Merge pull request #19 from dcolligan/new_common

Use newer ga4gh-* packages

.travis.yml

@@ -10,7 +10,6 @@ cache:
 install:
   - pip install pip --upgrade
   - pip install setuptools
-  - pip install ga4gh-common # need ga4gh_common.setup for sdist
   - python setup.py sdist
   - pip install dist/ga4gh_client*.tar.gz
 # every installable in setup.py's entry_points should be tested here
@@ -29,3 +28,7 @@ script:
               --cover-branches --cover-erase
   - make clean -C docs
   - make html -C docs
+
+after_success:
+# run codecov
+  - bash <(curl -s https://codecov.io/bash)

ga4gh_client/cli.py

@@ -8,14 +8,14 @@
 import json
 import logging
 import requests
-import argparse
-import operator
 
 import ga4gh_client
 import ga4gh_client.client as client
 import ga4gh_client.exceptions as exceptions
 import ga4gh_client.protocol as protocol
 
+import ga4gh_common.cli as cli
+
 
 ###############
 # Common
@@ -25,52 +25,12 @@
 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 addDisableUrllibWarningsArgument(parser):
     parser.add_argument(
         "--disable-urllib-warnings", default=False, action="store_true",
         help="Disable urllib3 warnings")
 
 
-def createArgumentParser(description):
-    parser = argparse.ArgumentParser(
-        description=description,
-        formatter_class=SortedHelpFormatter)
-    return parser
-
-
 def addVersionArgument(parser):
     # TODO argparse strips newlines from version output
     versionString = (
@@ -81,12 +41,6 @@ def addVersionArgument(parser):
         "--version", version=versionString, action="version")
 
 
-def addSubparser(subparsers, subcommand, description):
-    parser = subparsers.add_parser(
-        subcommand, description=description, help=description)
-    return parser
-
-
 ###############
 # Client
 ###############
@@ -1262,7 +1216,7 @@ def addHelpParser(subparsers):
 
 
 def addVariantsSearchParser(subparsers):
-    parser = addSubparser(
+    parser = cli.addSubparser(
         subparsers, "variants-search", "Search for variants")
     parser.set_defaults(runner=SearchVariantsRunner)
     addUrlArgument(parser)
@@ -1272,7 +1226,7 @@ def addVariantsSearchParser(subparsers):
 
 
 def addVariantSetsSearchParser(subparsers):
-    parser = addSubparser(
+    parser = cli.addSubparser(
         subparsers, "variantsets-search", "Search for variantSets")
     parser.set_defaults(runner=SearchVariantSetsRunner)
     addOutputFormatArgument(parser)
@@ -1308,42 +1262,42 @@ def addVariantAnnotationSetsSearchParser(subparsers):
 
 
 def addVariantAnnotationSetsGetParser(subparsers):
-    parser = addSubparser(
+    parser = cli.addSubparser(
         subparsers, "variantannotationsets-get", "Get a variantAnnotationSet")
     parser.set_defaults(runner=GetVariantAnnotationSetRunner)
     addGetArguments(parser)
 
 
 def addVariantSetsGetParser(subparsers):
-    parser = addSubparser(
+    parser = cli.addSubparser(
         subparsers, "variantsets-get", "Get a variantSet")
     parser.set_defaults(runner=GetVariantSetRunner)
     addGetArguments(parser)
 
 
 def addFeaturesGetParser(subparsers):
-    parser = addSubparser(
+    parser = cli.addSubparser(
         subparsers, "features-get", "Get a feature by ID")
     parser.set_defaults(runner=GetFeatureRunner)
     addGetArguments(parser)
 
 
 def addFeatureSetsGetParser(subparsers):
-    parser = addSubparser(
+    parser = cli.addSubparser(
         subparsers, "featuresets-get", "Get a featureSet by ID")
     parser.set_defaults(runner=GetFeatureSetRunner)
     addGetArguments(parser)
 
 
 def addBioSamplesGetParser(subparsers):
-    parser = addSubparser(
+    parser = cli.addSubparser(
         subparsers, "biosamples-get", "Get a biosample by ID")
     parser.set_defaults(runner=GetBioSampleRunner)
     addGetArguments(parser)
 
 
 def addIndividualsGetParser(subparsers):
-    parser = addSubparser(
+    parser = cli.addSubparser(
         subparsers, "individuals-get", "Get a individual by ID")
     parser.set_defaults(runner=GetIndividualRunner)
     addGetArguments(parser)
@@ -1405,7 +1359,7 @@ def addFeatureSetsSearchParser(subparsers):
 
 
 def addReferenceSetsSearchParser(subparsers):
-    parser = addSubparser(
+    parser = cli.addSubparser(
         subparsers, "referencesets-search", "Search for referenceSets")
     parser.set_defaults(runner=SearchReferenceSetsRunner)
     addUrlArgument(parser)
@@ -1420,7 +1374,7 @@ def addReferenceSetsSearchParser(subparsers):
 
 
 def addReferencesSearchParser(subparsers):
-    parser = addSubparser(
+    parser = cli.addSubparser(
         subparsers, "references-search", "Search for references")
     parser.set_defaults(runner=SearchReferencesRunner)
     addUrlArgument(parser)
@@ -1433,7 +1387,7 @@ def addReferencesSearchParser(subparsers):
 
 
 def addReadGroupSetsSearchParser(subparsers):
-    parser = addSubparser(
+    parser = cli.addSubparser(
         subparsers, "readgroupsets-search", "Search for readGroupSets")
     parser.set_defaults(runner=SearchReadGroupSetsRunner)
     addUrlArgument(parser)
@@ -1446,7 +1400,7 @@ def addReadGroupSetsSearchParser(subparsers):
 
 
 def addCallSetsSearchParser(subparsers):
-    parser = addSubparser(
+    parser = cli.addSubparser(
         subparsers, "callsets-search", "Search for callSets")
     parser.set_defaults(runner=SearchCallSetsRunner)
     addUrlArgument(parser)
@@ -1459,7 +1413,7 @@ def addCallSetsSearchParser(subparsers):
 
 
 def addReadsSearchParser(subparsers):
-    parser = addSubparser(
+    parser = cli.addSubparser(
         subparsers, "reads-search", "Search for reads")
     parser.set_defaults(runner=SearchReadsRunner)
     addOutputFormatArgument(parser)
@@ -1468,14 +1422,14 @@ def addReadsSearchParser(subparsers):
 
 
 def addDatasetsGetParser(subparsers):
-    parser = addSubparser(
+    parser = cli.addSubparser(
         subparsers, "datasets-get", "Get a dataset")
     parser.set_defaults(runner=GetDatasetRunner)
     addGetArguments(parser)
 
 
 def addDatasetsSearchParser(subparsers):
-    parser = addSubparser(
+    parser = cli.addSubparser(
         subparsers, "datasets-search", "Search for datasets")
     parser.set_defaults(runner=SearchDatasetsRunner)
     addUrlArgument(parser)
@@ -1498,71 +1452,71 @@ def addReadsSearchParserArguments(parser):
 
 
 def addReferenceSetsGetParser(subparsers):
-    parser = addSubparser(
+    parser = cli.addSubparser(
         subparsers, "referencesets-get", "Get a referenceset")
     parser.set_defaults(runner=GetReferenceSetRunner)
     addGetArguments(parser)
 
 
 def addReferencesGetParser(subparsers):
-    parser = addSubparser(
+    parser = cli.addSubparser(
         subparsers, "references-get", "Get a reference")
     parser.set_defaults(runner=GetReferenceRunner)
     addGetArguments(parser)
 
 
 def addReadGroupSetsGetParser(subparsers):
-    parser = addSubparser(
+    parser = cli.addSubparser(
         subparsers, "readgroupsets-get", "Get a read group set")
     parser.set_defaults(runner=GetReadGroupSetRunner)
     addGetArguments(parser)
 
 
 def addReadGroupsGetParser(subparsers):
-    parser = addSubparser(
+    parser = cli.addSubparser(
         subparsers, "readgroups-get", "Get a read group")
     parser.set_defaults(runner=GetReadGroupRunner)
     addGetArguments(parser)
 
 
 def addCallSetsGetParser(subparsers):
-    parser = addSubparser(
+    parser = cli.addSubparser(
         subparsers, "callsets-get", "Get a callSet")
     parser.set_defaults(runner=GetCallSetRunner)
     addGetArguments(parser)
 
 
 def addVariantsGetParser(subparsers):
-    parser = addSubparser(
+    parser = cli.addSubparser(
         subparsers, "variants-get", "Get a variant")
     parser.set_defaults(runner=GetVariantRunner)
     addGetArguments(parser)
 
 
 def addRnaQuantificationSetGetParser(subparsers):
-    parser = addSubparser(
+    parser = cli.addSubparser(
         subparsers, "rnaquantificationsets-get",
         "Get a rna quantification set")
     parser.set_defaults(runner=GetRnaQuantificationSetRunner)
     addGetArguments(parser)
 
 
 def addRnaQuantificationGetParser(subparsers):
-    parser = addSubparser(
+    parser = cli.addSubparser(
         subparsers, "rnaquantifications-get", "Get a rna quantification")
     parser.set_defaults(runner=GetRnaQuantificationRunner)
     addGetArguments(parser)
 
 
 def addExpressionLevelGetParser(subparsers):
-    parser = addSubparser(
+    parser = cli.addSubparser(
         subparsers, "expressionlevels-get", "Get a expression level")
     parser.set_defaults(runner=GetExpressionLevelRunner)
     addGetArguments(parser)
 
 
 def addReferencesBasesListParser(subparsers):
-    parser = addSubparser(
+    parser = cli.addSubparser(
         subparsers, "references-list-bases", "List bases of a reference")
     parser.add_argument(
         "--outputFormat", "-O", choices=['text', 'fasta'], default="text",
@@ -1625,7 +1579,7 @@ def addExpressionLevelsSearchParser(subparsers):
 
 
 def addGenotypePhenotypeSearchParser(subparsers):
-    parser = addSubparser(
+    parser = cli.addSubparser(
         subparsers, "genotypephenotype-search",
         "Search for genotype to phenotype associations")
     parser.set_defaults(runner=SearchGenotypePhenotypeRunner)
@@ -1637,7 +1591,7 @@ def addGenotypePhenotypeSearchParser(subparsers):
 
 
 def addPhenotypeSearchParser(subparsers):
-    parser = addSubparser(
+    parser = cli.addSubparser(
         subparsers, "phenotype-search", "Search for phenotypes")
     parser.set_defaults(runner=SearchPhenotypeRunner)
     addUrlArgument(parser)
@@ -1648,7 +1602,7 @@ def addPhenotypeSearchParser(subparsers):
 
 
 def addPhenotypeAssociationSetsSearchParser(subparsers):
-    parser = addSubparser(
+    parser = cli.addSubparser(
         subparsers, "phenotypeassociationsets-search",
         "Search for phenotypeassociationsets")
     parser.set_defaults(runner=SearchPhenotypeAssociationSetsRunner)
@@ -1659,7 +1613,7 @@ def addPhenotypeAssociationSetsSearchParser(subparsers):
 
 
 def getClientParser():
-    parser = createArgumentParser("GA4GH reference client")
+    parser = cli.createArgumentParser("GA4GH reference client")
     addClientGlobalOptions(parser)
     subparsers = parser.add_subparsers(title='subcommands',)
     addHelpParser(subparsers)

requirements.txt

@@ -3,7 +3,7 @@
 #
 # These requirements are read directly into setup.py, so specify them
 # in the order that they should be in in setup.py
-ga4gh_common
-ga4gh_schemas
+ga4gh_common==0.0.4
+ga4gh_schemas==0.0.7
 requests
 protobuf==3.0.0b3