mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Functional tests for automatically determining the target changeset revision in repository dependencies.
This commit is contained in:
Dave Bouvier
@@ -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 )
|
||||
|
||||
@@ -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://<tool shed url>/repos/user1/hg_tool_dependency_0460.
|
||||
|
||||
9) Upload to complex_dependency_test_5_0460 using the url hg://<tool shed url>/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://<tool shed url>/repos/user1/hg_repository_dependency_0460.
|
||||
|
||||
16) Upload to repository_dependency_test_5_0460 using the url hg://<tool shed url>/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://<tool shed url>/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://<tool shed url>/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://<tool shed url>/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://<tool shed url>/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 ] )
|
||||
@@ -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
|
||||
|
||||
|
||||
@@ -0,0 +1,4 @@
|
||||
<?xml version="1.0"?>
|
||||
<repositories description="">
|
||||
<repository name="emboss_datatypes_0460" owner="user1" />
|
||||
</repositories>
|
||||
Binary file not shown.
Binary file not shown.
@@ -0,0 +1,6 @@
|
||||
<?xml version="1.0"?>
|
||||
<tool_dependency>
|
||||
<package name="bwa" version="0.5.9">
|
||||
<repository name="package_bwa_0_5_9_0460" owner="user1" />
|
||||
</package>
|
||||
</tool_dependency>
|
||||
Binary file not shown.
Binary file not shown.
@@ -1,2 +1 @@
|
||||
These characters should not result in a unicode decoding error: ®Ãâ�âèÃ
|
||||
....
|
||||
This is a third readme file.
|
||||
Reference in New Issue
Block a user