minor: code style guides

1 files changed, 27 insertions, 23 deletions

diff --git a/examples/graph_digest_benchmark.py b/examples/graph_digest_benchmark.py
index c7c374f8..d987cf18 100644
--- a/examples/graph_digest_benchmark.py
+++ b/examples/graph_digest_benchmark.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 
 '''
-This benchmark will produce graph digests for all of the 
+This benchmark will produce graph digests for all of the
 downloadable ontologies available in Bioportal.
 '''
 
@@ -25,36 +25,38 @@ select distinct ?ontology ?title ?download where {
               metadata:links ?links.
     ?links metadata:Ontology ?download.
     filter(regex(?download, "/download"))
-} 
+}
 '''
 
 stat_cols = [
     'id',
     'ontology',
     'download_url',
-    'tree_depth', 
-    'color_count', 
-    'individuations', 
+    'tree_depth',
+    'color_count',
+    'individuations',
     'prunings',
-    'initial_color_count', 
-    'adjacent_nodes', 
-    'initial_coloring_runtime', 
-    'triple_count', 
+    'initial_color_count',
+    'adjacent_nodes',
+    'initial_coloring_runtime',
+    'triple_count',
     'graph_digest',
     'to_hash_runtime',
     'canonicalize_triples_runtime',
     'error',
-    ]     
+    ]
+
 
 def files_benchmark(ontologies, output_file, threads):
     w = open(output_file, 'w')
-    writer = csv.DictWriter(w,stat_cols)
+    writer = csv.DictWriter(w, stat_cols)
     writer.writeheader()
     tasks = Queue()
     finished_tasks = Queue()
     dl_lock = Semaphore(4)
     task_count = len(ontologies)
-    def worker(q,finished_tasks, dl_lock):
+
+    def worker(q, finished_tasks, dl_lock):
         try:
             while True:
                 stats = q.get()
@@ -73,13 +75,13 @@ def files_benchmark(ontologies, output_file, threads):
             pass
     for i in range(int(threads)):
         print "Starting worker", i
-        t = Process(target=worker, args=[tasks,finished_tasks, dl_lock])
+        t = Process(target=worker, args=[tasks, finished_tasks, dl_lock])
         t.daemon = True
         t.start()
     for download in ontologies:
         stats = defaultdict(str)
         stats.update({
-            "id":download.split("/")[-1].split(".")[0],
+            "id": download.split("/")[-1].split(".")[0],
             "ontology": download.split("/")[-1].split(".")[0],
             "download_url": download
         })
@@ -88,27 +90,29 @@ def files_benchmark(ontologies, output_file, threads):
     written_tasks = 0
     while written_tasks < task_count:
         stats = finished_tasks.get()
-        #print "Writing", stats['ontology']
+        # print "Writing", stats['ontology']
         writer.writerow(stats)
         w.flush()
         written_tasks += 1
 
+
 def bioportal_benchmark(apikey, output_file, threads):
     metadata = Namespace("http://data.bioontology.org/metadata/")
-    url = 'http://data.bioontology.org/ontologies?apikey=%s'%apikey
+    url = 'http://data.bioontology.org/ontologies?apikey=%s' % apikey
     ontology_graph = Graph()
     print url
     ontology_list_json = urlopen(url).read()
     ontology_graph.parse(StringIO(unicode(ontology_list_json)), format="json-ld")
     ontologies = ontology_graph.query(bioportal_query)
     w = open(output_file, 'w')
-    writer = csv.DictWriter(w,stat_cols)
+    writer = csv.DictWriter(w, stat_cols)
     writer.writeheader()
     tasks = Queue()
     finished_tasks = Queue()
     dl_lock = Semaphore(4)
     task_count = len(ontologies)
-    def worker(q,finished_tasks, dl_lock):
+
+    def worker(q, finished_tasks, dl_lock):
         try:
             while True:
                 stats = q.get()
@@ -116,7 +120,7 @@ def bioportal_benchmark(apikey, output_file, threads):
                 try:
                     try:
                         dl_lock.acquire()
-                        og.load(stats['download_url']+"?apikey=%s"%apikey)
+                        og.load(stats['download_url'] + "?apikey=%s" % apikey)
                     finally:
                         dl_lock.release()
                     print stats['ontology'], stats['id']
@@ -131,13 +135,13 @@ def bioportal_benchmark(apikey, output_file, threads):
             pass
     for i in range(int(threads)):
         print "Starting worker", i
-        t = Process(target=worker, args=[tasks,finished_tasks, dl_lock])
+        t = Process(target=worker, args=[tasks, finished_tasks, dl_lock])
         t.daemon = True
         t.start()
     for ontology, title, download in ontologies:
         stats = defaultdict(str)
         stats.update({
-            "id":ontology,
+            "id": ontology,
             "ontology": title,
             "download_url": download
         })
@@ -146,13 +150,13 @@ def bioportal_benchmark(apikey, output_file, threads):
     written_tasks = 0
     while written_tasks < task_count:
         stats = finished_tasks.get()
-        #print "Writing", stats['ontology']
+        # print "Writing", stats['ontology']
         writer.writerow(stats)
         w.flush()
         written_tasks += 1
 
 if __name__ == '__main__':
     if len(sys.argv) > 4:
-        files_benchmark(sys.argv[1:-2],sys.argv[-2],sys.argv[-1])
+        files_benchmark(sys.argv[1:-2], sys.argv[-2], sys.argv[-1])
     else:
         bioportal_benchmark(sys.argv[1], sys.argv[2], sys.argv[3])