def test_0025_delete_repository_dependency( self ):
'''Delete the repository_dependencies.xml from convert_chars_0440.'''
'''
We are at simple repository dependencies, steps 5 and 6 - Delete repository_dependencies.xml from convert_chars_0440.
Make sure convert_chars_0440 now has two installable revisions: 1 and 2
'''
repository = test_db_util.get_repository_by_name_and_owner( convert_repository_name, common.test_user_1_name )
# Record the current tip, so we can verify that it's still a downloadable revision after repository_dependencies.xml
# is deleted and a new downloadable revision is created.
old_changeset_revision = self.get_repository_tip( repository )
self.delete_files_from_repository( repository, filenames=[ 'repository_dependencies.xml' ] )
new_changeset_revision = self.get_repository_tip( repository )
# Check that the old changeset revision is still downloadable.
metadata_record = self.get_repository_metadata_by_changeset_revision( repository, old_changeset_revision )
assert metadata_record.downloadable, 'The revision of %s that contains repository_dependencies.xml is no longer downloadable.' % \
repository.name
# Check that the new tip is also downloadable.
metadata_record = self.get_repository_metadata_by_changeset_revision( repository, new_changeset_revision )
assert metadata_record.downloadable, 'The revision of %s that does not contain repository_dependencies.xml is not downloadable.' % \
repository.name
# Explicitly reload the repository instance from the database, to avoid potential caching issues.
test_db_util.refresh( repository )
# Verify that there are only two downloadable revisions.
assert len( repository.downloadable_revisions ) == 2, 'Repository %s has %d downloadable revisions, expected 2.' % \
( repository.name, len( repository.downloadable_revisions ) )
def test_0025_delete_repository_dependency(self):
'''Delete the repository_dependencies.xml from convert_chars_0440.'''
'''
We are at simple repository dependencies, steps 5 and 6 - Delete repository_dependencies.xml from convert_chars_0440.
Make sure convert_chars_0440 now has two installable revisions: 1 and 2
'''
repository = test_db_util.get_repository_by_name_and_owner(
convert_repository_name, common.test_user_1_name)
# Record the current tip, so we can verify that it's still a downloadable revision after repository_dependencies.xml
# is deleted and a new downloadable revision is created.
old_changeset_revision = self.get_repository_tip(repository)
self.delete_files_from_repository(
repository, filenames=['repository_dependencies.xml'])
new_changeset_revision = self.get_repository_tip(repository)
# Check that the old changeset revision is still downloadable.
metadata_record = self.get_repository_metadata_by_changeset_revision(
repository, old_changeset_revision)
assert metadata_record.downloadable, 'The revision of %s that contains repository_dependencies.xml is no longer downloadable.' % \
repository.name
# Check that the new tip is also downloadable.
metadata_record = self.get_repository_metadata_by_changeset_revision(
repository, new_changeset_revision)
assert metadata_record.downloadable, 'The revision of %s that does not contain repository_dependencies.xml is not downloadable.' % \
repository.name
# Explicitly reload the repository instance from the database, to avoid potential caching issues.
test_db_util.refresh(repository)
# Verify that there are only two downloadable revisions.
assert len( repository.downloadable_revisions ) == 2, 'Repository %s has %d downloadable revisions, expected 2.' % \
( repository.name, len( repository.downloadable_revisions ) )
def test_0005_create_category_and_repository(self):
"""Create a category for this test suite, then create and populate a bismark repository. It should contain at least one each valid and invalid tool."""
category = self.create_category(
name=category_name,
description='Tests for a repository with invalid tool revisions.')
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=[])
self.upload_file(repository,
'bismark/bismark.tar',
valid_tools_only=False,
strings_displayed=[],
commit_message='Uploaded the tool tarball.')
self.display_manage_repository_page(
repository, strings_displayed=['Invalid tools'])
invalid_revision = self.get_repository_tip(repository)
self.upload_file(repository,
'bismark/bismark_methylation_extractor.xml',
valid_tools_only=False,
strings_displayed=[],
remove_repo_files_not_in_tar='No',
commit_message='Uploaded an updated tool xml.')
valid_revision = self.get_repository_tip(repository)
test_db_util.refresh(repository)
self.check_repository_tools_for_changeset_revision(
repository, valid_revision)
self.check_repository_invalid_tools_for_changeset_revision(
repository, invalid_revision)
def test_0005_create_category_and_repository( self ):
"""Create a category for this test suite, then create and populate a bismark repository. It should contain at least one each valid and invalid tool."""
category = self.create_category( name=category_name, description='Tests for a repository with invalid tool revisions.' )
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=[] )
self.upload_file( repository,
'bismark/bismark.tar',
valid_tools_only=False,
strings_displayed=[],
commit_message='Uploaded the tool tarball.' )
self.display_manage_repository_page( repository, strings_displayed=[ 'Invalid tools' ] )
invalid_revision = self.get_repository_tip( repository )
self.upload_file( repository,
'bismark/bismark_methylation_extractor.xml',
valid_tools_only=False,
strings_displayed=[],
remove_repo_files_not_in_tar='No',
commit_message='Uploaded an updated tool xml.' )
valid_revision = self.get_repository_tip( repository )
test_db_util.refresh( repository )
self.check_repository_tools_for_changeset_revision( repository, valid_revision )
self.check_repository_invalid_tools_for_changeset_revision( repository, invalid_revision )
def test_0110_delete_filtering_repository( self ):
'''Delete the filtering_0000 repository and verify that it no longer has any downloadable revisions.'''
repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name )
self.logout()
self.login( email=common.admin_email, username=common.admin_username )
self.delete_repository( repository )
# Explicitly reload all metadata revisions from the database, to ensure that we have the current status of the downloadable flag.
for metadata_revision in repository.metadata_revisions:
test_db_util.refresh( metadata_revision )
# Marking a repository as deleted should result in no metadata revisions being downloadable.
assert True not in [ metadata.downloadable for metadata in repository.metadata_revisions ]
def test_0005_create_category_and_repository(self):
"""Create a category for this test suite, then create and populate a bismark repository. It should contain at least one each valid and invalid tool."""
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=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=[])
self.upload_file(repository,
filename='bismark/bismark.tar',
filepath=None,
valid_tools_only=False,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded bismark tarball.',
strings_displayed=[],
strings_not_displayed=[])
self.display_manage_repository_page(
repository, strings_displayed=['Invalid tools'])
invalid_revision = self.get_repository_tip(repository)
self.upload_file(repository,
filename='bismark/bismark_methylation_extractor.xml',
filepath=None,
valid_tools_only=False,
uncompress_file=False,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded an updated tool xml.',
strings_displayed=[],
strings_not_displayed=[])
valid_revision = self.get_repository_tip(repository)
test_db_util.refresh(repository)
tool_guid = '%s/repos/user1/bismark_0070/bismark_methylation_extractor/0.7.7.3' % self.url.replace(
'http://', '').rstrip('/')
tool_metadata_strings_displayed = [
tool_guid,
'0.7.7.3', # The tool version.
'bismark_methylation_extractor', # The tool ID.
'Bismark', # The tool name.
'methylation extractor'
] # The tool description.
tool_page_strings_displayed = ['Bismark (version 0.7.7.3)']
self.check_repository_tools_for_changeset_revision(
repository,
valid_revision,
tool_metadata_strings_displayed=tool_metadata_strings_displayed,
tool_page_strings_displayed=tool_page_strings_displayed)
self.check_repository_invalid_tools_for_changeset_revision(
repository, invalid_revision)
def test_0115_undelete_filtering_repository( self ):
'''Undelete the filtering_0000 repository and verify that it now has two downloadable revisions.'''
repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name )
self.logout()
self.login( email=common.admin_email, username=common.admin_username )
self.undelete_repository( repository )
# Explicitly reload all metadata revisions from the database, to ensure that we have the current status of the downloadable flag.
for metadata_revision in repository.metadata_revisions:
test_db_util.refresh( metadata_revision )
# Marking a repository as undeleted should result in all previously downloadable metadata revisions being downloadable again.
# In this case, there should be two downloadable revisions, one for filtering 1.1.0 and one for filtering 2.2.0.
assert True in [ metadata.downloadable for metadata in repository.metadata_revisions ]
assert len( repository.downloadable_revisions ) == 2
def test_0110_delete_filtering_repository(self):
'''Delete the filtering_0000 repository and verify that it no longer has any downloadable revisions.'''
repository = test_db_util.get_repository_by_name_and_owner(
repository_name, common.test_user_1_name)
self.logout()
self.login(email=common.admin_email, username=common.admin_username)
self.delete_repository(repository)
# Explicitly reload all metadata revisions from the database, to ensure that we have the current status of the downloadable flag.
for metadata_revision in repository.metadata_revisions:
test_db_util.refresh(metadata_revision)
# Marking a repository as deleted should result in no metadata revisions being downloadable.
assert True not in [
metadata.downloadable for metadata in repository.metadata_revisions
]
def test_0115_undelete_filtering_repository(self):
'''Undelete the filtering_0000 repository and verify that it now has two downloadable revisions.'''
repository = test_db_util.get_repository_by_name_and_owner(
repository_name, common.test_user_1_name)
self.logout()
self.login(email=common.admin_email, username=common.admin_username)
self.undelete_repository(repository)
# Explicitly reload all metadata revisions from the database, to ensure that we have the current status of the downloadable flag.
for metadata_revision in repository.metadata_revisions:
test_db_util.refresh(metadata_revision)
# Marking a repository as undeleted should result in all previously downloadable metadata revisions being downloadable again.
# In this case, there should be two downloadable revisions, one for filtering 1.1.0 and one for filtering 2.2.0.
assert True in [
metadata.downloadable for metadata in repository.metadata_revisions
]
assert len(repository.downloadable_revisions) == 2
def test_0005_create_category_and_repository( self ):
"""Create a category for this test suite, then create and populate a bismark repository. It should contain at least one each valid and invalid tool."""
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=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=[] )
self.upload_file( repository,
filename='bismark/bismark.tar',
filepath=None,
valid_tools_only=False,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded bismark tarball.',
strings_displayed=[],
strings_not_displayed=[] )
self.display_manage_repository_page( repository, strings_displayed=[ 'Invalid tools' ] )
invalid_revision = self.get_repository_tip( repository )
self.upload_file( repository,
filename='bismark/bismark_methylation_extractor.xml',
filepath=None,
valid_tools_only=False,
uncompress_file=False,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded an updated tool xml.',
strings_displayed=[],
strings_not_displayed=[] )
valid_revision = self.get_repository_tip( repository )
test_db_util.refresh( repository )
tool_guid = '%s/repos/user1/bismark_0070/bismark_methylation_extractor/0.7.7.3' % self.url.replace( 'http://', '' ).rstrip( '/' )
tool_metadata_strings_displayed = [ tool_guid,
'0.7.7.3', # The tool version.
'bismark_methylation_extractor', # The tool ID.
'Bismark', # The tool name.
'methylation extractor' ] # The tool description.
tool_page_strings_displayed = [ 'Bismark (version 0.7.7.3)' ]
self.check_repository_tools_for_changeset_revision( repository,
valid_revision,
tool_metadata_strings_displayed=tool_metadata_strings_displayed,
tool_page_strings_displayed=tool_page_strings_displayed )
self.check_repository_invalid_tools_for_changeset_revision( repository, invalid_revision )