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Tool shed functional tests for repository dependency features. Cleaned up import *s.

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This commit is contained in:
Dave Bouvier
2012-12-07 12:05:43 -05:00
parent 72a505290d
commit 9f657f2f1f
8 changed files with 217 additions and 68 deletions
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test/tool_shed/base/common.py
+1 -1
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@@ -9,7 +9,7 @@ test_user_1_email = 'test-1@bx.psu.edu'
test_user_1_name = 'user1'
new_repository_dependencies_xml = '''<?xml version="1.0"?>
<repositories>
<repositories${description}>
<repository toolshed="${toolshed_url}" name="${repository_name}" owner="${owner}" changeset_revision="${changeset_revision}" />
</repositories>
'''
test/tool_shed/base/twilltestcase.py
+27 -12
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@@ -1,8 +1,7 @@
from base.twilltestcase import *
from galaxy.webapps.community.util.hgweb_config import *
from test_db_util import *
from common import *
import string
import galaxy.webapps.community.util.hgweb_config
import common, string, os
from base.twilltestcase import tc, from_json_string, TwillTestCase, security
from test_db_util import get_repository_metadata_by_repository_id_changeset_revision
from galaxy import eggs
eggs.require('mercurial')
@@ -14,7 +13,7 @@ class ShedTwillTestCase( TwillTestCase ):
self.security = security.SecurityHelper( id_secret='changethisinproductiontoo' )
self.history_id = None
self.hgweb_config_dir = os.environ.get( 'TEST_HG_WEB_CONFIG_DIR' )
self.hgweb_config_manager = HgWebConfigManager()
self.hgweb_config_manager = galaxy.webapps.community.util.hgweb_config.HgWebConfigManager()
self.hgweb_config_manager.hgweb_config_dir = self.hgweb_config_dir
self.host = os.environ.get( 'TOOL_SHED_TEST_HOST' )
self.port = os.environ.get( 'TOOL_SHED_TEST_PORT' )
@@ -138,8 +137,12 @@ class ShedTwillTestCase( TwillTestCase ):
tc.fv( "1", "selected_files_to_delete", ','.join( files_to_delete ) )
tc.submit( 'select_files_to_delete_button' )
self.check_for_strings( strings_displayed, strings_not_displayed )
def display_manage_repository_page( self, repository, strings_displayed=[], strings_not_displayed=[] ):
url = '/repository/manage_repository?id=%s' % self.security.encode_id( repository.id )
def display_manage_repository_page( self, repository, changeset_revision=None, strings_displayed=[], strings_not_displayed=[] ):
base_url = '/repository/manage_repository?id=%s' % self.security.encode_id( repository.id )
if changeset_revision is not None:
url = '%s&changeset_revision=%s' % ( base_url, changeset_revision )
else:
url = base_url
self.visit_url( url )
self.check_for_strings( strings_displayed, strings_not_displayed )
def display_repository_clone_page( self, owner_name, repository_name, strings_displayed=[], strings_not_displayed=[] ):
@@ -209,14 +212,19 @@ class ShedTwillTestCase( TwillTestCase ):
else:
string = string.replace( character, replacement )
return string
def generate_repository_dependency_xml( self, repository, xml_filename ):
def generate_repository_dependency_xml( self, repository, xml_filename, dependency_description='' ):
changeset_revision = self.get_repository_tip( repository )
template_parser = string.Template( new_repository_dependencies_xml )
if dependency_description:
description = ' description="%s"' % dependency_description
else:
description = dependency_description
template_parser = string.Template( common.new_repository_dependencies_xml )
repository_dependency_xml = template_parser.safe_substitute( toolshed_url=self.url,
owner=repository.user.username,
repository_name=repository.name,
changeset_revision=changeset_revision )
# Save the generated xml to test-data/emboss_5/repository_dependencies.xml.
changeset_revision=changeset_revision,
description=description )
# Save the generated xml to the specified location.
file( xml_filename, 'w' ).write( repository_dependency_xml )
def get_latest_repository_metadata_for_repository( self, repository ):
# TODO: This will not work as expected. Fix it.
@@ -293,6 +301,13 @@ class ShedTwillTestCase( TwillTestCase ):
( self.security.encode_id( repository.id ), tool_xml_path, changeset_revision )
self.visit_url( url )
self.check_for_strings( strings_displayed, strings_not_displayed )
def repository_is_new( self, repository ):
repo = hg.repository( ui.ui(), self.get_repo_path( repository ) )
tip_ctx = repo.changectx( repo.changelog.tip() )
return tip_ctx.rev() < 0
def reset_repository_metadata( self, repository ):
url = '/repository/reset_all_metadata?id=%s' % self.security.encode_id( repository.id )
self.visit_url( url )
def revoke_write_access( self, repository, username ):
url = '/repository/manage_repository?user_access_button=Remove&id=%s&remove_auth=%s' % \
( self.security.encode_id( repository.id ), username )
test/tool_shed/functional/test_0000_basic_repository_features.py
+24 -24
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@@ -1,5 +1,5 @@
from tool_shed.base.twilltestcase import *
from tool_shed.base.test_db_util import *
from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os
from tool_shed.base.test_db_util import get_repository_by_name_and_owner, get_user, get_private_role
repository_name = 'filtering'
repository_description = "Galaxy's filtering tool"
@@ -9,14 +9,14 @@ class TestBasicRepositoryFeatures( ShedTwillTestCase ):
def test_0000_initiate_users( self ):
"""Create necessary user accounts and login as an admin user."""
self.login( email=test_user_1_email, username=test_user_1_name )
test_user_1 = get_user( test_user_1_email )
self.login( email=common.test_user_1_email, username=common.test_user_1_name )
test_user_1 = 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 = get_private_role( test_user_1 )
self.logout()
self.login( email=admin_email, username=admin_username )
admin_user = get_user( admin_email )
assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email
self.login( email=common.admin_email, username=common.admin_username )
admin_user = 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 = get_private_role( admin_user )
def test_0005_create_categories( self ):
"""Create categories"""
@@ -33,27 +33,27 @@ class TestBasicRepositoryFeatures( ShedTwillTestCase ):
strings_displayed=strings_displayed )
def test_0015_edit_repository( self ):
"""Edit the repository name, description, and long description"""
repository = get_repository_by_name_and_owner( repository_name, admin_username )
repository = get_repository_by_name_and_owner( repository_name, common.admin_username )
new_name = "renamed_filtering"
new_description = "Edited filtering tool"
new_long_description = "Edited long description"
self.edit_repository_information( repository, repo_name=new_name, description=new_description, long_description=new_long_description )
def test_0020_change_repository_category( self ):
"""Change the categories associated with the filtering repository"""
repository = get_repository_by_name_and_owner( repository_name, admin_username )
repository = get_repository_by_name_and_owner( repository_name, common.admin_username )
self.edit_repository_categories( repository, categories_to_add=[ "Text Analysis" ], categories_to_remove=[ "Text Manipulation" ] )
def test_0025_grant_write_access( self ):
'''Grant write access to another user'''
repository = get_repository_by_name_and_owner( repository_name, admin_username )
self.grant_write_access( repository, usernames=[ test_user_1_name ] )
self.revoke_write_access( repository, test_user_1_name )
repository = get_repository_by_name_and_owner( repository_name, common.admin_username )
self.grant_write_access( repository, usernames=[ common.test_user_1_name ] )
self.revoke_write_access( repository, common.test_user_1_name )
def test_0030_upload_filtering_1_1_0( self ):
"""Upload filtering_1.1.0.tar to the repository"""
repository = get_repository_by_name_and_owner( repository_name, admin_username )
repository = get_repository_by_name_and_owner( repository_name, common.admin_username )
self.upload_file( repository, 'filtering/filtering_1.1.0.tar', commit_message="Uploaded filtering 1.1.0" )
def test_0035_verify_repository( self ):
'''Display basic repository pages'''
repository = get_repository_by_name_and_owner( repository_name, admin_username )
repository = get_repository_by_name_and_owner( repository_name, common.admin_username )
latest_changeset_revision = self.get_repository_tip( repository )
self.check_for_valid_tools( repository, strings_displayed=[ 'Filter1' ] )
self.check_count_of_metadata_revisions_associated_with_repository( repository, metadata_count=1 )
@@ -61,12 +61,12 @@ class TestBasicRepositoryFeatures( ShedTwillTestCase ):
self.check_repository_tools_for_changeset_revision( repository, tip )
self.check_repository_metadata( repository, tip_only=False )
self.browse_repository( repository, strings_displayed=[ 'Browse %s revision' % repository.name, '(repository tip)' ] )
self.display_repository_clone_page( admin_username,
self.display_repository_clone_page( common.admin_username,
repository_name,
strings_displayed=[ 'Uploaded filtering 1.1.0', latest_changeset_revision ] )
def test_0040_alter_repository_states( self ):
'''Test toggling the malicious and deprecated repository flags.'''
repository = get_repository_by_name_and_owner( repository_name, admin_username )
repository = get_repository_by_name_and_owner( repository_name, common.admin_username )
self.set_repository_malicious( repository, set_malicious=True, strings_displayed=[ 'The repository tip has been defined as malicious.' ] )
self.set_repository_malicious( repository,
set_malicious=False,
@@ -82,7 +82,7 @@ class TestBasicRepositoryFeatures( ShedTwillTestCase ):
set_deprecated=False )
def test_0045_display_repository_tip_file( self ):
'''Display the contents of filtering.xml in the repository tip revision'''
repository = get_repository_by_name_and_owner( repository_name, admin_username )
repository = get_repository_by_name_and_owner( repository_name, common.admin_username )
self.display_repository_file_contents( repository=repository,
filename='filtering.xml',
filepath=None,
@@ -90,7 +90,7 @@ class TestBasicRepositoryFeatures( ShedTwillTestCase ):
strings_not_displayed=[] )
def test_0050_upload_filtering_txt_file( self ):
'''Upload filtering.txt file associated with tool version 1.1.0.'''
repository = get_repository_by_name_and_owner( repository_name, admin_username )
repository = get_repository_by_name_and_owner( repository_name, common.admin_username )
self.upload_file( repository,
'filtering/filtering.txt',
commit_message="Uploaded filtering.txt",
@@ -99,7 +99,7 @@ class TestBasicRepositoryFeatures( ShedTwillTestCase ):
self.display_manage_repository_page( repository, strings_displayed=[ 'Readme file for filtering 1.1.0' ] )
def test_0055_upload_filtering_test_data( self ):
'''Upload filtering test data.'''
repository = get_repository_by_name_and_owner( repository_name, admin_username )
repository = get_repository_by_name_and_owner( repository_name, common.admin_username )
self.upload_file( repository, 'filtering/filtering_test_data.tar', commit_message="Uploaded filtering test data", remove_repo_files_not_in_tar='No' )
self.display_repository_file_contents( repository=repository,
filename='1.bed',
@@ -109,14 +109,14 @@ class TestBasicRepositoryFeatures( ShedTwillTestCase ):
self.check_repository_metadata( repository, tip_only=True )
def test_0060_upload_filtering_2_2_0( self ):
'''Upload filtering version 2.2.0'''
repository = get_repository_by_name_and_owner( repository_name, admin_username )
repository = get_repository_by_name_and_owner( repository_name, common.admin_username )
self.upload_file( repository,
'filtering/filtering_2.2.0.tar',
commit_message="Uploaded filtering 2.2.0",
remove_repo_files_not_in_tar='No' )
def test_0065_verify_filtering_repository( self ):
'''Verify the new tool versions and repository metadata.'''
repository = get_repository_by_name_and_owner( repository_name, admin_username )
repository = get_repository_by_name_and_owner( repository_name, common.admin_username )
tip = self.get_repository_tip( repository )
self.check_for_valid_tools( repository )
strings_displayed = self.get_repository_metadata_revisions( repository ).append( 'Select a revision' )
@@ -126,7 +126,7 @@ class TestBasicRepositoryFeatures( ShedTwillTestCase ):
self.check_repository_metadata( repository, tip_only=False )
def test_0070_upload_readme_txt_file( self ):
'''Upload readme.txt file associated with tool version 2.2.0.'''
repository = get_repository_by_name_and_owner( repository_name, admin_username )
repository = get_repository_by_name_and_owner( repository_name, common.admin_username )
self.upload_file( repository, 'readme.txt', commit_message="Uploaded readme.txt" )
self.display_manage_repository_page( repository, strings_displayed=[ 'This is a readme file.' ] )
# Verify that there is a different readme file for each metadata revision.
@@ -134,13 +134,13 @@ class TestBasicRepositoryFeatures( ShedTwillTestCase ):
self.display_manage_repository_page( repository, strings_displayed=[ 'Readme file for filtering 1.1.0', 'This is a readme file.' ] )
def test_0075_delete_readme_txt_file( self ):
'''Delete the readme.txt file.'''
repository = get_repository_by_name_and_owner( repository_name, admin_username )
repository = get_repository_by_name_and_owner( repository_name, common.admin_username )
self.delete_files_from_repository( repository, filenames=[ 'readme.txt' ] )
self.check_count_of_metadata_revisions_associated_with_repository( repository, metadata_count=2 )
self.display_manage_repository_page( repository, strings_displayed=[ 'Readme file for filtering 1.1.0' ] )
def test_0080_search_for_valid_filter_tool( self ):
'''Search for the filtering tool by tool ID, name, and version.'''
repository = get_repository_by_name_and_owner( repository_name, admin_username )
repository = get_repository_by_name_and_owner( repository_name, common.admin_username )
tip_changeset = self.get_repository_tip( repository )
search_fields = dict( tool_id='Filter1', tool_name='filter', tool_version='2.2.0' )
self.search_for_valid_tools( search_fields=search_fields, strings_displayed=[ tip_changeset ], strings_not_displayed=[] )
test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py
+10 -10
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@@ -1,5 +1,5 @@
from tool_shed.base.twilltestcase import *
from tool_shed.base.test_db_util import *
from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os
from tool_shed.base.test_db_util import get_repository_by_name_and_owner, get_user, get_private_role
repository_name = 'freebayes'
repository_description = "Galaxy's freebayes tool"
@@ -10,8 +10,8 @@ class TestFreebayesRepository( ShedTwillTestCase ):
def test_0000_create_or_login_admin_user( self ):
"""Create necessary user accounts and login as an admin user."""
self.logout()
self.login( email=admin_email, username=admin_username )
admin_user = get_user( admin_email )
self.login( email=common.admin_email, username=common.admin_username )
admin_user = 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 = get_private_role( admin_user )
def test_0005_create_category( self ):
@@ -24,7 +24,7 @@ class TestFreebayesRepository( ShedTwillTestCase ):
repository_long_description=repository_long_description,
categories=[ 'SNP Analysis' ],
strings_displayed=[] )
repository = get_repository_by_name_and_owner( repository_name, admin_username )
repository = get_repository_by_name_and_owner( repository_name, common.admin_username )
self.upload_file( repository,
'freebayes/freebayes.xml',
valid_tools_only=False,
@@ -37,7 +37,7 @@ class TestFreebayesRepository( ShedTwillTestCase ):
strings_displayed=[ 'requires an entry', 'tool_data_table_conf.xml' ] )
def test_0015_upload_missing_tool_data_table_conf_file( self ):
'''Upload the missing tool_data_table_conf.xml.sample file to the repository.'''
repository = get_repository_by_name_and_owner( repository_name, admin_username )
repository = get_repository_by_name_and_owner( repository_name, common.admin_username )
self.upload_file( repository,
'freebayes/tool_data_table_conf.xml.sample',
valid_tools_only=False,
@@ -50,27 +50,27 @@ class TestFreebayesRepository( ShedTwillTestCase ):
strings_displayed=[ 'refers to a file', 'sam_fa_indices.loc' ] )
def test_0020_upload_missing_sample_loc_file( self ):
'''Upload the missing sam_fa_indices.loc.sample file to the repository.'''
repository = get_repository_by_name_and_owner( repository_name, admin_username )
repository = get_repository_by_name_and_owner( repository_name, common.admin_username )
self.upload_file( repository,
'freebayes/sam_fa_indices.loc.sample',
strings_displayed=[],
commit_message='Uploaded tool data table .loc file.' )
def test_0025_upload_invalid_tool_dependency_xml( self ):
'''Upload tool_dependencies.xml defining version 0.9.5 of the freebayes package.'''
repository = get_repository_by_name_and_owner( repository_name, admin_username )
repository = get_repository_by_name_and_owner( repository_name, common.admin_username )
self.upload_file( repository,
os.path.join( 'freebayes', 'invalid_tool_dependencies', 'tool_dependencies.xml' ),
strings_displayed=[ 'Name, version and type from a tool requirement tag does not match' ],
commit_message='Uploaded invalid tool dependency XML.' )
def test_0030_upload_valid_tool_dependency_xml( self ):
'''Upload tool_dependencies.xml defining version 0.9.4_9696d0ce8a962f7bb61c4791be5ce44312b81cf8 of the freebayes package.'''
repository = get_repository_by_name_and_owner( repository_name, admin_username )
repository = get_repository_by_name_and_owner( repository_name, common.admin_username )
self.upload_file( repository,
os.path.join( 'freebayes', 'tool_dependencies.xml' ),
commit_message='Uploaded valid tool dependency XML.' )
def test_0035_verify_tool_dependencies( self ):
'''Verify that the uploaded tool_dependencies.xml specifies the correct package versions.'''
repository = get_repository_by_name_and_owner( repository_name, admin_username )
repository = get_repository_by_name_and_owner( repository_name, common.admin_username )
self.display_manage_repository_page( repository,
strings_displayed=[ 'freebayes', '0.9.4_9696d0ce8a9', 'samtools', '0.1.18', 'Valid tools' ],
strings_not_displayed=[ 'Invalid tools' ] )
test/tool_shed/functional/test_0020_basic_repository_dependencies.py
+21 -21
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@@ -1,11 +1,11 @@
from tool_shed.base.twilltestcase import *
from tool_shed.base.test_db_util import *
from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os
from tool_shed.base.test_db_util import get_repository_by_name_and_owner, get_user, get_private_role
datatypes_repository_name = 'emboss_datatypes'
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."
emboss_repository_name = 'emboss_5'
emboss_repository_name = 'emboss_0020'
emboss_repository_description = 'Galaxy wrappers for Emboss version 5.0.0 tools'
emboss_repository_long_description = 'Galaxy wrappers for Emboss version 5.0.0 tools'
@@ -14,56 +14,56 @@ class TestBasicRepositoryDependencies( ShedTwillTestCase ):
def test_0000_initiate_users( self ):
"""Create necessary user accounts and login as an admin user."""
self.logout()
self.login( email=admin_email, username=admin_username )
admin_user = get_user( admin_email )
assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email
self.login( email=common.admin_email, username=common.admin_username )
admin_user = 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 = get_private_role( admin_user )
self.logout()
self.login( email=test_user_1_email, username=test_user_1_name )
test_user_1 = get_user( test_user_1_email )
assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % regular_email
self.login( email=common.test_user_1_email, username=common.test_user_1_name )
test_user_1 = 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 = get_private_role( test_user_1 )
def test_0005_create_category( self ):
"""Create Sequence Analysis category"""
self.logout()
self.login( email=admin_email, username=admin_username )
self.login( email=common.admin_email, username=common.admin_username )
self.create_category( 'Sequence Analysis', 'Tools for performing Protein and DNA/RNA analysis' )
def test_0010_create_emboss_datatypes_repository_and_upload_tarball( self ):
'''Create and populate the emboss_datatypes repository.'''
self.logout()
self.login( email=test_user_1_email, username=test_user_1_name )
self.login( email=common.test_user_1_email, username=common.test_user_1_name )
self.create_repository( datatypes_repository_name,
datatypes_repository_description,
repository_long_description=datatypes_repository_long_description,
categories=[ 'Sequence Analysis' ],
strings_displayed=[] )
repository = get_repository_by_name_and_owner( datatypes_repository_name, test_user_1_name )
repository = get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name )
self.upload_file( repository, 'emboss/datatypes/datatypes_conf.xml', commit_message='Uploaded datatypes_conf.xml.' )
def test_0015_verify_datatypes_in_datatypes_repository( self ):
'''Verify that the emboss_datatypes repository contains datatype entries.'''
repository = get_repository_by_name_and_owner( datatypes_repository_name, test_user_1_name )
repository = get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name )
self.display_manage_repository_page( repository, strings_displayed=[ 'Datatypes', 'equicktandem', 'hennig86', 'vectorstrip' ] )
def test_0020_create_emboss_5_repository_and_upload_files( self ):
'''Create and populate the emboss_5 repository.'''
'''Create and populate the emboss_5_0020 repository.'''
self.create_repository( emboss_repository_name,
emboss_repository_description,
repository_long_description=emboss_repository_long_description,
categories=[ 'Text Manipulation' ],
strings_displayed=[] )
repository = get_repository_by_name_and_owner( emboss_repository_name, test_user_1_name )
self.upload_file( repository, 'emboss/5/emboss.tar', commit_message='Uploaded emboss_5.tar' )
repository = get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name )
self.upload_file( repository, 'emboss/emboss.tar', commit_message='Uploaded emboss_5.tar' )
def test_0025_generate_and_upload_repository_dependencies_xml( self ):
'''Generate and upload the repository_dependencies.xml file'''
repository = get_repository_by_name_and_owner( emboss_repository_name, test_user_1_name )
datatypes_repository = get_repository_by_name_and_owner( datatypes_repository_name, test_user_1_name )
repository = get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name )
datatypes_repository = get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name )
self.generate_repository_dependency_xml( datatypes_repository, self.get_filename( 'emboss/5/repository_dependencies.xml' ) )
self.upload_file( repository, 'emboss/5/repository_dependencies.xml', commit_message='Uploaded repository_dependencies.xml' )
def test_0030_verify_emboss_5_repository_dependency_on_emboss_datatypes( self ):
'''Verify that the emboss_5 repository now depends on the emboss_datatypes repository with correct name, owner, and changeset revision.'''
repository = get_repository_by_name_and_owner( emboss_repository_name, test_user_1_name )
datatypes_repository = get_repository_by_name_and_owner( datatypes_repository_name, test_user_1_name )
repository = get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name )
datatypes_repository = get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name )
changeset_revision = self.get_repository_tip( datatypes_repository )
strings_displayed = [ datatypes_repository_name, test_user_1_name, changeset_revision, 'Repository dependencies' ]
strings_displayed = [ datatypes_repository_name, common.test_user_1_name, changeset_revision, 'Repository dependencies' ]
self.display_manage_repository_page( repository, strings_displayed=strings_displayed )
def test_0035_cleanup( self ):
'''Clean up generated test data.'''
test/tool_shed/functional/test_0030_repository_dependency_revisions.py
+134
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@@ -0,0 +1,134 @@
from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os
from tool_shed.base.test_db_util import get_repository_by_name_and_owner, get_user, get_private_role
datatypes_repository_name = 'emboss_datatypes'
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."
emboss_repository_name = 'emboss'
emboss_5_repository_name = 'emboss_5_0030'
emboss_6_repository_name = 'emboss_6_0030'
emboss_repository_description = 'Galaxy wrappers for Emboss version 5.0.0 tools'
emboss_repository_long_description = 'Galaxy wrappers for Emboss version 5.0.0 tools'
class TestRepositoryDependencyRevisions( ShedTwillTestCase ):
'''Test dependencies on different revisions of a repository.'''
'''
create repository emboss_5_0030
create repository emboss_6_0030
create repository emboss_datatypes if necessary
create repository emboss
emboss_5 has repository_dependency.xml file that defines emboss_datatypes
emboss_6 has repository_dependency.xml file that defines emboss_datatypes
get information to create repository dependency imformation for emboss
emboss depends on emboss_5
then emboss depends on emboss_6
verify per-changeset dependencies
'''
def test_0000_initiate_users( self ):
"""Create necessary user accounts."""
self.logout()
self.login( email=common.admin_email, username=common.admin_username )
admin_user = 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 = get_private_role( admin_user )
self.logout()
self.login( email=common.test_user_1_email, username=common.test_user_1_name )
test_user_1 = get_user( common.test_user_1_email )
assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % regular_email
test_user_1_private_role = get_private_role( test_user_1 )
def test_0005_create_repositories( self ):
'''Create the emboss_5_0030, emboss_6_0030, emboss_datatypes, and emboss repositories and populate the emboss_datatypes repository.'''
emboss_5_repository = get_repository_by_name_and_owner( emboss_5_repository_name, common.test_user_1_name )
if emboss_5_repository is None:
self.create_repository( emboss_5_repository_name,
emboss_repository_description,
repository_long_description=emboss_repository_long_description,
categories=[ 'Sequence Analysis' ],
strings_displayed=[] )
emboss_5_repository = get_repository_by_name_and_owner( emboss_5_repository_name, common.test_user_1_name )
self.upload_file( emboss_5_repository, 'emboss/emboss.tar', commit_message='Uploaded tool tarball.' )
emboss_6_repository = get_repository_by_name_and_owner( emboss_6_repository_name, common.test_user_1_name )
if emboss_6_repository is None:
self.create_repository( emboss_6_repository_name,
emboss_repository_description,
repository_long_description=emboss_repository_long_description,
categories=[ 'Sequence Analysis' ],
strings_displayed=[] )
emboss_6_repository = get_repository_by_name_and_owner( emboss_6_repository_name, common.test_user_1_name )
self.upload_file( emboss_6_repository, 'emboss/emboss.tar', commit_message='Uploaded tool tarball..' )
datatypes_repository = get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name )
if datatypes_repository is None:
self.create_repository( datatypes_repository_name,
datatypes_repository_description,
repository_long_description=datatypes_repository_long_description,
categories=[ 'Sequence Analysis' ],
strings_displayed=[] )
datatypes_repository = get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name )
if self.repository_is_new( datatypes_repository ):
self.upload_file( datatypes_repository, 'emboss/datatypes/datatypes_conf.xml', commit_message='Uploaded datatypes_conf.xml.' )
emboss_repository = get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name )
if emboss_repository is None:
self.create_repository( emboss_repository_name,
emboss_repository_description,
repository_long_description=emboss_repository_long_description,
categories=[ 'Sequence Analysis' ],
strings_displayed=[] )
emboss_repository = get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name )
self.upload_file( emboss_5_repository, 'emboss/emboss.tar', commit_message='Uploaded tool tarball.' )
def test_0010_generate_repository_dependencies_for_emboss_5( self ):
'''Generate a repository_dependencies.xml file specifying emboss_datatypes and upload it to the emboss_5 repository.'''
datatypes_repository = get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name )
self.generate_repository_dependency_xml( datatypes_repository, self.get_filename( 'emboss/repository_dependencies.xml' ) )
emboss_5_repository = get_repository_by_name_and_owner( emboss_5_repository_name, common.test_user_1_name )
self.upload_file( emboss_5_repository, 'emboss/repository_dependencies.xml', commit_message='Uploaded repository_depepndencies.xml.' )
def test_0015_generate_repository_dependencies_for_emboss_6( self ):
'''Generate a repository_dependencies.xml file specifying emboss_datatypes and upload it to the emboss_6 repository.'''
emboss_6_repository = get_repository_by_name_and_owner( emboss_6_repository_name, common.test_user_1_name )
self.upload_file( emboss_6_repository, 'emboss/repository_dependencies.xml', commit_message='Uploaded repository_depepndencies.xml.' )
def test_0020_generate_repository_dependency_on_emboss_5( self ):
'''Create and upload repository_dependencies.xml for the emboss_5_0030 repository.'''
emboss_repository = get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name )
emboss_5_repository = get_repository_by_name_and_owner( emboss_5_repository_name, common.test_user_1_name )
self.generate_repository_dependency_xml( emboss_5_repository,
self.get_filename( 'emboss/5/repository_dependencies.xml' ),
dependency_description='Emboss requires the Emboss 5 repository.' )
self.upload_file( emboss_repository,
'emboss/5/repository_dependencies.xml',
commit_message='Uploaded dependency configuration specifying emboss_5' )
def test_0025_generate_repository_dependency_on_emboss_6( self ):
'''Create and upload repository_dependencies.xml for the emboss_6_0030 repository.'''
emboss_repository = get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name )
emboss_6_repository = get_repository_by_name_and_owner( emboss_6_repository_name, common.test_user_1_name )
self.generate_repository_dependency_xml( emboss_6_repository,
self.get_filename( 'emboss/6/repository_dependencies.xml' ),
dependency_description='Emboss requires the Emboss 6 repository.' )
self.upload_file( emboss_repository,
'emboss/6/repository_dependencies.xml',
commit_message='Uploaded dependency configuration specifying emboss_6' )
def test_0030_verify_repository_dependency_revisions( self ):
'''Verify that different metadata revisions of the emboss repository have different repository dependencies.'''
repository = get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name )
# Reset emboss metadata to pick up the repository dependency changes.
# self.reset_repository_metadata( repository )
repository_metadata = [ ( metadata.metadata, metadata.changeset_revision ) for metadata in self.get_repository_metadata( repository ) ]
datatypes_repository = get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name )
datatypes_tip = self.get_repository_tip( datatypes_repository )
# Iterate through all metadata revisions and check for repository dependencies.
for metadata, changeset_revision in repository_metadata:
repository_dependency_metadata = metadata[ 'repository_dependencies' ][ 'repository_dependencies' ][ 0 ]
# Remove the tool shed URL, because that's not displayed on the page (yet?)
repository_dependency_metadata.pop( repository_dependency_metadata.index( self.url ) )
# Add the dependency description and datatypes repository details to the strings to check.
repository_dependency_metadata.extend( [ metadata[ 'repository_dependencies' ][ 'description' ],
datatypes_repository_name,
datatypes_repository.user.username,
datatypes_tip ] )
self.display_manage_repository_page( repository,
changeset_revision=changeset_revision,
strings_displayed=[ str( metadata ) for metadata in repository_dependency_metadata ] )
def test_0035_cleanup( self ):
'''Clean up generated repository dependency XML files.'''
for filename in [ 'emboss/5/repository_dependencies.xml', 'emboss/6/repository_dependencies.xml', 'emboss/repository_dependencies.xml' ]:
if os.path.exists( self.get_filename( filename ) ):
os.remove( self.get_filename( filename ) )
test/tool_shed/test_data/emboss/6/emboss.tar
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test/tool_shed/test_data/emboss/5/emboss.tar → test/tool_shed/test_data/emboss/emboss.tar
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