def test_0060_search_for_bwa_tools( self ):
'''Search for and install the repositories with BWA tools, and verify that this reinstalls emboss_datatypes and reactivates filtering.'''
bwa_color_repository = test_db_util.get_repository_by_name_and_owner( bwa_color_repository_name, common.test_user_1_name )
bwa_base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name )
bwa_base_revision = self.get_repository_tip( bwa_base_repository )
bwa_color_revision = self.get_repository_tip( bwa_color_repository )
self.search_for_valid_tools( search_fields={ 'tool_id': 'bwa' },
exact_matches=False, from_galaxy=True,
strings_displayed=[ 'bwa_color_0090', 'bwa_base_0090', bwa_base_revision, bwa_color_revision ] )
strings_displayed=[ 'freebayes_0090', 'emboss_0090', 'filtering_0090' ]
strings_displayed.extend( [ 'bwa_color_0090', 'bwa_base_0090' ] )
strings_displayed.extend( [ 'bwa', 'Handle', 'tool dependencies' ] )
repositories_to_install = [ bwa_color_repository, bwa_base_repository ]
# BWA is a good candidate for testing the installation of tool dependencies, but it is a core requirement of functional
# tests that they be able to run independently of any network connection or remote data.
#
# After this test, the repositories should be in the following state:
# Installed: bwa_color, bwa_base, emboss_datatypes, emboss, filtering, freebayes
self.install_repositories_from_search_results( repositories_to_install,
install_repository_dependencies='True',
install_tool_dependencies=False,
new_tool_panel_section='bwa_1090',
strings_displayed=strings_displayed )
installed_repositories = [ ( emboss_repository_name, common.test_user_1_name ),
( filtering_repository_name, common.test_user_1_name ),
( bwa_color_repository_name, common.test_user_1_name ),
( bwa_base_repository_name, common.test_user_1_name ),
( emboss_datatypes_repository_name, common.test_user_1_name ),
( freebayes_repository_name, common.test_user_1_name ) ]
strings_displayed = [ 'emboss_datatypes_0090', 'filtering_0090', 'emboss_0090', 'bwa_color_0090', 'bwa_base_0090', 'freebayes_0090' ]
self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed )
self.verify_installed_repositories( installed_repositories )
def test_0035_generate_repository_dependencies_for_emboss_6( self ):
'''Generate a repository_dependencies.xml file specifying emboss_datatypes and upload it to the emboss_6 repository.'''
emboss_6_repository = test_db_util.get_repository_by_name_and_owner( emboss_6_repository_name, common.test_user_1_name )
datatypes_repository = test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name )
repository_dependencies_path = self.generate_temp_path( 'test_0030', additional_paths=[ 'emboss6' ] )
datatypes_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=[ datatypes_tuple ], filepath=repository_dependencies_path )
def test_0080_url_upload_to_complex_test( self ):
'''Populate repository_dependency_test_4_0460.'''
'''
This is step 16 - Upload to repository_dependency_test_5_0460 using the url
hg://<tool shed url>/repos/user1/hg_subfolder_repository_dependency_0460.
'''
url = 'hg://%s:%s/repos/user1/hg_subfolder_repository_dependency_0460' % ( self.host, self.port )
repository = test_db_util.get_repository_by_name_and_owner( 'repository_dependency_test_5_0460', common.test_user_1_name )
package_repository = test_db_util.get_repository_by_name_and_owner( 'emboss_datatypes_0460', common.test_user_1_name )
self.upload_url( repository,
url=url,
filepath=None,
valid_tools_only=True,
uncompress_file=False,
remove_repo_files_not_in_tar=True,
commit_message='Uploaded repository dependency definition.',
strings_displayed=[],
strings_not_displayed=[] )
changeset_revision = self.get_repository_tip( package_repository )
strings_displayed = [ 'emboss_datatypes_0460', 'user1', changeset_revision ]
self.display_manage_repository_page( repository, strings_displayed=strings_displayed )
self.display_repository_file_contents( repository,
filename='repository_dependencies.xml',
filepath='subfolder',
strings_displayed=[ changeset_revision ] )
def test_0025_generate_and_upload_repository_dependencies_xml( self ):
'''Generate and upload the repository_dependencies.xml file'''
repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name )
datatypes_repository = test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name )
repository_dependencies_path = self.generate_temp_path( 'test_0020', additional_paths=[ 'emboss', '5' ] )
repository_tuple = ( self.url, datatypes_repository.name, datatypes_repository.user.username, self.get_repository_tip( datatypes_repository ) )
self.create_repository_dependency( repository=repository, repository_tuples=[ repository_tuple ], filepath=repository_dependencies_path )
def test_0045_generate_repository_dependency_on_emboss_6( self ):
'''Create and upload repository_dependencies.xml for the emboss_6_0030 repository.'''
emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name )
emboss_6_repository = test_db_util.get_repository_by_name_and_owner( emboss_6_repository_name, common.test_user_1_name )
repository_dependencies_path = self.generate_temp_path( 'test_0030', additional_paths=[ 'emboss', '5' ] )
emboss_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=[ emboss_tuple ], filepath=repository_dependencies_path )
def test_0020_create_repository_dependency( self ):
'''Create a repository dependency specifying convert_chars.'''
'''
Each of the three repositories should depend on the other two, to make this as circular as possible.
'''
filter_repository = test_db_util.get_repository_by_name_and_owner( filter_repository_name, common.test_user_1_name )
column_repository = test_db_util.get_repository_by_name_and_owner( column_repository_name, common.test_user_1_name )
convert_repository = test_db_util.get_repository_by_name_and_owner( convert_repository_name, common.test_user_1_name )
dependency_xml_path = self.generate_temp_path( 'test_0160', additional_paths=[ 'column' ] )
filter_revision = self.get_repository_tip( filter_repository )
column_revision = self.get_repository_tip( column_repository )
convert_revision = self.get_repository_tip( convert_repository )
column_tuple = ( self.url, column_repository.name, column_repository.user.username, column_revision )
convert_tuple = ( self.url, convert_repository.name, convert_repository.user.username, convert_revision )
filter_tuple = ( self.url, filter_repository.name, filter_repository.user.username, filter_revision )
self.create_repository_dependency( repository=column_repository,
repository_tuples=[ convert_tuple, filter_tuple],
filepath=dependency_xml_path,
prior_installation_required=False )
self.create_repository_dependency( repository=convert_repository,
repository_tuples=[ column_tuple, filter_tuple ],
filepath=dependency_xml_path,
prior_installation_required=False )
self.create_repository_dependency( repository=filter_repository,
repository_tuples=[ convert_tuple, column_tuple ],
filepath=dependency_xml_path,
prior_installation_required=True )
def test_0020_create_repository_dependencies( self ):
'''Set up the filtering and freebayes repository dependencies.'''
# The dependency structure should look like:
# Filtering revision 0 -> freebayes revision 0.
# Freebayes revision 0 -> filtering revision 1.
# Filtering will have two revisions, one with just the filtering tool, and one with the filtering tool and a dependency on freebayes.
global running_standalone
if running_standalone:
repository = test_db_util.get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name )
filtering_repository = test_db_util.get_repository_by_name_and_owner( filtering_repository_name, common.test_user_1_name )
repository_dependencies_path = self.generate_temp_path( 'test_0040', additional_paths=[ 'filtering' ] )
self.generate_repository_dependency_xml( [ 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' )
repository = test_db_util.get_repository_by_name_and_owner( filtering_repository_name, common.test_user_1_name )
freebayes_repository = test_db_util.get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name )
repository_dependencies_path = self.generate_temp_path( 'test_0040', additional_paths=[ 'freebayes' ] )
self.generate_repository_dependency_xml( [ 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' )
def test_0050_verify_tool_dependencies( self ):
'''Check that freebayes and emboss display tool dependencies.'''
freebayes_repository = test_db_util.get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name )
emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name )
self.display_manage_repository_page( freebayes_repository,
strings_displayed=[ 'freebayes', '0.9.4_9696d0ce8a9', 'samtools', '0.1.18', 'Tool dependencies', 'package' ] )
self.display_manage_repository_page( emboss_repository, strings_displayed=[ 'Tool dependencies', 'emboss', '5.0.0', 'package' ] )
def test_0025_verify_repository_dependency( self ):
'''Verify that the previously generated repositiory dependency displays correctly.'''
filter_repository = test_db_util.get_repository_by_name_and_owner( filter_repository_name, common.test_user_1_name )
column_repository = test_db_util.get_repository_by_name_and_owner( column_repository_name, common.test_user_1_name )
convert_repository = test_db_util.get_repository_by_name_and_owner( convert_repository_name, common.test_user_1_name )
self.check_repository_dependency( repository=column_repository,
depends_on_repository=convert_repository,
depends_on_changeset_revision=None,
changeset_revision=None )
self.check_repository_dependency( repository=column_repository,
depends_on_repository=filter_repository,
depends_on_changeset_revision=None,
changeset_revision=None )
self.check_repository_dependency( repository=convert_repository,
depends_on_repository=column_repository,
depends_on_changeset_revision=None,
changeset_revision=None )
self.check_repository_dependency( repository=convert_repository,
depends_on_repository=filter_repository,
depends_on_changeset_revision=None,
changeset_revision=None )
self.check_repository_dependency( repository=filter_repository,
depends_on_repository=column_repository,
depends_on_changeset_revision=None,
changeset_revision=None )
self.check_repository_dependency( repository=filter_repository,
depends_on_repository=convert_repository,
depends_on_changeset_revision=None,
changeset_revision=None )
def test_0040_generate_tool_dependency(self):
"""Generate and upload a new tool_dependencies.xml file that specifies an arbitrary file on the filesystem, and verify that bwa_base depends on the new changeset revision."""
base_repository = test_db_util.get_repository_by_name_and_owner(
bwa_base_repository_name, common.test_user_1_name
)
tool_repository = test_db_util.get_repository_by_name_and_owner(
bwa_tool_repository_name, common.test_user_1_name
)
previous_changeset = self.get_repository_tip(tool_repository)
old_tool_dependency = self.get_filename(os.path.join("bwa", "complex", "readme", "tool_dependencies.xml"))
new_tool_dependency_path = self.generate_temp_path("test_1100", additional_paths=["tool_dependency"])
xml_filename = os.path.abspath(os.path.join(new_tool_dependency_path, "tool_dependencies.xml"))
# Generate a tool_dependencies.xml file that points to an arbitrary file in the local filesystem.
file(xml_filename, "w").write(
file(old_tool_dependency, "r").read().replace("__PATH__", self.get_filename("bwa/complex"))
)
self.upload_file(
tool_repository,
xml_filename,
filepath=new_tool_dependency_path,
strings_displayed=[],
commit_message="Uploaded new tool_dependencies.xml.",
)
# Verify that the dependency display has been updated as a result of the new tool_dependencies.xml file.
self.display_manage_repository_page(
base_repository,
strings_displayed=[self.get_repository_tip(tool_repository), "bwa", "0.5.9", "package"],
strings_not_displayed=[previous_changeset],
)
def test_0035_generate_complex_repository_dependency(self):
"""Generate and upload a valid tool_dependencies.xml file that specifies bwa_tool_repository_0100."""
base_repository = test_db_util.get_repository_by_name_and_owner(
bwa_base_repository_name, common.test_user_1_name
)
tool_repository = test_db_util.get_repository_by_name_and_owner(
bwa_tool_repository_name, common.test_user_1_name
)
dependency_path = self.generate_temp_path("test_0100", additional_paths=["complex"])
xml_filename = self.get_filename("tool_dependencies.xml", filepath=dependency_path)
url = self.url
name = tool_repository.name
owner = tool_repository.user.username
changeset_revision = self.get_repository_tip(tool_repository)
self.generate_repository_dependency_xml(
[tool_repository], xml_filename, complex=True, package="bwa", version="0.5.9"
)
self.upload_file(
base_repository,
"tool_dependencies.xml",
valid_tools_only=True,
filepath=dependency_path,
commit_message="Uploaded valid complex dependency on bwa_tool_0100.",
)
self.check_repository_dependency(base_repository, tool_repository)
self.display_manage_repository_page(base_repository, strings_displayed=["bwa", "0.5.9", "package"])
def test_0040_update_tool_repository( self ):
'''Upload a new tool_dependencies.xml to the tool repository, and verify that the base repository displays the new changeset.'''
global running_standalone
if running_standalone:
base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name )
tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_package_repository_name, common.test_user_1_name )
previous_changeset = self.get_repository_tip( tool_repository )
old_tool_dependency = self.get_filename( os.path.join( 'bwa', 'complex', 'readme', 'tool_dependencies.xml' ) )
new_tool_dependency_path = self.generate_temp_path( 'test_1100', additional_paths=[ 'tool_dependency' ] )
xml_filename = os.path.abspath( os.path.join( new_tool_dependency_path, 'tool_dependencies.xml' ) )
file( xml_filename, 'w' ).write( file( old_tool_dependency, 'r' )
.read().replace( '__PATH__', self.get_filename( 'bwa/complex' ) ) )
self.upload_file( tool_repository,
filename=xml_filename,
filepath=new_tool_dependency_path,
valid_tools_only=True,
uncompress_file=False,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded new tool_dependencies.xml.',
strings_displayed=[],
strings_not_displayed=[] )
# Verify that the dependency display has been updated as a result of the new tool_dependencies.xml file.
self.display_manage_repository_page( base_repository,
strings_displayed=[ self.get_repository_tip( tool_repository ), 'bwa', '0.5.9', 'package' ],
strings_not_displayed=[ previous_changeset ] )
def test_0025_create_dependency_on_filtering( self ):
'''Upload a repository_dependencies.xml file that specifies the current revision of filtering to the freebayes_0040 repository.'''
convert_repository = test_db_util.get_repository_by_name_and_owner( convert_repository_name, common.test_user_1_name )
column_repository = test_db_util.get_repository_by_name_and_owner( column_repository_name, common.test_user_1_name )
repository_dependencies_path = self.generate_temp_path( 'test_0080', additional_paths=[ 'convert' ] )
repository_tuple = ( self.url, column_repository.name, column_repository.user.username, self.get_repository_tip( column_repository ) )
self.create_repository_dependency( repository=convert_repository, repository_tuples=[ repository_tuple ], filepath=repository_dependencies_path )
def test_0015_create_dependency_on_datatypes_repository( self ):
'''Create a dependency definition file that specifies emboss_datatypes_0430 and upload it to emboss_0430.'''
emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name )
datatypes_repository = test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name )
dependency_xml_path = self.generate_temp_path( 'test_0430', additional_paths=[ 'dependencies' ] )
datatypes_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=[ datatypes_tuple ], filepath=dependency_xml_path )
self.check_repository_dependency( emboss_repository, datatypes_repository )
def test_0055_verify_repository_metadata( self ):
'''Verify that resetting the metadata does not change it.'''
emboss_datatypes_repository = test_db_util.get_repository_by_name_and_owner( emboss_datatypes_repository_name, common.test_user_1_name )
emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name )
filtering_repository = test_db_util.get_repository_by_name_and_owner( filtering_repository_name, common.test_user_1_name )
freebayes_repository = test_db_util.get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name )
for repository in [ emboss_datatypes_repository, emboss_repository, freebayes_repository, filtering_repository ]:
self.verify_unchanged_repository_metadata( repository )
def test_0015_create_and_upload_dependency_files( self ):
convert_repository = test_db_util.get_repository_by_name_and_owner( convert_repository_name, common.test_user_1_name )
column_repository = test_db_util.get_repository_by_name_and_owner( column_repository_name, common.test_user_1_name )
repository_dependencies_path = self.generate_temp_path( 'test_1085', additional_paths=[ 'column' ] )
repository_tuple = ( self.url, convert_repository.name, convert_repository.user.username, self.get_repository_tip( convert_repository ) )
self.create_repository_dependency( repository=column_repository, repository_tuples=[ repository_tuple ], filepath=repository_dependencies_path )
repository_tuple = ( self.url, column_repository.name, column_repository.user.username, self.get_repository_tip( column_repository ) )
self.create_repository_dependency( repository=convert_repository, repository_tuples=[ repository_tuple ], filepath=repository_dependencies_path )
def test_0040_verify_repository_dependency( self ):
'''Verify the created repository dependency.'''
'''
We are at step 3a.
Check the newly created repository dependency to ensure that it was defined and displays correctly.
'''
datatypes_repository = test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_2_name )
tool_repository = test_db_util.get_repository_by_name_and_owner( tool_repository_name, common.test_user_1_name )
self.check_repository_dependency( tool_repository, datatypes_repository )
def test_0025_generate_and_upload_repository_dependencies_xml( self ):
'''Generate and upload the repository_dependencies.xml file'''
repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name )
datatypes_repository = test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name )
repository_dependencies_path = self.generate_temp_path( 'test_0020', additional_paths=[ 'emboss', '5' ] )
self.generate_repository_dependency_xml( [ datatypes_repository ],
self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ) )
self.upload_file( repository,
'repository_dependencies.xml',
filepath=repository_dependencies_path,
commit_message='Uploaded repository_dependencies.xml' )
def test_0060_create_dependency_structure( self ):
'''Create the dependency structure for test 0040.'''
global running_standalone
if running_standalone:
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' ] )
freebayes_tuple = ( self.url, freebayes_repository.name, freebayes_repository.user.username, self.get_repository_tip( freebayes_repository ) )
filtering_tuple = ( self.url, filtering_repository.name, filtering_repository.user.username, self.get_repository_tip( filtering_repository ) )
self.create_repository_dependency( repository=filtering_repository, repository_tuples=[ freebayes_tuple ], filepath=repository_dependencies_path )
self.create_repository_dependency( repository=freebayes_repository, repository_tuples=[ filtering_tuple ], filepath=repository_dependencies_path )
def test_0025_create_dependency_on_filtering( self ):
'''Upload a repository_dependencies.xml file that specifies the current revision of filtering to the freebayes_0040 repository.'''
# The dependency structure should look like:
# Filtering revision 0 -> freebayes revision 0.
# Freebayes revision 0 -> filtering revision 1.
# Filtering will have two revisions, one with just the filtering tool, and one with the filtering tool and a dependency on freebayes.
repository = test_db_util.get_repository_by_name_and_owner( filtering_repository_name, common.test_user_1_name )
freebayes_repository = test_db_util.get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name )
repository_dependencies_path = self.generate_temp_path( 'test_0040', additional_paths=[ 'freebayes' ] )
repository_tuple = ( self.url, repository.name, repository.user.username, self.get_repository_tip( repository ) )
self.create_repository_dependency( repository=freebayes_repository, repository_tuples=[ repository_tuple ], filepath=repository_dependencies_path )
def test_0030_verify_repository_dependencies( self ):
'''Verify that each repository can depend on the other without causing an infinite loop.'''
filtering_repository = test_db_util.get_repository_by_name_and_owner( filtering_repository_name, common.test_user_1_name )
freebayes_repository = test_db_util.get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name )
# The dependency structure should look like:
# Filtering revision 0 -> freebayes revision 0.
# Freebayes revision 0 -> filtering revision 1.
# Filtering will have two revisions, one with just the filtering tool, and one with the filtering tool and a dependency on freebayes.
# In this case, the displayed dependency will specify the tip revision, but this will not always be the case.
self.check_repository_dependency( filtering_repository, freebayes_repository, self.get_repository_tip( freebayes_repository ) )
self.check_repository_dependency( freebayes_repository, filtering_repository, self.get_repository_tip( filtering_repository ) )
def test_0015_upload_dependency_xml_if_needed( self ):
'''If this test is being run by itself, it will not have repository dependencies configured yet.'''
global running_standalone
if running_standalone:
convert_repository = test_db_util.get_repository_by_name_and_owner( convert_repository_name, common.test_user_1_name )
column_repository = test_db_util.get_repository_by_name_and_owner( column_repository_name, common.test_user_1_name )
repository_dependencies_path = self.generate_temp_path( 'test_1080', additional_paths=[ 'convert' ] )
repository_tuple = ( self.url, convert_repository.name, convert_repository.user.username, self.get_repository_tip( convert_repository ) )
self.create_repository_dependency( repository=column_repository, repository_tuples=[ repository_tuple ], filepath=repository_dependencies_path )
repository_tuple = ( self.url, column_repository.name, column_repository.user.username, self.get_repository_tip( column_repository ) )
self.create_repository_dependency( repository=convert_repository, repository_tuples=[ repository_tuple ], filepath=repository_dependencies_path )
def test_0015_generate_repository_dependencies_for_emboss_5( self ):
'''Generate a repository_dependencies.xml file specifying emboss_datatypes and upload it to the emboss_5 repository.'''
datatypes_repository = test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name )
repository_dependencies_path = self.generate_temp_path( 'test_0030', additional_paths=[ 'emboss' ] )
self.generate_repository_dependency_xml( [ datatypes_repository ],
self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ) )
emboss_5_repository = test_db_util.get_repository_by_name_and_owner( emboss_5_repository_name, common.test_user_1_name )
self.upload_file( emboss_5_repository,
'repository_dependencies.xml',
filepath=repository_dependencies_path,
commit_message='Uploaded repository_depepndencies.xml.' )
def test_0025_create_repository_dependency( self ):
'''Create a repository dependency on blast_datatypes_0120.'''
'''
We are at step 3.
Create a simple repository dependency for blastxml_to_top_descr_0120 that defines a dependency on blast_datatypes_0120.
'''
datatypes_repository = test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_2_name )
tool_repository = test_db_util.get_repository_by_name_and_owner( tool_repository_name, common.test_user_1_name )
dependency_xml_path = self.generate_temp_path( 'test_0120', additional_paths=[ 'dependencies' ] )
datatypes_tuple = ( self.url, datatypes_repository.name, datatypes_repository.user.username, self.get_repository_tip( datatypes_repository ) )
self.create_repository_dependency( repository=tool_repository, repository_tuples=[ datatypes_tuple ], filepath=dependency_xml_path )
def test_0030_generate_repository_dependency_on_emboss_6( self ):
'''Create and upload repository_dependencies.xml for the emboss_6_0030 repository.'''
emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name )
emboss_6_repository = test_db_util.get_repository_by_name_and_owner( emboss_6_repository_name, common.test_user_1_name )
repository_dependencies_path = self.generate_temp_path( 'test_0030', additional_paths=[ 'emboss', '6' ] )
self.generate_repository_dependency_xml( [ emboss_6_repository ],
self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ),
dependency_description='Emboss requires the Emboss 6 repository.' )
self.upload_file( emboss_repository,
'repository_dependencies.xml',
filepath=repository_dependencies_path,
commit_message='Uploaded dependency configuration specifying emboss_6' )
def test_0025_create_dependency_on_filtering( self ):
'''Upload a repository_dependencies.xml file that specifies the current revision of filtering to the freebayes_0040 repository.'''
convert_repository = test_db_util.get_repository_by_name_and_owner( convert_repository_name, common.test_user_1_name )
column_repository = test_db_util.get_repository_by_name_and_owner( column_repository_name, common.test_user_1_name )
repository_dependencies_path = self.generate_temp_path( 'test_0080', additional_paths=[ 'convert' ] )
self.generate_repository_dependency_xml( [ column_repository ],
self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ),
dependency_description='Convert chars depends on the column_maker repository.' )
self.upload_file( convert_repository,
'repository_dependencies.xml',
filepath=repository_dependencies_path,
commit_message='Uploaded dependency on column' )
def test_0035_browse_repository_dependencies( self ):
'''Browse repository dependencies and look for a dependency on emboss_datatypes_0430.'''
'''
We are at step 3.
Verify that the browse repository dependencies page shows emboss_datatypes_0430 as a dependency of emboss_0430.
'''
emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name )
datatypes_repository = test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name )
datatypes_changeset_revision = self.get_repository_tip( datatypes_repository )
emboss_changeset_revision = self.get_repository_tip( emboss_repository )
strings_displayed = [ datatypes_changeset_revision, emboss_changeset_revision, 'emboss_datatypes_0430', 'user1', 'emboss_0430' ]
self.browse_repository_dependencies( strings_displayed=strings_displayed )
def test_0020_verify_generated_dependency( self ):
'''Verify that matplotlib now has a package tool dependency and a complex repository dependency.'''
'''
This is step 3 - Verify that package_matplotlib_1_2_0170 now depends on package_numpy_1_7_0170, and that the inherited tool
dependency displays correctly.
'Inhherited' in this case means that matplotlib should show a package tool dependency on numpy version 1.7, and a repository
dependency on the latest revision of package_numpy_1_7_0170.
'''
numpy_repository = test_db_util.get_repository_by_name_and_owner( numpy_repository_name, common.test_user_1_name )
matplotlib_repository = test_db_util.get_repository_by_name_and_owner( matplotlib_repository_name, common.test_user_1_name )
changeset_revision = self.get_repository_tip( numpy_repository )
self.check_repository_dependency( matplotlib_repository, depends_on_repository=numpy_repository )
self.display_manage_repository_page( matplotlib_repository, strings_displayed=[ 'numpy', '1.7', 'package', changeset_revision ] )
def test_0045_reset_repository_metadata( self ):
'''Reset metadata on package_emboss_5_0_0_0470 and package_x11_client_1_5_proto_7_0.'''
'''
This is step 9 - Reset metadata on the package_emboss_5_0_0 and package_x11_client_1_5_proto_7_0 repositories. They should
now have only their tip as the installable revision.
'''
package_emboss_repository = test_db_util.get_repository_by_name_and_owner( package_emboss_repository_name, common.test_user_1_name )
package_x11_repository = test_db_util.get_repository_by_name_and_owner( package_libx11_repository_name, common.test_user_1_name )
self.reset_repository_metadata( package_emboss_repository )
self.reset_repository_metadata( package_x11_repository )
assert len( package_emboss_repository.metadata_revisions ) == 1, 'Repository package_emboss_5_0_0 has %d installable revisions, expected 1.' % \
len( package_emboss_repository.metadata_revisions )
assert len( package_x11_repository.metadata_revisions ) == 1, 'Repository package_x11_client_1_5_proto_7_0 has %d installable revisions, expected 1.' % \
len( package_x11_repository.metadata_revisions )
def test_0045_install_base_repository( self ):
'''Verify installation of the repository with complex repository dependencies.'''
self.galaxy_logout()
self.galaxy_login( email=common.admin_email, username=common.admin_username )
base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name )
tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name )
preview_strings_displayed = [ tool_repository.name, self.get_repository_tip( tool_repository ) ]
self.install_repository( bwa_base_repository_name,
common.test_user_1_name,
category_name,
install_tool_dependencies=True,
preview_strings_displayed=preview_strings_displayed,
post_submit_strings_displayed=[ base_repository.name, tool_repository.name, 'new' ],
includes_tools=True )
def test_0030_browse_with_other_user(self):
'''Verify that test_user_3 is blocked from browsing the review.'''
'''
We are at step 4 - Have test_user_3 browse the repository and make sure they are not allowed to browse the review.
'''
self.logout()
self.login(email=common.test_user_3_email,
username=common.test_user_3_name)
repository = test_db_util.get_repository_by_name_and_owner(
repository_name, common.test_user_1_name)
user = test_db_util.get_user(common.test_user_2_email)
strings_not_displayed = ['Browse reviews of this repository']
self.display_manage_repository_page(
repository, strings_not_displayed=strings_not_displayed)
strings_not_displayed = [
'A good set of functional tests.',
'Clear and concise readme file, a true pleasure to read.'
]
strings_not_displayed.append('Excellent tool, easy to use.')
changeset_revision = self.get_repository_tip(repository)
review = test_db_util.get_repository_review_by_user_id_changeset_revision(
user.id, repository.id, changeset_revision)
self.browse_component_review(
review, strings_not_displayed=strings_not_displayed)
def test_0035_verify_repository(self):
'''Display basic repository pages'''
repository = test_db_util.get_repository_by_name_and_owner(
repository_name, common.test_user_1_name)
latest_changeset_revision = self.get_repository_tip(repository)
self.check_for_valid_tools(repository, strings_displayed=['Filter1'])
self.check_count_of_metadata_revisions_associated_with_repository(
repository, metadata_count=1)
tip = self.get_repository_tip(repository)
tool_guid = '%s/repos/user1/filtering_0000/Filter1/1.1.0' % self.url.replace(
'http://', '').rstrip('/')
tool_metadata_strings_displayed = [
tool_guid,
'1.1.0', # The tool version.
'Filter1', # The tool ID.
'Filter', # The tool name.
'data on any column using simple expressions'
] # The tool description.
tool_page_strings_displayed = ['Filter (version 1.1.0)']
self.check_repository_tools_for_changeset_revision(
repository,
tip,
tool_metadata_strings_displayed=tool_metadata_strings_displayed,
tool_page_strings_displayed=tool_page_strings_displayed)
self.check_repository_metadata(repository, tip_only=False)
self.browse_repository(repository,
strings_displayed=[
"Repository '%s' revision" %
repository.name, '(repository tip)'
])
self.display_repository_clone_page(common.test_user_1_name,
repository_name,
strings_displayed=[
'Uploaded filtering 1.1.0',
latest_changeset_revision
])
def test_0070_upload_readme_txt_file(self):
'''Upload readme.txt file associated with tool version 2.2.0.'''
repository = test_db_util.get_repository_by_name_and_owner(
repository_name, common.test_user_1_name)
self.upload_file(repository,
filename='readme.txt',
filepath=None,
valid_tools_only=True,
uncompress_file=False,
remove_repo_files_not_in_tar=False,
commit_message="Uploaded readme.txt",
strings_displayed=[],
strings_not_displayed=[])
self.display_manage_repository_page(
repository,
strings_displayed=['This is a readme file.'])
# Verify that there is a different readme file for each metadata revision.
metadata_revisions = self.get_repository_metadata_revisions(repository)
self.display_manage_repository_page(
repository,
strings_displayed=[
'Readme file for filtering 1.1.0',
'This is a readme file.'
])
def test_0030_upload_updated_tool_dependency_to_emboss_5_repository(self):
'''Upload a new tool_dependencies.xml to emboss_5_0470.'''
'''
This is step 6 - Add a comment to the tool_dependencies.xml file in the emboss_5 repository, eliminating the
changeset_revision attribute so that it gets automatically populated when uploaded. After uploading the file,
the emboss5 repository should have 2 installable metadata revisions.
'''
emboss_repository = test_db_util.get_repository_by_name_and_owner(
emboss_repository_name, common.test_user_1_name)
# Populate package_emboss_5_0_0_0470 with updated tool dependency definition.
self.upload_file(
emboss_repository,
filename='emboss/0470_files/tool_dependencies.xml',
filepath=None,
valid_tools_only=True,
uncompress_file=False,
remove_repo_files_not_in_tar=False,
commit_message=
'Upload updated complex repository dependency definition to emboss_5_0470.',
strings_displayed=[],
strings_not_displayed=[])
assert len(
emboss_repository.metadata_revisions
) == 2, 'package_emboss_5_0_0_0470 has incorrect number of metadata revisions'
def test_0020_upload_updated_tool_dependency_to_package_x11(self):
'''Upload a new tool_dependencies.xml to package_x11_client_1_5_proto_7_0_0470.'''
'''
This is step 4 - Add a comment to the tool_dependencies.xml file to be uploaded to the package_x11_client_1_5_prot_7_0 repository, creating
a new installable changeset revision at the repository tip.
'''
package_x11_repository = test_db_util.get_repository_by_name_and_owner(
package_libx11_repository_name, common.test_user_1_name)
# Upload the tool dependency definition to the package_x11_client_1_5_proto_7_0_0470 repository.
self.upload_file(
package_x11_repository,
filename=
'emboss/libx11_proto/second_tool_dependency/tool_dependencies.xml',
filepath=None,
valid_tools_only=True,
uncompress_file=False,
remove_repo_files_not_in_tar=False,
commit_message=
'Populate package_x11_client_1_5_proto_7_0_0470 with tool dependency definitions.',
strings_displayed=[],
strings_not_displayed=[])
assert len(
package_x11_repository.metadata_revisions
) == 1, 'package_x11_client_1_5_proto_7_0_0470 has incorrect number of metadata revisions'
def test_0135_verify_review_for_new_version(self):
'''Verify that the reviews display correctly for this changeset revision.'''
self.logout()
self.login(email=common.test_user_1_email,
username=common.test_user_1_name)
repository = test_db_util.get_repository_by_name_and_owner(
repository_name, common.test_user_1_name)
user = test_db_util.get_user(common.test_user_2_email)
strings_displayed = [
'Data types', 'Functional tests', 'yes',
'A good set of functional tests.', 'README', 'yes', 'Workflows',
'Tools'
]
strings_displayed.extend([
'Clear and concise readme file, a true pleasure to read.',
'Tool dependencies', 'not_applicable'
])
strings_displayed.extend([
'Repository dependencies',
'Version 2.2.0 does the impossible and improves this tool.'
])
self.verify_repository_reviews(repository,
reviewer=user,
strings_displayed=strings_displayed)
def test_0035_create_and_upload_dependency_definitions( self ):
'''Create and upload repository dependency definitions.'''
global running_standalone
if running_standalone:
bwa_color_repository = test_db_util.get_repository_by_name_and_owner( bwa_color_repository_name, common.test_user_1_name )
bwa_base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name )
emboss_datatypes_repository = test_db_util.get_repository_by_name_and_owner( emboss_datatypes_repository_name, common.test_user_1_name )
emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name )
filtering_repository = test_db_util.get_repository_by_name_and_owner( filtering_repository_name, common.test_user_1_name )
freebayes_repository = test_db_util.get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name )
dependency_xml_path = self.generate_temp_path( 'test_0090', additional_paths=[ 'freebayes' ] )
freebayes_tuple = ( self.url, freebayes_repository.name, freebayes_repository.user.username, self.get_repository_tip( freebayes_repository ) )
emboss_tuple = ( self.url, emboss_repository.name, emboss_repository.user.username, self.get_repository_tip( emboss_repository ) )
datatypes_tuple = ( self.url, emboss_datatypes_repository.name, emboss_datatypes_repository.user.username, self.get_repository_tip( emboss_datatypes_repository ) )
filtering_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=[ datatypes_tuple ], filepath=dependency_xml_path )
self.create_repository_dependency( repository=filtering_repository, repository_tuples=[ freebayes_tuple ], filepath=dependency_xml_path )
self.create_repository_dependency( repository=bwa_base_repository, repository_tuples=[ emboss_tuple ], filepath=dependency_xml_path )
self.create_repository_dependency( repository=bwa_color_repository, repository_tuples=[ filtering_tuple ], filepath=dependency_xml_path )
def test_0040_verify_repository_dependencies(self):
'''Verify the generated dependency structure.'''
bwa_color_repository = test_db_util.get_repository_by_name_and_owner(
bwa_color_repository_name, common.test_user_1_name)
bwa_base_repository = test_db_util.get_repository_by_name_and_owner(
bwa_base_repository_name, common.test_user_1_name)
emboss_datatypes_repository = test_db_util.get_repository_by_name_and_owner(
emboss_datatypes_repository_name, common.test_user_1_name)
emboss_repository = test_db_util.get_repository_by_name_and_owner(
emboss_repository_name, common.test_user_1_name)
filtering_repository = test_db_util.get_repository_by_name_and_owner(
filtering_repository_name, common.test_user_1_name)
freebayes_repository = test_db_util.get_repository_by_name_and_owner(
freebayes_repository_name, common.test_user_1_name)
self.check_repository_dependency(emboss_repository,
emboss_datatypes_repository)
self.check_repository_dependency(filtering_repository,
freebayes_repository)
self.check_repository_dependency(bwa_base_repository,
emboss_repository)
self.check_repository_dependency(bwa_color_repository,
filtering_repository)
def test_0030_verify_repository_dependencies( self ):
'''Verify that each repository can depend on the other without causing an infinite loop.'''
convert_repository = test_db_util.get_repository_by_name_and_owner( convert_repository_name, common.test_user_1_name )
column_repository = test_db_util.get_repository_by_name_and_owner( column_repository_name, common.test_user_1_name )
self.check_repository_dependency( convert_repository, column_repository, self.get_repository_tip( column_repository ) )
self.check_repository_dependency( column_repository, convert_repository, self.get_repository_tip( convert_repository ) )
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=[])
def test_0085_verify_repository_metadata(self):
'''Verify that resetting the metadata does not change it.'''
repository = test_db_util.get_repository_by_name_and_owner(
repository_name, common.test_user_1_name)
self.verify_unchanged_repository_metadata(repository)
def test_0100_create_and_upload_dependency_definitions(self):
'''Create the dependency structure for test 0050.'''
global running_standalone
if running_standalone:
self.logout()
self.login(email=common.test_user_1_email,
username=common.test_user_1_name)
column_repository = test_db_util.get_repository_by_name_and_owner(
column_repository_name, common.test_user_1_name)
convert_repository = test_db_util.get_repository_by_name_and_owner(
convert_repository_name, common.test_user_1_name)
datatypes_repository = test_db_util.get_repository_by_name_and_owner(
emboss_datatypes_repository_name, common.test_user_1_name)
emboss_repository = test_db_util.get_repository_by_name_and_owner(
emboss_repository_name, common.test_user_1_name)
filtering_repository = test_db_util.get_repository_by_name_and_owner(
filtering_repository_name, common.test_user_1_name)
freebayes_repository = test_db_util.get_repository_by_name_and_owner(
freebayes_repository_name, common.test_user_1_name)
bismark_repository = test_db_util.get_repository_by_name_and_owner(
bismark_repository_name, common.test_user_1_name)
dependency_xml_path = self.generate_temp_path(
'test_0050', additional_paths=['freebayes'])
# convert_chars depends on column_maker
# column_maker depends on convert_chars
# emboss depends on emboss_datatypes
# emboss_datatypes depends on bismark
# freebayes depends on freebayes, emboss, emboss_datatypes, and column_maker
# filtering depends on emboss
column_tuple = (self.url, column_repository.name,
column_repository.user.username,
self.get_repository_tip(column_repository))
convert_tuple = (self.url, convert_repository.name,
convert_repository.user.username,
self.get_repository_tip(convert_repository))
freebayes_tuple = (self.url, freebayes_repository.name,
freebayes_repository.user.username,
self.get_repository_tip(freebayes_repository))
emboss_tuple = (self.url, emboss_repository.name,
emboss_repository.user.username,
self.get_repository_tip(emboss_repository))
datatypes_tuple = (self.url, datatypes_repository.name,
datatypes_repository.user.username,
self.get_repository_tip(datatypes_repository))
bismark_tuple = (self.url, bismark_repository.name,
bismark_repository.user.username,
self.get_repository_tip(bismark_repository))
self.create_repository_dependency(repository=convert_repository,
repository_tuples=[column_tuple],
filepath=dependency_xml_path)
self.create_repository_dependency(
repository=column_repository,
repository_tuples=[convert_tuple],
filepath=dependency_xml_path)
self.create_repository_dependency(
repository=datatypes_repository,
repository_tuples=[bismark_tuple],
filepath=dependency_xml_path)
self.create_repository_dependency(
repository=emboss_repository,
repository_tuples=[datatypes_tuple],
filepath=dependency_xml_path)
self.create_repository_dependency(repository=freebayes_repository,
repository_tuples=[
freebayes_tuple,
datatypes_tuple,
emboss_tuple, column_tuple
],
filepath=dependency_xml_path)
self.create_repository_dependency(repository=filtering_repository,
repository_tuples=[emboss_tuple],
filepath=dependency_xml_path)
def test_0035_verify_repository_metadata( self ):
'''Verify that resetting the metadata does not change it.'''
column_repository = test_db_util.get_repository_by_name_and_owner( column_repository_name, common.test_user_1_name )
convert_repository = test_db_util.get_repository_by_name_and_owner( convert_repository_name, common.test_user_1_name )
for repository in [ column_repository, convert_repository ]:
self.verify_unchanged_repository_metadata( repository )
def test_0015_verify_datatypes_in_datatypes_repository( self ):
'''Verify that the emboss_datatypes repository contains datatype entries.'''
repository = test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name )
self.display_manage_repository_page( repository, strings_displayed=[ 'Datatypes', 'equicktandem', 'hennig86', 'vectorstrip' ] )
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_0035_verify_tool_dependencies( self ):
'''Verify that the uploaded tool_dependencies.xml specifies the correct package versions.'''
repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name )
self.display_manage_repository_page( repository,
strings_displayed=[ 'freebayes', '0.9.4_9696d0ce8a9', 'samtools', '0.1.18', 'Valid tools' ],
strings_not_displayed=[ 'Invalid tools' ] )
def test_0025_grant_write_access(self):
'''Grant write access to another user'''
repository = test_db_util.get_repository_by_name_and_owner(
repository_name, common.test_user_1_name)
self.grant_write_access(repository, usernames=[common.admin_username])
self.revoke_write_access(repository, common.admin_username)
def test_0025_verify_repository_dependency( self ):
'''Verify that the new revision of column_maker now depends on convert_chars.'''
convert_repository = test_db_util.get_repository_by_name_and_owner( convert_repository_name, common.test_user_1_name )
column_repository = test_db_util.get_repository_by_name_and_owner( column_repository_name, common.test_user_1_name )
self.check_repository_dependency( column_repository, convert_repository )
def test_0030_upload_valid_tool_dependency_xml( self ):
'''Upload tool_dependencies.xml defining version 0.9.4_9696d0ce8a962f7bb61c4791be5ce44312b81cf8 of the freebayes package.'''
repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name )
self.upload_file( repository,
os.path.join( 'freebayes', 'tool_dependencies.xml' ),
commit_message='Uploaded valid tool dependency XML.' )
