diff options
Diffstat (limited to 'python')
| -rw-r--r-- | python/README.md | 41 | ||||
| -rw-r--r-- | python/TODO | 6 | ||||
| -rwxr-xr-x | python/codegen_python_client.sh | 5 | ||||
| -rw-r--r-- | python/fatcat/templates/base.html | 1 | ||||
| -rw-r--r-- | python/fatcat/templates/release_view.html | 2 | ||||
| -rw-r--r-- | python/fatcat_client/api/default_api.py | 20 | ||||
| -rw-r--r-- | python/tests/grobid_metadata_importer.py | 8 |
7 files changed, 62 insertions, 21 deletions
diff --git a/python/README.md b/python/README.md index 1369051a..9ba6b990 100644 --- a/python/README.md +++ b/python/README.md @@ -1,18 +1,47 @@ -## Python Web Interface and API Client Library +## Python Web Interface -Use `pipenv` (which you can install with `pip`). +This project uses `pipenv` to manage dependencies, and assumes Python 3.5 +(which pipenv may install if you are running a different local version). You +can can install `pipenv` with `pip`. You may want to set the +`PIPENV_VENV_IN_PROJECT` environment variable on your development machine (see +pipenv docs for details). +To just run the web interface (which will try to connect to a back-end API +server on the same machine by default), use: + + # will listen on http://localhost:9810 by default pipenv run fatcat_webface.py -Run tests: +## Python Client Library + +An auto-generated python client library for the fatcat API lives under +`./fatcat_client`. It includes entity model objects and functions to call all +API endpoints; see `./README_codegen.md` for details. + +To re-generate swagger-codegen python client library (requires docker installed +locally): + + ./codegen_python_client.sh + +## Running Tests + +Many (though not all) python tests depend on access to a local running API +server (the `fatcatd` rust daemon, code in `../rust/`), which itself depends on +a local PostgreSQL database server. Tests will fail if this endpoint isn't +found. See the README there to get that set up first. The CI integration tests +build and start this daemon automatically. + +To run the python tests (with `fatcatd` running locally on port 9411): pipenv install --dev pipenv run pytest - # for coverage: +To calculate code coverage (of python code): + pipenv run pytest --cov --cov-report html -Regeneate swagger-codegen python client library (requires docker): +To run 'lint' on the code base (note that this is pretty noisy and isn't +enforced by CI yet): - ./codegen_python_client.sh + pipenv run pylint --disable bad-continuation,arguments-differ,unidiomatic-typecheck fatcat diff --git a/python/TODO b/python/TODO index 54b63dd3..7a6eb10f 100644 --- a/python/TODO +++ b/python/TODO @@ -1,4 +1,10 @@ +Idea for new module structure: refactor 'fatcat_client' into 'fatcat' and have +that be the general purpose API client. create a new 'fatcat_services' for web +interface, importers, workers, etc, which depends on the other module. +potentially, move library module into subdirectory or another top-level folder +("python-fatcat"? "python-library"?). + - use dict counter type (in python collections) instead of currently janky counters - schema.org metadata for releases diff --git a/python/codegen_python_client.sh b/python/codegen_python_client.sh index 4cd30c44..3344c214 100755 --- a/python/codegen_python_client.sh +++ b/python/codegen_python_client.sh @@ -6,7 +6,7 @@ set -o pipefail OUTPUT=`pwd`/codegen-out mkdir -p $OUTPUT # Strip tags, so entire API is under a single class -cat ../fatcat-openapi2.yml | grep -v "TAGLINE$" > $OUTPUT/api.yml +cat ../fatcat-openapi2.yml | grep -v "TAGLINE$" | sed 's/\[https\]/\[http\]/g' > $OUTPUT/api.yml docker run \ -v $OUTPUT:/tmp/swagger/ \ @@ -23,4 +23,5 @@ mkdir -p tests/codegen_tests cp -r $OUTPUT/fatcat_client/* fatcat_client cp -r $OUTPUT/test/* tests/codegen_tests cp $OUTPUT/README.md README_codegen.md -#rm -rf $OUTPUT +# safer than 'rm -rf $OUTPUT' +mv $OUTPUT /tmp diff --git a/python/fatcat/templates/base.html b/python/fatcat/templates/base.html index 670d854f..856a6e03 100644 --- a/python/fatcat/templates/base.html +++ b/python/fatcat/templates/base.html @@ -5,6 +5,7 @@ <meta name="viewport" content="width=device-width"> <title>{% block title %}fatcat!{% endblock %}</title> + <meta name="referrer" content="origin-when-cross-origin"> <meta name="viewport" content="width=device-width, initial-scale=1"> <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/semantic-ui@2.3.2/dist/semantic.min.css"> <script diff --git a/python/fatcat/templates/release_view.html b/python/fatcat/templates/release_view.html index 3c05653b..39dcf8fd 100644 --- a/python/fatcat/templates/release_view.html +++ b/python/fatcat/templates/release_view.html @@ -22,7 +22,7 @@ <div class="one wide column"></div> <div class="ten wide column" style="font-size: 16px;"> -{% if release.release_date != None %}<p><b>Date (published):</b> {{ release.release_date[:10] }}{% endif %} +{% if release.release_date != None %}<p><b>Date (published):</b> {{ release.release_date }}{% endif %} {% if release.pmid != None %} <br><b>PubMed:</b> <a href="https://www.ncbi.nlm.nih.gov/pubmed/{{ release.pmid }}"> <code>{{ release.pmid }}</code></a> {% endif %} diff --git a/python/fatcat_client/api/default_api.py b/python/fatcat_client/api/default_api.py index a5971279..d3ce3cee 100644 --- a/python/fatcat_client/api/default_api.py +++ b/python/fatcat_client/api/default_api.py @@ -1970,7 +1970,7 @@ class DefaultApi(object): :param async bool :param str id: (required) - :param str expand: List of sub-entities to expand in response. For now, only 'all' accepted. + :param str expand: List of sub-entities to expand in response. For containers, none accepted (yet). :return: ContainerEntity If the method is called asynchronously, returns the request thread. @@ -1992,7 +1992,7 @@ class DefaultApi(object): :param async bool :param str id: (required) - :param str expand: List of sub-entities to expand in response. For now, only 'all' accepted. + :param str expand: List of sub-entities to expand in response. For containers, none accepted (yet). :return: ContainerEntity If the method is called asynchronously, returns the request thread. @@ -2172,7 +2172,7 @@ class DefaultApi(object): :param async bool :param str id: (required) - :param str expand: List of sub-entities to expand in response. For now, only 'all' accepted. + :param str expand: List of sub-entities to expand in response. For creators, none accepted (yet). :return: CreatorEntity If the method is called asynchronously, returns the request thread. @@ -2194,7 +2194,7 @@ class DefaultApi(object): :param async bool :param str id: (required) - :param str expand: List of sub-entities to expand in response. For now, only 'all' accepted. + :param str expand: List of sub-entities to expand in response. For creators, none accepted (yet). :return: CreatorEntity If the method is called asynchronously, returns the request thread. @@ -2770,7 +2770,7 @@ class DefaultApi(object): :param async bool :param str id: (required) - :param str expand: List of sub-entities to expand in response. For now, only 'all' accepted. + :param str expand: List of sub-entities to expand in response. For files, none accepted (yet). :return: FileEntity If the method is called asynchronously, returns the request thread. @@ -2792,7 +2792,7 @@ class DefaultApi(object): :param async bool :param str id: (required) - :param str expand: List of sub-entities to expand in response. For now, only 'all' accepted. + :param str expand: List of sub-entities to expand in response. For files, none accepted (yet). :return: FileEntity If the method is called asynchronously, returns the request thread. @@ -2972,7 +2972,7 @@ class DefaultApi(object): :param async bool :param str id: (required) - :param str expand: List of sub-entities to expand in response. For now, only 'all' accepted. + :param str expand: List of sub-entities to expand in response. For releases, 'files' and 'container' are valid. :return: ReleaseEntity If the method is called asynchronously, returns the request thread. @@ -2994,7 +2994,7 @@ class DefaultApi(object): :param async bool :param str id: (required) - :param str expand: List of sub-entities to expand in response. For now, only 'all' accepted. + :param str expand: List of sub-entities to expand in response. For releases, 'files' and 'container' are valid. :return: ReleaseEntity If the method is called asynchronously, returns the request thread. @@ -3364,7 +3364,7 @@ class DefaultApi(object): :param async bool :param str id: (required) - :param str expand: List of sub-entities to expand in response. For now, only 'all' accepted. + :param str expand: List of sub-entities to expand in response. For works, none accepted (yet). :return: WorkEntity If the method is called asynchronously, returns the request thread. @@ -3386,7 +3386,7 @@ class DefaultApi(object): :param async bool :param str id: (required) - :param str expand: List of sub-entities to expand in response. For now, only 'all' accepted. + :param str expand: List of sub-entities to expand in response. For works, none accepted (yet). :return: WorkEntity If the method is called asynchronously, returns the request thread. diff --git a/python/tests/grobid_metadata_importer.py b/python/tests/grobid_metadata_importer.py index 7bbabb39..2c8565aa 100644 --- a/python/tests/grobid_metadata_importer.py +++ b/python/tests/grobid_metadata_importer.py @@ -1,5 +1,7 @@ +import os import json +import base64 import pytest from fatcat.grobid_metadata_importer import FatcatGrobidMetadataImporter @@ -34,10 +36,12 @@ def test_file_metadata_parse(grobid_metadata_importer): with open('tests/files/example_grobid_metadata_lines.tsv', 'r') as f: f.readline() raw = f.readline().split('\t') + # randomize sha1 so tests are repeatable + random_sha1 = "sha1:{}".format(base64.b32encode(os.urandom(20)).decode('utf-8').upper()) fe = grobid_metadata_importer.parse_file_metadata( - raw[0], json.loads(raw[1]), raw[2], int(raw[3])) + random_sha1, json.loads(raw[1]), raw[2], int(raw[3])) assert fe - assert fe.sha1 == "d4a841744719518bf8bdd5d91576ccedc55efbb5" # "sha1:2SUEC5CHDFIYX6F52XMRK5WM5XCV565V" + #assert fe.sha1 == "d4a841744719518bf8bdd5d91576ccedc55efbb5" # "sha1:2SUEC5CHDFIYX6F52XMRK5WM5XCV565V" assert fe.md5 == None assert fe.mimetype == "application/pdf" assert fe.size == 142710 |