Merge pull request #150 from AllenNeuralDynamics/build-transfer-service

Release v1.4.0

pyproject.toml

@@ -18,9 +18,10 @@ dynamic = ["version"]
 
 dependencies = [
     'boto3',
-    'pydantic>=2.0',
+    'pydantic>=2.7,<2.9',
     'pydantic-settings>=2.0',
-    'aind-data-transfer-models==0.6.2'
+    'aind-data-schema>=1.0.0',
+    'aind-data-transfer-models==0.8.3'
 ]
 
 [project.optional-dependencies]

src/aind_data_transfer_service/__init__.py

@@ -1,7 +1,7 @@
 """Init package"""
 import os
 
-__version__ = "1.3.0"
+__version__ = "1.4.0"
 
 # Global constants
 OPEN_DATA_BUCKET_NAME = os.getenv("OPEN_DATA_BUCKET_NAME", "open")

src/aind_data_transfer_service/configs/job_configs.py

@@ -33,7 +33,7 @@ class ModalityConfigs(BaseSettings):
     # added to the Modality class
     _MODALITY_MAP: ClassVar = {
         m().abbreviation.upper().replace("-", "_"): m().abbreviation
-        for m in Modality._ALL
+        for m in Modality.ALL
     }
 
     # Optional number id to assign to modality config
@@ -116,10 +116,10 @@ class BasicUploadJobConfigs(BaseSettings):
         extra="allow",
     )
 
-    # Need some way to extract abbreviations. Maybe a public method can be
-    # added to the Platform class
+    # Legacy way required users to input platform in screaming snake case
     _PLATFORM_MAP: ClassVar = {
-        p().abbreviation.upper(): p().abbreviation for p in Platform._ALL
+        a.upper().replace("-", "_"): a
+        for a in Platform.abbreviation_map.keys()
     }
     _MODALITY_ENTRY_PATTERN: ClassVar = re.compile(r"^modality(\d*)$")
     _DATETIME_PATTERN1: ClassVar = re.compile(

src/aind_data_transfer_service/configs/job_upload_template.py

@@ -84,13 +84,13 @@ def validators(self) -> List[Dict[str, Any]]:
             {
                 "name": "platform",
                 "type": "list",
-                "options": [p().abbreviation for p in Platform._ALL],
+                "options": list(Platform.abbreviation_map.keys()),
                 "column_indexes": [self.HEADERS.index("platform")],
             },
             {
                 "name": "modality",
                 "type": "list",
-                "options": [m().abbreviation for m in Modality._ALL],
+                "options": list(Modality.abbreviation_map.keys()),
                 "column_indexes": [
                     self.HEADERS.index("modality0"),
                     self.HEADERS.index("modality1"),

tests/test_server.py

@@ -18,6 +18,7 @@
     SubmitJobRequest,
     V0036JobProperties,
 )
+from aind_data_transfer_models.trigger import TriggerConfigModel, ValidJobType
 from fastapi.responses import StreamingResponse
 from fastapi.testclient import TestClient
 from pydantic import SecretStr
@@ -1604,6 +1605,59 @@ def test_submit_v1_jobs_200_session_settings_config_file(
                 )
             self.assertEqual(200, submit_job_response.status_code)
 
+    @patch.dict(os.environ, EXAMPLE_ENV_VAR1, clear=True)
+    @patch("requests.post")
+    def test_submit_v1_jobs_200_trigger_capsule_configs(
+        self,
+        mock_post: MagicMock,
+    ):
+        """Tests suubmission when user adds trigger_capsule_configs"""
+
+        mock_response = Response()
+        mock_response.status_code = 200
+        mock_response._content = json.dumps({"message": "sent"}).encode(
+            "utf-8"
+        )
+        mock_post.return_value = mock_response
+        ephys_source_dir = PurePosixPath("shared_drive/ephys_data/690165")
+
+        s3_bucket = "private"
+        subject_id = "690165"
+        acq_datetime = datetime(2024, 2, 19, 11, 25, 17)
+        platform = Platform.ECEPHYS
+
+        trigger_capsule_settings = TriggerConfigModel(
+            job_type=ValidJobType.RUN_GENERIC_PIPELINE, capsule_id="abc-123"
+        )
+        ephys_config = ModalityConfigs(
+            modality=Modality.ECEPHYS,
+            source=ephys_source_dir,
+        )
+        project_name = "Ephys Platform"
+
+        upload_job_configs = BasicUploadJobConfigs(
+            project_name=project_name,
+            s3_bucket=s3_bucket,
+            platform=platform,
+            subject_id=subject_id,
+            acq_datetime=acq_datetime,
+            modalities=[ephys_config],
+            trigger_capsule_configs=trigger_capsule_settings,
+        )
+
+        upload_jobs = [upload_job_configs]
+        submit_request = SubmitJobRequest(upload_jobs=upload_jobs)
+
+        post_request_content = json.loads(
+            submit_request.model_dump_json(round_trip=True)
+        )
+
+        with TestClient(app) as client:
+            submit_job_response = client.post(
+                url="/api/v1/submit_jobs", json=post_request_content
+            )
+        self.assertEqual(200, submit_job_response.status_code)
+
 
 if __name__ == "__main__":
     unittest.main()