Tool shed functional test enhancements. Functional tests for displaying images on a tool's page. Updated test string in tool migration stage test.

test/tool_shed/base/twilltestcase.py

@@ -838,6 +838,11 @@ class ShedTwillTestCase( TwillTestCase ):
         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 )

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=[] )

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'

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 ] )

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 @@ class TestToolMigrationStages( 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' % 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',