Added create test for Metagenomics Batch and Batch Items

dinapy/schemas/metagenomics_batch_item_schema.py

@@ -26,7 +26,7 @@ class Meta:
 class MetagenomicsBatchItemSchema(Schema):
     id = fields.Str(load_only=True)
     createdBy = SkipUndefinedField(fields.Str, attribute="attributes.createdBy")
-    createdOn = SkipUndefinedField(fields.Str, attribute="attributes.createdOn")
+    createdOn = SkipUndefinedField(fields.Str, load_only=True, attribute="attributes.createdOn")
 
     metagenomicsBatch = create_relationship("metagenomics-batch-item", "metagenomics-batch", "metagenomicsBatch")
     pcrBatchItem = create_relationship("metagenomics-batch-item", "pcr-batch-item", "pcrBatchItem")

tests/metagenomic_batch_create_test.py

@@ -0,0 +1,100 @@
+import json
+from pprint import pprint
+
+import sys
+import os
+
+# Import for Metagenomics Batch
+from dinapy.apis.seqdbapi.metagenomics_batch_api import MetagenomicsBatchApi
+from dinapy.schemas.metagenomics_batch_schema import MetagenomicsBatchSchema
+from dinapy.entities.MetagenomicsBatch import *
+
+# Import for Metagenomics Batch Item
+from dinapy.apis.seqdbapi.metagenomics_batch_item_api import MetagenomicsBatchItemApi
+from dinapy.schemas.metagenomics_batch_item_schema import MetagenomicsBatchItemSchema
+from dinapy.entities.MetagenomicsBatchItem import *
+
+from dinapy.entities.Relationships import RelationshipDTO
+
+# Add the root directory of the project to the Python path
+project_root = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
+sys.path.insert(0, project_root)
+
+# List of pre-made PCR Batch Item UUIDs
+PCR_BATCH_ITEMS = [
+    "bae9440e-7029-43e2-9ddb-ab3912187189",
+    "e0eb9dba-c588-4252-b97a-92576f5613d2",
+    "ffdc42d2-5701-401e-bb2e-b13eec9fb22b",
+    "5e6b7a61-5a8d-43ec-8dee-4c5aa24ca31b",
+    "300b6407-b67b-49be-9013-5379d7989f9f"
+    ]
+
+def main():
+    # Build Relationship for Metagenomics Batch
+    # using a pre-made Index Set in DINA-dev2
+    batch_relationship = (
+        RelationshipDTO.Builder()
+            .add_relationship(
+                "indexSet",
+                "index-set",
+                "456036bc-6fa6-4779-b028-ec26a7b7e6dd"
+            ).build()
+    )
+
+    # Set Metagenomics Batch Attributes and Relationships
+    metagenomics_batch_api = MetagenomicsBatchApi()
+    metagenomics_batch_schema = MetagenomicsBatchSchema()
+    metagenomics_batch_attributes = MetagenomicsBatchAttributesDTOBuilder(
+      ).set_createdBy("dina-admin").set_group("aafc").set_name("metagenomics-batch-test").build()
+    metagenomics_batch = MetagenomicsBatchDTOBuilder(
+      ).set_relationships(batch_relationship).set_attributes(metagenomics_batch_attributes).build()
+
+    serialized_metagenomics_batch = metagenomics_batch_schema.dump(metagenomics_batch)
+
+    # print(f"{serialized_metagenomics_batch}\n")
+
+    # Create Metagenomics Batch
+    metagenomics_batch_response = metagenomics_batch_api.create_entity(serialized_metagenomics_batch)
+    batch_id = metagenomics_batch_response.json()['data']['id']
+    print(f"Metagenomics Batch: {batch_id} created\n")
+
+    with open("./uuids.txt", "a") as f:
+        print(f"Metagenomics Batch: {batch_id} created", file=f)
+
+    for item in PCR_BATCH_ITEMS:
+        # Build Relationships for Metagenomics Batch Items
+        batch_item_relationship = (
+            RelationshipDTO.Builder()
+                .add_relationship(
+                    "metagenomicsBatch",
+                    "metagenomics-batch",
+                    batch_id
+                ).add_relationship(
+                    "pcrBatchItem",
+                    "pcr-batch-item",
+                    item
+                ).build()
+        )
+
+        # Set Metagenomics Batch Item Attributes and Relationships
+        metagenomics_batch_item_api = MetagenomicsBatchItemApi()
+        metagenomics_batch_item_schema = MetagenomicsBatchItemSchema()
+        metagenomics_batch_item_attributes = MetagenomicsBatchItemAttributesDTOBuilder(
+            ).set_createdBy("dina-admin").build()
+        metagenomics_batch_item = MetagenomicsBatchItemDTOBuilder(
+            ).set_relationships(batch_item_relationship).set_attributes(metagenomics_batch_item_attributes).build()
+
+        serialized_metagenomics_batch_item = metagenomics_batch_item_schema.dump(metagenomics_batch_item)
+
+        # print(f"{serialized_metagenomics_batch_item}\n")
+
+        # Create Metagenomics Batch Item
+        metagenomics_batch_item_response = metagenomics_batch_item_api.create_entity(serialized_metagenomics_batch_item)
+        batch_item_id = metagenomics_batch_item_response.json()['data']['id']
+        print(f"Metagenomics Batch Item: {batch_item_id} created\n")
+
+        with open("./uuids.txt", "a") as f:
+            print(f"Metagenomics Batch Item: {batch_item_id} created",file=f)
+
+if __name__ == "__main__":
+    main()

tests/molecular_analysis_run_create_test.py

@@ -27,9 +27,6 @@
 
 from dinapy.entities.Relationships import RelationshipDTO
 
-os.environ["keycloak_username"] = "dina-admin"
-os.environ["keycloak_password"] = "dina-admin"
-
 def main():
     # Create a Molecular Analysis Run
     MOCK_RUN_NAME = "test run with results"