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dcolligandcolligan
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-181
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‎.gitignore

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@@ -12,7 +12,7 @@ scripts/auth.yml
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*.bak
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*.db-shm
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*.db-wal
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ga4gh_client/_version.py
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_version.py
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tests/data/registry.db
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# Below based off of https://gist.github.com/octocat/9257657

‎.travis.yml

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@@ -21,9 +21,9 @@ before_script:
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# run_tests.py runs everything under the script: tag so only put commands
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# under it that we want to run (and want to be able to run) as local tests
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script:
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- flake8 client_dev.py setup.py tests ga4gh_client scripts
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- flake8 client_dev.py setup.py tests ga4gh scripts
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- nosetests tests
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--with-coverage --cover-package ga4gh_client
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--with-coverage --cover-package ga4gh.client
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--cover-inclusive --cover-min-percentage=50
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--cover-branches --cover-erase
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- make clean -C docs

‎client_dev.py

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"""
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Simple shim for running the client program during development.
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"""
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import ga4gh_client.cli as cli
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import ga4gh.client.cli as cli
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if __name__ == "__main__":
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cli.client_main()

‎docs/api.rst

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.. todo:: Add overview documentation for the client API.
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.. autoclass:: ga4gh_client.client.HttpClient
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.. autoclass:: ga4gh.client.client.HttpClient
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:members: get_reference_set, get_reference,
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get_dataset, get_variant_set, get_variant,
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get_read_group_set, get_read_group,

‎docs/conf.py

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import os
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import sys
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sys.path.insert(0, os.path.abspath('..'))
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import ga4gh_client
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import ga4gh.client
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# -- General configuration ------------------------------------------------
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‎ga4gh/__init__.py

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"""
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Client for servers implementing the GA4GH api
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"""
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from __future__ import division
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from __future__ import print_function
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from __future__ import unicode_literals
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__import__('pkg_resources').declare_namespace(__name__)

‎ga4gh_client/__init__.py renamed to ‎ga4gh/client/__init__.py

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"""
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Reference implementation of the GA4GH client
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"""
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# Don't include future imports here; we don't want to export them as
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# part of the package
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__version__ = "undefined"
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try:
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from . import _version

‎ga4gh_client/cli.py renamed to ‎ga4gh/client/cli.py

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import logging
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import requests
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import ga4gh_client
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import ga4gh_client.client as client
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import ga4gh_client.exceptions as exceptions
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import ga4gh_client.protocol as protocol
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import ga4gh.client
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import ga4gh.client.client as client
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import ga4gh.client.exceptions as exceptions
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import ga4gh.client.protocol as protocol
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import ga4gh_common.cli as cli
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import ga4gh.common.cli as cli
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###############
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versionString = (
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"GA4GH Client Version {}\n"
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"(Protocol Version {})".format(
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ga4gh_client.__version__, protocol.version))
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ga4gh.client.__version__, protocol.version))
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parser.add_argument(
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"--version", version=versionString, action="version")
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‎ga4gh_client/client.py renamed to ‎ga4gh/client/client.py

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import posixpath
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import logging
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import ga4gh_client.protocol as protocol
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import ga4gh_client.exceptions as exceptions
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import ga4gh.client.protocol as protocol
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import ga4gh.client.exceptions as exceptions
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import ga4gh_schemas.pb as pb
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import ga4gh.schemas.pb as pb
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class AbstractClient(object):

‎ga4gh_client/exceptions.py renamed to ‎ga4gh/client/exceptions.py

File renamed without changes.

‎ga4gh_client/protocol.py renamed to ‎ga4gh/client/protocol.py

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import google.protobuf.message as message
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import google.protobuf.struct_pb2 as struct_pb2
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import ga4gh_schemas.pb as pb
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from ga4gh_schemas._protocol_version import version # noqa
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from ga4gh_schemas.ga4gh.common_pb2 import * # noqa
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from ga4gh_schemas.ga4gh.assay_metadata_pb2 import * # noqa
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from ga4gh_schemas.ga4gh.metadata_pb2 import * # noqa
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from ga4gh_schemas.ga4gh.metadata_service_pb2 import * # noqa
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from ga4gh_schemas.ga4gh.read_service_pb2 import * # noqa
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from ga4gh_schemas.ga4gh.reads_pb2 import * # noqa
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from ga4gh_schemas.ga4gh.reference_service_pb2 import * # noqa
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from ga4gh_schemas.ga4gh.references_pb2 import * # noqa
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from ga4gh_schemas.ga4gh.variant_service_pb2 import * # noqa
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from ga4gh_schemas.ga4gh.variants_pb2 import * # noqa
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from ga4gh_schemas.ga4gh.allele_annotations_pb2 import * # noqa
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from ga4gh_schemas.ga4gh.allele_annotation_service_pb2 import * # noqa
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from ga4gh_schemas.ga4gh.sequence_annotations_pb2 import * # noqa
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from ga4gh_schemas.ga4gh.sequence_annotation_service_pb2 import * # noqa
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from ga4gh_schemas.ga4gh.bio_metadata_pb2 import * # noqa
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from ga4gh_schemas.ga4gh.bio_metadata_service_pb2 import * # noqa
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from ga4gh_schemas.ga4gh.genotype_phenotype_pb2 import * # noqa
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from ga4gh_schemas.ga4gh.genotype_phenotype_service_pb2 import * # noqa
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from ga4gh_schemas.ga4gh.rna_quantification_pb2 import * # noqa
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from ga4gh_schemas.ga4gh.rna_quantification_service_pb2 import * # noqa
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import ga4gh.schemas.pb as pb
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from ga4gh.schemas._protocol_version import version # noqa
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from ga4gh.schemas.ga4gh.common_pb2 import * # noqa
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from ga4gh.schemas.ga4gh.assay_metadata_pb2 import * # noqa
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from ga4gh.schemas.ga4gh.metadata_pb2 import * # noqa
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from ga4gh.schemas.ga4gh.metadata_service_pb2 import * # noqa
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from ga4gh.schemas.ga4gh.read_service_pb2 import * # noqa
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from ga4gh.schemas.ga4gh.reads_pb2 import * # noqa
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from ga4gh.schemas.ga4gh.reference_service_pb2 import * # noqa
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from ga4gh.schemas.ga4gh.references_pb2 import * # noqa
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from ga4gh.schemas.ga4gh.variant_service_pb2 import * # noqa
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from ga4gh.schemas.ga4gh.variants_pb2 import * # noqa
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from ga4gh.schemas.ga4gh.allele_annotations_pb2 import * # noqa
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from ga4gh.schemas.ga4gh.allele_annotation_service_pb2 import * # noqa
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from ga4gh.schemas.ga4gh.sequence_annotations_pb2 import * # noqa
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from ga4gh.schemas.ga4gh.sequence_annotation_service_pb2 import * # noqa
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from ga4gh.schemas.ga4gh.bio_metadata_pb2 import * # noqa
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from ga4gh.schemas.ga4gh.bio_metadata_service_pb2 import * # noqa
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from ga4gh.schemas.ga4gh.genotype_phenotype_pb2 import * # noqa
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from ga4gh.schemas.ga4gh.genotype_phenotype_service_pb2 import * # noqa
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from ga4gh.schemas.ga4gh.rna_quantification_pb2 import * # noqa
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from ga4gh.schemas.ga4gh.rna_quantification_service_pb2 import * # noqa
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# A map of response objects to the name of the attribute used to

‎ga4gh_client/_protocol_version.py

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‎requirements.txt

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#
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# These requirements are read directly into setup.py, so specify them
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# in the order that they should be in in setup.py
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ga4gh_common==0.0.4
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ga4gh_schemas==0.0.7
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ga4gh_common==0.0.5
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ga4gh_schemas==0.0.8
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requests
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protobuf==3.0.0b3

‎scripts/process_schemas.py

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This file was deleted.

‎setup.py

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# END BOILERPLATE
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name="ga4gh_client",
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description="A client for the GA4GH reference server",
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packages=["ga4gh_client"],
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packages=["ga4gh", "ga4gh.client"],
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namespace_packages=["ga4gh"],
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url="https://github.com/ga4gh/ga4gh-client",
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use_scm_version={"write_to": "ga4gh_client/_version.py"},
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use_scm_version={"write_to": "ga4gh/client/_version.py"},
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entry_points={
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'console_scripts': [
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'ga4gh_client=ga4gh_client.cli:client_main',
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'ga4gh_client=ga4gh.client.cli:client_main',
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]
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},
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# BEGIN BOILERPLATE

‎tests/unit/test_cli.py

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import mock
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import unittest
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import ga4gh_client.cli as cli_client
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import ga4gh_client.protocol as protocol
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import google.protobuf.descriptor as descriptor
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import google.protobuf.internal.python_message as python_message
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import ga4gh_common.utils as utils
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import ga4gh.client.cli as cli_client
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import ga4gh.client.protocol as protocol
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import ga4gh.common.utils as utils
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class TestClientArguments(unittest.TestCase):

‎tests/unit/test_client.py

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import mock
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import ga4gh_client.protocol as protocol
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import ga4gh_client.client as client
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import ga4gh_client.exceptions as exceptions
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import ga4gh.client.protocol as protocol
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import ga4gh.client.client as client
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import ga4gh.client.exceptions as exceptions
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class TestSearchMethodsCallRunRequest(unittest.TestCase):

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