Linting

Removing old workflow mapping for PAS
Refactoring to make use of UBKG for assay name

src/ingest-pipeline/airflow/dags/pas_ftu_segmentation.py

@@ -50,16 +50,15 @@
 
 
 with HMDAG(
-        "pas_ftu_segmentation",
-        schedule_interval=None,
-        is_paused_upon_creation=False,
-        default_args=default_args,
-        user_defined_macros={
-            "tmp_dir_path": get_tmp_dir_path,
-            'preserve_scratch': get_preserve_scratch_resource('pas_ftu_segmentation'),
-        },
+    "pas_ftu_segmentation",
+    schedule_interval=None,
+    is_paused_upon_creation=False,
+    default_args=default_args,
+    user_defined_macros={
+        "tmp_dir_path": get_tmp_dir_path,
+        "preserve_scratch": get_preserve_scratch_resource("pas_ftu_segmentation"),
+    },
 ) as dag:
-
     pipeline_name = "pas-ftu-segmentation-pipeline"
     cwl_workflows = get_named_absolute_workflows(
         segmentation=Path(pipeline_name, "pipeline.cwl"),
@@ -84,13 +83,10 @@ def build_cwltool_cwl_segmentation(**kwargs):
         meta_yml_path = workflow.parent / "meta.yaml"
 
         # get organ type
-        ds_rslt = pythonop_get_dataset_state(
-            dataset_uuid_callable=get_dataset_uuid,
-            **kwargs
-        )
+        ds_rslt = pythonop_get_dataset_state(dataset_uuid_callable=get_dataset_uuid, **kwargs)
 
-        organ_list = list(set(ds_rslt['organs']))
-        organ_code = organ_list[0] if len(organ_list) == 1 else 'multi'
+        organ_list = list(set(ds_rslt["organs"]))
+        organ_code = organ_list[0] if len(organ_list) == 1 else "multi"
 
         command = [
             *get_cwltool_base_cmd(tmpdir),
@@ -99,7 +95,7 @@ def build_cwltool_cwl_segmentation(**kwargs):
             "--data_directory",
             data_dir,
             "--tissue_type",
-            organ_code
+            organ_code,
         ]
 
         return join_quote_command_str(command)
@@ -132,7 +128,6 @@ def build_cwltool_cwl_segmentation(**kwargs):
         },
     )
 
-
     prepare_cwl_ome_tiff_pyramid = DummyOperator(task_id="prepare_cwl_ome_tiff_pyramid")
 
     def build_cwltool_cwl_ome_tiff_pyramid(**kwargs):
@@ -278,6 +273,7 @@ def build_cwltool_cmd_ome_tiff_offsets(**kwargs):
         ],
         cwl_workflows=list(cwl_workflows.values()),
     )
+
     t_send_status = PythonOperator(
         task_id="send_status_msg", python_callable=send_status_msg, provide_context=True
     )

src/ingest-pipeline/airflow/dags/workflow_map.yml

@@ -47,9 +47,9 @@ workflow_map:
   - 'collection_type': '.*'
     'assay_type': 'PAS'
     'workflow': 'pas_ftu_segmentation'
-  - 'collection_type': '.*'
-    'assay_type': 'PAS'
-    'workflow': 'ometiff_pyramid'
+#  - 'collection_type': '.*'
+#    'assay_type': 'PAS'
+#    'workflow': 'ometiff_pyramid'
   - 'collection_type': '.*'
     'assay_type': 'AF'
     'workflow': 'ometiff_pyramid'

src/ingest-pipeline/misc/tools/airflow_environments/env_dev.sh

@@ -7,5 +7,5 @@ HM_AF_CONN_UUID_API_CONNECTION=http://https%3a%2f%2fuuid-api.dev.hubmapconsortiu
 HM_AF_CONN_FILES_API_CONNECTION=http://https%3a%2f%2ffiles-api.dev.hubmapconsortium.org/
 HM_AF_CONN_SPATIAL_API_CONNECTION=http://https%3a%2f%2fspatial-api.dev.hubmapconsortium.org/
 HM_AF_CONN_CELLS_API_CONNECTION=http://https%3a%2f%2fcells-api.dev.hubmapconsortium.org/
-HM_AF_CONN_SEARCH_API_CONNECTION=http://https%3a%2f%2fsearch-api.dev.hubmapconsortium.org%2fv3/
+HM_AF_CONN_SEARCH_API_CONNECTION=http://https%3a%2f%2fontoly-api.dev.hubmapconsortium.org%2fv3/
 HM_AF_CONN_ENTITY_API_CONNECTION=http://https%3a%2f%2fentity-api.dev.hubmapconsortium.org/

src/ingest-pipeline/misc/tools/airflow_environments/env_prod.sh

@@ -7,5 +7,5 @@ HM_AF_CONN_UUID_API_CONNECTION=http://https%3a%2f%2fuuid.api.hubmapconsortium.or
 HM_AF_CONN_FILES_API_CONNECTION=http://https%3a%2f%2ffiles.api.hubmapconsortium.org/
 HM_AF_CONN_SPATIAL_API_CONNECTION=http://https%3a%2f%2fspatial.api.hubmapconsortium.org/
 HM_AF_CONN_CELLS_API_CONNECTION=http://https%3a%2f%2fcells.api.hubmapconsortium.org/
-HM_AF_CONN_SEARCH_API_CONNECTION=http://https%3a%2f%2fsearch.api.hubmapconsortium.org%2fv3/
+HM_AF_CONN_SEARCH_API_CONNECTION=http://https%3a%2f%2fontology.api.hubmapconsortium.org%2fv3/
 HM_AF_CONN_ENTITY_API_CONNECTION=http://https%3a%2f%2fentity.api.hubmapconsortium.org/

src/ingest-pipeline/misc/tools/airflow_environments/env_stage.sh

@@ -8,5 +8,5 @@ HM_AF_CONN_UUID_API_CONNECTION=http://https%3a%2f%2fuuid-api.stage.hubmapconsort
 HM_AF_CONN_FILES_API_CONNECTION=http://https%3a%2f%2ffiles-api.stage.hubmapconsortium.org/
 HM_AF_CONN_SPATIAL_API_CONNECTION=http://https%3a%2f%2fspatial-api.stage.hubmapconsortium.org/
 HM_AF_CONN_CELLS_API_CONNECTION=http://https%3a%2f%2fcells-api.stage.hubmapconsortium.org/
-HM_AF_CONN_SEARCH_API_CONNECTION=http://https%3a%2f%2fsearch-api.stage.hubmapconsortium.org%2fv3/
+HM_AF_CONN_SEARCH_API_CONNECTION=http://https%3a%2f%2fontology-api.stage.hubmapconsortium.org%2fv3/
 HM_AF_CONN_ENTITY_API_CONNECTION=http://https%3a%2f%2fentity-api.stage.hubmapconsortium.org/

src/ingest-pipeline/misc/tools/airflow_environments/env_test.sh

@@ -7,5 +7,5 @@ HM_AF_CONN_UUID_API_CONNECTION=http://https%3a%2f%2fuuid-api.test.hubmapconsorti
 HM_AF_CONN_FILES_API_CONNECTION=http://https%3a%2f%2ffiles-api.test.hubmapconsortium.org/
 HM_AF_CONN_SPATIAL_API_CONNECTION=http://https%3a%2f%2fspatial-api.test.hubmapconsortium.org/
 HM_AF_CONN_CELLS_API_CONNECTION=http://https%3a%2f%2fcells-api.test.hubmapconsortium.org/
-HM_AF_CONN_SEARCH_API_CONNECTION=http://https%3a%2f%2fsearch-api.test.hubmapconsortium.org%2fv3/
+HM_AF_CONN_SEARCH_API_CONNECTION=http://https%3a%2f%2fontology-api.test.hubmapconsortium.org%2fv3/
 HM_AF_CONN_ENTITY_API_CONNECTION=http://https%3a%2f%2fentity-api.test.hubmapconsortium.org/