diff --git a/test/tool_shed/base/twilltestcase.py b/test/tool_shed/base/twilltestcase.py index efdcc41efbe..eaebb1e6d8c 100644 --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -1119,6 +1119,41 @@ class ShedTwillTestCase( TwillTestCase ): # time.sleep( 1 ) # continue + def upload_url( self, + repository, + url, + filepath, + valid_tools_only, + uncompress_file, + remove_repo_files_not_in_tar, + commit_message, + strings_displayed=[], + strings_not_displayed=[] ): + removed_message = 'files were removed from the repository' + if remove_repo_files_not_in_tar: + if not self.repository_is_new( repository ): + if removed_message not in strings_displayed: + strings_displayed.append( removed_message ) + else: + if removed_message not in strings_not_displayed: + strings_not_displayed.append( removed_message ) + self.visit_url( '/upload/upload?repository_id=%s' % self.security.encode_id( repository.id ) ) + if valid_tools_only: + strings_displayed.extend( [ 'has been successfully', 'uploaded to the repository.' ] ) + tc.fv( "1", "url", url ) + if uncompress_file: + tc.fv( 1, 'uncompress_file', 'Yes' ) + else: + tc.fv( 1, 'uncompress_file', 'No' ) + if not self.repository_is_new( repository ): + if remove_repo_files_not_in_tar: + tc.fv( 1, 'remove_repo_files_not_in_tar', 'Yes' ) + else: + tc.fv( 1, 'remove_repo_files_not_in_tar', 'No' ) + tc.fv( 1, 'commit_message', commit_message ) + tc.submit( "upload_button" ) + self.check_for_strings( strings_displayed, strings_not_displayed ) + def verify_installed_repositories( self, installed_repositories=[], uninstalled_repositories=[] ): for repository_name, repository_owner in installed_repositories: galaxy_repository = test_db_util.get_installed_repository_by_name_owner( repository_name, repository_owner ) diff --git a/test/tool_shed/functional/test_0460_upload_to_repository.py b/test/tool_shed/functional/test_0460_upload_to_repository.py new file mode 100644 index 00000000000..4e795ad32e7 --- /dev/null +++ b/test/tool_shed/functional/test_0460_upload_to_repository.py @@ -0,0 +1,485 @@ +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__ ) + +category_name = 'Test 0460 Automatic repository revision completion' +category_description = 'Test 0460 Automatic repository revision completion' +datatypes_repository_name = 'emboss_datatypes_0460' +datatypes_repository_description = "Galaxy applicable data formats used by Emboss tools." +datatypes_repository_long_description = "Galaxy applicable data formats used by Emboss tools. This repository contains no tools." +bwa_repository_name = 'package_bwa_0_5_9_0460' +bwa_repository_description = "Contains a tool dependency definition that downloads and compiles version 0.5.9 of the BWA package" +bwa_repository_long_description = "bwa (alignment via Burrows-Wheeler transformation) 0.5.9-r16 by Heng Li" + +''' +For all steps, verify that the generated dependency points to the tip of the specified repository. + +1) Create and populate emboss_datatypes_0460. + +2) Create and populate package_bwa_0_5_9_0460 + +3) Create complex_dependency_test_1_0460, complex_dependency_test_2_0460, complex_dependency_test_3_0460, + complex_dependency_test_4_0460, complex_dependency_test_5_0460. + +4) Upload an uncompressed tool_dependencies.xml to complex_dependency_test_1_0460 that specifies a complex + repository dependency on package_bwa_0_5_9_0460 without a specified changeset revision or tool shed url. + +5) Upload a tarball to complex_dependency_test_2_0460 with a tool_dependencies.xml in the root of the tarball. + +6) Upload a tarball to complex_dependency_test_3_0460 with a tool_dependencies.xml in a subfolder within the tarball. + +7) Create hg_tool_dependency_0460 and hg_subfolder_tool_dependency_0460 and populate with orphan tool dependencies. + +8) Upload to complex_dependency_test_4_0460 using the url hg:///repos/user1/hg_tool_dependency_0460. + +9) Upload to complex_dependency_test_5_0460 using the url hg:///repos/user1/hg_subfolder_tool_dependency_0460. + +10) Create repository_dependency_test_1_0460, repository_dependency_test_2_0460, repository_dependency_test_3_0460, + repository_dependency_test_4_0460, repository_dependency_test_4_0460. + +11) Upload an uncompressed repository_dependencies.xml to repository_dependency_test_1_0460 that specifies a + repository dependency on emboss_datatypes_0460 without a specified changeset revision or tool shed url. + +12) Upload a tarball to repository_dependency_test_1_0460 with a repository_dependencies.xml in the root of the tarball. + +13) Upload a tarball to repository_dependency_test_1_0460 with a repository_dependencies.xml in a subfolder within the tarball. + +14) Create hg_repository_dependency_0460 and populate with repository_dependencies.xml. + +15) Upload to repository_dependency_test_4_0460 using the url hg:///repos/user1/hg_repository_dependency_0460. + +16) Upload to repository_dependency_test_5_0460 using the url hg:///repos/user1/hg_repository_dependency_0460. +''' + +class TestAutomaticDependencyRevision( ShedTwillTestCase ): + '''Test defining repository dependencies without specifying the changeset revision.''' + + def test_0000_initiate_users( self ): + """Create necessary user accounts and login as an admin user.""" + 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_2_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 emboss_datatypes_0460 repository''' + ''' + This is step 1 - Create and populate emboss_datatypes_0460. + ''' + self.create_category( name=category_name, description=category_description ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + category = test_db_util.get_category_by_name( category_name ) + repository = self.get_or_create_repository( name=datatypes_repository_name, + description=datatypes_repository_description, + long_description=datatypes_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + self.upload_file( repository, + filename='emboss/datatypes/datatypes_conf.xml', + filepath=None, + valid_tools_only=True, + uncompress_file=False, + remove_repo_files_not_in_tar=False, + commit_message='Populate emboss_datatypes_0460 with datatype definitions.', + strings_displayed=[], + strings_not_displayed=[] ) + + def test_0010_create_bwa_package_repository( self ): + '''Create and populate the package_bwa_0_5_9_0460 repository.''' + ''' + This is step 2 - Create and populate package_bwa_0_5_9_0460. + ''' + category = test_db_util.get_category_by_name( category_name ) + repository = self.get_or_create_repository( name=bwa_repository_name, + description=bwa_repository_description, + long_description=bwa_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + self.upload_file( repository, + filename='bwa/complex/tool_dependencies.xml', + filepath=None, + valid_tools_only=True, + uncompress_file=False, + remove_repo_files_not_in_tar=False, + commit_message='Populate package_bwa_0_5_9_0460 with an orphan tool dependency definition.', + strings_displayed=[], + strings_not_displayed=[] ) + + def test_0015_create_tool_dependency_repositories( self ): + '''Create repositories for testing complex dependency generation.''' + ''' + This is step 3 - Create complex_dependency_test_1_0460, complex_dependency_test_2_0460, complex_dependency_test_3_0460, + complex_dependency_test_4_0460, complex_dependency_test_5_0460. Each of these repositories will be populated in a way + that tests a different way to achieve the same resulting dependency structure using complex tool dependencies. + The different methods being tested are: + - Upload an uncompressed tool_dependencies.xml to the root of the repository. + - Upload a tool_dependencies.xml in a tarball, not in a subfolder. + - Upload a tool_dependencies.xml in a subfolder within a tarball. + - Upload via url, with the tool_dependencies.xml in the root of another repository. + - Upload via url, with the tool_dependencies.xml in a subfolder within another repository. + ''' + category = test_db_util.get_category_by_name( category_name ) + repository_base_name = 'complex_dependency_test_%d_0460' + repository_base_description = 'Test #%d for complex repository dependency definitions.' + repository_base_long_description = 'Test #%d for complex repository dependency definitions.' + for number in range( 1, 6 ): + repository = self.get_or_create_repository( name=repository_base_name % number, + description=repository_base_description % number, + long_description=repository_base_long_description % number, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + + def test_0020_populate_complex_dependency_test_1_0460( self ): + '''Populate complex_dependency_test_1_0460.''' + ''' + This is step 4 - Upload an uncompressed tool_dependencies.xml to complex_dependency_test_1_0460 that specifies + a complex repository dependency on package_bwa_0_5_9_0460 without a specified changeset revision or tool shed url. + ''' + repository = test_db_util.get_repository_by_name_and_owner( 'complex_dependency_test_1_0460', common.test_user_1_name ) + package_repository = test_db_util.get_repository_by_name_and_owner( 'package_bwa_0_5_9_0460', common.test_user_1_name ) + self.upload_file( repository, + filename='0460_files/tool_dependencies.xml', + filepath=None, + valid_tools_only=True, + uncompress_file=False, + remove_repo_files_not_in_tar=False, + commit_message='Uploaded complex repository dependency definition.', + strings_displayed=[], + strings_not_displayed=[] ) + changeset_revision = self.get_repository_tip( package_repository ) + strings_displayed = [ 'package_bwa_0_5_9_0460', 'bwa', '0.5.9', 'package', changeset_revision ] + self.display_manage_repository_page( repository, strings_displayed=strings_displayed ) + self.display_repository_file_contents( repository, filename='tool_dependencies.xml', strings_displayed=[ changeset_revision ] ) + + def test_0025_populate_complex_dependency_test_2_0460( self ): + '''Populate complex_dependency_test_2_0460.''' + ''' + This is step 5 - Upload an tarball with tool_dependencies.xml to complex_dependency_test_2_0460 that specifies + a complex repository dependency on package_bwa_0_5_9_0460 without a specified changeset revision or tool shed url. + ''' + repository = test_db_util.get_repository_by_name_and_owner( 'complex_dependency_test_2_0460', common.test_user_1_name ) + package_repository = test_db_util.get_repository_by_name_and_owner( 'package_bwa_0_5_9_0460', common.test_user_1_name ) + self.upload_file( repository, + filename='0460_files/tool_dependencies_in_root.tar', + filepath=None, + valid_tools_only=True, + uncompress_file=False, + remove_repo_files_not_in_tar=True, + commit_message='Uploaded complex repository dependency definition.', + strings_displayed=[], + strings_not_displayed=[] ) + changeset_revision = self.get_repository_tip( package_repository ) + strings_displayed = [ 'package_bwa_0_5_9_0460', 'bwa', '0.5.9', 'package', changeset_revision ] + self.display_manage_repository_page( repository, strings_displayed=strings_displayed ) + self.display_repository_file_contents( repository, filename='tool_dependencies.xml', strings_displayed=[ changeset_revision ] ) + + def test_0030_populate_complex_dependency_test_3_0460( self ): + '''Populate complex_dependency_test_3_0460.''' + ''' + This is step 6 - Upload an tarball with tool_dependencies.xml in a subfolder to complex_dependency_test_3_0460 that + specifies a complex repository dependency on package_bwa_0_5_9_0460 without a specified changeset revision or tool shed url. + ''' + repository = test_db_util.get_repository_by_name_and_owner( 'complex_dependency_test_3_0460', common.test_user_1_name ) + package_repository = test_db_util.get_repository_by_name_and_owner( 'package_bwa_0_5_9_0460', common.test_user_1_name ) + self.upload_file( repository, + filename='0460_files/tool_dependencies_in_subfolder.tar', + filepath=None, + valid_tools_only=True, + uncompress_file=False, + remove_repo_files_not_in_tar=True, + commit_message='Uploaded complex repository dependency definition.', + strings_displayed=[], + strings_not_displayed=[] ) + changeset_revision = self.get_repository_tip( package_repository ) + strings_displayed = [ 'package_bwa_0_5_9_0460', 'bwa', '0.5.9', 'package', changeset_revision ] + self.display_manage_repository_page( repository, strings_displayed=strings_displayed ) + self.display_repository_file_contents( repository, + filename='tool_dependencies.xml', + filepath='subfolder', + strings_displayed=[ changeset_revision ] ) + + def test_0035_create_repositories_for_url_upload( self ): + '''Create and populate hg_tool_dependency_0460 and hg_subfolder_tool_dependency_0460.''' + ''' + This is step 7 - Create hg_tool_dependency_0460 and hg_subfolder_tool_dependency_0460 and populate with orphan tool dependencies. + ''' + category = test_db_util.get_category_by_name( category_name ) + repository = self.get_or_create_repository( name='hg_tool_dependency_0460', + description=bwa_repository_description, + long_description=bwa_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + self.upload_file( repository, + filename='0460_files/tool_dependencies.xml', + filepath=None, + valid_tools_only=True, + uncompress_file=False, + remove_repo_files_not_in_tar=False, + commit_message='Populate hg_tool_dependency_0460 with an orphan tool dependency definition.', + strings_displayed=[], + strings_not_displayed=[] ) + repository = self.get_or_create_repository( name='hg_subfolder_tool_dependency_0460', + description=bwa_repository_description, + long_description=bwa_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + self.upload_file( repository, + filename='0460_files/tool_dependencies_in_subfolder.tar', + filepath=None, + valid_tools_only=True, + uncompress_file=False, + remove_repo_files_not_in_tar=False, + commit_message='Populate hg_subfolder_tool_dependency_0460 with an orphan tool dependency definition.', + strings_displayed=[], + strings_not_displayed=[] ) + + def test_0040_url_upload_to_complex_test( self ): + '''Populate complex_dependency_test_4_0460.''' + ''' + This is step 8 - Upload to complex_dependency_test_4_0460 using the url hg:///repos/user1/hg_tool_dependency_0460. + ''' + url = 'hg://%s:%s/repos/user1/hg_tool_dependency_0460' % ( self.host, self.port ) + repository = test_db_util.get_repository_by_name_and_owner( 'complex_dependency_test_4_0460', common.test_user_1_name ) + package_repository = test_db_util.get_repository_by_name_and_owner( 'package_bwa_0_5_9_0460', common.test_user_1_name ) + self.upload_url( repository, + url=url, + filepath=None, + valid_tools_only=True, + uncompress_file=False, + remove_repo_files_not_in_tar=True, + commit_message='Uploaded complex repository dependency definition.', + strings_displayed=[], + strings_not_displayed=[] ) + changeset_revision = self.get_repository_tip( package_repository ) + strings_displayed = [ 'package_bwa_0_5_9_0460', 'bwa', '0.5.9', 'package', changeset_revision ] + self.display_manage_repository_page( repository, strings_displayed=strings_displayed ) + self.display_repository_file_contents( repository, + filename='tool_dependencies.xml', + strings_displayed=[ changeset_revision ] ) + + def test_0045_url_upload_to_complex_test( self ): + '''Populate complex_dependency_test_4_0460.''' + ''' + This is step 9 - Upload to complex_dependency_test_5_0460 using the url hg:///repos/user1/hg_subfolder_tool_dependency_0460. + ''' + url = 'hg://%s:%s/repos/user1/hg_subfolder_tool_dependency_0460' % ( self.host, self.port ) + repository = test_db_util.get_repository_by_name_and_owner( 'complex_dependency_test_5_0460', common.test_user_1_name ) + package_repository = test_db_util.get_repository_by_name_and_owner( 'package_bwa_0_5_9_0460', common.test_user_1_name ) + self.upload_url( repository, + url=url, + filepath=None, + valid_tools_only=True, + uncompress_file=False, + remove_repo_files_not_in_tar=True, + commit_message='Uploaded complex repository dependency definition.', + strings_displayed=[], + strings_not_displayed=[] ) + changeset_revision = self.get_repository_tip( package_repository ) + strings_displayed = [ 'package_bwa_0_5_9_0460', 'bwa', '0.5.9', 'package', changeset_revision ] + self.display_manage_repository_page( repository, strings_displayed=strings_displayed ) + self.display_repository_file_contents( repository, + filename='tool_dependencies.xml', + filepath='subfolder', + strings_displayed=[ changeset_revision ] ) + + def test_0050_create_repositories_for_simple_dependencies( self ): + '''Create repositories for testing simple dependency generation.''' + ''' + This is step 10 - Create repository_dependency_test_1_0460, repository_dependency_test_2_0460, repository_dependency_test_3_0460, + repository_dependency_test_4_0460, repository_dependency_test_4_0460.. Each of these repositories will be populated in a way + that tests a different way to achieve the same resulting dependency structure using complex tool dependencies. + The different methods being tested are: + - Upload an uncompressed repository_dependencies.xml to the root of the repository. + - Upload a repository_dependencies.xml in a tarball, not in a subfolder. + - Upload a repository_dependencies.xml in a subfolder within a tarball. + - Upload via url, with the repository_dependencies.xml in the root of another repository. + - Upload via url, with the repository_dependencies.xml in a subfolder within another repository. + ''' + category = test_db_util.get_category_by_name( category_name ) + repository_base_name = 'repository_dependency_test_%d_0460' + repository_base_description = 'Test #%d for repository dependency definitions.' + repository_base_long_description = 'Test #%d for repository dependency definitions.' + for number in range( 1, 6 ): + repository = self.get_or_create_repository( name=repository_base_name % number, + description=repository_base_description % number, + long_description=repository_base_long_description % number, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + + + def test_0055_populate_repository_dependency_test_1_0460( self ): + '''Populate repository_dependency_test_1_0460.''' + ''' + This is step 11 - Upload an uncompressed repository_dependencies.xml to repository_dependency_test_1_0460 that specifies a + repository dependency on emboss_datatypes_0460 without a specified changeset revision or tool shed url. + ''' + repository = test_db_util.get_repository_by_name_and_owner( 'repository_dependency_test_1_0460', common.test_user_1_name ) + package_repository = test_db_util.get_repository_by_name_and_owner( 'emboss_datatypes_0460', common.test_user_1_name ) + self.upload_file( repository, + filename='0460_files/repository_dependencies.xml', + filepath=None, + valid_tools_only=True, + uncompress_file=False, + remove_repo_files_not_in_tar=False, + commit_message='Uploaded complex repository dependency definition.', + strings_displayed=[], + strings_not_displayed=[] ) + changeset_revision = self.get_repository_tip( package_repository ) + strings_displayed = [ 'emboss_datatypes_0460', 'user1', changeset_revision ] + self.display_manage_repository_page( repository, strings_displayed=strings_displayed ) + self.display_repository_file_contents( repository, filename='repository_dependencies.xml', strings_displayed=[ changeset_revision ] ) + + def test_0060_populate_repository_dependency_test_2_0460( self ): + '''Populate repository_dependency_test_2_0460.''' + ''' + This is step 12 - Upload a tarball to repository_dependency_test_2_0460 with a repository_dependencies.xml in the root of the tarball. + ''' + repository = test_db_util.get_repository_by_name_and_owner( 'repository_dependency_test_2_0460', common.test_user_1_name ) + package_repository = test_db_util.get_repository_by_name_and_owner( 'emboss_datatypes_0460', common.test_user_1_name ) + self.upload_file( repository, + filename='0460_files/repository_dependencies_in_root.tar', + filepath=None, + valid_tools_only=True, + uncompress_file=False, + remove_repo_files_not_in_tar=True, + commit_message='Uploaded complex repository dependency definition.', + strings_displayed=[], + strings_not_displayed=[] ) + changeset_revision = self.get_repository_tip( package_repository ) + strings_displayed = [ 'emboss_datatypes_0460', 'user1', changeset_revision ] + self.display_manage_repository_page( repository, strings_displayed=strings_displayed ) + self.display_repository_file_contents( repository, filename='repository_dependencies.xml', strings_displayed=[ changeset_revision ] ) + + def test_0065_populate_repository_dependency_test_3_0460( self ): + '''Populate repository_dependency_test_3_0460.''' + ''' + This is step 13 - Upload a tarball to repository_dependency_test_3_0460 with a repository_dependencies.xml in a + subfolder within the tarball. + ''' + repository = test_db_util.get_repository_by_name_and_owner( 'repository_dependency_test_3_0460', common.test_user_1_name ) + package_repository = test_db_util.get_repository_by_name_and_owner( 'emboss_datatypes_0460', common.test_user_1_name ) + self.upload_file( repository, + filename='0460_files/repository_dependencies_in_subfolder.tar', + filepath=None, + valid_tools_only=True, + uncompress_file=False, + remove_repo_files_not_in_tar=True, + commit_message='Uploaded complex repository dependency definition.', + strings_displayed=[], + strings_not_displayed=[] ) + changeset_revision = self.get_repository_tip( package_repository ) + strings_displayed = [ 'emboss_datatypes_0460', 'user1', changeset_revision ] + self.display_manage_repository_page( repository, strings_displayed=strings_displayed ) + self.display_repository_file_contents( repository, + filename='repository_dependencies.xml', + filepath='subfolder', + strings_displayed=[ changeset_revision ] ) + + def test_0070_create_repositories_for_url_upload( self ): + '''Create and populate hg_repository_dependency_0460 and hg_subfolder_repository_dependency_0460.''' + ''' + This is step 14 - Create hg_repository_dependency_0460 and hg_subfolder_repository_dependency_0460 and populate + with repository dependencies. + ''' + category = test_db_util.get_category_by_name( category_name ) + repository = self.get_or_create_repository( name='hg_repository_dependency_0460', + description=bwa_repository_description, + long_description=bwa_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + self.upload_file( repository, + filename='0460_files/repository_dependencies.xml', + filepath=None, + valid_tools_only=True, + uncompress_file=False, + remove_repo_files_not_in_tar=False, + commit_message='Populate hg_repository_dependency_0460 with an orphan tool dependency definition.', + strings_displayed=[], + strings_not_displayed=[] ) + repository = self.get_or_create_repository( name='hg_subfolder_repository_dependency_0460', + description=bwa_repository_description, + long_description=bwa_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + self.upload_file( repository, + filename='0460_files/repository_dependencies_in_subfolder.tar', + filepath=None, + valid_tools_only=True, + uncompress_file=False, + remove_repo_files_not_in_tar=False, + commit_message='Populate hg_subfolder_repository_dependency_0460 with an orphan tool dependency definition.', + strings_displayed=[], + strings_not_displayed=[] ) + + def test_0075_url_upload_to_complex_test( self ): + '''Populate repository_dependency_test_4_0460.''' + ''' + This is step 15 - Upload to repository_dependency_test_4_0460 using the url + hg:///repos/user1/hg_repository_dependency_0460. + ''' + url = 'hg://%s:%s/repos/user1/hg_repository_dependency_0460' % ( self.host, self.port ) + repository = test_db_util.get_repository_by_name_and_owner( 'repository_dependency_test_4_0460', common.test_user_1_name ) + package_repository = test_db_util.get_repository_by_name_and_owner( 'emboss_datatypes_0460', common.test_user_1_name ) + self.upload_url( repository, + url=url, + filepath=None, + valid_tools_only=True, + uncompress_file=False, + remove_repo_files_not_in_tar=True, + commit_message='Uploaded repository dependency definition.', + strings_displayed=[], + strings_not_displayed=[] ) + changeset_revision = self.get_repository_tip( package_repository ) + strings_displayed = [ 'emboss_datatypes_0460', 'user1', changeset_revision ] + self.display_manage_repository_page( repository, strings_displayed=strings_displayed ) + self.display_repository_file_contents( repository, + filename='repository_dependencies.xml', + strings_displayed=[ changeset_revision ] ) + + def test_0080_url_upload_to_complex_test( self ): + '''Populate repository_dependency_test_4_0460.''' + ''' + This is step 16 - Upload to repository_dependency_test_5_0460 using the url + hg:///repos/user1/hg_subfolder_repository_dependency_0460. + ''' + url = 'hg://%s:%s/repos/user1/hg_subfolder_repository_dependency_0460' % ( self.host, self.port ) + repository = test_db_util.get_repository_by_name_and_owner( 'repository_dependency_test_5_0460', common.test_user_1_name ) + package_repository = test_db_util.get_repository_by_name_and_owner( 'emboss_datatypes_0460', common.test_user_1_name ) + self.upload_url( repository, + url=url, + filepath=None, + valid_tools_only=True, + uncompress_file=False, + remove_repo_files_not_in_tar=True, + commit_message='Uploaded repository dependency definition.', + strings_displayed=[], + strings_not_displayed=[] ) + changeset_revision = self.get_repository_tip( package_repository ) + strings_displayed = [ 'emboss_datatypes_0460', 'user1', changeset_revision ] + self.display_manage_repository_page( repository, strings_displayed=strings_displayed ) + self.display_repository_file_contents( repository, + filename='repository_dependencies.xml', + filepath='subfolder', + strings_displayed=[ changeset_revision ] ) \ No newline at end of file diff --git a/test/tool_shed/functional_tests.py b/test/tool_shed/functional_tests.py index 0d531082274..f9c1ffff324 100644 --- a/test/tool_shed/functional_tests.py +++ b/test/tool_shed/functional_tests.py @@ -15,7 +15,7 @@ new_path = [ os.path.join( cwd, "lib" ) ] new_path.extend( sys.path[1:] ) sys.path = new_path -from galaxy import eggs +from galaxy import eggs, model eggs.require( "nose" ) eggs.require( "NoseHTML" ) @@ -38,7 +38,6 @@ import galaxy.webapps.tool_shed.app from galaxy.webapps.tool_shed.app import UniverseApplication as ToolshedUniverseApplication from galaxy.webapps.tool_shed import buildapp as toolshedbuildapp # This is for the galaxy application. -import galaxy.app from galaxy.app import UniverseApplication as GalaxyUniverseApplication from galaxy.web import buildapp as galaxybuildapp diff --git a/test/tool_shed/test_data/0460_files/repository_dependencies.xml b/test/tool_shed/test_data/0460_files/repository_dependencies.xml new file mode 100644 index 00000000000..f39196b0b3b --- /dev/null +++ b/test/tool_shed/test_data/0460_files/repository_dependencies.xml @@ -0,0 +1,4 @@ + + + + \ No newline at end of file diff --git a/test/tool_shed/test_data/0460_files/repository_dependencies_in_root.tar b/test/tool_shed/test_data/0460_files/repository_dependencies_in_root.tar new file mode 100644 index 00000000000..e39a9db1cb8 Binary files /dev/null and b/test/tool_shed/test_data/0460_files/repository_dependencies_in_root.tar differ diff --git a/test/tool_shed/test_data/0460_files/repository_dependencies_in_subfolder.tar b/test/tool_shed/test_data/0460_files/repository_dependencies_in_subfolder.tar new file mode 100644 index 00000000000..eb82fe8e928 Binary files /dev/null and b/test/tool_shed/test_data/0460_files/repository_dependencies_in_subfolder.tar differ diff --git a/test/tool_shed/test_data/0460_files/tool_dependencies.xml b/test/tool_shed/test_data/0460_files/tool_dependencies.xml new file mode 100644 index 00000000000..d0bbbfa4f5b --- /dev/null +++ b/test/tool_shed/test_data/0460_files/tool_dependencies.xml @@ -0,0 +1,6 @@ + + + + + + \ No newline at end of file diff --git a/test/tool_shed/test_data/0460_files/tool_dependencies_in_root.tar b/test/tool_shed/test_data/0460_files/tool_dependencies_in_root.tar new file mode 100644 index 00000000000..8dc097bf940 Binary files /dev/null and b/test/tool_shed/test_data/0460_files/tool_dependencies_in_root.tar differ diff --git a/test/tool_shed/test_data/0460_files/tool_dependencies_in_subfolder.tar b/test/tool_shed/test_data/0460_files/tool_dependencies_in_subfolder.tar new file mode 100644 index 00000000000..515f4d993cb Binary files /dev/null and b/test/tool_shed/test_data/0460_files/tool_dependencies_in_subfolder.tar differ diff --git a/test/tool_shed/test_data/filtering/README b/test/tool_shed/test_data/filtering/README index 9ad35df358c..c030be8ce43 100644 --- a/test/tool_shed/test_data/filtering/README +++ b/test/tool_shed/test_data/filtering/README @@ -1,2 +1 @@ -These characters should not result in a unicode decoding error: -.... \ No newline at end of file +This is a third readme file. \ No newline at end of file