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Merge pull request #11179 from jmchilton/unused_ts

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Remove unused TS methods.
This commit is contained in:
Martin Cech
2021-01-19 12:05:49 +01:00
committed by GitHub
parent 405372d8d3 b3af6948c9
commit 4def8f9721
1 changed files with 0 additions and 114 deletions
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lib/galaxy/tool_shed/galaxy_install/installed_repository_manager.py
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@@ -56,24 +56,6 @@ class InstalledRepositoryManager:
# and whose values are a list of tuples defining tool_shed_repository objects (whose status is 'Installed') that require
# the key.
self.installed_dependent_repositories_of_installed_repositories = {}
# Keep an in-memory dictionary whose keys are tuples defining tool_shed_repository objects (whose status is 'Installed')
# and whose values are a list of tuples defining its immediate tool_dependency objects (whose status can be anything).
# The value defines only the immediate tool dependencies of the repository and does not include any dependencies of the
# tool dependencies.
self.tool_dependencies_of_installed_repositories = {}
# Keep an in-memory dictionary whose keys are tuples defining tool_shed_repository objects (whose status is 'Installed')
# and whose values are a list of tuples defining its immediate tool_dependency objects (whose status is 'Installed').
# The value defines only the immediate tool dependencies of the repository and does not include any dependencies of the
# tool dependencies.
self.installed_tool_dependencies_of_installed_repositories = {}
# Keep an in-memory dictionary whose keys are tuples defining tool_dependency objects (whose status is 'Installed') and
# whose values are a list of tuples defining tool_dependency objects (whose status can be anything) required by the
# installed tool dependency at runtime. The value defines the entire tool dependency tree.
self.runtime_tool_dependencies_of_installed_tool_dependencies = {}
# Keep an in-memory dictionary whose keys are tuples defining tool_dependency objects (whose status is 'Installed') and
# whose values are a list of tuples defining tool_dependency objects (whose status is 'Installed') that require the key
# at runtime. The value defines the entire tool dependency tree.
self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies = {}
@property
def tool_paths(self):
@@ -176,35 +158,6 @@ class InstalledRepositoryManager:
else:
self.installed_dependent_repositories_of_installed_repositories[required_repository_tup] = [repository_tup]
def add_entry_to_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies(self, tool_dependency):
"""Add an entry to self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies."""
tool_dependency_tup = self.get_tool_dependency_tuple_for_installed_repository_manager(tool_dependency)
if tool_dependency_tup not in self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies:
tool_shed_repository_id, name, version, type = tool_dependency_tup
debug_msg = f"Adding an entry for version {version} of {type} {name} "
debug_msg += "to installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies."
log.debug(debug_msg)
status = self.install_model.ToolDependency.installation_status.INSTALLED
installed_runtime_dependent_tool_dependency_tups = self.get_runtime_dependent_tool_dependency_tuples(tool_dependency,
status=status)
self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies[tool_dependency_tup] = \
installed_runtime_dependent_tool_dependency_tups
def add_entry_to_installed_tool_dependencies_of_installed_repositories(self, repository):
"""Add an entry to self.installed_tool_dependencies_of_installed_repositories."""
repository_tup = self.get_repository_tuple_for_installed_repository_manager(repository)
if repository_tup not in self.installed_tool_dependencies_of_installed_repositories:
tool_shed, name, owner, installed_changeset_revision = repository_tup
debug_msg = f"Adding an entry for revision {installed_changeset_revision} of repository {name} owned by {owner} "
debug_msg += "to installed_tool_dependencies_of_installed_repositories."
log.debug(debug_msg)
installed_tool_dependency_tups = []
for tool_dependency in repository.tool_dependencies:
if tool_dependency.status == self.app.install_model.ToolDependency.installation_status.INSTALLED:
tool_dependency_tup = self.get_tool_dependency_tuple_for_installed_repository_manager(tool_dependency)
installed_tool_dependency_tups.append(tool_dependency_tup)
self.installed_tool_dependencies_of_installed_repositories[repository_tup] = installed_tool_dependency_tups
def add_entry_to_repository_dependencies_of_installed_repositories(self, repository):
"""Add an entry to self.repository_dependencies_of_installed_repositories."""
repository_tup = self.get_repository_tuple_for_installed_repository_manager(repository)
@@ -216,33 +169,6 @@ class InstalledRepositoryManager:
repository_dependency_tups = self.get_repository_dependency_tups_for_installed_repository(repository, status=None)
self.repository_dependencies_of_installed_repositories[repository_tup] = repository_dependency_tups
def add_entry_to_runtime_tool_dependencies_of_installed_tool_dependencies(self, tool_dependency):
"""Add an entry to self.runtime_tool_dependencies_of_installed_tool_dependencies."""
tool_dependency_tup = self.get_tool_dependency_tuple_for_installed_repository_manager(tool_dependency)
if tool_dependency_tup not in self.runtime_tool_dependencies_of_installed_tool_dependencies:
tool_shed_repository_id, name, version, type = tool_dependency_tup
debug_msg = f"Adding an entry for version {version} of {type} {name} "
debug_msg += "to runtime_tool_dependencies_of_installed_tool_dependencies."
log.debug(debug_msg)
runtime_dependent_tool_dependency_tups = self.get_runtime_dependent_tool_dependency_tuples(tool_dependency,
status=None)
self.runtime_tool_dependencies_of_installed_tool_dependencies[tool_dependency_tup] = \
runtime_dependent_tool_dependency_tups
def add_entry_to_tool_dependencies_of_installed_repositories(self, repository):
"""Add an entry to self.tool_dependencies_of_installed_repositories."""
repository_tup = self.get_repository_tuple_for_installed_repository_manager(repository)
if repository_tup not in self.tool_dependencies_of_installed_repositories:
tool_shed, name, owner, installed_changeset_revision = repository_tup
debug_msg = f"Adding an entry for revision {installed_changeset_revision} of repository {name} owned by {owner} "
debug_msg += "to tool_dependencies_of_installed_repositories."
log.debug(debug_msg)
tool_dependency_tups = []
for tool_dependency in repository.tool_dependencies:
tool_dependency_tup = self.get_tool_dependency_tuple_for_installed_repository_manager(tool_dependency)
tool_dependency_tups.append(tool_dependency_tup)
self.tool_dependencies_of_installed_repositories[repository_tup] = tool_dependency_tups
def get_containing_repository_for_tool_dependency(self, tool_dependency_tup):
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)
@@ -883,26 +809,6 @@ class InstalledRepositoryManager:
log.debug(debug_msg)
del self.installed_repository_dependencies_of_installed_repositories[repository_tup]
def remove_entry_from_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies(self, tool_dependency):
"""Remove an entry from self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies."""
tool_dependency_tup = self.get_tool_dependency_tuple_for_installed_repository_manager(tool_dependency)
if tool_dependency_tup in self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies:
tool_shed_repository_id, name, version, type = tool_dependency_tup
debug_msg = f"Removing entry for version {version} of {type} {name} "
debug_msg += "from installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies."
log.debug(debug_msg)
del self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies[tool_dependency_tup]
def remove_entry_from_installed_tool_dependencies_of_installed_repositories(self, repository):
"""Remove an entry from self.installed_tool_dependencies_of_installed_repositories."""
repository_tup = self.get_repository_tuple_for_installed_repository_manager(repository)
if repository_tup in self.installed_tool_dependencies_of_installed_repositories:
tool_shed, name, owner, installed_changeset_revision = repository_tup
debug_msg = f"Removing entry for revision {installed_changeset_revision} of repository {name} owned by {owner} "
debug_msg += "from installed_tool_dependencies_of_installed_repositories."
log.debug(debug_msg)
del self.installed_tool_dependencies_of_installed_repositories[repository_tup]
def remove_entry_from_repository_dependencies_of_installed_repositories(self, repository):
"""Remove an entry from self.repository_dependencies_of_installed_repositories."""
repository_tup = self.get_repository_tuple_for_installed_repository_manager(repository)
@@ -913,26 +819,6 @@ class InstalledRepositoryManager:
log.debug(debug_msg)
del self.repository_dependencies_of_installed_repositories[repository_tup]
def remove_entry_from_runtime_tool_dependencies_of_installed_tool_dependencies(self, tool_dependency):
"""Remove an entry from self.runtime_tool_dependencies_of_installed_tool_dependencies."""
tool_dependency_tup = self.get_tool_dependency_tuple_for_installed_repository_manager(tool_dependency)
if tool_dependency_tup in self.runtime_tool_dependencies_of_installed_tool_dependencies:
tool_shed_repository_id, name, version, type = tool_dependency_tup
debug_msg = "Removing entry for version %s of %s %s from runtime_tool_dependencies_of_installed_tool_dependencies." % \
(version, type, name)
log.debug(debug_msg)
del self.runtime_tool_dependencies_of_installed_tool_dependencies[tool_dependency_tup]
def remove_entry_from_tool_dependencies_of_installed_repositories(self, repository):
"""Remove an entry from self.tool_dependencies_of_installed_repositories."""
repository_tup = self.get_repository_tuple_for_installed_repository_manager(repository)
if repository_tup in self.tool_dependencies_of_installed_repositories:
tool_shed, name, owner, installed_changeset_revision = repository_tup
debug_msg = "Removing entry for revision %s of repository %s owned by %s from tool_dependencies_of_installed_repositories." % \
(installed_changeset_revision, name, owner)
log.debug(debug_msg)
del self.tool_dependencies_of_installed_repositories[repository_tup]
def repository_dependency_needed_only_for_compiling_tool_dependency(self, repository, repository_dependency):
for rd_tup in repository.tuples_of_repository_dependencies_needed_for_compiling_td:
tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = rd_tup