Merge branch 'master' into mgrmaster

Author: Will Trimble

mglib/mglib.py

@@ -212,6 +212,9 @@ def post_file(url, keyname, filename, data={}, auth=None, debug=False):
             finally:
                 # sys.exit(1)
                 return None
+        except OSError as error: 
+            sys.stderr.write("ERROR with post_file\n")
+            sys.stderr.write("ERROR (%s): %s\n" %(error.code, error.read()))
         if not res:
             sys.stderr.write("ERROR: no results returned for %s\n"% (filename))
             # sys.exit(1)

scripts/mg-display-statistics.py

@@ -83,7 +83,7 @@ def main(args):
     token = get_auth_token(opts)
 
     # build call url
-    url = opts.url+'/metagenome/'+opts.id+'?verbosity=stats'
+    url = opts.url+'/metagenome/'+opts.id+'?verbosity=stats&public=1'
 
     # retrieve / output data
     result = obj_from_url(url, auth=token)

tests/test_api.py

@@ -81,21 +81,21 @@ def test_matrix_04():
     o.write(str(obj))
 
 def test_large_01():
-    URI = API_URL + '/matrix/organism?group_level=phylum&source=RDP&hit_type=single&result_type=abundance&evalue=1&identity=60&length=15&taxid=0&id=mgm4510219.3'
+    URI = API_URL + '/matrix/organism?group_level=phylum&source=RDP&hit_type=single&result_type=abundance&evalue=1&identity=60&length=15&taxid=0&id=mgm4440026.3'
     obj = obj_from_url(URI)
     o = open("5.txt", "w")
     o.write(str(obj))
     os.remove("5.txt")
 
 def test_large_02():
-    URI = API_URL + '/matrix/organism?group_level=phylum&source=RefSeq&hit_type=single&result_type=abundance&evalue=1&identity=60&length=15&taxid=0&id=mgm4510219.3'
+    URI = API_URL + '/matrix/organism?group_level=phylum&source=RefSeq&hit_type=single&result_type=abundance&evalue=1&identity=60&length=15&taxid=0&id=mgm4440026.3'
     obj = obj_from_url(URI)
     o = open("6.txt", "w")
     o.write(str(obj))
     os.remove("6.txt")
 
 def test_large_03():
-    URI = API_URL + '/matrix/organism?group_level=phylum&source=SEED&hit_type=single&result_type=abundance&evalue=1&identity=60&length=15&taxid=0&id=mgm4510219.3'
+    URI = API_URL + '/matrix/organism?group_level=phylum&source=SEED&hit_type=single&result_type=abundance&evalue=1&identity=60&length=15&taxid=0&id=mgm4440026.3'
     obj = obj_from_url(URI)
     o = open("7.txt", "w")
     o.write(str(obj))