def test_0025_create_repository_with_only_workflow( self ):
"""Create and populate the filtering_workflow_0060 repository"""
category = self.create_category( name=category_name, description=category_description )
self.logout()
self.login( email=common.test_user_1_email, username=common.test_user_1_name )
self.get_or_create_repository( name=workflow_repository_name,
description=workflow_repository_description,
long_description=workflow_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id( category.id ),
strings_displayed=[] )
workflow = file( self.get_filename( 'filtering_workflow/Workflow_for_0060_filter_workflow_repository.ga' ), 'r' ).read()
workflow = workflow.replace( '__TEST_TOOL_SHED_URL__', self.url.replace( 'http://', '' ) )
workflow = workflow.replace( 'Workflow for 0060_filter_workflow_repository',
'New workflow for 0060_filter_workflow_repository' )
workflow_filepath = self.generate_temp_path( 'test_0060', additional_paths=[ 'filtering_workflow_2' ] )
if not os.path.exists( workflow_filepath ):
os.makedirs( workflow_filepath )
file( os.path.join( workflow_filepath, workflow_filename ), 'w+' ).write( workflow )
repository = test_db_util.get_repository_by_name_and_owner( workflow_repository_name, common.test_user_1_name )
self.upload_file( repository,
filename=workflow_filename,
filepath=workflow_filepath,
valid_tools_only=True,
uncompress_file=False,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded filtering workflow.',
strings_displayed=[],
strings_not_displayed=[] )
self.load_workflow_image_in_tool_shed( repository, workflow_name, strings_displayed=[ '#EBBCB2' ] )
def test_0005_ensure_category_exists( self ):
'''Create the 0060 category.'''
category = self.create_category( name='Test 0060 Workflow Features', description='Test 0060 Workflow Features' )
self.logout()
self.login( email=common.test_user_1_email, username=common.test_user_1_name )
repository = self.get_or_create_repository( name=repository_name,
description=repository_description,
long_description=repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id( category.id ),
strings_displayed=[] )
if self.repository_is_new( repository ):
workflow = file( self.get_filename( 'filtering_workflow/Workflow_for_0060_filter_workflow_repository.ga' ), 'r' ).read()
workflow = workflow.replace( '__TEST_TOOL_SHED_URL__', self.url.replace( 'http://', '' ) )
workflow_filepath = self.generate_temp_path( 'test_1060', additional_paths=[ 'filtering_workflow' ] )
os.makedirs( workflow_filepath )
file( os.path.join( workflow_filepath, workflow_filename ), 'w+' ).write( workflow )
self.upload_file( repository,
workflow_filename,
filepath=workflow_filepath,
commit_message='Uploaded filtering workflow.' )
self.upload_file( repository,
'filtering/filtering_2.2.0.tar',
commit_message="Uploaded filtering 2.2.0",
remove_repo_files_not_in_tar='No' )
def test_0015_upload_workflow(self):
'''Upload a workflow with a missing tool, and verify that the tool specified is marked as missing.'''
repository = self.test_db_util.get_repository_by_name_and_owner(
repository_name, common.test_user_1_name)
workflow = file(
self.get_filename(
'filtering_workflow/Workflow_for_0060_filter_workflow_repository.ga'
), 'r').read()
workflow = workflow.replace('__TEST_TOOL_SHED_URL__',
self.url.replace('http://', ''))
workflow_filepath = self.generate_temp_path(
'test_0060', additional_paths=['filtering_workflow'])
if not os.path.exists(workflow_filepath):
os.makedirs(workflow_filepath)
file(os.path.join(workflow_filepath, workflow_filename),
'w+').write(workflow)
self.upload_file(repository,
filename=workflow_filename,
filepath=workflow_filepath,
valid_tools_only=True,
uncompress_file=False,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded filtering workflow.',
strings_displayed=[],
strings_not_displayed=[])
self.load_workflow_image_in_tool_shed(repository,
workflow_name,
strings_displayed=['#EBBCB2'])
def test_0035_create_repositories_from_0060_series( self ):
category = self.create_category( name=category_0060_name, description='' )
workflow_repository = self.get_or_create_repository( name='filtering_0060',
description="Galaxy's filtering tool",
long_description="Long description of Galaxy's filtering tool",
owner=common.test_user_1_name,
category_id=self.security.encode_id( category.id ),
strings_displayed=[] )
if self.repository_is_new( workflow_repository ):
workflow = file( self.get_filename( 'filtering_workflow/Workflow_for_0060_filter_workflow_repository.ga' ), 'r' ).read()
workflow = workflow.replace( '__TEST_TOOL_SHED_URL__', self.url.replace( 'http://', '' ) )
workflow_filepath = self.generate_temp_path( 'test_0360', additional_paths=[ 'filtering_workflow' ] )
if not os.path.exists( workflow_filepath ):
os.makedirs( workflow_filepath )
file( os.path.join( workflow_filepath, workflow_filename ), 'w+' ).write( workflow )
self.upload_file( workflow_repository,
filename=workflow_filename,
filepath=workflow_filepath,
valid_tools_only=True,
uncompress_file=False,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded filtering workflow.',
strings_displayed=[],
strings_not_displayed=[] )
self.upload_file( workflow_repository,
filename='filtering/filtering_2.2.0.tar',
filepath=None,
valid_tools_only=True,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded filtering 2.2.0 tarball.',
strings_displayed=[],
strings_not_displayed=[] )
def test_0015_upload_workflow( self ):
'''Upload a workflow with a missing tool, and verify that the tool specified is marked as missing.'''
repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name )
workflow = file( self.get_filename( 'filtering_workflow/Workflow_for_0060_filter_workflow_repository.ga' ), 'r' ).read()
workflow = workflow.replace( '__TEST_TOOL_SHED_URL__', self.url.replace( 'http://', '' ) )
workflow_filepath = self.generate_temp_path( 'test_0060', additional_paths=[ 'filtering_workflow' ] )
if not os.path.exists( workflow_filepath ):
os.makedirs( workflow_filepath )
file( os.path.join( workflow_filepath, workflow_filename ), 'w+' ).write( workflow )
self.upload_file( repository,
workflow_filename,
filepath=workflow_filepath,
commit_message='Uploaded filtering workflow.' )
self.load_workflow_image_in_tool_shed( repository, workflow_name, strings_displayed=[ '#EBBCB2' ] )
def test_0020_create_filter_workflow_repository(self):
'''Create, if necessary, a filtering repository with only a workflow.'''
category = self.create_category(name=category_name,
description=category_description)
self.logout()
self.login(email=common.test_user_1_email,
username=common.test_user_1_name)
repository = self.get_or_create_repository(
name=workflow_repository_name,
description=workflow_repository_description,
long_description=workflow_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
strings_displayed=[])
if self.repository_is_new(repository):
workflow = file(
self.get_filename(
'filtering_workflow/Workflow_for_0060_filter_workflow_repository.ga'
), 'r').read()
workflow = workflow.replace('__TEST_TOOL_SHED_URL__',
self.url.replace('http://', ''))
workflow = workflow.replace(
'Workflow for 0060_filter_workflow_repository',
'New workflow for 0060_filter_workflow_repository')
workflow_filepath = self.generate_temp_path(
'test_0060', additional_paths=['filtering_workflow_2'])
if not os.path.exists(workflow_filepath):
os.makedirs(workflow_filepath)
file(os.path.join(workflow_filepath, workflow_filename),
'w+').write(workflow)
self.upload_file(repository,
filename=workflow_filename,
filepath=workflow_filepath,
valid_tools_only=True,
uncompress_file=False,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded filtering workflow.',
strings_displayed=[],
strings_not_displayed=[])
self.load_workflow_image_in_tool_shed(
repository,
'New workflow for 0060_filter_workflow_repository',
strings_displayed=['#EBBCB2'])
def test_0005_create_repositories_and_categories(self):
category_0000 = self.create_category(
name='Test 0000 Basic Repository Features 1',
description='Test 0000 Basic Repository Features 1')
category_0001 = self.create_category(
name='Test 0000 Basic Repository Features 2',
description='Test 0000 Basic Repository Features 2')
category_0010 = self.create_category(
name='Test 0010 Repository With Tool Dependencies',
description='Tests for a repository with tool dependencies.')
category_0020 = self.create_category(
name='Test 0020 Basic Repository Dependencies',
description='Testing basic repository dependency features.')
category_0030 = self.create_category(
name='Test 0030 Repository Dependency Revisions',
description='Testing repository dependencies by revision.')
category_0040 = self.create_category(
name='test_0040_repository_circular_dependencies',
description='Testing handling of circular repository dependencies.'
)
category_0050 = self.create_category(
name='test_0050_repository_n_level_circular_dependencies',
description=
'Testing handling of circular repository dependencies to n levels.'
)
category_0060 = self.create_category(
name='Test 0060 Workflow Features',
description='Test 0060 - Workflow Features')
self.logout()
self.login(email=common.test_user_1_email,
username=common.test_user_1_name)
repository = self.get_or_create_repository(
name='filtering_0000',
description="Galaxy's filtering tool",
long_description="Long description of Galaxy's filtering tool",
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0000.id))
if self.repository_is_new(repository):
self.upload_file(repository,
'filtering/filtering_1.1.0.tar',
commit_message="Uploaded filtering 1.1.0")
self.upload_file(repository,
'filtering/filtering_2.2.0.tar',
commit_message="Uploaded filtering 2.2.0")
repository = self.get_or_create_repository(
name='freebayes_0010',
description="Galaxy's freebayes tool",
long_description="Long description of Galaxy's freebayes tool",
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0000.id),
strings_displayed=[])
if self.repository_is_new(repository):
self.upload_file(repository,
'freebayes/freebayes.xml',
valid_tools_only=False,
commit_message='Uploaded.',
strings_displayed=[])
self.upload_file(repository,
'freebayes/tool_data_table_conf.xml.sample',
valid_tools_only=False,
commit_message='Uploaded.',
strings_displayed=[])
self.upload_file(repository,
'freebayes/sam_fa_indices.loc.sample',
valid_tools_only=False,
commit_message='Uploaded.',
strings_displayed=[])
self.upload_file(repository,
'freebayes/tool_dependencies.xml',
commit_message='Uploaded.')
repository = self.get_or_create_repository(
name='emboss_datatypes_0020',
description="Galaxy applicable data formats used by Emboss tools.",
long_description=
"Galaxy applicable data formats used by Emboss tools. This repository contains no tools.",
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0010.id),
strings_displayed=[])
if self.repository_is_new(repository):
self.upload_file(repository,
'emboss/datatypes/datatypes_conf.xml',
commit_message='Uploaded datatypes_conf.xml.')
repository = self.get_or_create_repository(
name='emboss_0020',
description='Galaxy wrappers for Emboss version 5.0.0 tools',
long_description=
'Galaxy wrappers for Emboss version 5.0.0 tools',
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0020.id),
strings_displayed=[])
self.upload_file(repository,
'emboss/emboss.tar',
commit_message='Uploaded emboss_5.tar')
datatypes_repository = self.get_or_create_repository(
name='emboss_datatypes_0030',
description=datatypes_repository_description,
long_description=datatypes_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0030.id),
strings_displayed=[])
if self.repository_is_new(datatypes_repository):
self.upload_file(datatypes_repository,
'emboss/datatypes/datatypes_conf.xml',
commit_message='Uploaded datatypes_conf.xml.')
emboss_5_repository = self.get_or_create_repository(
name='emboss_5_0030',
description=emboss_repository_description,
long_description=emboss_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0030.id),
strings_displayed=[])
self.upload_file(emboss_5_repository,
'emboss/emboss.tar',
commit_message='Uploaded emboss.tar')
repository_dependencies_path = self.generate_temp_path(
'test_0330', additional_paths=['emboss', '5'])
self.generate_repository_dependency_xml(
[datatypes_repository],
self.get_filename('repository_dependencies.xml',
filepath=repository_dependencies_path))
self.upload_file(
emboss_5_repository,
'repository_dependencies.xml',
filepath=repository_dependencies_path,
commit_message='Uploaded repository_dependencies.xml')
emboss_6_repository = self.get_or_create_repository(
name='emboss_6_0030',
description=emboss_repository_description,
long_description=emboss_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0030.id),
strings_displayed=[])
self.upload_file(emboss_6_repository,
'emboss/emboss.tar',
commit_message='Uploaded emboss.tar')
repository_dependencies_path = self.generate_temp_path(
'test_0330', additional_paths=['emboss', '6'])
self.generate_repository_dependency_xml(
[datatypes_repository],
self.get_filename('repository_dependencies.xml',
filepath=repository_dependencies_path))
self.upload_file(
emboss_6_repository,
'repository_dependencies.xml',
filepath=repository_dependencies_path,
commit_message='Uploaded repository_dependencies.xml')
emboss_repository = self.get_or_create_repository(
name='emboss_0030',
description=emboss_repository_description,
long_description=emboss_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0030.id),
strings_displayed=[])
self.upload_file(emboss_repository,
'emboss/emboss.tar',
commit_message='Uploaded emboss.tar')
repository_dependencies_path = self.generate_temp_path(
'test_0330', additional_paths=['emboss', '5'])
self.generate_repository_dependency_xml(
[emboss_5_repository],
self.get_filename('repository_dependencies.xml',
filepath=repository_dependencies_path))
self.upload_file(
emboss_repository,
'repository_dependencies.xml',
filepath=repository_dependencies_path,
commit_message='Uploaded repository_dependencies.xml')
self.generate_repository_dependency_xml(
[emboss_6_repository],
self.get_filename('repository_dependencies.xml',
filepath=repository_dependencies_path))
self.upload_file(
emboss_repository,
'repository_dependencies.xml',
filepath=repository_dependencies_path,
commit_message='Uploaded repository_dependencies.xml')
repository = self.get_or_create_repository(
name='freebayes_0040',
description="Galaxy's freebayes tool",
long_description="Long description of Galaxy's freebayes tool",
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0040.id),
strings_displayed=[])
if self.repository_is_new(repository):
self.upload_file(repository,
'freebayes/freebayes.tar',
commit_message='Uploaded freebayes.tar.')
repository = self.get_or_create_repository(
name='filtering_0040',
description="Galaxy's filtering tool",
long_description="Long description of Galaxy's filtering tool",
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0040.id),
strings_displayed=[])
self.upload_file(repository,
'filtering/filtering_1.1.0.tar',
commit_message='Uploaded filtering.tar.')
freebayes_repository = test_db_util.get_repository_by_name_and_owner(
'freebayes_0040', common.test_user_1_name)
filtering_repository = test_db_util.get_repository_by_name_and_owner(
'filtering_0040', common.test_user_1_name)
repository_dependencies_path = self.generate_temp_path(
'test_0340', additional_paths=['dependencies'])
self.generate_repository_dependency_xml(
[freebayes_repository],
self.get_filename('repository_dependencies.xml',
filepath=repository_dependencies_path),
dependency_description=
'Filtering 1.1.0 depends on the freebayes repository.')
self.upload_file(filtering_repository,
'repository_dependencies.xml',
filepath=repository_dependencies_path,
commit_message='Uploaded dependency on freebayes')
self.generate_repository_dependency_xml(
[filtering_repository],
self.get_filename('repository_dependencies.xml',
filepath=repository_dependencies_path),
dependency_description=
'Freebayes depends on the filtering repository.')
self.upload_file(freebayes_repository,
'repository_dependencies.xml',
filepath=repository_dependencies_path,
commit_message='Uploaded dependency on filtering')
datatypes_repository = self.get_or_create_repository(
name='emboss_datatypes_0050',
description="Datatypes for emboss",
long_description="Long description of Emboss' datatypes",
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0050.id),
strings_displayed=[])
if self.repository_is_new(datatypes_repository):
emboss_repository = self.get_or_create_repository(
name='emboss_0050',
description="Galaxy's emboss tool",
long_description="Long description of Galaxy's emboss tool",
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0050.id),
strings_displayed=[])
filtering_repository = self.get_or_create_repository(
name='filtering_0050',
description="Galaxy's filtering tool",
long_description="Long description of Galaxy's filtering tool",
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0050.id),
strings_displayed=[])
freebayes_repository = self.get_or_create_repository(
name='freebayes_0050',
description="Galaxy's freebayes tool",
long_description="Long description of Galaxy's freebayes tool",
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0050.id),
strings_displayed=[])
self.upload_file(datatypes_repository,
'emboss/datatypes/datatypes_conf.xml',
commit_message='Uploaded datatypes_conf.xml.')
self.upload_file(emboss_repository,
'emboss/emboss.tar',
commit_message='Uploaded tool tarball.')
self.upload_file(freebayes_repository,
'freebayes/freebayes.tar',
commit_message='Uploaded freebayes.tar.')
self.upload_file(filtering_repository,
'filtering/filtering_1.1.0.tar',
commit_message='Uploaded filtering.tar.')
repository_dependencies_path = self.generate_temp_path(
'test_0350', additional_paths=['emboss'])
self.generate_repository_dependency_xml(
[datatypes_repository],
self.get_filename('repository_dependencies.xml',
filepath=repository_dependencies_path),
dependency_description=
'Emboss depends on the emboss_datatypes repository.')
self.upload_file(
emboss_repository,
'repository_dependencies.xml',
filepath=repository_dependencies_path,
commit_message='Uploaded dependency on emboss_datatypes.')
repository_dependencies_path = self.generate_temp_path(
'test_0350', additional_paths=['filtering'])
self.generate_repository_dependency_xml(
[emboss_repository],
self.get_filename('repository_dependencies.xml',
filepath=repository_dependencies_path),
dependency_description=
'Filtering depends on the emboss repository.')
self.upload_file(filtering_repository,
'repository_dependencies.xml',
filepath=repository_dependencies_path,
commit_message='Uploaded dependency on emboss.')
repository_dependencies_path = self.generate_temp_path(
'test_0350', additional_paths=['freebayes'])
self.generate_repository_dependency_xml(
[filtering_repository],
self.get_filename('repository_dependencies.xml',
filepath=repository_dependencies_path),
dependency_description=
'Emboss depends on the filtering repository.')
self.upload_file(
emboss_repository,
'repository_dependencies.xml',
filepath=repository_dependencies_path,
commit_message='Uploaded dependency on filtering.')
self.generate_repository_dependency_xml(
[
datatypes_repository, emboss_repository,
filtering_repository, freebayes_repository
],
self.get_filename('repository_dependencies.xml',
filepath=repository_dependencies_path),
dependency_description=
'Freebayes depends on the filtering repository.')
self.upload_file(
freebayes_repository,
'repository_dependencies.xml',
filepath=repository_dependencies_path,
commit_message='Uploaded dependency on filtering.')
workflow_repository = self.get_or_create_repository(
name='filtering_0060',
description="Galaxy's filtering tool",
long_description="Long description of Galaxy's filtering tool",
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0060.id),
strings_displayed=[])
if self.repository_is_new(workflow_repository):
workflow = file(
self.get_filename(
'filtering_workflow/Workflow_for_0060_filter_workflow_repository.ga'
), 'r').read()
workflow = workflow.replace('__TEST_TOOL_SHED_URL__',
self.url.replace('http://', ''))
workflow_filepath = self.generate_temp_path(
'test_0360', additional_paths=['filtering_workflow'])
os.makedirs(workflow_filepath)
file(os.path.join(workflow_filepath, workflow_filename),
'w+').write(workflow)
self.upload_file(workflow_repository,
workflow_filename,
filepath=workflow_filepath,
commit_message='Uploaded filtering workflow.')
self.upload_file(workflow_repository,
'filtering/filtering_2.2.0.tar',
commit_message='Uploaded filtering tool.')
def test_0005_create_repositories_and_categories(self):
"""Ensure that the necessary categories and repositories exist for these tests."""
global repository_datatypes_count
global running_standalone
category_0000 = self.create_category(
name="Test 0000 Basic Repository Features 1", description="Test 0000 Basic Repository Features 1"
)
category_0001 = self.create_category(
name="Test 0000 Basic Repository Features 2", description="Test 0000 Basic Repository Features 2"
)
category_0010 = self.create_category(
name="Test 0010 Repository With Tool Dependencies",
description="Tests for a repository with tool dependencies.",
)
category_0020 = self.create_category(
name="Test 0020 Basic Repository Dependencies", description="Testing basic repository dependency features."
)
category_0030 = self.create_category(
name="Test 0030 Repository Dependency Revisions", description="Testing repository dependencies by revision."
)
category_0040 = self.create_category(
name="test_0040_repository_circular_dependencies",
description="Testing handling of circular repository dependencies.",
)
category_0050 = self.create_category(
name="test_0050_repository_n_level_circular_dependencies",
description="Testing handling of circular repository dependencies to n levels.",
)
category_0060 = self.create_category(
name="Test 0060 Workflow Features", description="Test 0060 - Workflow Features"
)
self.logout()
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
repository = self.get_or_create_repository(
name="filtering_0000",
description="Galaxy's filtering tool",
long_description="Long description of Galaxy's filtering tool",
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0000.id),
)
if self.repository_is_new(repository):
self.upload_file(repository, "filtering/filtering_1.1.0.tar", commit_message="Uploaded filtering 1.1.0")
self.upload_file(repository, "filtering/filtering_2.2.0.tar", commit_message="Uploaded filtering 2.2.0")
repository = self.get_or_create_repository(
name="freebayes_0010",
description="Galaxy's freebayes tool",
long_description="Long description of Galaxy's freebayes tool",
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0010.id),
strings_displayed=[],
)
if self.repository_is_new(repository):
self.upload_file(
repository,
"freebayes/freebayes.xml",
valid_tools_only=False,
commit_message="Uploaded.",
strings_displayed=[],
)
self.upload_file(
repository,
"freebayes/tool_data_table_conf.xml.sample",
valid_tools_only=False,
commit_message="Uploaded.",
strings_displayed=[],
)
self.upload_file(
repository,
"freebayes/sam_fa_indices.loc.sample",
valid_tools_only=False,
commit_message="Uploaded.",
strings_displayed=[],
)
self.upload_file(repository, "freebayes/tool_dependencies.xml", commit_message="Uploaded.")
repository = self.get_or_create_repository(
name="emboss_datatypes_0020",
description="Galaxy applicable data formats used by Emboss tools.",
long_description="Galaxy applicable data formats used by Emboss tools. This repository contains no tools.",
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0010.id),
strings_displayed=[],
)
if self.repository_is_new(repository):
self.upload_file(
repository, "emboss/datatypes/datatypes_conf.xml", commit_message="Uploaded datatypes_conf.xml."
)
repository = self.get_or_create_repository(
name="emboss_0020",
description="Galaxy wrappers for Emboss version 5.0.0 tools",
long_description="Galaxy wrappers for Emboss version 5.0.0 tools",
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0020.id),
strings_displayed=[],
)
self.upload_file(repository, "emboss/emboss.tar", commit_message="Uploaded emboss_5.tar")
datatypes_repository = self.get_or_create_repository(
name="emboss_datatypes_0030",
description=datatypes_repository_description,
long_description=datatypes_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0030.id),
strings_displayed=[],
)
if self.repository_is_new(datatypes_repository):
running_standalone = True
self.upload_file(
datatypes_repository,
"emboss/datatypes/datatypes_conf.xml",
commit_message="Uploaded datatypes_conf.xml.",
)
repository_datatypes_count = int(self.get_repository_datatypes_count(datatypes_repository))
emboss_5_repository = self.get_or_create_repository(
name="emboss_5_0030",
description=emboss_repository_description,
long_description=emboss_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0030.id),
strings_displayed=[],
)
self.upload_file(emboss_5_repository, "emboss/emboss.tar", commit_message="Uploaded emboss.tar")
repository_dependencies_path = self.generate_temp_path("test_0330", additional_paths=["emboss", "5"])
self.generate_repository_dependency_xml(
[datatypes_repository],
self.get_filename("repository_dependencies.xml", filepath=repository_dependencies_path),
)
self.upload_file(
emboss_5_repository,
"repository_dependencies.xml",
filepath=repository_dependencies_path,
commit_message="Uploaded repository_dependencies.xml",
)
emboss_6_repository = self.get_or_create_repository(
name="emboss_6_0030",
description=emboss_repository_description,
long_description=emboss_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0030.id),
strings_displayed=[],
)
self.upload_file(emboss_6_repository, "emboss/emboss.tar", commit_message="Uploaded emboss.tar")
repository_dependencies_path = self.generate_temp_path("test_0330", additional_paths=["emboss", "6"])
self.generate_repository_dependency_xml(
[datatypes_repository],
self.get_filename("repository_dependencies.xml", filepath=repository_dependencies_path),
)
self.upload_file(
emboss_6_repository,
"repository_dependencies.xml",
filepath=repository_dependencies_path,
commit_message="Uploaded repository_dependencies.xml",
)
emboss_repository = self.get_or_create_repository(
name="emboss_0030",
description=emboss_repository_description,
long_description=emboss_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0030.id),
strings_displayed=[],
)
self.upload_file(emboss_repository, "emboss/emboss.tar", commit_message="Uploaded emboss.tar")
repository_dependencies_path = self.generate_temp_path("test_0330", additional_paths=["emboss", "5"])
self.generate_repository_dependency_xml(
[emboss_5_repository],
self.get_filename("repository_dependencies.xml", filepath=repository_dependencies_path),
)
self.upload_file(
emboss_repository,
"repository_dependencies.xml",
filepath=repository_dependencies_path,
commit_message="Uploaded repository_dependencies.xml",
)
self.generate_repository_dependency_xml(
[emboss_6_repository],
self.get_filename("repository_dependencies.xml", filepath=repository_dependencies_path),
)
self.upload_file(
emboss_repository,
"repository_dependencies.xml",
filepath=repository_dependencies_path,
commit_message="Uploaded repository_dependencies.xml",
)
repository = self.get_or_create_repository(
name="freebayes_0040",
description="Galaxy's freebayes tool",
long_description="Long description of Galaxy's freebayes tool",
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0040.id),
strings_displayed=[],
)
if self.repository_is_new(repository):
self.upload_file(repository, "freebayes/freebayes.tar", commit_message="Uploaded freebayes.tar.")
repository = self.get_or_create_repository(
name="filtering_0040",
description="Galaxy's filtering tool",
long_description="Long description of Galaxy's filtering tool",
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0040.id),
strings_displayed=[],
)
self.upload_file(repository, "filtering/filtering_1.1.0.tar", commit_message="Uploaded filtering.tar.")
freebayes_repository = test_db_util.get_repository_by_name_and_owner(
"freebayes_0040", common.test_user_1_name
)
filtering_repository = test_db_util.get_repository_by_name_and_owner(
"filtering_0040", common.test_user_1_name
)
repository_dependencies_path = self.generate_temp_path("test_0340", additional_paths=["dependencies"])
self.generate_repository_dependency_xml(
[freebayes_repository],
self.get_filename("repository_dependencies.xml", filepath=repository_dependencies_path),
dependency_description="Filtering 1.1.0 depends on the freebayes repository.",
)
self.upload_file(
filtering_repository,
"repository_dependencies.xml",
filepath=repository_dependencies_path,
commit_message="Uploaded dependency on freebayes",
)
self.generate_repository_dependency_xml(
[filtering_repository],
self.get_filename("repository_dependencies.xml", filepath=repository_dependencies_path),
dependency_description="Freebayes depends on the filtering repository.",
)
self.upload_file(
freebayes_repository,
"repository_dependencies.xml",
filepath=repository_dependencies_path,
commit_message="Uploaded dependency on filtering",
)
datatypes_repository = self.get_or_create_repository(
name="emboss_datatypes_0050",
description="Datatypes for emboss",
long_description="Long description of Emboss' datatypes",
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0050.id),
strings_displayed=[],
)
if self.repository_is_new(datatypes_repository):
emboss_repository = self.get_or_create_repository(
name="emboss_0050",
description="Galaxy's emboss tool",
long_description="Long description of Galaxy's emboss tool",
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0050.id),
strings_displayed=[],
)
filtering_repository = self.get_or_create_repository(
name="filtering_0050",
description="Galaxy's filtering tool",
long_description="Long description of Galaxy's filtering tool",
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0050.id),
strings_displayed=[],
)
freebayes_repository = self.get_or_create_repository(
name="freebayes_0050",
description="Galaxy's freebayes tool",
long_description="Long description of Galaxy's freebayes tool",
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0050.id),
strings_displayed=[],
)
self.upload_file(
datatypes_repository,
"emboss/datatypes/datatypes_conf.xml",
commit_message="Uploaded datatypes_conf.xml.",
)
self.upload_file(emboss_repository, "emboss/emboss.tar", commit_message="Uploaded tool tarball.")
self.upload_file(freebayes_repository, "freebayes/freebayes.tar", commit_message="Uploaded freebayes.tar.")
self.upload_file(
filtering_repository, "filtering/filtering_1.1.0.tar", commit_message="Uploaded filtering.tar."
)
repository_dependencies_path = self.generate_temp_path("test_0350", additional_paths=["emboss"])
self.generate_repository_dependency_xml(
[datatypes_repository],
self.get_filename("repository_dependencies.xml", filepath=repository_dependencies_path),
dependency_description="Emboss depends on the emboss_datatypes repository.",
)
self.upload_file(
emboss_repository,
"repository_dependencies.xml",
filepath=repository_dependencies_path,
commit_message="Uploaded dependency on emboss_datatypes.",
)
repository_dependencies_path = self.generate_temp_path("test_0350", additional_paths=["filtering"])
self.generate_repository_dependency_xml(
[emboss_repository],
self.get_filename("repository_dependencies.xml", filepath=repository_dependencies_path),
dependency_description="Filtering depends on the emboss repository.",
)
self.upload_file(
filtering_repository,
"repository_dependencies.xml",
filepath=repository_dependencies_path,
commit_message="Uploaded dependency on emboss.",
)
repository_dependencies_path = self.generate_temp_path("test_0350", additional_paths=["freebayes"])
self.generate_repository_dependency_xml(
[filtering_repository],
self.get_filename("repository_dependencies.xml", filepath=repository_dependencies_path),
dependency_description="Emboss depends on the filtering repository.",
)
self.upload_file(
emboss_repository,
"repository_dependencies.xml",
filepath=repository_dependencies_path,
commit_message="Uploaded dependency on filtering.",
)
self.generate_repository_dependency_xml(
[datatypes_repository, emboss_repository, filtering_repository, freebayes_repository],
self.get_filename("repository_dependencies.xml", filepath=repository_dependencies_path),
dependency_description="Freebayes depends on the filtering repository.",
)
self.upload_file(
freebayes_repository,
"repository_dependencies.xml",
filepath=repository_dependencies_path,
commit_message="Uploaded dependency on filtering.",
)
workflow_repository = self.get_or_create_repository(
name="filtering_0060",
description="Galaxy's filtering tool",
long_description="Long description of Galaxy's filtering tool",
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0060.id),
strings_displayed=[],
)
if self.repository_is_new(workflow_repository):
workflow = file(
self.get_filename("filtering_workflow/Workflow_for_0060_filter_workflow_repository.ga"), "r"
).read()
workflow = workflow.replace("__TEST_TOOL_SHED_URL__", self.url.replace("http://", ""))
workflow_filepath = self.generate_temp_path("test_0360", additional_paths=["filtering_workflow"])
os.makedirs(workflow_filepath)
file(os.path.join(workflow_filepath, workflow_filename), "w+").write(workflow)
self.upload_file(
workflow_repository,
workflow_filename,
filepath=workflow_filepath,
commit_message="Uploaded filtering workflow.",
)
self.upload_file(
workflow_repository, "filtering/filtering_2.2.0.tar", commit_message="Uploaded filtering tool."
)
def test_0005_create_repositories_and_categories( self ):
category_0000 = self.create_category( name='Test 0000 Basic Repository Features 1', description='Test 0000 Basic Repository Features 1' )
category_0001 = self.create_category( name='Test 0000 Basic Repository Features 2', description='Test 0000 Basic Repository Features 2' )
category_0010 = self.create_category( name='Test 0010 Repository With Tool Dependencies', description='Tests for a repository with tool dependencies.' )
category_0020 = self.create_category( name='Test 0020 Basic Repository Dependencies', description='Testing basic repository dependency features.' )
category_0030 = self.create_category( name='Test 0030 Repository Dependency Revisions', description='Testing repository dependencies by revision.' )
category_0040 = self.create_category( name='test_0040_repository_circular_dependencies', description='Testing handling of circular repository dependencies.' )
category_0050 = self.create_category( name='test_0050_repository_n_level_circular_dependencies', description='Testing handling of circular repository dependencies to n levels.' )
category_0060 = self.create_category( name='Test 0060 Workflow Features', description='Test 0060 - Workflow Features' )
self.logout()
self.login( email=common.test_user_1_email, username=common.test_user_1_name )
repository = self.get_or_create_repository( name='filtering_0000',
description="Galaxy's filtering tool",
long_description="Long description of Galaxy's filtering tool",
owner=common.test_user_1_name,
category_id=self.security.encode_id( category_0000.id ) )
if self.repository_is_new( repository ):
self.upload_file( repository, 'filtering/filtering_1.1.0.tar', commit_message="Uploaded filtering 1.1.0" )
self.upload_file( repository, 'filtering/filtering_2.2.0.tar', commit_message="Uploaded filtering 2.2.0" )
repository = self.get_or_create_repository( name='freebayes_0010',
description="Galaxy's freebayes tool",
long_description="Long description of Galaxy's freebayes tool",
owner=common.test_user_1_name,
category_id=self.security.encode_id( category_0000.id ),
strings_displayed=[] )
if self.repository_is_new( repository ):
self.upload_file( repository, 'freebayes/freebayes.xml', valid_tools_only=False, commit_message='Uploaded.', strings_displayed=[] )
self.upload_file( repository, 'freebayes/tool_data_table_conf.xml.sample', valid_tools_only=False, commit_message='Uploaded.', strings_displayed=[] )
self.upload_file( repository, 'freebayes/sam_fa_indices.loc.sample', valid_tools_only=False, commit_message='Uploaded.', strings_displayed=[] )
self.upload_file( repository, 'freebayes/tool_dependencies.xml', commit_message='Uploaded.' )
repository = self.get_or_create_repository( name='emboss_datatypes_0020',
description="Galaxy applicable data formats used by Emboss tools.",
long_description="Galaxy applicable data formats used by Emboss tools. This repository contains no tools.",
owner=common.test_user_1_name,
category_id=self.security.encode_id( category_0010.id ),
strings_displayed=[] )
if self.repository_is_new( repository ):
self.upload_file( repository, 'emboss/datatypes/datatypes_conf.xml', commit_message='Uploaded datatypes_conf.xml.' )
repository = self.get_or_create_repository( name='emboss_0020',
description='Galaxy wrappers for Emboss version 5.0.0 tools',
long_description='Galaxy wrappers for Emboss version 5.0.0 tools',
owner=common.test_user_1_name,
category_id=self.security.encode_id( category_0020.id ),
strings_displayed=[] )
self.upload_file( repository, 'emboss/emboss.tar', commit_message='Uploaded emboss_5.tar' )
datatypes_repository = self.get_or_create_repository( name='emboss_datatypes_0030',
description=datatypes_repository_description,
long_description=datatypes_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id( category_0030.id ),
strings_displayed=[] )
if self.repository_is_new( datatypes_repository ):
self.upload_file( datatypes_repository, 'emboss/datatypes/datatypes_conf.xml', commit_message='Uploaded datatypes_conf.xml.' )
emboss_5_repository = self.get_or_create_repository( name='emboss_5_0030',
description=emboss_repository_description,
long_description=emboss_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id( category_0030.id ),
strings_displayed=[] )
self.upload_file( emboss_5_repository, 'emboss/emboss.tar', commit_message='Uploaded emboss.tar' )
repository_dependencies_path = self.generate_temp_path( 'test_0330', additional_paths=[ 'emboss', '5' ] )
self.generate_repository_dependency_xml( [ datatypes_repository ],
self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ) )
self.upload_file( emboss_5_repository,
'repository_dependencies.xml',
filepath=repository_dependencies_path,
commit_message='Uploaded repository_dependencies.xml' )
emboss_6_repository = self.get_or_create_repository( name='emboss_6_0030',
description=emboss_repository_description,
long_description=emboss_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id( category_0030.id ),
strings_displayed=[] )
self.upload_file( emboss_6_repository, 'emboss/emboss.tar', commit_message='Uploaded emboss.tar' )
repository_dependencies_path = self.generate_temp_path( 'test_0330', additional_paths=[ 'emboss', '6' ] )
self.generate_repository_dependency_xml( [ datatypes_repository ],
self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ) )
self.upload_file( emboss_6_repository,
'repository_dependencies.xml',
filepath=repository_dependencies_path,
commit_message='Uploaded repository_dependencies.xml' )
emboss_repository = self.get_or_create_repository( name='emboss_0030',
description=emboss_repository_description,
long_description=emboss_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id( category_0030.id ),
strings_displayed=[] )
self.upload_file( emboss_repository, 'emboss/emboss.tar', commit_message='Uploaded emboss.tar' )
repository_dependencies_path = self.generate_temp_path( 'test_0330', additional_paths=[ 'emboss', '5' ] )
self.generate_repository_dependency_xml( [ emboss_5_repository ],
self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ) )
self.upload_file( emboss_repository,
'repository_dependencies.xml',
filepath=repository_dependencies_path,
commit_message='Uploaded repository_dependencies.xml' )
self.generate_repository_dependency_xml( [ emboss_6_repository ],
self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ) )
self.upload_file( emboss_repository,
'repository_dependencies.xml',
filepath=repository_dependencies_path,
commit_message='Uploaded repository_dependencies.xml' )
repository = self.get_or_create_repository( name='freebayes_0040',
description="Galaxy's freebayes tool",
long_description="Long description of Galaxy's freebayes tool",
owner=common.test_user_1_name,
category_id=self.security.encode_id( category_0040.id ),
strings_displayed=[] )
if self.repository_is_new( repository ):
self.upload_file( repository, 'freebayes/freebayes.tar', commit_message='Uploaded freebayes.tar.' )
repository = self.get_or_create_repository( name='filtering_0040',
description="Galaxy's filtering tool",
long_description="Long description of Galaxy's filtering tool",
owner=common.test_user_1_name,
category_id=self.security.encode_id( category_0040.id ),
strings_displayed=[] )
self.upload_file( repository, 'filtering/filtering_1.1.0.tar', commit_message='Uploaded filtering.tar.' )
freebayes_repository = test_db_util.get_repository_by_name_and_owner( 'freebayes_0040', common.test_user_1_name )
filtering_repository = test_db_util.get_repository_by_name_and_owner( 'filtering_0040', common.test_user_1_name )
repository_dependencies_path = self.generate_temp_path( 'test_0340', additional_paths=[ 'dependencies' ] )
self.generate_repository_dependency_xml( [ freebayes_repository ],
self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ),
dependency_description='Filtering 1.1.0 depends on the freebayes repository.' )
self.upload_file( filtering_repository,
'repository_dependencies.xml',
filepath=repository_dependencies_path,
commit_message='Uploaded dependency on freebayes' )
self.generate_repository_dependency_xml( [ filtering_repository ],
self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ),
dependency_description='Freebayes depends on the filtering repository.' )
self.upload_file( freebayes_repository,
'repository_dependencies.xml',
filepath=repository_dependencies_path,
commit_message='Uploaded dependency on filtering' )
datatypes_repository = self.get_or_create_repository( name='emboss_datatypes_0050',
description="Datatypes for emboss",
long_description="Long description of Emboss' datatypes",
owner=common.test_user_1_name,
category_id=self.security.encode_id( category_0050.id ),
strings_displayed=[] )
if self.repository_is_new( datatypes_repository ):
emboss_repository = self.get_or_create_repository( name='emboss_0050',
description="Galaxy's emboss tool",
long_description="Long description of Galaxy's emboss tool",
owner=common.test_user_1_name,
category_id=self.security.encode_id( category_0050.id ),
strings_displayed=[] )
filtering_repository = self.get_or_create_repository( name='filtering_0050',
description="Galaxy's filtering tool",
long_description="Long description of Galaxy's filtering tool",
owner=common.test_user_1_name,
category_id=self.security.encode_id( category_0050.id ),
strings_displayed=[] )
freebayes_repository = self.get_or_create_repository( name='freebayes_0050',
description="Galaxy's freebayes tool",
long_description="Long description of Galaxy's freebayes tool",
owner=common.test_user_1_name,
category_id=self.security.encode_id( category_0050.id ),
strings_displayed=[] )
self.upload_file( datatypes_repository, 'emboss/datatypes/datatypes_conf.xml', commit_message='Uploaded datatypes_conf.xml.' )
self.upload_file( emboss_repository, 'emboss/emboss.tar', commit_message='Uploaded tool tarball.' )
self.upload_file( freebayes_repository, 'freebayes/freebayes.tar', commit_message='Uploaded freebayes.tar.' )
self.upload_file( filtering_repository, 'filtering/filtering_1.1.0.tar', commit_message='Uploaded filtering.tar.' )
repository_dependencies_path = self.generate_temp_path( 'test_0350', additional_paths=[ 'emboss' ] )
self.generate_repository_dependency_xml( [ datatypes_repository ],
self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ),
dependency_description='Emboss depends on the emboss_datatypes repository.' )
self.upload_file( emboss_repository,
'repository_dependencies.xml',
filepath=repository_dependencies_path,
commit_message='Uploaded dependency on emboss_datatypes.' )
repository_dependencies_path = self.generate_temp_path( 'test_0350', additional_paths=[ 'filtering' ] )
self.generate_repository_dependency_xml( [ emboss_repository ],
self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ),
dependency_description='Filtering depends on the emboss repository.' )
self.upload_file( filtering_repository,
'repository_dependencies.xml',
filepath=repository_dependencies_path,
commit_message='Uploaded dependency on emboss.' )
repository_dependencies_path = self.generate_temp_path( 'test_0350', additional_paths=[ 'freebayes' ] )
self.generate_repository_dependency_xml( [ filtering_repository ],
self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ),
dependency_description='Emboss depends on the filtering repository.' )
self.upload_file( emboss_repository,
'repository_dependencies.xml',
filepath=repository_dependencies_path,
commit_message='Uploaded dependency on filtering.' )
self.generate_repository_dependency_xml( [ datatypes_repository, emboss_repository, filtering_repository, freebayes_repository ],
self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ),
dependency_description='Freebayes depends on the filtering repository.' )
self.upload_file( freebayes_repository,
'repository_dependencies.xml',
filepath=repository_dependencies_path,
commit_message='Uploaded dependency on filtering.' )
workflow_repository = self.get_or_create_repository( name='filtering_0060',
description="Galaxy's filtering tool",
long_description="Long description of Galaxy's filtering tool",
owner=common.test_user_1_name,
category_id=self.security.encode_id( category_0060.id ),
strings_displayed=[] )
if self.repository_is_new( workflow_repository ):
workflow = file( self.get_filename( 'filtering_workflow/Workflow_for_0060_filter_workflow_repository.ga' ), 'r' ).read()
workflow = workflow.replace( '__TEST_TOOL_SHED_URL__', self.url.replace( 'http://', '' ) )
workflow_filepath = self.generate_temp_path( 'test_0360', additional_paths=[ 'filtering_workflow' ] )
os.makedirs( workflow_filepath )
file( os.path.join( workflow_filepath, workflow_filename ), 'w+' ).write( workflow )
self.upload_file( workflow_repository,
workflow_filename,
filepath=workflow_filepath,
commit_message='Uploaded filtering workflow.' )
self.upload_file( workflow_repository,
'filtering/filtering_2.2.0.tar',
commit_message='Uploaded filtering tool.' )
def test_0005_create_repositories_and_categories( self ):
'''Ensure that the necessary categories and repositories exist for these tests.'''
global repository_datatypes_count
global running_standalone
category_0000 = self.create_category( name='Test 0000 Basic Repository Features 1', description='Test 0000 Basic Repository Features 1' )
category_0001 = self.create_category( name='Test 0000 Basic Repository Features 2', description='Test 0000 Basic Repository Features 2' )
category_0010 = self.create_category( name='Test 0010 Repository With Tool Dependencies', description='Tests for a repository with tool dependencies.' )
category_0020 = self.create_category( name='Test 0020 Basic Repository Dependencies', description='Testing basic repository dependency features.' )
category_0030 = self.create_category( name='Test 0030 Repository Dependency Revisions', description='Testing repository dependencies by revision.' )
category_0040 = self.create_category( name='test_0040_repository_circular_dependencies', description='Testing handling of circular repository dependencies.' )
category_0050 = self.create_category( name='test_0050_repository_n_level_circular_dependencies', description='Testing handling of circular repository dependencies to n levels.' )
category_0060 = self.create_category( name='Test 0060 Workflow Features', description='Test 0060 - Workflow Features' )
self.logout()
self.login( email=common.test_user_1_email, username=common.test_user_1_name )
repository = self.get_or_create_repository( name='filtering_0000',
description="Galaxy's filtering tool",
long_description="Long description of Galaxy's filtering tool",
owner=common.test_user_1_name,
category_id=self.security.encode_id( category_0000.id ) )
if self.repository_is_new( repository ):
self.upload_file( repository,
filename='filtering/filtering_1.1.0.tar',
filepath=None,
valid_tools_only=True,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded filtering 1.1.0 tarball.',
strings_displayed=[],
strings_not_displayed=[] )
self.upload_file( repository,
filename='filtering/filtering_2.2.0.tar',
filepath=None,
valid_tools_only=True,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded filtering 2.2.0 tarball.',
strings_displayed=[],
strings_not_displayed=[] )
repository = self.get_or_create_repository( name='freebayes_0010',
description="Galaxy's freebayes tool",
long_description="Long description of Galaxy's freebayes tool",
owner=common.test_user_1_name,
category_id=self.security.encode_id( category_0010.id ),
strings_displayed=[] )
if self.repository_is_new( repository ):
self.upload_file( repository,
filename='freebayes/freebayes.xml',
filepath=None,
valid_tools_only=False,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded freebayes.xml.',
strings_displayed=[],
strings_not_displayed=[] )
self.upload_file( repository,
filename='freebayes/tool_data_table_conf.xml.sample',
filepath=None,
valid_tools_only=False,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded tool_data_table_conf.xml.sample',
strings_displayed=[],
strings_not_displayed=[] )
self.upload_file( repository,
filename='freebayes/sam_fa_indices.loc.sample',
filepath=None,
valid_tools_only=False,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded sam_fa_indices.loc.sample',
strings_displayed=[],
strings_not_displayed=[] )
self.upload_file( repository,
filename='freebayes/tool_dependencies.xml',
filepath=None,
valid_tools_only=False,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded tool_dependencies.xml',
strings_displayed=[],
strings_not_displayed=[] )
repository = self.get_or_create_repository( name='emboss_datatypes_0020',
description="Galaxy applicable data formats used by Emboss tools.",
long_description="Galaxy applicable data formats used by Emboss tools. This repository contains no tools.",
owner=common.test_user_1_name,
category_id=self.security.encode_id( category_0010.id ),
strings_displayed=[] )
if self.repository_is_new( repository ):
self.upload_file( repository,
filename='emboss/datatypes/datatypes_conf.xml',
filepath=None,
valid_tools_only=False,
uncompress_file=False,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded datatypes_conf.xml.',
strings_displayed=[],
strings_not_displayed=[] )
repository = self.get_or_create_repository( name='emboss_0020',
description='Galaxy wrappers for Emboss version 5.0.0 tools',
long_description='Galaxy wrappers for Emboss version 5.0.0 tools',
owner=common.test_user_1_name,
category_id=self.security.encode_id( category_0020.id ),
strings_displayed=[] )
self.upload_file( repository,
filename='emboss/emboss.tar',
filepath=None,
valid_tools_only=True,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded emboss.tar',
strings_displayed=[],
strings_not_displayed=[] )
datatypes_repository = self.get_or_create_repository( name='emboss_datatypes_0030',
description=datatypes_repository_description,
long_description=datatypes_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id( category_0030.id ),
strings_displayed=[] )
if self.repository_is_new( datatypes_repository ):
running_standalone = True
self.upload_file( datatypes_repository,
filename='emboss/datatypes/datatypes_conf.xml',
filepath=None,
valid_tools_only=False,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded datatypes_conf.xml.',
strings_displayed=[],
strings_not_displayed=[] )
repository_datatypes_count = int( self.get_repository_datatypes_count( datatypes_repository ) )
emboss_5_repository = self.get_or_create_repository( name='emboss_5_0030',
description=emboss_repository_description,
long_description=emboss_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id( category_0030.id ),
strings_displayed=[] )
self.upload_file( emboss_5_repository,
filename='emboss/emboss.tar',
filepath=None,
valid_tools_only=True,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded emboss.tar',
strings_displayed=[],
strings_not_displayed=[] )
repository_dependencies_path = self.generate_temp_path( 'test_0330', additional_paths=[ 'emboss', '5' ] )
dependency_tuple = ( self.url, datatypes_repository.name, datatypes_repository.user.username, self.get_repository_tip( datatypes_repository ) )
self.create_repository_dependency( repository=emboss_5_repository, repository_tuples=[ dependency_tuple ], filepath=repository_dependencies_path )
emboss_6_repository = self.get_or_create_repository( name='emboss_6_0030',
description=emboss_repository_description,
long_description=emboss_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id( category_0030.id ),
strings_displayed=[] )
self.upload_file( emboss_6_repository,
filename='emboss/emboss.tar',
filepath=None,
valid_tools_only=True,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded emboss.tar',
strings_displayed=[],
strings_not_displayed=[] )
repository_dependencies_path = self.generate_temp_path( 'test_0330', additional_paths=[ 'emboss', '6' ] )
dependency_tuple = ( self.url, datatypes_repository.name, datatypes_repository.user.username, self.get_repository_tip( datatypes_repository ) )
self.create_repository_dependency( repository=emboss_6_repository, repository_tuples=[ dependency_tuple ], filepath=repository_dependencies_path )
emboss_repository = self.get_or_create_repository( name='emboss_0030',
description=emboss_repository_description,
long_description=emboss_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id( category_0030.id ),
strings_displayed=[] )
self.upload_file( emboss_repository,
filename='emboss/emboss.tar',
filepath=None,
valid_tools_only=True,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded emboss.tar',
strings_displayed=[],
strings_not_displayed=[] )
repository_dependencies_path = self.generate_temp_path( 'test_0330', additional_paths=[ 'emboss', '5' ] )
dependency_tuple = ( self.url, emboss_5_repository.name, emboss_5_repository.user.username, self.get_repository_tip( emboss_5_repository ) )
self.create_repository_dependency( repository=emboss_repository, repository_tuples=[ dependency_tuple ], filepath=repository_dependencies_path )
dependency_tuple = ( self.url, emboss_6_repository.name, emboss_6_repository.user.username, self.get_repository_tip( emboss_6_repository ) )
self.create_repository_dependency( repository=emboss_repository, repository_tuples=[ dependency_tuple ], filepath=repository_dependencies_path )
repository = self.get_or_create_repository( name='freebayes_0040',
description="Galaxy's freebayes tool",
long_description="Long description of Galaxy's freebayes tool",
owner=common.test_user_1_name,
category_id=self.security.encode_id( category_0040.id ),
strings_displayed=[] )
if self.repository_is_new( repository ):
self.upload_file( repository,
filename='freebayes/freebayes.tar',
filepath=None,
valid_tools_only=True,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded freebayes tarball.',
strings_displayed=[],
strings_not_displayed=[] )
repository = self.get_or_create_repository( name='filtering_0040',
description="Galaxy's filtering tool",
long_description="Long description of Galaxy's filtering tool",
owner=common.test_user_1_name,
category_id=self.security.encode_id( category_0040.id ),
strings_displayed=[] )
self.upload_file( repository,
filename='filtering/filtering_1.1.0.tar',
filepath=None,
valid_tools_only=True,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded filtering 1.1.0 tarball.',
strings_displayed=[],
strings_not_displayed=[] )
freebayes_repository = self.test_db_util.get_repository_by_name_and_owner( 'freebayes_0040', common.test_user_1_name )
filtering_repository = self.test_db_util.get_repository_by_name_and_owner( 'filtering_0040', common.test_user_1_name )
repository_dependencies_path = self.generate_temp_path( 'test_0340', additional_paths=[ 'dependencies' ] )
dependency_tuple = ( self.url, freebayes_repository.name, freebayes_repository.user.username, self.get_repository_tip( freebayes_repository ) )
self.create_repository_dependency( repository=filtering_repository, repository_tuples=[ dependency_tuple ], filepath=repository_dependencies_path )
dependency_tuple = ( self.url, filtering_repository.name, filtering_repository.user.username, self.get_repository_tip( filtering_repository ) )
self.create_repository_dependency( repository=freebayes_repository, repository_tuples=[ dependency_tuple ], filepath=repository_dependencies_path )
datatypes_repository = self.get_or_create_repository( name='emboss_datatypes_0050',
description="Datatypes for emboss",
long_description="Long description of Emboss' datatypes",
owner=common.test_user_1_name,
category_id=self.security.encode_id( category_0050.id ),
strings_displayed=[] )
if self.repository_is_new( datatypes_repository ):
emboss_repository = self.get_or_create_repository( name='emboss_0050',
description="Galaxy's emboss tool",
long_description="Long description of Galaxy's emboss tool",
owner=common.test_user_1_name,
category_id=self.security.encode_id( category_0050.id ),
strings_displayed=[] )
filtering_repository = self.get_or_create_repository( name='filtering_0050',
description="Galaxy's filtering tool",
long_description="Long description of Galaxy's filtering tool",
owner=common.test_user_1_name,
category_id=self.security.encode_id( category_0050.id ),
strings_displayed=[] )
freebayes_repository = self.get_or_create_repository( name='freebayes_0050',
description="Galaxy's freebayes tool",
long_description="Long description of Galaxy's freebayes tool",
owner=common.test_user_1_name,
category_id=self.security.encode_id( category_0050.id ),
strings_displayed=[] )
self.upload_file( datatypes_repository,
filename='emboss/datatypes/datatypes_conf.xml',
filepath=None,
valid_tools_only=False,
uncompress_file=False,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded datatypes_conf.xml.',
strings_displayed=[],
strings_not_displayed=[] )
self.upload_file( emboss_repository,
filename='emboss/emboss.tar',
filepath=None,
valid_tools_only=True,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded emboss.tar',
strings_displayed=[],
strings_not_displayed=[] )
self.upload_file( freebayes_repository,
filename='freebayes/freebayes.tar',
filepath=None,
valid_tools_only=True,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded freebayes tarball.',
strings_displayed=[],
strings_not_displayed=[] )
self.upload_file( filtering_repository,
filename='filtering/filtering_1.1.0.tar',
filepath=None,
valid_tools_only=True,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded filtering 1.1.0 tarball.',
strings_displayed=[],
strings_not_displayed=[] )
repository_dependencies_path = self.generate_temp_path( 'test_0350', additional_paths=[ 'emboss' ] )
dependency_tuple = ( self.url, datatypes_repository.name, datatypes_repository.user.username, self.get_repository_tip( datatypes_repository ) )
self.create_repository_dependency( repository=emboss_repository, repository_tuples=[ dependency_tuple ], filepath=repository_dependencies_path )
repository_dependencies_path = self.generate_temp_path( 'test_0350', additional_paths=[ 'filtering' ] )
dependency_tuple = ( self.url, emboss_repository.name, emboss_repository.user.username, self.get_repository_tip( emboss_repository ) )
self.create_repository_dependency( repository=filtering_repository, repository_tuples=[ dependency_tuple ], filepath=repository_dependencies_path )
repository_dependencies_path = self.generate_temp_path( 'test_0350', additional_paths=[ 'freebayes' ] )
dependency_tuple = ( self.url, filtering_repository.name, filtering_repository.user.username, self.get_repository_tip( filtering_repository ) )
self.create_repository_dependency( repository=emboss_repository, repository_tuples=[ dependency_tuple ], filepath=repository_dependencies_path )
dependency_tuples = [ ( self.url, datatypes_repository.name, datatypes_repository.user.username, self.get_repository_tip( datatypes_repository ) ),
( self.url, emboss_repository.name, emboss_repository.user.username, self.get_repository_tip( emboss_repository ) ),
( self.url, filtering_repository.name, filtering_repository.user.username, self.get_repository_tip( filtering_repository ) ),
( self.url, freebayes_repository.name, freebayes_repository.user.username, self.get_repository_tip( freebayes_repository ) ) ]
self.create_repository_dependency( repository=freebayes_repository, repository_tuples=dependency_tuples, filepath=repository_dependencies_path )
workflow_repository = self.get_or_create_repository( name='filtering_0060',
description="Galaxy's filtering tool",
long_description="Long description of Galaxy's filtering tool",
owner=common.test_user_1_name,
category_id=self.security.encode_id( category_0060.id ),
strings_displayed=[] )
if self.repository_is_new( workflow_repository ):
workflow = file( self.get_filename( 'filtering_workflow/Workflow_for_0060_filter_workflow_repository.ga' ), 'r' ).read()
workflow = workflow.replace( '__TEST_TOOL_SHED_URL__', self.url.replace( 'http://', '' ) )
workflow_filepath = self.generate_temp_path( 'test_0360', additional_paths=[ 'filtering_workflow' ] )
if not os.path.exists( workflow_filepath ):
os.makedirs( workflow_filepath )
file( os.path.join( workflow_filepath, workflow_filename ), 'w+' ).write( workflow )
self.upload_file( workflow_repository,
filename=workflow_filename,
filepath=workflow_filepath,
valid_tools_only=True,
uncompress_file=False,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded filtering workflow.',
strings_displayed=[],
strings_not_displayed=[] )
self.upload_file( workflow_repository,
filename='filtering/filtering_2.2.0.tar',
filepath=None,
valid_tools_only=True,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded filtering 2.2.0 tarball.',
strings_displayed=[],
strings_not_displayed=[] )
def test_0005_create_repositories_and_categories(self):
'''Ensure that the necessary categories and repositories exist for these tests.'''
global repository_datatypes_count
global running_standalone
category_0000 = self.create_category(
name='Test 0000 Basic Repository Features 1',
description='Test 0000 Basic Repository Features 1')
category_0001 = self.create_category(
name='Test 0000 Basic Repository Features 2',
description='Test 0000 Basic Repository Features 2')
category_0010 = self.create_category(
name='Test 0010 Repository With Tool Dependencies',
description='Tests for a repository with tool dependencies.')
category_0020 = self.create_category(
name='Test 0020 Basic Repository Dependencies',
description='Testing basic repository dependency features.')
category_0030 = self.create_category(
name='Test 0030 Repository Dependency Revisions',
description='Testing repository dependencies by revision.')
category_0040 = self.create_category(
name='test_0040_repository_circular_dependencies',
description='Testing handling of circular repository dependencies.'
)
category_0050 = self.create_category(
name='test_0050_repository_n_level_circular_dependencies',
description=
'Testing handling of circular repository dependencies to n levels.'
)
category_0060 = self.create_category(
name='Test 0060 Workflow Features',
description='Test 0060 - Workflow Features')
self.logout()
self.login(email=common.test_user_1_email,
username=common.test_user_1_name)
repository = self.get_or_create_repository(
name='filtering_0000',
description="Galaxy's filtering tool",
long_description="Long description of Galaxy's filtering tool",
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0000.id))
if self.repository_is_new(repository):
self.upload_file(
repository,
filename='filtering/filtering_1.1.0.tar',
filepath=None,
valid_tools_only=True,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded filtering 1.1.0 tarball.',
strings_displayed=[],
strings_not_displayed=[])
self.upload_file(
repository,
filename='filtering/filtering_2.2.0.tar',
filepath=None,
valid_tools_only=True,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded filtering 2.2.0 tarball.',
strings_displayed=[],
strings_not_displayed=[])
repository = self.get_or_create_repository(
name='freebayes_0010',
description="Galaxy's freebayes tool",
long_description="Long description of Galaxy's freebayes tool",
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0010.id),
strings_displayed=[])
if self.repository_is_new(repository):
self.upload_file(repository,
filename='freebayes/freebayes.xml',
filepath=None,
valid_tools_only=False,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded freebayes.xml.',
strings_displayed=[],
strings_not_displayed=[])
self.upload_file(
repository,
filename='freebayes/tool_data_table_conf.xml.sample',
filepath=None,
valid_tools_only=False,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded tool_data_table_conf.xml.sample',
strings_displayed=[],
strings_not_displayed=[])
self.upload_file(
repository,
filename='freebayes/sam_fa_indices.loc.sample',
filepath=None,
valid_tools_only=False,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded sam_fa_indices.loc.sample',
strings_displayed=[],
strings_not_displayed=[])
self.upload_file(repository,
filename='freebayes/tool_dependencies.xml',
filepath=None,
valid_tools_only=False,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded tool_dependencies.xml',
strings_displayed=[],
strings_not_displayed=[])
repository = self.get_or_create_repository(
name='emboss_datatypes_0020',
description="Galaxy applicable data formats used by Emboss tools.",
long_description=
"Galaxy applicable data formats used by Emboss tools. This repository contains no tools.",
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0010.id),
strings_displayed=[])
if self.repository_is_new(repository):
self.upload_file(repository,
filename='emboss/datatypes/datatypes_conf.xml',
filepath=None,
valid_tools_only=False,
uncompress_file=False,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded datatypes_conf.xml.',
strings_displayed=[],
strings_not_displayed=[])
repository = self.get_or_create_repository(
name='emboss_0020',
description='Galaxy wrappers for Emboss version 5.0.0 tools',
long_description=
'Galaxy wrappers for Emboss version 5.0.0 tools',
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0020.id),
strings_displayed=[])
self.upload_file(repository,
filename='emboss/emboss.tar',
filepath=None,
valid_tools_only=True,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded emboss.tar',
strings_displayed=[],
strings_not_displayed=[])
datatypes_repository = self.get_or_create_repository(
name='emboss_datatypes_0030',
description=datatypes_repository_description,
long_description=datatypes_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0030.id),
strings_displayed=[])
if self.repository_is_new(datatypes_repository):
running_standalone = True
self.upload_file(datatypes_repository,
filename='emboss/datatypes/datatypes_conf.xml',
filepath=None,
valid_tools_only=False,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded datatypes_conf.xml.',
strings_displayed=[],
strings_not_displayed=[])
repository_datatypes_count = int(
self.get_repository_datatypes_count(datatypes_repository))
emboss_5_repository = self.get_or_create_repository(
name='emboss_5_0030',
description=emboss_repository_description,
long_description=emboss_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0030.id),
strings_displayed=[])
self.upload_file(emboss_5_repository,
filename='emboss/emboss.tar',
filepath=None,
valid_tools_only=True,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded emboss.tar',
strings_displayed=[],
strings_not_displayed=[])
repository_dependencies_path = self.generate_temp_path(
'test_0330', additional_paths=['emboss', '5'])
dependency_tuple = (self.url, datatypes_repository.name,
datatypes_repository.user.username,
self.get_repository_tip(datatypes_repository))
self.create_repository_dependency(
repository=emboss_5_repository,
repository_tuples=[dependency_tuple],
filepath=repository_dependencies_path)
emboss_6_repository = self.get_or_create_repository(
name='emboss_6_0030',
description=emboss_repository_description,
long_description=emboss_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0030.id),
strings_displayed=[])
self.upload_file(emboss_6_repository,
filename='emboss/emboss.tar',
filepath=None,
valid_tools_only=True,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded emboss.tar',
strings_displayed=[],
strings_not_displayed=[])
repository_dependencies_path = self.generate_temp_path(
'test_0330', additional_paths=['emboss', '6'])
dependency_tuple = (self.url, datatypes_repository.name,
datatypes_repository.user.username,
self.get_repository_tip(datatypes_repository))
self.create_repository_dependency(
repository=emboss_6_repository,
repository_tuples=[dependency_tuple],
filepath=repository_dependencies_path)
emboss_repository = self.get_or_create_repository(
name='emboss_0030',
description=emboss_repository_description,
long_description=emboss_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0030.id),
strings_displayed=[])
self.upload_file(emboss_repository,
filename='emboss/emboss.tar',
filepath=None,
valid_tools_only=True,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded emboss.tar',
strings_displayed=[],
strings_not_displayed=[])
repository_dependencies_path = self.generate_temp_path(
'test_0330', additional_paths=['emboss', '5'])
dependency_tuple = (self.url, emboss_5_repository.name,
emboss_5_repository.user.username,
self.get_repository_tip(emboss_5_repository))
self.create_repository_dependency(
repository=emboss_repository,
repository_tuples=[dependency_tuple],
filepath=repository_dependencies_path)
dependency_tuple = (self.url, emboss_6_repository.name,
emboss_6_repository.user.username,
self.get_repository_tip(emboss_6_repository))
self.create_repository_dependency(
repository=emboss_repository,
repository_tuples=[dependency_tuple],
filepath=repository_dependencies_path)
repository = self.get_or_create_repository(
name='freebayes_0040',
description="Galaxy's freebayes tool",
long_description="Long description of Galaxy's freebayes tool",
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0040.id),
strings_displayed=[])
if self.repository_is_new(repository):
self.upload_file(repository,
filename='freebayes/freebayes.tar',
filepath=None,
valid_tools_only=True,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded freebayes tarball.',
strings_displayed=[],
strings_not_displayed=[])
repository = self.get_or_create_repository(
name='filtering_0040',
description="Galaxy's filtering tool",
long_description="Long description of Galaxy's filtering tool",
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0040.id),
strings_displayed=[])
self.upload_file(
repository,
filename='filtering/filtering_1.1.0.tar',
filepath=None,
valid_tools_only=True,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded filtering 1.1.0 tarball.',
strings_displayed=[],
strings_not_displayed=[])
freebayes_repository = test_db_util.get_repository_by_name_and_owner(
'freebayes_0040', common.test_user_1_name)
filtering_repository = test_db_util.get_repository_by_name_and_owner(
'filtering_0040', common.test_user_1_name)
repository_dependencies_path = self.generate_temp_path(
'test_0340', additional_paths=['dependencies'])
dependency_tuple = (self.url, freebayes_repository.name,
freebayes_repository.user.username,
self.get_repository_tip(freebayes_repository))
self.create_repository_dependency(
repository=filtering_repository,
repository_tuples=[dependency_tuple],
filepath=repository_dependencies_path)
dependency_tuple = (self.url, filtering_repository.name,
filtering_repository.user.username,
self.get_repository_tip(filtering_repository))
self.create_repository_dependency(
repository=freebayes_repository,
repository_tuples=[dependency_tuple],
filepath=repository_dependencies_path)
datatypes_repository = self.get_or_create_repository(
name='emboss_datatypes_0050',
description="Datatypes for emboss",
long_description="Long description of Emboss' datatypes",
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0050.id),
strings_displayed=[])
if self.repository_is_new(datatypes_repository):
emboss_repository = self.get_or_create_repository(
name='emboss_0050',
description="Galaxy's emboss tool",
long_description="Long description of Galaxy's emboss tool",
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0050.id),
strings_displayed=[])
filtering_repository = self.get_or_create_repository(
name='filtering_0050',
description="Galaxy's filtering tool",
long_description="Long description of Galaxy's filtering tool",
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0050.id),
strings_displayed=[])
freebayes_repository = self.get_or_create_repository(
name='freebayes_0050',
description="Galaxy's freebayes tool",
long_description="Long description of Galaxy's freebayes tool",
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0050.id),
strings_displayed=[])
self.upload_file(datatypes_repository,
filename='emboss/datatypes/datatypes_conf.xml',
filepath=None,
valid_tools_only=False,
uncompress_file=False,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded datatypes_conf.xml.',
strings_displayed=[],
strings_not_displayed=[])
self.upload_file(emboss_repository,
filename='emboss/emboss.tar',
filepath=None,
valid_tools_only=True,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded emboss.tar',
strings_displayed=[],
strings_not_displayed=[])
self.upload_file(freebayes_repository,
filename='freebayes/freebayes.tar',
filepath=None,
valid_tools_only=True,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded freebayes tarball.',
strings_displayed=[],
strings_not_displayed=[])
self.upload_file(
filtering_repository,
filename='filtering/filtering_1.1.0.tar',
filepath=None,
valid_tools_only=True,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded filtering 1.1.0 tarball.',
strings_displayed=[],
strings_not_displayed=[])
repository_dependencies_path = self.generate_temp_path(
'test_0350', additional_paths=['emboss'])
dependency_tuple = (self.url, datatypes_repository.name,
datatypes_repository.user.username,
self.get_repository_tip(datatypes_repository))
self.create_repository_dependency(
repository=emboss_repository,
repository_tuples=[dependency_tuple],
filepath=repository_dependencies_path)
repository_dependencies_path = self.generate_temp_path(
'test_0350', additional_paths=['filtering'])
dependency_tuple = (self.url, emboss_repository.name,
emboss_repository.user.username,
self.get_repository_tip(emboss_repository))
self.create_repository_dependency(
repository=filtering_repository,
repository_tuples=[dependency_tuple],
filepath=repository_dependencies_path)
repository_dependencies_path = self.generate_temp_path(
'test_0350', additional_paths=['freebayes'])
dependency_tuple = (self.url, filtering_repository.name,
filtering_repository.user.username,
self.get_repository_tip(filtering_repository))
self.create_repository_dependency(
repository=emboss_repository,
repository_tuples=[dependency_tuple],
filepath=repository_dependencies_path)
dependency_tuples = [
(self.url, datatypes_repository.name,
datatypes_repository.user.username,
self.get_repository_tip(datatypes_repository)),
(self.url, emboss_repository.name,
emboss_repository.user.username,
self.get_repository_tip(emboss_repository)),
(self.url, filtering_repository.name,
filtering_repository.user.username,
self.get_repository_tip(filtering_repository)),
(self.url, freebayes_repository.name,
freebayes_repository.user.username,
self.get_repository_tip(freebayes_repository))
]
self.create_repository_dependency(
repository=freebayes_repository,
repository_tuples=dependency_tuples,
filepath=repository_dependencies_path)
workflow_repository = self.get_or_create_repository(
name='filtering_0060',
description="Galaxy's filtering tool",
long_description="Long description of Galaxy's filtering tool",
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0060.id),
strings_displayed=[])
if self.repository_is_new(workflow_repository):
workflow = file(
self.get_filename(
'filtering_workflow/Workflow_for_0060_filter_workflow_repository.ga'
), 'r').read()
workflow = workflow.replace('__TEST_TOOL_SHED_URL__',
self.url.replace('http://', ''))
workflow_filepath = self.generate_temp_path(
'test_0360', additional_paths=['filtering_workflow'])
if not os.path.exists(workflow_filepath):
os.makedirs(workflow_filepath)
file(os.path.join(workflow_filepath, workflow_filename),
'w+').write(workflow)
self.upload_file(workflow_repository,
filename=workflow_filename,
filepath=workflow_filepath,
valid_tools_only=True,
uncompress_file=False,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded filtering workflow.',
strings_displayed=[],
strings_not_displayed=[])
self.upload_file(
workflow_repository,
filename='filtering/filtering_2.2.0.tar',
filepath=None,
valid_tools_only=True,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded filtering 2.2.0 tarball.',
strings_displayed=[],
strings_not_displayed=[])
