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more use six.moves to import StringIO
author
Diane Trout
<diane@ghic.org>
Thu, 29 Jan 2015 18:59:48 +0000
(10:59 -0800)
committer
Diane Trout
<diane@ghic.org>
Thu, 29 Jan 2015 18:59:48 +0000
(10:59 -0800)
19 files changed:
encode_submission/encode3.py
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encode_submission/geo_gather.py
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encode_submission/ucsc_gather.py
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htsworkflow/pipelines/test/test_eland.py
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htsworkflow/pipelines/test/test_genome_mapper.py
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htsworkflow/pipelines/test/test_genomemap.py
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htsworkflow/pipelines/test/test_retrieve_config.py
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htsworkflow/pipelines/test/test_run_xml.py
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htsworkflow/pipelines/test/test_samplekey.py
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htsworkflow/pipelines/test/test_summary.py
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htsworkflow/submission/daf.py
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htsworkflow/submission/test/test_daf.py
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htsworkflow/submission/test/test_submission.py
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htsworkflow/submission/test/test_ucsc.py
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htsworkflow/util/test/test_makebed.py
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htsworkflow/util/test/test_validate.py
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samples/views.py
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test/test_copier.py
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test/test_srf2fastq.py
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diff --git
a/encode_submission/encode3.py
b/encode_submission/encode3.py
index 4e9b46640aa22ae306dcd00baae150ff84b35ca0..525edfd45427dae22c857185c6afa54197298d47 100644
(file)
--- a/
encode_submission/encode3.py
+++ b/
encode_submission/encode3.py
@@
-12,7
+12,7
@@
from optparse import OptionParser, OptionGroup
import os
from pprint import pprint, pformat
import shlex
import os
from pprint import pprint, pformat
import shlex
-from
StringIO
import StringIO
+from
six.moves
import StringIO
import stat
import sys
import time
import stat
import sys
import time
diff --git
a/encode_submission/geo_gather.py
b/encode_submission/geo_gather.py
index 751264cc4276a658491c387852a180fff94929a0..1aadb8398f92fec7a661e33cc9f219b4d656857a 100644
(file)
--- a/
encode_submission/geo_gather.py
+++ b/
encode_submission/geo_gather.py
@@
-9,7
+9,7
@@
from optparse import OptionParser, OptionGroup
import os
from pprint import pprint, pformat
import shlex
import os
from pprint import pprint, pformat
import shlex
-from
StringIO
import StringIO
+from
six.moves
import StringIO
import stat
import sys
import time
import stat
import sys
import time
diff --git
a/encode_submission/ucsc_gather.py
b/encode_submission/ucsc_gather.py
index a9fa72a83ddc1c4263e509070f50053d238fa405..bc3515b5c6511f101107d6a0dc94a6ac72c882f3 100644
(file)
--- a/
encode_submission/ucsc_gather.py
+++ b/
encode_submission/ucsc_gather.py
@@
-9,7
+9,7
@@
from optparse import OptionParser, OptionGroup
import os
from pprint import pprint, pformat
import shlex
import os
from pprint import pprint, pformat
import shlex
-from
StringIO
import StringIO
+from
six.moves
import StringIO
import stat
import sys
import time
import stat
import sys
import time
diff --git
a/htsworkflow/pipelines/test/test_eland.py
b/htsworkflow/pipelines/test/test_eland.py
index f6851883952332ab4005e06b6713bb011dc928ef..3e5820e30bc9303a09f2a865959e11b155a8ac61 100644
(file)
--- a/
htsworkflow/pipelines/test/test_eland.py
+++ b/
htsworkflow/pipelines/test/test_eland.py
@@
-1,7
+1,7
@@
#!/usr/bin/env python
"""More direct synthetic test cases for the eland output file processing
"""
#!/usr/bin/env python
"""More direct synthetic test cases for the eland output file processing
"""
-from
StringIO
import StringIO
+from
six.moves
import StringIO
from unittest import TestCase
from htsworkflow.pipelines.eland import ELAND, ElandLane, ElandMatches, \
from unittest import TestCase
from htsworkflow.pipelines.eland import ELAND, ElandLane, ElandMatches, \
diff --git
a/htsworkflow/pipelines/test/test_genome_mapper.py
b/htsworkflow/pipelines/test/test_genome_mapper.py
index d71755c90c7e639f24b83ad0683614379b04a263..011a42d04cad546923920bcfde9e6e197f3462b0 100644
(file)
--- a/
htsworkflow/pipelines/test/test_genome_mapper.py
+++ b/
htsworkflow/pipelines/test/test_genome_mapper.py
@@
-1,6
+1,6
@@
from unittest import TestCase
from unittest import TestCase
-from
StringIO
import StringIO
+from
six.moves
import StringIO
from htsworkflow.pipelines import genome_mapper
class testGenomeMapper(TestCase):
from htsworkflow.pipelines import genome_mapper
class testGenomeMapper(TestCase):
diff --git
a/htsworkflow/pipelines/test/test_genomemap.py
b/htsworkflow/pipelines/test/test_genomemap.py
index 7640910afd0ae6078a658237049ac89d75f62957..2734676106f917d11dc9efc8aee5ea98f09f920d 100644
(file)
--- a/
htsworkflow/pipelines/test/test_genomemap.py
+++ b/
htsworkflow/pipelines/test/test_genomemap.py
@@
-2,7
+2,7
@@
"""More direct synthetic test cases for the eland output file processing
"""
import os
"""More direct synthetic test cases for the eland output file processing
"""
import os
-from
StringIO
import StringIO
+from
six.moves
import StringIO
import shutil
import tempfile
from unittest import TestCase
import shutil
import tempfile
from unittest import TestCase
diff --git
a/htsworkflow/pipelines/test/test_retrieve_config.py
b/htsworkflow/pipelines/test/test_retrieve_config.py
index 7ca87905d623e0ff6ce0c5c880851a283490176f..1b412c7d98832760cce6a9c4482638fe8b531508 100644
(file)
--- a/
htsworkflow/pipelines/test/test_retrieve_config.py
+++ b/
htsworkflow/pipelines/test/test_retrieve_config.py
@@
-1,7
+1,7
@@
import csv
import os
import re
import csv
import os
import re
-from
StringIO
import StringIO
+from
six.moves
import StringIO
try:
import json
try:
import json
diff --git
a/htsworkflow/pipelines/test/test_run_xml.py
b/htsworkflow/pipelines/test/test_run_xml.py
index 42dedf9be9ed160fc2c6308ce88e3036e98fd1f6..9ef8dd08882b1df30a118d9aeb6a06eb2e2a03b8 100644
(file)
--- a/
htsworkflow/pipelines/test/test_run_xml.py
+++ b/
htsworkflow/pipelines/test/test_run_xml.py
@@
-1,6
+1,6
@@
import os
from unittest import TestCase
import os
from unittest import TestCase
-from
StringIO
import StringIO
+from
six.moves
import StringIO
from simulate_runfolder import TESTDATA_DIR
from htsworkflow.pipelines.runfolder import load_pipeline_run_xml
from simulate_runfolder import TESTDATA_DIR
from htsworkflow.pipelines.runfolder import load_pipeline_run_xml
diff --git
a/htsworkflow/pipelines/test/test_samplekey.py
b/htsworkflow/pipelines/test/test_samplekey.py
index 7861a58763f3d764df43bd3942496fcf218b2e7f..aa0b96c52392d117c3862af0e388e37b27225915 100644
(file)
--- a/
htsworkflow/pipelines/test/test_samplekey.py
+++ b/
htsworkflow/pipelines/test/test_samplekey.py
@@
-1,7
+1,7
@@
#!/usr/bin/env python
"""More direct synthetic test cases for the eland output file processing
"""
#!/usr/bin/env python
"""More direct synthetic test cases for the eland output file processing
"""
-from
StringIO
import StringIO
+from
six.moves
import StringIO
from unittest import TestCase
from htsworkflow.pipelines.samplekey import SampleKey
from unittest import TestCase
from htsworkflow.pipelines.samplekey import SampleKey
diff --git
a/htsworkflow/pipelines/test/test_summary.py
b/htsworkflow/pipelines/test/test_summary.py
index fbc025bd2aa79c8759bff1fcaaa93631856bdbf4..835d2069d22d714c2185cef8ae821648782fb70d 100644
(file)
--- a/
htsworkflow/pipelines/test/test_summary.py
+++ b/
htsworkflow/pipelines/test/test_summary.py
@@
-1,6
+1,6
@@
#!/usr/bin/env python
import os
#!/usr/bin/env python
import os
-from
StringIO
import StringIO
+from
six.moves
import StringIO
from unittest import TestCase
from htsworkflow.pipelines import summary
from unittest import TestCase
from htsworkflow.pipelines import summary
diff --git
a/htsworkflow/submission/daf.py
b/htsworkflow/submission/daf.py
index 30edcdc54ba3ca60fc231334c5de2b3a38909568..35b9a6c7d22a55cd52c833f4db8e599d2c34bea3 100644
(file)
--- a/
htsworkflow/submission/daf.py
+++ b/
htsworkflow/submission/daf.py
@@
-5,7
+5,7
@@
import os
from pprint import pformat
import re
import string
from pprint import pformat
import re
import string
-from
StringIO
import StringIO
+from
six.moves
import StringIO
import types
import urlparse
import types
import urlparse
diff --git
a/htsworkflow/submission/test/test_daf.py
b/htsworkflow/submission/test/test_daf.py
index 5bc9014267cfbbb2c1536e8c21ac83d3d7f57d23..87a0cd1c6afe4a3d82156e8c343e2a9752457599 100644
(file)
--- a/
htsworkflow/submission/test/test_daf.py
+++ b/
htsworkflow/submission/test/test_daf.py
@@
-1,7
+1,7
@@
from contextlib import contextmanager
import logging
import os
from contextlib import contextmanager
import logging
import os
-from
StringIO
import StringIO
+from
six.moves
import StringIO
import shutil
import tempfile
from unittest import TestCase, TestSuite, defaultTestLoader
import shutil
import tempfile
from unittest import TestCase, TestSuite, defaultTestLoader
diff --git
a/htsworkflow/submission/test/test_submission.py
b/htsworkflow/submission/test/test_submission.py
index 0c4e0870399eb30dbc1702d5fa1912de2a3ab837..a59fc9d9a8d0d066f37b01f2d1b69b4dcc57aeff 100644
(file)
--- a/
htsworkflow/submission/test/test_submission.py
+++ b/
htsworkflow/submission/test/test_submission.py
@@
-1,6
+1,6
@@
import os
import os
-from
StringIO
import StringIO
+from
six.moves
import StringIO
import shutil
import tempfile
from unittest import TestCase, TestSuite, defaultTestLoader
import shutil
import tempfile
from unittest import TestCase, TestSuite, defaultTestLoader
diff --git
a/htsworkflow/submission/test/test_ucsc.py
b/htsworkflow/submission/test/test_ucsc.py
index b4cb2d8bef2a24be839c2d631392c2311e6cac98..ebc461074152be6ea144aaa7e23bac811c7572ec 100644
(file)
--- a/
htsworkflow/submission/test/test_ucsc.py
+++ b/
htsworkflow/submission/test/test_ucsc.py
@@
-1,5
+1,5
@@
from unittest import TestCase, TestSuite, defaultTestLoader
from unittest import TestCase, TestSuite, defaultTestLoader
-from
StringIO
import StringIO
+from
six.moves
import StringIO
from htsworkflow.submission import ucsc
from htsworkflow.submission import ucsc
diff --git
a/htsworkflow/util/test/test_makebed.py
b/htsworkflow/util/test/test_makebed.py
index 50d2c64a638f5f8b84bff93f0418090c3fc7094d..daf618b2136132f8287bec33b57e6b62857d5285 100644
(file)
--- a/
htsworkflow/util/test/test_makebed.py
+++ b/
htsworkflow/util/test/test_makebed.py
@@
-1,5
+1,5
@@
import os
import os
-from
StringIO
import StringIO
+from
six.moves
import StringIO
from unittest import TestCase
from htsworkflow.util import makebed
from unittest import TestCase
from htsworkflow.util import makebed
diff --git
a/htsworkflow/util/test/test_validate.py
b/htsworkflow/util/test/test_validate.py
index c906cd5592fdc689509fe8e67d6339c20091b668..dc253b8d3edbfc7f375d9198b63cbf97c1a7b12a 100644
(file)
--- a/
htsworkflow/util/test/test_validate.py
+++ b/
htsworkflow/util/test/test_validate.py
@@
-1,5
+1,5
@@
import os
import os
-from
StringIO
import StringIO
+from
six.moves
import StringIO
from unittest import TestCase
from htsworkflow.util import validate
from unittest import TestCase
from htsworkflow.util import validate
diff --git
a/samples/views.py
b/samples/views.py
index e506c7d68789783e118ca6132d44a7e5e044c549..0684ee7f5589cf8436a5a1e6c1fff1cb8e023150 100644
(file)
--- a/
samples/views.py
+++ b/
samples/views.py
@@
-1,7
+1,6
@@
from __future__ import absolute_import, print_function
# Create your views here.
from __future__ import absolute_import, print_function
# Create your views here.
-import StringIO
import logging
import os
import sys
import logging
import os
import sys
diff --git
a/test/test_copier.py
b/test/test_copier.py
index 52bd8e2879dfe47e4bf444ead9924873728942ee..b88b1a49248ba7d539003163f6f468ade4f551a7 100644
(file)
--- a/
test/test_copier.py
+++ b/
test/test_copier.py
@@
-1,6
+1,6
@@
from unittest import TestCase, skipIf
from unittest import TestCase, skipIf
-from
StringIO
import StringIO
+from
six.moves
import StringIO
from htsworkflow.automation.solexa import is_runfolder
try:
from htsworkflow.automation.solexa import is_runfolder
try:
diff --git
a/test/test_srf2fastq.py
b/test/test_srf2fastq.py
index e06ec82ed31e197e464665d2a68e9c99bb53d3b5..bbd1e4132462ad1dd6cb18d1ba4d763152c0d5fb 100644
(file)
--- a/
test/test_srf2fastq.py
+++ b/
test/test_srf2fastq.py
@@
-1,5
+1,5
@@
import os
import os
-from
StringIO
import StringIO
+from
six.moves
import StringIO
import sys
from unittest import TestCase
import sys
from unittest import TestCase