mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Refactor the tool shed functional tests' upload_file method for clarity.
This commit is contained in:
Dave Bouvier
@@ -168,11 +168,11 @@ class ShedTwillTestCase( TwillTestCase ):
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raise AssertionError( errmsg )
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def create_category( self, **kwd ):
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category = test_db_util.get_category_by_name( kwd[ 'name' ] )
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if category is not None:
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return category
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self.visit_url( '/admin/manage_categories?operation=create' )
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self.submit_form( form_no=1, button="create_category_button", **kwd )
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return test_db_util.get_category_by_name( kwd[ 'name' ] )
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if category is None:
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self.visit_url( '/admin/manage_categories?operation=create' )
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self.submit_form( form_no=1, button="create_category_button", **kwd )
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category = test_db_util.get_category_by_name( kwd[ 'name' ] )
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return category
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def create_checkbox_query_string( self, field_name, value ):
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'''
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From galaxy.web.form_builder.CheckboxField:
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@@ -213,8 +213,13 @@ class ShedTwillTestCase( TwillTestCase ):
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dependency_description=dependency_description )
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self.upload_file( repository,
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'repository_dependencies.xml',
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filepath=filepath,
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commit_message='Uploaded dependency on %s.' % ', '.join( repo.name for repo in depends_on ) )
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filepath=filepath,
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valid_tools_only=True,
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uncompress_file=False,
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remove_repo_files_not_in_tar=False,
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commit_message='Uploaded dependency on %s.' % ', '.join( repo.name for repo in depends_on ),
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strings_displayed=[],
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strings_not_displayed=[] )
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def create_repository_review( self, repository, review_contents_dict, changeset_revision=None, copy_from=None):
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strings_displayed = []
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if not copy_from:
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@@ -860,17 +865,35 @@ class ShedTwillTestCase( TwillTestCase ):
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def upload_file( self,
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repository,
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filename,
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filepath=None,
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valid_tools_only=True,
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filepath,
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valid_tools_only,
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uncompress_file,
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remove_repo_files_not_in_tar,
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commit_message,
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strings_displayed=[],
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strings_not_displayed=[],
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**kwd ):
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strings_not_displayed=[] ):
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removed_message = 'files were removed from the repository'
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if remove_repo_files_not_in_tar:
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if not self.repository_is_new( repository ):
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if removed_message not in strings_displayed:
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strings_displayed.append( removed_message )
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else:
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if removed_message not in strings_not_displayed:
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strings_not_displayed.append( removed_message )
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self.visit_url( '/upload/upload?repository_id=%s' % self.security.encode_id( repository.id ) )
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if valid_tools_only:
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strings_displayed.extend( [ 'has been successfully', 'uploaded to the repository.' ] )
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for key in kwd:
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tc.fv( "1", key, kwd[ key ] )
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tc.formfile( "1", "file_data", self.get_filename( filename, filepath ) )
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if uncompress_file:
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tc.fv( 1, 'uncompress_file', 'Yes' )
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else:
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tc.fv( 1, 'uncompress_file', 'No' )
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if not self.repository_is_new( repository ):
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if remove_repo_files_not_in_tar:
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tc.fv( 1, 'remove_repo_files_not_in_tar', 'Yes' )
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else:
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tc.fv( 1, 'remove_repo_files_not_in_tar', 'No' )
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tc.fv( 1, 'commit_message', commit_message )
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tc.submit( "upload_button" )
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self.check_for_strings( strings_displayed, strings_not_displayed )
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# Uncomment this if it becomes necessary to wait for an asynchronous process to complete after submitting an upload.
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@@ -56,7 +56,15 @@ class TestBasicRepositoryFeatures( ShedTwillTestCase ):
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def test_0030_upload_filtering_1_1_0( self ):
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"""Upload filtering_1.1.0.tar to the repository"""
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repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name )
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self.upload_file( repository, 'filtering/filtering_1.1.0.tar', commit_message="Uploaded filtering 1.1.0" )
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self.upload_file( repository,
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filename='filtering/filtering_1.1.0.tar',
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filepath=None,
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valid_tools_only=True,
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uncompress_file=True,
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remove_repo_files_not_in_tar=True,
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commit_message="Uploaded filtering 1.1.0",
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strings_displayed=[],
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strings_not_displayed=[] )
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def test_0035_verify_repository( self ):
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'''Display basic repository pages'''
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repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name )
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@@ -102,15 +110,27 @@ class TestBasicRepositoryFeatures( ShedTwillTestCase ):
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'''Upload filtering.txt file associated with tool version 1.1.0.'''
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repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name )
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self.upload_file( repository,
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'filtering/filtering_0000.txt',
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commit_message="Uploaded filtering.txt",
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uncompress_file='No',
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remove_repo_files_not_in_tar='No' )
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filename='filtering/filtering_0000.txt',
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filepath=None,
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valid_tools_only=True,
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uncompress_file=False,
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remove_repo_files_not_in_tar=False,
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commit_message="Uploaded filtering.txt",
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strings_displayed=[],
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strings_not_displayed=[] )
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self.display_manage_repository_page( repository, strings_displayed=[ 'Readme file for filtering 1.1.0' ] )
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def test_0055_upload_filtering_test_data( self ):
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'''Upload filtering test data.'''
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repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name )
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self.upload_file( repository, 'filtering/filtering_test_data.tar', commit_message="Uploaded filtering test data", remove_repo_files_not_in_tar='No' )
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self.upload_file( repository,
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filename='filtering/filtering_test_data.tar',
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filepath=None,
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valid_tools_only=True,
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uncompress_file=True,
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remove_repo_files_not_in_tar=False,
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commit_message="Uploaded filtering test data",
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strings_displayed=[],
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strings_not_displayed=[] )
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self.display_repository_file_contents( repository=repository,
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filename='1.bed',
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filepath='test-data',
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@@ -121,9 +141,14 @@ class TestBasicRepositoryFeatures( ShedTwillTestCase ):
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'''Upload filtering version 2.2.0'''
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repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name )
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self.upload_file( repository,
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'filtering/filtering_2.2.0.tar',
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commit_message="Uploaded filtering 2.2.0",
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remove_repo_files_not_in_tar='No' )
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filename='filtering/filtering_2.2.0.tar',
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filepath=None,
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valid_tools_only=True,
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uncompress_file=True,
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remove_repo_files_not_in_tar=False,
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commit_message="Uploaded filtering 2.2.0",
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strings_displayed=[],
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strings_not_displayed=[] )
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def test_0065_verify_filtering_repository( self ):
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'''Verify the new tool versions and repository metadata.'''
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repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name )
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@@ -138,7 +163,15 @@ class TestBasicRepositoryFeatures( ShedTwillTestCase ):
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def test_0070_upload_readme_txt_file( self ):
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'''Upload readme.txt file associated with tool version 2.2.0.'''
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repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name )
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self.upload_file( repository, 'readme.txt', commit_message="Uploaded readme.txt" )
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self.upload_file( repository,
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filename='readme.txt',
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filepath=None,
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valid_tools_only=True,
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uncompress_file=False,
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remove_repo_files_not_in_tar=False,
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commit_message="Uploaded readme.txt",
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strings_displayed=[],
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strings_not_displayed=[] )
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self.display_manage_repository_page( repository, strings_displayed=[ 'This is a readme file.' ] )
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# Verify that there is a different readme file for each metadata revision.
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metadata_revisions = self.get_repository_metadata_revisions( repository )
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@@ -34,10 +34,14 @@ class TestFreebayesRepository( ShedTwillTestCase ):
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category_id=self.security.encode_id( category.id ),
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strings_displayed=[] )
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self.upload_file( repository,
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'freebayes/freebayes.xml',
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filename='freebayes/freebayes.xml',
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filepath=None,
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valid_tools_only=False,
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uncompress_file=False,
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remove_repo_files_not_in_tar=False,
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commit_message='Uploaded the tool xml.',
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strings_displayed=[ 'Metadata may have been defined', 'This file requires an entry', 'tool_data_table_conf' ],
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commit_message='Uploaded the tool xml.' )
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strings_not_displayed=[] )
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self.display_manage_repository_page( repository, strings_displayed=[ 'Invalid tools' ], strings_not_displayed=[ 'Valid tools' ] )
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tip = self.get_repository_tip( repository )
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self.check_repository_invalid_tools_for_changeset_revision( repository,
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@@ -47,10 +51,14 @@ class TestFreebayesRepository( ShedTwillTestCase ):
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'''Upload the missing tool_data_table_conf.xml.sample file to the repository.'''
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repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name )
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self.upload_file( repository,
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'freebayes/tool_data_table_conf.xml.sample',
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filename='freebayes/tool_data_table_conf.xml.sample',
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filepath=None,
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valid_tools_only=False,
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uncompress_file=False,
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remove_repo_files_not_in_tar=False,
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commit_message='Uploaded the tool data table sample file.',
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strings_displayed=[],
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commit_message='Uploaded the tool data table sample file.' )
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strings_not_displayed=[] )
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self.display_manage_repository_page( repository, strings_displayed=[ 'Invalid tools' ], strings_not_displayed=[ 'Valid tools' ] )
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tip = self.get_repository_tip( repository )
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self.check_repository_invalid_tools_for_changeset_revision( repository,
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@@ -60,30 +68,50 @@ class TestFreebayesRepository( ShedTwillTestCase ):
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'''Upload the missing sam_fa_indices.loc.sample file to the repository.'''
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repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name )
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self.upload_file( repository,
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'freebayes/sam_fa_indices.loc.sample',
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filename='freebayes/sam_fa_indices.loc.sample',
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filepath=None,
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valid_tools_only=True,
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uncompress_file=False,
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remove_repo_files_not_in_tar=False,
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commit_message='Uploaded tool data table .loc file.',
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strings_displayed=[],
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commit_message='Uploaded tool data table .loc file.' )
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strings_not_displayed=[] )
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def test_0025_upload_malformed_tool_dependency_xml( self ):
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'''Upload tool_dependencies.xml with bad characters in the readme tag.'''
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repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name )
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self.upload_file( repository,
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os.path.join( 'freebayes', 'malformed_tool_dependencies', 'tool_dependencies.xml' ),
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filename=os.path.join( 'freebayes', 'malformed_tool_dependencies', 'tool_dependencies.xml' ),
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filepath=None,
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valid_tools_only=False,
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uncompress_file=False,
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remove_repo_files_not_in_tar=False,
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commit_message='Uploaded malformed tool dependency XML.',
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strings_displayed=[ 'Exception attempting to parse tool_dependencies.xml', 'not well-formed' ],
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commit_message='Uploaded malformed tool dependency XML.' )
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strings_not_displayed=[] )
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def test_0030_upload_invalid_tool_dependency_xml( self ):
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'''Upload tool_dependencies.xml defining version 0.9.5 of the freebayes package.'''
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repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name )
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self.upload_file( repository,
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os.path.join( 'freebayes', 'invalid_tool_dependencies', 'tool_dependencies.xml' ),
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filename=os.path.join( 'freebayes', 'invalid_tool_dependencies', 'tool_dependencies.xml' ),
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filepath=None,
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valid_tools_only=False,
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uncompress_file=False,
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remove_repo_files_not_in_tar=False,
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commit_message='Uploaded invalid tool dependency XML.',
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strings_displayed=[ 'Name, version and type from a tool requirement tag does not match' ],
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commit_message='Uploaded invalid tool dependency XML.' )
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strings_not_displayed=[] )
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def test_0035_upload_valid_tool_dependency_xml( self ):
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'''Upload tool_dependencies.xml defining version 0.9.4_9696d0ce8a962f7bb61c4791be5ce44312b81cf8 of the freebayes package.'''
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repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name )
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self.upload_file( repository,
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os.path.join( 'freebayes', 'tool_dependencies.xml' ),
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commit_message='Uploaded valid tool dependency XML.' )
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filename=os.path.join( 'freebayes', 'tool_dependencies.xml' ),
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filepath=None,
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valid_tools_only=True,
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uncompress_file=False,
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remove_repo_files_not_in_tar=False,
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commit_message='Uploaded valid tool dependency XML.',
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strings_displayed=[],
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strings_not_displayed=[] )
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def test_0040_verify_tool_dependencies( self ):
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'''Verify that the uploaded tool_dependencies.xml specifies the correct package versions.'''
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repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name )
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@@ -37,7 +37,15 @@ class TestBasicRepositoryDependencies( ShedTwillTestCase ):
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owner=common.test_user_1_name,
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category_id=self.security.encode_id( category.id ),
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strings_displayed=[] )
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self.upload_file( repository, 'emboss/datatypes/datatypes_conf.xml', commit_message='Uploaded datatypes_conf.xml.' )
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self.upload_file( repository,
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filename='emboss/datatypes/datatypes_conf.xml',
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filepath=None,
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valid_tools_only=True,
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uncompress_file=False,
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remove_repo_files_not_in_tar=False,
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commit_message='Uploaded datatypes_conf.xml.',
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strings_displayed=[],
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strings_not_displayed=[] )
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def test_0015_verify_datatypes_in_datatypes_repository( self ):
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'''Verify that the emboss_datatypes repository contains datatype entries.'''
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repository = test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name )
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@@ -51,7 +59,15 @@ class TestBasicRepositoryDependencies( ShedTwillTestCase ):
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owner=common.test_user_1_name,
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category_id=self.security.encode_id( category.id ),
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strings_displayed=[] )
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self.upload_file( repository, 'emboss/emboss.tar', commit_message='Uploaded emboss_5.tar' )
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self.upload_file( repository,
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filename='emboss/emboss.tar',
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filepath=None,
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valid_tools_only=True,
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uncompress_file=True,
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remove_repo_files_not_in_tar=False,
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commit_message='Uploaded emboss.tar',
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strings_displayed=[],
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strings_not_displayed=[] )
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def test_0025_generate_and_upload_repository_dependencies_xml( self ):
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'''Generate and upload the repository_dependencies.xml file'''
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repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name )
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@@ -60,9 +76,14 @@ class TestBasicRepositoryDependencies( ShedTwillTestCase ):
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self.generate_repository_dependency_xml( [ datatypes_repository ],
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self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ) )
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self.upload_file( repository,
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'repository_dependencies.xml',
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filepath=repository_dependencies_path,
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commit_message='Uploaded repository_dependencies.xml' )
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filename='repository_dependencies.xml',
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filepath=repository_dependencies_path,
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valid_tools_only=True,
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uncompress_file=False,
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remove_repo_files_not_in_tar=False,
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commit_message='Uploaded repository_dependencies.xml.',
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strings_displayed=[],
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strings_not_displayed=[] )
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def test_0030_verify_emboss_5_dependencies( self ):
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'''Verify that the emboss_5 repository now depends on the emboss_datatypes repository with correct name, owner, and changeset revision.'''
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repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name )
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@@ -28,36 +28,83 @@ class TestRepositoryDependencyRevisions( ShedTwillTestCase ):
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def test_0005_create_category( self ):
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"""Create a category for this test suite"""
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self.create_category( name='Test 0030 Repository Dependency Revisions', description='Testing repository dependencies by revision.' )
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def test_0010_create_repositories( self ):
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'''Create the emboss_5_0030, emboss_6_0030, emboss_datatypes_0030, and emboss_0030 repositories and populate the emboss_datatypes repository.'''
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def test_0010_create_emboss_5_repository( self ):
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'''Create and populate the emboss_5_0030 repository.'''
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self.logout()
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self.login( email=common.test_user_1_email, username=common.test_user_1_name )
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category = test_db_util.get_category_by_name( 'Test 0030 Repository Dependency Revisions' )
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emboss_5_repository = self.get_or_create_repository( name=emboss_5_repository_name,
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description=emboss_repository_description,
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long_description=emboss_repository_long_description,
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owner=common.test_user_1_name,
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category_id=self.security.encode_id( category.id ) )
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emboss_6_repository = self.get_or_create_repository( name=emboss_6_repository_name,
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description=emboss_repository_description,
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long_description=emboss_repository_long_description,
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owner=common.test_user_1_name,
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category_id=self.security.encode_id( category.id ) )
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datatypes_repository = self.get_or_create_repository( name=datatypes_repository_name,
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description=emboss_repository_description,
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long_description=emboss_repository_long_description,
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owner=common.test_user_1_name,
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category_id=self.security.encode_id( category.id ) )
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emboss_repository = self.get_or_create_repository( name=emboss_repository_name,
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repository = self.get_or_create_repository( name=emboss_5_repository_name,
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description=emboss_repository_description,
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long_description=emboss_repository_long_description,
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owner=common.test_user_1_name,
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category_id=self.security.encode_id( category.id ) )
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self.upload_file( repository,
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filename='emboss/emboss.tar',
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filepath=None,
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valid_tools_only=True,
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uncompress_file=False,
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remove_repo_files_not_in_tar=False,
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commit_message='Uploaded tool tarball.',
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strings_displayed=[],
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strings_not_displayed=[] )
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def test_0015_create_emboss_6_repository( self ):
|
||||
'''Create and populate the emboss_6_0030 repository.'''
|
||||
self.logout()
|
||||
self.login( email=common.test_user_1_email, username=common.test_user_1_name )
|
||||
category = test_db_util.get_category_by_name( 'Test 0030 Repository Dependency Revisions' )
|
||||
repository = self.get_or_create_repository( name=emboss_6_repository_name,
|
||||
description=emboss_repository_description,
|
||||
long_description=emboss_repository_long_description,
|
||||
owner=common.test_user_1_name,
|
||||
category_id=self.security.encode_id( category.id ) )
|
||||
self.upload_file( repository,
|
||||
filename='emboss/emboss.tar',
|
||||
filepath=None,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded tool tarball.',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
def test_0020_create_emboss_datatypes_repository( self ):
|
||||
'''Create and populate the emboss_datatypes_0030 repository.'''
|
||||
self.logout()
|
||||
self.login( email=common.test_user_1_email, username=common.test_user_1_name )
|
||||
category = test_db_util.get_category_by_name( 'Test 0030 Repository Dependency Revisions' )
|
||||
repository = self.get_or_create_repository( name=datatypes_repository_name,
|
||||
description=emboss_repository_description,
|
||||
long_description=emboss_repository_long_description,
|
||||
owner=common.test_user_1_name,
|
||||
category_id=self.security.encode_id( category.id ) )
|
||||
self.upload_file( repository,
|
||||
filename='emboss/datatypes/datatypes_conf.xml',
|
||||
filepath=None,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded datatypes_conf.xml.',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
def test_0025_create_emboss_repository( self ):
|
||||
'''Create and populate the emboss_0030 repository.'''
|
||||
self.logout()
|
||||
self.login( email=common.test_user_1_email, username=common.test_user_1_name )
|
||||
category = test_db_util.get_category_by_name( 'Test 0030 Repository Dependency Revisions' )
|
||||
repository = self.get_or_create_repository( name=emboss_repository_name,
|
||||
description=emboss_repository_description,
|
||||
long_description=emboss_repository_long_description,
|
||||
owner=common.test_user_1_name,
|
||||
category_id=self.security.encode_id( category.id ) )
|
||||
self.upload_file( emboss_5_repository, 'emboss/emboss.tar', commit_message='Uploaded tool tarball.' )
|
||||
self.upload_file( emboss_6_repository, 'emboss/emboss.tar', commit_message='Uploaded tool tarball.' )
|
||||
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.' )
|
||||
def test_0015_generate_repository_dependencies_for_emboss_5( self ):
|
||||
self.upload_file( repository,
|
||||
filename='emboss/emboss.tar',
|
||||
filepath=None,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded the tool tarball.',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
def test_0030_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' ] )
|
||||
@@ -65,18 +112,28 @@ class TestRepositoryDependencyRevisions( ShedTwillTestCase ):
|
||||
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_0020_generate_repository_dependencies_for_emboss_6( self ):
|
||||
filename='repository_dependencies.xml',
|
||||
filepath=repository_dependencies_path,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded repository_dependencies.xml.',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
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 )
|
||||
repository_dependencies_path = self.generate_temp_path( 'test_0030', additional_paths=[ 'emboss' ] )
|
||||
self.upload_file( emboss_6_repository,
|
||||
'repository_dependencies.xml',
|
||||
filepath=repository_dependencies_path,
|
||||
commit_message='Uploaded repository_depepndencies.xml.' )
|
||||
def test_0025_generate_repository_dependency_on_emboss_5( self ):
|
||||
filename='repository_dependencies.xml',
|
||||
filepath=repository_dependencies_path,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded repository_dependencies.xml.',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
def test_0040_generate_repository_dependency_on_emboss_5( self ):
|
||||
'''Create and upload repository_dependencies.xml for the emboss_5_0030 repository.'''
|
||||
emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name )
|
||||
emboss_5_repository = test_db_util.get_repository_by_name_and_owner( emboss_5_repository_name, common.test_user_1_name )
|
||||
@@ -85,10 +142,15 @@ class TestRepositoryDependencyRevisions( ShedTwillTestCase ):
|
||||
self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ),
|
||||
dependency_description='Emboss requires the Emboss 5 repository.' )
|
||||
self.upload_file( emboss_repository,
|
||||
'repository_dependencies.xml',
|
||||
filepath=repository_dependencies_path,
|
||||
commit_message='Uploaded dependency configuration specifying emboss_5' )
|
||||
def test_0030_generate_repository_dependency_on_emboss_6( self ):
|
||||
filename='repository_dependencies.xml',
|
||||
filepath=repository_dependencies_path,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded repository_dependencies.xml.',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
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 )
|
||||
@@ -97,10 +159,15 @@ class TestRepositoryDependencyRevisions( ShedTwillTestCase ):
|
||||
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_0035_verify_repository_dependency_revisions( self ):
|
||||
filename='repository_dependencies.xml',
|
||||
filepath=repository_dependencies_path,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded repository_dependencies.xml.',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
def test_0050_verify_repository_dependency_revisions( self ):
|
||||
'''Verify that different metadata revisions of the emboss repository have different repository dependencies.'''
|
||||
repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name )
|
||||
repository_metadata = [ ( metadata.metadata, metadata.changeset_revision ) for metadata in self.get_repository_metadata( repository ) ]
|
||||
@@ -120,7 +187,7 @@ class TestRepositoryDependencyRevisions( ShedTwillTestCase ):
|
||||
self.display_manage_repository_page( repository,
|
||||
changeset_revision=changeset_revision,
|
||||
strings_displayed=strings_displayed )
|
||||
def test_0040_verify_repository_metadata( self ):
|
||||
def test_0055_verify_repository_metadata( self ):
|
||||
'''Verify that resetting the metadata does not change it.'''
|
||||
emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name )
|
||||
emboss_5_repository = test_db_util.get_repository_by_name_and_owner( emboss_5_repository_name, common.test_user_1_name )
|
||||
|
||||
@@ -37,9 +37,14 @@ class TestRepositoryCircularDependencies( ShedTwillTestCase ):
|
||||
categories=[ 'test_0040_repository_circular_dependencies' ],
|
||||
strings_displayed=[] )
|
||||
self.upload_file( repository,
|
||||
'freebayes/freebayes.tar',
|
||||
filename='freebayes/freebayes.tar',
|
||||
filepath=None,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=True,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded the tool tarball.',
|
||||
strings_displayed=[],
|
||||
commit_message='Uploaded freebayes.tar.' )
|
||||
strings_not_displayed=[] )
|
||||
def test_0015_create_filtering_repository( self ):
|
||||
'''Create and populate filtering_0040.'''
|
||||
self.logout()
|
||||
@@ -51,9 +56,14 @@ class TestRepositoryCircularDependencies( ShedTwillTestCase ):
|
||||
categories=[ 'test_0040_repository_circular_dependencies' ],
|
||||
strings_displayed=[] )
|
||||
self.upload_file( repository,
|
||||
'filtering/filtering_1.1.0.tar',
|
||||
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 the tool tarball for filtering 1.1.0.',
|
||||
strings_displayed=[],
|
||||
commit_message='Uploaded filtering.tar.' )
|
||||
strings_not_displayed=[] )
|
||||
def test_0020_create_dependency_on_freebayes( self ):
|
||||
'''Upload a repository_dependencies.xml file that specifies the current revision of freebayes to the filtering_0040 repository.'''
|
||||
# The dependency structure should look like:
|
||||
@@ -67,9 +77,14 @@ class TestRepositoryCircularDependencies( ShedTwillTestCase ):
|
||||
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',
|
||||
filename='repository_dependencies.xml',
|
||||
filepath=repository_dependencies_path,
|
||||
commit_message='Uploaded dependency on freebayes' )
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded dependency on freebayes.',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
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:
|
||||
@@ -83,9 +98,14 @@ class TestRepositoryCircularDependencies( ShedTwillTestCase ):
|
||||
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',
|
||||
filename='repository_dependencies.xml',
|
||||
filepath=repository_dependencies_path,
|
||||
commit_message='Uploaded dependency on filtering' )
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded dependency on filtering.',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
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 )
|
||||
|
||||
@@ -58,9 +58,14 @@ class TestRepositoryCircularDependenciesToNLevels( ShedTwillTestCase ):
|
||||
category_id=self.security.encode_id( category.id ),
|
||||
strings_displayed=[] )
|
||||
self.upload_file( repository,
|
||||
'convert_chars/convert_chars.tar',
|
||||
filename='convert_chars/convert_chars.tar',
|
||||
filepath=None,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=True,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded convert_chars tarball.',
|
||||
strings_displayed=[],
|
||||
commit_message='Uploaded convert_chars.tar.' )
|
||||
strings_not_displayed=[] )
|
||||
def test_0010_create_column_repository( self ):
|
||||
'''Create and populate convert_chars_0050.'''
|
||||
category = self.create_category( name=category_name, description=category_description )
|
||||
@@ -71,9 +76,14 @@ class TestRepositoryCircularDependenciesToNLevels( ShedTwillTestCase ):
|
||||
category_id=self.security.encode_id( category.id ),
|
||||
strings_displayed=[] )
|
||||
self.upload_file( repository,
|
||||
'column_maker/column_maker.tar',
|
||||
filename='column_maker/column_maker.tar',
|
||||
filepath=None,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=True,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded column_maker tarball.',
|
||||
strings_displayed=[],
|
||||
commit_message='Uploaded column_maker.tar.' )
|
||||
strings_not_displayed=[] )
|
||||
def test_0015_create_emboss_datatypes_repository( self ):
|
||||
'''Create and populate emboss_datatypes_0050.'''
|
||||
category = self.create_category( name=category_name, description=category_description )
|
||||
@@ -86,9 +96,14 @@ class TestRepositoryCircularDependenciesToNLevels( ShedTwillTestCase ):
|
||||
category_id=self.security.encode_id( category.id ),
|
||||
strings_displayed=[] )
|
||||
self.upload_file( repository,
|
||||
'emboss/datatypes/datatypes_conf.xml',
|
||||
filename='emboss/datatypes/datatypes_conf.xml',
|
||||
filepath=None,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded datatypes_conf.xml.',
|
||||
strings_displayed=[],
|
||||
commit_message='Uploaded datatypes_conf.xml.' )
|
||||
strings_not_displayed=[] )
|
||||
def test_0020_create_emboss_repository( self ):
|
||||
'''Create and populate emboss_0050.'''
|
||||
category = self.create_category( name=category_name, description=category_description )
|
||||
@@ -99,18 +114,28 @@ class TestRepositoryCircularDependenciesToNLevels( ShedTwillTestCase ):
|
||||
category_id=self.security.encode_id( category.id ),
|
||||
strings_displayed=[] )
|
||||
self.upload_file( repository,
|
||||
'emboss/emboss.tar',
|
||||
filename='emboss/emboss.tar',
|
||||
filepath=None,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=True,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded emboss tarball.',
|
||||
strings_displayed=[],
|
||||
commit_message='Uploaded tool tarball.' )
|
||||
strings_not_displayed=[] )
|
||||
datatypes_repository = test_db_util.get_repository_by_name_and_owner( emboss_datatypes_repository_name, common.test_user_1_name )
|
||||
repository_dependencies_path = self.generate_temp_path( 'test_0050', 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( repository,
|
||||
'repository_dependencies.xml',
|
||||
filename='repository_dependencies.xml',
|
||||
filepath=repository_dependencies_path,
|
||||
commit_message='Uploaded dependency on emboss_datatypes.' )
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded dependency on emboss_datatypes.',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
def test_0025_create_filtering_repository( self ):
|
||||
'''Create and populate filtering_0050.'''
|
||||
category = self.create_category( name=category_name, description=category_description )
|
||||
@@ -121,18 +146,28 @@ class TestRepositoryCircularDependenciesToNLevels( ShedTwillTestCase ):
|
||||
category_id=self.security.encode_id( category.id ),
|
||||
strings_displayed=[] )
|
||||
self.upload_file( filtering_repository,
|
||||
'filtering/filtering_1.1.0.tar',
|
||||
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=[],
|
||||
commit_message='Uploaded filtering.tar.' )
|
||||
strings_not_displayed=[] )
|
||||
emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name )
|
||||
repository_dependencies_path = self.generate_temp_path( 'test_0050', 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',
|
||||
filename='repository_dependencies.xml',
|
||||
filepath=repository_dependencies_path,
|
||||
commit_message='Uploaded dependency on emboss.' )
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded dependency on emboss.',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
def test_0030_create_freebayes_repository( self ):
|
||||
'''Create and populate freebayes_0050.'''
|
||||
category = self.create_category( name=category_name, description=category_description )
|
||||
@@ -143,9 +178,14 @@ class TestRepositoryCircularDependenciesToNLevels( ShedTwillTestCase ):
|
||||
category_id=self.security.encode_id( category.id ),
|
||||
strings_displayed=[] )
|
||||
self.upload_file( repository,
|
||||
'freebayes/freebayes.tar',
|
||||
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=[],
|
||||
commit_message='Uploaded freebayes.tar.' )
|
||||
strings_not_displayed=[] )
|
||||
def test_0035_create_bismark_repository( self ):
|
||||
'''Create and populate bismark_0050.'''
|
||||
category = self.create_category( name=category_name, description=category_description )
|
||||
@@ -156,10 +196,14 @@ class TestRepositoryCircularDependenciesToNLevels( ShedTwillTestCase ):
|
||||
category_id=self.security.encode_id( category.id ),
|
||||
strings_displayed=[] )
|
||||
self.upload_file( repository,
|
||||
'bismark/bismark.tar',
|
||||
strings_displayed=[],
|
||||
filename='bismark/bismark.tar',
|
||||
filepath=None,
|
||||
valid_tools_only=False,
|
||||
commit_message='Uploaded bismark.tar.' )
|
||||
uncompress_file=True,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded bismark tarball.',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
def test_0040_create_and_upload_dependency_definitions( self ):
|
||||
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 )
|
||||
|
||||
@@ -6,6 +6,8 @@ repository_description="Galaxy's filtering tool for test 0060"
|
||||
repository_long_description="Long description of Galaxy's filtering tool for test 0060"
|
||||
workflow_filename = 'Workflow_for_0060_filter_workflow_repository.ga'
|
||||
workflow_name = 'Workflow for 0060_filter_workflow_repository'
|
||||
category_name = 'Test 0060 Workflow Features'
|
||||
category_description = 'Test 0060 for workflow features'
|
||||
|
||||
class TestToolShedWorkflowFeatures( ShedTwillTestCase ):
|
||||
'''Test valid and invalid workflows.'''
|
||||
@@ -26,13 +28,14 @@ class TestToolShedWorkflowFeatures( ShedTwillTestCase ):
|
||||
self.create_category( name='Test 0060 Workflow Features', description='Test 0060 - Workflow Features' )
|
||||
def test_0010_create_repository( self ):
|
||||
"""Create and populate the filtering 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=repository_name,
|
||||
description=repository_description,
|
||||
long_description=repository_long_description,
|
||||
owner=common.test_user_1_name,
|
||||
categories=[ 'Test 0060 Workflow Features' ],
|
||||
category_id=self.security.encode_id( category.id ),
|
||||
strings_displayed=[] )
|
||||
def test_0015_upload_workflow( self ):
|
||||
'''Upload a workflow with a missing tool, and verify that the tool specified is marked as missing.'''
|
||||
@@ -44,18 +47,27 @@ class TestToolShedWorkflowFeatures( ShedTwillTestCase ):
|
||||
os.makedirs( workflow_filepath )
|
||||
file( os.path.join( workflow_filepath, workflow_filename ), 'w+' ).write( workflow )
|
||||
self.upload_file( repository,
|
||||
workflow_filename,
|
||||
filename=workflow_filename,
|
||||
filepath=workflow_filepath,
|
||||
commit_message='Uploaded filtering workflow.' )
|
||||
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_0020_upload_tool( self ):
|
||||
'''Upload the missing tool for the workflow in the previous step, and verify that the error is no longer present.'''
|
||||
repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name )
|
||||
self.upload_file( repository,
|
||||
'filtering/filtering_2.2.0.tar',
|
||||
commit_message="Uploaded filtering 2.2.0",
|
||||
remove_repo_files_not_in_tar='No' )
|
||||
# raise Exception( self.get_repository_tip( 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.',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
self.load_workflow_image_in_tool_shed( repository, workflow_name, strings_not_displayed=[ '#EBBCB2' ] )
|
||||
def test_0025_verify_repository_metadata( self ):
|
||||
'''Verify that resetting the metadata does not change it.'''
|
||||
|
||||
@@ -5,6 +5,7 @@ repository_name = 'bismark_0070'
|
||||
repository_description = "Galaxy's bismark wrapper"
|
||||
repository_long_description = "Long description of Galaxy's bismark wrapper"
|
||||
category_name = 'Test 0070 Invalid Tool Revisions'
|
||||
category_description = 'Tests for a repository with invalid tool revisions.'
|
||||
|
||||
class TestBismarkRepository( ShedTwillTestCase ):
|
||||
'''Testing bismark with valid and invalid tool entries.'''
|
||||
@@ -22,7 +23,7 @@ class TestBismarkRepository( ShedTwillTestCase ):
|
||||
admin_user_private_role = test_db_util.get_private_role( admin_user )
|
||||
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.' )
|
||||
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,
|
||||
@@ -32,18 +33,25 @@ class TestBismarkRepository( ShedTwillTestCase ):
|
||||
category_id=self.security.encode_id( category.id ),
|
||||
strings_displayed=[] )
|
||||
self.upload_file( repository,
|
||||
'bismark/bismark.tar',
|
||||
filename='bismark/bismark.tar',
|
||||
filepath=None,
|
||||
valid_tools_only=False,
|
||||
strings_displayed=[],
|
||||
commit_message='Uploaded the tool tarball.' )
|
||||
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,
|
||||
'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.' )
|
||||
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 )
|
||||
self.check_repository_tools_for_changeset_revision( repository, valid_revision )
|
||||
|
||||
@@ -26,8 +26,8 @@ class TestRepositoryCircularDependencies( ShedTwillTestCase ):
|
||||
admin_user = test_db_util.get_user( common.admin_email )
|
||||
assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email
|
||||
admin_user_private_role = test_db_util.get_private_role( admin_user )
|
||||
def test_0005_initiate_category_repositories( self ):
|
||||
"""Create a category for this test suite and add repositories to it."""
|
||||
def test_0005_create_column_repository( self ):
|
||||
"""Create and populate the column_maker 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 )
|
||||
@@ -38,9 +38,21 @@ class TestRepositoryCircularDependencies( ShedTwillTestCase ):
|
||||
category_id=self.security.encode_id( category.id ),
|
||||
strings_displayed=[] )
|
||||
self.upload_file( repository,
|
||||
'column_maker/column_maker.tar',
|
||||
filename='column_maker/column_maker.tar',
|
||||
filepath=None,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=True,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded column_maker tarball.',
|
||||
strings_displayed=[],
|
||||
commit_message='Uploaded column_maker.tar.' )
|
||||
strings_not_displayed=[] )
|
||||
def test_0005_create_convert_repository( self ):
|
||||
"""Create and populate the convert_chars repository."""
|
||||
self.logout()
|
||||
self.login( email=common.admin_email, username=common.admin_username )
|
||||
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=convert_repository_name,
|
||||
description=convert_repository_description,
|
||||
long_description=convert_repository_long_description,
|
||||
@@ -48,9 +60,14 @@ class TestRepositoryCircularDependencies( ShedTwillTestCase ):
|
||||
category_id=self.security.encode_id( category.id ),
|
||||
strings_displayed=[] )
|
||||
self.upload_file( repository,
|
||||
'convert_chars/convert_chars.tar',
|
||||
filename='convert_chars/convert_chars.tar',
|
||||
filepath=None,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=True,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded convert_chars tarball.',
|
||||
strings_displayed=[],
|
||||
commit_message='Uploaded convert_chars.tar.' )
|
||||
strings_not_displayed=[] )
|
||||
def test_0020_create_repository_dependencies( self ):
|
||||
'''Upload a repository_dependencies.xml file that specifies the current revision of freebayes to the filtering_0040 repository.'''
|
||||
convert_repository = test_db_util.get_repository_by_name_and_owner( convert_repository_name, common.test_user_1_name )
|
||||
@@ -60,9 +77,14 @@ class TestRepositoryCircularDependencies( ShedTwillTestCase ):
|
||||
self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ),
|
||||
dependency_description='Column maker depends on the convert repository.' )
|
||||
self.upload_file( column_repository,
|
||||
'repository_dependencies.xml',
|
||||
filepath=repository_dependencies_path,
|
||||
commit_message='Uploaded dependency on convert' )
|
||||
filename='repository_dependencies.xml',
|
||||
filepath=repository_dependencies_path,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=True,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded dependency on convert_chars.',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
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 )
|
||||
@@ -72,9 +94,14 @@ class TestRepositoryCircularDependencies( ShedTwillTestCase ):
|
||||
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' )
|
||||
filename='repository_dependencies.xml',
|
||||
filepath=repository_dependencies_path,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=True,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded dependency on column_maker.',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
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 )
|
||||
|
||||
@@ -54,9 +54,14 @@ class TestRepositoryCircularDependenciesAgain( ShedTwillTestCase ):
|
||||
category_id=self.security.encode_id( category.id ),
|
||||
strings_displayed=[] )
|
||||
self.upload_file( repository,
|
||||
'bwa/bwa_base.tar',
|
||||
filename='bwa/bwa_base.tar',
|
||||
filepath=None,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=True,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded BWA tarball.',
|
||||
strings_displayed=[],
|
||||
commit_message='Uploaded bwa_base.tar.' )
|
||||
strings_not_displayed=[] )
|
||||
def test_0010_create_bwa_color_repository( self ):
|
||||
'''Create and populate bwa_color_0090.'''
|
||||
category = self.create_category( name=category_name, description=category_description )
|
||||
@@ -69,9 +74,14 @@ class TestRepositoryCircularDependenciesAgain( ShedTwillTestCase ):
|
||||
category_id=self.security.encode_id( category.id ),
|
||||
strings_displayed=[] )
|
||||
self.upload_file( repository,
|
||||
'bwa/bwa_color.tar',
|
||||
filename='bwa/bwa_color.tar',
|
||||
filepath=None,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=True,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded BWA color tarball.',
|
||||
strings_displayed=[],
|
||||
commit_message='Uploaded bwa_color.tar.' )
|
||||
strings_not_displayed=[] )
|
||||
def test_0015_create_emboss_datatypes_repository( self ):
|
||||
'''Create and populate emboss_datatypes_0090.'''
|
||||
category = self.create_category( name=category_name, description=category_description )
|
||||
@@ -84,9 +94,14 @@ class TestRepositoryCircularDependenciesAgain( ShedTwillTestCase ):
|
||||
category_id=self.security.encode_id( category.id ),
|
||||
strings_displayed=[] )
|
||||
self.upload_file( repository,
|
||||
'emboss/datatypes/datatypes_conf.xml',
|
||||
filename='emboss/datatypes/datatypes_conf.xml',
|
||||
filepath=None,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded datatypes_conf.xml.',
|
||||
strings_displayed=[],
|
||||
commit_message='Uploaded datatypes_conf.xml.' )
|
||||
strings_not_displayed=[] )
|
||||
def test_0020_create_emboss_repository( self ):
|
||||
'''Create and populate emboss_0090.'''
|
||||
category = self.create_category( name=category_name, description=category_description )
|
||||
@@ -97,18 +112,28 @@ class TestRepositoryCircularDependenciesAgain( ShedTwillTestCase ):
|
||||
category_id=self.security.encode_id( category.id ),
|
||||
strings_displayed=[] )
|
||||
self.upload_file( repository,
|
||||
'emboss/emboss.tar',
|
||||
filename='emboss/emboss.tar',
|
||||
filepath=None,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded emboss tarball.',
|
||||
strings_displayed=[],
|
||||
commit_message='Uploaded tool tarball.' )
|
||||
strings_not_displayed=[] )
|
||||
datatypes_repository = test_db_util.get_repository_by_name_and_owner( emboss_datatypes_repository_name, common.test_user_1_name )
|
||||
repository_dependencies_path = self.generate_temp_path( 'test_0090', 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( repository,
|
||||
'repository_dependencies.xml',
|
||||
filepath=repository_dependencies_path,
|
||||
commit_message='Uploaded dependency on emboss_datatypes.' )
|
||||
filename='repository_dependencies.xml',
|
||||
filepath=repository_dependencies_path,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=True,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded dependency on emboss_datatypes.',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
def test_0025_create_filtering_repository( self ):
|
||||
'''Create and populate filtering_0090.'''
|
||||
category = self.create_category( name=category_name, description=category_description )
|
||||
@@ -119,18 +144,28 @@ class TestRepositoryCircularDependenciesAgain( ShedTwillTestCase ):
|
||||
category_id=self.security.encode_id( category.id ),
|
||||
strings_displayed=[] )
|
||||
self.upload_file( filtering_repository,
|
||||
'filtering/filtering_1.1.0.tar',
|
||||
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=[],
|
||||
commit_message='Uploaded filtering.tar.' )
|
||||
strings_not_displayed=[] )
|
||||
emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name )
|
||||
repository_dependencies_path = self.generate_temp_path( 'test_0090', 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.' )
|
||||
filename='repository_dependencies.xml',
|
||||
filepath=repository_dependencies_path,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded dependency on emboss.',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
def test_0030_create_freebayes_repository( self ):
|
||||
'''Create and populate freebayes_0090.'''
|
||||
category = self.create_category( name=category_name, description=category_description )
|
||||
@@ -141,9 +176,14 @@ class TestRepositoryCircularDependenciesAgain( ShedTwillTestCase ):
|
||||
category_id=self.security.encode_id( category.id ),
|
||||
strings_displayed=[] )
|
||||
self.upload_file( repository,
|
||||
'freebayes/freebayes.tar',
|
||||
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=[],
|
||||
commit_message='Uploaded freebayes.tar.' )
|
||||
strings_not_displayed=[] )
|
||||
def test_0035_create_and_upload_dependency_definitions( self ):
|
||||
'''Create and upload repository dependency definitions.'''
|
||||
bwa_color_repository = test_db_util.get_repository_by_name_and_owner( bwa_color_repository_name, common.test_user_1_name )
|
||||
|
||||
@@ -38,9 +38,14 @@ class TestComplexRepositoryDependencies( ShedTwillTestCase ):
|
||||
category_id=self.security.encode_id( category.id ),
|
||||
strings_displayed=[] )
|
||||
self.upload_file( repository,
|
||||
'bwa/complex/tool_dependencies.xml',
|
||||
filename='bwa/complex/tool_dependencies.xml',
|
||||
filepath=None,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded tool_dependencies.xml.',
|
||||
strings_displayed=[ 'Name, version and type from a tool requirement tag does not match' ],
|
||||
commit_message='Uploaded tool_dependencies.xml.' )
|
||||
strings_not_displayed=[] )
|
||||
self.display_manage_repository_page( repository, strings_displayed=[ 'Tool dependencies', 'may not be', 'in this repository' ] )
|
||||
def test_0010_create_bwa_base_repository( self ):
|
||||
'''Create and populate bwa_base_0100.'''
|
||||
@@ -55,9 +60,14 @@ class TestComplexRepositoryDependencies( ShedTwillTestCase ):
|
||||
strings_displayed=[] )
|
||||
tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name )
|
||||
self.upload_file( repository,
|
||||
'bwa/complex/bwa_base.tar',
|
||||
filename='bwa/complex/bwa_base.tar',
|
||||
filepath=None,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=True,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded bwa_base.tar with tool wrapper XML, but without tool dependency XML.',
|
||||
strings_displayed=[],
|
||||
commit_message='Uploaded bwa_base.tar with tool wrapper XML, but without tool dependency XML.' )
|
||||
strings_not_displayed=[] )
|
||||
def test_0015_generate_complex_repository_dependency_invalid_shed_url( self ):
|
||||
'''Generate and upload a complex repository definition that specifies an invalid tool shed URL.'''
|
||||
dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex', 'invalid' ] )
|
||||
@@ -71,34 +81,40 @@ class TestComplexRepositoryDependencies( ShedTwillTestCase ):
|
||||
self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=True, package='bwa', version='0.5.9' )
|
||||
strings_displayed = [ 'Invalid tool shed <b>%s</b> defined' % url ]
|
||||
self.upload_file( repository,
|
||||
'tool_dependencies.xml',
|
||||
valid_tools_only=False,
|
||||
filename='tool_dependencies.xml',
|
||||
filepath=dependency_path,
|
||||
valid_tools_only=False,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded dependency on bwa_tool_0100 with invalid url.',
|
||||
strings_displayed=strings_displayed )
|
||||
strings_displayed=strings_displayed,
|
||||
strings_not_displayed=[] )
|
||||
def test_0020_generate_complex_repository_dependency_invalid_repository_name( self ):
|
||||
'''Generate and upload a complex repository definition that specifies an invalid repository name.'''
|
||||
dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex', 'invalid' ] )
|
||||
xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path )
|
||||
repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name )
|
||||
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 )
|
||||
url = self.url
|
||||
name = 'invalid_repository!?'
|
||||
owner = tool_repository.user.username
|
||||
changeset_revision = self.get_repository_tip( tool_repository )
|
||||
self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=True, package='bwa', version='0.5.9' )
|
||||
strings_displayed = 'Invalid repository name <b>%s</b> defined.' % name
|
||||
self.upload_file( repository,
|
||||
'tool_dependencies.xml',
|
||||
valid_tools_only=False,
|
||||
strings_displayed = [ 'Invalid repository name <b>%s</b> defined.' % name ]
|
||||
self.upload_file( base_repository,
|
||||
filename='tool_dependencies.xml',
|
||||
filepath=dependency_path,
|
||||
valid_tools_only=False,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded dependency on bwa_tool_0100 with invalid repository name.',
|
||||
strings_displayed=[ strings_displayed ] )
|
||||
strings_displayed=strings_displayed,
|
||||
strings_not_displayed=[] )
|
||||
def test_0025_generate_complex_repository_dependency_invalid_owner_name( self ):
|
||||
'''Generate and upload a complex repository definition that specifies an invalid owner.'''
|
||||
dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex', 'invalid' ] )
|
||||
xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path )
|
||||
repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name )
|
||||
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 )
|
||||
url = self.url
|
||||
name = tool_repository.name
|
||||
@@ -106,30 +122,36 @@ class TestComplexRepositoryDependencies( ShedTwillTestCase ):
|
||||
changeset_revision = self.get_repository_tip( tool_repository )
|
||||
self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=True, package='bwa', version='0.5.9' )
|
||||
strings_displayed = [ 'Invalid owner <b>%s</b> defined' % owner ]
|
||||
self.upload_file( repository,
|
||||
'tool_dependencies.xml',
|
||||
valid_tools_only=False,
|
||||
self.upload_file( base_repository,
|
||||
filename='tool_dependencies.xml',
|
||||
filepath=dependency_path,
|
||||
valid_tools_only=False,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded dependency on bwa_tool_0100 with invalid owner.',
|
||||
strings_displayed=strings_displayed )
|
||||
strings_displayed=strings_displayed,
|
||||
strings_not_displayed=[] )
|
||||
def test_0030_generate_complex_repository_dependency_invalid_changeset_revision( self ):
|
||||
'''Generate and upload a complex repository definition that specifies an invalid changeset revision.'''
|
||||
dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex', 'invalid' ] )
|
||||
xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path )
|
||||
repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name )
|
||||
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 )
|
||||
url = self.url
|
||||
name = tool_repository.name
|
||||
owner = tool_repository.user.username
|
||||
changeset_revision = '1234abcd'
|
||||
self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=True, package='bwa', version='0.5.9' )
|
||||
strings_displayed = 'Invalid changeset revision <b>%s</b> defined.' % changeset_revision
|
||||
self.upload_file( repository,
|
||||
'tool_dependencies.xml',
|
||||
valid_tools_only=False,
|
||||
strings_displayed = [ 'Invalid changeset revision <b>%s</b> defined.' % changeset_revision ]
|
||||
self.upload_file( base_repository,
|
||||
filename='tool_dependencies.xml',
|
||||
filepath=dependency_path,
|
||||
valid_tools_only=False,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded dependency on bwa_tool_0100 with invalid changeset revision.',
|
||||
strings_displayed=[ strings_displayed ] )
|
||||
strings_displayed=strings_displayed,
|
||||
strings_not_displayed=[] )
|
||||
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 )
|
||||
@@ -142,10 +164,14 @@ class TestComplexRepositoryDependencies( ShedTwillTestCase ):
|
||||
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,
|
||||
filename='tool_dependencies.xml',
|
||||
filepath=dependency_path,
|
||||
commit_message='Uploaded valid complex dependency on bwa_tool_0100.' )
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded valid complex dependency on bwa_tool_0100.',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
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_generate_tool_dependency( self ):
|
||||
@@ -160,10 +186,14 @@ class TestComplexRepositoryDependencies( ShedTwillTestCase ):
|
||||
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,
|
||||
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=[],
|
||||
commit_message='Uploaded new tool_dependencies.xml.' )
|
||||
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' ],
|
||||
|
||||
@@ -40,7 +40,15 @@ class TestBasicRepositoryDependencies( ShedTwillTestCase ):
|
||||
owner=common.test_user_1_name,
|
||||
category_id=self.security.encode_id( category.id ),
|
||||
strings_displayed=[] )
|
||||
self.upload_file( repository, 'emboss/datatypes/datatypes_conf.xml', commit_message='Uploaded datatypes_conf.xml.' )
|
||||
self.upload_file( repository,
|
||||
filename='emboss/datatypes/datatypes_conf.xml',
|
||||
filepath=None,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=True,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded datatypes_conf.xml.',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
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 )
|
||||
@@ -54,7 +62,15 @@ class TestBasicRepositoryDependencies( ShedTwillTestCase ):
|
||||
owner=common.test_user_1_name,
|
||||
category_id=self.security.encode_id( category.id ),
|
||||
strings_displayed=[] )
|
||||
self.upload_file( repository, 'emboss/emboss.tar', commit_message='Uploaded emboss_5.tar' )
|
||||
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 tool tarball.',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
def test_0025_generate_repository_dependency_with_invalid_url( self ):
|
||||
'''Generate a repository dependency for emboss 5 with an invalid URL.'''
|
||||
dependency_path = self.generate_temp_path( 'test_0110', additional_paths=[ 'simple' ] )
|
||||
@@ -68,11 +84,14 @@ class TestBasicRepositoryDependencies( ShedTwillTestCase ):
|
||||
self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=False, description='This is invalid.' )
|
||||
strings_displayed = [ 'Invalid tool shed <b>%s</b> defined for repository <b>%s</b>' % ( url, repository.name ) ]
|
||||
self.upload_file( emboss_repository,
|
||||
'repository_dependencies.xml',
|
||||
filename='repository_dependencies.xml',
|
||||
filepath=dependency_path,
|
||||
valid_tools_only=False,
|
||||
filepath=dependency_path,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded dependency on emboss_datatypes_0110 with invalid url.',
|
||||
strings_displayed=strings_displayed )
|
||||
strings_displayed=strings_displayed,
|
||||
strings_not_displayed=[] )
|
||||
def test_0030_generate_repository_dependency_with_invalid_name( self ):
|
||||
'''Generate a repository dependency for emboss 5 with an invalid name.'''
|
||||
dependency_path = self.generate_temp_path( 'test_0110', additional_paths=[ 'simple' ] )
|
||||
@@ -86,11 +105,14 @@ class TestBasicRepositoryDependencies( ShedTwillTestCase ):
|
||||
self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=False, description='This is invalid.' )
|
||||
strings_displayed = [ 'Invalid repository name <b>%s</b> defined.' % name ]
|
||||
self.upload_file( emboss_repository,
|
||||
'repository_dependencies.xml',
|
||||
filename='repository_dependencies.xml',
|
||||
filepath=dependency_path,
|
||||
valid_tools_only=False,
|
||||
filepath=dependency_path,
|
||||
commit_message='Uploaded dependency on emboss_datatypes_0110 with invalid url.',
|
||||
strings_displayed=strings_displayed )
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded dependency on emboss_datatypes_0110 with invalid name.',
|
||||
strings_displayed=strings_displayed,
|
||||
strings_not_displayed=[] )
|
||||
def test_0035_generate_repository_dependency_with_invalid_owner( self ):
|
||||
'''Generate a repository dependency for emboss 5 with an invalid owner.'''
|
||||
dependency_path = self.generate_temp_path( 'test_0110', additional_paths=[ 'simple' ] )
|
||||
@@ -104,11 +126,14 @@ class TestBasicRepositoryDependencies( ShedTwillTestCase ):
|
||||
self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=False, description='This is invalid.' )
|
||||
strings_displayed = [ 'Invalid owner <b>%s</b> defined for repository <b>%s</b>' % ( owner, repository.name ) ]
|
||||
self.upload_file( emboss_repository,
|
||||
'repository_dependencies.xml',
|
||||
filename='repository_dependencies.xml',
|
||||
filepath=dependency_path,
|
||||
valid_tools_only=False,
|
||||
filepath=dependency_path,
|
||||
commit_message='Uploaded dependency on emboss_datatypes_0110 with invalid url.',
|
||||
strings_displayed=strings_displayed )
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded dependency on emboss_datatypes_0110 with invalid owner.',
|
||||
strings_displayed=strings_displayed,
|
||||
strings_not_displayed=[] )
|
||||
def test_0040_generate_repository_dependency_with_invalid_changeset_revision( self ):
|
||||
'''Generate a repository dependency for emboss 5 with an invalid changeset revision.'''
|
||||
dependency_path = self.generate_temp_path( 'test_0110', additional_paths=[ 'simple', 'invalid' ] )
|
||||
@@ -122,8 +147,11 @@ class TestBasicRepositoryDependencies( ShedTwillTestCase ):
|
||||
self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=False, description='This is invalid.' )
|
||||
strings_displayed = [ 'Invalid changeset revision <b>%s</b> defined.' % changeset_revision ]
|
||||
self.upload_file( emboss_repository,
|
||||
'repository_dependencies.xml',
|
||||
filename='repository_dependencies.xml',
|
||||
filepath=dependency_path,
|
||||
valid_tools_only=False,
|
||||
filepath=dependency_path,
|
||||
commit_message='Uploaded dependency on emboss_datatypes_0110 with invalid url.',
|
||||
strings_displayed=strings_displayed )
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded dependency on emboss_datatypes_0110 with invalid changeset revision.',
|
||||
strings_displayed=strings_displayed,
|
||||
strings_not_displayed=[] )
|
||||
|
||||
@@ -23,15 +23,12 @@ class TestResetAllRepositoryMetadata( ShedTwillTestCase ):
|
||||
admin_user = test_db_util.get_user( common.admin_email )
|
||||
assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email
|
||||
admin_user_private_role = test_db_util.get_private_role( admin_user )
|
||||
def test_0005_create_repositories_and_categories( self ):
|
||||
def test_0005_create_filtering_repository( self ):
|
||||
'''Create and populate the filtering_0000 repository.'''
|
||||
self.logout()
|
||||
self.login( email=common.admin_email, username=common.admin_username )
|
||||
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',
|
||||
@@ -40,34 +37,119 @@ class TestResetAllRepositoryMetadata( ShedTwillTestCase ):
|
||||
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" )
|
||||
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=[] )
|
||||
def test_0010_create_freebayes_repository( self ):
|
||||
'''Create and populate the freebayes_0010 repository.'''
|
||||
self.logout()
|
||||
self.login( email=common.admin_email, username=common.admin_username )
|
||||
category_0010 = self.create_category( name='Test 0010 Repository With Tool Dependencies', description='Tests for a repository with tool dependencies.' )
|
||||
self.logout()
|
||||
self.login( email=common.test_user_1_email, username=common.test_user_1_name )
|
||||
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 ),
|
||||
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.' )
|
||||
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=[] )
|
||||
def test_0015_create_emboss_repository( self ):
|
||||
'''Create and populate the emboss_0020 repository.'''
|
||||
self.logout()
|
||||
self.login( email=common.admin_email, username=common.admin_username )
|
||||
category_0020 = self.create_category( name='Test 0020 Basic Repository Dependencies', description='Testing basic repository dependency features.' )
|
||||
self.logout()
|
||||
self.login( email=common.test_user_1_email, username=common.test_user_1_name )
|
||||
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 ),
|
||||
category_id=self.security.encode_id( category_0020.id ),
|
||||
strings_displayed=[] )
|
||||
if self.repository_is_new( repository ):
|
||||
self.upload_file( repository, 'emboss/datatypes/datatypes_conf.xml', commit_message='Uploaded datatypes_conf.xml.' )
|
||||
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, 'emboss/emboss.tar', commit_message='Uploaded emboss_5.tar' )
|
||||
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=[] )
|
||||
def test_0020_create_emboss_datatypes_repository( self ):
|
||||
'''Create and populate the emboss_0030 repository.'''
|
||||
self.logout()
|
||||
self.login( email=common.admin_email, username=common.admin_username )
|
||||
category_0030 = self.create_category( name='Test 0030 Repository Dependency Revisions', description='Testing repository dependencies by revision.' )
|
||||
self.logout()
|
||||
self.login( email=common.test_user_1_email, username=common.test_user_1_name )
|
||||
datatypes_repository = self.get_or_create_repository( name='emboss_datatypes_0030',
|
||||
description=datatypes_repository_description,
|
||||
long_description=datatypes_repository_long_description,
|
||||
@@ -75,55 +157,114 @@ class TestResetAllRepositoryMetadata( ShedTwillTestCase ):
|
||||
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.' )
|
||||
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=[] )
|
||||
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' )
|
||||
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' ] )
|
||||
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',
|
||||
filename='repository_dependencies.xml',
|
||||
filepath=repository_dependencies_path,
|
||||
commit_message='Uploaded repository_dependencies.xml' )
|
||||
valid_tools_only=True,
|
||||
uncompress_file=True,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded repository_dependencies.xml',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
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' )
|
||||
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' ] )
|
||||
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',
|
||||
filename='repository_dependencies.xml',
|
||||
filepath=repository_dependencies_path,
|
||||
commit_message='Uploaded repository_dependencies.xml' )
|
||||
valid_tools_only=True,
|
||||
uncompress_file=True,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded repository_dependencies.xml',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
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' )
|
||||
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' ] )
|
||||
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',
|
||||
filename='repository_dependencies.xml',
|
||||
filepath=repository_dependencies_path,
|
||||
commit_message='Uploaded repository_dependencies.xml' )
|
||||
valid_tools_only=True,
|
||||
uncompress_file=True,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded repository_dependencies.xml',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
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',
|
||||
filename='repository_dependencies.xml',
|
||||
filepath=repository_dependencies_path,
|
||||
commit_message='Uploaded repository_dependencies.xml' )
|
||||
valid_tools_only=True,
|
||||
uncompress_file=True,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded repository_dependencies.xml',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
def test_0025_create_freebayes_repository( self ):
|
||||
'''Create and populate the freebayes_0040 repository.'''
|
||||
self.logout()
|
||||
self.login( email=common.admin_email, username=common.admin_username )
|
||||
category_0040 = self.create_category( name='test_0040_repository_circular_dependencies', description='Testing handling of circular repository dependencies.' )
|
||||
self.logout()
|
||||
self.login( email=common.test_user_1_email, username=common.test_user_1_name )
|
||||
repository = self.get_or_create_repository( name='freebayes_0040',
|
||||
description="Galaxy's freebayes tool",
|
||||
long_description="Long description of Galaxy's freebayes tool",
|
||||
@@ -131,14 +272,30 @@ class TestResetAllRepositoryMetadata( ShedTwillTestCase ):
|
||||
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.' )
|
||||
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, 'filtering/filtering_1.1.0.tar', commit_message='Uploaded filtering.tar.' )
|
||||
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' ] )
|
||||
@@ -146,16 +303,33 @@ class TestResetAllRepositoryMetadata( ShedTwillTestCase ):
|
||||
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',
|
||||
filename='repository_dependencies.xml',
|
||||
filepath=repository_dependencies_path,
|
||||
commit_message='Uploaded dependency on freebayes' )
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded repository_dependencies.xml specifying freebayes',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
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',
|
||||
filename='repository_dependencies.xml',
|
||||
filepath=repository_dependencies_path,
|
||||
commit_message='Uploaded dependency on filtering' )
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded repository_dependencies.xml specifying filtering',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
def test_0030_create_emboss_repository( self ):
|
||||
'''Create and populate the emboss_0050 repository.'''
|
||||
self.logout()
|
||||
self.login( email=common.admin_email, username=common.admin_username )
|
||||
category_0050 = self.create_category( name='test_0050_repository_n_level_circular_dependencies', description='Testing handling of circular repository dependencies to n levels.' )
|
||||
self.logout()
|
||||
self.login( email=common.test_user_1_email, username=common.test_user_1_name )
|
||||
datatypes_repository = self.get_or_create_repository( name='emboss_datatypes_0050',
|
||||
description="Datatypes for emboss",
|
||||
long_description="Long description of Emboss' datatypes",
|
||||
@@ -181,41 +355,100 @@ class TestResetAllRepositoryMetadata( ShedTwillTestCase ):
|
||||
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.' )
|
||||
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' ] )
|
||||
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',
|
||||
filename='repository_dependencies.xml',
|
||||
filepath=repository_dependencies_path,
|
||||
commit_message='Uploaded dependency on emboss_datatypes.' )
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded repository_dependencies.xml',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
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',
|
||||
filename='repository_dependencies.xml',
|
||||
filepath=repository_dependencies_path,
|
||||
commit_message='Uploaded dependency on emboss.' )
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded repository_dependencies.xml',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
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',
|
||||
filename='repository_dependencies.xml',
|
||||
filepath=repository_dependencies_path,
|
||||
commit_message='Uploaded dependency on filtering.' )
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded repository_dependencies.xml',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
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',
|
||||
filename='repository_dependencies.xml',
|
||||
filepath=repository_dependencies_path,
|
||||
commit_message='Uploaded dependency on filtering.' )
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded repository_dependencies.xml',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
def test_0035_create_filtering_repository( self ):
|
||||
'''Create and populate the filtering_0060 repository.'''
|
||||
self.logout()
|
||||
self.login( email=common.admin_email, username=common.admin_username )
|
||||
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 )
|
||||
workflow_repository = self.get_or_create_repository( name='filtering_0060',
|
||||
description="Galaxy's filtering tool",
|
||||
long_description="Long description of Galaxy's filtering tool",
|
||||
@@ -226,16 +459,28 @@ class TestResetAllRepositoryMetadata( ShedTwillTestCase ):
|
||||
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 )
|
||||
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,
|
||||
workflow_filename,
|
||||
filename=workflow_filename,
|
||||
filepath=workflow_filepath,
|
||||
commit_message='Uploaded filtering workflow.' )
|
||||
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,
|
||||
'filtering/filtering_2.2.0.tar',
|
||||
commit_message='Uploaded filtering tool.' )
|
||||
def test_0010_reset_metadata_on_all_repositories( self ):
|
||||
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_0040_reset_metadata_on_all_repositories( self ):
|
||||
'''Reset metadata on all repositories, then verify that it has not changed.'''
|
||||
self.logout()
|
||||
self.login( email=common.admin_email, username=common.admin_username )
|
||||
|
||||
@@ -100,7 +100,15 @@ class TestRepositoryComponentReviews( ShedTwillTestCase ):
|
||||
owner=common.test_user_1_name,
|
||||
category_id=self.security.encode_id( category.id ),
|
||||
strings_displayed=strings_displayed )
|
||||
self.upload_file( repository, 'filtering/filtering_1.1.0.tar', commit_message="Uploaded filtering 1.1.0" )
|
||||
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=[] )
|
||||
def test_0020_review_initial_revision_data_types( self ):
|
||||
'''Review the datatypes component for the current tip revision.'''
|
||||
"""
|
||||
@@ -396,7 +404,15 @@ class TestRepositoryComponentReviews( ShedTwillTestCase ):
|
||||
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 )
|
||||
self.upload_file( repository, 'readme.txt', commit_message="Uploaded readme.txt" )
|
||||
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=[] )
|
||||
def test_0095_review_new_changeset_readme_component( self ):
|
||||
'''Update the filtering repository's readme component review to reflect the presence of the readme file.'''
|
||||
"""
|
||||
@@ -452,10 +468,15 @@ class TestRepositoryComponentReviews( ShedTwillTestCase ):
|
||||
"""
|
||||
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 )
|
||||
self.upload_file( repository,
|
||||
'filtering/filtering_test_data.tar',
|
||||
commit_message="Uploaded test data.",
|
||||
remove_repo_files_not_in_tar='No' )
|
||||
self.upload_file( repository,
|
||||
filename='filtering/filtering_test_data.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=[] )
|
||||
def test_0110_review_new_changeset_functional_tests( self ):
|
||||
'''Update the filtering repository's readme component review to reflect the presence of the readme file.'''
|
||||
"""
|
||||
@@ -509,9 +530,14 @@ class TestRepositoryComponentReviews( ShedTwillTestCase ):
|
||||
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 )
|
||||
self.upload_file( repository,
|
||||
'filtering/filtering_2.2.0.tar',
|
||||
commit_message="Uploaded filtering 2.2.0",
|
||||
remove_repo_files_not_in_tar='No' )
|
||||
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_0125_review_new_changeset_functional_tests( self ):
|
||||
'''Update the filtering repository's review to apply to the new changeset with filtering 2.2.0.'''
|
||||
"""
|
||||
|
||||
@@ -32,10 +32,42 @@ class BasicToolShedFeatures( ShedTwillTestCase ):
|
||||
owner=common.test_user_1_name,
|
||||
category_id=self.security.encode_id( category.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_0000.txt', commit_message="Uploaded readme for 1.1.0", remove_repo_files_not_in_tar='No' )
|
||||
self.upload_file( repository, 'filtering/filtering_2.2.0.tar', commit_message="Uploaded filtering 2.2.0", remove_repo_files_not_in_tar='No' )
|
||||
self.upload_file( repository, 'readme.txt', commit_message="Uploaded readme for 2.2.0", remove_repo_files_not_in_tar='No' )
|
||||
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_0000.txt',
|
||||
filepath=None,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded readme for 1.1.0',
|
||||
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=[] )
|
||||
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 for 2.2.0',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
def test_0010_browse_tool_sheds( self ):
|
||||
"""Browse the available tool sheds in this Galaxy instance."""
|
||||
self.galaxy_logout()
|
||||
|
||||
@@ -38,34 +38,59 @@ class ToolWithToolDependencies( ShedTwillTestCase ):
|
||||
category_id=self.security.encode_id( category.id ) )
|
||||
if self.repository_is_new( repository ):
|
||||
self.upload_file( repository,
|
||||
'freebayes/freebayes.xml',
|
||||
valid_tools_only=False,
|
||||
commit_message="Uploaded freebayes.xml." )
|
||||
self.upload_file( repository,
|
||||
'freebayes/tool_data_table_conf.xml.sample',
|
||||
filename='freebayes/freebayes.xml',
|
||||
filepath=None,
|
||||
valid_tools_only=False,
|
||||
commit_message="Uploaded tool_data_table_conf.xml.",
|
||||
remove_repo_files_not_in_tar='No' )
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded the tool xml.',
|
||||
strings_displayed=[ 'Metadata may have been defined', 'This file requires an entry', 'tool_data_table_conf' ],
|
||||
strings_not_displayed=[] )
|
||||
self.upload_file( repository,
|
||||
'freebayes/sam_fa_indices.loc.sample',
|
||||
commit_message="Uploaded sam_fa_indices.loc.sample.",
|
||||
filename='freebayes/tool_data_table_conf.xml.sample',
|
||||
filepath=None,
|
||||
valid_tools_only=False,
|
||||
remove_repo_files_not_in_tar='No' )
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded the tool data table sample file.',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
self.upload_file( repository,
|
||||
'freebayes/invalid_tool_dependencies/tool_dependencies.xml',
|
||||
valid_tools_only=False,
|
||||
commit_message="Uploaded invalid_tool_dependencies/tool_dependencies.xml.",
|
||||
remove_repo_files_not_in_tar='No' )
|
||||
filename='freebayes/sam_fa_indices.loc.sample',
|
||||
filepath=None,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded tool data table .loc file.',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
self.upload_file( repository,
|
||||
os.path.join( 'freebayes', 'malformed_tool_dependencies', 'tool_dependencies.xml' ),
|
||||
filename=os.path.join( 'freebayes', 'malformed_tool_dependencies', 'tool_dependencies.xml' ),
|
||||
filepath=None,
|
||||
valid_tools_only=False,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded malformed tool dependency XML.',
|
||||
strings_displayed=[ 'Exception attempting to parse tool_dependencies.xml', 'not well-formed' ],
|
||||
commit_message='Uploaded malformed tool dependency XML.' )
|
||||
strings_not_displayed=[] )
|
||||
self.upload_file( repository,
|
||||
'freebayes/tool_dependencies.xml',
|
||||
filename=os.path.join( 'freebayes', 'invalid_tool_dependencies', 'tool_dependencies.xml' ),
|
||||
filepath=None,
|
||||
valid_tools_only=False,
|
||||
commit_message="Uploaded tool_dependencies.xml",
|
||||
remove_repo_files_not_in_tar='No' )
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded invalid tool dependency XML.',
|
||||
strings_displayed=[ 'Name, version and type from a tool requirement tag does not match' ],
|
||||
strings_not_displayed=[] )
|
||||
self.upload_file( repository,
|
||||
filename=os.path.join( 'freebayes', 'tool_dependencies.xml' ),
|
||||
filepath=None,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded valid tool dependency XML.',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
def test_0010_browse_tool_shed( self ):
|
||||
"""Browse the available tool sheds in this Galaxy instance and preview the freebayes tool."""
|
||||
self.galaxy_logout()
|
||||
|
||||
+26
-5
@@ -44,21 +44,42 @@ class ToolWithRepositoryDependencies( ShedTwillTestCase ):
|
||||
category_id=self.security.encode_id( category.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.' )
|
||||
self.upload_file( datatypes_repository,
|
||||
filename='emboss/datatypes/datatypes_conf.xml',
|
||||
filepath=None,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded datatypes_conf.xml.',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
emboss_repository = self.get_or_create_repository( name=emboss_repository_name,
|
||||
description=emboss_repository_description,
|
||||
long_description=emboss_repository_long_description,
|
||||
owner=common.test_user_1_name,
|
||||
category_id=self.security.encode_id( category.id ),
|
||||
strings_displayed=[] )
|
||||
self.upload_file( emboss_repository, 'emboss/emboss.tar', commit_message='Uploaded emboss_5.tar' )
|
||||
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_1020', 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_repository,
|
||||
'repository_dependencies.xml',
|
||||
filepath=repository_dependencies_path,
|
||||
commit_message='Uploaded repository_dependencies.xml' )
|
||||
filename='repository_dependencies.xml',
|
||||
filepath=repository_dependencies_path,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded repository_dependencies.xml.',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
repository_datatypes_count = int( self.get_repository_datatypes_count( datatypes_repository ) )
|
||||
def test_0010_browse_tool_shed( self ):
|
||||
"""Browse the available tool sheds in this Galaxy instance and preview the emboss tool."""
|
||||
|
||||
+68
-16
@@ -49,55 +49,107 @@ class RepositoryWithDependencyRevisions( ShedTwillTestCase ):
|
||||
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.' )
|
||||
self.upload_file( datatypes_repository,
|
||||
filename='emboss/datatypes/datatypes_conf.xml',
|
||||
filepath=None,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded datatypes_conf.xml.',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
emboss_5_repository = self.get_or_create_repository( name=emboss_5_repository_name,
|
||||
description=emboss_repository_description,
|
||||
long_description=emboss_repository_long_description,
|
||||
owner=common.test_user_1_name,
|
||||
category_id=self.security.encode_id( category.id ),
|
||||
strings_displayed=[] )
|
||||
self.upload_file( emboss_5_repository, 'emboss/emboss.tar', commit_message='Uploaded emboss.tar' )
|
||||
self.upload_file( emboss_5_repository,
|
||||
filename='emboss/emboss.tar',
|
||||
filepath=None,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded tool tarball.',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
repository_dependencies_path = self.generate_temp_path( 'test_1030', 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' )
|
||||
filename='repository_dependencies.xml',
|
||||
filepath=repository_dependencies_path,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded repository_dependencies.xml.',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
emboss_6_repository = self.get_or_create_repository( name=emboss_6_repository_name,
|
||||
description=emboss_repository_description,
|
||||
long_description=emboss_repository_long_description,
|
||||
owner=common.test_user_1_name,
|
||||
category_id=self.security.encode_id( category.id ),
|
||||
strings_displayed=[] )
|
||||
self.upload_file( emboss_6_repository, 'emboss/emboss.tar', commit_message='Uploaded emboss.tar' )
|
||||
self.upload_file( emboss_6_repository,
|
||||
filename='emboss/emboss.tar',
|
||||
filepath=None,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded tool tarball.',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
repository_dependencies_path = self.generate_temp_path( 'test_1030', 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' )
|
||||
filename='repository_dependencies.xml',
|
||||
filepath=repository_dependencies_path,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded repository_dependencies.xml.',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
emboss_repository = self.get_or_create_repository( name=emboss_repository_name,
|
||||
description=emboss_repository_description,
|
||||
long_description=emboss_repository_long_description,
|
||||
owner=common.test_user_1_name,
|
||||
category_id=self.security.encode_id( category.id ),
|
||||
strings_displayed=[] )
|
||||
self.upload_file( emboss_repository, 'emboss/emboss.tar', commit_message='Uploaded emboss.tar' )
|
||||
self.upload_file( emboss_repository,
|
||||
filename='emboss/emboss.tar',
|
||||
filepath=None,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded tool tarball.',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
repository_dependencies_path = self.generate_temp_path( 'test_1030', 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' )
|
||||
filename='repository_dependencies.xml',
|
||||
filepath=repository_dependencies_path,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded repository_dependencies.xml.',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
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' )
|
||||
filename='repository_dependencies.xml',
|
||||
filepath=repository_dependencies_path,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded repository_dependencies.xml.',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
repository_datatypes_count = int( self.get_repository_datatypes_count( datatypes_repository ) )
|
||||
def test_0010_browse_tool_shed( self ):
|
||||
"""Browse the available tool sheds in this Galaxy instance and preview the emboss tool."""
|
||||
|
||||
+28
-8
@@ -42,9 +42,14 @@ class TestInstallingCircularDependencies( ShedTwillTestCase ):
|
||||
if self.repository_is_new( repository ):
|
||||
running_standalone = True
|
||||
self.upload_file( repository,
|
||||
'freebayes/freebayes.tar',
|
||||
filename='freebayes/freebayes.tar',
|
||||
filepath=None,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=True,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded the tool tarball.',
|
||||
strings_displayed=[],
|
||||
commit_message='Uploaded freebayes.tar.' )
|
||||
strings_not_displayed=[] )
|
||||
def test_0015_create_filtering_repository( self ):
|
||||
'''Create and populate filtering_0040.'''
|
||||
global running_standalone
|
||||
@@ -60,9 +65,14 @@ class TestInstallingCircularDependencies( ShedTwillTestCase ):
|
||||
if self.repository_is_new( repository ):
|
||||
running_standalone = True
|
||||
self.upload_file( repository,
|
||||
'filtering/filtering_1.1.0.tar',
|
||||
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 the tool tarball for filtering 1.1.0.',
|
||||
strings_displayed=[],
|
||||
commit_message='Uploaded filtering.tar.' )
|
||||
strings_not_displayed=[] )
|
||||
def test_0020_create_repository_dependencies( self ):
|
||||
'''Set up the filtering and freebayes repository dependencies.'''
|
||||
# The dependency structure should look like:
|
||||
@@ -78,9 +88,14 @@ class TestInstallingCircularDependencies( ShedTwillTestCase ):
|
||||
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',
|
||||
filename='repository_dependencies.xml',
|
||||
filepath=repository_dependencies_path,
|
||||
commit_message='Uploaded dependency on freebayes' )
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded dependency on freebayes.',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
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' ] )
|
||||
@@ -88,9 +103,14 @@ class TestInstallingCircularDependencies( ShedTwillTestCase ):
|
||||
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',
|
||||
filename='repository_dependencies.xml',
|
||||
filepath=repository_dependencies_path,
|
||||
commit_message='Uploaded dependency on filtering' )
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded dependency on filtering.',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
def test_0025_install_freebayes_repository( self ):
|
||||
'''Install freebayes with blank tool panel section, without tool dependencies but with repository dependencies.'''
|
||||
self.galaxy_logout()
|
||||
|
||||
@@ -63,9 +63,14 @@ class TestInstallRepositoryCircularDependencies( ShedTwillTestCase ):
|
||||
if self.repository_is_new( repository ):
|
||||
running_standalone = True
|
||||
self.upload_file( repository,
|
||||
'convert_chars/convert_chars.tar',
|
||||
filename='convert_chars/convert_chars.tar',
|
||||
filepath=None,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=True,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded convert_chars tarball.',
|
||||
strings_displayed=[],
|
||||
commit_message='Uploaded convert_chars.tar.' )
|
||||
strings_not_displayed=[] )
|
||||
def test_0010_create_column_repository( self ):
|
||||
'''Create and populate convert_chars_0050.'''
|
||||
category = self.create_category( name=category_name, description=category_description )
|
||||
@@ -77,9 +82,14 @@ class TestInstallRepositoryCircularDependencies( ShedTwillTestCase ):
|
||||
strings_displayed=[] )
|
||||
if self.repository_is_new( repository ):
|
||||
self.upload_file( repository,
|
||||
'column_maker/column_maker.tar',
|
||||
filename='column_maker/column_maker.tar',
|
||||
filepath=None,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=True,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded column_maker tarball.',
|
||||
strings_displayed=[],
|
||||
commit_message='Uploaded column_maker.tar.' )
|
||||
strings_not_displayed=[] )
|
||||
def test_0015_create_emboss_datatypes_repository( self ):
|
||||
'''Create and populate emboss_datatypes_0050.'''
|
||||
category = self.create_category( name=category_name, description=category_description )
|
||||
@@ -91,9 +101,14 @@ class TestInstallRepositoryCircularDependencies( ShedTwillTestCase ):
|
||||
strings_displayed=[] )
|
||||
if self.repository_is_new( repository ):
|
||||
self.upload_file( repository,
|
||||
'emboss/datatypes/datatypes_conf.xml',
|
||||
filename='emboss/datatypes/datatypes_conf.xml',
|
||||
filepath=None,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded datatypes_conf.xml.',
|
||||
strings_displayed=[],
|
||||
commit_message='Uploaded datatypes_conf.xml.' )
|
||||
strings_not_displayed=[] )
|
||||
def test_0020_create_emboss_repository( self ):
|
||||
'''Create and populate emboss_0050.'''
|
||||
category = self.create_category( name=category_name, description=category_description )
|
||||
@@ -105,9 +120,14 @@ class TestInstallRepositoryCircularDependencies( ShedTwillTestCase ):
|
||||
strings_displayed=[] )
|
||||
if self.repository_is_new( repository ):
|
||||
self.upload_file( repository,
|
||||
'emboss/emboss.tar',
|
||||
filename='emboss/emboss.tar',
|
||||
filepath=None,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=True,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded emboss tarball.',
|
||||
strings_displayed=[],
|
||||
commit_message='Uploaded tool tarball.' )
|
||||
strings_not_displayed=[] )
|
||||
def test_0025_create_filtering_repository( self ):
|
||||
'''Create and populate filtering_0050.'''
|
||||
category = self.create_category( name=category_name, description=category_description )
|
||||
@@ -119,9 +139,14 @@ class TestInstallRepositoryCircularDependencies( ShedTwillTestCase ):
|
||||
strings_displayed=[] )
|
||||
if self.repository_is_new( repository ):
|
||||
self.upload_file( repository,
|
||||
'filtering/filtering_1.1.0.tar',
|
||||
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=[],
|
||||
commit_message='Uploaded filtering.tar.' )
|
||||
strings_not_displayed=[] )
|
||||
def test_0030_create_freebayes_repository( self ):
|
||||
'''Create and populate freebayes_0050.'''
|
||||
category = self.create_category( name=category_name, description=category_description )
|
||||
@@ -133,9 +158,14 @@ class TestInstallRepositoryCircularDependencies( ShedTwillTestCase ):
|
||||
strings_displayed=[] )
|
||||
if self.repository_is_new( repository ):
|
||||
self.upload_file( repository,
|
||||
'freebayes/freebayes.tar',
|
||||
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=[],
|
||||
commit_message='Uploaded freebayes.tar.' )
|
||||
strings_not_displayed=[] )
|
||||
def test_0035_create_bismark_repository( self ):
|
||||
'''Create and populate bismark_0050.'''
|
||||
category = self.create_category( name=category_name, description=category_description )
|
||||
@@ -147,10 +177,14 @@ class TestInstallRepositoryCircularDependencies( ShedTwillTestCase ):
|
||||
strings_displayed=[] )
|
||||
if self.repository_is_new( repository ):
|
||||
self.upload_file( repository,
|
||||
'bismark/bismark.tar',
|
||||
strings_displayed=[],
|
||||
filename='bismark/bismark.tar',
|
||||
filepath=None,
|
||||
valid_tools_only=False,
|
||||
commit_message='Uploaded bismark.tar.' )
|
||||
uncompress_file=True,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded bismark tarball.',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
def test_0040_create_and_upload_dependency_definitions( self ):
|
||||
'''Set up the dependency structure.'''
|
||||
global running_standalone
|
||||
|
||||
@@ -1,11 +1,14 @@
|
||||
from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os
|
||||
import tool_shed.base.test_db_util as test_db_util
|
||||
|
||||
import logging
|
||||
log = logging.getLogger(__name__)
|
||||
repository_name = 'filtering_0060'
|
||||
repository_description="Galaxy's filtering tool for test 0060",
|
||||
repository_long_description="Long description of Galaxy's filtering tool for test 0060",
|
||||
repository_description="Galaxy's filtering tool for test 0060"
|
||||
repository_long_description="Long description of Galaxy's filtering tool for test 0060"
|
||||
workflow_filename = 'Workflow_for_0060_filter_workflow_repository.ga'
|
||||
workflow_name = 'Workflow for 0060_filter_workflow_repository'
|
||||
category_name = 'Test 0060 Workflow Features'
|
||||
category_description = 'Test 0060 for workflow features'
|
||||
|
||||
class ToolWithRepositoryDependencies( ShedTwillTestCase ):
|
||||
'''Test installing a repository with repository dependencies.'''
|
||||
@@ -28,7 +31,7 @@ class ToolWithRepositoryDependencies( ShedTwillTestCase ):
|
||||
admin_user_private_role = test_db_util.get_private_role( admin_user )
|
||||
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' )
|
||||
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,
|
||||
@@ -41,16 +44,27 @@ class ToolWithRepositoryDependencies( ShedTwillTestCase ):
|
||||
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 )
|
||||
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,
|
||||
filename=workflow_filename,
|
||||
filepath=workflow_filepath,
|
||||
commit_message='Uploaded filtering workflow.' )
|
||||
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( repository,
|
||||
'filtering/filtering_2.2.0.tar',
|
||||
commit_message="Uploaded filtering 2.2.0",
|
||||
remove_repo_files_not_in_tar='No' )
|
||||
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.',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
def test_0010_install_repository_with_workflow( self ):
|
||||
"""Browse the available tool sheds in this Galaxy instance and preview the filtering tool."""
|
||||
self.preview_repository_in_tool_shed( repository_name,
|
||||
|
||||
@@ -5,6 +5,7 @@ repository_name = 'bismark_0070'
|
||||
repository_description = "Galaxy's bismark wrapper"
|
||||
repository_long_description = "Long description of Galaxy's bismark wrapper"
|
||||
category_name = 'Test 0070 Invalid Tool Revisions'
|
||||
category_description = 'Test 1070 for a repository with an invalid tool.'
|
||||
|
||||
class TestFreebayesRepository( ShedTwillTestCase ):
|
||||
'''Test repository with multiple revisions with invalid tools.'''
|
||||
@@ -27,8 +28,7 @@ class TestFreebayesRepository( ShedTwillTestCase ):
|
||||
admin_user_private_role = test_db_util.get_private_role( admin_user )
|
||||
def test_0005_ensure_existence_of_repository_and_category( self ):
|
||||
'''Create freebayes repository and upload only freebayes.xml. This should result in an error message and invalid tool.'''
|
||||
self.create_category( name=category_name,
|
||||
description='Test 1070 for a repository with an invalid tool.' )
|
||||
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 )
|
||||
category = test_db_util.get_category_by_name( category_name )
|
||||
@@ -40,16 +40,23 @@ class TestFreebayesRepository( ShedTwillTestCase ):
|
||||
strings_displayed=[] )
|
||||
if self.repository_is_new( repository ):
|
||||
self.upload_file( repository,
|
||||
'bismark/bismark.tar',
|
||||
filename='bismark/bismark.tar',
|
||||
filepath=None,
|
||||
valid_tools_only=False,
|
||||
strings_displayed=[],
|
||||
commit_message='Uploaded the tool tarball.' )
|
||||
uncompress_file=True,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded bismark tarball.',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
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.' )
|
||||
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=[] )
|
||||
def test_0010_browse_tool_shed( self ):
|
||||
"""Browse the available tool sheds in this Galaxy instance and preview the bismark repository."""
|
||||
self.galaxy_logout()
|
||||
|
||||
@@ -49,9 +49,14 @@ class TestRepositoryDependencies( ShedTwillTestCase ):
|
||||
strings_displayed=[] )
|
||||
if self.repository_is_new( repository ):
|
||||
self.upload_file( repository,
|
||||
'column_maker/column_maker.tar',
|
||||
filename='column_maker/column_maker.tar',
|
||||
filepath=None,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=True,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded column_maker tarball.',
|
||||
strings_displayed=[],
|
||||
commit_message='Uploaded column_maker.tar.' )
|
||||
strings_not_displayed=[] )
|
||||
running_standalone = True
|
||||
def test_0010_create_and_populate_convert_repository( self ):
|
||||
'''Create and populate the convert_chars repository.'''
|
||||
@@ -69,9 +74,14 @@ class TestRepositoryDependencies( ShedTwillTestCase ):
|
||||
strings_displayed=[] )
|
||||
if self.repository_is_new( repository ):
|
||||
self.upload_file( repository,
|
||||
'convert_chars/convert_chars.tar',
|
||||
filename='convert_chars/convert_chars.tar',
|
||||
filepath=None,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=True,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded convert_chars tarball.',
|
||||
strings_displayed=[],
|
||||
commit_message='Uploaded convert_chars.tar.' )
|
||||
strings_not_displayed=[] )
|
||||
running_standalone = True
|
||||
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.'''
|
||||
@@ -84,9 +94,14 @@ class TestRepositoryDependencies( ShedTwillTestCase ):
|
||||
self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ),
|
||||
dependency_description='Column maker depends on the convert repository.' )
|
||||
self.upload_file( column_repository,
|
||||
'repository_dependencies.xml',
|
||||
filepath=repository_dependencies_path,
|
||||
commit_message='Uploaded dependency on convert' )
|
||||
filename='repository_dependencies.xml',
|
||||
filepath=repository_dependencies_path,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=True,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded dependency on convert_chars.',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
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' ] )
|
||||
@@ -94,9 +109,14 @@ class TestRepositoryDependencies( ShedTwillTestCase ):
|
||||
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' )
|
||||
filename='repository_dependencies.xml',
|
||||
filepath=repository_dependencies_path,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=True,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded dependency on column_maker.',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
def test_0020_install_convert_repository( self ):
|
||||
'''Install convert_chars without repository dependencies into convert_chars tool panel section.'''
|
||||
self.galaxy_logout()
|
||||
|
||||
@@ -46,9 +46,14 @@ class TestRepositoryDependencies( ShedTwillTestCase ):
|
||||
strings_displayed=[] )
|
||||
if self.repository_is_new( repository ):
|
||||
self.upload_file( repository,
|
||||
'column_maker/column_maker.tar',
|
||||
filename='column_maker/column_maker.tar',
|
||||
filepath=None,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=True,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded column_maker tarball.',
|
||||
strings_displayed=[],
|
||||
commit_message='Uploaded column_maker.tar.' )
|
||||
strings_not_displayed=[] )
|
||||
def test_0010_create_and_populate_convert_repository( self ):
|
||||
self.logout()
|
||||
self.login( email=common.admin_email, username=common.admin_username )
|
||||
@@ -63,9 +68,14 @@ class TestRepositoryDependencies( ShedTwillTestCase ):
|
||||
strings_displayed=[] )
|
||||
if self.repository_is_new( repository ):
|
||||
self.upload_file( repository,
|
||||
'convert_chars/convert_chars.tar',
|
||||
filename='convert_chars/convert_chars.tar',
|
||||
filepath=None,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=True,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded convert_chars tarball.',
|
||||
strings_displayed=[],
|
||||
commit_message='Uploaded convert_chars.tar.' )
|
||||
strings_not_displayed=[] )
|
||||
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 )
|
||||
@@ -74,9 +84,14 @@ class TestRepositoryDependencies( ShedTwillTestCase ):
|
||||
self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ),
|
||||
dependency_description='Column maker depends on the convert_chars repository.' )
|
||||
self.upload_file( column_repository,
|
||||
'repository_dependencies.xml',
|
||||
filepath=repository_dependencies_path,
|
||||
commit_message='Uploaded dependency on convert' )
|
||||
filename='repository_dependencies.xml',
|
||||
filepath=repository_dependencies_path,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=True,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded dependency on convert_chars.',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
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=[ 'convert' ] )
|
||||
@@ -84,9 +99,14 @@ class TestRepositoryDependencies( ShedTwillTestCase ):
|
||||
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' )
|
||||
filename='repository_dependencies.xml',
|
||||
filepath=repository_dependencies_path,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=True,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded dependency on column_maker.',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
def test_0020_install_repositories( self ):
|
||||
'''Install column_maker into column_maker tool panel section and install repository dependencies.'''
|
||||
self.galaxy_logout()
|
||||
|
||||
@@ -44,9 +44,14 @@ class TestRepositoryDependencies( ShedTwillTestCase ):
|
||||
strings_displayed=[] )
|
||||
if self.repository_is_new( repository ):
|
||||
self.upload_file( repository,
|
||||
'column_maker/column_maker.tar',
|
||||
filename='column_maker/column_maker.tar',
|
||||
filepath=None,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=True,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded column_maker tarball.',
|
||||
strings_displayed=[],
|
||||
commit_message='Uploaded column_maker.tar.' )
|
||||
strings_not_displayed=[] )
|
||||
def test_0010_create_and_populate_convert_repository( self ):
|
||||
'''Create and populate the convert_chars repository.'''
|
||||
self.logout()
|
||||
@@ -62,9 +67,14 @@ class TestRepositoryDependencies( ShedTwillTestCase ):
|
||||
strings_displayed=[] )
|
||||
if self.repository_is_new( repository ):
|
||||
self.upload_file( repository,
|
||||
'convert_chars/convert_chars.tar',
|
||||
filename='convert_chars/convert_chars.tar',
|
||||
filepath=None,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=True,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded convert_chars tarball.',
|
||||
strings_displayed=[],
|
||||
commit_message='Uploaded convert_chars.tar.' )
|
||||
strings_not_displayed=[] )
|
||||
def test_0015_install_and_uninstall_column_repository( self ):
|
||||
'''Install and uninstall the column_maker repository.'''
|
||||
self.galaxy_logout()
|
||||
|
||||
@@ -59,9 +59,14 @@ class TestToolSearchAndInstall( ShedTwillTestCase ):
|
||||
if self.repository_is_new( repository ):
|
||||
running_standalone = True
|
||||
self.upload_file( repository,
|
||||
'bwa/bwa_base.tar',
|
||||
filename='bwa/bwa_base.tar',
|
||||
filepath=None,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=True,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded BWA tarball.',
|
||||
strings_displayed=[],
|
||||
commit_message='Uploaded bwa_base.tar.' )
|
||||
strings_not_displayed=[] )
|
||||
def test_0010_create_bwa_color_repository( self ):
|
||||
'''Create and populate bwa_color_0090.'''
|
||||
category = self.create_category( name=category_name, description=category_description )
|
||||
@@ -75,9 +80,14 @@ class TestToolSearchAndInstall( ShedTwillTestCase ):
|
||||
if self.repository_is_new( repository ):
|
||||
running_standalone = True
|
||||
self.upload_file( repository,
|
||||
'bwa/bwa_color.tar',
|
||||
filename='bwa/bwa_color.tar',
|
||||
filepath=None,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=True,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded BWA color tarball.',
|
||||
strings_displayed=[],
|
||||
commit_message='Uploaded bwa_color.tar.' )
|
||||
strings_not_displayed=[] )
|
||||
def test_0015_create_emboss_datatypes_repository( self ):
|
||||
'''Create and populate emboss_datatypes_0090.'''
|
||||
category = self.create_category( name=category_name, description=category_description )
|
||||
@@ -91,9 +101,14 @@ class TestToolSearchAndInstall( ShedTwillTestCase ):
|
||||
if self.repository_is_new( repository ):
|
||||
running_standalone = True
|
||||
self.upload_file( repository,
|
||||
'emboss/datatypes/datatypes_conf.xml',
|
||||
filename='emboss/datatypes/datatypes_conf.xml',
|
||||
filepath=None,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded datatypes_conf.xml.',
|
||||
strings_displayed=[],
|
||||
commit_message='Uploaded datatypes_conf.xml.' )
|
||||
strings_not_displayed=[] )
|
||||
def test_0020_create_emboss_repository( self ):
|
||||
'''Create and populate emboss_0090.'''
|
||||
category = self.create_category( name=category_name, description=category_description )
|
||||
@@ -107,9 +122,14 @@ class TestToolSearchAndInstall( ShedTwillTestCase ):
|
||||
if self.repository_is_new( repository ):
|
||||
running_standalone = True
|
||||
self.upload_file( repository,
|
||||
'emboss/emboss.tar',
|
||||
filename='emboss/emboss.tar',
|
||||
filepath=None,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded emboss tarball.',
|
||||
strings_displayed=[],
|
||||
commit_message='Uploaded tool tarball.' )
|
||||
strings_not_displayed=[] )
|
||||
def test_0025_create_filtering_repository( self ):
|
||||
'''Create and populate filtering_0090.'''
|
||||
category = self.create_category( name=category_name, description=category_description )
|
||||
@@ -123,9 +143,14 @@ class TestToolSearchAndInstall( ShedTwillTestCase ):
|
||||
if self.repository_is_new( repository ):
|
||||
running_standalone = True
|
||||
self.upload_file( repository,
|
||||
'filtering/filtering_1.1.0.tar',
|
||||
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=[],
|
||||
commit_message='Uploaded filtering.tar.' )
|
||||
strings_not_displayed=[] )
|
||||
def test_0030_create_freebayes_repository( self ):
|
||||
'''Create and populate freebayes_0090.'''
|
||||
category = self.create_category( name=category_name, description=category_description )
|
||||
@@ -139,9 +164,14 @@ class TestToolSearchAndInstall( ShedTwillTestCase ):
|
||||
if self.repository_is_new( repository ):
|
||||
running_standalone = True
|
||||
self.upload_file( repository,
|
||||
'freebayes/freebayes.tar',
|
||||
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=[],
|
||||
commit_message='Uploaded freebayes.tar.' )
|
||||
strings_not_displayed=[] )
|
||||
def test_0035_create_and_upload_dependency_definitions( self ):
|
||||
'''Create and upload repository dependency definitions.'''
|
||||
global running_standalone
|
||||
|
||||
+60
-31
@@ -47,10 +47,14 @@ class TestInstallingComplexRepositoryDependencies( ShedTwillTestCase ):
|
||||
file( xml_filename, 'w' ).write( file( old_tool_dependency, 'r' )
|
||||
.read().replace( '__PATH__', self.get_filename( 'bwa/complex' ) ) )
|
||||
self.upload_file( repository,
|
||||
xml_filename,
|
||||
filepath=new_tool_dependency_path,
|
||||
strings_displayed=[],
|
||||
commit_message='Uploaded tool_dependencies.xml.' )
|
||||
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 tool_dependencies.xml.',
|
||||
strings_displayed=[ 'Name, version and type from a tool requirement tag does not match' ],
|
||||
strings_not_displayed=[] )
|
||||
self.display_manage_repository_page( repository, strings_displayed=[ 'Tool dependencies', 'may not be', 'in this repository' ] )
|
||||
def test_0010_create_bwa_base_repository( self ):
|
||||
'''Create and populate bwa_base_0100.'''
|
||||
@@ -67,9 +71,14 @@ class TestInstallingComplexRepositoryDependencies( ShedTwillTestCase ):
|
||||
strings_displayed=[] )
|
||||
tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name )
|
||||
self.upload_file( repository,
|
||||
'bwa/complex/bwa_base.tar',
|
||||
filename='bwa/complex/bwa_base.tar',
|
||||
filepath=None,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=True,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded bwa_base.tar with tool wrapper XML, but without tool dependency XML.',
|
||||
strings_displayed=[],
|
||||
commit_message='Uploaded bwa_base.tar with tool wrapper XML, but without tool dependency XML.' )
|
||||
strings_not_displayed=[] )
|
||||
def test_0015_generate_complex_repository_dependency_invalid_shed_url( self ):
|
||||
'''Generate and upload a complex repository definition that specifies an invalid tool shed URL.'''
|
||||
global running_standalone
|
||||
@@ -85,38 +94,44 @@ class TestInstallingComplexRepositoryDependencies( ShedTwillTestCase ):
|
||||
self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=True, package='bwa', version='0.5.9' )
|
||||
strings_displayed = [ 'Invalid tool shed <b>%s</b> defined' % url ]
|
||||
self.upload_file( repository,
|
||||
'tool_dependencies.xml',
|
||||
valid_tools_only=False,
|
||||
filename='tool_dependencies.xml',
|
||||
filepath=dependency_path,
|
||||
valid_tools_only=False,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded dependency on bwa_tool_0100 with invalid url.',
|
||||
strings_displayed=strings_displayed )
|
||||
strings_displayed=strings_displayed,
|
||||
strings_not_displayed=[] )
|
||||
def test_0020_generate_complex_repository_dependency_invalid_repository_name( self ):
|
||||
'''Generate and upload a complex repository definition that specifies an invalid repository name.'''
|
||||
global running_standalone
|
||||
if running_standalone:
|
||||
dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex', 'shed' ] )
|
||||
xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path )
|
||||
repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name )
|
||||
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 )
|
||||
url = self.url
|
||||
name = 'invalid_repository!?'
|
||||
owner = tool_repository.user.username
|
||||
changeset_revision = self.get_repository_tip( tool_repository )
|
||||
self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=True, package='bwa', version='0.5.9' )
|
||||
strings_displayed = 'Invalid repository name <b>%s</b> defined.' % name
|
||||
self.upload_file( repository,
|
||||
'tool_dependencies.xml',
|
||||
valid_tools_only=False,
|
||||
strings_displayed = [ 'Invalid repository name <b>%s</b> defined.' % name ]
|
||||
self.upload_file( base_repository,
|
||||
filename='tool_dependencies.xml',
|
||||
filepath=dependency_path,
|
||||
valid_tools_only=False,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded dependency on bwa_tool_0100 with invalid repository name.',
|
||||
strings_displayed=[ strings_displayed ] )
|
||||
strings_displayed=strings_displayed,
|
||||
strings_not_displayed=[] )
|
||||
def test_0025_generate_complex_repository_dependency_invalid_owner_name( self ):
|
||||
'''Generate and upload a complex repository definition that specifies an invalid owner.'''
|
||||
global running_standalone
|
||||
if running_standalone:
|
||||
dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex', 'shed' ] )
|
||||
xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path )
|
||||
repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name )
|
||||
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 )
|
||||
url = self.url
|
||||
name = tool_repository.name
|
||||
@@ -124,32 +139,38 @@ class TestInstallingComplexRepositoryDependencies( ShedTwillTestCase ):
|
||||
changeset_revision = self.get_repository_tip( tool_repository )
|
||||
self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=True, package='bwa', version='0.5.9' )
|
||||
strings_displayed = [ 'Invalid owner <b>%s</b> defined' % owner ]
|
||||
self.upload_file( repository,
|
||||
'tool_dependencies.xml',
|
||||
valid_tools_only=False,
|
||||
self.upload_file( base_repository,
|
||||
filename='tool_dependencies.xml',
|
||||
filepath=dependency_path,
|
||||
valid_tools_only=False,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded dependency on bwa_tool_0100 with invalid owner.',
|
||||
strings_displayed=strings_displayed )
|
||||
strings_displayed=strings_displayed,
|
||||
strings_not_displayed=[] )
|
||||
def test_0030_generate_complex_repository_dependency_invalid_changeset_revision( self ):
|
||||
'''Generate and upload a complex repository definition that specifies an invalid changeset revision.'''
|
||||
global running_standalone
|
||||
if running_standalone:
|
||||
dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex', 'shed' ] )
|
||||
xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path )
|
||||
repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name )
|
||||
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 )
|
||||
url = self.url
|
||||
name = tool_repository.name
|
||||
owner = tool_repository.user.username
|
||||
changeset_revision = '1234abcd'
|
||||
self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=True, package='bwa', version='0.5.9' )
|
||||
strings_displayed = 'Invalid changeset revision <b>%s</b> defined.' % changeset_revision
|
||||
self.upload_file( repository,
|
||||
'tool_dependencies.xml',
|
||||
valid_tools_only=False,
|
||||
strings_displayed = [ 'Invalid changeset revision <b>%s</b> defined.' % changeset_revision ]
|
||||
self.upload_file( base_repository,
|
||||
filename='tool_dependencies.xml',
|
||||
filepath=dependency_path,
|
||||
valid_tools_only=False,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded dependency on bwa_tool_0100 with invalid changeset revision.',
|
||||
strings_displayed=[ strings_displayed ] )
|
||||
strings_displayed=strings_displayed,
|
||||
strings_not_displayed=[] )
|
||||
def test_0035_generate_valid_complex_repository_dependency( self ):
|
||||
'''Generate and upload a valid tool_dependencies.xml file that specifies bwa_tool_repository_0100.'''
|
||||
global running_standalone
|
||||
@@ -164,10 +185,14 @@ class TestInstallingComplexRepositoryDependencies( ShedTwillTestCase ):
|
||||
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,
|
||||
filename='tool_dependencies.xml',
|
||||
filepath=dependency_path,
|
||||
commit_message='Uploaded valid complex dependency on bwa_tool_0100.' )
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded valid complex dependency on bwa_tool_0100.',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
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 ):
|
||||
@@ -183,10 +208,14 @@ class TestInstallingComplexRepositoryDependencies( ShedTwillTestCase ):
|
||||
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,
|
||||
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=[],
|
||||
commit_message='Uploaded new tool_dependencies.xml.' )
|
||||
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' ],
|
||||
|
||||
+42
-14
@@ -44,7 +44,15 @@ class TestBasicRepositoryDependencies( ShedTwillTestCase ):
|
||||
strings_displayed=[] )
|
||||
if self.repository_is_new( repository ):
|
||||
running_standalone = True
|
||||
self.upload_file( repository, 'emboss/datatypes/datatypes_conf.xml', commit_message='Uploaded datatypes_conf.xml.' )
|
||||
self.upload_file( repository,
|
||||
filename='emboss/datatypes/datatypes_conf.xml',
|
||||
filepath=None,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=True,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded datatypes_conf.xml.',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
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 )
|
||||
@@ -60,7 +68,15 @@ class TestBasicRepositoryDependencies( ShedTwillTestCase ):
|
||||
owner=common.test_user_1_name,
|
||||
category_id=self.security.encode_id( category.id ),
|
||||
strings_displayed=[] )
|
||||
self.upload_file( repository, 'emboss/emboss.tar', commit_message='Uploaded emboss_5.tar' )
|
||||
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 tool tarball.',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
def test_0025_generate_repository_dependency_with_invalid_url( self ):
|
||||
'''Generate a repository dependency for emboss 5 with an invalid URL.'''
|
||||
global running_standalone
|
||||
@@ -76,11 +92,14 @@ class TestBasicRepositoryDependencies( ShedTwillTestCase ):
|
||||
self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=False, description='This is invalid.' )
|
||||
strings_displayed = [ 'Invalid tool shed <b>%s</b> defined for repository <b>%s</b>' % ( url, repository.name ) ]
|
||||
self.upload_file( emboss_repository,
|
||||
'repository_dependencies.xml',
|
||||
filename='repository_dependencies.xml',
|
||||
filepath=dependency_path,
|
||||
valid_tools_only=False,
|
||||
filepath=dependency_path,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded dependency on emboss_datatypes_0110 with invalid url.',
|
||||
strings_displayed=strings_displayed )
|
||||
strings_displayed=strings_displayed,
|
||||
strings_not_displayed=[] )
|
||||
def test_0030_generate_repository_dependency_with_invalid_name( self ):
|
||||
'''Generate a repository dependency for emboss 5 with an invalid name.'''
|
||||
global running_standalone
|
||||
@@ -96,11 +115,14 @@ class TestBasicRepositoryDependencies( ShedTwillTestCase ):
|
||||
self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=False, description='This is invalid.' )
|
||||
strings_displayed = [ 'Invalid repository name <b>%s</b> defined.' % name ]
|
||||
self.upload_file( emboss_repository,
|
||||
'repository_dependencies.xml',
|
||||
filename='repository_dependencies.xml',
|
||||
filepath=dependency_path,
|
||||
valid_tools_only=False,
|
||||
filepath=dependency_path,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded dependency on emboss_datatypes_0110 with invalid name.',
|
||||
strings_displayed=strings_displayed )
|
||||
strings_displayed=strings_displayed,
|
||||
strings_not_displayed=[] )
|
||||
def test_0035_generate_repository_dependency_with_invalid_owner( self ):
|
||||
'''Generate a repository dependency for emboss 5 with an invalid owner.'''
|
||||
global running_standalone
|
||||
@@ -116,11 +138,14 @@ class TestBasicRepositoryDependencies( ShedTwillTestCase ):
|
||||
self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=False, description='This is invalid.' )
|
||||
strings_displayed = [ 'Invalid owner <b>%s</b> defined for repository <b>%s</b>' % ( owner, repository.name ) ]
|
||||
self.upload_file( emboss_repository,
|
||||
'repository_dependencies.xml',
|
||||
filename='repository_dependencies.xml',
|
||||
filepath=dependency_path,
|
||||
valid_tools_only=False,
|
||||
filepath=dependency_path,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded dependency on emboss_datatypes_0110 with invalid owner.',
|
||||
strings_displayed=strings_displayed )
|
||||
strings_displayed=strings_displayed,
|
||||
strings_not_displayed=[] )
|
||||
def test_0040_generate_repository_dependency_with_invalid_changeset_revision( self ):
|
||||
'''Generate a repository dependency for emboss 5 with an invalid changeset revision.'''
|
||||
global running_standalone
|
||||
@@ -136,11 +161,14 @@ class TestBasicRepositoryDependencies( ShedTwillTestCase ):
|
||||
self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=False, description='This is invalid.' )
|
||||
strings_displayed = [ 'Invalid changeset revision <b>%s</b> defined.' % changeset_revision ]
|
||||
self.upload_file( emboss_repository,
|
||||
'repository_dependencies.xml',
|
||||
filename='repository_dependencies.xml',
|
||||
filepath=dependency_path,
|
||||
valid_tools_only=False,
|
||||
filepath=dependency_path,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded dependency on emboss_datatypes_0110 with invalid changeset revision.',
|
||||
strings_displayed=strings_displayed )
|
||||
strings_displayed=strings_displayed,
|
||||
strings_not_displayed=[] )
|
||||
def test_0045_install_repository_with_invalid_repository_dependency( self ):
|
||||
'''Install the repository and verify that galaxy detects invalid repository dependencies.'''
|
||||
self.galaxy_logout()
|
||||
|
||||
@@ -32,10 +32,42 @@ class UninstallingAndReinstallingRepositories( ShedTwillTestCase ):
|
||||
owner=common.test_user_1_name,
|
||||
category_id=self.security.encode_id( category.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_0000.txt', commit_message="Uploaded readme for 1.1.0", remove_repo_files_not_in_tar='No' )
|
||||
self.upload_file( repository, 'filtering/filtering_2.2.0.tar', commit_message="Uploaded filtering 2.2.0", remove_repo_files_not_in_tar='No' )
|
||||
self.upload_file( repository, 'readme.txt', commit_message="Uploaded readme for 2.2.0", remove_repo_files_not_in_tar='No' )
|
||||
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_0000.txt',
|
||||
filepath=None,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded readme for 1.1.0',
|
||||
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=[] )
|
||||
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 for 2.2.0',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
def test_0010_install_filtering_repository( self ):
|
||||
'''Install the filtering repository into the Galaxy instance.'''
|
||||
self.galaxy_logout()
|
||||
|
||||
+47
-17
@@ -32,29 +32,59 @@ class UninstallingAndReinstallingRepositories( ShedTwillTestCase ):
|
||||
category_id=self.security.encode_id( category.id ) )
|
||||
if self.repository_is_new( repository ):
|
||||
self.upload_file( repository,
|
||||
'freebayes/freebayes.xml',
|
||||
valid_tools_only=False,
|
||||
commit_message="Uploaded freebayes.xml." )
|
||||
self.upload_file( repository,
|
||||
'freebayes/tool_data_table_conf.xml.sample',
|
||||
filename='freebayes/freebayes.xml',
|
||||
filepath=None,
|
||||
valid_tools_only=False,
|
||||
commit_message="Uploaded tool_data_table_conf.xml.",
|
||||
remove_repo_files_not_in_tar='No' )
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded the tool xml.',
|
||||
strings_displayed=[ 'Metadata may have been defined', 'This file requires an entry', 'tool_data_table_conf' ],
|
||||
strings_not_displayed=[] )
|
||||
self.upload_file( repository,
|
||||
'freebayes/sam_fa_indices.loc.sample',
|
||||
commit_message="Uploaded sam_fa_indices.loc.sample.",
|
||||
filename='freebayes/tool_data_table_conf.xml.sample',
|
||||
filepath=None,
|
||||
valid_tools_only=False,
|
||||
remove_repo_files_not_in_tar='No' )
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded the tool data table sample file.',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
self.upload_file( repository,
|
||||
'freebayes/invalid_tool_dependencies/tool_dependencies.xml',
|
||||
valid_tools_only=False,
|
||||
commit_message="Uploaded invalid_tool_dependencies/tool_dependencies.xml.",
|
||||
remove_repo_files_not_in_tar='No' )
|
||||
filename='freebayes/sam_fa_indices.loc.sample',
|
||||
filepath=None,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded tool data table .loc file.',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
self.upload_file( repository,
|
||||
'freebayes/tool_dependencies.xml',
|
||||
filename=os.path.join( 'freebayes', 'malformed_tool_dependencies', 'tool_dependencies.xml' ),
|
||||
filepath=None,
|
||||
valid_tools_only=False,
|
||||
commit_message="Uploaded tool_dependencies.xml",
|
||||
remove_repo_files_not_in_tar='No' )
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded malformed tool dependency XML.',
|
||||
strings_displayed=[ 'Exception attempting to parse tool_dependencies.xml', 'not well-formed' ],
|
||||
strings_not_displayed=[] )
|
||||
self.upload_file( repository,
|
||||
filename=os.path.join( 'freebayes', 'invalid_tool_dependencies', 'tool_dependencies.xml' ),
|
||||
filepath=None,
|
||||
valid_tools_only=False,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded invalid tool dependency XML.',
|
||||
strings_displayed=[ 'Name, version and type from a tool requirement tag does not match' ],
|
||||
strings_not_displayed=[] )
|
||||
self.upload_file( repository,
|
||||
filename=os.path.join( 'freebayes', 'tool_dependencies.xml' ),
|
||||
filepath=None,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded valid tool dependency XML.',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
def test_0010_install_freebayes_repository( self ):
|
||||
'''Install the freebayes repository into the Galaxy instance.'''
|
||||
self.galaxy_logout()
|
||||
|
||||
+26
-5
@@ -47,21 +47,42 @@ class UninstallingAndReinstallingRepositories( ShedTwillTestCase ):
|
||||
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.' )
|
||||
self.upload_file( datatypes_repository,
|
||||
filename='emboss/datatypes/datatypes_conf.xml',
|
||||
filepath=None,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded datatypes_conf.xml.',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
emboss_repository = self.get_or_create_repository( name=emboss_repository_name,
|
||||
description=emboss_repository_description,
|
||||
long_description=emboss_repository_long_description,
|
||||
owner=common.test_user_1_name,
|
||||
category_id=self.security.encode_id( category.id ),
|
||||
strings_displayed=[] )
|
||||
self.upload_file( emboss_repository, 'emboss/emboss.tar', commit_message='Uploaded emboss_5.tar' )
|
||||
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_1020', 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_repository,
|
||||
'repository_dependencies.xml',
|
||||
filepath=repository_dependencies_path,
|
||||
commit_message='Uploaded repository_dependencies.xml' )
|
||||
filename='repository_dependencies.xml',
|
||||
filepath=repository_dependencies_path,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded repository_dependencies.xml.',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
repository_datatypes_count = int( self.get_repository_datatypes_count( datatypes_repository ) )
|
||||
def test_0010_install_emboss_repository( self ):
|
||||
'''Install the emboss repository into the Galaxy instance.'''
|
||||
|
||||
+59
-15
@@ -56,48 +56,92 @@ class UninstallingAndReinstallingRepositories( ShedTwillTestCase ):
|
||||
owner=common.test_user_1_name,
|
||||
category_id=self.security.encode_id( category.id ),
|
||||
strings_displayed=[] )
|
||||
self.upload_file( emboss_5_repository, 'emboss/emboss.tar', commit_message='Uploaded emboss.tar' )
|
||||
self.upload_file( datatypes_repository,
|
||||
filename='emboss/datatypes/datatypes_conf.xml',
|
||||
filepath=None,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded datatypes_conf.xml.',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
repository_dependencies_path = self.generate_temp_path( 'test_1030', 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' )
|
||||
filename='repository_dependencies.xml',
|
||||
filepath=repository_dependencies_path,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded repository_dependencies.xml.',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
emboss_6_repository = self.get_or_create_repository( name=emboss_6_repository_name,
|
||||
description=emboss_repository_description,
|
||||
long_description=emboss_repository_long_description,
|
||||
owner=common.test_user_1_name,
|
||||
category_id=self.security.encode_id( category.id ),
|
||||
strings_displayed=[] )
|
||||
self.upload_file( emboss_6_repository, 'emboss/emboss.tar', commit_message='Uploaded emboss.tar' )
|
||||
self.upload_file( emboss_6_repository,
|
||||
filename='emboss/emboss.tar',
|
||||
filepath=None,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded tool tarball.',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
repository_dependencies_path = self.generate_temp_path( 'test_1030', 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' )
|
||||
filename='repository_dependencies.xml',
|
||||
filepath=repository_dependencies_path,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded repository_dependencies.xml.',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
emboss_repository = self.get_or_create_repository( name=emboss_repository_name,
|
||||
description=emboss_repository_description,
|
||||
long_description=emboss_repository_long_description,
|
||||
owner=common.test_user_1_name,
|
||||
category_id=self.security.encode_id( category.id ),
|
||||
strings_displayed=[] )
|
||||
self.upload_file( emboss_repository, 'emboss/emboss.tar', commit_message='Uploaded emboss.tar' )
|
||||
self.upload_file( emboss_repository,
|
||||
filename='emboss/emboss.tar',
|
||||
filepath=None,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded tool tarball.',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
repository_dependencies_path = self.generate_temp_path( 'test_1030', 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' )
|
||||
filename='repository_dependencies.xml',
|
||||
filepath=repository_dependencies_path,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded repository_dependencies.xml.',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
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' )
|
||||
filename='repository_dependencies.xml',
|
||||
filepath=repository_dependencies_path,
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded repository_dependencies.xml.',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
repository_datatypes_count = int( self.get_repository_datatypes_count( datatypes_repository ) )
|
||||
def test_0010_install_emboss_repository( self ):
|
||||
'''Install the emboss repository into the Galaxy instance.'''
|
||||
|
||||
@@ -47,8 +47,24 @@ class TestResetInstalledRepositoryMetadata( ShedTwillTestCase ):
|
||||
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" )
|
||||
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",
|
||||
@@ -56,10 +72,42 @@ class TestResetInstalledRepositoryMetadata( ShedTwillTestCase ):
|
||||
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.' )
|
||||
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.",
|
||||
@@ -67,14 +115,30 @@ class TestResetInstalledRepositoryMetadata( ShedTwillTestCase ):
|
||||
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.' )
|
||||
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, 'emboss/emboss.tar', commit_message='Uploaded emboss_5.tar' )
|
||||
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,
|
||||
@@ -83,7 +147,15 @@ class TestResetInstalledRepositoryMetadata( ShedTwillTestCase ):
|
||||
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.' )
|
||||
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,
|
||||
@@ -91,48 +163,92 @@ class TestResetInstalledRepositoryMetadata( ShedTwillTestCase ):
|
||||
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' )
|
||||
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' ] )
|
||||
self.generate_repository_dependency_xml( [ datatypes_repository ],
|
||||
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',
|
||||
filename='repository_dependencies.xml',
|
||||
filepath=repository_dependencies_path,
|
||||
commit_message='Uploaded repository_dependencies.xml' )
|
||||
valid_tools_only=True,
|
||||
uncompress_file=True,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded repository_dependencies.xml',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
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' )
|
||||
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' ] )
|
||||
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',
|
||||
filename='repository_dependencies.xml',
|
||||
filepath=repository_dependencies_path,
|
||||
commit_message='Uploaded repository_dependencies.xml' )
|
||||
valid_tools_only=True,
|
||||
uncompress_file=True,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded repository_dependencies.xml',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
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' )
|
||||
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' ] )
|
||||
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',
|
||||
filename='repository_dependencies.xml',
|
||||
filepath=repository_dependencies_path,
|
||||
commit_message='Uploaded repository_dependencies.xml' )
|
||||
valid_tools_only=True,
|
||||
uncompress_file=True,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded repository_dependencies.xml',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
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',
|
||||
filename='repository_dependencies.xml',
|
||||
filepath=repository_dependencies_path,
|
||||
commit_message='Uploaded repository_dependencies.xml' )
|
||||
valid_tools_only=True,
|
||||
uncompress_file=True,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded repository_dependencies.xml',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
repository = self.get_or_create_repository( name='freebayes_0040',
|
||||
description="Galaxy's freebayes tool",
|
||||
long_description="Long description of Galaxy's freebayes tool",
|
||||
@@ -140,14 +256,30 @@ class TestResetInstalledRepositoryMetadata( ShedTwillTestCase ):
|
||||
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.' )
|
||||
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, 'filtering/filtering_1.1.0.tar', commit_message='Uploaded filtering.tar.' )
|
||||
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' ] )
|
||||
@@ -155,16 +287,26 @@ class TestResetInstalledRepositoryMetadata( ShedTwillTestCase ):
|
||||
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',
|
||||
filename='repository_dependencies.xml',
|
||||
filepath=repository_dependencies_path,
|
||||
commit_message='Uploaded dependency on freebayes' )
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded repository_dependencies.xml specifying freebayes',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
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',
|
||||
filename='repository_dependencies.xml',
|
||||
filepath=repository_dependencies_path,
|
||||
commit_message='Uploaded dependency on filtering' )
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded repository_dependencies.xml specifying filtering',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
datatypes_repository = self.get_or_create_repository( name='emboss_datatypes_0050',
|
||||
description="Datatypes for emboss",
|
||||
long_description="Long description of Emboss' datatypes",
|
||||
@@ -190,41 +332,93 @@ class TestResetInstalledRepositoryMetadata( ShedTwillTestCase ):
|
||||
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.' )
|
||||
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' ] )
|
||||
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',
|
||||
filename='repository_dependencies.xml',
|
||||
filepath=repository_dependencies_path,
|
||||
commit_message='Uploaded dependency on emboss_datatypes.' )
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded repository_dependencies.xml',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
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',
|
||||
filename='repository_dependencies.xml',
|
||||
filepath=repository_dependencies_path,
|
||||
commit_message='Uploaded dependency on emboss.' )
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded repository_dependencies.xml',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
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',
|
||||
filename='repository_dependencies.xml',
|
||||
filepath=repository_dependencies_path,
|
||||
commit_message='Uploaded dependency on filtering.' )
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded repository_dependencies.xml',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
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',
|
||||
filename='repository_dependencies.xml',
|
||||
filepath=repository_dependencies_path,
|
||||
commit_message='Uploaded dependency on filtering.' )
|
||||
valid_tools_only=True,
|
||||
uncompress_file=False,
|
||||
remove_repo_files_not_in_tar=False,
|
||||
commit_message='Uploaded repository_dependencies.xml',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
workflow_repository = self.get_or_create_repository( name='filtering_0060',
|
||||
description="Galaxy's filtering tool",
|
||||
long_description="Long description of Galaxy's filtering tool",
|
||||
@@ -235,15 +429,27 @@ class TestResetInstalledRepositoryMetadata( ShedTwillTestCase ):
|
||||
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 )
|
||||
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,
|
||||
workflow_filename,
|
||||
filename=workflow_filename,
|
||||
filepath=workflow_filepath,
|
||||
commit_message='Uploaded filtering workflow.' )
|
||||
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,
|
||||
'filtering/filtering_2.2.0.tar',
|
||||
commit_message='Uploaded filtering tool.' )
|
||||
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_0010_install_all_missing_repositories( self ):
|
||||
'''Call the install_repository method to ensure that all required repositories are installed.'''
|
||||
global repository_datatypes_count
|
||||
|
||||
Reference in New Issue
Block a user