X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=htsworkflow.git;a=blobdiff_plain;f=encode_submission%2Fencode_find.py;h=6c8b94223ef2fdd1a80194d43422917f558b63a7;hp=7589f5487aef5ef85a6c4ec65072aa3d025ef5bc;hb=refs%2Fheads%2Fpython3-django1.5;hpb=4262586d10cc0cc227390873b301b55244204c11
diff --git a/encode_submission/encode_find.py b/encode_submission/encode_find.py
index 7589f54..6c8b942 100644
--- 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 "\
- " ."
- print ""
+ print("# {0}".format(name))
+ print("<{0}>".format(subid.uri))
+ print(" encodeSubmit:library_urn "\
+ " .")
+ 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