Fixed engine parameter mid path issue

* Since we use centralise location for root directory mid path need to be specific enough to avoid clashes
umccr · Aug 27, 2021 · 33860d4 · 33860d4
1 parent b9f8eca
commit 33860d4
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Showing 6 changed files with 15 additions and 8 deletions.
diff --git a/data_processors/pipeline/lambdas/dragen_tso_ctdna.py b/data_processors/pipeline/lambdas/dragen_tso_ctdna.py
@@ -173,7 +173,9 @@ def handler(event, context) -> dict:
     )
 
     subject_id = metadata_srv.get_subject_id_from_library_id(library_id)
-    workflow_engine_parameters = wfl_helper.get_engine_parameters(subject_id)
+    # NOTE: event['tso500_sample']['sample_id'] is already in the form of sample_id + "_" + library_id
+    mid_path = subject_id + "/" + event['tso500_sample']['sample_id']
+    workflow_engine_parameters = wfl_helper.get_engine_parameters(mid_path)
 
     wfl_run = wes_handler.launch({
         'workflow_id': workflow_id,

diff --git a/data_processors/pipeline/lambdas/dragen_wgs_qc.py b/data_processors/pipeline/lambdas/dragen_wgs_qc.py
@@ -157,7 +157,8 @@ def handler(event, context) -> dict:
     )
 
     subject_id = metadata_srv.get_subject_id_from_library_id(library_id)
-    workflow_engine_parameters = wfl_helper.get_engine_parameters(subject_id)
+    mid_path = subject_id + "/" + library_id
+    workflow_engine_parameters = wfl_helper.get_engine_parameters(mid_path)
 
     wfl_run = wes_handler.launch({
         'workflow_id': workflow_id,

diff --git a/data_processors/pipeline/lambdas/tests/test_dragen_tso_ctdna.py b/data_processors/pipeline/lambdas/tests/test_dragen_tso_ctdna.py
@@ -25,7 +25,7 @@ def test_handler(self):
 
         workflow: dict = dragen_tso_ctdna.handler({
             "tso500_sample": {
-                "sample_id": "sample_id",
+                "sample_id": "PRJ000001_L0000001",
                 "sample_name": "sample_name",
                 "sample_type": "DNA",
                 "pair_id": "sample_name"

diff --git a/data_processors/pipeline/lambdas/tests/test_dragen_wgs_qc.py b/data_processors/pipeline/lambdas/tests/test_dragen_wgs_qc.py
@@ -24,12 +24,12 @@ def test_handler(self):
         when(metadata_srv).get_subject_id_from_library_id(...).thenReturn("SBJ0001")
 
         workflow: dict = dragen_wgs_qc.handler({
-            "library_id": "SAMPLE_NAME",
+            "library_id": "L0000001",
             "fastq_list_rows": [
                 {
                     "rgid": "index1.index2.lane",
                     "rgsm": "sample_name",
-                    "rglb": "sample_library",
+                    "rglb": "L0000001",
                     "lane": 1,
                     "read_1": {
                       "class": "File",

diff --git a/data_processors/pipeline/lambdas/tests/test_tumor_normal.py b/data_processors/pipeline/lambdas/tests/test_tumor_normal.py
@@ -18,7 +18,7 @@ def test_handler(self):
             "fastq_list_rows": [{
                 "rgid": "index1.index2.lane",
                 "rgsm": "sample_name",
-                "rglb": "UnknownLibrary",
+                "rglb": "L0000001",
                 "lane": 1,
                 "read_1": {
                     "class": "File",
@@ -32,7 +32,7 @@ def test_handler(self):
             "tumor_fastq_list_rows": [{
                 "rgid": "index1.index2.lane",
                 "rgsm": "sample_name",
-                "rglb": "UnknownLibrary",
+                "rglb": "L0000002",
                 "lane": 1,
                 "read_1": {
                     "class": "File",

diff --git a/data_processors/pipeline/lambdas/tumor_normal.py b/data_processors/pipeline/lambdas/tumor_normal.py
@@ -115,6 +115,9 @@ def handler(event, context) -> dict:
     tumor_fastq_list_rows = event['tumor_fastq_list_rows']
     sample_name = event['sample_name']
 
+    normal_library_id = fastq_list_rows[0]['rglb']
+    tumor_library_id = tumor_fastq_list_rows[0]['rglb']
+
     # Set workflow helper
     wfl_helper = SecondaryAnalysisHelper(WorkflowType.TUMOR_NORMAL)
 
@@ -171,7 +174,8 @@ def handler(event, context) -> dict:
 
     # If no running workflows were found, we proceed to preparing and kicking it off
     workflow_run_name = wfl_helper.construct_workflow_name(subject_id=subject_id)
-    workflow_engine_parameters = wfl_helper.get_engine_parameters(subject_id)
+    mid_path = subject_id + "/" + tumor_library_id + "_" + normal_library_id
+    workflow_engine_parameters = wfl_helper.get_engine_parameters(mid_path)
 
     wfl_run = wes_handler.launch({
         'workflow_id': workflow_id,