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Replace all remaining instances of TSR.metadata

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This commit is contained in:
Sergey Golitsynskiy
2021-10-20 18:51:46 -04:00
parent 5acbb140b1
commit bd765b0b24
14 changed files with 27 additions and 27 deletions
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lib/galaxy/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py
+1 -1
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@@ -154,7 +154,7 @@ class CustomDatatypeLoader:
Load proprietary datatypes and return information needed for loading custom
datatypes converters and display applications later.
"""
metadata = repository.metadata
metadata = repository.metadata_
repository_dict = None
datatypes_config = get_config_from_disk(DATATYPES_CONFIG_FILENAME, relative_install_dir)
if datatypes_config:
lib/galaxy/tool_shed/galaxy_install/install_manager.py
+3 -3
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@@ -515,7 +515,7 @@ class InstallRepositoryManager:
persist=True)
irmm.generate_metadata_for_changeset_revision()
irmm_metadata_dict = irmm.get_metadata_dict()
tool_shed_repository.metadata = irmm_metadata_dict
tool_shed_repository.metadata_ = irmm_metadata_dict
# Update the tool_shed_repository.tool_shed_status column in the database.
tool_shed_status_dict = repository_util.get_tool_shed_status_for_installed_repository(self.app, tool_shed_repository)
if tool_shed_status_dict:
@@ -934,7 +934,7 @@ class InstallRepositoryManager:
shed_tool_conf=shed_tool_conf,
reinstalling=reinstalling,
tool_panel_section_mapping=tool_panel_section_mapping)
metadata = tool_shed_repository.metadata
metadata = tool_shed_repository.metadata_
if 'tools' in metadata and install_resolver_dependencies:
self.update_tool_shed_repository_status(tool_shed_repository,
self.install_model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES)
@@ -964,7 +964,7 @@ class InstallRepositoryManager:
def update_tool_shed_repository(self, repository, tool_shed_url, latest_ctx_rev, latest_changeset_revision,
install_new_dependencies=True, install_options=None):
install_options = install_options or {}
original_metadata_dict = repository.metadata
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', {})
lib/galaxy/tool_shed/galaxy_install/installed_repository_manager.py
+5 -5
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@@ -87,10 +87,10 @@ class InstalledRepositoryManager:
tpm=tpm,
repository=repository,
changeset_revision=repository.changeset_revision,
metadata_dict=repository.metadata)
metadata_dict=repository.metadata_)
repository_tools_tups = irmm.get_repository_tools_tups()
# Reload tools into the appropriate tool panel section.
tool_panel_dict = repository.metadata['tool_panel_section']
tool_panel_dict = repository.metadata_['tool_panel_section']
tpm.add_to_tool_panel(repository.name,
repository_clone_url,
repository.installed_changeset_revision,
@@ -105,7 +105,7 @@ class InstalledRepositoryManager:
data_manager_relative_install_dir = os.path.join(data_manager_relative_install_dir, repository.name)
dmh = data_manager.DataManagerHandler(self.app)
dmh.install_data_managers(self.app.config.shed_data_manager_config_file,
repository.metadata,
repository.metadata_,
repository.get_shed_config_dict(self.app),
data_manager_relative_install_dir,
repository,
@@ -204,7 +204,7 @@ class InstalledRepositoryManager:
name,
repository_owner,
changeset_revision)
if not updating and repository and repository.metadata:
if not updating and repository and repository.metadata_:
installed_rd, missing_rd = self.get_installed_and_missing_repository_dependencies(repository)
else:
installed_rd, missing_rd = \
@@ -286,7 +286,7 @@ class InstalledRepositoryManager:
if has_repository_dependencies:
# The repository dependencies container will include only the immediate repository
# dependencies of this repository, so the container will be only a single level in depth.
metadata = repository.metadata
metadata = repository.metadata_
installed_rd_tups = []
missing_rd_tups = []
for tsr in repository.repository_dependencies:
lib/galaxy/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py
+2 -2
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@@ -87,10 +87,10 @@ class InstalledRepositoryMetadataManager(MetadataGenerator):
def reset_all_metadata_on_installed_repository(self):
"""Reset all metadata on a single tool shed repository installed into a Galaxy instance."""
if self.relative_install_dir:
original_metadata_dict = self.repository.metadata
original_metadata_dict = self.repository.metadata_
self.generate_metadata_for_changeset_revision()
if self.metadata_dict != original_metadata_dict:
self.repository.metadata = self.metadata_dict
self.repository.metadata_ = self.metadata_dict
self.update_in_shed_tool_config()
self.app.install_model.context.add(self.repository)
self.app.install_model.context.flush()
lib/galaxy/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
+2 -2
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@@ -233,10 +233,10 @@ class RepositoryDependencyInstallManager:
# The database record for the tool shed repository currently being processed can be updated.
# Get the repository metadata to see where it was previously located in the tool panel.
tpm = tool_panel_manager.ToolPanelManager(self.app)
if repository_db_record and repository_db_record.metadata:
if repository_db_record and repository_db_record.metadata_:
_, tool_panel_section_key = \
tpm.handle_tool_panel_selection(toolbox=self.app.toolbox,
metadata=repository_db_record.metadata,
metadata=repository_db_record.metadata_,
no_changes_checked=no_changes_checked,
tool_panel_section_id=tool_panel_section_id,
new_tool_panel_section_label=new_tool_panel_section_label)
lib/galaxy/tool_shed/galaxy_install/tool_migration_manager.py
+1 -1
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@@ -442,7 +442,7 @@ class ToolMigrationManager:
persist=True)
irmm.generate_metadata_for_changeset_revision()
irmm_metadata_dict = irmm.get_metadata_dict()
tool_shed_repository.metadata = irmm_metadata_dict
tool_shed_repository.metadata_ = irmm_metadata_dict
self.app.install_model.context.add(tool_shed_repository)
self.app.install_model.context.flush()
has_tool_dependencies = self.__has_tool_dependencies(irmm_metadata_dict)
lib/galaxy/tool_shed/galaxy_install/tools/data_manager.py
+1 -1
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@@ -149,7 +149,7 @@ class DataManagerHandler:
return rval
def remove_from_data_manager(self, repository):
metadata_dict = repository.metadata
metadata_dict = repository.metadata_
if metadata_dict and 'data_manager' in metadata_dict:
shed_data_manager_conf_filename = self.app.config.shed_data_manager_config_file
tree, error_message = parse_xml(shed_data_manager_conf_filename)
lib/galaxy/tool_shed/galaxy_install/tools/tool_panel_manager.py
+3 -3
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@@ -212,7 +212,7 @@ class ToolPanelManager:
tool_panel_dict = {}
shed_tool_conf, tool_path, relative_install_dir = \
get_tool_panel_config_tool_path_install_dir(self.app, repository)
metadata = repository.metadata
metadata = repository.metadata_
# Create a dictionary of tool guid and tool config file name for each tool in the repository.
guids_and_configs = {}
if 'tools' in metadata:
@@ -467,7 +467,7 @@ class ToolPanelManager:
# information so the tools can be displayed in the same way when the repository is
# activated or reinstalled.
tool_panel_dict = self.generate_tool_panel_dict_from_shed_tool_conf_entries(repository)
repository.metadata['tool_panel_section'] = tool_panel_dict
repository.metadata_['tool_panel_section'] = tool_panel_dict
self.app.install_model.context.add(repository)
self.app.install_model.context.flush()
# Create a list of guids for all tools that will be removed from the in-memory tool panel
@@ -481,7 +481,7 @@ class ToolPanelManager:
shed_tool_conf_dict = self.get_shed_tool_conf_dict(shed_tool_conf)
if uninstall:
# Remove from the shed_tool_conf file on disk.
self.remove_from_shed_tool_config(shed_tool_conf_dict, repository.metadata)
self.remove_from_shed_tool_config(shed_tool_conf_dict, repository.metadata_)
def update_tool_panel_dict(self, tool_panel_dict, tool_panel_section_mapping, repository_tools_tups):
for tool_guid in tool_panel_dict:
lib/galaxy/tool_shed/galaxy_install/update_repository_manager.py
+1 -1
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@@ -109,7 +109,7 @@ class UpdateRepositoryManager:
Update a tool_shed_repository database record with new information retrieved from the
Tool Shed. This happens when updating an installed repository to a new changeset revision.
"""
repository.metadata = updated_metadata_dict
repository.metadata_ = updated_metadata_dict
tool_shed_url = get_tool_shed_url_from_tool_shed_registry(self.app, repository.tool_shed)
clean_dependency_relationships(self.app, updated_metadata_dict, repository, tool_shed_url)
# Update the repository.changeset_revision column in the database.
lib/galaxy/tool_shed/metadata/metadata_generator.py
+1 -1
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@@ -317,7 +317,7 @@ class MetadataGenerator:
if self.updating_installed_repository:
# Keep the original tool shed repository metadata if setting metadata on a repository
# installed into a local Galaxy instance for which we have pulled updates.
original_repository_metadata = self.repository.metadata
original_repository_metadata = self.repository.metadata_
else:
original_repository_metadata = None
readme_file_names = _get_readme_file_names(str(self.repository.name))
lib/galaxy/tool_shed/util/repository_util.py
+2 -2
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@@ -112,7 +112,7 @@ def create_or_update_tool_shed_repository(app, name, description, installed_chan
tool_shed_repository.description = description
tool_shed_repository.changeset_revision = current_changeset_revision
tool_shed_repository.ctx_rev = ctx_rev
tool_shed_repository.metadata = metadata_dict
tool_shed_repository.metadata_ = metadata_dict
tool_shed_repository.includes_datatypes = includes_datatypes
tool_shed_repository.deleted = deleted
tool_shed_repository.uninstalled = uninstalled
@@ -127,7 +127,7 @@ def create_or_update_tool_shed_repository(app, name, description, installed_chan
installed_changeset_revision=installed_changeset_revision,
changeset_revision=current_changeset_revision,
ctx_rev=ctx_rev,
metadata=metadata_dict,
metadata_=metadata_dict,
includes_datatypes=includes_datatypes,
dist_to_shed=dist_to_shed,
deleted=deleted,
lib/galaxy/tools/cache.py
+1 -1
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@@ -301,7 +301,7 @@ class ToolShedRepositoryCache:
def rebuild(self):
self.repositories = self.session.query(ToolShedRepository).options(
defer(ToolShedRepository.metadata), joinedload('tool_dependencies')
defer(ToolShedRepository.metadata_), joinedload('tool_dependencies')
).all()
repos_by_tuple = defaultdict(list)
for repository in self.repositories + self.local_repositories:
lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+3 -3
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@@ -177,7 +177,7 @@ class AdminToolshed(AdminGalaxy):
message = escape(kwd.get('message', ''))
status = kwd.get('status', 'done')
repository = repository_util.get_installed_tool_shed_repository(trans.app, repository_id)
repository_metadata = repository.metadata
repository_metadata = repository.metadata_
shed_config_dict = repository.get_shed_config_dict(trans.app)
tool_metadata = {}
tool_lineage = []
@@ -863,7 +863,7 @@ class AdminToolshed(AdminGalaxy):
new_tool_panel_section_label = kwd.get('new_tool_panel_section_label', '')
tool_panel_section_key = None
tool_panel_section_keys = []
metadata = tool_shed_repository.metadata
metadata = tool_shed_repository.metadata_
# Keep track of tool dependencies defined for the current repository or those defined for any of
# its repository dependencies.
includes_tool_dependencies = tool_shed_repository.includes_tool_dependencies
@@ -1024,7 +1024,7 @@ class AdminToolshed(AdminGalaxy):
latest_ctx_rev = kwd.get('latest_ctx_rev', None)
tool_shed_repository = repository_util.get_installed_tool_shed_repository(trans.app, repository_id)
repository_clone_url = common_util.generate_clone_url_for_installed_repository(trans.app, tool_shed_repository)
metadata = tool_shed_repository.metadata
metadata = tool_shed_repository.metadata_
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(trans.app, str(tool_shed_repository.tool_shed))
tool_path = tool_shed_repository.get_tool_relative_path(trans.app)[0]
if latest_changeset_revision and latest_ctx_rev:
test/unit/app/tools/test_toolbox.py
+1 -1
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@@ -111,7 +111,7 @@ class BaseToolBoxTestCase(unittest.TestCase, UsesTools):
}
if config_filename:
metadata['shed_config_filename'] = config_filename
repository = tool_shed_install.ToolShedRepository(metadata=metadata)
repository = tool_shed_install.ToolShedRepository(metadata_=metadata)
repository.tool_shed = DEFAULT_TEST_REPO.tool_shed
repository.owner = DEFAULT_TEST_REPO.owner
repository.name = DEFAULT_TEST_REPO.name