Merge pull request #247 from bento-platform/develop

Version 2.2.1
bento-platform · Jul 28, 2021 · 58aac95 · 58aac95
2 parents b89a4b8 + be3d7a6
commit 58aac95
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Showing 4 changed files with 25 additions and 7 deletions.
diff --git a/chord_metadata_service/chord/ingest.py b/chord_metadata_service/chord/ingest.py
@@ -8,6 +8,7 @@
 import shutil
 import tempfile
 import uuid
+import jsonschema
 
 from dateutil.parser import isoparse
 from typing import Callable
@@ -30,6 +31,7 @@
 )
 from chord_metadata_service.mcode.parse_fhir_mcode import parse_bundle
 from chord_metadata_service.mcode.mcode_ingest import ingest_mcodepacket
+from chord_metadata_service.phenopackets.schemas import PHENOPACKET_SCHEMA
 
 requests_unixsocket.monkeypatch()
 
@@ -344,9 +346,27 @@ def ingest_experiment(experiment_data, table_id) -> em.Experiment:
     return new_experiment
 
 
-def ingest_phenopacket(phenopacket_data, table_id) -> pm.Phenopacket:
+def ingest_phenopacket(phenopacket_data, table_id):
     """Ingests a single phenopacket."""
 
+    v = jsonschema.Draft7Validator(PHENOPACKET_SCHEMA, format_checker=jsonschema.FormatChecker())
+    try:
+        jsonschema.validate(
+            phenopacket_data,
+            PHENOPACKET_SCHEMA,
+            format_checker=jsonschema.FormatChecker(),
+        )
+        logger.info("JSON schema validation passed.")
+
+    except jsonschema.exceptions.ValidationError:
+        errors = [e for e in v.iter_errors(phenopacket_data)]
+        logger.info(f"JSON schema validation failed. Errors: {errors}")
+        for i, error in enumerate(errors, 1):
+            logger.error(
+                f"{i} Validation error in {'.'.join(str(v) for v in error.path)}: {error.message}",
+            )
+        return
+
     new_phenopacket_id = phenopacket_data.get("id", str(uuid.uuid4()))
 
     subject = phenopacket_data.get("subject")

diff --git a/chord_metadata_service/chord/tests/example_phenopacket.json b/chord_metadata_service/chord/tests/example_phenopacket.json
@@ -13,8 +13,7 @@
                 "label": "Hematuria"
             },
             "negated": false,
-            "modifier": [],
-            "evidence": []
+            "modifier": []
         },
         {
             "description": "",
@@ -27,8 +26,7 @@
                 "id": "HP:0012828",
                 "label": "Severe"
             },
-            "modifier": [],
-            "evidence": []
+            "modifier": []
         }
     ],
     "diseases": [

diff --git a/chord_metadata_service/package.cfg b/chord_metadata_service/package.cfg
@@ -1,4 +1,4 @@
 [package]
 name = katsu
-version = 2.2.0
+version = 2.2.1
 authors = Ksenia Zaytseva, David Lougheed, Simon Chénard, Romain Grégoire
diff --git a/chord_metadata_service/phenopackets/schemas.py b/chord_metadata_service/phenopackets/schemas.py
@@ -360,5 +360,5 @@
         "meta_data": PHENOPACKET_META_DATA_SCHEMA,
         "extra_properties": EXTRA_PROPERTIES_SCHEMA
     },
-    "required": ["id", "meta_data"],
+    "required": ["meta_data"],
 }, descriptions.PHENOPACKET)