Merge pull request #167 from pagreene/api-update-db-side

API Update: Database Side

.github/workflows/tests.yml

@@ -0,0 +1,78 @@
+name: Tests
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - uses: actions/cache@v2
+      with:
+        path: ~/.cache/pip
+        key: ${{ runner.os }}-pip-${{ hashFiles('**/setup.py') }}
+        restore-keys: |
+          ${{ runner.os }}-pip-
+    - name: Set up Python 3.6
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.6
+    - name: Install dependencies
+      run: |
+        echo $GITHUB_EVENT_NAME
+        export WRKDIR=`pwd`
+        echo "home dir:" $WRKDIR
+        sudo apt-get update
+        sudo apt-get install libstdc++6 graphviz python3-dev libgraphviz-dev pkg-config
+        # Install test/github-workflows-specific dependencies not covered elsewhere
+        pip install jsonschema coverage nose-timer doctest-ignore-unicode awscli pycodestyle
+        pip install cython psycopg2
+        # Now install INDRA DB with all its extras
+        pip install git+https://github.com/pagreene/indra.git@api-update
+        cd ..
+        git clone https://github.com/indralab/ui_util
+        cd ui_util/indralab_auth_tools
+        echo "indralab_auth_tools dir:" pwd
+        pip install .
+        cd $WRKDIR
+        echo "indra_db dir:" pwd
+        pip install .[all]
+    - name: Run API tests
+      env:
+        AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
+        AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+        INDRADBPRIMARY: ${{ secrets.INDRADBPRIMARY }}
+        INDRAROPRIMARY: ${{ secrets.INDRAROPRIMARY }}
+        SUPERSECRETSECREST: ${{ secrets.SUPERSECRETSECRET }}
+      run: |
+        # Set nose attributes based on the context in which we are running
+        export NOSEATTR="!notravis,!slow,!cron";
+        export NOSEATTR=$(if [ "$GITHUB_EVENT_NAME" == "pull_request" ]; then echo $NOSEATTR,!nonpublic; else echo $NOSEATTR; fi)
+        echo $NOSEATTR
+        # These are files that are ignored so that doctests don't fail
+        export NOSE_IGNORE_FILES="find_full_text_sentence.py";
+
+        echo $NOSEATTR
+        #- cd $TRAVIS_BUILD_DIR
+        # Now run all INDRA DB REST API tests
+        cd rest_api
+        nosetests -v -a $NOSEATTR --with-coverage --cover-inclusive --cover-package=indra --with-doctest --with-doctest-ignore-unicode --with-timer --timer-top-n 10 --processes=0
+    #- name: Run all other tests
+    #  env:
+    #    AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
+    #    AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+    #    INDRADBPRIMARY: ${{ secrets.INDRADBPRIMARY }}
+    #    INDRAROPRIMARY: ${{ secrets.INDRAROPRIMARY }}
+    #  run: |
+    #    # Set nose attributes based on the context in which we are running
+    #    export NOSEATTR="!notravis,!slow,!cron";
+    #    export NOSEATTR=$(if [ "$GITHUB_EVENT_NAME" == "pull_request" ]; then echo $NOSEATTR,!nonpublic; else echo $NOSEATTR; fi)
+    #    echo $NOSEATTR
+    #    # These are files that are ignored so that doctests don't fail
+    #    export NOSE_IGNORE_FILES="find_full_text_sentence.py";
+    #    echo $NOSEATTR
+    #    #- cd $TRAVIS_BUILD_DIR
+    #    # Now run all INDRA DB REST API tests
+    #    cd indra_db
+    #    nosetests -v -a $NOSEATTR --with-coverage --cover-inclusive --cover-package=indra --with-doctest --with-doctest-ignore-unicode --with-timer --timer-top-n 10 --processes=0
+

indra_db/client/principal/curation.py

@@ -1,6 +1,7 @@
 __all__ = ['submit_curation', 'get_curations', 'get_grounding_curations']
 
 import re
+import json
 import logging
 import datetime
 from collections import Counter
@@ -14,7 +15,7 @@
 
 
 def submit_curation(hash_val, tag, curator, ip, text=None, ev_hash=None,
-                    source='direct_client', stmt_json=None, ev_json=None,
+                    source='direct_client', pa_json=None, ev_json=None,
                     db=None):
     """Submit a curation for a given preassembled or raw extraction.
 
@@ -37,19 +38,27 @@ def submit_curation(hash_val, tag, curator, ip, text=None, ev_hash=None,
         The name of the access point through which the curation was performed.
         The default is 'direct_client', meaning this function was used
         directly. Any higher-level application should identify itself here.
-    stmt_json : Optional[dict]
-        The JSON of a preassembled or raw statement that was curated.
+    pa_json : Optional[dict]
+        The JSON of a preassembled or raw statement that was curated. If None,
+        we will try to get the pa_json from the database.
     ev_json : Optional[dict]
-        The JSON of the evidence that was curated.
+        The JSON of the evidence that was curated. This cannot be retrieved from
+        the database if not given.
     db : DatabaseManager
         A database manager object used to access the database.
     """
     if db is None:
         db = get_db('primary')
 
+    if pa_json is None:
+        pa_json_strs = db.select_one(db.PAStatements.json,
+                                     db.PAStatements.mk_hash == int(hash_val))
+        if pa_json_strs is not None:
+            pa_json = json.loads(pa_json_strs[0])
+
     inp = {'tag': tag, 'text': text, 'curator': curator, 'ip': ip,
            'source': source, 'pa_hash': hash_val, 'source_hash': ev_hash,
-           'pa_json': stmt_json, 'ev_json': ev_json}
+           'pa_json': pa_json, 'ev_json': ev_json}
 
     logger.info("Adding curation: %s" % str(inp))