Merge pull request #83 from c3g/develop

Release v0.5.1

.travis.yml

@@ -9,12 +9,12 @@ addons:
       - postgresql-11
       - postgresql-contrib-11
 before_install:
-  - sudo -u postgres psql -U postgres -p 5433 -d postgres -c "alter user postgres with password 'hj38f3Ntr';"
+  - sudo -u postgres psql -U postgres -p 5432 -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=5433
+  - export POSTGRES_USER="postgres" && export POSTGRES_PASSWORD="hj38f3Ntr" && export POSTGRES_PORT=5432
   - python3 -m coverage run ./manage.py test
   - codecov
   - rm -rf chord_metadata_service

chord_metadata_service/chord/tests/constants.py

@@ -92,7 +92,11 @@ def dats_dataset(project_id, creators):
           }
        ],
        "title": "1000 Genomes Project",
-       "description": "The 1000 Genomes Project provides a comprehensive description of common human variation by applying a combination of whole-genome sequencing, deep exome sequencing and dense microarray genotyping to a diverse set of 2504 individuals from 26 populations.  Over 88 million variants are characterised, including >99% of SNP variants with a frequency of >1% for a variety of ancestries.",
+       "description": "The 1000 Genomes Project provides a comprehensive description of common human variation by "
+                      "applying a combination of whole-genome sequencing, deep exome sequencing and dense microarray "
+                      "genotyping to a diverse set of 2504 individuals from 26 populations.  Over 88 million variants "
+                      "are characterised, including >99% of SNP variants with a frequency of >1% for a variety of "
+                      "ancestries.",
        "storedIn": {
           "name": "European Bioinformatics Institute"
        },
@@ -140,13 +144,14 @@ def dats_dataset(project_id, creators):
              "category": "contact",
              "values": [
                 {
-                   "value": "Jennifer Tremblay-Mercier, Research Co-ordinator, [email protected], 514-761-6131 #3329"
+                   "value": "Jennifer Tremblay-Mercier, Research Co-ordinator, "
+                            "[email protected], 514-761-6131 #3329"
                 }
              ]
           }
        ],
        "data_use": VALID_DATA_USE_1
-}
+    }
 
 
 TEST_SEARCH_QUERY_1 = ["#eq", ["#resolve", "subject", "sex"], "FEMALE"]

chord_metadata_service/chord/tests/example_ingest.py

@@ -0,0 +1,234 @@
+EXAMPLE_INGEST = {
+    "subject": {
+        "id": "patient1",
+        "date_of_birth": "1964-03-15T00:00:00Z",
+        "sex": "MALE",
+        "karyotypic_sex": "UNKNOWN_KARYOTYPE"
+    },
+    "phenotypic_features": [
+        {
+            "description": "",
+            "type": {
+                "id": "HP:0000790",
+                "label": "Hematuria"
+            },
+            "negated": False,
+            "modifier": [],
+            "evidence": []
+        },
+        {
+            "description": "",
+            "type": {
+                "id": "HP:0100518",
+                "label": "Dysuria"
+            },
+            "negated": False,
+            "severity": {
+                "id": "HP:0012828",
+                "label": "Severe"
+            },
+            "modifier": [],
+            "evidence": []
+        }
+    ],
+    "diseases": [
+        {
+            "term": {
+                "id": "NCIT:C39853",
+                "label": "Infiltrating Urothelial Carcinoma"
+            },
+            "disease_stage": [
+                {
+                    "id": "NCIT:C48766",
+                    "label": "pT2b Stage Finding"
+                },
+                {
+                    "id": "NCIT:C48750",
+                    "label": "pN2 Stage Finding"
+                }
+            ]
+        }
+    ],
+    "meta_data": {
+        "created": "2019-04-03T15:31:40.765Z",
+        "created_by": "Peter R",
+        "submitted_by": "Peter R",
+        "resources": [
+            {
+                "id": "hp",
+                "name": "human phenotype ontology",
+                "namespace_prefix": "HP",
+                "url": "http://purl.obolibrary.org/obo/hp.owl",
+                "version": "2019-04-08",
+                "iri_prefix": "http://purl.obolibrary.org/obo/HP_"
+            },
+            {
+                "id": "uberon",
+                "name": "uber anatomy ontology",
+                "namespace_prefix": "UBERON",
+                "url": "http://purl.obolibrary.org/obo/uberon.owl",
+                "version": "2019-03-08",
+                "iri_prefix": "http://purl.obolibrary.org/obo/UBERON_"
+            },
+            {
+                "id": "ncit",
+                "name": "NCI Thesaurus OBO Edition",
+                "namespace_prefix": "NCIT",
+                "url": "http://purl.obolibrary.org/obo/ncit.owl",
+                "version": "18.05d",
+                "iri_prefix": "http://purl.obolibrary.org/obo/NCIT_"
+            }
+        ],
+        "updated": [],
+        "external_references": [
+            {
+                "id": "PMID:29221636",
+                "description": "Urothelial neoplasms in pediatric and young adult patients: A large single-center "
+                               "series"
+            }
+        ]
+    },
+    "biosamples": [
+        {
+            "id": "sample1",
+            "individual_id": "patient1",
+            "description": "",
+            "sampled_tissue": {
+                "id": "UBERON_0001256",
+                "label": "wall of urinary bladder"
+            },
+            "phenotypic_features": [],
+            "individual_age_at_collection": {
+                "age": "P52Y2M"
+            },
+            "histological_diagnosis": {
+                "id": "NCIT:C39853",
+                "label": "Infiltrating Urothelial Carcinoma"
+            },
+            "tumor_progression": {
+                "id": "NCIT:C84509",
+                "label": "Primary Malignant Neoplasm"
+            },
+            "diagnostic_markers": [],
+            "procedure": {
+                "code": {
+                    "id": "NCIT:C5189",
+                    "label": "Radical Cystoprostatectomy"
+                }
+            },
+            "is_control_sample": False
+        },
+        {
+            "id": "sample2",
+            "individual_id": "patient1",
+            "description": "",
+            "sampled_tissue": {
+                "id": "UBERON:0002367",
+                "label": "prostate gland"
+            },
+            "phenotypic_features": [],
+            "individual_age_at_collection": {
+                "age": "P52Y2M"
+            },
+            "histological_diagnosis": {
+                "id": "NCIT:C5596",
+                "label": "Prostate Acinar Adenocarcinoma"
+            },
+            "tumor_progression": {
+                "id": "NCIT:C95606",
+                "label": "Second Primary Malignant Neoplasm"
+            },
+            "tumor_grade": {
+                "id": "NCIT:C28091",
+                "label": "Gleason Score 7"
+            },
+            "disease_stage": [],
+            "diagnostic_markers": [],
+            "procedure": {
+                "code": {
+                    "id": "NCIT:C15189",
+                    "label": "Biopsy"
+                }
+            },
+            "is_control_sample": False
+        },
+        {
+            "id": "sample3",
+            "individual_id": "patient1",
+            "description": "",
+            "sampled_tissue": {
+                "id": "UBERON:0001223",
+                "label": "left ureter"
+            },
+            "phenotypic_features": [],
+            "individual_age_at_collection": {
+                "age": "P52Y2M"
+            },
+            "histological_diagnosis": {
+                "id": "NCIT:C38757",
+                "label": "Negative Finding"
+            },
+            "disease_stage": [],
+            "diagnostic_markers": [],
+            "procedure": {
+                "code": {
+                    "id": "NCIT:C15189",
+                    "label": "Biopsy"
+                }
+            },
+            "is_control_sample": False
+        },
+        {
+            "id": "sample4",
+            "individual_id": "patient1",
+            "description": "",
+            "sampled_tissue": {
+                "id": "UBERON:0001222",
+                "label": "right ureter"
+            },
+            "phenotypic_features": [],
+            "individual_age_at_collection": {
+                "age": "P52Y2M"
+            },
+            "histological_diagnosis": {
+                "id": "NCIT:C38757",
+                "label": "Negative Finding"
+            },
+            "disease_stage": [],
+            "diagnostic_markers": [],
+            "procedure": {
+                "code": {
+                    "id": "NCIT:C15189",
+                    "label": "Biopsy"
+                }
+            },
+            "is_control_sample": False
+        },
+        {
+            "id": "sample5",
+            "individual_id": "patient1",
+            "description": "",
+            "sampled_tissue": {
+                "id": "UBERON:0015876",
+                "label": "pelvic lymph node"
+            },
+            "phenotypic_features": [],
+            "individual_age_at_collection": {
+                "age": "P52Y2M"
+            },
+            "tumor_progression": {
+                "id": "NCIT:C3261",
+                "label": "Metastatic Neoplasm"
+            },
+            "disease_stage": [],
+            "diagnostic_markers": [],
+            "procedure": {
+                "code": {
+                    "id": "NCIT:C15189",
+                    "label": "Biopsy"
+                }
+            },
+            "is_control_sample": False
+        }
+    ]
+}

chord_metadata_service/chord/tests/test_api_ingest.py

@@ -0,0 +1,89 @@
+import json
+
+from django.test import override_settings
+from django.urls import reverse
+from rest_framework import status
+from rest_framework.test import APITestCase
+from uuid import uuid4
+
+from .constants import *
+from ..views_ingest import METADATA_WORKFLOWS
+
+
+def generate_ingest(table_id):
+    return {
+        "table_id": table_id,
+        "workflow_id": "phenopackets_json",
+        "workflow_metadata": METADATA_WORKFLOWS["ingestion"]["phenopackets_json"],
+        "workflow_outputs": {
+            "json_document": ""  # TODO
+        },
+        "workflow_params": {
+            "json_document": ""  # TODO
+        }
+    }
+
+
+class WorkflowTest(APITestCase):
+    def test_workflows(self):
+        r = self.client.get(reverse("workflows"), content_type="application/json")
+        self.assertEqual(r.status_code, status.HTTP_200_OK)
+        self.assertDictEqual(r.json(), METADATA_WORKFLOWS)
+
+        # Non-existent workflow
+        r = self.client.get(reverse("workflow-detail", args=("invalid_workflow",)), content_type="application/json")
+        self.assertEqual(r.status_code, status.HTTP_404_NOT_FOUND)
+
+        # Valid workflow
+        r = self.client.get(reverse("workflow-detail", args=("phenopackets_json",)), content_type="application/json")
+        self.assertEqual(r.status_code, status.HTTP_200_OK)
+        self.assertDictEqual(r.json(), METADATA_WORKFLOWS["ingestion"]["phenopackets_json"])
+
+        # Non-existent workflow file
+        r = self.client.get(reverse("workflow-file", args=("invalid_workflow",)), content_type="text/plain")
+        self.assertEqual(r.status_code, status.HTTP_404_NOT_FOUND)
+
+        # Valid workflow file
+        r = self.client.get(reverse("workflow-file", args=("phenopackets_json",)), content_type="text/plain")
+        self.assertEqual(r.status_code, status.HTTP_200_OK)
+        # TODO: Check file contents
+
+
+class IngestTest(APITestCase):
+    @override_settings(AUTH_OVERRIDE=True)  # For permissions
+    def setUp(self) -> None:
+        r = self.client.post(reverse("project-list"), data=json.dumps(VALID_PROJECT_1), content_type="application/json")
+        self.project = r.json()
+
+        r = self.client.post(reverse("dataset-list"), data=json.dumps(valid_dataset_1(self.project["identifier"])),
+                             content_type="application/json")
+        self.dataset = r.json()
+
+    @override_settings(AUTH_OVERRIDE=True)  # For permissions
+    def test_ingest(self):
+        # No ingestion body
+        r = self.client.post(reverse("ingest"), content_type="application/json")
+        self.assertEqual(r.status_code, status.HTTP_400_BAD_REQUEST)
+
+        # Invalid ingestion request
+        r = self.client.post(reverse("ingest"), data=json.dumps({}), content_type="application/json")
+        self.assertEqual(r.status_code, status.HTTP_400_BAD_REQUEST)
+
+        # Non-existent dataset ID
+        r = self.client.post(reverse("ingest"), data=json.dumps(generate_ingest(str(uuid4()))),
+                             content_type="application/json")
+        self.assertEqual(r.status_code, status.HTTP_400_BAD_REQUEST)
+
+        # Non-existent workflow ID
+        bad_wf = generate_ingest(self.dataset["identifier"])
+        bad_wf["workflow_id"] += "_invalid"
+        r = self.client.post(reverse("ingest"), data=json.dumps(bad_wf), content_type="application/json")
+        self.assertEqual(r.status_code, status.HTTP_400_BAD_REQUEST)
+
+        # json_document not in output
+        bad_wf = generate_ingest(self.dataset["identifier"])
+        bad_wf["workflow_outputs"] = {}
+        r = self.client.post(reverse("ingest"), data=json.dumps(bad_wf), content_type="application/json")
+        self.assertEqual(r.status_code, status.HTTP_400_BAD_REQUEST)
+
+        # TODO: More