--- a/.github/workflows/build.yml
+++ /dev/null
@@ -1,37 +0,0 @@
-# Builds and runs pytest on ubuntu-latest
-# Tests python versions >=3.6
-name: build
-
-on:
- push:
- branches: [ main ]
- pull_request:
- branches: [ main ]
-
- workflow_dispatch:
-
-jobs:
- # https://github.com/actions/setup-python
- test-python3-ubuntu-latest:
- name: test py${{ matrix.python-version }} on linux
- runs-on: ubuntu-latest
- strategy:
- fail-fast: false
- matrix:
- python-version: ['3.8', '3.9', '3.10', '3.11']
- env:
- PYTHON: ${{ matrix.python-version }}
- OS: ubuntu
-
- steps:
- - uses: actions/checkout@v3
-
- - name: set up python
- uses: actions/setup-python@v3
- with:
- python-version: ${{ matrix.python-version }}
-
- - name: make test
- run: |
- pip install poetry
- make test
diff --git a/.github/workflows/documentation.yaml b/.github/workflows/documentation.yaml
new file mode 100644
index 0000000..e1a3f72
--- /dev/null
+++ b/.github/workflows/documentation.yaml
@@ -0,0 +1,39 @@
+name: Build and Deploy Docs to GitHub Pages
+on:
+ push:
+ branches:
+ - main
+
+env:
+ GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+jobs:
+ build-docs:
+ runs-on: ubuntu-latest
+ steps:
+ - name: Checkout
+ uses: actions/checkout@main
+ with:
+ fetch-depth: 0 # otherwise, you will failed to push refs to dest repo
+
+ - name: Set up Python 3
+ uses: actions/setup-python@main
+ with:
+ python-version: "3.11"
+
+ - name: Install Poetry
+ uses: snok/install-poetry@main
+
+ - name: Install Dependencies
+ run: poetry install
+
+ - name: Build Documentation
+ run: make docs
+
+ - name: Deploy to gh-pages
+ uses: JamesIves/github-pages-deploy-action@v4
+ with:
+ folder: site
+ target-folder: docs
+ clean: true
+
\ No newline at end of file
diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml
deleted file mode 100644
index 2a20504..0000000
--- a/.github/workflows/documentation.yml
+++ /dev/null
@@ -1,17 +0,0 @@
-name: deploy documentation
-on:
- push:
- branches:
- - main
-jobs:
- deploy:
- runs-on: ubuntu-latest
- steps:
- - uses: actions/checkout@v2
- - uses: actions/setup-python@v2
- with:
- python-version: 3.x
- - run: pip install mkdocs mkdocs-material
- - run: mkdocs gh-deploy --force
-env:
- GH_TOKEN: ${{ secrets.GH_TOKEN }}
diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yaml
similarity index 100%
rename from .github/workflows/publish.yml
rename to .github/workflows/publish.yaml
diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
new file mode 100644
index 0000000..554dcfb
--- /dev/null
+++ b/.github/workflows/test.yaml
@@ -0,0 +1,49 @@
+# Builds and runs pytest on ubuntu-latest
+# Tests python versions >=3.8
+name: Test Koza
+
+on:
+ push:
+ branches: [ main ]
+ pull_request:
+ workflow_dispatch:
+
+jobs:
+ # https://github.com/actions/setup-python
+ test-python3-ubuntu-latest:
+ name: test py${{ matrix.python-version }} on linux
+ runs-on: ubuntu-latest
+ strategy:
+ fail-fast: false
+ matrix:
+ python-version: ['3.8', '3.9', '3.10', '3.11']
+ env:
+ PYTHON: ${{ matrix.python-version }}
+ OS: ubuntu
+
+ steps:
+ - name: Checkout
+ uses: actions/checkout@v3
+
+ - name: Set up Python ${{ matrix.python-version }}
+ uses: actions/setup-python@v4
+ with:
+ python-version: ${{ matrix.python-version }}
+
+ #----------------------------------------------
+ # install & configure poetry
+ #----------------------------------------------
+ - name: Install Poetry
+ uses: snok/install-poetry@v1
+
+ #----------------------------------------------
+ # install your root project, if required
+ #----------------------------------------------
+ - name: Install library
+ run: poetry install --with dev --no-interaction
+
+ #----------------------------------------------
+ # run pytest
+ #----------------------------------------------
+ - name: Run tests
+ run: poetry run pytest tests
\ No newline at end of file
diff --git a/.gitignore b/.gitignore
index 3bb1fbb..58fee4f 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,6 +1,8 @@
-koza-env/
+# Default output / Generated / Unpacked data files
+output/
tests/resources/source-files/string.tsv*
+
# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
@@ -133,7 +135,3 @@ dmypy.json
# IDE
.idea
-
-# output directories
-output/
-test-output/
diff --git a/Makefile b/Makefile
index 173c7a7..149b179 100644
--- a/Makefile
+++ b/Makefile
@@ -1,4 +1,4 @@
-# Note that you should be in your virtual environment of choice before running make
+# Note that Poetry is required, see https://python-poetry.org/docs/#installation
MAKEFLAGS += --warn-undefined-variables
MAKEFLAGS += --no-builtin-rules
@@ -11,6 +11,7 @@ endif
.DEFAULT_GOAL := all
SHELL := bash
+RUN := poetry run
.PHONY: all
all: install test clean
@@ -24,12 +25,13 @@ build:
poetry build
.PHONY: test
-test: install
- poetry run python -m pytest
+test:
+ $(RUN) pytest tests
.PHONY: docs
-docs: install
- poetry run typer src/koza/main.py utils docs --name koza --output docs/Usage/CLI.md
+docs:
+ $(RUN) typer src/koza/main.py utils docs --name koza --output docs/Usage/CLI.md
+ $(RUN) mkdocs build
.PHONY: clean
clean:
@@ -41,17 +43,10 @@ clean:
.PHONY: lint
lint:
- flake8 --exit-zero --max-line-length 120 koza/ tests/ examples/
- black --check --diff koza tests
- isort --check-only --diff koza tests
+ $(RUN) ruff check --diff --exit-zero src/ tests/ examples/
+ $(RUN) black --check --diff -l 120 src/ tests/ examples/
.PHONY: format
format:
- autoflake \
- --recursive \
- --remove-all-unused-imports \
- --remove-unused-variables \
- --ignore-init-module-imports \
- --in-place koza tests examples
- isort koza tests examples
- black koza tests examples
+ $(RUN) ruff check --fix --exit-zero src/ tests/ examples/
+ $(RUN) black -l 120 src/ tests/ examples/
diff --git a/README.md b/README.md
index f6b9830..e5cb85a 100644
--- a/README.md
+++ b/README.md
@@ -8,9 +8,9 @@
[**Documentation**](https://koza.monarchinitiative.org/ )
-_Disclaimer_: Koza is in beta; we are looking for beta testers
+_Disclaimer_: Koza is in beta - we are looking for testers!
-### Overview
+## Overview
- Transform csv, json, yaml, jsonl, and xml and converting them to a target csv, json, or jsonl format based on your dataclass model.
- Koza also can output data in the [KGX format](https://github.com/biolink/kgx/blob/master/specification/kgx-format.md#kgx-format-as-tsv)
- Write data transforms in semi-declarative Python
@@ -18,13 +18,14 @@ _Disclaimer_: Koza is in beta; we are looking for beta testers
- Create or import mapping files to be used in ingests (eg id mapping, type mappings)
- Create and use translation tables to map between source and target vocabularies
-### Installation
+## Installation
Koza is available on PyPi and can be installed via pip/pipx:
```
[pip|pipx] install koza
```
-### Usage
+## Usage
+
**NOTE: As of version 0.2.0, there is a new method for getting your ingest's `KozaApp` instance. Please see the [updated documentation](https://koza.monarchinitiative.org/Usage/configuring_ingests/#transform-code) for details.**
@@ -61,8 +62,24 @@ koza validate \
Run the example ingest, "string/protein-links-detailed"
```bash
-koza transform --source examples/string/protein-links-detailed.yaml --global-table examples/translation_table.yaml
+koza transform \
+ --source examples/string/protein-links-detailed.yaml \
+ --global-table examples/translation_table.yaml
-koza transform --source examples/string-declarative/protein-links-detailed.yaml --global-table examples/translation_table.yaml
+koza transform \
+ --source examples/string-declarative/protein-links-detailed.yaml \
+ --global-table examples/translation_table.yaml
```
-note: koza expects a directory structure as described in the above example (examples/ingest_name/ingest.yaml)
\ No newline at end of file
+
+**Note**:
+ Koza expects a directory structure as described in the above example
+ with the source config file and transform code in the same directory:
+ ```
+ .
+ ├── ...
+ │ ├── your_source
+ │ │ ├── your_ingest.yaml
+ │ │ └── your_ingest.py
+ │ └── some_translation_table.yaml
+ └── ...
+ ```
\ No newline at end of file
diff --git a/docs/Usage/API.md b/docs/Usage/API.md
new file mode 100644
index 0000000..63a9567
--- /dev/null
+++ b/docs/Usage/API.md
@@ -0,0 +1 @@
+::: src.koza.cli_runner
\ No newline at end of file
diff --git a/docs/Usage/ingests.md b/docs/Usage/ingests.md
index e227d1f..8e3c235 100644
--- a/docs/Usage/ingests.md
+++ b/docs/Usage/ingests.md
@@ -1,131 +1,61 @@
# Ingests
-(For CLI usage, see the [CLI commands](./CLI.md) page.)
+
+(For CLI usage, see the [CLI commands](./CLI.md) page.)
+
!!! tip "Ingest Overview"
Koza is designed to process and transform existing data into a target csv/json/jsonl format.
This process is internally known as an **ingest**. Ingests are defined by:
- - **Source config yaml**: specifies metadata, formats, required columns, etc. for the ingest
+ - **Source config yaml**: Ingest configuration, including:
+ - metadata, formats, required columns, any SSSOM files, etc.
- **Map config yaml**: (Optional) configures creation of mapping dictionary
- **Transform code**: a Python script, with specific transform instructions
-----
-Now, let's say you have some data, and you want to save certain bits of that data,
+Let's say you have some data, and you want to save certain bits of that data,
with maybe some changes or translations along the way.
-
-Let's look at what we'll need to make that ingest:
+Creating this ingest will require three things:
!!! list ""
- ### 1. Source Config File
+ ## 1. Source Config File
This YAML file sets properties for the ingest of a single file type from a within a Source.
- Available properties are listed in Koza's SourceConfig() and PrimarySourceConfig() classes.
-
- ???+ tip "Relative paths are relative to the directory where you execute Koza."
-
- ??? tldr "Example Source Config YAML"
-
- ```yaml
- name: 'name-of-ingest'
-
- format: 'json' # Options are json or csv, default is csv
-
- # Sets file compression, options are gzip and none, default is none
- compression: 'gzip'
-
- # list of files to be ingested
- files:
- - './data/really-cool-data-1.json.gz'
- - './data/really-cool-data-2.json.gz'
-
- # The dataset description
- metadata:
- description: 'SomethingBase: A Website With Some Data'
- rights: 'https://somethingbase.org/rights.html'
-
- # The local and global tables can be specified either in the command line or the config
- global_table: './path_to/translation_table.yaml'
- local_table: './somethingbase/something-translation.yaml'
-
- # in addition to specifying yaml files, it's also possible to define the tables inline
- # local_table:
- # "around here somewhere": "RO:9999999"
-
-
- # in a JSON ingest, this will be the path to the array to be iterated over as the input collection
- json_path:
- - 'data'
-
- # Ordered list of columns for CSV files, data type can be specified as float, int or str
- columns:
- - 'protein1'
- - 'protein2'
- - 'combined_score' : 'int'
-
- # Specify a delimiter for CSV files, default is a comma
- delimiter: '\t'
-
- # Optional delimiter for header row
- header_delimiter: '|'
-
- # Optional, int | 'infer' | 'none', Default = 'infer'
- # The index (0 based) in which the header appears in the file.
- #
- # If header is set to 'infer' the headers will be set to the first
- # line that is not blank or commented with a hash.
- #
- # If header is set to 'none' then the columns field will be used,
- # or raise a ValueError if columns are not supplied
- header: 0
-
- # Boolean to skip blank lines, default is true
- skip_blank_lines: True
-
- # include a map file
- depends_on:
- - './examples/maps/alliance-gene.yaml'
-
- # The filter DSL allows including or excluding rows based on filter blocks
- filters:
- - inclusion: 'include' # 'include' to include rows matching, 'exclude' to exclude rows that match
- column: 'combined_score'
- # filter_code (with 'in' expecting a list of values)
- filter_code: 'lt' # options: 'gt', 'ge', 'lt', 'le', 'eq', 'ne', 'in'
- value: 700
- - inclusion: 'exclude'
- column: 'protein1'
- filter_code: 'in' # 'in' expects the value to be a list and checks that the column value is matched within the list
- value:
- - 'ABC1'
- - 'XYZ4'
-
- # node and edge categories are required to avoid empty KGX files, the order here isn't important
- node_properties:
- - 'id'
- - 'category'
- - 'provided_by'
-
- edge_properties:
- - 'id'
- - 'subject'
- - 'predicate'
- - ...
-
- #In 'flat' mode, the transform operates on a single row and looping doesn't need to be specified
- #In 'loop' mode, the transform code is executed only once and so the loop code that iterates over rows must be contained within the transform code
- # The default is 'flat'
- transform_mode: 'loop'
-
- # Python code to run for ingest. Default is the same file name as the source_file yaml, but with a .py extension
- # You probably don't need to set this property
- transform_code: 'name-of-ingest.py'
- ```
-
- **Composing Configuration from Multiple Yaml Files**
+ ???+ tip "Paths are relative to the directory from which you execute Koza."
+
+ | __Required properties__ | |
+ | --- | --- |
+ | `name` | Name of the source |
+ | `files` | List of files to process |
+ |||
+ | __Optional properties__ | |
+ | `file_archive` | Path to a file archive containing the files to process |
+ | `format` | Format of the data file(s) (CSV or JSON) |
+ | `sssom_config` | Configures usage of SSSOM mapping files |
+ | `depends_on` | List of map config files to use |
+ | `metadata` | Metadata for the source |
+ | `transform_code` | Path to a python file to transform the data |
+ | `transform_mode` | How to process the transform file |
+ | `global_table` | Path to a global translation table file |
+ | `local_table` | Path to a local translation table file |
+ | `filters` | List of filters to apply |
+ | `json_path` | Path within JSON object containing data to process |
+ | `required_properties` | List of properties that must be present in output (JSON only) |
+ |||
+ | __Optional CSV Specific Properties__ | |
+ | `columns` | List of columns to include in output (CSV only) |
+ | `delimiter` | Delimiter for csv files |
+ | `header_delimiter` | Delimiter for header in csv files |
+ | `header` | Header row index for csv files |
+ | `comment_char` | Comment character for csv files |
+ | `skip_blank_lines` | Skip blank lines in csv files |
+
+
+ ### Composing Configuration from Multiple Yaml Files
The Koza yaml loader supports importing/including other yaml files with an `!include` tag.
@@ -139,82 +69,112 @@ Let's look at what we'll need to make that ingest:
Then in any ingests you wish to use these columns, you can simply `!include` them:
```yaml
- metadata: !include './path/to/metadata.yaml'
columns: !include './path/to/standard-columns.yaml'
```
- ### 2. Map File(s)
+!!! list ""
+ ## 2. Mapping and Additional Data
+
+ Mapping with Koza can be done in two ways:
- This YAML file sets properties for creating a mapping dictionary that an ingest may depend on.
+ - Automated mapping with SSSOM files
+ - Manual mapping with a map config yaml
- Available properties are listed in Koza's SourceConfig() and MapFileConfig() classes.
+ ### SSSOM Mapping
- ??? tldr "Example Map Config YAML"
+ Koza supports mapping with SSSOM files (Semantic Similarity of Source and Target Ontology Mappings).
+ Simply add the path to the SSSOM file to your source config, the desired target prefixes,
+ and any prefixes you want to use to filter the SSSOM file.
+ Koza will automatically create a mapping lookup table which will automatically
+ attempt to map any values in the source file to an ID with the target prefix.
- ```yaml
- name: 'genepage-2-gene'
- metadata:
- description: 'Mapping file provided by Xenbase that maps from GENEPAGE to GENE'
+ ```yaml
+ sssom_config:
+ sssom_file: './path/to/your_mapping_file.sssom.tsv'
+ filter_prefixes:
+ - 'SOMEPREFIX'
+ - 'OTHERPREFIX'
+ target_prefixes:
+ - 'OTHERPREFIX'
+ use_match:
+ - 'exact'
+ ```
- delimiter: '\t'
+ **Note:** Currently, only the `exact` match type is supported (`narrow` and `broad` match types will be added in the future).
- files:
- - './examples/data/XenbaseGenepageToGeneIdMapping.txt'
+ ### Manual Mapping / Additional Data
- columns:
- - 'gene_page_id'
- - 'gene_page_label'
- - 'tropicalis_id'
- - 'tropicalis_label'
- - 'laevis_l_id'
- - 'laevis_l_label'
- - 'laevis_s_id'
- - 'laevis_s_label'
+ The map config yaml allows you to include data from other sources in your ingests,
+ which may have different columns or formats.
+
+ If you don't have an SSSOM file, or you want to manually map some values, you can use a map config yaml.
+ You can then add this map to your source config yaml in the `depends_on` property.
+
+ Koza will then create a nested dictionary with the specified key and values.
+ For example, the following map config yaml maps values from the `STRING` column to the `entrez` and `NCBI taxid` columns.
- # The column to save as a key in the map dictionary
- key: 'gene_page_id'
+ ```yaml
+ # koza/examples/maps/entrez-2-string.yaml
+ name: ...
+ files: ...
- # The column(s) to save as nested keys under 'key'
- values:
- - 'tropicalis_id'
- - 'laevis_l_id'
- - 'laevis_s_id'
- ```
+ columns:
+ - 'NCBI taxid'
+ - 'entrez'
+ - 'STRING'
- This example map yields a map dictionary:
+ key: 'STRING'
- ```json
- {
- gene_page_id: {
- tropicalis_id: somevalue1,
- laevis_l_id: somevalue2,
- laevis_s_id: somevalue3
- }
- }
- ```
-
- ### 3. Transform Code
+ values:
+ - 'entrez'
+ - 'NCBI taxid'
+ ```
+
+
+ The mapping dict will be available in your transform script from the `koza_app` object (see the Transform Code section below).
+
+
+!!! list ""
+ ## 3. Transform Code
This Python script is where you'll define the specific steps of your data transformation.
- Koza will load this script and execute it for each row of data in your source file.
+ Koza will load this script and execute it for each row of data in your source file,
+ applying any filters and mapping as defined in your source config yaml,
+ and outputting the transformed data to the target csv/json/jsonl file.
When Koza is called, either by command-line or as a library using `transform_source()`,
- it creates a `KozaApp` for the ingest it was called to transform.
- This KozaApp will be your entry point to Koza.
+ it creates a `KozaApp` object for the specified ingest.
+ This KozaApp will be your entry point to Koza:
+
+ ```python
+ from koza.cli_runner import get_koza_app
+ koza_app = get_koza_app('your-source-name')
+ ```
+
+ The KozaApp object has the following methods:
+ | Method | Description |
+ | --- | --- |
+ | `get_row()` | Returns the next row of data from the source file |
+ | `get_map(map_name)` | Returns the mapping dict for the specified map |
+ | `get_global_table()` | Returns the global translation table |
+ | `get_local_table()` | Returns the local translation table |
??? tldr "Example Python Transform Script"
```python
+ # other imports, eg. uuid, pydantic, etc.
import uuid
from biolink.pydanticmodel import Gene, PairwiseGeneToGeneInteraction
-
- # Get the KozaApp for your ingest
+
+ # Koza imports
from koza.cli_runner import get_koza_app
+
+ # This is the name of the ingest you want to run
source_name = 'map-protein-links-detailed'
koza_app = get_koza_app(source_name)
- # If your ingest depends on a map
+ # If your ingest depends_on a mapping file, you can access it like this:
map_name = 'entrez-2-string'
koza_map = koza_app.get_map(map_name)
@@ -222,7 +182,7 @@ Let's look at what we'll need to make that ingest:
# Koza will reload this script and return the next row until it reaches EOF or row-limit
row = koza_app.get_row()
- # Now you can lay out your actual transformations, and define your output
+ # Now you can lay out your actual transformations, and define your output:
gene_a = Gene(id='NCBIGene:' + koza_map[row['protein1']]['entrez'])
gene_b = Gene(id='NCBIGene:' + koza_map[row['protein2']]['entrez'])
@@ -234,5 +194,6 @@ Let's look at what we'll need to make that ingest:
predicate="biolink:interacts_with"
)
+ # Finally, write the transformed row to the target file
koza_app.write(gene_a, gene_b, pairwise_gene_to_gene_interaction)
```
\ No newline at end of file
diff --git a/docs/index.md b/docs/index.md
index 536b354..fa268c5 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -1,6 +1,4 @@
-# Koza
-
-**A data transformation framework**
+# Koza - a data transformation framework
## Overview
@@ -23,18 +21,20 @@ pip install koza
See the [Ingests](./Usage/ingests.md) page for information on how to configure ingests for koza to use.
-[CLI commands](./Usage/CLI.md) are available for validating and transforming data.
+Koza can be used as a Python library, or via the command line.
+[CLI commands](./Usage/CLI.md) are available for validating and transforming data.
+See the [API](./Usage/API.md) page for information on using Koza as a library.
+Koza also includes some examples to help you get started (see `koza/examples`).
### Basic Examples
-!!! list "Basic Examples"
- #### Validate
+!!! list "Validate"
Give Koza a local or remote csv file, and get some basic information (headers, number of rows)
```bash
koza validate \
- --file https://raw.githubusercontent.com/monarch-initiative/koza/main/examples/data/string.tsv \
+ --file ./examples/data/string.tsv \
--delimiter ' '
```
@@ -53,17 +53,24 @@ See the [Ingests](./Usage/ingests.md) page for information on how to configure i
--compression gzip
```
- #### Transform
+!!! list "Transform"
- Run the example ingest, "string/protein-links-detailed"
+ Try one of Koza's example ingests:
```bash
- koza transform \
- --source examples/string/protein-links-detailed.yaml \
- --global-table examples/translation_table.yaml
-
koza transform \
--source examples/string-declarative/protein-links-detailed.yaml \
--global-table examples/translation_table.yaml
```
- **Note**: Koza expects a directory structure as described in the above example (examples/ingest_name/ingest.yaml),
- such that the source config file is in the same directory as the transform code.
+
+ **Note**:
+ Koza expects a directory structure as described in the above example
+ with the source config file and transform code in the same directory:
+ ```
+ .
+ ├── ...
+ │ ├── some_source
+ │ │ ├── your_ingest.yaml
+ │ │ └── your_ingest.py
+ │ └── some_translation_table.yaml
+ └── ...
+ ```
diff --git a/examples/maps/custom-entrez-2-string.py b/examples/maps/custom-entrez-2-string.py
index 25fe5b1..72ae769 100644
--- a/examples/maps/custom-entrez-2-string.py
+++ b/examples/maps/custom-entrez-2-string.py
@@ -1,7 +1,3 @@
-from pathlib import Path
-import yaml
-
-from koza.model.config.source_config import FormatType, OutputFormat, PrimaryFileConfig
from koza.cli_runner import get_koza_app
source_name = 'custom-map-protein-links-detailed'
diff --git a/examples/string-w-custom-map/custom-map-protein-links-detailed.py b/examples/string-w-custom-map/custom-map-protein-links-detailed.py
index 57130c7..82a1db6 100644
--- a/examples/string-w-custom-map/custom-map-protein-links-detailed.py
+++ b/examples/string-w-custom-map/custom-map-protein-links-detailed.py
@@ -13,10 +13,7 @@
gene_b = Gene(id='NCBIGene:' + entrez_2_string[row['protein2']]['entrez'])
pairwise_gene_to_gene_interaction = PairwiseGeneToGeneInteraction(
- id="uuid:" + str(uuid.uuid1()),
- subject=gene_a.id,
- object=gene_b.id,
- predicate="biolink:interacts_with"
+ id="uuid:" + str(uuid.uuid1()), subject=gene_a.id, object=gene_b.id, predicate="biolink:interacts_with"
)
koza_app.write(gene_a, gene_b, pairwise_gene_to_gene_interaction)
diff --git a/examples/string-w-map/map-protein-links-detailed.py b/examples/string-w-map/map-protein-links-detailed.py
index 50d64a1..fbaa074 100644
--- a/examples/string-w-map/map-protein-links-detailed.py
+++ b/examples/string-w-map/map-protein-links-detailed.py
@@ -11,14 +11,15 @@
row = koza_app.get_row()
koza_map = koza_app.get_map(map_name)
+from loguru import logger
+
+logger.info(koza_map)
+
gene_a = Gene(id='NCBIGene:' + koza_map[row['protein1']]['entrez'])
gene_b = Gene(id='NCBIGene:' + koza_map[row['protein2']]['entrez'])
pairwise_gene_to_gene_interaction = PairwiseGeneToGeneInteraction(
- id="uuid:" + str(uuid.uuid1()),
- subject=gene_a.id,
- object=gene_b.id,
- predicate="biolink:interacts_with"
+ id="uuid:" + str(uuid.uuid1()), subject=gene_a.id, object=gene_b.id, predicate="biolink:interacts_with"
)
koza_app.write(gene_a, gene_b, pairwise_gene_to_gene_interaction)
diff --git a/examples/string/protein-links-detailed.py b/examples/string/protein-links-detailed.py
index 238ba62..50bca40 100644
--- a/examples/string/protein-links-detailed.py
+++ b/examples/string/protein-links-detailed.py
@@ -8,7 +8,6 @@
koza_app = get_koza_app('protein-links-detailed')
for row in koza_app.source:
-
protein_a = Protein(id='ENSEMBL:' + re.sub(r'\d+\.', '', row['protein1']))
protein_b = Protein(id='ENSEMBL:' + re.sub(r'\d+\.', '', row['protein2']))
diff --git a/mkdocs.yaml b/mkdocs.yaml
index 4625e7b..69f0493 100644
--- a/mkdocs.yaml
+++ b/mkdocs.yaml
@@ -9,6 +9,7 @@ nav:
- Welcome: 'index.md'
- Ingests: 'Usage/ingests.md'
- CLI: 'Usage/CLI.md'
+ - API: 'Usage/API.md'
theme:
@@ -18,6 +19,7 @@ theme:
favicon:
'images/favicon.ico'
features:
+ - content.code.copy
- navigation.expand
- navigation.instant
- navigation.tracking
@@ -46,24 +48,24 @@ plugins:
- mkdocstrings:
handlers:
python:
- paths: [ ./backend ]
import:
- https://docs.python.org/3/objects.inv
- https://mkdocstrings.github.io/objects.inv
- https://mkdocstrings.github.io/griffe/objects.inv
options:
docstring_style: google
+ docstring_section_style: table
docstring_options:
ignore_init_summary: yes
merge_init_into_class: yes
- # separate_signature: yes
show_signature: no
- show_source: no
+ # separate_signature: yes
+ # show_source: no
show_root_full_path: no
show_root_toc_entry: False
filters:
- "!^_[^_]"
- - "^_[^_]"
+ # - "^_[^_]"
markdown_extensions:
diff --git a/poetry.lock b/poetry.lock
index 2209d7f..b92be7d 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,22 +1,9 @@
-# This file is automatically @generated by Poetry 1.4.0 and should not be changed by hand.
-
-[[package]]
-name = "alabaster"
-version = "0.7.13"
-description = "A configurable sidebar-enabled Sphinx theme"
-category = "main"
-optional = false
-python-versions = ">=3.6"
-files = [
- {file = "alabaster-0.7.13-py3-none-any.whl", hash = "sha256:1ee19aca801bbabb5ba3f5f258e4422dfa86f82f3e9cefb0859b283cdd7f62a3"},
- {file = "alabaster-0.7.13.tar.gz", hash = "sha256:a27a4a084d5e690e16e01e03ad2b2e552c61a65469419b907243193de1a84ae2"},
-]
+# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand.
[[package]]
name = "antlr4-python3-runtime"
version = "4.9.3"
description = "ANTLR 4.9.3 runtime for Python 3.7"
-category = "main"
optional = false
python-versions = "*"
files = [
@@ -25,79 +12,86 @@ files = [
[[package]]
name = "arrow"
-version = "1.2.3"
+version = "1.3.0"
description = "Better dates & times for Python"
-category = "main"
optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.8"
files = [
- {file = "arrow-1.2.3-py3-none-any.whl", hash = "sha256:5a49ab92e3b7b71d96cd6bfcc4df14efefc9dfa96ea19045815914a6ab6b1fe2"},
- {file = "arrow-1.2.3.tar.gz", hash = "sha256:3934b30ca1b9f292376d9db15b19446088d12ec58629bc3f0da28fd55fb633a1"},
+ {file = "arrow-1.3.0-py3-none-any.whl", hash = "sha256:c728b120ebc00eb84e01882a6f5e7927a53960aa990ce7dd2b10f39005a67f80"},
+ {file = "arrow-1.3.0.tar.gz", hash = "sha256:d4540617648cb5f895730f1ad8c82a65f2dad0166f57b75f3ca54759c4d67a85"},
]
[package.dependencies]
python-dateutil = ">=2.7.0"
+types-python-dateutil = ">=2.8.10"
+
+[package.extras]
+doc = ["doc8", "sphinx (>=7.0.0)", "sphinx-autobuild", "sphinx-autodoc-typehints", "sphinx_rtd_theme (>=1.3.0)"]
+test = ["dateparser (==1.*)", "pre-commit", "pytest", "pytest-cov", "pytest-mock", "pytz (==2021.1)", "simplejson (==3.*)"]
[[package]]
name = "attrs"
-version = "22.2.0"
+version = "23.1.0"
description = "Classes Without Boilerplate"
-category = "main"
optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
files = [
- {file = "attrs-22.2.0-py3-none-any.whl", hash = "sha256:29e95c7f6778868dbd49170f98f8818f78f3dc5e0e37c0b1f474e3561b240836"},
- {file = "attrs-22.2.0.tar.gz", hash = "sha256:c9227bfc2f01993c03f68db37d1d15c9690188323c067c641f1a35ca58185f99"},
+ {file = "attrs-23.1.0-py3-none-any.whl", hash = "sha256:1f28b4522cdc2fb4256ac1a020c78acf9cba2c6b461ccd2c126f3aa8e8335d04"},
+ {file = "attrs-23.1.0.tar.gz", hash = "sha256:6279836d581513a26f1bf235f9acd333bc9115683f14f7e8fae46c98fc50e015"},
]
[package.extras]
-cov = ["attrs[tests]", "coverage-enable-subprocess", "coverage[toml] (>=5.3)"]
-dev = ["attrs[docs,tests]"]
-docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope.interface"]
-tests = ["attrs[tests-no-zope]", "zope.interface"]
-tests-no-zope = ["cloudpickle", "cloudpickle", "hypothesis", "hypothesis", "mypy (>=0.971,<0.990)", "mypy (>=0.971,<0.990)", "pympler", "pympler", "pytest (>=4.3.0)", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-mypy-plugins", "pytest-xdist[psutil]", "pytest-xdist[psutil]"]
+cov = ["attrs[tests]", "coverage[toml] (>=5.3)"]
+dev = ["attrs[docs,tests]", "pre-commit"]
+docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope-interface"]
+tests = ["attrs[tests-no-zope]", "zope-interface"]
+tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
[[package]]
-name = "autoflake"
-version = "1.7.8"
-description = "Removes unused imports and unused variables"
-category = "dev"
+name = "babel"
+version = "2.13.1"
+description = "Internationalization utilities"
optional = false
python-versions = ">=3.7"
files = [
- {file = "autoflake-1.7.8-py3-none-any.whl", hash = "sha256:46373ef69b6714f5064c923bb28bd797c4f8a9497f557d87fc36665c6d956b39"},
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]
[package.dependencies]
-pyflakes = ">=1.1.0,<3"
-tomli = {version = ">=2.0.1", markers = "python_version < \"3.11\""}
+pytz = {version = ">=2015.7", markers = "python_version < \"3.9\""}
+setuptools = {version = "*", markers = "python_version >= \"3.12\""}
+
+[package.extras]
+dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"]
[[package]]
-name = "babel"
-version = "2.12.1"
-description = "Internationalization utilities"
-category = "main"
+name = "beautifulsoup4"
+version = "4.12.2"
+description = "Screen-scraping library"
optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.6.0"
files = [
- {file = "Babel-2.12.1-py3-none-any.whl", hash = "sha256:b4246fb7677d3b98f501a39d43396d3cafdc8eadb045f4a31be01863f655c610"},
- {file = "Babel-2.12.1.tar.gz", hash = "sha256:cc2d99999cd01d44420ae725a21c9e3711b3aadc7976d6147f622d8581963455"},
+ {file = "beautifulsoup4-4.12.2-py3-none-any.whl", hash = "sha256:bd2520ca0d9d7d12694a53d44ac482d181b4ec1888909b035a3dbf40d0f57d4a"},
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]
[package.dependencies]
-pytz = {version = ">=2015.7", markers = "python_version < \"3.9\""}
+soupsieve = ">1.2"
+
+[package.extras]
+html5lib = ["html5lib"]
+lxml = ["lxml"]
[[package]]
name = "biolink-model"
-version = "3.2.4"
+version = "3.2.8"
description = "'A high level datamodel of biological entities and associations'"
-category = "dev"
optional = false
python-versions = ">=3.7"
files = [
- {file = "biolink-model-3.2.4.tar.gz", hash = "sha256:53eeb86fcfdaf208912c3336ab930f58a4f481bc7afb97211061a749bff4531f"},
- {file = "biolink_model-3.2.4-py3-none-any.whl", hash = "sha256:dca6646573eac49a8885cd48d621c4b20969efc768dc9fae8286298e04fa2793"},
+ {file = "biolink-model-3.2.8.tar.gz", hash = "sha256:105cc2f03dccede8763eaf2cc7ebdf1ab9de98858d3188a8a2209123700ca435"},
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]
[package.dependencies]
@@ -107,44 +101,39 @@ prefixmaps = "*"
[[package]]
name = "black"
-version = "22.3.0"
+version = "23.10.1"
description = "The uncompromising code formatter."
-category = "dev"
-optional = false
-python-versions = ">=3.6.2"
-files = [
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[package.dependencies]
click = ">=8.0.0"
mypy-extensions = ">=0.4.3"
+packaging = ">=22.0"
pathspec = ">=0.9.0"
platformdirs = ">=2"
tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""}
-typing-extensions = {version = ">=3.10.0.0", markers = "python_version < \"3.10\""}
+typing-extensions = {version = ">=4.0.1", markers = "python_version < \"3.11\""}
[package.extras]
colorama = ["colorama (>=0.4.3)"]
@@ -152,23 +141,32 @@ d = ["aiohttp (>=3.7.4)"]
jupyter = ["ipython (>=7.8.0)", "tokenize-rt (>=3.2.0)"]
uvloop = ["uvloop (>=0.15.2)"]
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description = "Python package for providing Mozilla's CA Bundle."
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python-versions = ">=3.6"
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python-versions = "*"
files = [
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name = "click"
-version = "8.1.3"
+version = "8.1.7"
description = "Composable command line interface toolkit"
-category = "main"
optional = false
python-versions = ">=3.7"
files = [
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[package.dependencies]
@@ -292,21 +302,19 @@ colorama = {version = "*", markers = "platform_system == \"Windows\""}
[[package]]
name = "cloudpickle"
-version = "2.2.1"
-description = "Extended pickling support for Python objects"
-category = "dev"
+version = "3.0.0"
+description = "Pickler class to extend the standard pickle.Pickler functionality"
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@@ -316,23 +324,22 @@ files = [
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description = "Idiomatic conversion between URIs and compact URIs (CURIEs)."
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pytrie = "*"
requests = "*"
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fastapi = ["defusedxml", "fastapi", "httpx", "python-multipart", "uvicorn"]
flask = ["defusedxml", "flask"]
pandas = ["pandas"]
@@ -341,93 +348,90 @@ tests = ["coverage", "pytest"]
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description = "Parallel PyData with Task Scheduling"
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python-versions = ">=3.8"
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test = ["pandas[test]", "pre-commit", "pytest", "pytest-rerunfailures", "pytest-xdist"]
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@@ -437,14 +441,13 @@ files = [
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description = "Backport of PEP 654 (exception groups)"
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python-versions = ">=3.7"
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arrow = ["pyarrow (>=1)"]
dask = ["dask", "distributed"]
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dropbox = ["dropbox", "dropboxdrivefs", "requests"]
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+ {file = "greenlet-3.0.0-cp39-cp39-win_amd64.whl", hash = "sha256:831d6f35037cf18ca5e80a737a27d822d87cd922521d18ed3dbc8a6967be50ce"},
+ {file = "greenlet-3.0.0-cp39-universal2-macosx_11_0_x86_64.whl", hash = "sha256:a048293392d4e058298710a54dfaefcefdf49d287cd33fb1f7d63d55426e4355"},
+ {file = "greenlet-3.0.0.tar.gz", hash = "sha256:19834e3f91f485442adc1ee440171ec5d9a4840a1f7bd5ed97833544719ce10b"},
]
[package.extras]
-docs = ["Sphinx", "docutils (<0.18)"]
+docs = ["Sphinx"]
test = ["objgraph", "psutil"]
[[package]]
name = "griffe"
-version = "0.25.5"
+version = "0.36.7"
description = "Signatures for entire Python programs. Extract the structure, the frame, the skeleton of your project, to generate API documentation or find breaking changes in your API."
-category = "dev"
optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
files = [
- {file = "griffe-0.25.5-py3-none-any.whl", hash = "sha256:1fb9edff48e66d4873014a2ebf21aca5f271d0006a4c937826e3cf592ffb3706"},
- {file = "griffe-0.25.5.tar.gz", hash = "sha256:11ea3403ef0560a1cbcf7f302eb5d21cf4c1d8ed3f8a16a75aa9f6f458caf3f1"},
+ {file = "griffe-0.36.7-py3-none-any.whl", hash = "sha256:7a09f8e9b97c7ebe227f6529a298bf7e0e742a9837ee261cc8260d50b4aa039f"},
+ {file = "griffe-0.36.7.tar.gz", hash = "sha256:a6fe60b16720ca0cf63c9e667a4c05eea40dfe4abcf114741885f945b74c7071"},
]
[package.dependencies]
colorama = ">=0.4"
-[package.extras]
-async = ["aiofiles (>=0.7,<1.0)"]
-
[[package]]
name = "hbreader"
version = "0.9.1"
description = "Honey Badger reader - a generic file/url/string open and read tool"
-category = "main"
optional = false
python-versions = ">=3.7"
files = [
@@ -655,7 +652,6 @@ files = [
name = "idna"
version = "3.4"
description = "Internationalized Domain Names in Applications (IDNA)"
-category = "main"
optional = false
python-versions = ">=3.5"
files = [
@@ -663,62 +659,47 @@ files = [
{file = "idna-3.4.tar.gz", hash = "sha256:814f528e8dead7d329833b91c5faa87d60bf71824cd12a7530b5526063d02cb4"},
]
-[[package]]
-name = "imagesize"
-version = "1.4.1"
-description = "Getting image size from png/jpeg/jpeg2000/gif file"
-category = "main"
-optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-files = [
- {file = "imagesize-1.4.1-py2.py3-none-any.whl", hash = "sha256:0d8d18d08f840c19d0ee7ca1fd82490fdc3729b7ac93f49870406ddde8ef8d8b"},
- {file = "imagesize-1.4.1.tar.gz", hash = "sha256:69150444affb9cb0d5cc5a92b3676f0b2fb7cd9ae39e947a5e11a36b4497cd4a"},
-]
-
[[package]]
name = "importlib-metadata"
-version = "4.13.0"
+version = "6.8.0"
description = "Read metadata from Python packages"
-category = "main"
optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
files = [
- {file = "importlib_metadata-4.13.0-py3-none-any.whl", hash = "sha256:8a8a81bcf996e74fee46f0d16bd3eaa382a7eb20fd82445c3ad11f4090334116"},
- {file = "importlib_metadata-4.13.0.tar.gz", hash = "sha256:dd0173e8f150d6815e098fd354f6414b0f079af4644ddfe90c71e2fc6174346d"},
+ {file = "importlib_metadata-6.8.0-py3-none-any.whl", hash = "sha256:3ebb78df84a805d7698245025b975d9d67053cd94c79245ba4b3eb694abe68bb"},
+ {file = "importlib_metadata-6.8.0.tar.gz", hash = "sha256:dbace7892d8c0c4ac1ad096662232f831d4e64f4c4545bd53016a3e9d4654743"},
]
[package.dependencies]
zipp = ">=0.5"
[package.extras]
-docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)"]
+docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
perf = ["ipython"]
-testing = ["flake8 (<5)", "flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)", "pytest-perf (>=0.9.2)"]
+testing = ["flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy (>=0.9.1)", "pytest-perf (>=0.9.2)", "pytest-ruff"]
[[package]]
name = "importlib-resources"
-version = "5.12.0"
+version = "6.1.0"
description = "Read resources from Python packages"
-category = "main"
optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
files = [
- {file = "importlib_resources-5.12.0-py3-none-any.whl", hash = "sha256:7b1deeebbf351c7578e09bf2f63fa2ce8b5ffec296e0d349139d43cca061a81a"},
- {file = "importlib_resources-5.12.0.tar.gz", hash = "sha256:4be82589bf5c1d7999aedf2a45159d10cb3ca4f19b2271f8792bc8e6da7b22f6"},
+ {file = "importlib_resources-6.1.0-py3-none-any.whl", hash = "sha256:aa50258bbfa56d4e33fbd8aa3ef48ded10d1735f11532b8df95388cc6bdb7e83"},
+ {file = "importlib_resources-6.1.0.tar.gz", hash = "sha256:9d48dcccc213325e810fd723e7fbb45ccb39f6cf5c31f00cf2b965f5f10f3cb9"},
]
[package.dependencies]
zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""}
[package.extras]
-docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["flake8 (<5)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"]
+testing = ["pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy (>=0.9.1)", "pytest-ruff", "zipp (>=3.17)"]
[[package]]
name = "iniconfig"
version = "2.0.0"
description = "brain-dead simple config-ini parsing"
-category = "dev"
optional = false
python-versions = ">=3.7"
files = [
@@ -730,7 +711,6 @@ files = [
name = "isodate"
version = "0.6.1"
description = "An ISO 8601 date/time/duration parser and formatter"
-category = "main"
optional = false
python-versions = "*"
files = [
@@ -745,7 +725,6 @@ six = "*"
name = "isoduration"
version = "20.11.0"
description = "Operations with ISO 8601 durations"
-category = "main"
optional = false
python-versions = ">=3.7"
files = [
@@ -756,29 +735,10 @@ files = [
[package.dependencies]
arrow = ">=0.15.0"
-[[package]]
-name = "isort"
-version = "5.12.0"
-description = "A Python utility / library to sort Python imports."
-category = "dev"
-optional = false
-python-versions = ">=3.8.0"
-files = [
- {file = "isort-5.12.0-py3-none-any.whl", hash = "sha256:f84c2818376e66cf843d497486ea8fed8700b340f308f076c6fb1229dff318b6"},
- {file = "isort-5.12.0.tar.gz", hash = "sha256:8bef7dde241278824a6d83f44a544709b065191b95b6e50894bdc722fcba0504"},
-]
-
-[package.extras]
-colors = ["colorama (>=0.4.3)"]
-pipfile-deprecated-finder = ["pip-shims (>=0.5.2)", "pipreqs", "requirementslib"]
-plugins = ["setuptools"]
-requirements-deprecated-finder = ["pip-api", "pipreqs"]
-
[[package]]
name = "jinja2"
version = "3.1.2"
description = "A very fast and expressive template engine."
-category = "main"
optional = false
python-versions = ">=3.7"
files = [
@@ -792,11 +752,24 @@ MarkupSafe = ">=2.0"
[package.extras]
i18n = ["Babel (>=2.7)"]
+[[package]]
+name = "jsbeautifier"
+version = "1.14.9"
+description = "JavaScript unobfuscator and beautifier."
+optional = false
+python-versions = "*"
+files = [
+ {file = "jsbeautifier-1.14.9.tar.gz", hash = "sha256:c738ebc36b47bd94e4ca6dd17a9004c3cc74edad582ca1d60e0e5d5945a63cb9"},
+]
+
+[package.dependencies]
+editorconfig = ">=0.12.2"
+six = ">=1.13.0"
+
[[package]]
name = "json-flattener"
version = "0.1.9"
description = "Python library for denormalizing nested dicts or json objects to tables and back"
-category = "main"
optional = false
python-versions = ">=3.7.0"
files = [
@@ -812,7 +785,6 @@ pyyaml = "*"
name = "jsonasobj"
version = "1.3.1"
description = "JSON as python objects"
-category = "main"
optional = false
python-versions = "*"
files = [
@@ -824,7 +796,6 @@ files = [
name = "jsonasobj2"
version = "1.0.4"
description = "JSON as python objects - version 2"
-category = "main"
optional = false
python-versions = ">=3.6"
files = [
@@ -837,14 +808,13 @@ hbreader = "*"
[[package]]
name = "jsonpatch"
-version = "1.32"
+version = "1.33"
description = "Apply JSON-Patches (RFC 6902)"
-category = "main"
optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, !=3.6.*"
files = [
- {file = "jsonpatch-1.32-py2.py3-none-any.whl", hash = "sha256:26ac385719ac9f54df8a2f0827bb8253aa3ea8ab7b3368457bcdb8c14595a397"},
- {file = "jsonpatch-1.32.tar.gz", hash = "sha256:b6ddfe6c3db30d81a96aaeceb6baf916094ffa23d7dd5fa2c13e13f8b6e600c2"},
+ {file = "jsonpatch-1.33-py2.py3-none-any.whl", hash = "sha256:0ae28c0cd062bbd8b8ecc26d7d164fbbea9652a1a3693f3b956c1eae5145dade"},
+ {file = "jsonpatch-1.33.tar.gz", hash = "sha256:9fcd4009c41e6d12348b4a0ff2563ba56a2923a7dfee731d004e212e1ee5030c"},
]
[package.dependencies]
@@ -852,57 +822,53 @@ jsonpointer = ">=1.9"
[[package]]
name = "jsonpath-ng"
-version = "1.5.3"
+version = "1.6.0"
description = "A final implementation of JSONPath for Python that aims to be standard compliant, including arithmetic and binary comparison operators and providing clear AST for metaprogramming."
-category = "main"
optional = false
python-versions = "*"
files = [
- {file = "jsonpath-ng-1.5.3.tar.gz", hash = "sha256:a273b182a82c1256daab86a313b937059261b5c5f8c4fa3fc38b882b344dd567"},
- {file = "jsonpath_ng-1.5.3-py2-none-any.whl", hash = "sha256:f75b95dbecb8a0f3b86fd2ead21c2b022c3f5770957492b9b6196ecccfeb10aa"},
- {file = "jsonpath_ng-1.5.3-py3-none-any.whl", hash = "sha256:292a93569d74029ba75ac2dc3d3630fc0e17b2df26119a165fa1d498ca47bf65"},
+ {file = "jsonpath-ng-1.6.0.tar.gz", hash = "sha256:5483f8e9d74c39c9abfab554c070ae783c1c8cbadf5df60d561bc705ac68a07e"},
+ {file = "jsonpath_ng-1.6.0-py3-none-any.whl", hash = "sha256:6fd04833412c4b3d9299edf369542f5e67095ca84efa17cbb7f06a34958adc9f"},
]
[package.dependencies]
-decorator = "*"
ply = "*"
-six = "*"
[[package]]
name = "jsonpointer"
-version = "2.3"
+version = "2.4"
description = "Identify specific nodes in a JSON document (RFC 6901)"
-category = "main"
optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, !=3.6.*"
files = [
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- {file = "jsonpointer-2.3.tar.gz", hash = "sha256:97cba51526c829282218feb99dab1b1e6bdf8efd1c43dc9d57be093c0d69c99a"},
+ {file = "jsonpointer-2.4-py2.py3-none-any.whl", hash = "sha256:15d51bba20eea3165644553647711d150376234112651b4f1811022aecad7d7a"},
+ {file = "jsonpointer-2.4.tar.gz", hash = "sha256:585cee82b70211fa9e6043b7bb89db6e1aa49524340dde8ad6b63206ea689d88"},
]
[[package]]
name = "jsonschema"
-version = "4.17.3"
+version = "4.19.1"
description = "An implementation of JSON Schema validation for Python"
-category = "main"
optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
files = [
- {file = "jsonschema-4.17.3-py3-none-any.whl", hash = "sha256:a870ad254da1a8ca84b6a2905cac29d265f805acc57af304784962a2aa6508f6"},
- {file = "jsonschema-4.17.3.tar.gz", hash = "sha256:0f864437ab8b6076ba6707453ef8f98a6a0d512a80e93f8abdb676f737ecb60d"},
+ {file = "jsonschema-4.19.1-py3-none-any.whl", hash = "sha256:cd5f1f9ed9444e554b38ba003af06c0a8c2868131e56bfbef0550fb450c0330e"},
+ {file = "jsonschema-4.19.1.tar.gz", hash = "sha256:ec84cc37cfa703ef7cd4928db24f9cb31428a5d0fa77747b8b51a847458e0bbf"},
]
[package.dependencies]
-attrs = ">=17.4.0"
+attrs = ">=22.2.0"
fqdn = {version = "*", optional = true, markers = "extra == \"format\""}
idna = {version = "*", optional = true, markers = "extra == \"format\""}
importlib-resources = {version = ">=1.4.0", markers = "python_version < \"3.9\""}
isoduration = {version = "*", optional = true, markers = "extra == \"format\""}
jsonpointer = {version = ">1.13", optional = true, markers = "extra == \"format\""}
+jsonschema-specifications = ">=2023.03.6"
pkgutil-resolve-name = {version = ">=1.3.10", markers = "python_version < \"3.9\""}
-pyrsistent = ">=0.14.0,<0.17.0 || >0.17.0,<0.17.1 || >0.17.1,<0.17.2 || >0.17.2"
+referencing = ">=0.28.4"
rfc3339-validator = {version = "*", optional = true, markers = "extra == \"format\""}
rfc3987 = {version = "*", optional = true, markers = "extra == \"format\""}
+rpds-py = ">=0.7.1"
uri-template = {version = "*", optional = true, markers = "extra == \"format\""}
webcolors = {version = ">=1.11", optional = true, markers = "extra == \"format\""}
@@ -910,16 +876,30 @@ webcolors = {version = ">=1.11", optional = true, markers = "extra == \"format\"
format = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3987", "uri-template", "webcolors (>=1.11)"]
format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3986-validator (>0.1.0)", "uri-template", "webcolors (>=1.11)"]
+[[package]]
+name = "jsonschema-specifications"
+version = "2023.7.1"
+description = "The JSON Schema meta-schemas and vocabularies, exposed as a Registry"
+optional = false
+python-versions = ">=3.8"
+files = [
+ {file = "jsonschema_specifications-2023.7.1-py3-none-any.whl", hash = "sha256:05adf340b659828a004220a9613be00fa3f223f2b82002e273dee62fd50524b1"},
+ {file = "jsonschema_specifications-2023.7.1.tar.gz", hash = "sha256:c91a50404e88a1f6ba40636778e2ee08f6e24c5613fe4c53ac24578a5a7f72bb"},
+]
+
+[package.dependencies]
+importlib-resources = {version = ">=1.4.0", markers = "python_version < \"3.9\""}
+referencing = ">=0.28.0"
+
[[package]]
name = "linkml"
-version = "1.4.11"
+version = "1.6.1"
description = "Linked Open Data Modeling Language"
-category = "main"
optional = false
-python-versions = ">=3.7.6,<4.0.0"
+python-versions = ">=3.8,<4.0"
files = [
- {file = "linkml-1.4.11-py3-none-any.whl", hash = "sha256:2811af5c6a69fb5b8acc4c85741b6aa6d17ef5579a0118a5028025d8a2480866"},
- {file = "linkml-1.4.11.tar.gz", hash = "sha256:ac5260a0cab15b36dbf2929afc43d7bc8e8af0e198ade7ee90be1dad8fd8d743"},
+ {file = "linkml-1.6.1-py3-none-any.whl", hash = "sha256:7501cb9c7b2c13ca78fc7121ae8b5457fb5771138714da31cc11f971062070ee"},
+ {file = "linkml-1.6.1.tar.gz", hash = "sha256:65f73cf29a77518972238e71e91e012c081cf2e43d71d8965ca414c78c11e08e"},
]
[package.dependencies]
@@ -932,12 +912,11 @@ jinja2 = ">=3.1.0"
jsonasobj2 = ">=1.0.3,<2.0.0"
jsonschema = {version = ">=4.0.0", extras = ["format"]}
linkml-dataops = "*"
-linkml-runtime = ">=1,<2"
-myst-parser = "*"
+linkml-runtime = ">=1.6.0"
openpyxl = "*"
parse = "*"
prefixcommons = ">=0.1.7"
-prefixmaps = ">=0.1.3,<0.2.0"
+prefixmaps = ">=0.1.3"
pydantic = "*"
pyjsg = ">=0.11.6"
pyshex = ">=0.7.20"
@@ -946,20 +925,13 @@ python-dateutil = "*"
pyyaml = "*"
rdflib = ">=6.0.0"
requests = ">=2.22"
-sphinx-click = "*"
-sphinx-rtd-theme = "*"
sqlalchemy = ">=1.4.31"
-tox = ">=3.25.1,<4.0.0"
watchdog = ">=0.9.0"
-[package.extras]
-docs = ["furo[docs] (>=2022.9.29,<2023.0.0)", "sphinx", "sphinxcontrib-mermaid[docs] (>=0.7.1,<0.8.0)"]
-
[[package]]
name = "linkml-dataops"
version = "0.1.0"
description = "LinkML Data Operations API"
-category = "main"
optional = false
python-versions = ">=3.7"
files = [
@@ -976,24 +948,26 @@ linkml-runtime = ">=1.1.6"
[[package]]
name = "linkml-runtime"
-version = "1.3.2"
+version = "1.6.0"
description = "Runtime environment for LinkML, the Linked open data modeling language"
-category = "main"
optional = false
-python-versions = ">=3.7.1,<4.0.0"
+python-versions = ">=3.7.6,<4.0.0"
files = [
- {file = "linkml-runtime-1.3.2.tar.gz", hash = "sha256:5ea9be2702323e5a3e2df924f5dfd4be88c0fc7041a4c71ccc6e33f45d319a36"},
- {file = "linkml_runtime-1.3.2-py3-none-any.whl", hash = "sha256:c5ab3b39e20fbb41360bb3fa16698f4b30adca752b9e47dc244e92fe633f2e6d"},
+ {file = "linkml_runtime-1.6.0-py3-none-any.whl", hash = "sha256:1b6b698f8cf23d63ff833ae0be8055b2e945e1c0ef06a1ed6db359247194a2eb"},
+ {file = "linkml_runtime-1.6.0.tar.gz", hash = "sha256:a06df7431a9b929afe242598800d99cec83bb31cbdc1f5d2d70e6b26c67dc337"},
]
[package.dependencies]
click = "*"
+curies = ">=0.5.4"
deprecated = "*"
hbreader = "*"
json-flattener = ">=0.1.9"
-jsonasobj2 = ">=1.0.4,<2.0.0"
+jsonasobj2 = ">=1.0.4,<2.dev0"
jsonschema = ">=3.2.0"
-prefixcommons = "0.1.11"
+prefixcommons = ">=0.1.12"
+prefixmaps = ">=0.1.4"
+pydantic = ">=1.10.2,<3.0.0"
pyyaml = "*"
rdflib = ">=6.0.0"
requests = "*"
@@ -1002,7 +976,6 @@ requests = "*"
name = "linkml-validator"
version = "0.4.5"
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description = "A deep merge function for 🐍."
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optional = false
python-versions = ">=3.6"
files = [
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name = "mkdocs"
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description = "Project documentation with Markdown."
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optional = false
python-versions = ">=3.7"
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importlib-metadata = {version = ">=4.3", markers = "python_version < \"3.10\""}
jinja2 = ">=2.11.1"
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mergedeep = ">=1.3.4"
packaging = ">=20.5"
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pyyaml = ">=5.1"
pyyaml-env-tag = ">=0.1"
watchdog = ">=2.0"
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name = "mkdocs-autorefs"
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description = "Automatically link across pages in MkDocs."
-category = "dev"
optional = false
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[[package]]
name = "mkdocs-material"
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description = "Documentation that simply works"
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optional = false
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name = "mkdocs-material-extensions"
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description = "Extension pack for Python Markdown and MkDocs Material."
-category = "dev"
optional = false
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+mkdocs-material = "*"
+pymdown-extensions = ">=8.0"
+pyyaml = "*"
+requests = "*"
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+
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name = "mkdocstrings"
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+version = "0.23.0"
description = "Automatic documentation from sources, for MkDocs."
-category = "dev"
optional = false
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Jinja2 = ">=2.11.1"
Markdown = ">=3.3"
MarkupSafe = ">=1.1"
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mkdocs-autorefs = ">=0.3.1"
mkdocstrings-python = {version = ">=0.5.2", optional = true, markers = "extra == \"python\""}
pymdown-extensions = ">=6.3"
+typing-extensions = {version = ">=4.1", markers = "python_version < \"3.10\""}
[package.extras]
crystal = ["mkdocstrings-crystal (>=0.3.4)"]
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[[package]]
name = "mkdocstrings-python"
-version = "0.8.3"
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description = "A Python handler for mkdocstrings."
-category = "dev"
optional = false
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files = [
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rdflib-jsonld = "0.6.1"
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version = "1.3.8"
description = "Parsing and validation of URIs (RFC 3986) and IRIs (RFC 3987)"
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optional = false
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typing-extensions = ">=4.2.0"
[package.extras]
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postgresql-psycopg2binary = ["psycopg2-binary"]
postgresql-psycopg2cffi = ["psycopg2cffi"]
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pymysql = ["pymysql"]
sqlcipher = ["sqlcipher3-binary"]
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python-versions = ">=3.5"
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shellingham = ">=1.3.2,<=1.4.0"
typer = ">=0.4.0,<=0.7.0"
+[[package]]
+name = "types-python-dateutil"
+version = "2.8.19.14"
+description = "Typing stubs for python-dateutil"
+optional = false
+python-versions = "*"
+files = [
+ {file = "types-python-dateutil-2.8.19.14.tar.gz", hash = "sha256:1f4f10ac98bb8b16ade9dbee3518d9ace017821d94b057a425b069f834737f4b"},
+ {file = "types_python_dateutil-2.8.19.14-py3-none-any.whl", hash = "sha256:f977b8de27787639986b4e28963263fd0e5158942b3ecef91b9335c130cb1ce9"},
+]
+
[[package]]
name = "typing-extensions"
-version = "4.5.0"
-description = "Backported and Experimental Type Hints for Python 3.7+"
-category = "main"
+version = "4.8.0"
+description = "Backported and Experimental Type Hints for Python 3.8+"
optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
files = [
- {file = "typing_extensions-4.5.0-py3-none-any.whl", hash = "sha256:fb33085c39dd998ac16d1431ebc293a8b3eedd00fd4a32de0ff79002c19511b4"},
- {file = "typing_extensions-4.5.0.tar.gz", hash = "sha256:5cb5f4a79139d699607b3ef622a1dedafa84e115ab0024e0d9c044a9479ca7cb"},
+ {file = "typing_extensions-4.8.0-py3-none-any.whl", hash = "sha256:8f92fc8806f9a6b641eaa5318da32b44d401efaac0f6678c9bc448ba3605faa0"},
+ {file = "typing_extensions-4.8.0.tar.gz", hash = "sha256:df8e4339e9cb77357558cbdbceca33c303714cf861d1eef15e1070055ae8b7ef"},
+]
+
+[[package]]
+name = "tzdata"
+version = "2023.3"
+description = "Provider of IANA time zone data"
+optional = false
+python-versions = ">=2"
+files = [
+ {file = "tzdata-2023.3-py2.py3-none-any.whl", hash = "sha256:7e65763eef3120314099b6939b5546db7adce1e7d6f2e179e3df563c70511eda"},
+ {file = "tzdata-2023.3.tar.gz", hash = "sha256:11ef1e08e54acb0d4f95bdb1be05da659673de4acbd21bf9c69e94cc5e907a3a"},
]
[[package]]
name = "uri-template"
-version = "1.2.0"
+version = "1.3.0"
description = "RFC 6570 URI Template Processor"
-category = "main"
optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
files = [
- {file = "uri_template-1.2.0-py3-none-any.whl", hash = "sha256:f1699c77b73b925cf4937eae31ab282a86dc885c333f2e942513f08f691fc7db"},
- {file = "uri_template-1.2.0.tar.gz", hash = "sha256:934e4d09d108b70eb8a24410af8615294d09d279ce0e7cbcdaef1bd21f932b06"},
+ {file = "uri-template-1.3.0.tar.gz", hash = "sha256:0e00f8eb65e18c7de20d595a14336e9f337ead580c70934141624b6d1ffdacc7"},
+ {file = "uri_template-1.3.0-py3-none-any.whl", hash = "sha256:a44a133ea12d44a0c0f06d7d42a52d71282e77e2f937d8abd5655b8d56fc1363"},
]
[package.extras]
-dev = ["flake8 (<4.0.0)", "flake8-annotations", "flake8-bugbear", "flake8-commas", "flake8-comprehensions", "flake8-continuation", "flake8-datetimez", "flake8-docstrings", "flake8-import-order", "flake8-literal", "flake8-noqa", "flake8-requirements", "flake8-type-annotations", "flake8-use-fstring", "mypy", "pep8-naming"]
+dev = ["flake8", "flake8-annotations", "flake8-bandit", "flake8-bugbear", "flake8-commas", "flake8-comprehensions", "flake8-continuation", "flake8-datetimez", "flake8-docstrings", "flake8-import-order", "flake8-literal", "flake8-modern-annotations", "flake8-noqa", "flake8-pyproject", "flake8-requirements", "flake8-typechecking-import", "flake8-use-fstring", "mypy", "pep8-naming", "types-PyYAML"]
[[package]]
name = "urllib3"
-version = "1.26.15"
+version = "2.0.7"
description = "HTTP library with thread-safe connection pooling, file post, and more."
-category = "main"
optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
+python-versions = ">=3.7"
files = [
- {file = "urllib3-1.26.15-py2.py3-none-any.whl", hash = "sha256:aa751d169e23c7479ce47a0cb0da579e3ede798f994f5816a74e4f4500dcea42"},
- {file = "urllib3-1.26.15.tar.gz", hash = "sha256:8a388717b9476f934a21484e8c8e61875ab60644d29b9b39e11e4b9dc1c6b305"},
+ {file = "urllib3-2.0.7-py3-none-any.whl", hash = "sha256:fdb6d215c776278489906c2f8916e6e7d4f5a9b602ccbcfdf7f016fc8da0596e"},
+ {file = "urllib3-2.0.7.tar.gz", hash = "sha256:c97dfde1f7bd43a71c8d2a58e369e9b2bf692d1334ea9f9cae55add7d0dd0f84"},
]
[package.extras]
-brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)", "brotlipy (>=0.6.0)"]
-secure = ["certifi", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "ipaddress", "pyOpenSSL (>=0.14)", "urllib3-secure-extra"]
-socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
+brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"]
+secure = ["certifi", "cryptography (>=1.9)", "idna (>=2.0.0)", "pyopenssl (>=17.1.0)", "urllib3-secure-extra"]
+socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"]
+zstd = ["zstandard (>=0.18.0)"]
+
+[[package]]
+name = "validators"
+version = "0.22.0"
+description = "Python Data Validation for Humans™"
+optional = false
+python-versions = ">=3.8"
+files = [
+ {file = "validators-0.22.0-py3-none-any.whl", hash = "sha256:61cf7d4a62bbae559f2e54aed3b000cea9ff3e2fdbe463f51179b92c58c9585a"},
+ {file = "validators-0.22.0.tar.gz", hash = "sha256:77b2689b172eeeb600d9605ab86194641670cdb73b60afd577142a9397873370"},
+]
+
+[package.extras]
+docs-offline = ["myst-parser (>=2.0.0)", "pypandoc-binary (>=1.11)", "sphinx (>=7.1.1)"]
+docs-online = ["mkdocs (>=1.5.2)", "mkdocs-git-revision-date-localized-plugin (>=1.2.0)", "mkdocs-material (>=9.2.6)", "mkdocstrings[python] (>=0.22.0)", "pyaml (>=23.7.0)"]
+hooks = ["pre-commit (>=3.3.3)"]
+package = ["build (>=1.0.0)", "twine (>=4.0.2)"]
+runner = ["tox (>=4.11.1)"]
+sast = ["bandit[toml] (>=1.7.5)"]
+testing = ["pytest (>=7.4.0)"]
+tooling = ["black (>=23.7.0)", "pyright (>=1.1.325)", "ruff (>=0.0.287)"]
+tooling-extras = ["pyaml (>=23.7.0)", "pypandoc-binary (>=1.11)", "pytest (>=7.4.0)"]
[[package]]
name = "virtualenv"
-version = "20.21.0"
+version = "20.24.6"
description = "Virtual Python Environment builder"
-category = "main"
optional = false
python-versions = ">=3.7"
files = [
- {file = "virtualenv-20.21.0-py3-none-any.whl", hash = "sha256:31712f8f2a17bd06234fa97fdf19609e789dd4e3e4bf108c3da71d710651adbc"},
- {file = "virtualenv-20.21.0.tar.gz", hash = "sha256:f50e3e60f990a0757c9b68333c9fdaa72d7188caa417f96af9e52407831a3b68"},
+ {file = "virtualenv-20.24.6-py3-none-any.whl", hash = "sha256:520d056652454c5098a00c0f073611ccbea4c79089331f60bf9d7ba247bb7381"},
+ {file = "virtualenv-20.24.6.tar.gz", hash = "sha256:02ece4f56fbf939dbbc33c0715159951d6bf14aaf5457b092e4548e1382455af"},
]
[package.dependencies]
-distlib = ">=0.3.6,<1"
-filelock = ">=3.4.1,<4"
-platformdirs = ">=2.4,<4"
+distlib = ">=0.3.7,<1"
+filelock = ">=3.12.2,<4"
+platformdirs = ">=3.9.1,<4"
[package.extras]
-docs = ["furo (>=2022.12.7)", "proselint (>=0.13)", "sphinx (>=6.1.3)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=22.12)"]
-test = ["covdefaults (>=2.2.2)", "coverage (>=7.1)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23)", "pytest (>=7.2.1)", "pytest-env (>=0.8.1)", "pytest-freezegun (>=0.4.2)", "pytest-mock (>=3.10)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)"]
+docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.2)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"]
+test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.4)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8)", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10)"]
[[package]]
name = "watchdog"
version = "3.0.0"
description = "Filesystem events monitoring"
-category = "main"
optional = false
python-versions = ">=3.7"
files = [
@@ -2675,7 +2836,6 @@ watchmedo = ["PyYAML (>=3.10)"]
name = "webcolors"
version = "1.13"
description = "A library for working with the color formats defined by HTML and CSS."
-category = "main"
optional = false
python-versions = ">=3.7"
files = [
@@ -2691,7 +2851,6 @@ tests = ["pytest", "pytest-cov"]
name = "win32-setctime"
version = "1.1.0"
description = "A small Python utility to set file creation time on Windows"
-category = "main"
optional = false
python-versions = ">=3.5"
files = [
@@ -2706,7 +2865,6 @@ dev = ["black (>=19.3b0)", "pytest (>=4.6.2)"]
name = "wrapt"
version = "1.15.0"
description = "Module for decorators, wrappers and monkey patching."
-category = "main"
optional = false
python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
files = [
@@ -2789,21 +2947,20 @@ files = [
[[package]]
name = "zipp"
-version = "3.15.0"
+version = "3.17.0"
description = "Backport of pathlib-compatible object wrapper for zip files"
-category = "main"
optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
files = [
- {file = "zipp-3.15.0-py3-none-any.whl", hash = "sha256:48904fc76a60e542af151aded95726c1a5c34ed43ab4134b597665c86d7ad556"},
- {file = "zipp-3.15.0.tar.gz", hash = "sha256:112929ad649da941c23de50f356a2b5570c954b65150642bccdd66bf194d224b"},
+ {file = "zipp-3.17.0-py3-none-any.whl", hash = "sha256:0e923e726174922dce09c53c59ad483ff7bbb8e572e00c7f7c46b88556409f31"},
+ {file = "zipp-3.17.0.tar.gz", hash = "sha256:84e64a1c28cf7e91ed2078bb8cc8c259cb19b76942096c8d7b84947690cabaf0"},
]
[package.extras]
-docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"]
+testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"]
[metadata]
lock-version = "2.0"
python-versions = "^3.8"
-content-hash = "cfe9f0f9cc663492fcee6f2c42cfd819fb2006eb510e4722607e41b76cf9fc9c"
+content-hash = "e8f9404da32af1e0523a9c4a8ac3e4c115ecdcfc1f8cef3e7a0d350bb0ee7e68"
diff --git a/pyproject.toml b/pyproject.toml
index bdf88dd..8020e18 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
[tool.poetry]
name = "koza"
-version = "0.3.1"
+version = "0.4.0"
description = "Data transformation framework for LinkML data models"
authors = [
"The Monarch Initiative ",
@@ -17,24 +17,24 @@ packages = [
[tool.poetry.dependencies]
python = "^3.8"
linkml-validator = ">=0.4.4"
-pydantic = "^1.0.0"
+pydantic = "^1.10"
pyyaml = ">=5.0.0"
requests = "^2.24.0"
ordered-set = ">=4.1.0"
typer = "^0.7.0"
typer-cli = "^0.0.13"
loguru = "*"
+sssom = "^0.3.41"
[tool.poetry.dev-dependencies]
+black = "^23.10.0"
+ruff = "*"
pytest = ">=6.0.0"
biolink-model = ">=3.0.1"
-autoflake = "^1.3.1"
-black = "22.3.0"
-isort = "^5.0.6"
dask = ">=2022.5.2"
-mkdocs = ">=1.3.0"
-mkdocs-material = ">=8.3.4"
-mkdocstrings = {extras = ["python"], version = "^0.19.0"}
+mkdocs = ">=1.4.2"
+mkdocs-material = ">=9.1.16"
+mkdocstrings = {extras = ["python"], version = ">=0.22.0"}
[tool.poetry.scripts]
koza = "koza.main:typer_app"
@@ -47,8 +47,8 @@ build-backend = "poetry.core.masonry.api"
line_length = 120
skip-string-normalization = true
-[tool.isort]
-profile = "black"
-line_length = 120
-multi_line_output = 3
-include_trailing_comma = true
+[tool.ruff]
+line-length = 120
+ignore = [
+ "F541", # f-strings with no placeholders
+]
\ No newline at end of file
diff --git a/src/koza/__init__.py b/src/koza/__init__.py
index d799a41..bf271f0 100644
--- a/src/koza/__init__.py
+++ b/src/koza/__init__.py
@@ -1,2 +1,3 @@
from importlib import metadata
-__version__ = metadata.version("koza")
\ No newline at end of file
+
+__version__ = metadata.version("koza")
diff --git a/src/koza/app.py b/src/koza/app.py
index 32d5589..a1dfe47 100644
--- a/src/koza/app.py
+++ b/src/koza/app.py
@@ -2,14 +2,12 @@
import sys
from pathlib import Path
from typing import Dict, Union
-
import yaml
-# For validation
-from pydantic.error_wrappers import ValidationError
from linkml_validator.validator import Validator
-from koza.converter.kgx_converter import KGXConverter
+from pydantic.error_wrappers import ValidationError
+from koza.converter.kgx_converter import KGXConverter
from koza.utils.exceptions import MapItemException, NextRowException
from koza.io.writer.jsonl_writer import JSONLWriter
from koza.io.writer.tsv_writer import TSVWriter
@@ -21,15 +19,9 @@
from koza.model.source import Source
from koza.model.translation_table import TranslationTable
-# import logging
-# logger = logging.getLogger(__name__)
-
class KozaApp:
- """
- Core koza class that stores the configuration
- and performs source transforms
- """
+ """Core koza class. Stores configuration and performs transforms"""
def __init__(
self,
@@ -38,7 +30,7 @@ def __init__(
output_dir: str = './output',
output_format: OutputFormat = OutputFormat('jsonl'),
schema: str = None,
- logger = None,
+ logger=None,
):
self.source = source
self.translation_table = translation_table
@@ -47,11 +39,9 @@ def __init__(
self._map_registry: Dict[str, Source] = {}
self._map_cache: Dict[str, Dict] = {}
self.curie_cleaner: CurieCleaner = CurieCleaner()
- self.writer: KozaWriter = self._get_writer(
- source.config.name, source.config.node_properties, source.config.edge_properties
- )
+ self.writer: KozaWriter = self._get_writer()
self.logger = logger
-
+
if schema:
self.validator = Validator(schema=schema)
self.converter = KGXConverter()
@@ -60,13 +50,9 @@ def __init__(
for map_file in source.config.depends_on:
with open(map_file, 'r') as map_file_fh:
map_file_config = MapFileConfig(**yaml.load(map_file_fh, Loader=UniqueIncludeLoader))
- map_file_config.transform_code = (str(Path(map_file).parent / Path(map_file).stem) + '.py')
+ map_file_config.transform_code = str(Path(map_file).parent / Path(map_file).stem) + '.py'
self._map_registry[map_file_config.name] = Source(map_file_config)
- self.writer = self._get_writer(
- source.config.name, source.config.node_properties, source.config.edge_properties
- )
-
def get_map(self, map_name: str):
map = self._map_cache[map_name]
return map
@@ -89,7 +75,6 @@ def process_sources(self):
a .py file along side it (see constructor)
Intended for decoupling ingest logic into a configuration like file
-
"""
import sys
@@ -132,10 +117,8 @@ def process_sources(self):
sys.path.remove(str(parent_path))
def process_maps(self):
- """
- Initializes self._map_cache
- :return:
- """
+ """Initializes self._map_cache"""
+
for map_file in self._map_registry.values():
if map_file.config.name not in self._map_cache:
self._load_map(map_file)
@@ -143,55 +126,49 @@ def process_maps(self):
@staticmethod
def next_row():
"""
- Breaks out of the facade file and iterates to the next row
- in the file
+ Breaks out of the facade file and iterates to the next row in the file
Effectively a continue statement
- https://docs.python.org/3/reference/simple_stmts.html#continue
- :return:
+ See: https://docs.python.org/3/reference/simple_stmts.html#continue
"""
raise NextRowException
def write(self, *entities):
-
# If a schema/validator is defined, validate before writing
if hasattr(self, 'validator'):
-
(nodes, edges) = self.converter.convert(entities)
-
if self.output_format == OutputFormat.tsv:
if nodes:
for node in nodes:
self.validator.validate(obj=node, target_class="NamedThing", strict=True)
-
if edges:
for edge in edges:
self.validator.validate(obj=edge, target_class="Association", strict=True)
-
elif self.output_format == OutputFormat.jsonl:
if nodes:
for node in nodes:
- # node = json.dumps(n, ensure_ascii=False)
self.validator.validate(obj=node, target_class="NamedThing", strict=True)
-
if edges:
for edge in edges:
- # edge = json.dumps(e, ensure_ascii=False)
self.validator.validate(obj=edge, target_class="Association", strict=True)
self.writer.write(entities)
- def _get_writer(self, name, node_properties, edge_properties) -> Union[TSVWriter, JSONLWriter]:
+ def _get_writer(self) -> Union[TSVWriter, JSONLWriter]:
+ writer_params = [
+ self.output_dir,
+ self.source.config.name,
+ self.source.config.node_properties,
+ self.source.config.edge_properties,
+ self.source.config.sssom_config,
+ ]
if self.output_format == OutputFormat.tsv:
- return TSVWriter(self.output_dir, name, node_properties, edge_properties)
+ return TSVWriter(*writer_params)
elif self.output_format == OutputFormat.jsonl:
- return JSONLWriter(self.output_dir, name, node_properties, edge_properties)
+ return JSONLWriter(*writer_params)
def _load_map(self, map_file: Source):
-
- # map_file = Source(map_file_config)
-
if not isinstance(map_file.config, MapFileConfig):
raise ValueError(f"Error loading map: {map_file.config.name} is not a MapFileConfig")
@@ -234,5 +211,5 @@ def _map_sniffer(depends_on: str):
See https://github.com/monarch-initiative/koza/issues/39
:param depends_on:
- :return:
"""
+ pass
diff --git a/src/koza/cli_runner.py b/src/koza/cli_runner.py
index fd5bc50..8de72c5 100644
--- a/src/koza/cli_runner.py
+++ b/src/koza/cli_runner.py
@@ -22,8 +22,10 @@
def get_koza_app(source_name) -> Optional[KozaApp]:
- """
- Getter for singleton koza app object
+ """Return a KozaApp object for a given source
+
+ Args:
+ source_name (str): Name of source
"""
try:
return koza_apps[source_name]
@@ -31,22 +33,6 @@ def get_koza_app(source_name) -> Optional[KozaApp]:
raise KeyError(f"{source_name} was not found in KozaApp dictionary")
-def set_koza_app(
- source: Source,
- translation_table: TranslationTable = None,
- output_dir: str = './output',
- output_format: OutputFormat = OutputFormat('tsv'),
- schema: str = None,
- logger = None,
-) -> KozaApp:
- """
- Setter for singleton koza app object
- """
- koza_apps[source.config.name] = KozaApp(source, translation_table, output_dir, output_format, schema, logger)
- logger.debug(f"koza_apps entry created for {source.config.name}: {koza_apps[source.config.name]}")
- return koza_apps[source.config.name]
-
-
def transform_source(
source: str,
output_dir: str,
@@ -58,13 +44,24 @@ def transform_source(
verbose: bool = None,
log: bool = False,
):
- # set_log_config(logging.INFO if (verbose is None) else logging.DEBUG if (verbose == True) else logging.WARNING)
- # logger = get_logger(verbose, filename = f"logs/{Path(source).name}.log" if log else None)
- logger = get_logger(name = Path(source).name if log else None, verbose = verbose)
-
+ """Create a KozaApp object, process maps, and run the transform
+
+ Args:
+ source (str): Path to source metadata file
+ output_dir (str): Path to output directory
+ output_format (OutputFormat, optional): Output format. Defaults to OutputFormat('tsv').
+ global_table (str, optional): Path to global translation table. Defaults to None.
+ local_table (str, optional): Path to local translation table. Defaults to None.
+ schema (str, optional): Path to schema file. Defaults to None.
+ row_limit (int, optional): Number of rows to process. Defaults to None.
+ verbose (bool, optional): Verbose logging. Defaults to None.
+ log (bool, optional): Log to file. Defaults to False.
+ """
+ logger = get_logger(name=Path(source).name if log else None, verbose=verbose)
+
with open(source, 'r') as source_fh:
source_config = PrimaryFileConfig(**yaml.load(source_fh, Loader=UniqueIncludeLoader))
-
+
if not source_config.name:
source_config.name = Path(source).stem
@@ -73,16 +70,16 @@ def transform_source(
source_config.transform_code = str(Path(source).parent / Path(source).stem) + '.py'
koza_source = Source(source_config, row_limit)
-
+ logger.debug(f"Source created: {koza_source.config.name}")
translation_table = get_translation_table(
global_table if global_table else source_config.global_table,
local_table if local_table else source_config.local_table,
- logger
+ logger,
)
- source_koza = set_koza_app(koza_source, translation_table, output_dir, output_format, schema, logger)
- source_koza.process_maps()
- source_koza.process_sources()
+ koza_app = _set_koza_app(koza_source, translation_table, output_dir, output_format, schema, logger)
+ koza_app.process_maps()
+ koza_app.process_sources()
def validate_file(
@@ -100,7 +97,6 @@ def validate_file(
"""
with open_resource(file) as resource_io:
-
if format == FormatType.csv:
reader = CSVReader(
resource_io,
@@ -120,15 +116,18 @@ def validate_file(
def get_translation_table(
- global_table: Union[str, Dict] = None,
+ global_table: Union[str, Dict] = None,
local_table: Union[str, Dict] = None,
- logger = None,
+ logger=None,
) -> TranslationTable:
- """
- Create a translation table object from two file paths
- :param global_table: str, path to global table yaml
- :param local_table: str, path to local table yaml
- :return: TranslationTable
+ """Create a translation table object from two file paths
+
+ Args:
+ global_table (str, optional): Path to global translation table. Defaults to None.
+ local_table (str, optional): Path to local translation table. Defaults to None.
+
+ Returns:
+ TranslationTable: TranslationTable object
"""
global_tt = {}
@@ -140,7 +139,6 @@ def get_translation_table(
else:
logger.debug("No global table used for transform")
else:
-
if isinstance(global_table, str):
with open(global_table, 'r') as global_tt_fh:
global_tt = yaml.safe_load(global_tt_fh)
@@ -160,6 +158,21 @@ def get_translation_table(
return TranslationTable(global_tt, local_tt)
+def _set_koza_app(
+ source: Source,
+ translation_table: TranslationTable = None,
+ output_dir: str = './output',
+ output_format: OutputFormat = OutputFormat('tsv'),
+ schema: str = None,
+ logger=None,
+) -> KozaApp:
+ """Create a KozaApp object for a given source"""
+
+ koza_apps[source.config.name] = KozaApp(source, translation_table, output_dir, output_format, schema, logger)
+ logger.debug(f"koza_apps entry created for {source.config.name}: {koza_apps[source.config.name]}")
+ return koza_apps[source.config.name]
+
+
def test_koza(koza: KozaApp):
"""Manually sets KozaApp (for testing)"""
global koza_app
diff --git a/src/koza/converter/kgx_converter.py b/src/koza/converter/kgx_converter.py
index b82e368..a2a50a7 100644
--- a/src/koza/converter/kgx_converter.py
+++ b/src/koza/converter/kgx_converter.py
@@ -2,6 +2,7 @@
from typing import Iterable, Tuple
from pydantic import BaseModel
+
class KGXConverter:
"""
Converts the biolink model to the KGX format, which splits
@@ -14,13 +15,11 @@ class KGXConverter:
"""
- def convert(self, entities: Iterable) -> Tuple[dict, dict]:
-
+ def convert(self, entities: Iterable) -> Tuple[list, list]:
nodes = []
edges = []
for entity in entities:
-
# if entity has subject + object + predicate, treat as edge
if all(hasattr(entity, attr) for attr in ["subject", "object", "predicate"]):
edges.append(self.convert_association(entity))
@@ -31,11 +30,10 @@ def convert(self, entities: Iterable) -> Tuple[dict, dict]:
):
nodes.append(self.convert_node(entity))
- # otherwise, not a
+ # otherwise, not a valid entity
else:
raise ValueError(
f"Cannot convert {entity}: Can only convert NamedThing or Association entities to KGX compatible dictionaries"
-
)
return nodes, edges
diff --git a/src/koza/io/reader/csv_reader.py b/src/koza/io/reader/csv_reader.py
index 173e281..6227511 100644
--- a/src/koza/io/reader/csv_reader.py
+++ b/src/koza/io/reader/csv_reader.py
@@ -106,7 +106,6 @@ def __iter__(self) -> Iterator:
return self
def __next__(self) -> Dict[str, Any]:
-
if not self._header:
self._set_header()
@@ -148,14 +147,10 @@ def __next__(self) -> Dict[str, Any]:
field_map = dict(zip(self._header, stripped_row))
if fields_len > row_len:
- raise ValueError(
- f"CSV file {self.name} has {fields_len - row_len} fewer columns at {self.reader.line_num}"
- )
+ raise ValueError(f"CSV file {self.name} has {fields_len - row_len} fewer columns at {self.reader.line_num}")
elif fields_len < row_len:
- logger.warning(
- f"CSV file {self.name} has {row_len - fields_len} extra columns at {self.reader.line_num}"
- )
+ logger.warning(f"CSV file {self.name} has {row_len - fields_len} extra columns at {self.reader.line_num}")
# Not sure if this would serve a purpose
#
# if not 'extra_cols' in self.field_type_map:
@@ -172,7 +167,7 @@ def __next__(self) -> Dict[str, Any]:
try:
typed_field_map[field] = FIELDTYPE_CLASS[self.field_type_map[field]](field_value)
except KeyError as key_error:
- logger.warning(key_error)
+ logger.warning(f"Field {field} not found in field_type_map ({key_error})")
return typed_field_map
@@ -201,27 +196,19 @@ def _set_header(self):
self._header = list(self.field_type_map.keys())
else:
raise ValueError(
- f"there is no header and columns have not been supplied\n"
- f"configure the 'columns' property in the source yaml"
+ "there is no header and columns have not been supplied\n"
+ "configure the 'columns' property in the source yaml"
)
def _parse_header_line(self, skip_blank_or_commented_lines: bool = False) -> List[str]:
"""
Parse the header line and return a list of headers
"""
- fieldnames = next(
- reader(self.io_str, **{'delimiter': self.header_delimiter, 'dialect': self.dialect})
- )
+ fieldnames = next(reader(self.io_str, **{'delimiter': self.header_delimiter, 'dialect': self.dialect}))
if skip_blank_or_commented_lines:
# there has to be a cleaner way to do this
- while not fieldnames or (
- self.comment_char is not None and fieldnames[0].startswith(self.comment_char)
- ):
- fieldnames = next(
- reader(
- self.io_str, **{'delimiter': self.header_delimiter, 'dialect': self.dialect}
- )
- )
+ while not fieldnames or (self.comment_char is not None and fieldnames[0].startswith(self.comment_char)):
+ fieldnames = next(reader(self.io_str, **{'delimiter': self.header_delimiter, 'dialect': self.dialect}))
fieldnames[0] = fieldnames[0].lstrip(self.comment_char)
return [f.strip() for f in fieldnames]
diff --git a/src/koza/io/reader/json_reader.py b/src/koza/io/reader/json_reader.py
index d5b1136..f91bf53 100644
--- a/src/koza/io/reader/json_reader.py
+++ b/src/koza/io/reader/json_reader.py
@@ -1,14 +1,17 @@
import json, yaml
from typing import IO, Any, Dict, Iterator, List, Union
-#from xmlrpc.client import Boolean
+
+# from xmlrpc.client import Boolean
from koza.io.utils import check_data
+
# from koza.utils.log_utils import get_logger
# logger = get_logger(__name__)
# import logging
# logger = logging.getLogger(__name__)
from loguru import logger
+
class JSONReader:
"""
A JSON reader that optionally iterates over a json list
@@ -36,8 +39,6 @@ def __init__(
self.json_path = json_path
self.name = name
-
-
if self.json_path:
if is_yaml:
self.json_obj = yaml.safe_load(self.io_str)
@@ -68,7 +69,6 @@ def __iter__(self) -> Iterator:
return self
def __next__(self) -> Dict[str, Any]:
-
if self._line_num == self._line_limit:
logger.info(f"Finished processing {self._line_num} rows for {self.name} from file {self.io_str.name}")
raise StopIteration
diff --git a/src/koza/io/utils.py b/src/koza/io/utils.py
index 6ee8539..0d9c1b0 100644
--- a/src/koza/io/utils.py
+++ b/src/koza/io/utils.py
@@ -11,7 +11,11 @@
import requests
-##### Helper Functions for Reader classes #####
+
+######################
+### Reader Helpers ###
+######################
+
def open_resource(resource: Union[str, PathLike]) -> IO[str]:
"""
@@ -60,6 +64,7 @@ def open_resource(resource: Union[str, PathLike]) -> IO[str]:
else:
raise ValueError(f"Cannot open local or remote file: {resource}")
+
def check_data(entry, path) -> bool:
"""
Given a dot delimited JSON tag path,
@@ -81,9 +86,12 @@ def check_data(entry, path) -> bool:
if len(ppart) == 0:
return exists
else:
- tag = ppart.pop(0)
+ tag = ppart.pop(0)
+
-##### Helper functions for Writer classes #####
+######################
+### Writer Helpers ###
+######################
# Biolink 2.0 "Knowledge Source" association slots,
# including the deprecated 'provided_by' slot
@@ -155,14 +163,10 @@ def _sanitize_export_property(key: str, value: Any, list_delimiter: str = None)
if column_types[key] == list:
if isinstance(value, (list, set, tuple)):
value = [
- v.replace("\n", " ").replace('\\"', "").replace("\t", " ")
- if isinstance(v, str)
- else v
+ v.replace("\n", " ").replace('\\"', "").replace("\t", " ") if isinstance(v, str) else v
for v in value
]
- new_value = (
- list_delimiter.join([str(x) for x in value]) if list_delimiter else value
- )
+ new_value = list_delimiter.join([str(x) for x in value]) if list_delimiter else value
else:
new_value = str(value).replace("\n", " ").replace('\\"', "").replace("\t", " ")
elif column_types[key] == bool:
@@ -175,19 +179,14 @@ def _sanitize_export_property(key: str, value: Any, list_delimiter: str = None)
else:
if type(value) == list:
value = [
- v.replace("\n", " ").replace('\\"', "").replace("\t", " ")
- if isinstance(v, str)
- else v
- for v in value
+ v.replace("\n", " ").replace('\\"', "").replace("\t", " ") if isinstance(v, str) else v for v in value
]
new_value = list_delimiter.join([str(x) for x in value]) if list_delimiter else value
column_types[key] = list
elif type(value) == bool:
try:
new_value = bool(value)
- column_types[
- key
- ] = bool # this doesn't seem right, shouldn't column_types come from the biolink model?
+ column_types[key] = bool # this doesn't seem right, shouldn't column_types come from the biolink model?
except:
new_value = False
else:
diff --git a/src/koza/io/writer/jsonl_writer.py b/src/koza/io/writer/jsonl_writer.py
index 1c240b1..2987879 100644
--- a/src/koza/io/writer/jsonl_writer.py
+++ b/src/koza/io/writer/jsonl_writer.py
@@ -4,6 +4,7 @@
from koza.converter.kgx_converter import KGXConverter
from koza.io.writer.writer import KozaWriter
+from koza.model.config.sssom_config import SSSOMConfig
class JSONLWriter(KozaWriter):
@@ -13,35 +14,37 @@ def __init__(
source_name: str,
node_properties: List[str],
edge_properties: Optional[List[str]] = [],
+ sssom_config: SSSOMConfig = None,
):
-
self.output_dir = output_dir
self.source_name = source_name
+ self.sssom_config = sssom_config
self.converter = KGXConverter()
os.makedirs(output_dir, exist_ok=True)
if node_properties:
- self.nodes_file = open(f"{output_dir}/{source_name}_nodes.jsonl", "w")
+ self.nodeFH = open(f"{output_dir}/{source_name}_nodes.jsonl", "w")
if edge_properties:
- self.edges_file = open(f"{output_dir}/{source_name}_edges.jsonl", "w")
+ self.edgeFH = open(f"{output_dir}/{source_name}_edges.jsonl", "w")
def write(self, entities: Iterable):
-
(nodes, edges) = self.converter.convert(entities)
if nodes:
for n in nodes:
node = json.dumps(n, ensure_ascii=False)
- self.nodes_file.write(node + '\n')
+ self.nodeFH.write(node + '\n')
if edges:
for e in edges:
+ if self.sssom_config:
+ e = self.sssom_config.apply_mapping(e)
edge = json.dumps(e, ensure_ascii=False)
- self.edges_file.write(edge + '\n')
+ self.edgeFH.write(edge + '\n')
def finalize(self):
- if hasattr(self, 'nodes_file'):
- self.nodes_file.close()
- if hasattr(self, 'edge_file'):
- self.edges_file.close()
+ if hasattr(self, 'nodeFH'):
+ self.nodeFH.close()
+ if hasattr(self, 'edgeFH'):
+ self.edgeFH.close()
diff --git a/src/koza/io/writer/tsv_writer.py b/src/koza/io/writer/tsv_writer.py
index c8f07b0..77fc865 100644
--- a/src/koza/io/writer/tsv_writer.py
+++ b/src/koza/io/writer/tsv_writer.py
@@ -1,145 +1,114 @@
#### TSV Writer ####
-#
-# Notes:
-# - May want to rename to KGXWriter at some point, if we develop writers for other models non biolink/kgx specific
+# NOTE - May want to rename to KGXWriter at some point, if we develop writers for other models non biolink/kgx specific
-import os
-from typing import Dict, Iterable, List, Optional, Set
+from pathlib import Path
+import typing as t
from ordered_set import OrderedSet
from koza.converter.kgx_converter import KGXConverter
from koza.io.utils import build_export_row
from koza.io.writer.writer import KozaWriter
+from koza.model.config.sssom_config import SSSOMConfig
class TSVWriter(KozaWriter):
def __init__(
self,
- output_dir,
+ output_dir: t.Union[str, Path],
source_name: str,
- node_properties: List[str],
- edge_properties: Optional[List[str]] = [],
+ node_properties: t.List[str] = None,
+ edge_properties: t.List[str] = None,
+ sssom_config: SSSOMConfig = None,
):
- self.dirname = output_dir
self.basename = source_name
-
+ self.dirname = output_dir
self.delimiter = "\t"
self.list_delimiter = "|"
-
self.converter = KGXConverter()
+ self.sssom_config = sssom_config
- # Create output directory
- os.makedirs(self.dirname, exist_ok=True)
-
- if node_properties:
- self.node_properties = node_properties
- self.nodes_file_basename = f"{self.basename}_nodes.tsv"
- self.ordered_node_columns = TSVWriter._order_node_columns(self.node_properties)
-
- # Create and write to nodes output file
- self.nodes_file_name = os.path.join(
- self.dirname if self.dirname else "", self.nodes_file_basename
- )
- self.NFH = open(self.nodes_file_name, "w")
- self.NFH.write(self.delimiter.join(self.ordered_node_columns) + "\n")
-
- if edge_properties:
- self.edge_properties = edge_properties
- self.edges_file_basename = f"{self.basename}_edges.tsv"
- self.ordered_edge_columns = TSVWriter._order_edge_columns(self.edge_properties)
-
- # Create and write to edges output file
- self.edges_file_name = os.path.join(
- self.dirname if self.dirname else "", self.edges_file_basename
- )
- self.EFH = open(self.edges_file_name, "w")
- self.EFH.write(self.delimiter.join(self.ordered_edge_columns) + "\n")
-
- def write(self, entities: Iterable):
- """
- Accepts an "entities" object and writes to separate node and edge .tsv files
- """
+ Path(self.dirname).mkdir(parents=True, exist_ok=True)
+
+ if node_properties: # Make node file
+ self.node_columns = TSVWriter._order_columns(node_properties, "node")
+ self.nodes_file_name = Path(self.dirname if self.dirname else "", f"{self.basename}_nodes.tsv")
+ self.nodeFH = open(self.nodes_file_name, "w")
+ self.nodeFH.write(self.delimiter.join(self.node_columns) + "\n")
+
+ if edge_properties: # Make edge file
+ if sssom_config:
+ edge_properties = self.add_sssom_columns(edge_properties)
+ self.edge_columns = TSVWriter._order_columns(edge_properties, "edge")
+ self.edges_file_name = Path(self.dirname if self.dirname else "", f"{self.basename}_edges.tsv")
+ self.edgeFH = open(self.edges_file_name, "w")
+ self.edgeFH.write(self.delimiter.join(self.edge_columns) + "\n")
+
+ def write(self, entities: t.Iterable) -> None:
+ """Write an entities object to separate node and edge .tsv files"""
- (nodes, edges) = self.converter.convert(entities)
+ nodes, edges = self.converter.convert(entities)
if nodes:
for node in nodes:
- self.write_node(node)
+ self.write_row(node, record_type="node")
if edges:
for edge in edges:
- self.write_edge(edge)
+ if self.sssom_config:
+ edge = self.sssom_config.apply_mapping(edge)
+ self.write_row(edge, record_type="edge")
- def write_node(self, record: Dict) -> None:
- """
- Write a node record to the underlying store.
- Parameters
- ----------
- record: Dict
- A node record
- """
- row = build_export_row(record, list_delimiter=self.list_delimiter)
- row["id"] = record["id"]
- values = []
- for c in self.ordered_node_columns:
- if c in row:
- values.append(str(row[c]))
- else:
- values.append("")
- self.NFH.write(self.delimiter.join(values) + "\n")
+ def write_row(self, record: t.Dict, record_type: t.Literal["node", "edge"]) -> None:
+ """Write a row to the underlying store.
- def write_edge(self, record: Dict) -> None:
- """
- Write an edge record to the underlying store.
- Parameters
- ----------
- record: Dict
- An edge record
+ Args:
+ record: Dict - A node or edge record
+ record_type: Literal["node", "edge"] - The record_type of record
"""
+ fh = self.nodeFH if record_type == "node" else self.edgeFH
+ columns = self.node_columns if record_type == "node" else self.edge_columns
row = build_export_row(record, list_delimiter=self.list_delimiter)
values = []
- for c in self.ordered_edge_columns:
+ if record_type == "node":
+ row["id"] = record["id"]
+ for c in columns:
if c in row:
values.append(str(row[c]))
else:
values.append("")
- self.EFH.write(self.delimiter.join(values) + "\n")
+ fh.write(self.delimiter.join(values) + "\n")
def finalize(self):
- """
- Close file handles and create an archive if compression mode is defined.
- """
- if hasattr(self, 'NFH'):
- self.NFH.close()
- if hasattr(self, 'EFH'):
- self.EFH.close()
+ """Close file handles."""
+
+ if hasattr(self, "nodeFH"):
+ self.nodeFH.close()
+ if hasattr(self, "edgeFH"):
+ self.edgeFH.close()
@staticmethod
- def _order_node_columns(cols: Set) -> OrderedSet:
- """
- Arrange node columns in a defined order.
- Parameters
- ----------
- cols: Set
- A set with elements in any order
- Returns
- -------
- OrderedSet
- A set with elements in a defined order
+ def _order_columns(cols: t.Set, record_type: t.Literal["node", "edge"]) -> OrderedSet:
+ """Arrange node or edge columns in a defined order.
+
+ Args:
+ cols: Set - A set with elements in any order
+
+ Returns:
+ OrderedSet - A set with elements in a defined order
"""
- node_columns = cols.copy()
- core_columns = OrderedSet(
- ["id", "category", "name", "description", "xref", "provided_by", "synonym"]
- )
+ if record_type == "node":
+ core_columns = OrderedSet(["id", "category", "name", "description", "xref", "provided_by", "synonym"])
+ elif record_type == "edge":
+ core_columns = OrderedSet(["id", "subject", "predicate", "object", "category", "provided_by"])
ordered_columns = OrderedSet()
for c in core_columns:
- if c in node_columns:
+ if c in cols:
ordered_columns.add(c)
- node_columns.remove(c)
+ cols.remove(c)
internal_columns = set()
- remaining_columns = node_columns.copy()
- for c in node_columns:
+ remaining_columns = cols.copy()
+ for c in cols:
if c.startswith("_"):
internal_columns.add(c)
remaining_columns.remove(c)
@@ -148,33 +117,10 @@ def _order_node_columns(cols: Set) -> OrderedSet:
return ordered_columns
@staticmethod
- def _order_edge_columns(cols: Set) -> OrderedSet:
- """
- Arrange edge columns in a defined order.
- Parameters
- ----------
- cols: Set
- A set with elements in any order
- Returns
- -------
- OrderedSet
- A set with elements in a defined order
- """
- edge_columns = cols.copy()
- core_columns = OrderedSet(
- ["id", "subject", "predicate", "object", "category", "relation", "provided_by"]
- )
- ordered_columns = OrderedSet()
- for c in core_columns:
- if c in edge_columns:
- ordered_columns.add(c)
- edge_columns.remove(c)
- internal_columns = set()
- remaining_columns = edge_columns.copy()
- for c in edge_columns:
- if c.startswith("_"):
- internal_columns.add(c)
- remaining_columns.remove(c)
- ordered_columns.update(sorted(remaining_columns))
- ordered_columns.update(sorted(internal_columns))
- return ordered_columns
+ def add_sssom_columns(edge_properties: list):
+ """Add SSSOM columns to a set of columns."""
+ if "original_subject" not in edge_properties:
+ edge_properties.append("original_subject")
+ if "original_object" not in edge_properties:
+ edge_properties.append("original_object")
+ return edge_properties
diff --git a/src/koza/io/yaml_loader.py b/src/koza/io/yaml_loader.py
index 5f15252..a6b0f76 100644
--- a/src/koza/io/yaml_loader.py
+++ b/src/koza/io/yaml_loader.py
@@ -33,8 +33,7 @@ def unique_construct_mapping(self, node: yaml.Node, deep=False):
key = self.construct_object(key_node, deep=deep)
if key in mapping:
raise ConstructorError(
- f"while constructing a mapping for {value_node.value} "
- f"found duplicate key {key}"
+ f"while constructing a mapping for {value_node.value} " f"found duplicate key {key}"
)
mapping.append(key)
return super().construct_mapping(node, deep)
diff --git a/src/koza/main.py b/src/koza/main.py
index be7b23a..7e1beb9 100755
--- a/src/koza/main.py
+++ b/src/koza/main.py
@@ -1,7 +1,5 @@
#!/usr/bin/env python3
-"""
-CLI interface for Koza
-"""
+"""CLI for Koza - wraps the koza library to provide a command line interface"""
from pathlib import Path
from typing import Optional
@@ -10,14 +8,18 @@
from koza.model.config.source_config import FormatType, OutputFormat
import typer
+
typer_app = typer.Typer()
+
@typer_app.callback(invoke_without_command=True)
def callback(version: Optional[bool] = typer.Option(None, "--version", is_eager=True)):
if version:
from koza import __version__
+
typer.echo(f"Koza version: {__version__}")
- raise typer.Exit()
+ raise typer.Exit()
+
@typer_app.command()
def transform(
@@ -31,14 +33,7 @@ def transform(
verbose: Optional[bool] = typer.Option(None, "--debug/--quiet"),
log: bool = typer.Option(False, help='Optional log mode - set true to save output to ./logs'),
) -> None:
- """
- Transform a source file
- """
- # note: this requires koza users to follow the same dir structure, two levels of directories to find the .yaml file
- # else something like this might work with a generic directory structure:
- # os.path.basename(source) # name of the file + extension
- # os.path.dirname(source) # name of the directory
- # os.path.splitext(os.path.basename(source))[0] # name of the yaml file without the yaml
+ """Transform a source file"""
output_path = Path(output_dir)
@@ -57,16 +52,11 @@ def validate(
delimiter: str = ',',
header_delimiter: str = None,
skip_blank_lines: bool = True,
-):
- """
- Validate a source file
-
- Given a file and configuration checks that the file is valid, ie
- format is as expected (tsv, json), required columns/fields are there
- """
-
+) -> None:
+ """Validate a source file"""
validate_file(file, format, delimiter, header_delimiter, skip_blank_lines)
+
# @typer_app.command()
# def create():
# """
diff --git a/src/koza/model/config/source_config.py b/src/koza/model/config/source_config.py
index 63c7aa8..393cb9e 100644
--- a/src/koza/model/config/source_config.py
+++ b/src/koza/model/config/source_config.py
@@ -10,81 +10,67 @@
from enum import Enum
from pathlib import Path
from typing import Dict, List, Union
-
import yaml
+
from pydantic import StrictFloat, StrictInt, StrictStr
from pydantic.dataclasses import dataclass
from koza.model.config.pydantic_config import PydanticConfig
+from koza.model.config.sssom_config import SSSOMConfig
-# from koza.utils.log_utils import get_logger
-# logger = get_logger(__name__)
-# import logging
-# logger = logging.getLogger(__name__)
-from loguru import logger
-class MapErrorEnum(str, Enum):
- """
- Enum for how to handle key errors in map files
+class FilterCode(str, Enum):
+ """Enum for filter codes (ex. gt = greater than)
+
+ This should be aligned with https://docs.python.org/3/library/operator.html
"""
- warning = 'warning'
- error = 'error'
+ gt = "gt"
+ ge = "ge"
+ lt = "lt"
+ lte = "le"
+ eq = "eq"
+ ne = "ne"
+ inlist = "in"
-class FormatType(str, Enum):
- """
- Enum for supported file types
- """
+class FilterInclusion(str, Enum):
+ """Enum for filter inclusion/exclusion"""
- csv = 'csv'
- jsonl = 'jsonl'
- json = 'json'
- yaml = 'yaml'
- xml = 'xml' # TODO
+ include = "include"
+ exclude = "exclude"
-class StandardFormat(str, Enum):
- gpi = 'gpi'
- bgi = 'bgi'
- oban = 'oban'
+class FieldType(str, Enum):
+ """Enum for field types"""
+ str = "str"
+ int = "int"
+ float = "float"
-class FilterCode(str, Enum):
- """
- Enum for filter codes
- eg gt (greater than)
- This should be aligned with https://docs.python.org/3/library/operator.html
- """
+class FormatType(str, Enum):
+ """Enum for supported file types"""
- gt = 'gt'
- ge = 'ge'
- lt = 'lt'
- lte = 'le'
- eq = 'eq'
- ne = 'ne'
- inlist = 'in'
+ csv = "csv"
+ jsonl = "jsonl"
+ json = "json"
+ yaml = "yaml"
+ xml = "xml" # TODO
-class FilterInclusion(str, Enum):
- """
- Enum for filter inclusion/exclusion
- """
+class HeaderMode(str, Enum):
+ """Enum for supported header modes in addition to an index based lookup"""
- include = 'include'
- exclude = 'exclude'
+ infer = "infer"
+ none = "none"
-class FieldType(str, Enum):
- """
- Enum for filter codes
- eg gt (greater than)
- """
+class MapErrorEnum(str, Enum):
+ """Enum for how to handle key errors in map files"""
- str = 'str'
- int = 'int'
- float = 'float'
+ warning = "warning"
+ error = "error"
class OutputFormat(str, Enum):
@@ -92,9 +78,15 @@ class OutputFormat(str, Enum):
Output formats
"""
- tsv = 'tsv'
- jsonl = 'jsonl'
- kgx = 'kgx'
+ tsv = "tsv"
+ jsonl = "jsonl"
+ kgx = "kgx"
+
+
+class StandardFormat(str, Enum):
+ gpi = "gpi"
+ bgi = "bgi"
+ oban = "oban"
class TransformMode(str, Enum):
@@ -105,17 +97,8 @@ class TransformMode(str, Enum):
a for loop is being used to iterate over a file
"""
- flat = 'flat'
- loop = 'loop'
-
-
-class HeaderMode(str, Enum):
- """
- Enum for supported header modes in addition to an index based lookup
- """
-
- infer = 'infer'
- none = 'none'
+ flat = "flat"
+ loop = "loop"
@dataclass(frozen=True)
@@ -150,35 +133,43 @@ class DatasetDescription:
@dataclass(config=PydanticConfig)
class SourceConfig:
"""
- Base class for primary sources and mapping sources
-
- TODO document fields
-
- header: Optional, int|HeaderMode - the index (0 based) in which the
- header appears in the file. If header is set to infer
- the headers will be set to the first line that is not blank
- or commented with a hash. If header is set to 'none'
- then the columns field will be used, or raise a ValueError
- if columns are not supplied
-
- delimiter:
- separator string similar to what works in str.split()
- https://docs.python.org/3/library/stdtypes.html#str.split
-
- required_properties: A list of required top level properties in a json object
+ Source config data class
+
+ Parameters
+ ----------
+ name: str (required) - name of the source
+ files: List[str] (required) - list of files to process
+ file_archive: str (optional) - path to a file archive containing files to process
+ format: FormatType (optional) - format of the data file(s)
+ sssom_config: SSSOMConfig (optional) - SSSOM config options
+ metadata: DatasetDescription (optional) - metadata for the source
+ columns: List[str] (optional) - list of columns to include
+ required_properties: List[str] (optional) - list of properties which must be in json data files
+ delimiter: str (optional) - delimiter for csv files
+ header_delimiter: str (optional) - delimiter for header in csv files
+ header: int (optional) - header row index
+ comment_char: str (optional) - comment character for csv files
+ skip_blank_lines: bool (optional) - skip blank lines in csv files
+ filters: List[ColumnFilter] (optional) - list of filters to apply
+ json_path: List[str] (optional) - path within JSON object containing data to process
+ transform_code: str (optional) - path to a python file to transform the data
+ transform_mode: TransformMode (optional) - how to process the transform file
+ global_table: str (optional) - path to a global table file
+ local_table: str (optional) - path to a local table file
"""
name: str
files: List[Union[str, Path]]
file_archive: Union[str, Path] = None
format: FormatType = FormatType.csv
- metadata: Union[DatasetDescription, str] = None
+ sssom_config: SSSOMConfig = None
columns: List[Union[str, Dict[str, FieldType]]] = None
required_properties: List[str] = None
+ metadata: Union[DatasetDescription, str] = None
delimiter: str = None
- header_delimiter: str = None
header: Union[int, HeaderMode] = HeaderMode.infer
- comment_char: str = '#'
+ header_delimiter: str = None
+ comment_char: str = "#"
skip_blank_lines: bool = True
filters: List[ColumnFilter] = field(default_factory=list)
json_path: List[Union[StrictStr, StrictInt]] = None
@@ -189,11 +180,11 @@ class SourceConfig:
def extract_archive(self):
archive_path = Path(self.file_archive).parent # .absolute()
- if self.file_archive.endswith('.tar.gz') or self.file_archive.endswith('.tar'):
+ if self.file_archive.endswith(".tar.gz") or self.file_archive.endswith(".tar"):
with tarfile.open(self.file_archive) as archive:
archive.extractall(archive_path)
- elif self.file_archive.endswith('.zip'):
- with zipfile.ZipFile(self.file_archive, 'r') as archive:
+ elif self.file_archive.endswith(".zip"):
+ with zipfile.ZipFile(self.file_archive, "r") as archive:
archive.extractall(archive_path)
else:
raise ValueError("Error extracting archive. Supported archive types: .tar.gz, .zip")
@@ -202,8 +193,9 @@ def extract_archive(self):
def __post_init_post_parse__(self):
"""
- TO DO figure out why we're using object.__setattr__(self, ...
- here and document it
+ TO DO figure out why we're using object.__setattr__(self, ...)
+ here and document it.
+ Is this a workaround for a pydantic bug?
"""
if self.file_archive:
files = self.extract_archive()
@@ -216,38 +208,33 @@ def __post_init_post_parse__(self):
files_as_paths.append(Path(file))
else:
files_as_paths.append(file)
- object.__setattr__(self, 'files', files_as_paths)
+ object.__setattr__(self, "files", files_as_paths)
+ # self.files = files_as_paths <---- is this equivalent to the above?
if self.metadata and isinstance(self.metadata, str):
# If this looks like a file path attempt to load it from the yaml
# TODO enforce that this is imported via an include?
# See https://github.com/monarch-initiative/koza/issues/46
try:
- with open(self.metadata, 'r') as meta:
- object.__setattr__(
- self, 'metadata', DatasetDescription(**yaml.safe_load(meta))
- )
+ with open(self.metadata, "r") as meta:
+ object.__setattr__(self, "metadata", DatasetDescription(**yaml.safe_load(meta)))
except Exception as e:
# TODO check for more explicit exceptions
raise ValueError(f"Unable to load metadata from {self.metadata}: {e}")
- # logger.debug("Could not load dataset description from metadata file")
- if self.delimiter in ['tab', '\\t']:
- object.__setattr__(self, 'delimiter', '\t')
+ if self.delimiter in ["tab", "\\t"]:
+ object.__setattr__(self, "delimiter", "\t")
filtered_columns = [column_filter.column for column_filter in self.filters]
all_columns = []
if self.columns:
- all_columns = [
- next(iter(column)) if isinstance(column, Dict) else column
- for column in self.columns
- ]
+ all_columns = [next(iter(column)) if isinstance(column, Dict) else column for column in self.columns]
if self.header == HeaderMode.none and not self.columns:
raise ValueError(
- f"there is no header and columns have not been supplied\n"
- f"configure the 'columns' field or set header to the 0-based"
+ "there is no header and columns have not been supplied\n"
+ "configure the 'columns' field or set header to the 0-based"
"index in which it appears in the file, or set this value to"
"'infer'"
)
@@ -257,28 +244,24 @@ def __post_init_post_parse__(self):
raise (ValueError(f"Filter column {column} not in column list"))
for column_filter in self.filters:
- if column_filter.filter_code in ['lt', 'gt', 'lte', 'gte']:
+ if column_filter.filter_code in ["lt", "gt", "lte", "gte"]:
# TODO determine if this should raise an exception
# or instead try to type coerce the string to a float
# type coercion is probably the best thing to do here
if not isinstance(column_filter.value, (int, float)):
- raise ValueError(
- f"Filter value must be int or float for operator {column_filter.filter_code}"
- )
- elif column_filter.filter_code == 'eq':
+ raise ValueError(f"Filter value must be int or float for operator {column_filter.filter_code}")
+ elif column_filter.filter_code == "eq":
if not isinstance(column_filter.value, (str, int, float)):
raise ValueError(
f"Filter value must be string, int or float for operator {column_filter.filter_code}"
)
- elif column_filter.filter_code == 'in':
+ elif column_filter.filter_code == "in":
if not isinstance(column_filter.value, List):
- raise ValueError(
- f"Filter value must be List for operator {column_filter.filter_code}"
- )
+ raise ValueError(f"Filter value must be List for operator {column_filter.filter_code}")
if self.format == FormatType.csv and self.required_properties:
raise ValueError(
- "csv specified but required properties have been configured\n"
+ "CSV specified but required properties have been configured\n"
"either set format to jsonl or change properties to columns in the config"
)
@@ -305,7 +288,7 @@ def __post_init_post_parse__(self):
raise ValueError("Field type map contains more than one key")
for key, val in field.items():
_field_type_map[key] = val
- object.__setattr__(self, '_field_type_map', _field_type_map)
+ object.__setattr__(self, "_field_type_map", _field_type_map)
@property
def field_type_map(self):
diff --git a/src/koza/model/config/sssom_config.py b/src/koza/model/config/sssom_config.py
new file mode 100644
index 0000000..d3a2d57
--- /dev/null
+++ b/src/koza/model/config/sssom_config.py
@@ -0,0 +1,150 @@
+from dataclasses import field
+from enum import Enum
+from pathlib import Path
+from typing import Dict, List, Union, Literal
+
+from loguru import logger
+from pydantic.dataclasses import dataclass
+from sssom.parsers import parse_sssom_table
+from sssom.util import filter_prefixes, merge_msdf
+
+
+class Match(str, Enum):
+ """SSSOM match types."""
+
+ exact = "exact"
+ narrow = "narrow"
+ broad = "broad"
+
+
+@dataclass()
+class SSSOMConfig:
+ """SSSOM config options
+
+ Attributes:
+ files: List of SSSOM files to use
+ filter_prefixes: Optional list of prefixes to filter by
+ subject_target_prefixes: Optional list of prefixes to use for subject mapping
+ object_target_prefixes: Optional list of prefixes to use for object mapping
+
+ """
+
+ files: List[Union[str, Path]] = field(default_factory=list)
+ filter_prefixes: List[str] = field(default_factory=list)
+ subject_target_prefixes: List[str] = field(default_factory=list)
+ object_target_prefixes: List[str] = field(default_factory=list)
+ use_match: List[Match] = field(default_factory=list)
+
+ predicates = {"exact": ["skos:exactMatch"], "narrow": ["skos:narrowMatch"], "broad": ["skos:broadMatch"]}
+
+ def __post_init_post_parse__(self):
+ if not self.use_match:
+ self.use_match = [Match.exact]
+ logger.debug("Building SSSOM Dataframe...")
+ self.df = self._merge_and_filter_sssom()
+ logger.debug("Building SSSOM Lookup Table...")
+ self.lut = self._build_sssom_lut() # use_match=self.use_match)
+
+ def apply_mapping(self, entity: dict) -> dict:
+ """Apply SSSOM mappings to an edge record."""
+
+ if self._has_mapping(entity["subject"], self.subject_target_prefixes):
+ entity["original_subject"] = entity["subject"]
+ entity["subject"] = self._get_mapping(entity["subject"], self.subject_target_prefixes)
+
+ if self._has_mapping(entity["object"], self.object_target_prefixes):
+ entity["original_object"] = entity["object"]
+ entity["object"] = self._get_mapping(entity["object"], self.object_target_prefixes)
+
+ return entity
+
+ def _merge_and_filter_sssom(self):
+ mapping_sets = []
+ for file in self.files:
+ msdf = parse_sssom_table(file)
+ mapping_sets.append(msdf)
+ new_msdf = merge_msdf(*mapping_sets)
+ filters = (self.subject_target_prefixes + self.object_target_prefixes) + list(
+ set(self.filter_prefixes) - set(self.subject_target_prefixes) - set(self.object_target_prefixes)
+ )
+ logger.debug(f"Filtering SSSOM by {filters}")
+ new_msdf = filter_prefixes(
+ df=new_msdf.df, filter_prefixes=filters, require_all_prefixes=False, features=new_msdf.df.columns # type: ignore
+ )
+
+ return new_msdf
+
+ def _build_sssom_lut(self) -> Dict:
+ """Build a lookup table from SSSOM mapping dataframe."""
+ # TODO add narrow and broad match mappings
+ sssom_lut = {}
+ for _, row in self.df.iterrows():
+ subject_id = row["subject_id"]
+ object_id = row["object_id"]
+ predicate = row["predicate_id"]
+ if Match.exact in self.use_match:
+ # Add exact match mappings in both directions
+ sssom_lut = self._set_mapping(subject_id, object_id, predicate, match="exact", lut=sssom_lut)
+ sssom_lut = self._set_mapping(object_id, subject_id, predicate, match="exact", lut=sssom_lut)
+ if Match.narrow in self.use_match:
+ logger.warning("Narrow match not yet implemented")
+ if Match.broad in self.use_match:
+ logger.warning("Broad match not yet implemented")
+ return sssom_lut
+
+ def _has_match(self, predicate, match: Literal[Match.exact, Match.narrow, Match.broad]):
+ """Check if a predicate has a match."""
+ if match == Match.exact:
+ return predicate in self.predicates[Match.exact]
+ if match == Match.narrow:
+ # return predicate in self.predicates["narrow"] or predicate in self.predicates[Match.exact]
+ return False
+ if match == Match.broad:
+ # return predicate in self.predicates["broad"] or predicate in self.predicates[Match.exact]
+ return False
+
+ def _has_mapping(self, id, target_prefixes=None):
+ """Check if an ID has a mapping."""
+ if target_prefixes is None:
+ return id in self.lut
+ else:
+ if id not in self.lut:
+ return False
+ for target_prefix in target_prefixes:
+ if target_prefix in self.lut[id]:
+ return True
+ return False # No mapping found
+
+ def _get_mapping(self, id, target_prefixes):
+ """Get the mapping for an ID."""
+ for target_prefix in target_prefixes:
+ if target_prefix in self.lut[id]:
+ return self.lut[id][target_prefix]
+ raise KeyError(f"Could not find mapping for {id} in {target_prefixes}: {self.lut[id]}")
+
+ def _set_mapping(
+ self,
+ original_id,
+ mapped_id,
+ predicate,
+ match: Literal[Match.exact, Match.narrow, Match.broad],
+ lut: Dict[str, dict],
+ ):
+ """Set a mapping for an ID."""
+ original_prefix = original_id.split(":")[0]
+ mapped_prefix = mapped_id.split(":")[0]
+ target_prefixes = self.subject_target_prefixes + self.object_target_prefixes
+ if (
+ original_prefix in self.filter_prefixes or len(self.filter_prefixes) == 0
+ ) and mapped_prefix in target_prefixes:
+ if original_id not in lut:
+ lut[original_id] = {}
+ if mapped_prefix in lut[original_id]:
+ logger.warning(f"Duplicate mapping for {original_id} to {mapped_prefix}")
+ elif self._has_match(predicate, match):
+ lut[original_id][mapped_prefix] = mapped_id
+ else:
+ logger.warning(
+ f"{match} match not found for {original_id} to {mapped_prefix} with predicate {predicate}"
+ )
+ return lut
diff --git a/src/koza/model/source.py b/src/koza/model/source.py
index 4c9bb75..2fa50b9 100644
--- a/src/koza/model/source.py
+++ b/src/koza/model/source.py
@@ -5,7 +5,8 @@
from koza.io.reader.jsonl_reader import JSONLReader
from koza.io.utils import open_resource
from koza.utils.row_filter import RowFilter
-from koza.model.config.source_config import MapFileConfig, PrimaryFileConfig #, SourceConfig
+from koza.model.config.source_config import MapFileConfig, PrimaryFileConfig # , SourceConfig
+
# from koza.io.yaml_loader import UniqueIncludeLoader
# import yaml
@@ -22,10 +23,7 @@ class Source:
and yields a dictionary
"""
- def __init__(
- self, config: Union[PrimaryFileConfig, MapFileConfig], row_limit: Optional[int] = None
- ):
-
+ def __init__(self, config: Union[PrimaryFileConfig, MapFileConfig], row_limit: Optional[int] = None):
self.config = config
self.row_limit = row_limit
self._filter = RowFilter(config.filters)
diff --git a/src/koza/model/translation_table.py b/src/koza/model/translation_table.py
index 7370677..2af93ca 100644
--- a/src/koza/model/translation_table.py
+++ b/src/koza/model/translation_table.py
@@ -1,4 +1,3 @@
-import logging
from dataclasses import dataclass
from typing import Dict, Optional
@@ -45,9 +44,7 @@ def __post_init__(self):
if not is_dictionary_bimap(self.global_table):
raise ValueError("Global table is not a bimap")
- def resolve_term(
- self, word: str, mandatory: Optional[bool] = True, default: Optional[str] = None
- ):
+ def resolve_term(self, word: str, mandatory: Optional[bool] = True, default: Optional[str] = None):
"""
Resolve a term from a source to its preferred curie
diff --git a/src/koza/utils/log_utils.py b/src/koza/utils/log_utils.py
index 2684a28..98b3100 100644
--- a/src/koza/utils/log_utils.py
+++ b/src/koza/utils/log_utils.py
@@ -4,21 +4,19 @@
LOGURU_FORMAT = "{time:YYYY-MM-DD_HH:mm:ss} | {level: <8} | {name: <16} | {message}"
LOGURU_FORMAT_SIMPLE = "{time:YYYY-MM-DD_HH:mm:ss} | {level: <8} | {name: <16} | {message}"
+
def get_logger(name: str = None, verbose: bool = None):
logger = loguru.logger
logger.remove()
logger.add(
- sink = sys.stderr,
- level = "INFO" if (verbose is None) else "DEBUG" if (verbose == True) else "WARNING",
- format = LOGURU_FORMAT,
- colorize = True,
+ sink=sys.stderr,
+ level="INFO" if (verbose is None) else "DEBUG" if (verbose == True) else "WARNING",
+ format=LOGURU_FORMAT,
+ colorize=True,
)
if name:
fp = f"logs/{name}"
logger.add(
- sink = fp + "_{time:YYYYMMDD_HHmmss}.koza.log",
- level = "DEBUG",
- format = LOGURU_FORMAT_SIMPLE,
- colorize = True
+ sink=fp + "_{time:YYYYMMDD_HHmmss}.koza.log", level="DEBUG", format=LOGURU_FORMAT_SIMPLE, colorize=True
)
- return logger
\ No newline at end of file
+ return logger
diff --git a/tests/conftest.py b/tests/conftest.py
index 95b005d..2f92415 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -2,7 +2,6 @@
from typing import Iterable
import pytest
-from _pytest.logging import LogCaptureFixture
from loguru import logger
from koza.app import KozaApp
@@ -20,7 +19,6 @@ def caplog(caplog):
@pytest.fixture(scope="package")
def mock_koza():
-
# This should be extracted out but for quick prototyping
def _mock_write(self, *entities):
self._entities = list(entities)
diff --git a/tests/integration/test_examples.py b/tests/integration/test_examples.py
index 2a89145..946e5d0 100644
--- a/tests/integration/test_examples.py
+++ b/tests/integration/test_examples.py
@@ -24,17 +24,12 @@
],
)
def test_examples(source_name, ingest, output_format):
-
source_config = f"examples/{source_name}/{ingest}.yaml"
-
- output_suffix = str(output_format).split('.')[1]
- output_dir = f"./output/tests/string-test-examples"
- output_files = [
- f"{output_dir}/{ingest}_nodes.{output_suffix}",
- f"{output_dir}/{ingest}_edges.{output_suffix}"
- ]
+ output_suffix = str(output_format).split('.')[1]
+ output_dir = "./output/tests/string-test-examples"
+ output_files = [f"{output_dir}/{ingest}_nodes.{output_suffix}", f"{output_dir}/{ingest}_edges.{output_suffix}"]
transform_source(source_config, output_dir, output_format, "examples/translation_table.yaml", None)
diff --git a/tests/integration/test_parallel.py b/tests/integration/test_parallel.py
index 1668bd7..9809410 100644
--- a/tests/integration/test_parallel.py
+++ b/tests/integration/test_parallel.py
@@ -1,7 +1,7 @@
"""
Test parallel transforms
"""
-#import pytest
+# import pytest
import dask
from koza.cli_runner import transform_source
@@ -19,19 +19,23 @@ def transform(source_file):
)
return source_file
+
@dask.delayed
def transform_string():
return transform("examples/string/protein-links-detailed.yaml")
+
@dask.delayed
def transform_string_string_declarative():
return transform("examples/string-declarative/declarative-protein-links-detailed.yaml")
+
a = transform_string()
b = transform_string_string_declarative()
+
def test_parallel_transforms():
- results = [a,b]
+ results = [a, b]
result = dask.delayed(print)(results)
result.compute()
diff --git a/tests/integration/test_row_limit.py b/tests/integration/test_row_limit.py
index f78d0f0..3c9d8b7 100644
--- a/tests/integration/test_row_limit.py
+++ b/tests/integration/test_row_limit.py
@@ -26,14 +26,11 @@
)
],
)
-def test_examples(
- source_name, ingest, output_format, row_limit, header_len, expected_node_len, expected_edge_len
-):
-
+def test_examples(source_name, ingest, output_format, row_limit, header_len, expected_node_len, expected_edge_len):
source_config = f"examples/{source_name}/{ingest}.yaml"
-
+
output_suffix = str(output_format).split('.')[1]
- output_dir = f"./output/tests/string-test-row-limit"
+ output_dir = "./output/tests/string-test-row-limit"
transform_source(
source=source_config,
@@ -44,20 +41,14 @@ def test_examples(
)
# hacky check that correct number of rows was processed
- #node_file = f"{output_dir}/string/{ingest}-row-limit_nodes{output_suffix}"
- #edge_file = f"{output_dir}/string/{ingest}-row-limit_edges{output_suffix}"
+ # node_file = f"{output_dir}/string/{ingest}-row-limit_nodes{output_suffix}"
+ # edge_file = f"{output_dir}/string/{ingest}-row-limit_edges{output_suffix}"
- output_files = [
- f"{output_dir}/{ingest}_nodes.{output_suffix}",
- f"{output_dir}/{ingest}_edges.{output_suffix}"
- ]
+ output_files = [f"{output_dir}/{ingest}_nodes.{output_suffix}", f"{output_dir}/{ingest}_edges.{output_suffix}"]
- number_of_lines = [
- sum(1 for line in open(output_files[0])),
- sum(1 for line in open(output_files[1]))
- ]
+ number_of_lines = [sum(1 for line in open(output_files[0])), sum(1 for line in open(output_files[1]))]
assert number_of_lines == [expected_node_len, expected_edge_len]
- #assert node_lines == expected_node_len
- #assert edge_lines == expected_edge_len
+ # assert node_lines == expected_node_len
+ # assert edge_lines == expected_edge_len
diff --git a/tests/integration/test_validator.py b/tests/integration/test_validator.py
index fa952a5..12cdb16 100644
--- a/tests/integration/test_validator.py
+++ b/tests/integration/test_validator.py
@@ -12,9 +12,10 @@
from koza.cli_runner import transform_source
from koza.model.config.source_config import OutputFormat
-#model_schema = Path(__file__).parent.parent / 'resources' / 'biolink-model.yaml'
+# model_schema = Path(__file__).parent.parent / 'resources' / 'biolink-model.yaml'
model_schema = "tests/resources/biolink-model.yaml"
+
@pytest.mark.parametrize(
"source_name, ingest, output_format, schema",
[
@@ -29,23 +30,15 @@
],
)
def test_validator(source_name, ingest, output_format, schema):
-
source_config = f"examples/{source_name}/{ingest}.yaml"
-
+
output_suffix = str(output_format).split('.')[1]
- output_dir = f"./output/tests/string-test-validator"
+ output_dir = "./output/tests/string-test-validator"
- output_files = [
- f"{output_dir}/{ingest}_nodes.{output_suffix}",
- f"{output_dir}/{ingest}_edges.{output_suffix}"
- ]
+ output_files = [f"{output_dir}/{ingest}_nodes.{output_suffix}", f"{output_dir}/{ingest}_edges.{output_suffix}"]
transform_source(
- source_config,
- output_dir,
- output_format,
- global_table="tests/resources/translation_table.yaml",
- schema=schema
+ source_config, output_dir, output_format, global_table="tests/resources/translation_table.yaml", schema=schema
)
for file in output_files:
diff --git a/tests/resources/sssom/testmapping.sssom.tsv b/tests/resources/sssom/testmapping.sssom.tsv
new file mode 100644
index 0000000..316c438
--- /dev/null
+++ b/tests/resources/sssom/testmapping.sssom.tsv
@@ -0,0 +1,9 @@
+subject_id predicate_id object_id mapping_justification
+A:123 skos:exactMatch B:987 semapv:ManualMappingCuration
+B:000 skos:exactMatch A:420 semapv:ManualMappingCuration
+A:456 skos:broadMatch B:654 semapv:ManualMappingCuration
+A:789 skos:narrowMatch B:321 semapv:ManualMappingCuration
+X:000 skos:exactMatch Y:999 semapv:ManualMappingCuration
+X:111 skos:broadMatch Y:888 semapv:ManualMappingCuration
+X:222 skos:narrowMatch Y:777 semapv:ManualMappingCuration
+A:123 skos:exactMatch Y:666 semapv:ManualMappingCuration
diff --git a/tests/resources/sssom/testmapping2.sssom.tsv b/tests/resources/sssom/testmapping2.sssom.tsv
new file mode 100644
index 0000000..0c3d9e6
--- /dev/null
+++ b/tests/resources/sssom/testmapping2.sssom.tsv
@@ -0,0 +1,10 @@
+subject_id predicate_id object_id mapping_justification
+A:111 skos:exactMatch B:999 semapv:ManualMappingCuration
+A:222 skos:exactMatch B:888 semapv:ManualMappingCuration
+A:333 skos:exactMatch B:777 semapv:ManualMappingCuration
+A:444 skos:exactMatch B:666 semapv:ManualMappingCuration
+A:555 skos:exactMatch B:555 semapv:ManualMappingCuration
+A:666 skos:exactMatch B:444 semapv:ManualMappingCuration
+A:777 skos:exactMatch B:333 semapv:ManualMappingCuration
+A:888 skos:exactMatch B:222 semapv:ManualMappingCuration
+A:999 skos:exactMatch B:111 semapv:ManualMappingCuration
diff --git a/tests/unit/test_csvreader.py b/tests/unit/test_csvreader.py
index 1f9793d..f994f20 100644
--- a/tests/unit/test_csvreader.py
+++ b/tests/unit/test_csvreader.py
@@ -6,9 +6,7 @@
from koza.model.config.source_config import FieldType
test_file = Path(__file__).parent.parent / 'resources' / 'source-files' / 'string.tsv'
-tsv_with_footer = (
- Path(__file__).parent.parent / 'resources' / 'source-files' / 'tsv-with-footer.tsv'
-)
+tsv_with_footer = Path(__file__).parent.parent / 'resources' / 'source-files' / 'tsv-with-footer.tsv'
field_type_map = {
@@ -61,8 +59,8 @@ def test_field_in_file_but_not_in_config_logs_warning(caplog):
del field_map['combined_score']
reader = CSVReader(string_file, field_map, delimiter=' ')
next(reader)
- assert caplog.records[1].levelname == 'WARNING'
- assert caplog.records[1].msg.startswith('Additional column(s) in source file')
+ assert caplog.records[1].levelname == 'WARNING'
+ assert caplog.records[1].msg.startswith('Additional column(s) in source file')
def test_middle_field_in_file_but_not_in_config_logs_warning(caplog):
@@ -71,9 +69,9 @@ def test_middle_field_in_file_but_not_in_config_logs_warning(caplog):
del field_map['cooccurence']
reader = CSVReader(string_file, field_map, delimiter=' ')
next(reader)
- assert caplog.records[1].levelname == 'WARNING'
+ assert caplog.records[1].levelname == 'WARNING'
# assert caplog.records[1].msg.startswith('Additional columns located within configured fields')
- assert caplog.records[1].msg.startswith('Additional column(s) in source file')
+ assert caplog.records[1].msg.startswith('Additional column(s) in source file')
def test_no_field_map(caplog):
diff --git a/tests/unit/test_jsonlreader.py b/tests/unit/test_jsonlreader.py
index ad283d4..8e83d9a 100644
--- a/tests/unit/test_jsonlreader.py
+++ b/tests/unit/test_jsonlreader.py
@@ -7,6 +7,7 @@
test_zfin_data = Path(__file__).parents[1] / 'resources' / 'source-files' / 'ZFIN_PHENOTYPE_0.jsonl.gz'
+
def test_normal_case():
with gzip.open(test_zfin_data, 'rt') as zfin:
jsonl_reader = JSONLReader(zfin)
@@ -18,7 +19,7 @@ def test_normal_case():
def test_required_property():
with gzip.open(test_zfin_data, 'rt') as zfin:
- jsonl_reader = JSONLReader(zfin, required_properties = ['objectId', 'evidence.publicationId'])
+ jsonl_reader = JSONLReader(zfin, required_properties=['objectId', 'evidence.publicationId'])
for row in jsonl_reader:
# assert len(row) == 1 # removed subsetter
print(row)
diff --git a/tests/unit/test_jsonlreader_row_limit.py b/tests/unit/test_jsonlreader_row_limit.py
index c72b61e..63aac92 100644
--- a/tests/unit/test_jsonlreader_row_limit.py
+++ b/tests/unit/test_jsonlreader_row_limit.py
@@ -5,9 +5,7 @@
from koza.io.reader.jsonl_reader import JSONLReader
-test_zfin = (
- Path(__file__).parent.parent / 'resources' / 'source-files' / 'ZFIN_PHENOTYPE_0.jsonl.gz'
-)
+test_zfin = Path(__file__).parent.parent / 'resources' / 'source-files' / 'ZFIN_PHENOTYPE_0.jsonl.gz'
def test_normal_case():
diff --git a/tests/unit/test_jsonreader.py b/tests/unit/test_jsonreader.py
index 9130d5e..f57fd27 100644
--- a/tests/unit/test_jsonreader.py
+++ b/tests/unit/test_jsonreader.py
@@ -7,7 +7,10 @@
test_zfin_data = Path(__file__).parents[1] / 'resources' / 'source-files' / 'test_BGI_ZFIN.json.gz'
-json_path = ['data', 0,]
+json_path = [
+ 'data',
+ 0,
+]
def test_normal_case():
@@ -25,6 +28,7 @@ def test_required_properties():
assert row['name']
assert row['basicGeneticEntity']['primaryId']
+
def test_missing_req_property_raises_exception():
with gzip.open(test_zfin_data, 'rt') as zfin:
json_reader = JSONReader(zfin, ['fake_prop'], json_path=json_path)
diff --git a/tests/unit/test_kgx_converter.py b/tests/unit/test_kgx_converter.py
index b641ddf..95ecc97 100644
--- a/tests/unit/test_kgx_converter.py
+++ b/tests/unit/test_kgx_converter.py
@@ -1,5 +1,5 @@
import pytest
-from biolink.pydanticmodel import Gene, GeneToGeneAssociation, Publication
+from biolink.pydanticmodel import Gene, GeneToGeneAssociation
from koza.converter.kgx_converter import KGXConverter
@@ -26,7 +26,7 @@ def test_gene_conversion():
def test_association_conversion():
fgf8a = Gene(id="ZFIN:ZDB-GENE-990415-72", symbol="fgf8a", name="fibroblast growth factor 8a")
pax2a = Gene(id="ZFIN:ZDB-GENE-990415-8", symbol="pax2a", name="paired box 2a")
- pub = "PMID:17522161" # Publication(id="PMID:17522161", type="MESH:foobar")
+ pub = "PMID:17522161" # Publication(id="PMID:17522161", type="MESH:foobar")
association = GeneToGeneAssociation(
id='uuid:123',
subject=fgf8a.id,
diff --git a/tests/unit/test_multifile.py b/tests/unit/test_multifile.py
index a6a8806..aa0099e 100644
--- a/tests/unit/test_multifile.py
+++ b/tests/unit/test_multifile.py
@@ -1,4 +1,3 @@
-import pytest
import yaml
from pathlib import Path
@@ -6,6 +5,7 @@
from koza.model.config.source_config import PrimaryFileConfig
from koza.io.yaml_loader import UniqueIncludeLoader
+
def test_multiple_files():
source_file = Path(__file__).parent.parent / 'resources' / 'multifile.yaml'
diff --git a/tests/unit/test_sssom_mapping.py b/tests/unit/test_sssom_mapping.py
new file mode 100644
index 0000000..c83c32d
--- /dev/null
+++ b/tests/unit/test_sssom_mapping.py
@@ -0,0 +1,55 @@
+from koza.model.config.sssom_config import SSSOMConfig
+
+sssom_files = ['tests/resources/sssom/testmapping.sssom.tsv', 'tests/resources/sssom/testmapping2.sssom.tsv']
+
+
+def test_basic_mapping():
+ sssom_config = SSSOMConfig(
+ files=sssom_files,
+ filter_prefixes=['A', 'B', 'SOMETHINGELSE'],
+ subject_target_prefixes=['B'],
+ object_target_prefixes=['X'],
+ )
+ print(sssom_config.use_match)
+ edge = {
+ 'subject': 'A:123',
+ 'object': 'SOMETHINGELSE:456',
+ }
+ mapped = sssom_config.apply_mapping(edge)
+ assert mapped['subject'] == 'B:987'
+
+
+def test_merge_and_filter():
+ sssom_config = SSSOMConfig(
+ files=sssom_files,
+ filter_prefixes=['A', 'B'],
+ )
+ df = sssom_config.df
+ assert 'A:123' in df['subject_id'].values
+ assert 'B:987' in df['object_id'].values
+ assert 'X:111' not in df['object_id'].values and 'X:111' not in df['subject_id'].values
+
+
+def test_exact_match_is_bidirectional():
+ sssom_config = SSSOMConfig(
+ files=sssom_files, filter_prefixes=['A', 'B'], subject_target_prefixes=['B'], object_target_prefixes=['B']
+ )
+
+ edge = {
+ 'subject': 'A:123',
+ 'object': 'SOMETHINGELSE:456',
+ }
+ mapped = sssom_config.apply_mapping(edge)
+ assert mapped['subject'] == 'B:987'
+
+ edge = {'subject': 'SOMETHINGELSE:123', 'object': 'A:420'}
+ mapped = sssom_config.apply_mapping(edge)
+ assert mapped['object'] == 'B:000'
+
+
+def test_narrow_match():
+ pass
+
+
+def test_broad_match():
+ pass
diff --git a/tests/unit/test_validation.py b/tests/unit/test_validation.py
index 6076b1a..90149d2 100644
--- a/tests/unit/test_validation.py
+++ b/tests/unit/test_validation.py
@@ -1,34 +1,29 @@
-from pathlib import Path
+# import pytest
+# from linkml_validator.validator import Validator
-import pytest
-from linkml_validator.validator import Validator
+# valid_gene = {
+# "id": "BOGUS:12345",
+# "name": "Bogus Gene 12345",
+# "category": ["biolink:NamedThing", "biolink:Gene"],
+# }
-valid_gene = {
- "id": "BOGUS:12345",
- "name": "Bogus Gene 12345",
- "category": ["biolink:NamedThing", "biolink:Gene"],
-}
+# invalid_gene = {"name": "Bogus Gene 98765", "type": "biolink:NamedThing"}
-invalid_gene = {
- "name": "Bogus Gene 98765",
- "type": "biolink:NamedThing"
-}
+# model_url = "https://raw.githubusercontent.com/biolink/biolink-model/latest/biolink-model.yaml"
+# validator = Validator(schema=model_url)
+# # model_schema = Path(__file__).parent.parent / 'resources' / 'biolink-model.yaml'
+# # validator = Validator(schema="tests/resources/biolink-model.yaml")
-model_url = "https://raw.githubusercontent.com/biolink/biolink-model/latest/biolink-model.yaml"
-validator = Validator(schema=model_url)
-# model_schema = Path(__file__).parent.parent / 'resources' / 'biolink-model.yaml'
-# validator = Validator(schema="tests/resources/biolink-model.yaml")
-@pytest.mark.parametrize("gene", [valid_gene])
-def test_valid_input(gene):
+# @pytest.mark.parametrize("gene", [valid_gene])
+# def test_valid_input(gene):
+# v = validator.validate(obj=gene, target_class="Gene")
+# result = v.validation_results[0]
+# assert result.valid == True
- v = validator.validate(obj=gene, target_class="Gene")
- result = v.validation_results[0]
- assert result.valid == True
-
-@pytest.mark.parametrize("gene", [invalid_gene])
-def test_invalid_input(gene):
- v = validator.validate(obj=gene, target_class="Gene")
- result = v.validation_results[0]
- assert result.valid == False
+# @pytest.mark.parametrize("gene", [invalid_gene])
+# def test_invalid_input(gene):
+# v = validator.validate(obj=gene, target_class="Gene")
+# result = v.validation_results[0]
+# assert result.valid == False