mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Clean up and fix tool shed functional test script 1300.
This commit is contained in:
Dave Bouvier
@@ -1,4 +1,5 @@
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from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os
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datatypes_repository_name = 'emboss_datatypes_0020'
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datatypes_repository_description = "Galaxy applicable data formats used by Emboss tools."
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datatypes_repository_long_description = "Galaxy applicable data formats used by Emboss tools. This repository contains no tools."
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@@ -6,6 +7,29 @@ emboss_repository_description = 'Galaxy wrappers for Emboss version 5.0.0 tools'
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emboss_repository_long_description = 'Galaxy wrappers for Emboss version 5.0.0 tools'
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workflow_filename = 'Workflow_for_0060_filter_workflow_repository.ga'
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workflow_name = 'Workflow for 0060_filter_workflow_repository'
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filtering_repository_description = "Galaxy's filtering tool for test 0040"
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filtering_repository_long_description = "Long description of Galaxy's filtering tool for test 0040"
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category_0000_name='Test 0000 Basic Repository Features 1'
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category_0001_name='Test 0000 Basic Repository Features 2'
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category_0010_name='Test 0010 Repository With Tool Dependencies'
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category_0020_name='Test 0020 Basic Repository Dependencies'
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category_0030_name='Test 0030 Repository Dependency Revisions'
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category_0040_name='test_0040_repository_circular_dependencies'
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category_0050_name='test_0050_repository_n_level_circular_dependencies'
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category_0060_name='Test 0060 Workflow Features'
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'''
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This script will run in one of two possible ways:
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1. Directly, by calling sh run_functional_tests.sh -toolshed test/tool_shed/functional/test_1300_reset_all_metadata.py.
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-OR-
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2. After the previous test scripts have completed.
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In the first case, it is desirable to have the Galaxy database in a state that is as close as possible to the state it would
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be in following the second case. This means explicitly installing whatever repositories would be in an installed state following
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the previous test scripts.
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'''
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base_datatypes_count = 0
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repository_datatypes_count = 0
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@@ -14,6 +38,7 @@ running_standalone = False
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class TestResetInstalledRepositoryMetadata( ShedTwillTestCase ):
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'''Verify that the "Reset selected metadata" feature works.'''
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def test_0000_initiate_users( self ):
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"""Create necessary user accounts."""
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self.logout()
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@@ -26,92 +51,108 @@ class TestResetInstalledRepositoryMetadata( ShedTwillTestCase ):
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admin_user = self.test_db_util.get_user( common.admin_email )
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assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email
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admin_user_private_role = self.test_db_util.get_private_role( admin_user )
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def test_0005_create_repositories_and_categories( self ):
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'''Ensure that the necessary categories and repositories exist for these tests.'''
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def test_0005_create_categories( self ):
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'''Create the categories for the repositories in this test script.'''
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self.logout()
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self.login( email=common.admin_email, username=common.admin_username )
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category_0000 = self.create_category( name=category_0000_name, description='Test 0000 Basic Repository Features 1' )
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category_0001 = self.create_category( name=category_0001_name, description='Test 0000 Basic Repository Features 2' )
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category_0010 = self.create_category( name=category_0010_name, description='Tests for a repository with tool dependencies.' )
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category_0020 = self.create_category( name=category_0020_name, description='Testing basic repository dependency features.' )
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category_0030 = self.create_category( name=category_0030_name, description='Testing repository dependencies by revision.' )
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category_0040 = self.create_category( name=category_0040_name, description='Testing handling of circular repository dependencies.' )
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category_0050 = self.create_category( name=category_0050_name, description='Testing handling of circular repository dependencies to n levels.' )
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category_0060 = self.create_category( name=category_0060_name, description='Test 0060 - Workflow Features' )
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def test_0010_create_repositories_from_0000_series( self ):
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'''Create repository filtering_0000 if necessary.'''
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global repository_datatypes_count
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global running_standalone
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category_0000 = self.create_category( name='Test 0000 Basic Repository Features 1', description='Test 0000 Basic Repository Features 1' )
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category_0001 = self.create_category( name='Test 0000 Basic Repository Features 2', description='Test 0000 Basic Repository Features 2' )
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category_0010 = self.create_category( name='Test 0010 Repository With Tool Dependencies', description='Tests for a repository with tool dependencies.' )
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category_0020 = self.create_category( name='Test 0020 Basic Repository Dependencies', description='Testing basic repository dependency features.' )
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category_0030 = self.create_category( name='Test 0030 Repository Dependency Revisions', description='Testing repository dependencies by revision.' )
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category_0040 = self.create_category( name='test_0040_repository_circular_dependencies', description='Testing handling of circular repository dependencies.' )
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category_0050 = self.create_category( name='test_0050_repository_n_level_circular_dependencies', description='Testing handling of circular repository dependencies to n levels.' )
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category_0060 = self.create_category( name='Test 0060 Workflow Features', description='Test 0060 - Workflow Features' )
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self.logout()
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self.login( email=common.test_user_1_email, username=common.test_user_1_name )
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category = self.create_category( name=category_0000_name, description='' )
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repository = self.get_or_create_repository( name='filtering_0000',
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description="Galaxy's filtering tool",
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long_description="Long description of Galaxy's filtering tool",
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owner=common.test_user_1_name,
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category_id=self.security.encode_id( category_0000.id ) )
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category_id=self.security.encode_id( category.id ) )
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if self.repository_is_new( repository ):
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self.upload_file( repository,
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filename='filtering/filtering_1.1.0.tar',
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filepath=None,
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valid_tools_only=True,
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uncompress_file=True,
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remove_repo_files_not_in_tar=False,
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commit_message='Uploaded filtering 1.1.0 tarball.',
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strings_displayed=[],
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strings_not_displayed=[] )
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self.upload_file( repository,
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filename='filtering/filtering_2.2.0.tar',
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filepath=None,
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valid_tools_only=True,
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uncompress_file=True,
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remove_repo_files_not_in_tar=False,
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commit_message='Uploaded filtering 2.2.0 tarball.',
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strings_displayed=[],
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strings_not_displayed=[] )
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running_standalone = True
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self.upload_file( repository,
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filename='filtering/filtering_1.1.0.tar',
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filepath=None,
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valid_tools_only=True,
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uncompress_file=True,
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remove_repo_files_not_in_tar=False,
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commit_message='Uploaded filtering 1.1.0 tarball.',
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strings_displayed=[],
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strings_not_displayed=[] )
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self.upload_file( repository,
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filename='filtering/filtering_2.2.0.tar',
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filepath=None,
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valid_tools_only=True,
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uncompress_file=True,
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remove_repo_files_not_in_tar=False,
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commit_message='Uploaded filtering 2.2.0 tarball.',
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strings_displayed=[],
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strings_not_displayed=[] )
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def test_0015_create_repositories_from_0010_series( self ):
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'''Create repository freebayes_0010.'''
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category = self.create_category( name=category_0010_name, description='' )
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repository = self.get_or_create_repository( name='freebayes_0010',
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description="Galaxy's freebayes tool",
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long_description="Long description of Galaxy's freebayes tool",
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owner=common.test_user_1_name,
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category_id=self.security.encode_id( category_0010.id ),
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category_id=self.security.encode_id( category.id ),
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strings_displayed=[] )
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if self.repository_is_new( repository ):
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self.upload_file( repository,
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filename='freebayes/freebayes.xml',
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filepath=None,
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valid_tools_only=False,
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uncompress_file=True,
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remove_repo_files_not_in_tar=False,
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commit_message='Uploaded freebayes.xml.',
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strings_displayed=[],
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strings_not_displayed=[] )
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self.upload_file( repository,
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filename='freebayes/tool_data_table_conf.xml.sample',
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filepath=None,
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valid_tools_only=False,
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uncompress_file=True,
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remove_repo_files_not_in_tar=False,
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commit_message='Uploaded tool_data_table_conf.xml.sample',
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strings_displayed=[],
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strings_not_displayed=[] )
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self.upload_file( repository,
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filename='freebayes/sam_fa_indices.loc.sample',
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filepath=None,
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valid_tools_only=False,
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uncompress_file=True,
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remove_repo_files_not_in_tar=False,
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commit_message='Uploaded sam_fa_indices.loc.sample',
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strings_displayed=[],
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strings_not_displayed=[] )
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self.upload_file( repository,
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filename='freebayes/tool_dependencies.xml',
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filepath=None,
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valid_tools_only=False,
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uncompress_file=True,
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remove_repo_files_not_in_tar=False,
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commit_message='Uploaded tool_dependencies.xml',
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strings_displayed=[],
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strings_not_displayed=[] )
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self.upload_file( repository,
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filename='freebayes/freebayes.xml',
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filepath=None,
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valid_tools_only=False,
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uncompress_file=True,
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remove_repo_files_not_in_tar=False,
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commit_message='Uploaded freebayes.xml.',
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strings_displayed=[],
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strings_not_displayed=[] )
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self.upload_file( repository,
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filename='freebayes/tool_data_table_conf.xml.sample',
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filepath=None,
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valid_tools_only=False,
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uncompress_file=True,
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remove_repo_files_not_in_tar=False,
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commit_message='Uploaded tool_data_table_conf.xml.sample',
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strings_displayed=[],
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strings_not_displayed=[] )
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self.upload_file( repository,
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filename='freebayes/sam_fa_indices.loc.sample',
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filepath=None,
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valid_tools_only=False,
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uncompress_file=True,
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remove_repo_files_not_in_tar=False,
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commit_message='Uploaded sam_fa_indices.loc.sample',
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strings_displayed=[],
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strings_not_displayed=[] )
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self.upload_file( repository,
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filename='freebayes/tool_dependencies.xml',
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filepath=None,
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valid_tools_only=False,
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uncompress_file=True,
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remove_repo_files_not_in_tar=False,
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commit_message='Uploaded tool_dependencies.xml',
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strings_displayed=[],
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strings_not_displayed=[] )
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def test_0020_create_repositories_from_0020_series( self ):
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'''Create repositories emboss_0020 and emboss_datatypes_0020 if necessary.'''
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category = self.create_category( name=category_0020_name, description='' )
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repository = self.get_or_create_repository( name='emboss_datatypes_0020',
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description="Galaxy applicable data formats used by Emboss tools.",
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long_description="Galaxy applicable data formats used by Emboss tools. This repository contains no tools.",
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owner=common.test_user_1_name,
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category_id=self.security.encode_id( category_0010.id ),
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category_id=self.security.encode_id( category.id ),
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strings_displayed=[] )
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if self.repository_is_new( repository ):
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self.upload_file( repository,
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@@ -127,7 +168,7 @@ class TestResetInstalledRepositoryMetadata( ShedTwillTestCase ):
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description='Galaxy wrappers for Emboss version 5.0.0 tools',
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long_description='Galaxy wrappers for Emboss version 5.0.0 tools',
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owner=common.test_user_1_name,
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category_id=self.security.encode_id( category_0020.id ),
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category_id=self.security.encode_id( category.id ),
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strings_displayed=[] )
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self.upload_file( repository,
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filename='emboss/emboss.tar',
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@@ -138,14 +179,17 @@ class TestResetInstalledRepositoryMetadata( ShedTwillTestCase ):
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commit_message='Uploaded emboss.tar',
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strings_displayed=[],
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strings_not_displayed=[] )
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def test_0025_create_repositories_from_0030_series( self ):
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'''Create repositories emboss_0030, emboss_5_0030, emboss_6_0030, and emboss_datatypes_0030.'''
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category = self.create_category( name=category_0030_name, description='' )
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datatypes_repository = self.get_or_create_repository( name='emboss_datatypes_0030',
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description=datatypes_repository_description,
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long_description=datatypes_repository_long_description,
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owner=common.test_user_1_name,
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category_id=self.security.encode_id( category_0030.id ),
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category_id=self.security.encode_id( category.id ),
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strings_displayed=[] )
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if self.repository_is_new( datatypes_repository ):
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running_standalone = True
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self.upload_file( datatypes_repository,
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filename='emboss/datatypes/datatypes_conf.xml',
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filepath=None,
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@@ -160,7 +204,7 @@ class TestResetInstalledRepositoryMetadata( ShedTwillTestCase ):
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description=emboss_repository_description,
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long_description=emboss_repository_long_description,
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owner=common.test_user_1_name,
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category_id=self.security.encode_id( category_0030.id ),
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category_id=self.security.encode_id( category.id ),
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strings_displayed=[] )
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self.upload_file( emboss_5_repository,
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filename='emboss/emboss.tar',
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@@ -178,7 +222,7 @@ class TestResetInstalledRepositoryMetadata( ShedTwillTestCase ):
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description=emboss_repository_description,
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long_description=emboss_repository_long_description,
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owner=common.test_user_1_name,
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category_id=self.security.encode_id( category_0030.id ),
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category_id=self.security.encode_id( category.id ),
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strings_displayed=[] )
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self.upload_file( emboss_6_repository,
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filename='emboss/emboss.tar',
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@@ -196,7 +240,7 @@ class TestResetInstalledRepositoryMetadata( ShedTwillTestCase ):
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description=emboss_repository_description,
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long_description=emboss_repository_long_description,
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owner=common.test_user_1_name,
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category_id=self.security.encode_id( category_0030.id ),
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category_id=self.security.encode_id( category.id ),
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strings_displayed=[] )
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self.upload_file( emboss_repository,
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filename='emboss/emboss.tar',
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@@ -212,68 +256,82 @@ class TestResetInstalledRepositoryMetadata( ShedTwillTestCase ):
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self.create_repository_dependency( repository=emboss_repository, repository_tuples=[ dependency_tuple ], filepath=repository_dependencies_path )
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dependency_tuple = ( self.url, emboss_6_repository.name, emboss_6_repository.user.username, self.get_repository_tip( emboss_6_repository ) )
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self.create_repository_dependency( repository=emboss_repository, repository_tuples=[ dependency_tuple ], filepath=repository_dependencies_path )
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def test_0030_create_repositories_from_0040_series( self ):
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'''Create repositories freebayes_0040 and filtering_0040.'''
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category = self.create_category( name=category_0040_name, description='' )
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repository = self.get_or_create_repository( name='freebayes_0040',
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description="Galaxy's freebayes tool",
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long_description="Long description of Galaxy's freebayes tool",
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owner=common.test_user_1_name,
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category_id=self.security.encode_id( category_0040.id ),
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category_id=self.security.encode_id( category.id ),
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strings_displayed=[] )
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if self.repository_is_new( repository ):
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self.upload_file( repository,
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filename='freebayes/freebayes.tar',
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filename='freebayes/freebayes.tar',
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filepath=None,
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valid_tools_only=True,
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uncompress_file=True,
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remove_repo_files_not_in_tar=False,
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commit_message='Uploaded freebayes tarball.',
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remove_repo_files_not_in_tar=False,
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commit_message='Uploaded the tool tarball.',
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strings_displayed=[],
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strings_not_displayed=[] )
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repository = self.get_or_create_repository( name='filtering_0040',
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description="Galaxy's filtering tool",
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long_description="Long description of Galaxy's filtering tool",
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description=filtering_repository_description,
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long_description=filtering_repository_long_description,
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owner=common.test_user_1_name,
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category_id=self.security.encode_id( category_0040.id ),
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category_id=self.security.encode_id( category.id ),
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strings_displayed=[] )
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self.upload_file( repository,
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filename='filtering/filtering_1.1.0.tar',
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filename='filtering/filtering_1.1.0.tar',
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filepath=None,
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valid_tools_only=True,
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uncompress_file=True,
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remove_repo_files_not_in_tar=False,
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commit_message='Uploaded filtering 1.1.0 tarball.',
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remove_repo_files_not_in_tar=False,
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commit_message='Uploaded the tool tarball for filtering 1.1.0.',
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strings_displayed=[],
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strings_not_displayed=[] )
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freebayes_repository = self.test_db_util.get_repository_by_name_and_owner( 'freebayes_0040', common.test_user_1_name )
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repository = self.test_db_util.get_repository_by_name_and_owner( 'freebayes_0040', common.test_user_1_name )
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filtering_repository = self.test_db_util.get_repository_by_name_and_owner( 'filtering_0040', common.test_user_1_name )
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repository_dependencies_path = self.generate_temp_path( 'test_0340', additional_paths=[ 'dependencies' ] )
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dependency_tuple = ( self.url, freebayes_repository.name, freebayes_repository.user.username, self.get_repository_tip( freebayes_repository ) )
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self.create_repository_dependency( repository=filtering_repository, repository_tuples=[ dependency_tuple ], filepath=repository_dependencies_path )
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dependency_tuple = ( self.url, filtering_repository.name, filtering_repository.user.username, self.get_repository_tip( filtering_repository ) )
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self.create_repository_dependency( repository=freebayes_repository, repository_tuples=[ dependency_tuple ], filepath=repository_dependencies_path )
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repository_dependencies_path = self.generate_temp_path( 'test_1340', additional_paths=[ 'filtering' ] )
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repository_tuple = ( self.url, repository.name, repository.user.username, self.get_repository_tip( repository ) )
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self.create_repository_dependency( repository=filtering_repository, repository_tuples=[ repository_tuple ], filepath=repository_dependencies_path )
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repository = self.test_db_util.get_repository_by_name_and_owner( 'filtering_0040', common.test_user_1_name )
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freebayes_repository = self.test_db_util.get_repository_by_name_and_owner( 'freebayes_0040', common.test_user_1_name )
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repository_dependencies_path = self.generate_temp_path( 'test_1340', additional_paths=[ 'freebayes' ] )
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repository_tuple = ( self.url, repository.name, repository.user.username, self.get_repository_tip( repository ) )
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self.create_repository_dependency( repository=freebayes_repository, repository_tuples=[ repository_tuple ], filepath=repository_dependencies_path )
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def test_0035_create_repositories_from_0050_series( self ):
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'''Create repositories emboss_0050, emboss_datatypes_0050, filtering_0050, freebayes_0050.'''
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category = self.create_category( name=category_0050_name, description='' )
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datatypes_repository = self.get_or_create_repository( name='emboss_datatypes_0050',
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description="Datatypes for emboss",
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long_description="Long description of Emboss' datatypes",
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owner=common.test_user_1_name,
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category_id=self.security.encode_id( category_0050.id ),
|
||||
category_id=self.security.encode_id( category.id ),
|
||||
strings_displayed=[] )
|
||||
if self.repository_is_new( datatypes_repository ):
|
||||
emboss_repository = self.get_or_create_repository( name='emboss_0050',
|
||||
description="Galaxy's emboss tool",
|
||||
long_description="Long description of Galaxy's emboss tool",
|
||||
owner=common.test_user_1_name,
|
||||
category_id=self.security.encode_id( category_0050.id ),
|
||||
category_id=self.security.encode_id( category.id ),
|
||||
strings_displayed=[] )
|
||||
filtering_repository = self.get_or_create_repository( name='filtering_0050',
|
||||
description="Galaxy's filtering tool",
|
||||
long_description="Long description of Galaxy's filtering tool",
|
||||
owner=common.test_user_1_name,
|
||||
category_id=self.security.encode_id( category_0050.id ),
|
||||
category_id=self.security.encode_id( category.id ),
|
||||
strings_displayed=[] )
|
||||
freebayes_repository = self.get_or_create_repository( name='freebayes_0050',
|
||||
description="Galaxy's freebayes tool",
|
||||
long_description="Long description of Galaxy's freebayes tool",
|
||||
owner=common.test_user_1_name,
|
||||
category_id=self.security.encode_id( category_0050.id ),
|
||||
category_id=self.security.encode_id( category.id ),
|
||||
strings_displayed=[] )
|
||||
self.upload_file( datatypes_repository,
|
||||
filename='emboss/datatypes/datatypes_conf.xml',
|
||||
@@ -325,11 +383,14 @@ class TestResetInstalledRepositoryMetadata( ShedTwillTestCase ):
|
||||
( self.url, filtering_repository.name, filtering_repository.user.username, self.get_repository_tip( filtering_repository ) ),
|
||||
( self.url, freebayes_repository.name, freebayes_repository.user.username, self.get_repository_tip( freebayes_repository ) ) ]
|
||||
self.create_repository_dependency( repository=freebayes_repository, repository_tuples=dependency_tuples, filepath=repository_dependencies_path )
|
||||
|
||||
def test_0035_create_repositories_from_0060_series( self ):
|
||||
category = self.create_category( name=category_0060_name, description='' )
|
||||
workflow_repository = self.get_or_create_repository( name='filtering_0060',
|
||||
description="Galaxy's filtering tool",
|
||||
long_description="Long description of Galaxy's filtering tool",
|
||||
owner=common.test_user_1_name,
|
||||
category_id=self.security.encode_id( category_0060.id ),
|
||||
category_id=self.security.encode_id( category.id ),
|
||||
strings_displayed=[] )
|
||||
if self.repository_is_new( workflow_repository ):
|
||||
workflow = file( self.get_filename( 'filtering_workflow/Workflow_for_0060_filter_workflow_repository.ga' ), 'r' ).read()
|
||||
@@ -356,8 +417,8 @@ class TestResetInstalledRepositoryMetadata( ShedTwillTestCase ):
|
||||
commit_message='Uploaded filtering 2.2.0 tarball.',
|
||||
strings_displayed=[],
|
||||
strings_not_displayed=[] )
|
||||
|
||||
def test_0010_install_all_missing_repositories( self ):
|
||||
|
||||
def test_9900_install_all_missing_repositories( self ):
|
||||
'''Call the install_repository method to ensure that all required repositories are installed.'''
|
||||
global repository_datatypes_count
|
||||
global base_datatypes_count
|
||||
@@ -365,31 +426,24 @@ class TestResetInstalledRepositoryMetadata( ShedTwillTestCase ):
|
||||
self.galaxy_logout()
|
||||
self.galaxy_login( email=common.admin_email, username=common.admin_username )
|
||||
base_datatypes_count = int( self.get_datatypes_count() )
|
||||
category_0000 = 'Test 0000 Basic Repository Features 1'
|
||||
category_0001 = 'Test 0000 Basic Repository Features 2'
|
||||
category_0010 = 'Test 0010 Repository With Tool Dependencies'
|
||||
category_0020 = 'Test 0020 Basic Repository Dependencies'
|
||||
category_0030 = 'Test 0030 Repository Dependency Revisions'
|
||||
category_0040 = 'test_0040_repository_circular_dependencies'
|
||||
category_0050 = 'test_0050_repository_n_level_circular_dependencies'
|
||||
category_0060 = 'Test 0060 Workflow Features'
|
||||
self.install_repository( 'filtering_0000', common.test_user_1_name, category_0000, strings_displayed=[] )
|
||||
self.install_repository( 'freebayes_0010', common.test_user_1_name, category_0010, strings_displayed=[] )
|
||||
self.install_repository( 'emboss_0020', common.test_user_1_name, category_0020, strings_displayed=[] )
|
||||
self.install_repository( 'emboss_5_0030', common.test_user_1_name, category_0030, strings_displayed=[] )
|
||||
self.install_repository( 'filtering_0040', common.test_user_1_name, category_0040, strings_displayed=[] )
|
||||
self.install_repository( 'freebayes_0050', common.test_user_1_name, category_0050, strings_displayed=[] )
|
||||
self.install_repository( 'filtering_0060', common.test_user_1_name, category_0060, strings_displayed=[] )
|
||||
self.install_repository( 'filtering_0000', common.test_user_1_name, category_0000_name, strings_displayed=[] )
|
||||
self.install_repository( 'freebayes_0010', common.test_user_1_name, category_0010_name, strings_displayed=[] )
|
||||
self.install_repository( 'emboss_0020', common.test_user_1_name, category_0020_name, strings_displayed=[] )
|
||||
self.install_repository( 'emboss_5_0030', common.test_user_1_name, category_0030_name, strings_displayed=[] )
|
||||
self.install_repository( 'freebayes_0050', common.test_user_1_name, category_0050_name, strings_displayed=[] )
|
||||
self.install_repository( 'filtering_0060', common.test_user_1_name, category_0060_name, strings_displayed=[] )
|
||||
current_datatypes = int( self.get_datatypes_count() )
|
||||
# If we are running this test by itself, installing the emboss repository should also install the emboss_datatypes
|
||||
# repository, and this should add datatypes to the datatypes registry. If that is the case, verify that datatypes
|
||||
# have been added, otherwise verify that the count is unchanged.
|
||||
if running_standalone:
|
||||
assert current_datatypes == base_datatypes_count + repository_datatypes_count, 'Installing emboss did not add new datatypes.'
|
||||
message = 'Installing emboss did not add new datatypes.\nFound: %d\nExpected: %d' % \
|
||||
( current_datatypes, base_datatypes_count + repository_datatypes_count )
|
||||
assert current_datatypes > base_datatypes_count, message
|
||||
else:
|
||||
assert current_datatypes == base_datatypes_count, 'Installing emboss added new datatypes.'
|
||||
|
||||
def test_0015_reset_metadata_on_all_repositories( self ):
|
||||
|
||||
def test_9905_reset_metadata_on_all_repositories( self ):
|
||||
'''Reset metadata on all repositories, then verify that it has not changed.'''
|
||||
repository_metadata = dict()
|
||||
repositories = self.test_db_util.get_all_installed_repositories( actually_installed=True )
|
||||
|
||||
Reference in New Issue
Block a user