Initial port to python3

[htsworkflow.git] / encode_submission / encode_find.py

diff --git a/encode_submission/encode_find.py b/encode_submission/encode_find.py
index 7589f5487aef5ef85a6c4ec65072aa3d025ef5bc..6c8b94223ef2fdd1a80194d43422917f558b63a7 100644 (file)
--- a/encode_submission/encode_find.py
+++ b/encode_submission/encode_find.py
@@ -17,8 +17,8 @@ import re
 # redland rdf lib
 import RDF
 import sys
-import urllib
-import urlparse
+import urllib.request, urllib.parse, urllib.error
+import urllib.parse
 
 if not 'DJANGO_SETTINGS_MODULE' in os.environ:
     os.environ['DJANGO_SETTINGS_MODULE'] = 'htsworkflow.settings'
@@ -130,7 +130,7 @@ def main(cmdline=None):
 
     if opts.print_rdf:
         serializer = get_serializer(name=opts.rdf_parser_name)
-        print serializer.serialize_model_to_string(model)
+        print(serializer.serialize_model_to_string(model))
 
 
 def make_parser():
@@ -261,11 +261,11 @@ def report_submissions_with_no_library(model):
     for row in results:
         subid = row['subid']
         name = row['name']
-        print "# {0}".format(name)
-        print "<{0}>".format(subid.uri)
-        print "  encodeSubmit:library_urn "\
-              "<http://jumpgate.caltech.edu/library/> ."
-        print ""
+        print("# {0}".format(name))
+        print("<{0}>".format(subid.uri))
+        print("  encodeSubmit:library_urn "\
+              "<http://jumpgate.caltech.edu/library/> .")
+        print("")
 
 def find_submissions_with_no_library(model):
     missing_lib_query_text = """
@@ -482,7 +482,7 @@ def reload_libraries(model, library_list):
         load_library_detail(model, library_urn)
 
 def user_library_id_to_library_urn(library_id):
-    split_url = urlparse.urlsplit(library_id)
+    split_url = urllib.parse.urlsplit(library_id)
     if len(split_url.scheme) == 0:
         return LIBRARY_NS[library_id]
     else:
@@ -536,11 +536,11 @@ def load_encodedcc_files(model, genome, composite):
 
     lib_term = submissionOntology['library_urn']
     sub_term = submissionOntology['submission_urn']
-    for filename, attributes in file_index.items():
+    for filename, attributes in list(file_index.items()):
         s = RDF.Node(RDF.Uri(filename))
         model.add_statement(
             RDF.Statement(s, TYPE_N, submissionOntology['ucsc_track']))
-        for name, value in attributes.items():
+        for name, value in list(attributes.items()):
             p = RDF.Node(DCC_NS[name])
             o = RDF.Node(value)
             model.add_statement(RDF.Statement(s,p,o))
@@ -566,7 +566,7 @@ def load_library_detail(model, libraryUrn):
         try:
             body = get_url_as_text(str(libraryUrn.uri), 'GET')
             rdfaParser.parse_string_into_model(model, body, libraryUrn.uri)
-        except httplib2.HttpLib2ErrorWithResponse, e:
+        except httplib2.HttpLib2ErrorWithResponse as e:
             LOGGER.error(str(e))
     elif len(results) == 1:
         pass  # Assuming that a loaded dataset has one record
@@ -644,7 +644,7 @@ def login(cookie=None):
     response, content = http.request(LOGIN_URL,
                                      'POST',
                                      headers=headers,
-                                     body=urllib.urlencode(credentials))
+                                     body=urllib.parse.urlencode(credentials))
     LOGGER.debug("Login to {0}, status {1}".format(LOGIN_URL,
                                                     response['status']))
 
@@ -709,7 +709,7 @@ def select_by_library_id(submission_list):
     for lib_id, subobj in subl:
         libraries.setdefault(lib_id, []).append(subobj)
 
-    for submission in libraries.values():
+    for submission in list(libraries.values()):
         submission.sort(key=attrgetter('date'), reverse=True)
 
     return libraries