8c99178b26a94e8808d87cc245ce693e0f2069f1
lrnassar
  Thu Feb 13 09:10:46 2025 -0800
Fixing the clinGenCspec otto that needed some continues when conditions were not met, no RM.

diff --git src/hg/utils/otto/clinGen/makeClinGenCspec.sh src/hg/utils/otto/clinGen/makeClinGenCspec.sh
index 59b0d691603..c41f2a7f05d 100755
--- src/hg/utils/otto/clinGen/makeClinGenCspec.sh
+++ src/hg/utils/otto/clinGen/makeClinGenCspec.sh
@@ -74,30 +74,31 @@
         disease = fields[2].strip('"')
         mondo[mondoID] = disease
 
 seen = [] 
 
 for panel in data:
     for rset in panel["ruleSets"]:
         if 'genes' in rset:
             for gene in rset['genes']:
                 name = gene['label']
                 if name in seen:
                     continue
                 seen.append(name)
                 if not name in mane:
                     print('WARNING, cannot find', name, file=sys.stderr)
+                    continue
                 disease = 'no MONDO ID specified'
                 if "diseases" in gene:
                     try:
                         mondoID = gene["diseases"][0]["label"].replace(':', '_')
                         disease = f'{mondoID}, {mondoDict[mondoID]}'
                     except:
                         mondoID = "No MONDO ID"
                         disease = f'{mondoID}'
                 url = panel['url']
                 diseaseURL = f'<a target="_blank" href="{url}">{disease}</a>'
                 affiliationURL = panel["affiliation"]["url"]
                 affURL = f'<a target="_blank" href="{affiliationURL}">{panel["affiliation"]["label"]}</a>'
                 status = panel['status']
                 color = '0'
                 print(f'{mane[name]}\t{color}\t{diseaseURL}\t{affURL}\t{status}')
@@ -180,30 +181,31 @@
         disease = fields[2].strip('"')
         mondo[mondoID] = disease
 
 seen = [] 
 
 for panel in data:
     for rset in panel["ruleSets"]:
         if 'genes' in rset:
             for gene in rset['genes']:
                 name = gene['label']
                 if name in seen:
                     continue
                 seen.append(name)
                 if not name in mane:
                     print('WARNING, cannot find', name, file=sys.stderr)
+                    continue
                 disease = 'no MONDO ID specified'
                 if "diseases" in gene:
                     try:
                         mondoID = gene["diseases"][0]["label"].replace(':', '_')
                         disease = f'{mondoID}, {mondoDict[mondoID]}'
                     except:
                         mondoID = "No MONDO ID"
                         disease = f'{mondoID}'
                 url = panel['url']
                 diseaseURL = f'<a target="_blank" href="{url}">{disease}</a>'
                 affiliationURL = panel["affiliation"]["url"]
                 affURL = f'<a target="_blank" href="{affiliationURL}">{panel["affiliation"]["label"]}</a>'
                 status = panel['status']
                 color = '0'
                 print(f'{mane[name]}\t{color}\t{diseaseURL}\t{affURL}\t{status}')