add func to prepare observed var section

Author: elewis2

pori_python/ipr/inputs.py

@@ -59,7 +59,7 @@
     'comments',
     'library',
     'germline',
-    'flags'
+    'flags',
 ]
 
 SMALL_MUT_REQ = ['gene', 'proteinChange']
@@ -98,7 +98,7 @@
     'tumourRefCount',
     'tumourRefCopies',
     'zygosity',
-    'flags'
+    'flags',
 ]
 
 EXP_REQ = ['gene', 'kbCategory']
@@ -131,7 +131,7 @@
     'rnaReads',
     'rpkm',
     'tpm',
-    'flags'
+    'flags',
 ]
 
 SV_REQ = [
@@ -164,7 +164,7 @@
     'tumourDepth',
     'germline',
     'mavis_product_id',
-    'flags'
+    'flags',
 ]
 
 SIGV_REQ = ['signatureName', 'variantTypeName']
@@ -335,6 +335,7 @@ def preprocess_expression_variants(rows: Iterable[Dict]) -> List[IprExprVariant]
     Validate the input rows contain the minimum required fields and
     generate any default values where possible
     """
+
     def row_key(row: Dict) -> Tuple[str, ...]:
         return tuple(['expression'] + [row[key] for key in EXP_KEY])
 
@@ -375,7 +376,6 @@ def row_key(row: Dict) -> Tuple[str, ...]:
 
     if errors:
         raise ValueError(f'{len(errors)} Invalid expression variants in file')
-
     return result
 
 

pori_python/ipr/ipr.py

@@ -668,7 +668,6 @@ def get_kb_disease_matches(
     verbose: bool = True,
     useSubgraphsRoute: bool = True,
 ) -> list[Dict]:
-
     disease_matches = []
 
     if not kb_disease_match:
@@ -736,9 +735,9 @@ def ensure_str_list(val):
             return [val]
         if isinstance(val, list):
             if not all(isinstance(item, str) for item in val):
-                raise TypeError("All items in flags must be strings")
+                raise TypeError('All items in flags must be strings')
             return val
-        raise TypeError(f"Unexpected type in flags field: {type(val).__name__}")
+        raise TypeError(f'Unexpected type in flags field: {type(val).__name__}')
 
     flags = []
 
@@ -748,19 +747,19 @@ def ensure_str_list(val):
         if not raw_flags:  # skips None and ''
             continue
 
-        flags.append({
-            'variant': item['key'],
-            'variantType': item['variantType'],
-            'flags': [f for f in ensure_str_list(raw_flags) if f]
-        })
+        flags.append(
+            {
+                'variant': item['key'],
+                'variantType': item['variantType'],
+                'flags': [f for f in ensure_str_list(raw_flags) if f],
+            }
+        )
         item.pop('flags', None)  # remove after extraction
 
         return flags
 
     observed_vars_section = [
-        flag
-        for variants in variant_sources
-        for flag in extract_flags(variants)
+        flag for variants in variant_sources for flag in extract_flags(variants)
     ]
 
     return observed_vars_section

pori_python/ipr/main.py

@@ -46,7 +46,7 @@
     get_kb_disease_matches,
     get_kb_matches_sections,
     select_expression_plots,
-    get_variant_flags
+    get_variant_flags,
 )
 from .summary import auto_analyst_comments, get_ipr_analyst_comments
 from .therapeutic_options import create_therapeutic_options
@@ -528,7 +528,7 @@ def ipr_report(
         gkb_matches, all_variants, kb_matched_sections['kbMatches']
     )
 
-    if True:
+    if False:
 
         def extract_flags(variant_list):
             # convert item to list of str, if it's just a str
@@ -541,12 +541,14 @@ def ensure_list(val):
 
             # extract only the relevant fields for creating an observed variant annotation record
             flags = [
-                {'variant': item['key'],
-                'variantType': item['variantType'],
-                'flags': ensure_list(item['flags'])
+                {
+                    'variant': item['key'],
+                    'variantType': item['variantType'],
+                    'flags': ensure_list(item['flags']),
                 }
-                for item in variant_list if item['flags'] is not None and item['flags'] != ''
-                ]
+                for item in variant_list
+                if item['flags'] is not None and item['flags'] != ''
+            ]
             _ = [item.pop('flags', '') for item in variant_list]
 
             return flags
@@ -556,11 +558,13 @@ def ensure_list(val):
             flags = extract_flags([item for item in varlist if item['gene'] in genes_with_variants])
             observed_vars_section.extend(flags)
         observed_vars_section.extend(extract_flags(signature_variants))
-        observed_vars_section.extend(extract_flags(filter_structural_variants(
-                        structural_variants, gkb_matches, gene_information
-                    )))
+        observed_vars_section.extend(
+            extract_flags(
+                filter_structural_variants(structural_variants, gkb_matches, gene_information)
+            )
+        )
 
-    if False:
+    if True:
         variant_sources = [
             v
             for source in [
@@ -606,7 +610,7 @@ def ensure_list(val):
             'variantCounts': variant_counts,
             'analystComments': comments,
             'therapeuticTarget': targets,
-            'observedVariantAnnotations': observed_vars_section
+            'observedVariantAnnotations': observed_vars_section,
         }
     )