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Source code for tool_shed.test.functional.test_0460_upload_to_repository
import logging
from ..base import common
from ..base.twilltestcase import ShedTwillTestCase
log = logging.getLogger(__name__)
category_name = "Test 0460 Automatic repository revision completion"
category_description = "Test 0460 Automatic repository revision completion"
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 category...
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 the package 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)
self.login(email=common.test_user_2_email, username=common.test_user_2_name)
self.login(email=common.admin_email, username=common.admin_username)
[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)
[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.populator.get_category_with_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=category,
strings_displayed=[],
)
self.add_file_to_repository(
repository,
"bwa/complex/tool_dependencies.xml",
commit_message="Populate package_bwa_0_5_9_0460 with a tool dependency definition.",
)
[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.populator.get_category_with_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=category,
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._get_repository_by_name_and_owner("complex_dependency_test_1_0460", common.test_user_1_name)
package_repository = self._get_repository_by_name_and_owner("package_bwa_0_5_9_0460", common.test_user_1_name)
self.add_file_to_repository(repository, "0460_files/tool_dependencies.xml")
if not self.is_v2:
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._get_repository_by_name_and_owner("complex_dependency_test_2_0460", common.test_user_1_name)
package_repository = self._get_repository_by_name_and_owner("package_bwa_0_5_9_0460", common.test_user_1_name)
self.commit_tar_to_repository(
repository,
"0460_files/tool_dependencies_in_root.tar",
commit_message="Uploaded complex repository dependency definition.",
)
if not self.is_v2:
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._get_repository_by_name_and_owner("complex_dependency_test_3_0460", common.test_user_1_name)
package_repository = self._get_repository_by_name_and_owner("package_bwa_0_5_9_0460", common.test_user_1_name)
self.commit_tar_to_repository(
repository,
"0460_files/tool_dependencies_in_subfolder.tar",
commit_message="Uploaded complex repository dependency definition.",
)
changeset_revision = self.get_repository_tip(package_repository)
if not self.is_v2:
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.populator.get_category_with_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=category,
strings_displayed=[],
)
self.add_file_to_repository(repository, "0460_files/tool_dependencies.xml")
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=category,
strings_displayed=[],
)
self.commit_tar_to_repository(
repository,
"0460_files/tool_dependencies_in_subfolder.tar",
commit_message="Populate hg_subfolder_tool_dependency_0460 with a tool dependency definition.",
)
[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.populator.get_category_with_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=category,
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._get_repository_by_name_and_owner(
"repository_dependency_test_1_0460", common.test_user_1_name
)
package_repository = self._get_repository_by_name_and_owner(bwa_repository_name, common.test_user_1_name)
self.add_file_to_repository(repository, "0460_files/repository_dependencies.xml")
changeset_revision = self.get_repository_tip(package_repository)
if not self.is_v2:
strings_displayed = [bwa_repository_name, "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._get_repository_by_name_and_owner(
"repository_dependency_test_2_0460", common.test_user_1_name
)
package_repository = self._get_repository_by_name_and_owner(bwa_repository_name, common.test_user_1_name)
self.commit_tar_to_repository(
repository,
"0460_files/in_root/repository_dependencies_in_root.tar",
commit_message="Uploaded complex repository dependency definition.",
)
changeset_revision = self.get_repository_tip(package_repository)
if not self.is_v2:
strings_displayed = [bwa_repository_name, "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._get_repository_by_name_and_owner(
"repository_dependency_test_3_0460", common.test_user_1_name
)
package_repository = self._get_repository_by_name_and_owner(bwa_repository_name, common.test_user_1_name)
self.commit_tar_to_repository(
repository,
"0460_files/in_subfolder/repository_dependencies_in_subfolder.tar",
commit_message="Uploaded complex repository dependency definition.",
)
changeset_revision = self.get_repository_tip(package_repository)
if not self.is_v2:
strings_displayed = [bwa_repository_name, "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.populator.get_category_with_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=category,
strings_displayed=[],
)
self.add_file_to_repository(repository, "0460_files/repository_dependencies.xml")
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=category,
strings_displayed=[],
)
self.commit_tar_to_repository(
repository,
"0460_files/in_subfolder/repository_dependencies_in_subfolder.tar",
commit_message="Populate hg_subfolder_repository_dependency_0460 with a tool dependency definition.",
)