More cleanup tool_dependencies.xml handling. (362a1807) · Commits · NDIP / Galaxy

lib/galaxy/tool_shed/galaxy_install/install_manager.py

+0 −12

Original line number	Diff line number	Diff line
		@@ -667,7 +667,6 @@ class InstallRepositoryManager:
		original_metadata_dict = repository.metadata_
		original_repository_dependencies_dict = original_metadata_dict.get("repository_dependencies", {})
		original_repository_dependencies = original_repository_dependencies_dict.get("repository_dependencies", [])
		original_tool_dependencies_dict = original_metadata_dict.get("tool_dependencies", {})
		shed_tool_conf, tool_path, relative_install_dir = suc.get_tool_panel_config_tool_path_install_dir(
		self.app, repository
		)
		@@ -740,7 +739,6 @@ class InstallRepositoryManager:
		if "repository_dependencies" in irmm_metadata_dict or "tool_dependencies" in irmm_metadata_dict:
		new_repository_dependencies_dict = irmm_metadata_dict.get("repository_dependencies", {})
		new_repository_dependencies = new_repository_dependencies_dict.get("repository_dependencies", [])
		new_tool_dependencies_dict = irmm_metadata_dict.get("tool_dependencies", {})
		if new_repository_dependencies:
		# [[http://localhost:9009', package_picard_1_56_0', devteam', 910b0b056666', False', False']]
		if new_repository_dependencies == original_repository_dependencies:
		@@ -792,16 +790,6 @@ class InstallRepositoryManager:
		self.install(
		tool_shed_url, new_name, new_owner, new_changeset_revision, install_options
		)
		# Updates received did not include any newly defined repository dependencies but did include
		# newly defined tool dependencies. If the newly defined tool dependencies are not the same
		# as the originally defined tool dependencies, we need to install them.
		if not install_new_dependencies:
		for new_key, new_val in new_tool_dependencies_dict.items():
		if new_key not in original_tool_dependencies_dict:
		return ("tool", irmm_metadata_dict)
		original_val = original_tool_dependencies_dict[new_key]
		if new_val != original_val:
		return ("tool", irmm_metadata_dict)
		# Updates received did not include any newly defined repository dependencies or newly defined
		# tool dependencies that need to be installed.
		repository = self.app.update_repository_manager.update_repository_record(

lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py

+0 −47

Original line number	Diff line number	Diff line
		@@ -856,19 +856,6 @@ class AdminToolshed(AdminGalaxy):
		containers_dicts.append(containers_dict)
		# Merge all containers into a single container.
		containers_dict = dd.merge_containers_dicts_for_new_install(containers_dicts)
		# Handle tool dependencies check box.
		if not trans.app.toolbox.dependency_manager.uses_tool_shed_dependencies:
		if includes_tool_dependencies:
		message = "Tool dependencies defined in this repository can be automatically installed if you set "
		message += "the value of your <b>tool_dependency_dir</b> setting in your Galaxy config file "
		message += "(galaxy.yml) and restart your Galaxy server before installing the repository."
		status = "warning"
		install_tool_dependencies_check_box_checked = False
		else:
		install_tool_dependencies_check_box_checked = True
		install_tool_dependencies_check_box = CheckboxField(
		"install_tool_dependencies", value=install_tool_dependencies_check_box_checked
		)
		# Handle repository dependencies check box.
		install_repository_dependencies_check_box = CheckboxField("install_repository_dependencies", value=True)
		view = views.DependencyResolversView(self.app)
		@@ -889,7 +876,6 @@ class AdminToolshed(AdminGalaxy):
		includes_tools=includes_tools,
		includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel,
		includes_tool_dependencies=includes_tool_dependencies,
		install_tool_dependencies_check_box=install_tool_dependencies_check_box,
		install_resolver_dependencies_check_box=install_resolver_dependencies_check_box,
		has_repository_dependencies=has_repository_dependencies,
		install_repository_dependencies_check_box=install_repository_dependencies_check_box,
		@@ -1252,18 +1238,6 @@ class AdminToolshed(AdminGalaxy):
		containers_dict = dd.merge_missing_repository_dependencies_to_installed_container(containers_dict)
		# Handle repository dependencies check box.
		install_repository_dependencies_check_box = CheckboxField("install_repository_dependencies", value=True)
		# Handle tool dependencies check box.
		if not trans.app.toolbox.dependency_manager.uses_tool_shed_dependencies:
		if includes_tool_dependencies:
		message += "Tool dependencies defined in this repository can be automatically installed if you set the value of your <b>tool_dependency_dir</b> "
		message += "setting in your Galaxy config file (galaxy.yml) and restart your Galaxy server before installing the repository. "
		status = "warning"
		install_tool_dependencies_check_box_checked = False
		else:
		install_tool_dependencies_check_box_checked = True
		install_tool_dependencies_check_box = CheckboxField(
		"install_tool_dependencies", value=install_tool_dependencies_check_box_checked
		)
		view = views.DependencyResolversView(self.app)
		if view.installable_resolvers:
		install_resolver_dependencies_check_box = CheckboxField("install_resolver_dependencies", value=True)
		@@ -1282,7 +1256,6 @@ class AdminToolshed(AdminGalaxy):
		includes_workflows=includes_workflows,
		has_repository_dependencies=has_repository_dependencies,
		install_repository_dependencies_check_box=install_repository_dependencies_check_box,
		install_tool_dependencies_check_box=install_tool_dependencies_check_box,
		install_resolver_dependencies_check_box=install_resolver_dependencies_check_box,
		containers_dict=containers_dict,
		tool_panel_section_select_field=tool_panel_section_select_field,
		@@ -1388,26 +1361,6 @@ class AdminToolshed(AdminGalaxy):
		updating=True,
		)
		return self.prepare_for_install(trans, **new_kwd)
		elif install_dependencies == "tool":
		# Updates received did not include any newly defined repository dependencies but did include
		# newly defined tool dependencies. If the newly defined tool dependencies are not the same
		# as the originally defined tool dependencies, we need to install them.
		relative_install_dir = suc.get_tool_panel_config_tool_path_install_dir(trans.app, repository)[2]
		encoded_tool_dependencies_dict = encoding_util.tool_shed_encode(
		irmm_metadata_dict.get("tool_dependencies", {})
		)
		encoded_relative_install_dir = encoding_util.tool_shed_encode(relative_install_dir)
		new_kwd = dict(
		updating_repository_id=trans.security.encode_id(repository.id),
		updating_to_ctx_rev=latest_ctx_rev,
		updating_to_changeset_revision=latest_changeset_revision,
		encoded_updated_metadata=encoding_util.tool_shed_encode(irmm_metadata_dict),
		encoded_relative_install_dir=encoded_relative_install_dir,
		encoded_tool_dependencies_dict=encoded_tool_dependencies_dict,
		message=message,
		status=status,
		)
		return self.install_tool_dependencies_with_update(trans, **new_kwd)
		message = f"The installed repository named '{name}' has been updated to change set revision '{latest_changeset_revision}'. "
		else:
		message = (

lib/tool_shed/test/functional/test_1010_install_repository_with_tool_dependencies.py

+0 −2

Original line number	Diff line number	Diff line
		@@ -136,8 +136,6 @@ class ToolWithToolDependencies(ShedTwillTestCase):
		strings_displayed = [
		"Never installed",
		"install all needed dependencies",
		"install Tool Shed managed",
		"tool dependencies",
		]
		strings_displayed.extend(["freebayes", "0.9.4_9696d0ce8a9", "samtools", "0.1.18"])
		self.install_repository(

lib/tool_shed/test/functional/test_1040_install_repository_basic_circular_dependencies.py

+0 −2

Original line number	Diff line number	Diff line
		@@ -153,7 +153,6 @@ class TestInstallingCircularDependencies(ShedTwillTestCase):
		self.display_installed_repository_manage_page(installed_filtering_repository)
		self.deactivate_repository(installed_filtering_repository)
		self.test_db_util.ga_refresh(installed_filtering_repository)
		self.check_galaxy_repository_tool_panel_section(installed_filtering_repository, "Get Data")
		strings_displayed = [
		"Missing repository",
		"filtering",
		@@ -191,7 +190,6 @@ class TestInstallingCircularDependencies(ShedTwillTestCase):
		self.display_installed_repository_manage_page(installed_filtering_repository)
		self.deactivate_repository(installed_freebayes_repository)
		self.test_db_util.ga_refresh(installed_freebayes_repository)
		self.check_galaxy_repository_tool_panel_section(installed_freebayes_repository, "Get Data")
		strings_displayed = [
		"Missing repository",
		"freebayes",

lib/tool_shed/test/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py

+1 −8

Original line number	Diff line number	Diff line
		@@ -117,14 +117,7 @@ class UninstallingAndReinstallingRepositories(ShedTwillTestCase):
		def test_0010_install_freebayes_repository(self):
		"""Install the freebayes repository into the Galaxy instance."""
		self.galaxy_login(email=common.admin_email, username=common.admin_username)
		strings_displayed = [
		"install Tool Shed managed",
		"tool dependencies",
		"freebayes",
		"0.9.4_9696d0ce8a9",
		"samtools",
		"0.1.18",
		]
		strings_displayed = []
		self.install_repository(
		"freebayes_0010",
		common.test_user_1_name,

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