From 38423171026af0a5c84fa81184fe5e208f10498c Mon Sep 17 00:00:00 2001 From: John Chilton Date: Mon, 12 Sep 2022 15:59:11 -0400 Subject: [PATCH 1/3] Clean up tool shed install model a bit. --- lib/galaxy/model/tool_shed_install/__init__.py | 7 +------ lib/galaxy/tool_shed/util/repository_util.py | 2 -- 2 files changed, 1 insertion(+), 8 deletions(-) diff --git a/lib/galaxy/model/tool_shed_install/__init__.py b/lib/galaxy/model/tool_shed_install/__init__.py index 4f9995ebcb9..e2f49907930 100644 --- a/lib/galaxy/model/tool_shed_install/__init__.py +++ b/lib/galaxy/model/tool_shed_install/__init__.py @@ -146,7 +146,6 @@ class ToolShedRepository(Base, _HasTable): changeset_revision=None, ctx_rev=None, metadata_=None, - includes_datatypes=False, tool_shed_status=None, deleted=False, uninstalled=False, @@ -164,7 +163,6 @@ class ToolShedRepository(Base, _HasTable): self.changeset_revision = changeset_revision self.ctx_rev = ctx_rev self.metadata_ = metadata_ or {} - self.includes_datatypes = includes_datatypes self.tool_shed_status = tool_shed_status self.deleted = deleted self.uninstalled = uninstalled @@ -331,10 +329,6 @@ class ToolShedRepository(Base, _HasTable): def includes_tool_dependencies(self): return "tool_dependencies" in self.metadata_ - @property - def includes_workflows(self): - return "workflows" in self.metadata_ - @property def installed_repository_dependencies(self): """Return the repository's repository dependencies that are currently installed.""" @@ -750,6 +744,7 @@ class ToolDependency(Base, _HasTable): self.tool_shed_repository.name, self.tool_shed_repository.installed_changeset_revision, ) + return None @property def is_installed(self): diff --git a/lib/galaxy/tool_shed/util/repository_util.py b/lib/galaxy/tool_shed/util/repository_util.py index cecdca834c1..ab6caade419 100644 --- a/lib/galaxy/tool_shed/util/repository_util.py +++ b/lib/galaxy/tool_shed/util/repository_util.py @@ -136,7 +136,6 @@ def create_or_update_tool_shed_repository( tool_shed_repository.changeset_revision = current_changeset_revision tool_shed_repository.ctx_rev = ctx_rev tool_shed_repository.metadata_ = metadata_dict - tool_shed_repository.includes_datatypes = False tool_shed_repository.deleted = deleted tool_shed_repository.uninstalled = uninstalled tool_shed_repository.status = status @@ -153,7 +152,6 @@ def create_or_update_tool_shed_repository( changeset_revision=current_changeset_revision, ctx_rev=ctx_rev, metadata_=metadata_dict, - includes_datatypes=False, dist_to_shed=dist_to_shed, deleted=deleted, uninstalled=uninstalled, From 4d03a56156598edeaa880333c1ac09d68b71b82a Mon Sep 17 00:00:00 2001 From: John Chilton Date: Wed, 14 Sep 2022 09:55:34 -0400 Subject: [PATCH 2/3] Remove broken block in metadata_generator. generate_workflow_metadata was removed at some point and this would cause an exception --- .../tool_shed/metadata/metadata_generator.py | 26 ------------------- 1 file changed, 26 deletions(-) diff --git a/lib/galaxy/tool_shed/metadata/metadata_generator.py b/lib/galaxy/tool_shed/metadata/metadata_generator.py index b831d19c9b1..0f8e26fd594 100644 --- a/lib/galaxy/tool_shed/metadata/metadata_generator.py +++ b/lib/galaxy/tool_shed/metadata/metadata_generator.py @@ -1,4 +1,3 @@ -import json import logging import os import tempfile @@ -388,31 +387,6 @@ class MetadataGenerator: else: for tup in invalid_files_and_errors_tups: self.invalid_file_tups.append(tup) - # Find all exported workflows. - elif name.endswith(".ga"): - relative_path = os.path.join(root, name) - if os.path.getsize(os.path.abspath(relative_path)) > 0: - fp = open(relative_path, "rb") - workflow_text = fp.read() - fp.close() - if workflow_text: - valid_exported_galaxy_workflow = True - try: - exported_workflow_dict = json.loads(workflow_text) - except Exception: - log.exception( - "Skipping file %s since it does not seem to be a valid exported Galaxy workflow", - str(relative_path), - ) - valid_exported_galaxy_workflow = False - if ( - valid_exported_galaxy_workflow - and "a_galaxy_workflow" in exported_workflow_dict - and exported_workflow_dict["a_galaxy_workflow"] == "true" - ): - metadata_dict = self.generate_workflow_metadata( - relative_path, exported_workflow_dict, metadata_dict - ) # Handle any data manager entries data_manager_config = get_config_from_disk(suc.REPOSITORY_DATA_MANAGER_CONFIG_FILENAME, files_dir) metadata_dict = self._generate_data_manager_metadata( From 7563356ca880032de1b97cba758af8d4bcee026f Mon Sep 17 00:00:00 2001 From: John Chilton Date: Thu, 15 Sep 2022 09:04:01 -0400 Subject: [PATCH 3/3] Cleanup comments in shed_index.py. --- lib/tool_shed/util/shed_index.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/lib/tool_shed/util/shed_index.py b/lib/tool_shed/util/shed_index.py index 5c14db7e566..4035a8c5c5c 100644 --- a/lib/tool_shed/util/shed_index.py +++ b/lib/tool_shed/util/shed_index.py @@ -69,8 +69,6 @@ def build_index(whoosh_index_dir, file_path, hgweb_config_dir, dburi, **kwargs): tool_index_writer.delete_by_term("repo_id", repo_id) for tool in tools_list: tool_contents = tool.copy() - # tool_id = tool_contents["id"] - # tool_contents["path"] = f"{repo_id}/{tool_id}" tool_contents["repo_owner_username"] = repo.get("repo_owner_username") tool_contents["repo_name"] = repo.get("name") tool_contents["repo_id"] = repo_id