Merge pull request #300 from bento-platform/develop

Version 2.8.0

Author: zxenia

.gitignore

@@ -27,3 +27,6 @@ htmlcov/
 # docs build
 
 docs/_build
+
+# project custom config file
+config.json

chord_metadata_service/chord/ingest.py

@@ -35,6 +35,7 @@
 from chord_metadata_service.mcode.mcode_ingest import ingest_mcodepacket
 from chord_metadata_service.phenopackets.schemas import PHENOPACKET_SCHEMA
 from chord_metadata_service.experiments.schemas import EXPERIMENT_SCHEMA
+from chord_metadata_service.restapi.utils import iso_duration_to_years
 
 requests_unixsocket.monkeypatch()
 
@@ -414,9 +415,19 @@ def ingest_phenopacket(phenopacket_data, table_id):
         subject_query = _query_and_check_nulls(subject, "date_of_birth", transform=isoparse)
         for k in ("alternate_ids", "age", "sex", "karyotypic_sex", "taxonomy"):
             subject_query.update(_query_and_check_nulls(subject, k))
+
+        # check if age is represented as a duration string (vs. age range values) and convert it to years
+        age_numeric_value = None
+        age_unit_value = None
+        if "age" in subject:
+            if "age" in subject["age"]:
+                age_numeric_value, age_unit_value = iso_duration_to_years(subject["age"]["age"])
+
         subject, _ = pm.Individual.objects.get_or_create(id=subject["id"],
                                                          race=subject.get("race", ""),
                                                          ethnicity=subject.get("ethnicity", ""),
+                                                         age_numeric=age_numeric_value,
+                                                         age_unit=age_unit_value if age_unit_value else "",
                                                          extra_properties=subject.get("extra_properties", {}),
                                                          **subject_query)
 

chord_metadata_service/chord/tests/example_ingest.py

@@ -4,7 +4,8 @@
 
 __all__ = ["EXAMPLE_INGEST_PHENOPACKET", "EXAMPLE_INGEST_OUTPUTS",
            "EXAMPLE_INGEST_EXPERIMENT", "EXAMPLE_INGEST_OUTPUTS_EXPERIMENT",
-           "EXAMPLE_INGEST_INVALID_PHENOPACKET"]
+           "EXAMPLE_INGEST_INVALID_PHENOPACKET",
+           "EXAMPLE_INGEST_MULTIPLE_PHENOPACKETS", "EXAMPLE_INGEST_MULTIPLE_OUTPUTS"]
 
 with open(os.path.join(os.path.dirname(__file__), "example_phenopacket.json"), "r") as pf:
     EXAMPLE_INGEST_PHENOPACKET = json.load(pf)
@@ -24,3 +25,11 @@
 
 with open(os.path.join(os.path.dirname(__file__), "example_invalid_phenopacket.json"), "r") as pf:
     EXAMPLE_INGEST_INVALID_PHENOPACKET = json.load(pf)
+
+
+with open(os.path.join(os.path.dirname(__file__), "example_multiple_phenopackets.json"), "r") as pf:
+    EXAMPLE_INGEST_MULTIPLE_PHENOPACKETS = json.load(pf)
+
+EXAMPLE_INGEST_MULTIPLE_OUTPUTS = {
+    "json_document": os.path.join(os.path.dirname(__file__), "example_multiple_phenopackets.json"),
+}