1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/e291341d0127/ changeset: e291341d0127 user: inithello date: 2012-11-28 21:21:23 summary: Added more functional tests for basic tool shed repository features. affected #: 9 files

diff -r 4eaa644dd47877c40ee7090d56379998d7aecafa -r e291341d0127df0fd9bf8f66ac1d9df3f58b9bd7 lib/galaxy/webapps/community/controllers/upload.py --- a/lib/galaxy/webapps/community/controllers/upload.py +++ b/lib/galaxy/webapps/community/controllers/upload.py @@ -77,7 +77,7 @@ elif file_data not in ( '', None ): uploaded_file = file_data.file uploaded_file_name = uploaded_file.name - uploaded_file_filename = file_data.filename + uploaded_file_filename = os.path.split( file_data.filename )[ -1 ] isempty = os.path.getsize( os.path.abspath( uploaded_file_name ) ) == 0 if uploaded_file or uploaded_directory: ok = True

diff -r 4eaa644dd47877c40ee7090d56379998d7aecafa -r e291341d0127df0fd9bf8f66ac1d9df3f58b9bd7 test/tool_shed/base/test_db_util.py --- a/test/tool_shed/base/test_db_util.py +++ b/test/tool_shed/base/test_db_util.py @@ -39,7 +39,7 @@ sa_session.flush() def refresh( obj ): sa_session.refresh( obj ) -def get_repository_by_name( name, owner_username ): +def get_repository_by_name_and_owner( name, owner_username ): owner = get_user_by_name( owner_username ) repository = sa_session.query( model.Repository ) \ .filter( model.Repository.table.c.name==name ) \

diff -r 4eaa644dd47877c40ee7090d56379998d7aecafa -r e291341d0127df0fd9bf8f66ac1d9df3f58b9bd7 test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -5,6 +5,7 @@ # Security helper self.security = security.SecurityHelper( id_secret='changethisinproductiontoo' ) self.history_id = None + self.hgweb_config_manager = None self.host = os.environ.get( 'TOOL_SHED_TEST_HOST' ) self.port = os.environ.get( 'TOOL_SHED_TEST_PORT' ) self.url = "http://%s:%s" % ( self.host, self.port ) @@ -29,18 +30,67 @@ if strings_not_displayed: for string in strings_not_displayed: self.check_string_not_in_page( string ) - def check_for_tool_metadata(self, repository, changeset_revision, tool_id, strings_displayed=[], strings_not_displayed=[] ): - url = '/repository/view_tool_metadata?repository_id=%s&changeset_revision=%s&tool_id=%s' % \ - ( self.security.encode_id( repository.id ), changeset_revision, tool_id ) - self.visit_url( url ) - self.check_for_strings( strings_displayed, strings_not_displayed ) - def check_for_valid_tools( self, repository ): - self.manage_repository( repository ) - self.check_page_for_string( 'Valid tools' ) + def check_for_valid_tools( self, repository, strings_displayed=[], strings_not_displayed=[] ): + strings_displayed.append( 'Valid tools' ) + self.manage_repository( repository, strings_displayed, strings_not_displayed ) + def check_metadata_in_repository_changelog( self, repository, metadata_count ): + self.check_repository_changelog( repository ) + self.check_string_count_in_page( 'Repository metadata is associated with this change set.', metadata_count ) def check_repository_changelog( self, repository, strings_displayed=[], strings_not_displayed=[] ): url = '/repository/view_changelog?id=%s' % self.security.encode_id( repository.id ) self.visit_url( url ) self.check_for_strings( strings_displayed, strings_not_displayed ) + def check_repository_metadata( self, repository, tip_only=True ): + assert self.tip_has_metadata( repository, tip_only ), \ + 'Repository tip is not a metadata revision: Repository tip - %s, metadata revisions - %s.' % \ + ( self.get_repository_tip( repository ), ', '.join( self.get_repository_metadata_revisions( repository ) ) ) + def check_repository_tools( self, repository, include_invalid=False ): + ''' + Loop through each repository_metadata dict in the repository object. + For each of these, check for a tools attribute, and load the tool metadata + page if it exists, then display that tool's page. + ''' + tool_list, invalid_tool_list = self.get_tools_from_repository_metadata( repository, include_invalid=include_invalid ) + for valid_tool_dict in tool_list: + changeset_revision = valid_tool_dict[ 'changeset_revision' ] + for tool in valid_tool_dict[ 'tools' ]: + metadata_strings_displayed = [ tool[ 'guid' ], + tool[ 'version' ], + tool[ 'id' ], + tool[ 'name' ], + tool[ 'description' ], + changeset_revision ] + url = '/repository/view_tool_metadata?repository_id=%s&changeset_revision=%s&tool_id=%s' % \ + ( self.security.encode_id( repository.id ), changeset_revision, tool[ 'id' ] ) + self.visit_url( url ) + self.check_for_strings( metadata_strings_displayed ) + self.load_display_tool_page( repository, tool_xml_path=tool[ 'tool_config' ], + changeset_revision=changeset_revision, + strings_displayed=[ '%s (version %s)' % ( tool[ 'name' ], tool[ 'version' ] ) ], + strings_not_displayed=[] ) + if include_invalid and invalid_tool_list: + for invalid_tool_dict in invalid_tool_list: + for tool in invalid_tool_dict[ 'tools' ]: + tool_path = '%s/%s' % ( self.get_repository_filesystem_path( repository ), tool ) + self.load_display_tool_page( repository, + tool_xml_path=tool_path, + changeset_revision=changeset_revision, + strings_displayed=[ 'properly loaded' ], + strings_not_displayed=[] ) + def check_string_count_in_page( self, pattern, min_count, max_count=None ): + """Checks the number of 'pattern' occurrences in the current browser page""" + page = self.last_page() + pattern_count = page.count( pattern ) + if max_count is None: + max_count = min_count + # The number of occurrences of pattern in the page should be between min_count + # and max_count, so show error if pattern_count is less than min_count or greater + # than max_count. + if pattern_count < min_count or pattern_count > max_count: + fname = self.write_temp_file( page ) + errmsg = "%i occurrences of '%s' found (min. %i, max. %i).\npage content written to '%s' " % \ + ( pattern_count, pattern, min_count, max_count, fname ) + raise AssertionError( errmsg ) def create_category( self, category_name, category_description ): self.visit_url( '/admin/manage_categories?operation=create' ) tc.fv( "1", "name", category_name ) @@ -56,10 +106,43 @@ tc.fv( "1", "category_id", "+%s" % category ) tc.submit( "create_repository_button" ) self.check_for_strings( strings_displayed, strings_not_displayed ) + def delete_files_from_repository( self, repository, filenames=[], strings_displayed=[ 'were deleted from the repository' ], strings_not_displayed=[] ): + files_to_delete = [] + basepath = self.get_repository_base_path_from_browse_page( repository ) + repository_files = self.get_repository_file_list( repository, basepath ) + # Verify that the files to delete actually exist in the repository. + for filename in repository_files: + if filename in filenames: + files_to_delete.append( os.path.join( basepath, filename ) ) + self.browse_repository( repository ) + # Twill sets hidden form fields to read-only by default. We need to write to this field. + form = tc.browser.get_form( 'select_files_to_delete' ) + form.find_control( "selected_files_to_delete" ).readonly = False + tc.fv( "1", "selected_files_to_delete", ','.join( files_to_delete ) ) + tc.submit( 'select_files_to_delete_button' ) + self.check_for_strings( strings_displayed, strings_not_displayed ) + def display_readme_file( self, repository, changeset_revision=None, strings_displayed=[], strings_not_displayed=[] ): + if changeset_revision is None: + changeset_revision = self.get_repository_tip( repository ) + repository_id = self.security.encode_id( repository.id ) + self.visit_url( '/repository/view_readme?changeset_revision=%s&id=%s' % ( changeset_revision, repository_id ) ) + self.check_for_strings( strings_displayed, strings_not_displayed ) def display_repository_clone_page( self, owner_name, repository_name, strings_displayed=[], strings_not_displayed=[] ): url = '/repos/%s/%s' % ( owner_name, repository_name ) self.visit_url( url ) self.check_for_strings( strings_displayed, strings_not_displayed ) + def display_repository_file_contents( self, repository, filename, filepath=None, strings_displayed=[], strings_not_displayed=[] ): + '''Find a file in the repository and display the contents.''' + basepath = self.get_repository_base_path_from_browse_page( repository ) + repository_file_list = [] + relative_path = filename + if filepath is not None: + relative_path = os.path.join( filepath, filename ) + repository_file_list = self.get_repository_file_list( repository, basepath ) + assert relative_path in repository_file_list, 'File %s not found in the repository under %s.' % ( filename, filepath ) + url = '/repository/get_file_contents?file_path=%s' % os.path.join( basepath, relative_path ).replace( '/', '%2f' ) + self.visit_url( url ) + self.check_for_strings( strings_displayed, strings_not_displayed ) def edit_repository_categories( self, repository, categories_to_add=[], categories_to_remove=[], restore_original=True ): url = '/repository/manage_repository?id=%s' % self.security.encode_id( repository.id ) self.visit_url( url ) @@ -67,10 +150,10 @@ strings_not_displayed = [] for category in categories_to_add: tc.fv( "2", "category_id", '+%s' % category) - strings_displayed.append( "selected>%s</option>" % category ) + strings_displayed.append( "selected>%s" % category ) for category in categories_to_remove: tc.fv( "2", "category_id", '-%s' % category) - strings_not_displayed.append( "selected>%s</option>" % category ) + strings_not_displayed.append( "selected>%s" % category ) tc.submit( "manage_categories_button" ) self.check_for_strings( strings_displayed, strings_not_displayed ) if restore_original: @@ -78,22 +161,22 @@ strings_not_displayed = [] for category in categories_to_remove: tc.fv( "2", "category_id", '+%s' % category) - strings_displayed.append( "selected>%s</option>" % category ) + strings_displayed.append( "selected>%s" % category ) for category in categories_to_add: tc.fv( "2", "category_id", '-%s' % category) - strings_not_displayed.append( "selected>%s</option>" % category ) + strings_not_displayed.append( "selected>%s" % category ) tc.submit( "manage_categories_button" ) self.check_for_strings( strings_displayed, strings_not_displayed ) - def edit_repository_information( self, repository, **kwargs ): + def edit_repository_information( self, repository, **kwd ): url = '/repository/manage_repository?id=%s' % self.security.encode_id( repository.id ) self.visit_url( url ) original_information = dict( repo_name=repository.name, description=repository.description, long_description=repository.long_description ) strings_displayed = [] strings_not_displayed = [] for input_elem_name in [ 'repo_name', 'description', 'long_description' ]: - if input_elem_name in kwargs: - tc.fv( "1", input_elem_name, kwargs[ input_elem_name ] ) - strings_displayed.append( self.escape_html( kwargs[ input_elem_name ] ) ) + if input_elem_name in kwd: + tc.fv( "1", input_elem_name, kwd[ input_elem_name ] ) + strings_displayed.append( self.escape_html( kwd[ input_elem_name ] ) ) tc.submit( "edit_repository_button" ) self.check_for_strings( strings_displayed ) strings_displayed = [] @@ -102,19 +185,84 @@ strings_displayed.append( self.escape_html( original_information[ input_elem_name ] ) ) tc.submit( "edit_repository_button" ) self.check_for_strings( strings_displayed ) - def escape_html( self, string ): + def escape_html( self, string, unescape=False ): html_entities = [ ('&', 'X' ), ( "'", '&#39;' ), ( '"', '&#34;' ) ] for character, replacement in html_entities: - string = string.replace( character, replacement ) + if unescape: + string = string.replace( replacement, character ) + else: + string = string.replace( character, replacement ) return string def get_latest_repository_metadata_for_repository( self, repository ): + # TODO: This will not work as expected. Fix it. return repository.metadata_revisions[ 0 ] - def get_readme( self, repository, strings_displayed=[], strings_not_displayed=[] ): - repository_metadata = self.get_latest_repository_metadata_for_repository( repository ) - changeset_revision = repository_metadata.changeset_revision - repository_id = self.security.encode_id( repository.id ) - self.visit_url( '/repository/view_readme?changeset_revision=%s&id=%s' % ( changeset_revision, repository_id ) ) - self.check_for_strings( strings_displayed, strings_not_displayed ) + def get_repository_base_path_from_browse_page( self, repository ): + '''Get the base path from the javascript dynatree parameters. This must be updated if the browse feature is altered.''' + self.visit_url( '/repository/browse_repository?id=%s' % self.security.encode_id( repository.id ) ) + html = self.last_page() + found_file = None + basepath = None + search = re.search( 'data: { folder_path: "([^"]+)" },', html ) + if search is not None: + basepath = search.group( 1 ) + return basepath + def get_repository_file_list( self, repository, base_path, current_path=None ): + ''' + Recursively load repository folder contents and append them to a list. Similar to os.walk, + but via /repository/open_folder. + ''' + if current_path is None: + full_path = base_path + else: + full_path = os.path.join( base_path, current_path ) + # Get the current folder's contents. + url = '/repository/open_folder?folder_path=%s' % full_path.replace( '/', '%2f' ) + self.visit_url( url ) + file_list = from_json_string( self.last_page() ) + returned_file_list = [] + if current_path is not None: + returned_file_list.append( current_path ) + # Loop through the json dict returned by /repository/open_folder. + for file_dict in file_list: + if file_dict[ 'isFolder' ]: + # This is a folder. Get the contents of the folder and append it to the list, + # prefixed with the path relative to the repository root, if any. + if current_path is None: + returned_file_list.extend( self.get_repository_file_list( repository, base_path, file_dict[ 'title' ] ) ) + else: + sub_path = os.path.join( current_path, file_dict[ 'title' ] ) + returned_file_list.extend( self.get_repository_file_list( repository, base_path, sub_path ) ) + else: + # This is a regular file, prefix the filename with the current path and append it to the list. + if current_path is not None: + returned_file_list.append( os.path.join( current_path, file_dict[ 'title' ] ) ) + else: + returned_file_list.append( file_dict[ 'title' ] ) + return returned_file_list + def get_repository_metadata( self, repository ): + return [ metadata_revision for metadata_revision in repository.metadata_revisions ] + def get_repository_metadata_revisions( self, repository ): + return [ str( repository_metadata.changeset_revision ) for repository_metadata in repository.metadata_revisions ] + def get_repository_tip( self, repository ): + self.browse_repository( repository ) + html = self.last_page() + revision_regex = re.search( 'revision ([0-9a-f]+) (repository tip)', html ) + if revision_regex is not None: + return revision_regex.group( 1 ) + return None + def get_repository_filesystem_path( self, repository ): + repo_subdirectory = '%03d' % int( repository.id / 1000 ) + return os.path.join( 'database', 'community_files', repo_subdirectory, 'repo_%d' % repository.id ) + def get_tools_from_repository_metadata( self, repository, include_invalid=False ): + '''Get a list of valid and (optionally) invalid tool dicts from the repository metadata.''' + valid_tools = [] + invalid_tools = [] + for repository_metadata in repository.metadata_revisions: + if 'tools' in repository_metadata.metadata: + valid_tools.append( dict( tools=repository_metadata.metadata[ 'tools' ], changeset_revision=repository_metadata.changeset_revision ) ) + if include_invalid and 'invalid_tools' in repository_metadata.metadata: + invalid_tools.append( dict( tools=repository_metadata.metadata[ 'invalid_tools' ], changeset_revision=repository_metadata.changeset_revision ) ) + return valid_tools, invalid_tools def grant_write_access( self, repository, usernames=[], strings_displayed=[], strings_not_displayed=[] ): self.manage_repository( repository ) tc.fv( "3", "allow_push", '-Select one' ) @@ -122,10 +270,8 @@ tc.fv( "3", "allow_push", '+%s' % username ) tc.submit( 'user_access_button' ) self.check_for_strings( strings_displayed, strings_not_displayed ) - def load_display_tool_page( self, repository, tool_xml_filename, changeset_revision, strings_displayed=[], strings_not_displayed=[] ): + def load_display_tool_page( self, repository, tool_xml_path, changeset_revision, strings_displayed=[], strings_not_displayed=[] ): repository_id = self.security.encode_id( repository.id ) - repo_subdirectory = '%03d' % int( repository.id / 1000 ) - tool_xml_path = '%2f'.join( [ 'database', 'community_files', repo_subdirectory, 'repo_%d' % repository.id, tool_xml_filename ] ) url = '/repository/display_tool?repository_id=%s&tool_config=%s&changeset_revision=%s' % \ ( repository_id, tool_xml_path, changeset_revision ) self.visit_url( url ) @@ -134,20 +280,37 @@ url = '/repository/manage_repository?id=%s' % self.security.encode_id( repository.id ) self.visit_url( url ) self.check_for_strings( strings_displayed, strings_not_displayed ) - def set_repository_malicious( self, repository, strings_displayed=[], strings_not_displayed=[] ): + def revoke_write_access( self, repository, username ): + url = '/repository/manage_repository?user_access_button=Remove&id=%s&remove_auth=%s' % \ + ( self.security.encode_id( repository.id ), username ) + self.visit_url( url ) + def set_repository_deprecated( self, repository, set_deprecated=True, strings_displayed=[], strings_not_displayed=[] ): + url = '/repository/deprecate?id=%s&mark_deprecated=%s' % ( self.security.encode_id( repository.id ), set_deprecated ) + self.visit_url( url ) + self.check_for_strings( strings_displayed, strings_not_displayed ) + def set_repository_malicious( self, repository, set_malicious=True, strings_displayed=[], strings_not_displayed=[] ): self.manage_repository( repository ) - tc.fv( "malicious", "malicious", True ) + tc.fv( "malicious", "malicious", set_malicious ) tc.submit( "malicious_button" ) self.check_for_strings( strings_displayed, strings_not_displayed ) - def unset_repository_malicious( self, repository, strings_displayed=[], strings_not_displayed=[] ): - self.manage_repository( repository ) - tc.fv( "malicious", "malicious", False ) - tc.submit( "malicious_button" ) - self.check_for_strings( strings_displayed, strings_not_displayed ) - def upload( self, repository, filename, strings_displayed=[], strings_not_displayed=[], **kwargs ): + def tip_has_metadata( self, repository, tip_only=True ): + tip = self.get_repository_tip( repository ) + changeset_revisions = [ str( repository_metadata.changeset_revision ) for repository_metadata in repository.metadata_revisions ] + if tip_only: + return len( changeset_revisions ) == 1 and tip in changeset_revisions + return tip in changeset_revisions + def upload_file( self, + repository, + filename, + valid_tools_only=True, + strings_displayed=[], + strings_not_displayed=[], + **kwd ): self.visit_url( '/upload/upload?repository_id=%s' % self.security.encode_id( repository.id ) ) - for key in kwargs: - tc.fv( "1", key, kwargs[ key ] ) + if valid_tools_only: + strings_displayed.append( "has been successfully uploaded to the repository." ) + for key in kwd: + tc.fv( "1", key, kwd[ key ] ) tc.formfile( "1", "file_data", self.get_filename( filename ) ) tc.submit( "upload_button" ) self.check_for_strings( strings_displayed, strings_not_displayed )

diff -r 4eaa644dd47877c40ee7090d56379998d7aecafa -r e291341d0127df0fd9bf8f66ac1d9df3f58b9bd7 test/tool_shed/functional/test_0000_basic_repository_features.py --- a/test/tool_shed/functional/test_0000_basic_repository_features.py +++ b/test/tool_shed/functional/test_0000_basic_repository_features.py @@ -11,14 +11,14 @@ regular_email = 'test-1@bx.psu.edu' regular_username = 'user1'

-repository_name = 'filter' -repository_description = "Galaxy's filter tool" -repository_long_description = "Long description of Galaxy's filter tool" +repository_name = 'filtering' +repository_description = "Galaxy's filtering tool" +repository_long_description = "Long description of Galaxy's filtering tool"

class TestCreateRepository( ShedTwillTestCase ):

def test_0000_initiate_users( self ): - """Create necessary users and login as an admin user.""" + """Create necessary user accounts and login as an admin user.""" self.login( email=regular_email, username=regular_username ) regular_user = get_user( regular_email ) assert regular_user is not None, 'Problem retrieving user with email %s from the database' % regular_email @@ -29,60 +29,117 @@ assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email admin_user_private_role = get_private_role( admin_user ) def test_0005_create_categories( self ): - """Create a category""" + """Create categories""" self.create_category( 'Text Manipulation', 'Tools for manipulating text' ) self.create_category( 'Text Analysis', 'Tools for analyzing text' ) def test_0010_create_repository( self ): - """Create a repository""" - strings_displayed = [ '<div class="toolFormTitle">Repository %s</div>' % "'%s'" % repository_name, \ + """Create the filtering repository""" + strings_displayed = [ 'Repository %s' % "'%s'" % repository_name, 'Repository %s has been created' % "'%s'" % repository_name ] - self.create_repository( repository_name, repository_description, \ - repository_long_description=repository_long_description, \ - categories=[ 'Text Manipulation' ], \ + self.create_repository( repository_name, + repository_description, + repository_long_description=repository_long_description, + categories=[ 'Text Manipulation' ], strings_displayed=strings_displayed ) def test_0015_edit_repository( self ): """Edit the repository name, description, and long description""" - repository = get_repository_by_name( repository_name, admin_username ) - new_name = "renamed_filter" - new_description = "Edited filter tool" + repository = get_repository_by_name_and_owner( repository_name, admin_username ) + new_name = "renamed_filtering" + new_description = "Edited filtering tool" new_long_description = "Edited long description" self.edit_repository_information( repository, repo_name=new_name, description=new_description, long_description=new_long_description ) def test_0020_change_repository_category( self ): - """Change the category of a repository""" - repository = get_repository_by_name( repository_name, admin_username ) + """Change the categories associated with the filtering repository""" + repository = get_repository_by_name_and_owner( repository_name, admin_username ) self.edit_repository_categories( repository, categories_to_add=[ "Text Analysis" ], categories_to_remove=[ "Text Manipulation" ] ) -# def test_0025_grant_write_access( self ): -# '''Grant write access to another user''' -# repository = get_repository_by_name( repository_name, admin_username ) -# self.grant_write_access( repository, usernames=[ regular_username ] ) - def test_0030_upload_tarball( self ): + def test_0025_grant_write_access( self ): + '''Grant write access to another user''' + repository = get_repository_by_name_and_owner( repository_name, admin_username ) + self.grant_write_access( repository, usernames=[ regular_username ] ) + self.revoke_write_access( repository, regular_username ) + def test_0030_upload_filtering_1_1_0( self ): """Upload filtering_1.1.0.tar to the repository""" - repository = get_repository_by_name( repository_name, admin_username ) - self.upload( repository, - 'filtering_1.1.0.tar', - strings_displayed=[ "has been successfully uploaded to the repository." ], - commit_message="Uploaded filtering 1.1.0" ) + repository = get_repository_by_name_and_owner( repository_name, admin_username ) + self.upload_file( repository, 'filtering_1.1.0.tar', commit_message="Uploaded filtering 1.1.0" ) + def test_0035_verify_repository( self ): + '''Display basic repository pages''' + repository = get_repository_by_name_and_owner( repository_name, admin_username ) + latest_changeset_revision = self.get_repository_tip( repository ) + self.check_for_valid_tools( repository, strings_displayed=[ 'Filter1' ] ) + self.check_metadata_in_repository_changelog( repository, metadata_count=1 ) + self.check_repository_tools( repository ) + self.check_repository_metadata( repository, tip_only=False ) + self.browse_repository( repository, strings_displayed=[ 'Browse %s revision' % repository.name, '(repository tip)' ] ) + self.display_repository_clone_page( admin_username, + repository_name, + strings_displayed=[ 'Uploaded filtering 1.1.0', latest_changeset_revision ] ) + def test_0040_alter_repository_states( self ): + '''Test toggling the malicious and deprecated repository flags.''' + repository = get_repository_by_name_and_owner( repository_name, admin_username ) + self.set_repository_malicious( repository, set_malicious=True, strings_displayed=[ 'The repository tip has been defined as malicious.' ] ) + self.set_repository_malicious( repository, + set_malicious=False, + strings_displayed=[ 'The repository tip has been defined as <b>not</b> malicious.' ] ) + self.set_repository_deprecated( repository, + strings_displayed=[ 'has been marked as deprecated', 'Mark as not deprecated' ] ) + self.manage_repository( repository, + strings_displayed=[ 'This repository has been marked as deprecated' ], + strings_not_displayed=[ 'Upload files', 'Reset all repository metadata' ] ) + self.set_repository_deprecated( repository, + strings_displayed=[ 'has been marked as not deprecated', 'Mark as deprecated' ], + set_deprecated=False ) + def test_0045_display_repository_tip_file( self ): + '''Display the contents of a file in the repository tip revision''' + repository = get_repository_by_name_and_owner( repository_name, admin_username ) + self.display_repository_file_contents( repository, filename='filtering.xml', strings_displayed=[ '1.1.0' ] ) + def test_0050_upload_filtering_txt_file( self ): + '''Upload filtering.txt file associated with tool version 1.1.0.''' + repository = get_repository_by_name_and_owner( repository_name, admin_username ) + self.upload_file( repository, + 'filtering.txt', + commit_message="Uploaded filtering.txt", + uncompress_file='No', + remove_repo_files_not_in_tar='No' ) + self.display_readme_file( repository, strings_displayed=[ 'Readme file for filtering 1.1.0' ] ) + def test_0055_upload_filtering_test_data( self ): + '''Upload filtering test data.''' + repository = get_repository_by_name_and_owner( repository_name, admin_username ) + self.upload_file( repository, 'filtering_test_data.tar', commit_message="Uploaded filtering test data", remove_repo_files_not_in_tar='No' ) + self.display_repository_file_contents( repository, filename='1.bed', filepath='test-data' ) + self.check_repository_metadata( repository, tip_only=True ) + def test_0060_upload_filtering_2_2_0( self ): + '''Upload filtering version 2.2.0''' + repository = get_repository_by_name_and_owner( repository_name, admin_username ) + self.upload_file( repository, + 'filtering_2.2.0.tar', + commit_message="Uploaded filtering 2.2.0", + remove_repo_files_not_in_tar='No' ) + def test_0065_verify_filtering_repository( self ): + '''Verify the new tool versions and repository metadata.''' + repository = get_repository_by_name_and_owner( repository_name, admin_username ) self.check_for_valid_tools( repository ) - latest_repository_metadata = self.get_latest_repository_metadata_for_repository( repository ) - changeset_revision = latest_repository_metadata.changeset_revision - self.check_repository_changelog( repository, strings_displayed=[ 'Repository metadata is associated with this change set.' ] ) - self.set_repository_malicious( repository, strings_displayed=[ 'The repository tip has been defined as malicious.' ] ) - self.unset_repository_malicious( repository, strings_displayed=[ 'The repository tip has been defined as <b>not</b> malicious.' ] ) - self.load_display_tool_page( repository, tool_xml_filename='filtering.xml', \ - changeset_revision=changeset_revision, \ - strings_displayed=[ 'Filter (version 1.1.0)', "c1=='chr1'" ], \ - strings_not_displayed=[] ) - tool = latest_repository_metadata.metadata[ 'tools' ][0] - metadata_strings_displayed = [ tool[ 'guid' ], tool[ 'version' ], tool[ 'id' ], tool[ 'name' ], tool[ 'description' ], changeset_revision ] - self.check_for_tool_metadata( repository, changeset_revision, 'Filter1', strings_displayed=metadata_strings_displayed ) - def test_0035_repository_browse_page( self ): - '''Visit the repository browse page''' - repository = get_repository_by_name( repository_name, admin_username ) - self.browse_repository( repository, strings_displayed=[ 'Browse %s revision' % repository.name, '(repository tip)' ] ) - def test_0040_visit_clone_url_via_hgweb( self ): - '''Visit the repository clone URL via hgweb''' - repository = get_repository_by_name( repository_name, admin_username ) - latest_changeset_revision = self.get_latest_repository_metadata_for_repository( repository ) - self.display_repository_clone_page( admin_username, \ - repository_name, \ - strings_displayed=[ 'Uploaded filtering 1.1.0', latest_changeset_revision.changeset_revision ] ) + strings_displayed = self.get_repository_metadata_revisions( repository ).append( 'Select a revision' ) + self.manage_repository( repository, strings_displayed=strings_displayed ) + self.check_metadata_in_repository_changelog( repository, metadata_count=2 ) + self.check_repository_tools( repository, include_invalid=False ) + self.check_repository_metadata( repository, tip_only=False ) + def test_0070_upload_readme_txt_file( self ): + '''Upload readme.txt file associated with tool version 2.2.0.''' + repository = get_repository_by_name_and_owner( repository_name, admin_username ) + self.upload_file( repository, 'readme.txt', commit_message="Uploaded readme.txt" ) + self.display_readme_file( repository, strings_displayed=[ 'This is a readme file.' ] ) + # Verify that there is a different readme file for each metadata revision. + metadata_revisions = self.get_repository_metadata_revisions( repository ) + strings_to_check = [ 'Readme file for filtering 1.1.0', 'This is a readme file.' ] + for key, metadata_revision in enumerate( metadata_revisions ): + # Metadata revisions are in order newest to oldest at this point. + self.display_readme_file( repository, metadata_revision, strings_not_displayed=[ strings_to_check[ key ] ] ) + def test_0075_delete_readme_txt_file( self ): + '''Delete the readme.txt file.''' + repository = get_repository_by_name_and_owner( repository_name, admin_username ) + self.delete_files_from_repository( repository, filenames=[ 'readme.txt' ] ) + self.check_metadata_in_repository_changelog( repository, metadata_count=2 ) + # Deleting a readme file for a specific revision should make the repository fall back + # to a previous revision's readme file, if one exists. + # TODO: All readme files should be displayed. + self.display_readme_file( repository, strings_displayed=[ 'Readme file for filtering 1.1.0' ] )

diff -r 4eaa644dd47877c40ee7090d56379998d7aecafa -r e291341d0127df0fd9bf8f66ac1d9df3f58b9bd7 test/tool_shed/functional_tests.py --- a/test/tool_shed/functional_tests.py +++ b/test/tool_shed/functional_tests.py @@ -31,6 +31,7 @@ import galaxy.webapps.community.app from galaxy.webapps.community.app import UniverseApplication from galaxy.webapps.community import buildapp +#from galaxy.webapps.community.util.hgweb_config import *

import nose.core import nose.config @@ -164,6 +165,8 @@ running_functional_tests = True, hgweb_config_dir = new_file_path, **kwargs ) +# app.hgweb_config_manager = HgWebConfigManager() + log.info( "Embedded Universe application started" )

# ---- Run webserver ------------------------------------------------------

diff -r 4eaa644dd47877c40ee7090d56379998d7aecafa -r e291341d0127df0fd9bf8f66ac1d9df3f58b9bd7 test/tool_shed/test_data/filtering.txt --- /dev/null +++ b/test/tool_shed/test_data/filtering.txt @@ -0,0 +1,1 @@ +Readme file for filtering 1.1.0

diff -r 4eaa644dd47877c40ee7090d56379998d7aecafa -r e291341d0127df0fd9bf8f66ac1d9df3f58b9bd7 test/tool_shed/test_data/filtering_2.2.0.tar Binary file test/tool_shed/test_data/filtering_2.2.0.tar has changed

diff -r 4eaa644dd47877c40ee7090d56379998d7aecafa -r e291341d0127df0fd9bf8f66ac1d9df3f58b9bd7 test/tool_shed/test_data/filtering_test_data.tar Binary file test/tool_shed/test_data/filtering_test_data.tar has changed

diff -r 4eaa644dd47877c40ee7090d56379998d7aecafa -r e291341d0127df0fd9bf8f66ac1d9df3f58b9bd7 test/tool_shed/test_data/readme.txt --- /dev/null +++ b/test/tool_shed/test_data/readme.txt @@ -0,0 +1,1 @@ +This is a readme file.

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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