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 ), f"Problem retrieving user with email {common.test_user_1_email} from the database" 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 ), f"Problem retrieving user with email {common.test_user_2_email} from the database" 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, f"Problem retrieving user with email {common.admin_email} from the database" 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 = f"hg://{self.host}:{self.port}/repos/user1/hg_tool_dependency_0460" 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 = f"hg://{self.host}:{self.port}/repos/user1/hg_subfolder_tool_dependency_0460" 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 = f"hg://{self.host}:{self.port}/repos/user1/hg_repository_dependency_0460" 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 = f"hg://{self.host}:{self.port}/repos/user1/hg_subfolder_repository_dependency_0460" 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], )