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Source code for tool_shed.test.functional.test_0460_upload_to_repository
import logging
from ..base.twilltestcase import common, ShedTwillTestCase
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 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.
'''
[docs]class TestAutomaticDependencyRevision(ShedTwillTestCase):
'''Test defining repository dependencies without specifying the changeset revision.'''
[docs] def test_0000_initiate_users(self):
"""Create necessary user accounts and login as an admin user."""
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.test_user_2_email, username=common.test_user_2_name)
test_user_2 = self.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
self.test_db_util.get_private_role(test_user_2)
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_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.login(email=common.test_user_1_email, username=common.test_user_1_name)
category = self.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=[])
[docs] 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 = self.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 a tool dependency definition.',
strings_displayed=[],
strings_not_displayed=[])
[docs] 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 = self.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):
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=[])
[docs] 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 = self.test_db_util.get_repository_by_name_and_owner('complex_dependency_test_1_0460', common.test_user_1_name)
package_repository = self.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])
[docs] 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 = self.test_db_util.get_repository_by_name_and_owner('complex_dependency_test_2_0460', common.test_user_1_name)
package_repository = self.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])
[docs] 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 = self.test_db_util.get_repository_by_name_and_owner('complex_dependency_test_3_0460', common.test_user_1_name)
package_repository = self.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])
[docs] 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 tool dependencies.
'''
category = self.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 a 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 a tool dependency definition.',
strings_displayed=[],
strings_not_displayed=[])
[docs] 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://{}:{}/repos/user1/hg_tool_dependency_0460'.format(self.host, self.port)
repository = self.test_db_util.get_repository_by_name_and_owner('complex_dependency_test_4_0460', common.test_user_1_name)
package_repository = self.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])
[docs] 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://{}:{}/repos/user1/hg_subfolder_tool_dependency_0460'.format(self.host, self.port)
repository = self.test_db_util.get_repository_by_name_and_owner('complex_dependency_test_5_0460', common.test_user_1_name)
package_repository = self.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])
[docs] 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 = self.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):
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=[])
[docs] 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 = self.test_db_util.get_repository_by_name_and_owner('repository_dependency_test_1_0460', common.test_user_1_name)
package_repository = self.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])
[docs] 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 = self.test_db_util.get_repository_by_name_and_owner('repository_dependency_test_2_0460', common.test_user_1_name)
package_repository = self.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])
[docs] 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 = self.test_db_util.get_repository_by_name_and_owner('repository_dependency_test_3_0460', common.test_user_1_name)
package_repository = self.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])
[docs] 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 = self.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 a 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 a tool dependency definition.',
strings_displayed=[],
strings_not_displayed=[])
[docs] 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://{}:{}/repos/user1/hg_repository_dependency_0460'.format(self.host, self.port)
repository = self.test_db_util.get_repository_by_name_and_owner('repository_dependency_test_4_0460', common.test_user_1_name)
package_repository = self.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])
[docs] 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://{}:{}/repos/user1/hg_subfolder_repository_dependency_0460'.format(self.host, self.port)
repository = self.test_db_util.get_repository_by_name_and_owner('repository_dependency_test_5_0460', common.test_user_1_name)
package_repository = self.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])