From afdd76bec535955c381b542782a7182eece36056 Mon Sep 17 00:00:00 2001 From: Diane Trout Date: Thu, 29 Jan 2015 10:59:48 -0800 Subject: [PATCH] more use six.moves to import StringIO --- encode_submission/encode3.py | 2 +- encode_submission/geo_gather.py | 2 +- encode_submission/ucsc_gather.py | 2 +- htsworkflow/pipelines/test/test_eland.py | 2 +- htsworkflow/pipelines/test/test_genome_mapper.py | 2 +- htsworkflow/pipelines/test/test_genomemap.py | 2 +- htsworkflow/pipelines/test/test_retrieve_config.py | 2 +- htsworkflow/pipelines/test/test_run_xml.py | 2 +- htsworkflow/pipelines/test/test_samplekey.py | 2 +- htsworkflow/pipelines/test/test_summary.py | 2 +- htsworkflow/submission/daf.py | 2 +- htsworkflow/submission/test/test_daf.py | 2 +- htsworkflow/submission/test/test_submission.py | 2 +- htsworkflow/submission/test/test_ucsc.py | 2 +- htsworkflow/util/test/test_makebed.py | 2 +- htsworkflow/util/test/test_validate.py | 2 +- samples/views.py | 1 - test/test_copier.py | 2 +- test/test_srf2fastq.py | 2 +- 19 files changed, 18 insertions(+), 19 deletions(-) diff --git a/encode_submission/encode3.py b/encode_submission/encode3.py index 4e9b466..525edfd 100644 --- 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 -from StringIO import StringIO +from six.moves import StringIO import stat import sys import time diff --git a/encode_submission/geo_gather.py b/encode_submission/geo_gather.py index 751264c..1aadb83 100644 --- 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 -from StringIO import StringIO +from six.moves import StringIO import stat import sys import time diff --git a/encode_submission/ucsc_gather.py b/encode_submission/ucsc_gather.py index a9fa72a..bc3515b 100644 --- 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 -from StringIO import StringIO +from six.moves import StringIO import stat import sys import time diff --git a/htsworkflow/pipelines/test/test_eland.py b/htsworkflow/pipelines/test/test_eland.py index f685188..3e5820e 100644 --- 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 """ -from StringIO import StringIO +from six.moves import StringIO 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 d71755c..011a42d 100644 --- 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 StringIO import StringIO +from six.moves import StringIO 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 7640910..2734676 100644 --- 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 -from StringIO import StringIO +from six.moves import StringIO 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 7ca8790..1b412c7 100644 --- 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 -from StringIO import StringIO +from six.moves import StringIO try: import json diff --git a/htsworkflow/pipelines/test/test_run_xml.py b/htsworkflow/pipelines/test/test_run_xml.py index 42dedf9..9ef8dd0 100644 --- 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 -from StringIO import StringIO +from six.moves import StringIO 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 7861a58..aa0b96c 100644 --- 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 """ -from StringIO import StringIO +from six.moves import StringIO 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 fbc025b..835d206 100644 --- a/htsworkflow/pipelines/test/test_summary.py +++ b/htsworkflow/pipelines/test/test_summary.py @@ -1,6 +1,6 @@ #!/usr/bin/env python import os -from StringIO import StringIO +from six.moves import StringIO from unittest import TestCase from htsworkflow.pipelines import summary diff --git a/htsworkflow/submission/daf.py b/htsworkflow/submission/daf.py index 30edcdc..35b9a6c 100644 --- 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 StringIO import StringIO +from six.moves import StringIO import types import urlparse diff --git a/htsworkflow/submission/test/test_daf.py b/htsworkflow/submission/test/test_daf.py index 5bc9014..87a0cd1 100644 --- 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 StringIO import StringIO +from six.moves import StringIO 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 0c4e087..a59fc9d 100644 --- a/htsworkflow/submission/test/test_submission.py +++ b/htsworkflow/submission/test/test_submission.py @@ -1,6 +1,6 @@ import os -from StringIO import StringIO +from six.moves import StringIO 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 b4cb2d8..ebc4610 100644 --- 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 StringIO import StringIO +from six.moves import StringIO from htsworkflow.submission import ucsc diff --git a/htsworkflow/util/test/test_makebed.py b/htsworkflow/util/test/test_makebed.py index 50d2c64..daf618b 100644 --- a/htsworkflow/util/test/test_makebed.py +++ b/htsworkflow/util/test/test_makebed.py @@ -1,5 +1,5 @@ import os -from StringIO import StringIO +from six.moves import StringIO 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 c906cd5..dc253b8 100644 --- a/htsworkflow/util/test/test_validate.py +++ b/htsworkflow/util/test/test_validate.py @@ -1,5 +1,5 @@ import os -from StringIO import StringIO +from six.moves import StringIO from unittest import TestCase from htsworkflow.util import validate diff --git a/samples/views.py b/samples/views.py index e506c7d..0684ee7 100644 --- a/samples/views.py +++ b/samples/views.py @@ -1,7 +1,6 @@ from __future__ import absolute_import, print_function # Create your views here. -import StringIO import logging import os import sys diff --git a/test/test_copier.py b/test/test_copier.py index 52bd8e2..b88b1a4 100644 --- a/test/test_copier.py +++ b/test/test_copier.py @@ -1,6 +1,6 @@ from unittest import TestCase, skipIf -from StringIO import StringIO +from six.moves import StringIO from htsworkflow.automation.solexa import is_runfolder try: diff --git a/test/test_srf2fastq.py b/test/test_srf2fastq.py index e06ec82..bbd1e41 100644 --- a/test/test_srf2fastq.py +++ b/test/test_srf2fastq.py @@ -1,5 +1,5 @@ import os -from StringIO import StringIO +from six.moves import StringIO import sys from unittest import TestCase -- 2.30.2