Merge pull request #14669 from jmchilton/misc_ts_cleanup

Various unsorted tool shed code cleanup.

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):

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(

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,

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