Use ga4gh-common for setup and utils

.flake8

@@ -0,0 +1,2 @@
+[flake8]
+exclude = ga4gh/*_pb2.py,ga4gh/datamodel/obo_parser.py,docs,ez_setup.py

.gitignore

@@ -39,6 +39,7 @@ tests/data/registry.db
 *.rar
 *.tar
 *.zip
+*.whl
 
 # Logs and databases #
 ######################

.travis.yml

@@ -22,25 +22,23 @@ install:
   - ga4gh_repo --version
 
 before_script:
-  # the following two lines are to prevent travis from
-  # verbosely complaining about a security problem; see issue 54
-  - mkdir $HOME/.python-eggs
-  - chmod og-w $HOME/.python-eggs
   - pip install -r dev-requirements.txt
   - python scripts/build_test_data.py 
 
 
 # run_tests.py runs everything under the script: tag so only put commands
 # under it that we want to run (and want to be able to run) as local tests
 script: 
-  - flake8 *.py tests ga4gh scripts
-              --exclude=ez_setup.py,ga4gh/*_pb2.py,ga4gh/datamodel/obo_parser.py
+  - flake8 client_dev.py configtest_dev.py convert_error_code.py
+           ga2sam_dev.py ga2vcf_dev.py repo_dev.py server_dev.py
+           setup.py
+           tests ga4gh scripts
   - nosetests --with-coverage --cover-package ga4gh
               --cover-inclusive --cover-min-percentage 80
               --cover-branches --cover-erase
   - make clean -C docs
   - make -C docs
 
-# run codecov !
 after_success:
-  - bash <(curl -s https://codecov.io/bash)
+# run codecov
+  - bash <(curl -s https://codecov.io/bash)

dev-requirements.txt

@@ -16,16 +16,18 @@ PyYAML==3.11
 # do not import them in any code that can be reached via 
 # an executable that we ship
 
+mock
+nose
+pep8
+flake8
+coverage
+
 PyVCF==0.6.7
-coverage==3.7.1
-flake8==2.3.0  # Set due to conflict with pep8 in version 2.4.0
 freezegun==0.3.6
 guppy==0.1.10
-mock==1.0.0
-nose==1.3.7
-pep8==1.6.2
 snakefood==1.4
 Sphinx==1.3.1
+
 # Requirements for OIDC provider
 pyaml==15.03.1
 cherrypy==3.2.4

ga4gh/cli/__init__.py

@@ -5,9 +5,6 @@
 from __future__ import print_function
 from __future__ import unicode_literals
 
-import argparse
-import operator
-
 import ga4gh
 import ga4gh.protocol as protocol
 
@@ -20,52 +17,6 @@
 AVRO_LONG_MAX = 2**31 - 1
 
 
-class SortedHelpFormatter(argparse.HelpFormatter):
-    """
-    An argparse HelpFormatter that sorts the flags and subcommands
-    in alphabetical order
-    """
-    def add_arguments(self, actions):
-        """
-        Sort the flags alphabetically
-        """
-        actions = sorted(
-            actions, key=operator.attrgetter('option_strings'))
-        super(SortedHelpFormatter, self).add_arguments(actions)
-
-    def _iter_indented_subactions(self, action):
-        """
-        Sort the subcommands alphabetically
-        """
-        try:
-            get_subactions = action._get_subactions
-        except AttributeError:
-            pass
-        else:
-            self._indent()
-            if isinstance(action, argparse._SubParsersAction):
-                for subaction in sorted(
-                        get_subactions(), key=lambda x: x.dest):
-                    yield subaction
-            else:
-                for subaction in get_subactions():
-                    yield subaction
-            self._dedent()
-
-
-def addSubparser(subparsers, subcommand, description):
-    parser = subparsers.add_parser(
-        subcommand, description=description, help=description)
-    return parser
-
-
-def createArgumentParser(description):
-    parser = argparse.ArgumentParser(
-        description=description,
-        formatter_class=SortedHelpFormatter)
-    return parser
-
-
 def addVersionArgument(parser):
     # TODO argparse strips newlines from version output
     versionString = (

ga4gh/cli/client.py

@@ -16,6 +16,8 @@
 import ga4gh.exceptions as exceptions
 import ga4gh.protocol as protocol
 
+import ga4gh_common.cli as common_cli
+
 
 def verbosityToLogLevel(verbosity):
     """
@@ -1194,7 +1196,7 @@ def addHelpParser(subparsers):
 
 
 def addVariantsSearchParser(subparsers):
-    parser = cli.addSubparser(
+    parser = common_cli.addSubparser(
         subparsers, "variants-search", "Search for variants")
     parser.set_defaults(runner=SearchVariantsRunner)
     addUrlArgument(parser)
@@ -1204,7 +1206,7 @@ def addVariantsSearchParser(subparsers):
 
 
 def addVariantSetsSearchParser(subparsers):
-    parser = cli.addSubparser(
+    parser = common_cli.addSubparser(
         subparsers, "variantsets-search", "Search for variantSets")
     parser.set_defaults(runner=SearchVariantSetsRunner)
     addOutputFormatArgument(parser)
@@ -1240,42 +1242,42 @@ def addVariantAnnotationSetsSearchParser(subparsers):
 
 
 def addVariantAnnotationSetsGetParser(subparsers):
-    parser = cli.addSubparser(
+    parser = common_cli.addSubparser(
         subparsers, "variantannotationsets-get", "Get a variantAnnotationSet")
     parser.set_defaults(runner=GetVariantAnnotationSetRunner)
     addGetArguments(parser)
 
 
 def addVariantSetsGetParser(subparsers):
-    parser = cli.addSubparser(
+    parser = common_cli.addSubparser(
         subparsers, "variantsets-get", "Get a variantSet")
     parser.set_defaults(runner=GetVariantSetRunner)
     addGetArguments(parser)
 
 
 def addFeaturesGetParser(subparsers):
-    parser = cli.addSubparser(
+    parser = common_cli.addSubparser(
         subparsers, "features-get", "Get a feature by ID")
     parser.set_defaults(runner=GetFeatureRunner)
     addGetArguments(parser)
 
 
 def addFeatureSetsGetParser(subparsers):
-    parser = cli.addSubparser(
+    parser = common_cli.addSubparser(
         subparsers, "featuresets-get", "Get a featureSet by ID")
     parser.set_defaults(runner=GetFeatureSetRunner)
     addGetArguments(parser)
 
 
 def addBioSamplesGetParser(subparsers):
-    parser = cli.addSubparser(
+    parser = common_cli.addSubparser(
         subparsers, "biosamples-get", "Get a biosample by ID")
     parser.set_defaults(runner=GetBioSampleRunner)
     addGetArguments(parser)
 
 
 def addIndividualsGetParser(subparsers):
-    parser = cli.addSubparser(
+    parser = common_cli.addSubparser(
         subparsers, "individuals-get", "Get a individual by ID")
     parser.set_defaults(runner=GetIndividualRunner)
     addGetArguments(parser)
@@ -1337,7 +1339,7 @@ def addFeatureSetsSearchParser(subparsers):
 
 
 def addReferenceSetsSearchParser(subparsers):
-    parser = cli.addSubparser(
+    parser = common_cli.addSubparser(
         subparsers, "referencesets-search", "Search for referenceSets")
     parser.set_defaults(runner=SearchReferenceSetsRunner)
     addUrlArgument(parser)
@@ -1352,7 +1354,7 @@ def addReferenceSetsSearchParser(subparsers):
 
 
 def addReferencesSearchParser(subparsers):
-    parser = cli.addSubparser(
+    parser = common_cli.addSubparser(
         subparsers, "references-search", "Search for references")
     parser.set_defaults(runner=SearchReferencesRunner)
     addUrlArgument(parser)
@@ -1365,7 +1367,7 @@ def addReferencesSearchParser(subparsers):
 
 
 def addReadGroupSetsSearchParser(subparsers):
-    parser = cli.addSubparser(
+    parser = common_cli.addSubparser(
         subparsers, "readgroupsets-search", "Search for readGroupSets")
     parser.set_defaults(runner=SearchReadGroupSetsRunner)
     addUrlArgument(parser)
@@ -1378,7 +1380,7 @@ def addReadGroupSetsSearchParser(subparsers):
 
 
 def addCallSetsSearchParser(subparsers):
-    parser = cli.addSubparser(
+    parser = common_cli.addSubparser(
         subparsers, "callsets-search", "Search for callSets")
     parser.set_defaults(runner=SearchCallSetsRunner)
     addUrlArgument(parser)
@@ -1391,7 +1393,7 @@ def addCallSetsSearchParser(subparsers):
 
 
 def addReadsSearchParser(subparsers):
-    parser = cli.addSubparser(
+    parser = common_cli.addSubparser(
         subparsers, "reads-search", "Search for reads")
     parser.set_defaults(runner=SearchReadsRunner)
     addOutputFormatArgument(parser)
@@ -1400,14 +1402,14 @@ def addReadsSearchParser(subparsers):
 
 
 def addDatasetsGetParser(subparsers):
-    parser = cli.addSubparser(
+    parser = common_cli.addSubparser(
         subparsers, "datasets-get", "Get a dataset")
     parser.set_defaults(runner=GetDatasetRunner)
     addGetArguments(parser)
 
 
 def addDatasetsSearchParser(subparsers):
-    parser = cli.addSubparser(
+    parser = common_cli.addSubparser(
         subparsers, "datasets-search", "Search for datasets")
     parser.set_defaults(runner=SearchDatasetsRunner)
     addUrlArgument(parser)
@@ -1430,71 +1432,71 @@ def addReadsSearchParserArguments(parser):
 
 
 def addReferenceSetsGetParser(subparsers):
-    parser = cli.addSubparser(
+    parser = common_cli.addSubparser(
         subparsers, "referencesets-get", "Get a referenceset")
     parser.set_defaults(runner=GetReferenceSetRunner)
     addGetArguments(parser)
 
 
 def addReferencesGetParser(subparsers):
-    parser = cli.addSubparser(
+    parser = common_cli.addSubparser(
         subparsers, "references-get", "Get a reference")
     parser.set_defaults(runner=GetReferenceRunner)
     addGetArguments(parser)
 
 
 def addReadGroupSetsGetParser(subparsers):
-    parser = cli.addSubparser(
+    parser = common_cli.addSubparser(
         subparsers, "readgroupsets-get", "Get a read group set")
     parser.set_defaults(runner=GetReadGroupSetRunner)
     addGetArguments(parser)
 
 
 def addReadGroupsGetParser(subparsers):
-    parser = cli.addSubparser(
+    parser = common_cli.addSubparser(
         subparsers, "readgroups-get", "Get a read group")
     parser.set_defaults(runner=GetReadGroupRunner)
     addGetArguments(parser)
 
 
 def addCallSetsGetParser(subparsers):
-    parser = cli.addSubparser(
+    parser = common_cli.addSubparser(
         subparsers, "callsets-get", "Get a callSet")
     parser.set_defaults(runner=GetCallSetRunner)
     addGetArguments(parser)
 
 
 def addVariantsGetParser(subparsers):
-    parser = cli.addSubparser(
+    parser = common_cli.addSubparser(
         subparsers, "variants-get", "Get a variant")
     parser.set_defaults(runner=GetVariantRunner)
     addGetArguments(parser)
 
 
 def addRnaQuantificationSetGetParser(subparsers):
-    parser = cli.addSubparser(
+    parser = common_cli.addSubparser(
         subparsers, "rnaquantificationsets-get",
         "Get a rna quantification set")
     parser.set_defaults(runner=GetRnaQuantificationSetRunner)
     addGetArguments(parser)
 
 
 def addRnaQuantificationGetParser(subparsers):
-    parser = cli.addSubparser(
+    parser = common_cli.addSubparser(
         subparsers, "rnaquantifications-get", "Get a rna quantification")
     parser.set_defaults(runner=GetRnaQuantificationRunner)
     addGetArguments(parser)
 
 
 def addExpressionLevelGetParser(subparsers):
-    parser = cli.addSubparser(
+    parser = common_cli.addSubparser(
         subparsers, "expressionlevels-get", "Get a expression level")
     parser.set_defaults(runner=GetExpressionLevelRunner)
     addGetArguments(parser)
 
 
 def addReferencesBasesListParser(subparsers):
-    parser = cli.addSubparser(
+    parser = common_cli.addSubparser(
         subparsers, "references-list-bases", "List bases of a reference")
     parser.add_argument(
         "--outputFormat", "-O", choices=['text', 'fasta'], default="text",
@@ -1557,7 +1559,7 @@ def addExpressionLevelsSearchParser(subparsers):
 
 
 def addGenotypePhenotypeSearchParser(subparsers):
-    parser = cli.addSubparser(
+    parser = common_cli.addSubparser(
         subparsers, "genotypephenotype-search",
         "Search for genotype to phenotype associations")
     parser.set_defaults(runner=SearchGenotypePhenotypeRunner)
@@ -1569,7 +1571,7 @@ def addGenotypePhenotypeSearchParser(subparsers):
 
 
 def addPhenotypeSearchParser(subparsers):
-    parser = cli.addSubparser(
+    parser = common_cli.addSubparser(
         subparsers, "phenotype-search", "Search for phenotypes")
     parser.set_defaults(runner=SearchPhenotypeRunner)
     addUrlArgument(parser)
@@ -1580,7 +1582,7 @@ def addPhenotypeSearchParser(subparsers):
 
 
 def addPhenotypeAssociationSetsSearchParser(subparsers):
-    parser = cli.addSubparser(
+    parser = common_cli.addSubparser(
         subparsers, "phenotypeassociationsets-search",
         "Search for phenotypeassociationsets")
     parser.set_defaults(runner=SearchPhenotypeAssociationSetsRunner)
@@ -1591,7 +1593,7 @@ def addPhenotypeAssociationSetsSearchParser(subparsers):
 
 
 def getClientParser():
-    parser = cli.createArgumentParser("GA4GH reference client")
+    parser = common_cli.createArgumentParser("GA4GH reference client")
     addClientGlobalOptions(parser)
     subparsers = parser.add_subparsers(title='subcommands',)
     addHelpParser(subparsers)