Merge pull request #47 from dougli1sqrd/turn-down-logging

setting default logging to just report warnings and above. Skipped lines are logged at INFO
biolink · Jun 26, 2017 · 28999bc · 28999bc
2 parents 2b4369e + 44daa2b
commit 28999bc
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Showing 9 changed files with 102 additions and 78 deletions.
diff --git a/bin/biogolr-bulk.py b/bin/biogolr-bulk.py
@@ -37,7 +37,7 @@ def main():
         description='Command line interface to python-ontobio.golr library'
         """
 
-        Provides command line interface onto the ontobio.golr python library, a high level 
+        Provides command line interface onto the ontobio.golr python library, a high level
         abstraction layer over Monarch and GO solr indices.
         """,
         formatter_class=argparse.RawTextHelpFormatter)
@@ -63,8 +63,11 @@ def main():
 
     if args.verbosity >= 2:
         logging.basicConfig(level=logging.DEBUG)
-    if args.verbosity == 1:
+    elif args.verbosity == 1:
         logging.basicConfig(level=logging.INFO)
+    else:
+        logging.basicConfig(level=logging.WARNING)
+
     logging.info("Welcome!")
 
     [subject_category, object_category] = args.category
@@ -75,12 +78,12 @@ def main():
                         rows=args.limit,
                         slim=args.slim,
                         url=args.url)
-    
+
     for a in assocs:
         print("{}\t{}\t{}".format(a['subject'],
                                     a['relation'],
                                     ";".join(a['objects'])))
 
-    
+
 if __name__ == "__main__":
     main()
diff --git a/bin/biogolr-fqm.py b/bin/biogolr-fqm.py
@@ -40,7 +40,7 @@ def main():
         description='Command line interface to python-ontobio.golr library'
         """
 
-        Provides command line interface onto the ontobio.golr python library, a high level 
+        Provides command line interface onto the ontobio.golr python library, a high level
         abstraction layer over Monarch and GO solr indices.
         """,
         formatter_class=argparse.RawTextHelpFormatter)
@@ -65,8 +65,11 @@ def main():
 
     if args.verbosity >= 2:
         logging.basicConfig(level=logging.DEBUG)
-    if args.verbosity == 1:
+    elif args.verbosity == 1:
         logging.basicConfig(level=logging.INFO)
+    else:
+        logging.basicConfig(level=logging.WARNING)
+
     logging.info("Welcome!")
 
     r = search_query_as_matrix(facet=args.facet,
@@ -82,6 +85,6 @@ def main():
     data=[trace]
     py.plot(data, filename='search-heatmap')
 
-    
+
 if __name__ == "__main__":
     main()
diff --git a/bin/biogolr-pivot.py b/bin/biogolr-pivot.py
@@ -40,7 +40,7 @@ def main():
         description='Command line interface to python-ontobio.golr library'
         """
 
-        Provides command line interface onto the ontobio.golr python library, a high level 
+        Provides command line interface onto the ontobio.golr python library, a high level
         abstraction layer over Monarch and GO solr indices.
         """,
         formatter_class=argparse.RawTextHelpFormatter)
@@ -67,15 +67,18 @@ def main():
 
     if args.verbosity >= 2:
         logging.basicConfig(level=logging.DEBUG)
-    if args.verbosity == 1:
+    elif args.verbosity == 1:
         logging.basicConfig(level=logging.INFO)
+    else:
+        logging.basicConfig(level=logging.WARNING)
+
     logging.info("Welcome!")
 
     r = pivot_query_as_matrix(facet=args.facet,
                               fq=args.fq,
                               facet_pivot_fields=args.pivot,
                               url=args.url,
-                              is_go=args.legacy_solr,                              
+                              is_go=args.legacy_solr,
                               **args.qargs)
 
     print(str(r))
@@ -85,6 +88,6 @@ def main():
     data=[trace]
     py.plot(data, filename='pivot-heatmap')
 
-    
+
 if __name__ == "__main__":
     main()
diff --git a/bin/biogolr-search.py b/bin/biogolr-search.py
@@ -41,7 +41,7 @@ def main():
         description='Command line interface to python-ontobio.golr library'
         """
 
-        Provides command line interface onto the ontobio.golr python library, a high level 
+        Provides command line interface onto the ontobio.golr python library, a high level
         abstraction layer over Monarch and GO solr indices.
         """,
         formatter_class=argparse.RawTextHelpFormatter)
@@ -67,13 +67,16 @@ def main():
 
     parser.add_argument('search', type=str,
                         help='Search terms')
-    
+
     args = parser.parse_args()
 
     if args.verbosity >= 2:
         logging.basicConfig(level=logging.DEBUG)
-    if args.verbosity == 1:
+    elif args.verbosity == 1:
         logging.basicConfig(level=logging.INFO)
+    else:
+        logging.basicConfig(level=logging.WARNING)
+
     logging.info("Welcome!")
 
     facets = []
@@ -96,7 +99,7 @@ def main():
                                  fq=args.fq,
                                  facet_fields=facets,
                                  url=args.url)
-    
+
         results = q.exec()
         #print("RESULTS={}".format(results))
         docs = results['associations']
@@ -109,14 +112,14 @@ def main():
                             fq=args.fq,
                             facet_fields=facets,
                             url=args.url)
-    
+
         results = q.exec()
         #print("RESULTS={}".format(results))
         docs = results['docs']
         print("RESULTS: {}".format(len(docs)))
         for r in docs:
             print(" {} '{}' {} // {}".format(r['id'],r['label'],r['score'], r['category']))
-            
+
     if len(facets) > 0:
         #from collections import OrderedDict
         fcs = results['facet_counts']
@@ -126,6 +129,6 @@ def main():
             print("## FACET: {}".format(f))
             for k,v in sorted(d.items(), key=lambda t: -t[1]):
                 print("  {:5d}: {}".format(v,k))
-    
+
 if __name__ == "__main__":
     main()
diff --git a/bin/ogr.py b/bin/ogr.py
@@ -63,12 +63,15 @@ def main():
 
     if args.verbosity >= 2:
         logging.basicConfig(level=logging.DEBUG)
-    if args.verbosity == 1:
+    elif args.verbosity == 1:
         logging.basicConfig(level=logging.INFO)
+    else:
+        logging.basicConfig(level=logging.WARNING)
+
     logging.info("Welcome!")
-    
+
     handle = args.resource
-    
+
     factory = OntologyFactory()
     logging.info("Creating ont object from: {} {}".format(handle, factory))
     ont = factory.create(handle)
@@ -79,7 +82,7 @@ def main():
     if dirn == '' and args.to is not None:
         dirn = 'u'
     searchp = args.search
-    
+
     if args.level is not None:
         logging.info("Query for level: {}".format(args.level))
         qids = qids + ont.get_level(args.level, relations=args.properties, prefix=args.prefix)
@@ -98,14 +101,14 @@ def main():
                     cset = cset.intersection(terms)
             dset = dset.union(cset)
         qids = qids + list(dset)
-                    
-        
+
+
     if args.query is not None:
         qids = qids + ont.sparql(select='*',
                                  body=args.query,
                                  inject_prefixes = ont.prefixes(),
                                  single_column=True)
-        
+
     for id in ont.resolve_names(args.ids,
                                 is_remote = searchp.find('x') > -1,
                                 is_partial_match = searchp.find('p') > -1,
@@ -127,7 +130,7 @@ def cmd_cycles(handle, args):
 
     cycles = nx.simple_cycles(g)
     print(list(cycles))
-    
+
 def cmd_search(handle, args):
     for t in args.terms:
         results = search(handle, t)
@@ -147,7 +150,7 @@ def render(ont, query_ids, args):
     w.write(ont, query_ids=query_ids, container_predicates=args.container_properties)
     #logging.info("Writing subgraph for {}, |nodes|={}".format(ont,len(nodes)))
     #w.write_subgraph(ont, nodes, query_ids=query_ids, container_predicates=args.container_properties)
-            
+
 def resolve_ids(ont, ids, args):
     r_ids = []
     for id in ids:
@@ -158,6 +161,6 @@ def resolve_ids(ont, ids, args):
             r_ids += matches
     return r_ids
 
-    
+
 if __name__ == "__main__":
     main()