1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/0dc6a4052711/ Changeset: 0dc6a4052711 User: inithello Date: 2013-04-03 17:56:58 Summary: Tool shed functional test enhancements. Functional tests for displaying images on a tool's page. Updated test string in tool migration stage test. Affected #: 5 files

diff -r 1c7460ba03f9363c9d96e35dc53c3d3f95002346 -r 0dc6a4052711af50bbfaa438f3d591ff9bae4175 test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -838,6 +838,11 @@ self.visit_url( url ) self.check_for_strings( strings_displayed, strings_not_displayed )

+ def load_page_for_installed_tool( self, tool_guid, strings_displayed=[], strings_not_displayed=[] ): + url = '/tool_runner?tool_id=%s' % tool_guid + self.visit_galaxy_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 1c7460ba03f9363c9d96e35dc53c3d3f95002346 -r 0dc6a4052711af50bbfaa438f3d591ff9bae4175 test/tool_shed/functional/test_0140_tool_help_images.py --- /dev/null +++ b/test/tool_shed/functional/test_0140_tool_help_images.py @@ -0,0 +1,86 @@ +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 = 'htseq_count_0140' +repository_description = "Converter: BED to GFF" +repository_long_description = "Convert bed to gff" + +category_name = 'Test 0140 Tool Help Images' +category_description = 'Test 0140 Tool Help Images' + +''' +1) Create and populate the htseq_count_0140 repository. +2) Visit the manage_repository page. +3) Simulate clicking the htseq_count tool button. +4) On the resulting display tool page, look for the image string similar to the following string where the encoded repository_id is previously determined: + +src="/repository/static/images/<id>/count_modes.png" + +''' + + +class TestToolHelpImages( ShedTwillTestCase ): + '''Test features related to tool help images.''' + + def test_0000_initiate_users( self ): + """Create necessary user accounts.""" + 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' % 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' % admin_email + admin_user_private_role = test_db_util.get_private_role( admin_user ) + + def test_0005_create_htseq_count_repository( self ): + '''Create and populate htseq_count_0140.''' + ''' + We are at step 1 - Create and populate the htseq_count_0140 repository. + Create the htseq_count_0140 repository and upload the tarball. + ''' + 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 ) + # Create a repository named htseq_count_0140 owned by user1. + 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=[] ) + # Upload htseq_count.tar to the repository. + self.upload_file( repository, + filename='htseq_count/htseq_count.tar', + filepath=None, + valid_tools_only=True, + uncompress_file=False, + remove_repo_files_not_in_tar=False, + commit_message='Uploaded htseq_count.tar.', + strings_displayed=[], + strings_not_displayed=[] ) + + def test_0010_load_tool_page( self ): + '''Load the tool page and check for the image.''' + ''' + We are at step 2 + Visit the manage_repository page and the tool page, and look for the image url + similar to the following string: + + src="/repository/static/images/<id>/count_modes.png" + ''' + repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) + # Get the repository tip. + changeset_revision = self.get_repository_tip( repository ) + self.display_manage_repository_page( repository ) + # Generate the image path. + image_path = 'src="/repository/static/images/%s/count_modes.png"' % self.security.encode_id( repository.id ) + # The repository uploaded in this test should only have one metadata revision, with one tool defined, which + # should be the tool that contains a link to the image. + repository_metadata = repository.metadata_revisions[ 0 ].metadata + tool_path = repository_metadata[ 'tools' ][ 0 ][ 'tool_config' ] + self.load_display_tool_page( repository, tool_path, changeset_revision, strings_displayed=[ image_path ], strings_not_displayed=[] )

diff -r 1c7460ba03f9363c9d96e35dc53c3d3f95002346 -r 0dc6a4052711af50bbfaa438f3d591ff9bae4175 test/tool_shed/functional/test_0430_browse_utilities.py --- a/test/tool_shed/functional/test_0430_browse_utilities.py +++ b/test/tool_shed/functional/test_0430_browse_utilities.py @@ -1,7 +1,8 @@ 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__) + +log = logging.getLogger( __name__ )

datatypes_repository_name = 'emboss_datatypes_0430' datatypes_repository_description = 'Galaxy applicable datatypes for EMBOSS for test 0430'

diff -r 1c7460ba03f9363c9d96e35dc53c3d3f95002346 -r 0dc6a4052711af50bbfaa438f3d591ff9bae4175 test/tool_shed/functional/test_1140_tool_help_images.py --- /dev/null +++ b/test/tool_shed/functional/test_1140_tool_help_images.py @@ -0,0 +1,119 @@ +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 = 'htseq_count_0140' +repository_description = "Converter: BED to GFF" +repository_long_description = "Convert bed to gff" + +category_name = 'Test 0140 Tool Help Images' +category_description = 'Test 0140 Tool Help Images' + +''' +1) Create and populate the htseq_count_0140 repository. +2) Visit the manage_repository page, then the tool page, and look for the image string +similar to the following string where the encoded repository_id is previously determined: + +src="/repository/static/images/<id>/count_modes.png" + +Galaxy side: +1) Install the htseq_count repository from the tool shed into Galaxy. +2) In the center tool panel, look for the image string similar to the following string where the encoded_repository_id is previously determined as the installed ToolShedRepository id: + +src="/tool_runner/static/images/<id>/count_modes.png" +''' + + +class TestToolHelpImages( ShedTwillTestCase ): + '''Test features related to tool help images.''' + + def test_0000_initiate_users( self ): + """Create necessary user accounts.""" + 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' % 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' % admin_email + admin_user_private_role = test_db_util.get_private_role( admin_user ) + + def test_0005_create_htseq_count_repository( self ): + '''Create and populate htseq_count_0140.''' + ''' + We are at step 1 - Create and populate the htseq_count_0140 repository. + Create the htseq_count_0140 repository and upload the tarball. + ''' + 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 ) + # Create a repository named htseq_count_0140 owned by user1. + 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=[] ) + if self.repository_is_new( repository ): + # Upload htseq_count.tar to the repository if it hasn't already been populated. + self.upload_file( repository, + filename='htseq_count/htseq_count.tar', + filepath=None, + valid_tools_only=True, + uncompress_file=False, + remove_repo_files_not_in_tar=False, + commit_message='Uploaded htseq_count.tar.', + strings_displayed=[], + strings_not_displayed=[] ) + + def test_0010_load_tool_page( self ): + '''Load the tool page and check for the image URL.''' + ''' + This is a duplicate of test method _0010 in test_0140_tool_help_images. + ''' + repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) + # Get the repository tip. + changeset_revision = self.get_repository_tip( repository ) + self.display_manage_repository_page( repository ) + # Generate the image path. + image_path = 'src="/repository/static/images/%s/count_modes.png"' % self.security.encode_id( repository.id ) + # The repository uploaded in this test should only have one metadata revision, with one tool defined, which + # should be the tool that contains a link to the image. + repository_metadata = repository.metadata_revisions[ 0 ].metadata + tool_path = repository_metadata[ 'tools' ][ 0 ][ 'tool_config' ] + self.load_display_tool_page( repository, tool_path, changeset_revision, strings_displayed=[ image_path ], strings_not_displayed=[] ) + + def test_0015_install_htseq_count_repository( self ): + '''Install the htseq_count_0140 repository into Galaxy.''' + ''' + We are at step 1 - Install the htseq_count_0140 repository from the tool shed into Galaxy. + ''' + repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) + self.galaxy_logout() + self.galaxy_login( email=common.admin_email, username=common.admin_username ) + self.install_repository( 'htseq_count_0140', + 'user1', + category_name, + strings_displayed=[], + install_tool_dependencies=False, + install_repository_dependencies=False ) + + def test_0020_verify_tool_image_link( self ): + '''Load the tool page and verify the image link.''' + ''' + We are at step 2 + + In the center tool panel, look for the image string similar to the following string where the + encoded_repository_id is previously determined as the installed ToolShedRepository id: + + src="/tool_runner/static/images/<id>/count_modes.png" + ''' + repository = test_db_util.get_installed_repository_by_name_owner( repository_name, common.test_user_1_name ) + image_path = 'src="/tool_runner/static/images/%s/count_modes.png"' % self.security.encode_id( repository.id ) + # The repository uploaded in this test should only define one tool, which should be the tool that contains a link to an image. + repository_metadata = repository.metadata + tool_id = repository_metadata[ 'tools' ][ 0 ][ 'guid' ] + self.load_page_for_installed_tool( tool_id, strings_displayed=[ image_path ] )

diff -r 1c7460ba03f9363c9d96e35dc53c3d3f95002346 -r 0dc6a4052711af50bbfaa438f3d591ff9bae4175 test/tool_shed/functional/test_1400_review_migration_stages.py --- a/test/tool_shed/functional/test_1400_review_migration_stages.py +++ b/test/tool_shed/functional/test_1400_review_migration_stages.py @@ -1,8 +1,10 @@ from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os import tool_shed.base.test_db_util as test_db_util

+ class TestToolMigrationStages( ShedTwillTestCase ): '''Verify that the migration stages display correctly.''' + def test_0000_initiate_users( self ): """Create necessary user accounts and login as an admin user.""" self.logout() @@ -15,11 +17,12 @@ 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_load_migration_stages_page( self ): '''Load the migration page and check for the appropriate migration stages.''' stages = [ 'emboss_5', 'emboss_datatypes', 'emboss', '5.0.0', '0002_tools.sh', - 'freebayes', '0.9.4_a46483351fd0196637614121868fb5c386612b55', 'samtools', '0.1.18', 'FreeBayes requires g++', + 'freebayes', '0.9.4_9696d0ce8a962f7bb61c4791be5ce44312b81cf8', 'samtools', '0.1.18', 'FreeBayes requires g++', 'ncurses', 'zlib', '0003_tools.sh', 'ncbi_blast_plus', 'blast_datatypes', 'blast+', '2.2.26+', 'blast.ncbi.nlm.nih.gov', 'NCBI BLAST+ tools', '0004_tools.sh', 'bwa_wrappers', '0.5.9', 'zlib and libpthread', 'Map with BWA for Illumina', '0005_tools.sh',

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

--

This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.