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Initial port to python3
[htsworkflow.git]
/
htsworkflow
/
submission
/
ucsc.py
diff --git
a/htsworkflow/submission/ucsc.py
b/htsworkflow/submission/ucsc.py
index f7734adbd972b26db9150b155a7cdeb39818e0c1..3fd83484096858207be4a7e056a56632ae049bb7 100644
(file)
--- a/
htsworkflow/submission/ucsc.py
+++ b/
htsworkflow/submission/ucsc.py
@@
-1,8
+1,8
@@
"""Utilities for extracting information from the ENCODE DCC
"""
import logging
"""Utilities for extracting information from the ENCODE DCC
"""
import logging
-import urlparse
-import urllib
2
+import url
lib.
parse
+import urllib
.request, urllib.error, urllib.parse
LOGGER = logging.getLogger(__name__)
LOGGER = logging.getLogger(__name__)
@@
-21,7
+21,7
@@
def ddf_download_url(submission_id):
'http://encodesubmit.ucsc.edu/pipeline/download_ddf/1234'
"""
fragment = 'download_ddf/%s' % (submission_id,)
'http://encodesubmit.ucsc.edu/pipeline/download_ddf/1234'
"""
fragment = 'download_ddf/%s' % (submission_id,)
- return urlparse.urljoin(UCSCEncodePipeline, fragment)
+ return url
lib.
parse.urljoin(UCSCEncodePipeline, fragment)
def daf_download_url(submission_id):
def daf_download_url(submission_id):
@@
-31,7
+31,7
@@
def daf_download_url(submission_id):
'http://encodesubmit.ucsc.edu/pipeline/download_daf/1234'
"""
fragment = 'download_daf/%s' % (submission_id,)
'http://encodesubmit.ucsc.edu/pipeline/download_daf/1234'
"""
fragment = 'download_daf/%s' % (submission_id,)
- return urlparse.urljoin(UCSCEncodePipeline, fragment)
+ return url
lib.
parse.urljoin(UCSCEncodePipeline, fragment)
def submission_view_url(submission_id):
def submission_view_url(submission_id):
@@
-41,7
+41,7
@@
def submission_view_url(submission_id):
'http://encodesubmit.ucsc.edu/pipeline/show/1234'
"""
fragment = 'show/%s' % (submission_id,)
'http://encodesubmit.ucsc.edu/pipeline/show/1234'
"""
fragment = 'show/%s' % (submission_id,)
- return urlparse.urljoin(UCSCEncodePipeline, fragment)
+ return url
lib.
parse.urljoin(UCSCEncodePipeline, fragment)
def get_encodedcc_file_index(genome, composite):
def get_encodedcc_file_index(genome, composite):
@@
-58,10
+58,10
@@
def get_encodedcc_file_index(genome, composite):
request_url = base_url + 'files.txt'
try:
request_url = base_url + 'files.txt'
try:
- request = urllib
2
.urlopen(request_url)
+ request = urllib
.request
.urlopen(request_url)
file_index = parse_ucsc_file_index(request, base_url)
return file_index
file_index = parse_ucsc_file_index(request, base_url)
return file_index
- except urllib
2.HTTPError,
e:
+ except urllib
.error.HTTPError as
e:
err = e
pass
err = e
pass