Warning
This document is for an in-development version of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.
Source code for tool_shed.test.functional.test_1190_complex_prior_installation_required
import os
from ..base.twilltestcase import common, ShedTwillTestCase
matplotlib_repository_name = 'package_matplotlib_1_2_0170'
matplotlib_repository_description = "Contains a tool dependency definition that downloads and compiles version 1.2.x of the the python matplotlib package."
matplotlib_repository_long_description = "This repository is intended to be defined as a complex repository dependency within a separate repository."
numpy_repository_name = 'package_numpy_1_7_0170'
numpy_repository_description = "Contains a tool dependency definition that downloads and compiles version 1.7 of the the python numpy package."
numpy_repository_long_description = "This repository is intended to be defined as a complex repository dependency within a separate repository."
category_name = 'Test 0170 Prior Installation Complex Dependencies'
category_description = 'Test 0170 Prior Installation Complex Dependencies'
'''
1. Create and populate repositories package_matplotlib_1_2_0170 and package_numpy_1_7_0170.
2. Create a complex repository dependency on package_numpy_1_7_0170, and upload this to package_matplotlib_1_2_0170.
3. Verify that package_matplotlib_1_2_0170 now depends on package_numpy_1_7_0170, and that the inherited tool dependency displays correctly.
4. Install package_matplotlib_1_2_0170 with repository dependencies.
5. Verify that the prior_installation_required attribute resulted in package_numpy_1_7_0170 being installed first.
'''
running_standalone = False
[docs]class TestComplexPriorInstallation(ShedTwillTestCase):
'''Test features related to datatype converters.'''
[docs] def test_0000_initiate_users(self):
"""Create necessary user accounts."""
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
test_user_1 = self.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
self.test_db_util.get_private_role(test_user_1)
self.login(email=common.admin_email, username=common.admin_username)
admin_user = self.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
self.test_db_util.get_private_role(admin_user)
[docs] def test_0005_create_matplotlib_repository(self):
'''Create and populate the package_matplotlib_1_2_0170 repository.'''
'''
This is step 1 - Create and populate repositories package_matplotlib_1_2_0170 and package_numpy_1_7_0170.
'''
global running_standalone
category = self.create_category(name=category_name, description=category_description)
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
repository = self.get_or_create_repository(name=matplotlib_repository_name,
description=matplotlib_repository_description,
long_description=matplotlib_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
strings_displayed=[])
if self.repository_is_new(repository):
running_standalone = True
self.upload_file(repository,
filename='package_matplotlib/package_matplotlib_1_2.tar',
filepath=None,
valid_tools_only=False,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded matplotlib tool dependency tarball.',
strings_displayed=['This repository currently contains a single file named <b>tool_dependencies.xml</b>'],
strings_not_displayed=[])
[docs] def test_0010_create_numpy_repository(self):
'''Create and populate the package_numpy_1_7_0170 repository.'''
'''
This is step 1 - Create and populate repositories package_matplotlib_1_2_0170 and package_numpy_1_7_0170.
'''
global running_standalone
category = self.create_category(name=category_name, description=category_description)
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
if running_standalone:
repository = self.get_or_create_repository(name=numpy_repository_name,
description=numpy_repository_description,
long_description=numpy_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
strings_displayed=[])
self.upload_file(repository,
filename='package_numpy/package_numpy_1_7.tar',
filepath=None,
valid_tools_only=False,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded numpy tool dependency tarball.',
strings_displayed=['This repository currently contains a single file named <b>tool_dependencies.xml</b>'],
strings_not_displayed=[])
[docs] def test_0015_create_complex_repository_dependency(self):
'''Create a dependency on package_numpy_1_7_0170.'''
'''
This is step 2 - Create a complex repository dependency on package_numpy_1_7_0170, and upload this to package_matplotlib_1_2_0170.
package_matplotlib_1_2_0170 should depend on package_numpy_1_7_0170, with prior_installation_required
set to True. When matplotlib is selected for installation, the result should be that numpy is compiled
and installed first.
'''
global running_standalone
numpy_repository = self.test_db_util.get_repository_by_name_and_owner(numpy_repository_name, common.test_user_1_name)
matplotlib_repository = self.test_db_util.get_repository_by_name_and_owner(matplotlib_repository_name, common.test_user_1_name)
# Generate the new dependency XML. Normally, the create_repository_dependency method would be used for this, but
# it replaces any existing tool or repository dependency XML file with the generated contents. This is undesirable
# in this case, because matplotlib already has an additional tool dependency definition that we don't want to
# overwrite.
new_xml = ' <package name="numpy" version="1.7">\n'
new_xml += ' <repository toolshed="%s" name="%s" owner="%s" changeset_revision="%s" prior_installation_required="True" />\n'
new_xml += ' </package>\n'
url = self.url
name = numpy_repository.name
owner = numpy_repository.user.username
if running_standalone:
changeset_revision = self.get_repository_tip(numpy_repository)
processed_xml = new_xml % (url, name, owner, changeset_revision)
original_xml = open(self.get_filename('package_matplotlib/tool_dependencies.xml'), 'r').read()
dependency_xml_path = self.generate_temp_path('test_0170', additional_paths=['matplotlib'])
new_xml_file = os.path.join(dependency_xml_path, 'tool_dependencies.xml')
open(new_xml_file, 'w').write(original_xml.replace('<!--NUMPY-->', processed_xml))
# Upload the generated complex repository dependency XML to the matplotlib repository.
self.upload_file(matplotlib_repository,
filename='tool_dependencies.xml',
filepath=dependency_xml_path,
valid_tools_only=True,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded complex repository dependency on numpy 1.7.',
strings_displayed=[],
strings_not_displayed=[])
[docs] def test_0020_verify_generated_dependency(self):
'''Verify that matplotlib now has a package tool dependency and a complex repository dependency.'''
'''
This is step 3 - Verify that package_matplotlib_1_2_0170 now depends on package_numpy_1_7_0170, and that the inherited tool
dependency displays correctly.
'Inhherited' in this case means that matplotlib should show a package tool dependency on numpy version 1.7, and a repository
dependency on the latest revision of package_numpy_1_7_0170.
'''
numpy_repository = self.test_db_util.get_repository_by_name_and_owner(numpy_repository_name, common.test_user_1_name)
matplotlib_repository = self.test_db_util.get_repository_by_name_and_owner(matplotlib_repository_name, common.test_user_1_name)
changeset_revision = self.get_repository_tip(numpy_repository)
self.check_repository_dependency(matplotlib_repository, depends_on_repository=numpy_repository)
self.display_manage_repository_page(matplotlib_repository, strings_displayed=['numpy', '1.7', 'package', changeset_revision])
[docs] def test_0025_install_matplotlib_repository(self):
'''Install the package_matplotlib_1_2_0170 repository.'''
'''
This is step 4 - Install package_matplotlib_1_2_0170 with repository dependencies.
'''
self.galaxy_login(email=common.admin_email, username=common.admin_username)
matplotlib_repository = self.test_db_util.get_repository_by_name_and_owner(matplotlib_repository_name, common.test_user_1_name)
preview_strings_displayed = ['package_matplotlib_1_2_0170', self.get_repository_tip(matplotlib_repository)]
strings_displayed = ['Handle repository dependencies', numpy_repository_name, 'Never installed']
self.install_repository(matplotlib_repository_name,
common.test_user_1_name,
category_name,
install_tool_dependencies=False,
install_repository_dependencies=True,
preview_strings_displayed=preview_strings_displayed,
strings_displayed=strings_displayed,
strings_not_displayed=[],
post_submit_strings_displayed=['package_matplotlib_1_2_0170', 'New'],
includes_tools_for_display_in_tool_panel=False)
[docs] def test_0030_verify_installation_order(self):
'''Verify that the numpy repository was installed before the matplotlib repository.'''
'''
This is step 5 - Verify that the prior_installation_required attribute resulted in package_numpy_1_7_0170 being installed first.
In the previous step, package_matplotlib_1_2_0170 was selected for installation, but package_numpy_1_7_0170 had the
prior_installation_required attribute set. Confirm that this resulted in package_numpy_1_7_0170 being installed before
package_matplotlib_1_2_0170.
'''
matplotlib_repository = self.test_db_util.get_installed_repository_by_name_owner(matplotlib_repository_name, common.test_user_1_name)
numpy_repository = self.test_db_util.get_installed_repository_by_name_owner(numpy_repository_name, common.test_user_1_name)
assert matplotlib_repository.update_time > numpy_repository.update_time, \
'Error: package_numpy_1_7_0170 shows a later update time than package_matplotlib_1_2_0170'