Merge pull request #121 from c3g/fix-literal-search

Fix issues with "true" queries which should return all phenopackets

.travis.yml

@@ -4,18 +4,18 @@ python:
   - "3.6"
   - "3.8"
 addons:
-  postgresql: "11"
+  postgresql: "12"
   apt:
     packages:
-      - postgresql-11
-      - postgresql-contrib-11
+      - postgresql-12
+      - postgresql-contrib-12
 before_install:
-  - sudo -u postgres psql -U postgres -p 5432 -d postgres -c "alter user postgres with password 'hj38f3Ntr';"
+  - sudo -u postgres psql -U postgres -p 5433 -d postgres -c "alter user postgres with password 'hj38f3Ntr';"
 install:
   - pip install -r requirements.txt
   - pip install .
 script:
-  - export POSTGRES_USER="postgres" && export POSTGRES_PASSWORD="hj38f3Ntr" && export POSTGRES_PORT=5432
+  - export POSTGRES_USER="postgres" && export POSTGRES_PASSWORD="hj38f3Ntr" && export POSTGRES_PORT=5433
   - python3 -m coverage run ./manage.py test
   - codecov
   - rm -rf chord_metadata_service

chord_metadata_service/chord/tests/test_api_search.py

@@ -243,6 +243,16 @@ def test_private_table_search_4(self):
         self.assertEqual(len(c["results"]), 1)
         self.assertEqual(self.phenopacket.id, c["results"][0]["id"])
 
+    def test_private_table_search_5(self):
+        # Valid query: literal "true"
+        r = self.client.post(reverse("private-table-search", args=[str(self.dataset.identifier)]), data=json.dumps({
+            "query": True
+        }), content_type="application/json")
+        self.assertEqual(r.status_code, status.HTTP_200_OK)
+        c = r.json()
+        self.assertEqual(len(c["results"]), 1)
+        self.assertEqual(self.phenopacket.id, c["results"][0]["id"])
+
     @patch('chord_metadata_service.chord.views_search.es')
     def test_fhir_search(self, mocked_es):
         mocked_es.search.return_value = SEARCH_SUCCESS

requirements.txt

@@ -3,7 +3,7 @@ attrs==19.3.0
 Babel==2.8.0
 certifi==2020.4.5.1
 chardet==3.0.4
-chord-lib==0.8.0
+chord_lib==0.9.0
 codecov==2.0.22
 colorama==0.4.3
 coreapi==2.3.3
@@ -40,7 +40,7 @@ pytz==2020.1
 PyYAML==5.3.1
 rdflib==4.2.2
 rdflib-jsonld==0.4.0
-redis==3.4.1
+redis==3.5.1
 requests==2.23.0
 rfc3987==1.3.8
 simplejson==3.17.0

setup.py

@@ -16,8 +16,8 @@
 
     python_requires=">=3.6",
     install_requires=[
-        "chord_lib[django]==0.8.0",
-        "Django>=2.2,<3.0",
+        "chord_lib[django]==0.9.0",
+        "Django>=2.2.12,<3.0",
         "django-filter>=2.2,<3.0",
         "django-nose>=1.4,<2.0",
         "djangorestframework>=3.11,<3.12",