From ab12625a196beacda59486781a3e3af63ecacba2 Mon Sep 17 00:00:00 2001 From: Gytha Ogg Date: Wed, 29 Nov 2023 12:33:50 +0100 Subject: [PATCH 1/5] Create a model for caching Zotero entries --- apis_ontology/migrations/0031_zoteroentry.py | 47 ++++++++++++++++++++ apis_ontology/models.py | 9 ++++ 2 files changed, 56 insertions(+) create mode 100644 apis_ontology/migrations/0031_zoteroentry.py diff --git a/apis_ontology/migrations/0031_zoteroentry.py b/apis_ontology/migrations/0031_zoteroentry.py new file mode 100644 index 0000000..07724fe --- /dev/null +++ b/apis_ontology/migrations/0031_zoteroentry.py @@ -0,0 +1,47 @@ +# Generated by Django 4.1.13 on 2023-11-29 11:27 + +from django.db import migrations, models + + +class Migration(migrations.Migration): + + dependencies = [ + ("apis_ontology", "0030_merge_20231016_0118"), + ] + + operations = [ + migrations.CreateModel( + name="ZoteroEntry", + fields=[ + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ( + "zoteroId", + models.CharField(max_length=255, verbose_name="Zotero ID"), + ), + ( + "shortTitle", + models.TextField(blank=True, null=True, verbose_name="Short title"), + ), + ( + "fullCitation", + models.TextField( + blank=True, null=True, verbose_name="Full Citation" + ), + ), + ( + "year", + models.IntegerField( + blank=True, null=True, verbose_name="Year of publication" + ), + ), + ], + ), + ] diff --git a/apis_ontology/models.py b/apis_ontology/models.py index 6537c5d..ac53ffe 100644 --- a/apis_ontology/models.py +++ b/apis_ontology/models.py @@ -193,3 +193,12 @@ class Place(TempEntityClass): alternative_names = models.TextField( blank=True, null=True, verbose_name="Alternative names" ) + + +class ZoteroEntry(models.Model): + zoteroId = models.CharField(max_length=255, verbose_name="Zotero ID") + shortTitle = models.TextField(blank=True, null=True, verbose_name="Short title") + fullCitation = models.TextField(blank=True, null=True, verbose_name="Full Citation") + year = models.IntegerField( + blank=True, null=True, verbose_name="Year of publication" + ) From d85a12a8ebaf85b8010a3209adb7cba412ba94ed Mon Sep 17 00:00:00 2001 From: Gytha Ogg Date: Wed, 29 Nov 2023 13:00:28 +0100 Subject: [PATCH 2/5] include dev dependencies to support shell-plus --- poetry.lock | 1731 ++++++++++++++++++++++++++++++++++++++++++++++-- pyproject.toml | 10 + 2 files changed, 1681 insertions(+), 60 deletions(-) diff --git a/poetry.lock b/poetry.lock index 53109f4..04ee996 100644 --- a/poetry.lock +++ b/poetry.lock @@ -11,6 +11,26 @@ files = [ {file = "acdh_django_charts-0.6.0-py2.py3-none-any.whl", hash = "sha256:e13a10e24fe7f275544384a759be5fcf3c52ce70c74465d449e5ba75f84f845f"}, ] +[[package]] +name = "anyio" +version = "4.1.0" +description = "High level compatibility layer for multiple asynchronous event loop implementations" +optional = false +python-versions = ">=3.8" +files = [ + {file = "anyio-4.1.0-py3-none-any.whl", 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"sha256:71ddfc23a0e03ef2df1c1397d859868d158c8276a0603b96cf86892bff58149f"}, + {file = "tornado-6.4-cp38-abi3-win32.whl", hash = "sha256:6f8a6c77900f5ae93d8b4ae1196472d0ccc2775cc1dfdc9e7727889145c45052"}, + {file = "tornado-6.4-cp38-abi3-win_amd64.whl", hash = "sha256:10aeaa8006333433da48dec9fe417877f8bcc21f48dda8d661ae79da357b2a63"}, + {file = "tornado-6.4.tar.gz", hash = "sha256:72291fa6e6bc84e626589f1c29d90a5a6d593ef5ae68052ee2ef000dfd273dee"}, +] + [[package]] name = "tqdm" version = "4.65.0" @@ -1378,6 +2921,21 @@ notebook = ["ipywidgets (>=6)"] slack = ["slack-sdk"] telegram = ["requests"] +[[package]] +name = "traitlets" +version = "5.14.0" +description = "Traitlets Python configuration system" +optional = false +python-versions = ">=3.8" +files = [ + {file = "traitlets-5.14.0-py3-none-any.whl", hash = "sha256:f14949d23829023013c47df20b4a76ccd1a85effb786dc060f34de7948361b33"}, + {file = "traitlets-5.14.0.tar.gz", hash = "sha256:fcdaa8ac49c04dfa0ed3ee3384ef6dfdb5d6f3741502be247279407679296772"}, +] + +[package.extras] +docs = ["myst-parser", "pydata-sphinx-theme", "sphinx"] +test = ["argcomplete (>=3.0.3)", "mypy (>=1.7.0)", "pre-commit", "pytest (>=7.0,<7.5)", "pytest-mock", "pytest-mypy-testing"] + [[package]] name = "tzdata" version = "2023.3" @@ -1426,6 +2984,32 @@ brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"] socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"] zstd = ["zstandard (>=0.18.0)"] +[[package]] +name = "wcwidth" +version = "0.2.12" +description = "Measures the displayed width of unicode strings in a terminal" +optional = false +python-versions = "*" +files = [ + {file = "wcwidth-0.2.12-py2.py3-none-any.whl", hash = "sha256:f26ec43d96c8cbfed76a5075dac87680124fa84e0855195a6184da9c187f133c"}, + {file = "wcwidth-0.2.12.tar.gz", hash = "sha256:f01c104efdf57971bcb756f054dd58ddec5204dd15fa31d6503ea57947d97c02"}, +] + +[[package]] +name = "webcolors" +version = "1.13" +description = "A library for working with the color formats defined by HTML and CSS." +optional = false +python-versions = ">=3.7" +files = [ + {file = "webcolors-1.13-py3-none-any.whl", hash = "sha256:29bc7e8752c0a1bd4a1f03c14d6e6a72e93d82193738fa860cbff59d0fcc11bf"}, + {file = "webcolors-1.13.tar.gz", hash = "sha256:c225b674c83fa923be93d235330ce0300373d02885cef23238813b0d5668304a"}, +] + +[package.extras] +docs = ["furo", "sphinx", "sphinx-copybutton", "sphinx-inline-tabs", "sphinx-notfound-page", "sphinxext-opengraph"] +tests = ["pytest", "pytest-cov"] + [[package]] name = "webencodings" version = "0.5.1" @@ -1455,6 +3039,22 @@ url = "https://github.com/acdh-oeaw/apis-webpage.git" reference = "v1.0.1" resolved_reference = "9e5334513576c533bce64669129895eb62818dfd" +[[package]] +name = "websocket-client" +version = "1.6.4" +description = "WebSocket client for Python with low level API options" +optional = false +python-versions = ">=3.8" +files = [ + {file = "websocket-client-1.6.4.tar.gz", hash = "sha256:b3324019b3c28572086c4a319f91d1dcd44e6e11cd340232978c684a7650d0df"}, + {file = "websocket_client-1.6.4-py3-none-any.whl", hash = "sha256:084072e0a7f5f347ef2ac3d8698a5e0b4ffbfcab607628cadabc650fc9a83a24"}, +] + +[package.extras] +docs = ["Sphinx (>=6.0)", "sphinx-rtd-theme (>=1.1.0)"] +optional = ["python-socks", "wsaccel"] +test = ["websockets"] + [[package]] name = "whitenoise" version = "5.3.0" @@ -1469,7 +3069,18 @@ files = [ [package.extras] brotli = ["Brotli"] +[[package]] +name = "widgetsnbextension" +version = "4.0.9" +description = "Jupyter interactive widgets for Jupyter Notebook" +optional = false +python-versions = ">=3.7" +files = [ + {file = "widgetsnbextension-4.0.9-py3-none-any.whl", hash = "sha256:91452ca8445beb805792f206e560c1769284267a30ceb1cec9f5bcc887d15175"}, + {file = "widgetsnbextension-4.0.9.tar.gz", hash = "sha256:3c1f5e46dc1166dfd40a42d685e6a51396fd34ff878742a3e47c6f0cc4a2a385"}, +] + [metadata] lock-version = "2.0" python-versions = ">=3.11,<3.12" -content-hash = "be55e11be7cc8f1e8149f69b3fd9b72c660a0a1b5d0b9e366e77b25d3479b19d" +content-hash = "e9644c06e898f93c03c860b37103563124916d005cf05b6ccd1cf2688c435275" diff --git a/pyproject.toml b/pyproject.toml index 4090227..b08ca20 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -26,6 +26,16 @@ django-csp = "^3.7" django-allow-cidr = "^0.3.1" apis-override-select2js = {git = "https://github.com/acdh-oeaw/apis-override-select2js.git", tag = "v0.1.0" } +[tool.poetry.group.dev] +optional = true + +[tool.poetry.group.dev.dependencies] +django-extensions = "^3.1.0" +jupyter = "^1.0.0" +jupyter-tabnine = "^1.2.3" +black = "^22.12.0" +flake8 = "^6.0.0" + [build-system] requires = ["poetry-core>=1.0.0"] build-backend = "poetry.core.masonry.api" From b0f8d1dd3353a8335747ef9fa7865ef05e70bf06 Mon Sep 17 00:00:00 2001 From: Gytha Ogg Date: Thu, 30 Nov 2023 13:12:14 +0100 Subject: [PATCH 3/5] Store pub year as string --- .../migrations/0032_alter_zoteroentry_year.py | 23 +++++++++++++++++++ apis_ontology/models.py | 4 ++-- 2 files changed, 25 insertions(+), 2 deletions(-) create mode 100644 apis_ontology/migrations/0032_alter_zoteroentry_year.py diff --git a/apis_ontology/migrations/0032_alter_zoteroentry_year.py b/apis_ontology/migrations/0032_alter_zoteroentry_year.py new file mode 100644 index 0000000..bce4c54 --- /dev/null +++ b/apis_ontology/migrations/0032_alter_zoteroentry_year.py @@ -0,0 +1,23 @@ +# Generated by Django 4.1.13 on 2023-11-30 12:11 + +from django.db import migrations, models + + +class Migration(migrations.Migration): + + dependencies = [ + ("apis_ontology", "0031_zoteroentry"), + ] + + operations = [ + migrations.AlterField( + model_name="zoteroentry", + name="year", + field=models.CharField( + blank=True, + max_length=255, + null=True, + verbose_name="Year of publication", + ), + ), + ] diff --git a/apis_ontology/models.py b/apis_ontology/models.py index ac53ffe..0d4cb2d 100644 --- a/apis_ontology/models.py +++ b/apis_ontology/models.py @@ -199,6 +199,6 @@ class ZoteroEntry(models.Model): zoteroId = models.CharField(max_length=255, verbose_name="Zotero ID") shortTitle = models.TextField(blank=True, null=True, verbose_name="Short title") fullCitation = models.TextField(blank=True, null=True, verbose_name="Full Citation") - year = models.IntegerField( - blank=True, null=True, verbose_name="Year of publication" + year = models.CharField( + max_length=255, blank=True, null=True, verbose_name="Year of publication" ) From 1effd47d312d7826c1264d6e25274b93de1720ee Mon Sep 17 00:00:00 2001 From: Gytha Ogg Date: Thu, 30 Nov 2023 14:39:50 +0100 Subject: [PATCH 4/5] Cache Zotero entries in the database --- .../management/commands/update_zotero_data.py | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 apis_ontology/management/commands/update_zotero_data.py diff --git a/apis_ontology/management/commands/update_zotero_data.py b/apis_ontology/management/commands/update_zotero_data.py new file mode 100644 index 0000000..31239e7 --- /dev/null +++ b/apis_ontology/management/commands/update_zotero_data.py @@ -0,0 +1,54 @@ +import logging +import os, requests +from django.core.management.base import BaseCommand +import requests, os +from requests.auth import HTTPBasicAuth +import pandas as pd +from tqdm.auto import tqdm +from apis_ontology.models import ZoteroEntry + +USER = os.environ.get("APIS_BIBSONOMY_USER") +KEY = os.environ.get("APIS_BIBSONOMY_PASSWORD") +GROUP = "4394244" + + +QUERY_URL = f"https://api.zotero.org/groups/{GROUP}/items" +HEADERS = {"Authorization": f"Bearer {KEY}"} +PARAMS = {"v": 3, "format": "json"} + +logger = logging.getLogger(__name__) + + +class Command(BaseCommand): + def add_arguments(self, parser): + parser.add_argument( + "--fake", action="store_true", help="Whether to fake or really update" + ) + + def handle(self, *args, **kwargs): + res = requests.get(QUERY_URL, headers=HEADERS, params=PARAMS) + res.raise_for_status() + num_records = res.headers["Total-Results"] + + all_items = [] + for start in tqdm(range(0, int(num_records), 25)): + PARAMS["start"] = start + res = requests.get(QUERY_URL, headers=HEADERS, params=PARAMS) + + res.raise_for_status() + items = res.json() + all_items.extend(items) + + df = pd.json_normalize(all_items) + + for i, row in tqdm(df.iterrows(), total=df.shape[0]): + if "apis" in [tag["tag"].lower() for tag in row["data.tags"]]: + zotero_entry, _ = ZoteroEntry.objects.get_or_create( + zoteroId=row["data.key"] + ) + zotero_entry.shortTitle = row["data.shortTitle"] + zotero_entry.fullCitation = row["data.title"] + zotero_entry.year = row["data.date"] + zotero_entry.save() + + print(f"Cached {len(ZoteroEntry.objects.all())} zotero entries.") From c57ff416c0fe7d82eda03c6660aa2891497920e1 Mon Sep 17 00:00:00 2001 From: Gytha Ogg Date: Thu, 30 Nov 2023 14:42:07 +0100 Subject: [PATCH 5/5] Organise imports --- .../management/commands/update_zotero_data.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/apis_ontology/management/commands/update_zotero_data.py b/apis_ontology/management/commands/update_zotero_data.py index 31239e7..132e6bb 100644 --- a/apis_ontology/management/commands/update_zotero_data.py +++ b/apis_ontology/management/commands/update_zotero_data.py @@ -1,11 +1,11 @@ import logging -import os, requests -from django.core.management.base import BaseCommand -import requests, os -from requests.auth import HTTPBasicAuth +import os + import pandas as pd -from tqdm.auto import tqdm +import requests from apis_ontology.models import ZoteroEntry +from django.core.management.base import BaseCommand +from tqdm.auto import tqdm USER = os.environ.get("APIS_BIBSONOMY_USER") KEY = os.environ.get("APIS_BIBSONOMY_PASSWORD")