1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/ca145a616aee/ changeset: ca145a616aee user: inithello date: 2013-02-18 21:58:52 summary: Tool shed functional tests for: Citable URLs, simple repository dependencies with multiple repository owners. affected #: 6 files
diff -r 9e36d1ed099fb31eccbc6bf55f20c1bd3fec1773 -r ca145a616aee1ccb2499b115be9aeacc9ca2ecbd test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -695,11 +695,37 @@ self.check_for_strings( post_submit_strings_displayed, strings_not_displayed ) repository_ids = self.initiate_installation_process( new_tool_panel_section=new_tool_panel_section ) self.wait_for_repository_installation( repository_ids ) - def load_invalid_tool_page( self, repository, tool_xml, changeset_revision, strings_displayed=[], strings_not_displayed=[] ): - url = '/repository/load_invalid_tool?repository_id=%s&tool_config=%s&changeset_revision=%s' % \ - ( self.security.encode_id( repository.id ), tool_xml, changeset_revision ) + def load_citable_url( self, + username, + repository_name, + changeset_revision, + encoded_user_id, + encoded_repository_id, + strings_displayed=[], + strings_not_displayed=[], + strings_displayed_in_iframe=[], + strings_not_displayed_in_iframe=[] ): + url = '%s/view/%s' % ( self.url, username ) + # If repository name is passed in, append that to the url. + if repository_name: + url += '/%s' % repository_name + if changeset_revision: + # Changeset revision should never be provided unless repository name also is. + assert repository_name is not None, 'Changeset revision is present, but repository name is not - aborting.' + url += '/%s' % changeset_revision self.visit_url( url ) self.check_for_strings( strings_displayed, strings_not_displayed ) + # Now load the page that should be displayed inside the iframe and check for strings. + if encoded_repository_id: + url = '/repository/view_repository?id=%s&operation=view_or_manage_repository' % encoded_repository_id + if changeset_revision: + url += '&changeset_revision=%s' % changeset_revision + self.visit_url( url ) + self.check_for_strings( strings_displayed_in_iframe, strings_not_displayed_in_iframe ) + elif encoded_user_id: + url = '/repository/browse_repositories?user_id=%s&operation=repositories_by_user' % encoded_user_id + self.visit_url( url ) + self.check_for_strings( strings_displayed_in_iframe, strings_not_displayed_in_iframe ) def load_display_tool_page( self, repository, tool_xml_path, changeset_revision, strings_displayed=[], strings_not_displayed=[] ): url = '/repository/display_tool?repository_id=%s&tool_config=%s&changeset_revision=%s' % \ ( self.security.encode_id( repository.id ), tool_xml_path, changeset_revision ) @@ -709,6 +735,11 @@ url = '/admin/review_tool_migration_stages' self.visit_galaxy_url( url ) self.check_for_strings( strings_displayed, strings_not_displayed ) + def load_invalid_tool_page( self, repository, tool_xml, changeset_revision, strings_displayed=[], strings_not_displayed=[] ): + url = '/repository/load_invalid_tool?repository_id=%s&tool_config=%s&changeset_revision=%s' % \ + ( self.security.encode_id( repository.id ), tool_xml, changeset_revision ) + self.visit_url( url ) + self.check_for_strings( strings_displayed, strings_not_displayed ) def load_workflow_image_in_tool_shed( self, repository, workflow_name, changeset_revision=None, strings_displayed=[], strings_not_displayed=[] ): if not changeset_revision: changeset_revision = self.get_repository_tip( repository )
diff -r 9e36d1ed099fb31eccbc6bf55f20c1bd3fec1773 -r ca145a616aee1ccb2499b115be9aeacc9ca2ecbd test/tool_shed/functional/test_0120_simple_repository_dependency_multiple_owners.py --- /dev/null +++ b/test/tool_shed/functional/test_0120_simple_repository_dependency_multiple_owners.py @@ -0,0 +1,140 @@ +from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os +import tool_shed.base.test_db_util as test_db_util + +datatypes_repository_name = 'blast_datatypes_0120' +datatypes_repository_description = 'Galaxy applicable datatypes for BLAST' +datatypes_repository_long_description = 'Galaxy datatypes for the BLAST top hit descriptons tool' + +tool_repository_name = 'blastxml_to_top_descr_0120' +tool_repository_description = 'BLAST top hit descriptions' +tool_repository_long_description = 'Make a table from BLAST XML' + +''' +Tool shed side: + +1) Create and populate blast_datatypes_0120. +1a) Check for appropriate strings. +2) Create and populate blastxml_to_top_descr_0120. +2a) Check for appropriate strings. +3) Upload repository_dependencies.xml to blastxml_to_top_descr_0120 that defines a relationship to blast_datatypes_0120. +3a) Check for appropriate strings. +''' + +base_datatypes_count = 0 +repository_datatypes_count = 0 + +class TestRepositoryMultipleOwners( ShedTwillTestCase ): + def test_0000_initiate_users( self ): + """Create necessary user accounts and login as an admin user.""" + """ + Create all the user accounts that are needed for this test script to run independently of other tests. + Previously created accounts will not be re-created. + """ + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + test_user_1 = test_db_util.get_user( common.test_user_1_email ) + assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % common.test_user_1_email + test_user_1_private_role = test_db_util.get_private_role( test_user_1 ) + self.logout() + self.login( email=common.test_user_2_email, username=common.test_user_2_name ) + test_user_2 = test_db_util.get_user( common.test_user_1_email ) + assert test_user_2 is not None, 'Problem retrieving user with email %s from the database' % common.test_user_2_email + test_user_2_private_role = test_db_util.get_private_role( test_user_2 ) + self.logout() + self.login( email=common.admin_email, username=common.admin_username ) + 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' % common.admin_email + admin_user_private_role = test_db_util.get_private_role( admin_user ) + def test_0005_create_datatypes_repository( self ): + """Create and populate the blast_datatypes_0120 repository""" + """ + We are at step 1. + Create and populate blast_datatypes. + """ + category = self.create_category( name='Test 0120', description='Description of test 0120' ) + self.logout() + self.login( email=common.test_user_2_email, username=common.test_user_2_name ) + strings_displayed = [ 'Repository %s' % "'%s'" % datatypes_repository_name, + 'Repository %s has been created' % "'%s'" % datatypes_repository_name ] + repository = self.get_or_create_repository( name=datatypes_repository_name, + description=datatypes_repository_description, + long_description=datatypes_repository_long_description, + owner=common.test_user_2_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=strings_displayed ) + self.upload_file( repository, + filename='blast/blast_datatypes.tar', + filepath=None, + valid_tools_only=True, + uncompress_file=True, + remove_repo_files_not_in_tar=False, + commit_message='Uploaded blast_datatypes tarball.', + strings_displayed=[], + strings_not_displayed=[] ) + def test_0010_verify_datatypes_repository( self ): + '''Verify the blast_datatypes_0120 repository.''' + ''' + We are at step 1a. + Check for appropriate strings, most importantly BlastXml, BlastNucDb, and BlastProtDb, + the datatypes that are defined in datatypes_conf.xml. + ''' + global repository_datatypes_count + repository = test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_2_name ) + strings_displayed = [ 'BlastXml', 'BlastNucDb', 'BlastProtDb', 'application/xml', 'text/html', 'blastxml', 'blastdbn', 'blastdbp'] + self.display_manage_repository_page( repository, strings_displayed=strings_displayed ) + repository_datatypes_count = int( self.get_repository_datatypes_count( repository ) ) + def test_0015_create_tool_repository( self ): + """Create and populate the blastxml_to_top_descr_0120 repository""" + """ + We are at step 2. + Create and populate blastxml_to_top_descr_0120. + """ + category = self.create_category( name='Test 0120', description='Description of test 0120' ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + strings_displayed = [ 'Repository %s' % "'%s'" % tool_repository_name, + 'Repository %s has been created' % "'%s'" % tool_repository_name ] + repository = self.get_or_create_repository( name=tool_repository_name, + description=tool_repository_description, + long_description=tool_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=strings_displayed ) + self.upload_file( repository, + filename='blast/blastxml_to_top_descr.tar', + filepath=None, + valid_tools_only=True, + uncompress_file=True, + remove_repo_files_not_in_tar=False, + commit_message='Uploaded blastxml_to_top_descr tarball.', + strings_displayed=[], + strings_not_displayed=[] ) + def test_0020_verify_tool_repository( self ): + '''Verify the blastxml_to_top_descr_0120 repository.''' + ''' + We are at step 2a. + Check for appropriate strings, such as tool name, description, and version. + ''' + repository = test_db_util.get_repository_by_name_and_owner( tool_repository_name, common.test_user_1_name ) + strings_displayed = [ 'blastxml_to_top_descr_0120', 'BLAST top hit descriptions', 'Make a table from BLAST XML' ] + strings_displayed.extend( [ '0.0.1', 'Valid tools'] ) + self.display_manage_repository_page( repository, strings_displayed=strings_displayed ) + def test_0025_create_repository_dependency( self ): + '''Create a repository dependency on blast_datatypes_0120.''' + ''' + We are at step 3. + Create a simple repository dependency for blastxml_to_top_descr_0120 that defines a dependency on blast_datatypes_0120. + ''' + datatypes_repository = test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_2_name ) + tool_repository = test_db_util.get_repository_by_name_and_owner( tool_repository_name, common.test_user_1_name ) + dependency_xml_path = self.generate_temp_path( 'test_0120', additional_paths=[ 'dependencies' ] ) + self.create_repository_dependency( repository=tool_repository, depends_on=[ datatypes_repository ], filepath=dependency_xml_path ) + def test_0040_verify_repository_dependency( self ): + '''Verify the created repository dependency.''' + ''' + We are at step 3a. + Check the newly created repository dependency to ensure that it was defined and displays correctly. + ''' + datatypes_repository = test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_2_name ) + tool_repository = test_db_util.get_repository_by_name_and_owner( tool_repository_name, common.test_user_1_name ) + self.check_repository_dependency( tool_repository, datatypes_repository )
diff -r 9e36d1ed099fb31eccbc6bf55f20c1bd3fec1773 -r ca145a616aee1ccb2499b115be9aeacc9ca2ecbd test/tool_shed/functional/test_0420_citable_urls_for_repositories.py --- /dev/null +++ b/test/tool_shed/functional/test_0420_citable_urls_for_repositories.py @@ -0,0 +1,233 @@ +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_0420' +repository_description = 'Galaxy filtering tool for test 0420' +repository_long_description = 'Long description of Galaxy filtering tool for test 0410' + +first_changeset_hash = '' + +''' +1. Add and populate a repository to the tool shed with change set revision 0 (assume owner is test). +2. Add valid change set revision 1. +3. Visit the following url and check for appropriate strings: <tool shed base url>/view/user1 +4. Visit the following url and check for appropriate strings: <tool shed base url>/view/user1/filtering_0420 + Resulting page should contain change set revision 1 +5. Visit the following url and check for appropriate strings: <tool shed base url>/view/user1/filtering_0420/<revision 0> + Resulting page should not contain change set revision 1, but should contain change set revision 0. +6. Visit the following url and check for appropriate strings: <tool shed base url>/view/user1/filtering_0420/<invalid revision> +7. Visit the following url and check for appropriate strings: <tool shed base url>/view/user1/<invalid repository name> +8. Visit the following url and check for appropriate strings: <tool shed base url>/view/<invalid owner> +''' + +class TestRepositoryCitableURLs( ShedTwillTestCase ): + '''Test repository citable url features.''' + def test_0000_initiate_users( self ): + """Create necessary user accounts and login as an admin user.""" + """ + Create all the user accounts that are needed for this test script to run independently of other tests. + Previously created accounts will not be re-created. + """ + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + test_user_1 = test_db_util.get_user( common.test_user_1_email ) + assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % common.test_user_1_email + test_user_1_private_role = test_db_util.get_private_role( test_user_1 ) + self.logout() + self.login( email=common.admin_email, username=common.admin_username ) + 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' % common.admin_email + admin_user_private_role = test_db_util.get_private_role( admin_user ) + def test_0005_create_repository( self ): + """Create and populate the filtering_0420 repository""" + """ + We are at step 1. + Add and populate a repository to the tool shed with change set revision 0 (assume owner is test_user_1). + """ + global first_changeset_hash + category = self.create_category( name='Test 0400 Repository Citable URLs', + description='Test 0400 Repository Citable URLs category' ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + strings_displayed = [ 'Repository %s' % "'%s'" % repository_name, + 'Repository %s has been created' % "'%s'" % repository_name ] + repository = self.get_or_create_repository( name=repository_name, + description=repository_description, + long_description=repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=strings_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=[] ) + # We'll be checking for this hash later, after uploading another file to the repository, making get_repository_tip() not usable. + first_changeset_hash = self.get_repository_tip( repository ) + def test_0010_upload_new_file_to_repository( self ): + '''Upload a readme file to the repository in order to create a second changeset revision.''' + ''' + We are at step 2. + Add valid change set revision 1. + The repository should now contain two changeset revisions, 0:<revision hash> and 1:<revision hash>. + ''' + repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) + self.upload_file( repository, + filename='readme.txt', + filepath=None, + valid_tools_only=True, + uncompress_file=True, + remove_repo_files_not_in_tar=False, + commit_message='Uploaded readme.txt.', + strings_displayed=[], + strings_not_displayed=[] ) + def test_0015_load_user_view_page( self ): + '''Load the /view/<username> page amd check for strings.''' + ''' + We are at step 3. + Visit the following url and check for appropriate strings: <tool shed base url>/view/user1 + ''' + repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) + test_user_1 = test_db_util.get_user( common.test_user_1_email ) + encoded_user_id = self.security.encode_id( test_user_1.id ) + # Since twill does not load the contents of an iframe, we need to check that the iframe has been generated correctly, + # then directly load the url that the iframe should be loading and check for the expected strings. + # The iframe should point to /repository/browse_repositories?user_id=<encoded user ID>&operation=repositories_by_user + strings_displayed = [ '/repository/browse_repositories', encoded_user_id, 'operation=repositories_by_user' ] + strings_displayed.append( encoded_user_id ) + strings_displayed_in_iframe = [ 'user1', 'filtering_0420', 'Galaxy filtering tool for test 0420' ] + strings_displayed_in_iframe.append( self.get_repository_tip( repository ) ) + self.load_citable_url( username='user1', + repository_name=None, + changeset_revision=None, + encoded_user_id=encoded_user_id, + encoded_repository_id=None, + strings_displayed=strings_displayed, + strings_displayed_in_iframe=strings_displayed_in_iframe ) + def test_0020_load_repository_view_page( self ): + '''Load the /view/<user>/<repository> page and check for the appropriate strings.''' + ''' + We are at step 4. + Visit the following url and check for strings: <tool shed base url>/view/user1/filtering_0420 + Resulting page should contain change set revision 1 + ''' + repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) + test_user_1 = test_db_util.get_user( common.test_user_1_email ) + encoded_user_id = self.security.encode_id( test_user_1.id ) + encoded_repository_id = self.security.encode_id( repository.id ) + # Since twill does not load the contents of an iframe, we need to check that the iframe has been generated correctly, + # then directly load the url that the iframe should be loading and check for the expected strings. + # The iframe should point to /repository/bview_repository?id=<encoded repository ID> + strings_displayed = [ '/repository', 'view_repository', 'id=', encoded_repository_id ] + strings_displayed_in_iframe = [ 'user1', 'filtering_0420', 'Galaxy filtering tool for test 0420' ] + strings_displayed_in_iframe.append( self.get_repository_tip( repository ) ) + strings_displayed_in_iframe.append( 'Sharable link to this repository:' ) + strings_displayed_in_iframe.append( '%s/view/user1/filtering_0420' % self.url ) + self.load_citable_url( username='user1', + repository_name='filtering_0420', + changeset_revision=None, + encoded_user_id=encoded_user_id, + encoded_repository_id=encoded_repository_id, + strings_displayed=strings_displayed, + strings_displayed_in_iframe=strings_displayed_in_iframe ) + def test_0025_load_view_page_for_previous_revision( self ): + '''Load a citable url for a past changeset revision and verify that strings display.''' + ''' + We are at step 5. + Visit the following url and check for appropriate strings: <tool shed base url>/view/user1/filtering_0420/<revision 0> + Resulting page should not contain change set revision 1, but should contain change set revision 0. + ''' + global first_changeset_hash + repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) + test_user_1 = test_db_util.get_user( common.test_user_1_email ) + encoded_user_id = self.security.encode_id( test_user_1.id ) + encoded_repository_id = self.security.encode_id( repository.id ) + # We are checking the changeset revision pointed to by first_changeset_hash, stored in a global variable at the end of + # test_0005. The tip changeset hash should not be displayed here, but first_changeset_hash should. + tip_changeset_hash = self.get_repository_tip( repository ) + # Since twill does not load the contents of an iframe, we need to check that the iframe has been generated correctly, + # then directly load the url that the iframe should be loading and check for the expected strings. + # The iframe should point to /repository/view_repository?id=<encoded repository ID> + strings_displayed = [ '/repository', 'view_repository', 'id=' + encoded_repository_id ] + strings_displayed_in_iframe = [ 'user1', 'filtering_0420', 'Galaxy filtering tool for test 0420', first_changeset_hash ] + strings_displayed_in_iframe.append( 'Sharable link to this repository revision:' ) + strings_displayed_in_iframe.append( '%s/view/user1/filtering_0420/%s' % ( self.url, first_changeset_hash ) ) + strings_not_displayed_in_iframe = [ tip_changeset_hash ] + self.load_citable_url( username='user1', + repository_name='filtering_0420', + changeset_revision=first_changeset_hash, + encoded_user_id=encoded_user_id, + encoded_repository_id=encoded_repository_id, + strings_displayed=strings_displayed, + strings_displayed_in_iframe=strings_displayed_in_iframe, + strings_not_displayed_in_iframe=strings_not_displayed_in_iframe ) + def test_0030_load_sharable_url_with_invalid_changeset_revision( self ): + '''Load a citable url with an invalid changeset revision specified.''' + repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) + test_user_1 = test_db_util.get_user( common.test_user_1_email ) + encoded_user_id = self.security.encode_id( test_user_1.id ) + encoded_repository_id = self.security.encode_id( repository.id ) + changeset_hash = '!!invalid!!' + tip_revision = self.get_repository_tip( repository ) + # Since twill does not load the contents of an iframe, we need to check that the iframe has been generated correctly, + # then directly load the url that the iframe should be loading and check for the expected strings. + # The iframe should point to /repository/view_repository?id=<encoded repository ID>&status=error + strings_displayed = [ '/repository', 'view_repository', 'id=' + encoded_repository_id ] + strings_displayed.extend( [ 'The+change+log', 'does+not+include+revision', '%21%21invalid%21%21', 'status=error' ] ) + strings_displayed_in_iframe = [ 'user1', 'filtering_0420', 'Galaxy filtering tool for test 0420' ] + strings_displayed_in_iframe.append( 'Sharable link to this repository revision:' ) + strings_displayed_in_iframe.append( '%s/view/user1/filtering_0420/%s' % ( self.url, changeset_hash ) ) + strings_not_displayed_in_iframe = [ tip_revision ] + self.load_citable_url( username='user1', + repository_name='filtering_0420', + changeset_revision=changeset_hash, + encoded_user_id=encoded_user_id, + encoded_repository_id=encoded_repository_id, + strings_displayed=strings_displayed, + strings_displayed_in_iframe=strings_displayed_in_iframe, + strings_not_displayed_in_iframe=strings_not_displayed_in_iframe ) + def test_0035_load_sharable_url_with_invalid_repository_name( self ): + '''Load a citable url with an invalid changeset revision specified.''' + ''' + We are at step 7 + Visit the following url and check for appropriate strings: <tool shed base url>/view/user1/!!invalid!! + ''' + repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) + test_user_1 = test_db_util.get_user( common.test_user_1_email ) + encoded_user_id = self.security.encode_id( test_user_1.id ) + tip_revision = self.get_repository_tip( repository ) + # Since twill does not load the contents of an iframe, we need to check that the iframe has been generated correctly, + # then directly load the url that the iframe should be loading and check for the expected strings. + # The iframe should point to /repository/browse_repositories?user_id=<encoded user ID>&operation=repositories_by_user + strings_displayed = [ '/repository', 'browse_repositories', 'user1' ] + strings_displayed.extend( [ 'list+of+repositories+owned', 'does+not+include+one+named', '%21%21invalid%21%21', 'status=error' ] ) + strings_displayed_in_iframe = [ 'user1', 'filtering_0420' ] + strings_displayed_in_iframe.append( 'Repositories owned by user1' ) + strings_displayed_in_iframe.append( tip_revision ) + self.load_citable_url( username='user1', + repository_name='!!invalid!!', + changeset_revision=None, + encoded_user_id=encoded_user_id, + encoded_repository_id=None, + strings_displayed=strings_displayed, + strings_displayed_in_iframe=strings_displayed_in_iframe ) + def test_0040_load_sharable_url_with_invalid_owner( self ): + '''Load a citable url with an invalid owner.''' + ''' + We are at step 8. + Visit the following url and check for appropriate strings: <tool shed base url>/view/!!invalid!! + ''' + strings_displayed = [ 'The tool shed', self.url, 'contains no repositories owned by', '!!invalid!!' ] + self.load_citable_url( username='!!invalid!!', + repository_name=None, + changeset_revision=None, + encoded_user_id=None, + encoded_repository_id=None, + strings_displayed=strings_displayed ) + \ No newline at end of file
diff -r 9e36d1ed099fb31eccbc6bf55f20c1bd3fec1773 -r ca145a616aee1ccb2499b115be9aeacc9ca2ecbd test/tool_shed/functional/test_1120_simple_repository_dependency_multiple_owners.py --- /dev/null +++ b/test/tool_shed/functional/test_1120_simple_repository_dependency_multiple_owners.py @@ -0,0 +1,190 @@ +from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os +import tool_shed.base.test_db_util as test_db_util + +datatypes_repository_name = 'blast_datatypes_0120' +datatypes_repository_description = 'Galaxy applicable datatypes for BLAST' +datatypes_repository_long_description = 'Galaxy datatypes for the BLAST top hit descriptons tool' + +tool_repository_name = 'blastxml_to_top_descr_0120' +tool_repository_description = 'BLAST top hit descriptions' +tool_repository_long_description = 'Make a table from BLAST XML' + +''' +Tool shed side: + +1) Create and populate blast_datatypes_0120. +1a) Check for appropriate strings. +2) Create and populate blastxml_to_top_descr_0120. +2a) Check for appropriate strings. +3) Upload repository_dependencies.xml to blastxml_to_top_descr_0120 that defines a relationship to blast_datatypes_0120. +3a) Check for appropriate strings. + + +Galaxy side: + +1) Install blastxml_to_top_descr_0120, with repository dependencies. +1a) Check for appropriate strings in the installed blastxml_to_top_descr_0120 and blast_datatypes_0120 repositories. +''' + +running_standalone = False + +class TestInstallRepositoryMultipleOwners( ShedTwillTestCase ): + def test_0000_initiate_users( self ): + """Create necessary user accounts and login as an admin user.""" + """ + Create all the user accounts that are needed for this test script to run independently of other tests. + Previously created accounts will not be re-created. + """ + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + test_user_1 = test_db_util.get_user( common.test_user_1_email ) + assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % common.test_user_1_email + test_user_1_private_role = test_db_util.get_private_role( test_user_1 ) + self.logout() + self.login( email=common.test_user_2_email, username=common.test_user_2_name ) + test_user_2 = test_db_util.get_user( common.test_user_1_email ) + assert test_user_2 is not None, 'Problem retrieving user with email %s from the database' % common.test_user_2_email + test_user_2_private_role = test_db_util.get_private_role( test_user_2 ) + self.logout() + self.login( email=common.admin_email, username=common.admin_username ) + 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' % common.admin_email + admin_user_private_role = test_db_util.get_private_role( admin_user ) + def test_0005_create_datatypes_repository( self ): + """Create and populate the blast_datatypes_0120 repository""" + """ + We are at step 1. + Create and populate blast_datatypes. + """ + category = self.create_category( name='Test 0120', description='Description of test 0120' ) + self.logout() + self.login( email=common.test_user_2_email, username=common.test_user_2_name ) + strings_displayed = [ 'Repository %s' % "'%s'" % datatypes_repository_name, + 'Repository %s has been created' % "'%s'" % datatypes_repository_name ] + repository = self.get_or_create_repository( name=datatypes_repository_name, + description=datatypes_repository_description, + long_description=datatypes_repository_long_description, + owner=common.test_user_2_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=strings_displayed ) + if self.repository_is_new( repository ): + self.upload_file( repository, + filename='blast/blast_datatypes.tar', + filepath=None, + valid_tools_only=True, + uncompress_file=True, + remove_repo_files_not_in_tar=False, + commit_message='Uploaded blast_datatypes tarball.', + strings_displayed=[], + strings_not_displayed=[] ) + def test_0010_verify_datatypes_repository( self ): + '''Verify the blast_datatypes_0120 repository.''' + ''' + We are at step 1a. + Check for appropriate strings, most importantly BlastXml, BlastNucDb, and BlastProtDb, + the datatypes that are defined in datatypes_conf.xml. + ''' + global repository_datatypes_count + repository = test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_2_name ) + strings_displayed = [ 'BlastXml', 'BlastNucDb', 'BlastProtDb', 'application/xml', 'text/html', 'blastxml', 'blastdbn', 'blastdbp'] + self.display_manage_repository_page( repository, strings_displayed=strings_displayed ) + repository_datatypes_count = int( self.get_repository_datatypes_count( repository ) ) + def test_0015_create_tool_repository( self ): + """Create and populate the blastxml_to_top_descr_0120 repository""" + """ + We are at step 2. + Create and populate blastxml_to_top_descr_0120. + """ + global running_standalone + category = self.create_category( name='Test 0120', description='Description of test 0120' ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + strings_displayed = [ 'Repository %s' % "'%s'" % tool_repository_name, + 'Repository %s has been created' % "'%s'" % tool_repository_name ] + repository = self.get_or_create_repository( name=tool_repository_name, + description=tool_repository_description, + long_description=tool_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=strings_displayed ) + if self.repository_is_new( repository ): + running_standalone = True + self.upload_file( repository, + filename='blast/blastxml_to_top_descr.tar', + filepath=None, + valid_tools_only=True, + uncompress_file=True, + remove_repo_files_not_in_tar=False, + commit_message='Uploaded blastxml_to_top_descr tarball.', + strings_displayed=[], + strings_not_displayed=[] ) + def test_0020_verify_tool_repository( self ): + '''Verify the blastxml_to_top_descr_0120 repository.''' + ''' + We are at step 2a. + Check for appropriate strings, such as tool name, description, and version. + ''' + repository = test_db_util.get_repository_by_name_and_owner( tool_repository_name, common.test_user_1_name ) + strings_displayed = [ 'blastxml_to_top_descr_0120', 'BLAST top hit descriptions', 'Make a table from BLAST XML' ] + strings_displayed.extend( [ '0.0.1', 'Valid tools'] ) + self.display_manage_repository_page( repository, strings_displayed=strings_displayed ) + def test_0025_create_repository_dependency( self ): + '''Create a repository dependency on blast_datatypes_0120.''' + ''' + We are at step 3. + Create a simple repository dependency for blastxml_to_top_descr_0120 that defines a dependency on blast_datatypes_0120. + ''' + global running_standalone + if running_standalone: + datatypes_repository = test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_2_name ) + tool_repository = test_db_util.get_repository_by_name_and_owner( tool_repository_name, common.test_user_1_name ) + dependency_xml_path = self.generate_temp_path( 'test_1120', additional_paths=[ 'dependencies' ] ) + self.create_repository_dependency( repository=tool_repository, depends_on=[ datatypes_repository ], filepath=dependency_xml_path ) + def test_0040_verify_repository_dependency( self ): + '''Verify the created repository dependency.''' + ''' + We are at step 3a. + Check the newly created repository dependency to ensure that it was defined and displays correctly. + ''' + datatypes_repository = test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_2_name ) + tool_repository = test_db_util.get_repository_by_name_and_owner( tool_repository_name, common.test_user_1_name ) + self.check_repository_dependency( tool_repository, datatypes_repository ) + def test_0045_install_blastxml_to_top_descr( self ): + '''Install the blastxml_to_top_descr_0120 repository to Galaxy.''' + ''' + We are at step 1, Galaxy side. + Install blastxml_to_top_descr_0120 to Galaxy, with repository dependencies, so that the datatypes repository is also installed. + ''' + global base_datatypes_count + self.galaxy_logout() + self.galaxy_login( email=common.admin_email, username=common.admin_username ) + base_datatypes_count = int( self.get_datatypes_count() ) + post_submit_strings_displayed = [ 'blastxml_to_top_descr_0120', 'blast_datatypes_0120', 'New' ] + self.install_repository( name='blastxml_to_top_descr_0120', + owner=common.test_user_1_name, + category_name='Test 0120', + install_repository_dependencies=True, + post_submit_strings_displayed=post_submit_strings_displayed, + new_tool_panel_section='Test 0120' ) + def test_0050_verify_repository_installation( self ): + '''Verify installation of blastxml_to_top_descr_0120 and blast_datatypes_0120.''' + ''' + We are at step 1a, Galaxy side. + Check that the blastxml_to_top_descr_0120 and blast_datatypes_0120 repositories installed correctly, and that there + are now new datatypes in the registry matching the ones defined in blast_datatypes_0120. Also check that + blast_datatypes_0120 is labeled as an installed repository dependency of blastxml_to_top_descr_0120. + ''' + global repository_datatypes_count + global base_datatypes_count + tool_repository = test_db_util.get_installed_repository_by_name_owner( tool_repository_name, common.test_user_1_name ) + datatypes_repository = test_db_util.get_installed_repository_by_name_owner( datatypes_repository_name, common.test_user_2_name ) + current_datatypes = int( self.get_datatypes_count() ) + expected_count = base_datatypes_count + repository_datatypes_count + assert current_datatypes == expected_count, 'Installing %s did not add new datatypes. Expected: %d. Found: %d' % \ + ( 'blastxml_to_top_descr_0120', expected_count, current_datatypes ) + strings_displayed = [ 'Installed repository dependencies', 'user1', 'blast_datatypes_0120' ] + strings_displayed.extend( [ 'Valid tools', 'BLAST top hit', 'Make a table', datatypes_repository.installed_changeset_revision ] ) + self.display_installed_repository_manage_page( tool_repository, strings_displayed=strings_displayed ) + strings_displayed = [ 'Datatypes', 'blastxml', 'blastdbp', 'blastdbn', 'BlastXml', 'BlastNucDb', 'BlastProtDb' ] + strings_displayed.extend( [ 'application/xml', 'text/html' ] ) + self.display_installed_repository_manage_page( datatypes_repository, strings_displayed=strings_displayed )
diff -r 9e36d1ed099fb31eccbc6bf55f20c1bd3fec1773 -r ca145a616aee1ccb2499b115be9aeacc9ca2ecbd test/tool_shed/test_data/blast/blast_datatypes.tar Binary file test/tool_shed/test_data/blast/blast_datatypes.tar has changed
diff -r 9e36d1ed099fb31eccbc6bf55f20c1bd3fec1773 -r ca145a616aee1ccb2499b115be9aeacc9ca2ecbd test/tool_shed/test_data/blast/blastxml_to_top_descr.tar Binary file test/tool_shed/test_data/blast/blastxml_to_top_descr.tar has changed
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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