get custom variant text from ipr for comments

Author: elewis2

pori_python/ipr/main.py

@@ -37,7 +37,7 @@
     germline_kb_matches,
     select_expression_plots,
 )
-from .summary import auto_analyst_comments
+from .summary import auto_analyst_comments, ipr_analyst_comments
 from .therapeutic_options import create_therapeutic_options
 from .util import LOG_LEVELS, logger, trim_empty_values
 
@@ -194,6 +194,7 @@ def clean_unsupported_content(upload_content: Dict, ipr_spec: Dict = {}) -> Dict
         "copyVariants",
         "structuralVariants",
         "probeResults",
+        "signatureVariants",
         "msi",
     ]
     for variant_list_section in VARIANT_LIST_KEYS:
@@ -446,12 +447,20 @@ def ipr_report(
         targets = []
 
     logger.info("generating analyst comments")
+
     if generate_comments:
-        comments = {
-            "comments": auto_analyst_comments(
+        graphkb_comments = auto_analyst_comments(
                 graphkb_conn, gkb_matches, disease_name=kb_disease_match, variants=all_variants
             )
-        }
+
+        ipr_comments = ipr_analyst_comments(
+                ipr_conn,
+                gkb_matches,
+                disease_name=kb_disease_match,
+                project_name=content['project'],
+                report_type=content['template']
+            )
+        comments = {"comments": "\n".join([ipr_comments, graphkb_comments])}
     else:
         comments = {"comments": ""}
 

pori_python/ipr/summary.py

@@ -342,6 +342,40 @@ def section_statements_by_genes(
     return genes
 
 
+def ipr_analyst_comments(
+    ipr_conn: IprConnection,
+    matches: Sequence[KbMatch] | Sequence[Hashabledict],
+    disease_name: str,
+    project_name: str,
+    report_type: str
+):
+    output: List[str] = [
+        "<h3>The comments below were automatically drawn from curated text stored in IPR for variant matches in this report, and have not been manually reviewed</h3>"
+    ]
+
+    items = []
+
+    templates = ipr_conn.get(f'templates?name={report_type}')
+    # if this is genomic expect two results - one 'pharmacogenomic'
+    template_ident = [item for item in templates if item['name']==report_type][0]['ident']
+
+    projects = ipr_conn.get(f'project')
+    project_ident = [item for item in projects if item['name']==project_name][0]['ident']
+
+    match_set = list(set([item['kbVariant'] for item in matches]))
+
+    for variant in match_set:
+        itemlist = ipr_conn.get('variant-text', data={
+            'variantName': variant,
+            'template': template_ident,
+            'project': project_ident
+        })
+        if itemlist:
+            for item in itemlist:
+                output.append(item['text'])
+    return "\n".join(output)
+
+
 def auto_analyst_comments(
     graphkb_conn: GraphKBConnection,
     matches: Sequence[KbMatch] | Sequence[Hashabledict],