diff --git a/lib/galaxy/tool_shed/galaxy_install/installed_repository_manager.py b/lib/galaxy/tool_shed/galaxy_install/installed_repository_manager.py
index ef0d56cb1e3..0ee698e62d6 100644
--- a/lib/galaxy/tool_shed/galaxy_install/installed_repository_manager.py
+++ b/lib/galaxy/tool_shed/galaxy_install/installed_repository_manager.py
@@ -15,7 +15,10 @@ from typing import (
)
from galaxy import util
-from galaxy.model.tool_shed_install import ToolShedRepository
+from galaxy.model.tool_shed_install import (
+ ToolDependency,
+ ToolShedRepository,
+)
from galaxy.structured_app import MinimalManagerApp
from galaxy.tool_shed.galaxy_install.metadata.installed_repository_metadata_manager import (
InstalledRepositoryMetadataManager,
@@ -102,7 +105,7 @@ class InstalledRepositoryManager:
self.app, repository
)
repository.deleted = False
- repository.status = self.install_model.ToolShedRepository.installation_status.INSTALLED
+ repository.status = ToolShedRepository.installation_status.INSTALLED
if repository.includes_tools_for_display_in_tool_panel:
repository_clone_url = common_util.generate_clone_url_for_installed_repository(self.app, repository)
tpm = tool_panel_manager.ToolPanelManager(self.app)
@@ -139,8 +142,8 @@ class InstalledRepositoryManager:
repository,
repository_tools_tups,
)
- self.install_model.session.add(repository)
- self.install_model.session.flush()
+ self.context.add(repository)
+ self.context.flush()
def add_entry_to_installed_repository_dependencies_of_installed_repositories(
self, repository: ToolShedRepository
@@ -153,7 +156,7 @@ class InstalledRepositoryManager:
repository_tup = self.get_repository_tuple_for_installed_repository_manager(repository)
tool_shed, name, owner, installed_changeset_revision = repository_tup
# Get the list of repository dependencies for this repository.
- status = self.install_model.ToolShedRepository.installation_status.INSTALLED
+ status = ToolShedRepository.installation_status.INSTALLED
repository_dependency_tups = self.get_repository_dependency_tups_for_installed_repository(
repository, status=status
)
@@ -199,9 +202,7 @@ class InstalledRepositoryManager:
def get_containing_repository_for_tool_dependency(self, tool_dependency_tup: tuple) -> ToolShedRepository:
tool_shed_repository_id, name, version, type = tool_dependency_tup
- return self.app.install_model.context.query(self.app.install_model.ToolShedRepository).get(
- tool_shed_repository_id
- )
+ return self.context.query(ToolShedRepository).get(tool_shed_repository_id)
def get_dependencies_for_repository(
self,
@@ -364,7 +365,7 @@ class InstalledRepositoryManager:
tsr.id,
tsr.status,
]
- if tsr.status == self.app.install_model.ToolShedRepository.installation_status.INSTALLED:
+ if tsr.status == ToolShedRepository.installation_status.INSTALLED:
installed_rd_tups.append(rd_tup)
else:
# We'll only add the rd_tup to the missing_rd_tups list if the received repository
@@ -458,7 +459,7 @@ class InstalledRepositoryManager:
repository.id,
repository.status,
]
- if repository.status == self.install_model.ToolShedRepository.installation_status.INSTALLED:
+ if repository.status == ToolShedRepository.installation_status.INSTALLED:
if new_rd_tup not in installed_rd_tups:
installed_rd_tups.append(new_rd_tup)
else:
@@ -519,7 +520,7 @@ class InstalledRepositoryManager:
tmp_tool_dependencies_dict: dict = copy.deepcopy(tool_dependencies_dict)
for td_key, val in tmp_tool_dependencies_dict.items():
# Default the status to NEVER_INSTALLED.
- tool_dependency_status = self.install_model.ToolDependency.installation_status.NEVER_INSTALLED
+ tool_dependency_status = ToolDependency.installation_status.NEVER_INSTALLED
if td_key == "set_environment":
# Set environment tool dependencies are a list.
assert isinstance(val, list)
@@ -541,7 +542,7 @@ class InstalledRepositoryManager:
tool_dependency_status = tool_dependency.status
requirement_dict["status"] = tool_dependency_status
new_val.append(requirement_dict)
- if tool_dependency_status in [self.install_model.ToolDependency.installation_status.INSTALLED]:
+ if tool_dependency_status in [ToolDependency.installation_status.INSTALLED]:
if td_key in installed_tool_dependencies:
installed_tool_dependencies[td_key].extend(new_val)
else:
@@ -565,7 +566,7 @@ class InstalledRepositoryManager:
if tool_dependency:
tool_dependency_status = tool_dependency.status
val["status"] = tool_dependency_status
- if tool_dependency_status in [self.install_model.ToolDependency.installation_status.INSTALLED]:
+ if tool_dependency_status in [ToolDependency.installation_status.INSTALLED]:
installed_tool_dependencies[td_key] = val
else:
missing_tool_dependencies[td_key] = val
@@ -688,151 +689,14 @@ class InstalledRepositoryManager:
errors = f"{errors} {error_message}"
repository.deleted = True
if remove_from_disk:
- repository.status = self.app.install_model.ToolShedRepository.installation_status.UNINSTALLED
+ repository.status = ToolShedRepository.installation_status.UNINSTALLED
repository.error_message = None
else:
- repository.status = self.app.install_model.ToolShedRepository.installation_status.DEACTIVATED
- self.app.install_model.session.add(repository)
- self.app.install_model.session.flush()
+ repository.status = ToolShedRepository.installation_status.DEACTIVATED
+ self.context.add(repository)
+ self.context.flush()
return errors
- def purge_repository(self, repository: ToolShedRepository) -> Tuple[str, str]:
- """Purge a repository with status New (a white ghost) from the database."""
- sa_session = self.app.model.session
- status = "ok"
- message = ""
- purged_tool_versions = 0
- purged_tool_dependencies = 0
- purged_required_repositories = 0
- purged_orphan_repository_repository_dependency_association_records = 0
- purged_orphan_repository_dependency_records = 0
- if repository.is_new:
- # Purge this repository's associated tool versions.
- if repository.tool_versions:
- for tool_version in repository.tool_versions:
- if tool_version.parent_tool_association:
- for tool_version_association in tool_version.parent_tool_association:
- try:
- sa_session.delete(tool_version_association)
- sa_session.flush()
- except Exception as e:
- status = "error"
- message = (
- "Error attempting to purge tool_versions for the repository named %s with status %s: %s."
- % (str(repository.name), str(repository.status), str(e))
- )
- return status, message
- if tool_version.child_tool_association:
- for tool_version_association in tool_version.child_tool_association:
- try:
- sa_session.delete(tool_version_association)
- sa_session.flush()
- except Exception as e:
- status = "error"
- message = (
- "Error attempting to purge tool_versions for the repository named %s with status %s: %s."
- % (str(repository.name), str(repository.status), str(e))
- )
- return status, message
- try:
- sa_session.delete(tool_version)
- sa_session.flush()
- purged_tool_versions += 1
- except Exception as e:
- status = "error"
- message = (
- "Error attempting to purge tool_versions for the repository named %s with status %s: %s."
- % (str(repository.name), str(repository.status), str(e))
- )
- return status, message
- # Purge this repository's associated tool dependencies.
- if repository.tool_dependencies:
- for tool_dependency in repository.tool_dependencies:
- try:
- sa_session.delete(tool_dependency)
- sa_session.flush()
- purged_tool_dependencies += 1
- except Exception as e:
- status = "error"
- message = (
- "Error attempting to purge tool_dependencies for the repository named %s with status %s: %s."
- % (str(repository.name), str(repository.status), str(e))
- )
- return status, message
- # Purge this repository's associated required repositories.
- if repository.required_repositories:
- for rrda in repository.required_repositories:
- try:
- sa_session.delete(rrda)
- sa_session.flush()
- purged_required_repositories += 1
- except Exception as e:
- status = "error"
- message = (
- "Error attempting to purge required_repositories for the repository named %s with status %s: %s."
- % (str(repository.name), str(repository.status), str(e))
- )
- return status, message
- # Purge any "orphan" repository_dependency records associated with the repository, but not with any
- # repository_repository_dependency_association records.
- for orphan_repository_dependency in sa_session.query(self.app.install_model.RepositoryDependency).filter(
- self.app.install_model.RepositoryDependency.table.c.tool_shed_repository_id == repository.id
- ):
- # Purge any repository_repository_dependency_association records whose repository_dependency_id is
- # the id of the orphan repository_dependency record.
- for orphan_rrda in sa_session.query(
- self.app.install_model.RepositoryRepositoryDependencyAssociation
- ).filter(
- self.app.install_model.RepositoryRepositoryDependencyAssociation.table.c.repository_dependency_id
- == orphan_repository_dependency.id
- ):
- try:
- sa_session.delete(orphan_rrda)
- sa_session.flush()
- purged_orphan_repository_repository_dependency_association_records += 1
- except Exception as e:
- status = "error"
- message = "Error attempting to purge repository_repository_dependency_association records associated with "
- message += (
- "an orphan repository_dependency record for the repository named %s with status %s: %s."
- % (str(repository.name), str(repository.status), str(e))
- )
- return status, message
- try:
- sa_session.delete(orphan_repository_dependency)
- sa_session.flush()
- purged_orphan_repository_dependency_records += 1
- except Exception as e:
- status = "error"
- message = (
- "Error attempting to purge orphan repository_dependency records for the repository named %s with status %s: %s."
- % (str(repository.name), str(repository.status), str(e))
- )
- return status, message
- # Purge the repository.
- sa_session.delete(repository)
- sa_session.flush()
- message = f"The repository named {repository.name} with status {repository.status} has been purged. "
- message += "Total associated tool_version records purged: %d " % purged_tool_versions
- message += "Total associated tool_dependency records purged: %d " % purged_tool_dependencies
- message += (
- "Total associated repository_repository_dependency_association records purged: %d "
- % purged_required_repositories
- )
- message += (
- "Total associated orphan repository_repository_dependency_association records purged: %d "
- % purged_orphan_repository_repository_dependency_association_records
- )
- message += (
- "Total associated orphan repository_dependency records purged: %d "
- % purged_orphan_repository_dependency_records
- )
- else:
- status = "error"
- message = "A repository must have the status New in order to be purged. This repository has "
- message += f" the status {repository.status}."
- return status, message
-
def remove_entry_from_installed_repository_dependencies_of_installed_repositories(
self, repository: ToolShedRepository
):
@@ -992,7 +856,7 @@ class InstalledRepositoryManager:
dependency_install_dir
)
if removed_from_disk:
- context = self.app.install_model.context
+ context = self.context
new_dependency_name = None
new_dependency_type = None
new_dependency_version = None
@@ -1017,7 +881,7 @@ class InstalledRepositoryManager:
)
tool_dependency.type = new_dependency_type
tool_dependency.version = new_dependency_version
- tool_dependency.status = self.app.install_model.ToolDependency.installation_status.UNINSTALLED
+ tool_dependency.status = ToolDependency.installation_status.UNINSTALLED
tool_dependency.error_message = None
context.add(tool_dependency)
context.flush()
diff --git a/lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py b/lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
index 18ec626b782..544c86735e5 100644
--- a/lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
+++ b/lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
@@ -166,13 +166,6 @@ class InstalledRepositoryGrid(grids.Grid):
target="center",
url_args=dict(controller="admin_toolshed", action="restore_repository"),
),
- grids.GridOperation(
- label="Purge",
- condition=(lambda item: item.is_new),
- allow_multiple=False,
- target="center",
- url_args=dict(controller="admin_toolshed", action="purge_repository"),
- ),
]
default_filter = dict(deleted="False")
num_rows_per_page = 50
diff --git a/templates/admin/tool_shed_repository/purge_repository_confirmation.mako b/templates/admin/tool_shed_repository/purge_repository_confirmation.mako
deleted file mode 100644
index 36a7f562b66..00000000000
--- a/templates/admin/tool_shed_repository/purge_repository_confirmation.mako
+++ /dev/null
@@ -1,74 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-<%namespace file="/admin/tool_shed_repository/repository_actions_menu.mako" import="*" />
-
-<%def name="stylesheets()">
- ${parent.stylesheets()}
- ${h.css( "library" )}
-
-
-<%def name="javascripts()">
- ${parent.javascripts()}
-
-
-${render_galaxy_repository_actions( repository )}
-
-%if message:
- ${render_msg( message, status )}
-%endif
-
-
-
- Purging the repository named ${repository.name|h} will result in deletion of all records for the
- following associated items from the database. Click the Purge button to purge this repository
- and its associated items.
-