mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Merge pull request #14746 from jmchilton/installed_repository_manager_cleanup
Cleanup installed_repository_manager.py and related code a bit more.
This commit is contained in:
Aysam Guerler
@@ -15,7 +15,10 @@ from typing import (
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)
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from galaxy import util
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from galaxy.model.tool_shed_install import ToolShedRepository
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from galaxy.model.tool_shed_install import (
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ToolDependency,
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ToolShedRepository,
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)
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from galaxy.structured_app import MinimalManagerApp
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from galaxy.tool_shed.galaxy_install.metadata.installed_repository_metadata_manager import (
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InstalledRepositoryMetadataManager,
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@@ -102,7 +105,7 @@ class InstalledRepositoryManager:
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self.app, repository
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)
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repository.deleted = False
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repository.status = self.install_model.ToolShedRepository.installation_status.INSTALLED
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repository.status = ToolShedRepository.installation_status.INSTALLED
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if repository.includes_tools_for_display_in_tool_panel:
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repository_clone_url = common_util.generate_clone_url_for_installed_repository(self.app, repository)
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tpm = tool_panel_manager.ToolPanelManager(self.app)
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@@ -139,8 +142,8 @@ class InstalledRepositoryManager:
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repository,
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repository_tools_tups,
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)
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self.install_model.session.add(repository)
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self.install_model.session.flush()
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self.context.add(repository)
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self.context.flush()
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def add_entry_to_installed_repository_dependencies_of_installed_repositories(
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self, repository: ToolShedRepository
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@@ -153,7 +156,7 @@ class InstalledRepositoryManager:
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repository_tup = self.get_repository_tuple_for_installed_repository_manager(repository)
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tool_shed, name, owner, installed_changeset_revision = repository_tup
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# Get the list of repository dependencies for this repository.
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status = self.install_model.ToolShedRepository.installation_status.INSTALLED
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status = ToolShedRepository.installation_status.INSTALLED
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repository_dependency_tups = self.get_repository_dependency_tups_for_installed_repository(
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repository, status=status
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)
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@@ -199,9 +202,7 @@ class InstalledRepositoryManager:
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def get_containing_repository_for_tool_dependency(self, tool_dependency_tup: tuple) -> ToolShedRepository:
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tool_shed_repository_id, name, version, type = tool_dependency_tup
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return self.app.install_model.context.query(self.app.install_model.ToolShedRepository).get(
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tool_shed_repository_id
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)
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return self.context.query(ToolShedRepository).get(tool_shed_repository_id)
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def get_dependencies_for_repository(
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self,
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@@ -364,7 +365,7 @@ class InstalledRepositoryManager:
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tsr.id,
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tsr.status,
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]
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if tsr.status == self.app.install_model.ToolShedRepository.installation_status.INSTALLED:
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if tsr.status == ToolShedRepository.installation_status.INSTALLED:
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installed_rd_tups.append(rd_tup)
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else:
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# We'll only add the rd_tup to the missing_rd_tups list if the received repository
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@@ -458,7 +459,7 @@ class InstalledRepositoryManager:
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repository.id,
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repository.status,
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]
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if repository.status == self.install_model.ToolShedRepository.installation_status.INSTALLED:
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if repository.status == ToolShedRepository.installation_status.INSTALLED:
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if new_rd_tup not in installed_rd_tups:
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installed_rd_tups.append(new_rd_tup)
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else:
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@@ -519,7 +520,7 @@ class InstalledRepositoryManager:
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tmp_tool_dependencies_dict: dict = copy.deepcopy(tool_dependencies_dict)
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for td_key, val in tmp_tool_dependencies_dict.items():
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# Default the status to NEVER_INSTALLED.
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tool_dependency_status = self.install_model.ToolDependency.installation_status.NEVER_INSTALLED
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tool_dependency_status = ToolDependency.installation_status.NEVER_INSTALLED
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if td_key == "set_environment":
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# Set environment tool dependencies are a list.
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assert isinstance(val, list)
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@@ -541,7 +542,7 @@ class InstalledRepositoryManager:
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tool_dependency_status = tool_dependency.status
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requirement_dict["status"] = tool_dependency_status
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new_val.append(requirement_dict)
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if tool_dependency_status in [self.install_model.ToolDependency.installation_status.INSTALLED]:
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if tool_dependency_status in [ToolDependency.installation_status.INSTALLED]:
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if td_key in installed_tool_dependencies:
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installed_tool_dependencies[td_key].extend(new_val)
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else:
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@@ -565,7 +566,7 @@ class InstalledRepositoryManager:
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if tool_dependency:
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tool_dependency_status = tool_dependency.status
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val["status"] = tool_dependency_status
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if tool_dependency_status in [self.install_model.ToolDependency.installation_status.INSTALLED]:
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if tool_dependency_status in [ToolDependency.installation_status.INSTALLED]:
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installed_tool_dependencies[td_key] = val
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else:
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missing_tool_dependencies[td_key] = val
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@@ -688,151 +689,14 @@ class InstalledRepositoryManager:
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errors = f"{errors} {error_message}"
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repository.deleted = True
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if remove_from_disk:
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repository.status = self.app.install_model.ToolShedRepository.installation_status.UNINSTALLED
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repository.status = ToolShedRepository.installation_status.UNINSTALLED
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repository.error_message = None
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else:
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repository.status = self.app.install_model.ToolShedRepository.installation_status.DEACTIVATED
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self.app.install_model.session.add(repository)
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self.app.install_model.session.flush()
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repository.status = ToolShedRepository.installation_status.DEACTIVATED
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self.context.add(repository)
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self.context.flush()
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return errors
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def purge_repository(self, repository: ToolShedRepository) -> Tuple[str, str]:
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"""Purge a repository with status New (a white ghost) from the database."""
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sa_session = self.app.model.session
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status = "ok"
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message = ""
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purged_tool_versions = 0
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purged_tool_dependencies = 0
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purged_required_repositories = 0
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purged_orphan_repository_repository_dependency_association_records = 0
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purged_orphan_repository_dependency_records = 0
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if repository.is_new:
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# Purge this repository's associated tool versions.
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if repository.tool_versions:
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for tool_version in repository.tool_versions:
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if tool_version.parent_tool_association:
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for tool_version_association in tool_version.parent_tool_association:
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try:
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sa_session.delete(tool_version_association)
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sa_session.flush()
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except Exception as e:
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status = "error"
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message = (
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"Error attempting to purge tool_versions for the repository named %s with status %s: %s."
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% (str(repository.name), str(repository.status), str(e))
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)
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return status, message
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if tool_version.child_tool_association:
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for tool_version_association in tool_version.child_tool_association:
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try:
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sa_session.delete(tool_version_association)
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sa_session.flush()
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except Exception as e:
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status = "error"
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message = (
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"Error attempting to purge tool_versions for the repository named %s with status %s: %s."
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% (str(repository.name), str(repository.status), str(e))
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)
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return status, message
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try:
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sa_session.delete(tool_version)
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sa_session.flush()
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purged_tool_versions += 1
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except Exception as e:
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status = "error"
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message = (
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"Error attempting to purge tool_versions for the repository named %s with status %s: %s."
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% (str(repository.name), str(repository.status), str(e))
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)
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return status, message
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# Purge this repository's associated tool dependencies.
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if repository.tool_dependencies:
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for tool_dependency in repository.tool_dependencies:
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try:
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sa_session.delete(tool_dependency)
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sa_session.flush()
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purged_tool_dependencies += 1
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except Exception as e:
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status = "error"
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message = (
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"Error attempting to purge tool_dependencies for the repository named %s with status %s: %s."
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% (str(repository.name), str(repository.status), str(e))
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)
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return status, message
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# Purge this repository's associated required repositories.
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if repository.required_repositories:
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for rrda in repository.required_repositories:
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try:
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sa_session.delete(rrda)
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sa_session.flush()
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purged_required_repositories += 1
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except Exception as e:
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status = "error"
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message = (
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"Error attempting to purge required_repositories for the repository named %s with status %s: %s."
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% (str(repository.name), str(repository.status), str(e))
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)
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return status, message
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# Purge any "orphan" repository_dependency records associated with the repository, but not with any
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# repository_repository_dependency_association records.
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for orphan_repository_dependency in sa_session.query(self.app.install_model.RepositoryDependency).filter(
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self.app.install_model.RepositoryDependency.table.c.tool_shed_repository_id == repository.id
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):
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# Purge any repository_repository_dependency_association records whose repository_dependency_id is
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# the id of the orphan repository_dependency record.
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for orphan_rrda in sa_session.query(
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self.app.install_model.RepositoryRepositoryDependencyAssociation
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).filter(
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self.app.install_model.RepositoryRepositoryDependencyAssociation.table.c.repository_dependency_id
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== orphan_repository_dependency.id
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):
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try:
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sa_session.delete(orphan_rrda)
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sa_session.flush()
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purged_orphan_repository_repository_dependency_association_records += 1
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except Exception as e:
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status = "error"
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message = "Error attempting to purge repository_repository_dependency_association records associated with "
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message += (
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"an orphan repository_dependency record for the repository named %s with status %s: %s."
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% (str(repository.name), str(repository.status), str(e))
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)
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return status, message
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try:
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sa_session.delete(orphan_repository_dependency)
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sa_session.flush()
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purged_orphan_repository_dependency_records += 1
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except Exception as e:
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status = "error"
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message = (
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"Error attempting to purge orphan repository_dependency records for the repository named %s with status %s: %s."
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% (str(repository.name), str(repository.status), str(e))
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)
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return status, message
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# Purge the repository.
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sa_session.delete(repository)
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sa_session.flush()
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message = f"The repository named <b>{repository.name}</b> with status <b>{repository.status}</b> has been purged.<br/>"
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message += "Total associated tool_version records purged: %d<br/>" % purged_tool_versions
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message += "Total associated tool_dependency records purged: %d<br/>" % purged_tool_dependencies
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message += (
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"Total associated repository_repository_dependency_association records purged: %d<br/>"
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% purged_required_repositories
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)
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message += (
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"Total associated orphan repository_repository_dependency_association records purged: %d<br/>"
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% purged_orphan_repository_repository_dependency_association_records
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)
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message += (
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"Total associated orphan repository_dependency records purged: %d<br/>"
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% purged_orphan_repository_dependency_records
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)
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else:
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status = "error"
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message = "A repository must have the status <b>New</b> in order to be purged. This repository has "
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message += f" the status {repository.status}."
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return status, message
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def remove_entry_from_installed_repository_dependencies_of_installed_repositories(
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self, repository: ToolShedRepository
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):
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@@ -992,7 +856,7 @@ class InstalledRepositoryManager:
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dependency_install_dir
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)
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if removed_from_disk:
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context = self.app.install_model.context
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context = self.context
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new_dependency_name = None
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new_dependency_type = None
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new_dependency_version = None
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@@ -1017,7 +881,7 @@ class InstalledRepositoryManager:
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)
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tool_dependency.type = new_dependency_type
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tool_dependency.version = new_dependency_version
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tool_dependency.status = self.app.install_model.ToolDependency.installation_status.UNINSTALLED
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tool_dependency.status = ToolDependency.installation_status.UNINSTALLED
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tool_dependency.error_message = None
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context.add(tool_dependency)
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context.flush()
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@@ -166,13 +166,6 @@ class InstalledRepositoryGrid(grids.Grid):
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target="center",
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url_args=dict(controller="admin_toolshed", action="restore_repository"),
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),
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grids.GridOperation(
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label="Purge",
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condition=(lambda item: item.is_new),
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allow_multiple=False,
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target="center",
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url_args=dict(controller="admin_toolshed", action="purge_repository"),
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),
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]
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default_filter = dict(deleted="False")
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num_rows_per_page = 50
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@@ -1,74 +0,0 @@
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<%inherit file="/base.mako"/>
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<%namespace file="/message.mako" import="render_msg" />
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<%namespace file="/admin/tool_shed_repository/repository_actions_menu.mako" import="*" />
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<%def name="stylesheets()">
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${parent.stylesheets()}
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${h.css( "library" )}
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</%def>
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<%def name="javascripts()">
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${parent.javascripts()}
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</%def>
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${render_galaxy_repository_actions( repository )}
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%if message:
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${render_msg( message, status )}
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%endif
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<div class="warningmessage">
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<p>
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Purging the repository named <b>${repository.name|h}</b> will result in deletion of all records for the
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following associated items from the database. Click the <b>Purge</b> button to purge this repository
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and its associated items.
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</p>
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</div>
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<div class="card">
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<div class="card-header">Purge tool shed repository <b>${repository.name|h}</b></div>
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<form name="purge_repository" id="purge_repository" action="${h.url_for( controller='admin_toolshed', action='purge_repository', id=trans.security.encode_id( repository.id ) )}" method="post" >
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<%
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tool_versions = 0
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tool_dependencies = 0
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required_repositories = 0
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orphan_repository_repository_dependency_association_records = 0
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orphan_repository_dependency_records = 0
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# Count this repository's tool version lineage chain links that will be purged.
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for tool_version in repository.tool_versions:
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for tool_version_association in tool_version.parent_tool_association:
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tool_versions += 1
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for tool_version_association in tool_version.child_tool_association:
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tool_versions += 1
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tool_versions += 1
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# Count this repository's associated tool dependencies that will be purged.
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for tool_dependency in repository.tool_dependencies:
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tool_dependencies += 1
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# Count this repository's associated required repositories that will be purged.
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for rrda in repository.required_repositories:
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required_repositories += 1
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# Count any "orphan" repository_dependency records associated with the repository but not with any
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# repository_repository_dependency_association records that will be purged.
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for orphan_repository_dependency in \
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trans.sa_session.query( trans.app.install_model.RepositoryDependency ) \
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.filter( trans.app.install_model.RepositoryDependency.table.c.tool_shed_repository_id == repository.id ):
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for orphan_rrda in \
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trans.sa_session.query( trans.app.install_model.RepositoryRepositoryDependencyAssociation ) \
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.filter( trans.app.install_model.RepositoryRepositoryDependencyAssociation.table.c.repository_dependency_id == orphan_repository_dependency.id ):
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orphan_repository_repository_dependency_association_records += 1
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orphan_repository_dependency_records += 1
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%>
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<table class="grid">
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<tr><td>Tool version records</td><td>${tool_versions|h}</td><tr>
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<tr><td>Tool dependency records</td><td>${tool_dependencies|h}</td><tr>
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<tr><td>Repository dependency records</td><td>${required_repositories|h}</td><tr>
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<tr><td>Orphan repository_repository_dependency_association records</td><td>${orphan_repository_repository_dependency_association_records|h}</td><tr>
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<tr><td>Orphan repository_dependency records</td><td>${orphan_repository_dependency_records|h}</td><tr>
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</table>
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<div style="clear: both"></div>
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<div class="form-row">
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<input type="submit" name="purge_repository_button" value="Purge"/>
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</div>
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</form>
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</div>
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</div>
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Reference in New Issue
Block a user