modify function's application to fit with the updated model

Health-Informatics-UoN · Dec 3, 2024 · cc276a0 · cc276a0
1 parent 2df9265
commit cc276a0
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Showing 3 changed files with 31 additions and 23 deletions.
diff --git a/app/workers/RulesConceptsActivity/__init__.py b/app/workers/RulesConceptsActivity/__init__.py
@@ -58,7 +58,9 @@ def _create_concepts(
     return concepts
 
 
-def _transform_concepts(table_values: List[ScanReportValueDict], table_id: str) -> None:
+def _transform_concepts(
+    table_values: List[ScanReportValueDict], table: ScanReportTable
+) -> None:
     """
     For each vocab, set "concept_id" and "standard_concept" in each entry in the vocab.
     Transforms the values in place.
@@ -91,7 +93,7 @@ def _transform_concepts(table_values: List[ScanReportValueDict], table_id: str)
             # Set to defaults, and skip all the remaining processing that a vocab would require
             _set_defaults_for_none_vocab(value)
         else:
-            _process_concepts_for_vocab(vocab, value, table_id)
+            _process_concepts_for_vocab(vocab, value, table)
 
 
 def _set_defaults_for_none_vocab(entries: List[ScanReportValueDict]) -> None:
@@ -111,7 +113,7 @@ def _set_defaults_for_none_vocab(entries: List[ScanReportValueDict]) -> None:
 
 
 def _process_concepts_for_vocab(
-    vocab: str, entries: List[ScanReportValueDict], table_id: str
+    vocab: str, entries: List[ScanReportValueDict], table: ScanReportTable
 ) -> None:
     """
     Process concepts for a specific vocabulary.
@@ -127,7 +129,7 @@ def _process_concepts_for_vocab(
     update_job(
         JobStageType.BUILD_CONCEPTS_FROM_DICT,
         StageStatusType.IN_PROGRESS,
-        scan_report_table_id=table_id,
+        scan_report_table=table,
         details=f"Building concepts for {vocab} vocabulary",
     )
     logger.info(f"begin {vocab}")
@@ -271,7 +273,7 @@ def _handle_table(
     # Add vocab id to each entry from the vocab dict
     helpers.add_vocabulary_id_to_entries(table_values, vocab, table.name)
 
-    _transform_concepts(table_values, table.pk)
+    _transform_concepts(table_values, table)
     logger.debug("finished standard concepts lookup")
 
     concepts = _create_concepts(table_values)
@@ -285,37 +287,37 @@ def _handle_table(
         update_job(
             JobStageType.BUILD_CONCEPTS_FROM_DICT,
             StageStatusType.COMPLETE,
-            scan_report_table_id=table.pk,
+            scan_report_table=table,
             details=f"No concepts was created for table {table.name}. The data dict. may not be provided or the vocabs building function was called before.",
         )
     else:
         update_job(
             JobStageType.BUILD_CONCEPTS_FROM_DICT,
             StageStatusType.COMPLETE,
-            scan_report_table_id=table.pk,
+            scan_report_table=table,
             details=f"Created {len(concepts)} concepts for table {table.name}.",
         )
 
     # Starting the concepts reusing process
     create_or_update_job(
         JobStageType.REUSE_CONCEPTS,
         StageStatusType.IN_PROGRESS,
-        scan_report_table_id=table.pk,
+        scan_report_table=table,
     )
     # handle reuse of concepts at field level
-    reuse_existing_field_concepts(table_fields, table.pk)
+    reuse_existing_field_concepts(table_fields, table)
     update_job(
         JobStageType.REUSE_CONCEPTS,
         StageStatusType.IN_PROGRESS,
-        scan_report_table_id=table.pk,
+        scan_report_table=table,
         details="Finished reusing concepts at field level. Reusing concepts at value level...",
     )
     # handle reuse of concepts at value level
-    reuse_existing_value_concepts(table_values, table.pk)
+    reuse_existing_value_concepts(table_values, table)
     update_job(
         JobStageType.REUSE_CONCEPTS,
         StageStatusType.COMPLETE,
-        scan_report_table_id=table.pk,
+        scan_report_table=table,
         details="Reusing concepts finished.",
     )
 
@@ -343,6 +345,6 @@ def main(msg: Dict[str, str]):
     create_or_update_job(
         JobStageType.BUILD_CONCEPTS_FROM_DICT,
         StageStatusType.IN_PROGRESS,
-        scan_report_table_id=table_id,
+        scan_report_table=table,
     )
     _handle_table(table, vocab_dictionary)
diff --git a/app/workers/RulesConceptsActivity/reuse.py b/app/workers/RulesConceptsActivity/reuse.py
@@ -1,6 +1,11 @@
 from typing import Dict, List, Tuple, Union
 from collections import defaultdict
-from shared.mapping.models import ScanReportConcept, ScanReportField, ScanReportValue
+from shared.mapping.models import (
+    ScanReportConcept,
+    ScanReportField,
+    ScanReportValue,
+    ScanReportTable,
+)
 from shared_code import db
 from shared_code.logger import logger
 from shared_code.models import (
@@ -25,7 +30,7 @@
 
 
 def reuse_existing_value_concepts(
-    new_values_map: List[ScanReportValueDict], table_id: str
+    new_values_map: List[ScanReportValueDict], table: ScanReportTable
 ) -> None:
     """
     This expects a dict of value names to ids which have been generated in a newly
@@ -169,7 +174,7 @@ def reuse_existing_value_concepts(
         new_values_full_details,
         value_details_to_value_and_concept_id_map,
         content_type,
-        table_id,
+        table,
     ):
         ScanReportConcept.objects.bulk_create(concepts_to_post)
         logger.info("POST concepts all finished in reuse_existing_value_concepts")
@@ -178,7 +183,7 @@ def reuse_existing_value_concepts(
 
 
 def reuse_existing_field_concepts(
-    new_fields_map: List[ScanReportFieldDict], table_id: str
+    new_fields_map: List[ScanReportFieldDict], table: ScanReportTable
 ) -> None:
     """
     Creates new concepts associated to any field that matches the name of an existing
@@ -283,7 +288,7 @@ def reuse_existing_field_concepts(
         new_fields_full_details,
         existing_field_name_to_field_and_concept_id_map,
         content_type,
-        table_id,
+        table,
     ):
         ScanReportConcept.objects.bulk_create(concepts_to_post)
         logger.info("POST concepts all finished in reuse_existing_field_concepts")
@@ -301,7 +306,7 @@ def select_concepts_to_post(
         ],
     ],
     content_type: ScanReportConceptContentType,
-    table_id,
+    table: ScanReportTable,
 ) -> List[ScanReportConcept]:
     """
     Depending on the content_type, generate a list of `ScanReportConcepts` to be created.
@@ -342,7 +347,7 @@ def select_concepts_to_post(
             update_job(
                 JobStageType.REUSE_CONCEPTS,
                 StageStatusType.FAILED,
-                scan_report_table_id=table_id,
+                scan_report_table=table,
                 details=f"Reusing concepts failed: Unsupported content_type: {content_type}",
             )
             raise ValueError(f"Unsupported content_type: {content_type}")

diff --git a/app/workers/RulesOrchestrator/__init__.py b/app/workers/RulesOrchestrator/__init__.py
@@ -16,6 +16,7 @@
     JobStageType,
     StageStatusType,
 )
+from shared.mapping.models import ScanReportTable
 
 
 def orchestrator_function(context: df.DurableOrchestrationContext):
@@ -49,7 +50,7 @@ def orchestrator_function(context: df.DurableOrchestrationContext):
         create_or_update_job(
             JobStageType.GENERATE_RULES,
             StageStatusType.IN_PROGRESS,
-            scan_report_table_id=table_id,
+            scan_report_table=ScanReportTable.objects.get(id=table_id),
             details=f"Generating mapping rules from {concepts_count} concepts found.",
         )
         # Fan out
@@ -65,7 +66,7 @@ def orchestrator_function(context: df.DurableOrchestrationContext):
         update_job(
             JobStageType.GENERATE_RULES,
             StageStatusType.COMPLETE,
-            scan_report_table_id=table_id,
+            scan_report_table=ScanReportTable.objects.get(id=table_id),
             details="Automatic mapping rules generation finished.",
         )
         return [result, results]
@@ -74,7 +75,7 @@ def orchestrator_function(context: df.DurableOrchestrationContext):
         update_job(
             JobStageType.GENERATE_RULES,
             StageStatusType.FAILED,
-            scan_report_table_id=table_id,
+            scan_report_table=ScanReportTable.objects.get(id=table_id),
             details=f"Rules Orchestrator function failed: {e}",
         )
         raise