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Mark dependency_display internal-only methods as such.

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This commit is contained in:
John Chilton
2022-10-17 16:09:55 -04:00
parent 6915c5c556
commit 2dd9065926
1 changed files with 19 additions and 19 deletions
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lib/tool_shed/galaxy_install/dependency_display.py
+19 -19
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@@ -25,7 +25,7 @@ class DependencyDisplayer:
def __init__(self, app):
self.app = app
def add_installation_directories_to_tool_dependencies(self, tool_dependencies):
def _add_installation_directories_to_tool_dependencies(self, tool_dependencies):
"""
Determine the path to the installation directory for each of the received
tool dependencies. This path will be displayed within the tool dependencies
@@ -172,7 +172,7 @@ class DependencyDisplayer:
for env_requirements_dict in requirements_dict:
name = env_requirements_dict["name"]
type = env_requirements_dict["type"]
if self.tool_dependency_is_orphan(type, name, None, tools):
if self._tool_dependency_is_orphan(type, name, None, tools):
if not has_orphan_set_environment_dependencies:
has_orphan_set_environment_dependencies = True
set_environment_orphans_str += f"<b>* name:</b> {name}, <b>type:</b> {type}<br/>"
@@ -181,7 +181,7 @@ class DependencyDisplayer:
name = requirements_dict["name"]
type = requirements_dict["type"]
version = requirements_dict["version"]
if self.tool_dependency_is_orphan(type, name, version, tools):
if self._tool_dependency_is_orphan(type, name, version, tools):
if not has_orphan_package_dependencies:
has_orphan_package_dependencies = True
package_orphans_str += (
@@ -203,7 +203,7 @@ class DependencyDisplayer:
message += set_environment_orphans_str
return message
def get_installed_and_missing_tool_dependencies_for_installed_repository(self, repository, all_tool_dependencies):
def _get_installed_and_missing_tool_dependencies_for_installed_repository(self, repository, all_tool_dependencies):
"""
Return the lists of installed tool dependencies and missing tool dependencies for a Tool Shed
repository that has been installed into Galaxy.
@@ -263,7 +263,7 @@ class DependencyDisplayer:
missing_tool_dependencies = None
return tool_dependencies, missing_tool_dependencies
def merge_missing_repository_dependencies_to_installed_container(self, containers_dict):
def _merge_missing_repository_dependencies_to_installed_container(self, containers_dict):
"""
Merge the list of missing repository dependencies into the list of installed
repository dependencies.
@@ -295,7 +295,7 @@ class DependencyDisplayer:
containers_dict["missing_repository_dependencies"] = None
return containers_dict
def merge_missing_tool_dependencies_to_installed_container(self, containers_dict):
def _merge_missing_tool_dependencies_to_installed_container(self, containers_dict):
"""
Merge the list of missing tool dependencies into the list of installed tool
dependencies.
@@ -343,7 +343,7 @@ class DependencyDisplayer:
or for an installed repository that is being updated and the updates include newly
defined repository (and possibly tool) dependencies.
"""
installed_tool_dependencies, missing_tool_dependencies = self.populate_tool_dependencies_dicts(
installed_tool_dependencies, missing_tool_dependencies = self._populate_tool_dependencies_dicts(
tool_shed_url=tool_shed_url,
tool_path=tool_path,
repository_installed_tool_dependencies=installed_tool_dependencies,
@@ -372,9 +372,9 @@ class DependencyDisplayer:
# the missing_repository_dependencies container contents to the installed_repository_dependencies
# container. When updating an installed repository, merging will result in losing newly defined
# dependencies included in the updates.
containers_dict = self.merge_missing_repository_dependencies_to_installed_container(containers_dict)
containers_dict = self._merge_missing_repository_dependencies_to_installed_container(containers_dict)
# Merge the missing_tool_dependencies container contents to the installed_tool_dependencies container.
containers_dict = self.merge_missing_tool_dependencies_to_installed_container(containers_dict)
containers_dict = self._merge_missing_tool_dependencies_to_installed_container(containers_dict)
return containers_dict
def populate_containers_dict_from_repository_metadata(
@@ -433,11 +433,11 @@ class DependencyDisplayer:
(
repository_installed_tool_dependencies,
repository_missing_tool_dependencies,
) = self.get_installed_and_missing_tool_dependencies_for_installed_repository(
) = self._get_installed_and_missing_tool_dependencies_for_installed_repository(
repository, repository_tool_dependencies
)
if reinstalling:
installed_tool_dependencies, missing_tool_dependencies = self.populate_tool_dependencies_dicts(
installed_tool_dependencies, missing_tool_dependencies = self._populate_tool_dependencies_dicts(
tool_shed_url,
tool_path,
repository_installed_tool_dependencies,
@@ -485,7 +485,7 @@ class DependencyDisplayer:
)
return containers_dict
def populate_tool_dependencies_dicts(
def _populate_tool_dependencies_dicts(
self,
tool_shed_url,
tool_path,
@@ -503,14 +503,14 @@ class DependencyDisplayer:
repository_installed_tool_dependencies = {}
else:
# Add the install_dir attribute to the tool_dependencies.
repository_installed_tool_dependencies = self.add_installation_directories_to_tool_dependencies(
repository_installed_tool_dependencies = self._add_installation_directories_to_tool_dependencies(
repository_installed_tool_dependencies
)
if repository_missing_tool_dependencies is None:
repository_missing_tool_dependencies = {}
else:
# Add the install_dir attribute to the tool_dependencies.
repository_missing_tool_dependencies = self.add_installation_directories_to_tool_dependencies(
repository_missing_tool_dependencies = self._add_installation_directories_to_tool_dependencies(
repository_missing_tool_dependencies
)
if required_repo_info_dicts:
@@ -528,7 +528,7 @@ class DependencyDisplayer:
) = get_repo_info_tuple_contents(repo_info_tuple)
if tool_dependencies:
# Add the install_dir attribute to the tool_dependencies.
tool_dependencies = self.add_installation_directories_to_tool_dependencies(tool_dependencies)
tool_dependencies = self._add_installation_directories_to_tool_dependencies(tool_dependencies)
# The required_repository may have been installed with a different changeset revision.
(
required_repository,
@@ -540,13 +540,13 @@ class DependencyDisplayer:
(
required_repository_installed_tool_dependencies,
required_repository_missing_tool_dependencies,
) = self.get_installed_and_missing_tool_dependencies_for_installed_repository(
) = self._get_installed_and_missing_tool_dependencies_for_installed_repository(
required_repository, tool_dependencies
)
if required_repository_installed_tool_dependencies:
# Add the install_dir attribute to the tool_dependencies.
required_repository_installed_tool_dependencies = (
self.add_installation_directories_to_tool_dependencies(
self._add_installation_directories_to_tool_dependencies(
required_repository_installed_tool_dependencies
)
)
@@ -556,7 +556,7 @@ class DependencyDisplayer:
if required_repository_missing_tool_dependencies:
# Add the install_dir attribute to the tool_dependencies.
required_repository_missing_tool_dependencies = (
self.add_installation_directories_to_tool_dependencies(
self._add_installation_directories_to_tool_dependencies(
required_repository_missing_tool_dependencies
)
)
@@ -569,7 +569,7 @@ class DependencyDisplayer:
missing_tool_dependencies = repository_missing_tool_dependencies
return installed_tool_dependencies, missing_tool_dependencies
def tool_dependency_is_orphan(self, type, name, version, tools):
def _tool_dependency_is_orphan(self, type, name, version, tools):
"""
Determine if the combination of the received type, name and version is defined in the <requirement>
tag for at least one tool in the received list of tools. If not, the tool dependency defined by the