Remove unnecessary calls to get_repo_for_repository()

lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py

@@ -1634,10 +1634,9 @@ def update_to_changeset_revision(self, trans, **kwd):
                         repo_files_dir = os.path.abspath(os.path.join(tool_path, relative_install_dir, name))
                     else:
                         repo_files_dir = os.path.abspath(os.path.join(relative_install_dir, name))
-                    repo = hg_util.get_repo_for_repository(trans.app, repo_path=repo_files_dir)
                     repository_clone_url = os.path.join(tool_shed_url, 'repos', owner, name)
                     hg_util.pull_repository(repo_files_dir, repository_clone_url, latest_ctx_rev)
-                    hg_util.update_repository(repo, latest_ctx_rev)
+                    hg_util.update_repository(repo_files_dir, latest_ctx_rev)
                     # Remove old Data Manager entries
                     if repository.includes_data_managers:
                         dmh = data_manager.DataManagerHandler(trans.app)

lib/galaxy/webapps/tool_shed/api/repositories.py

@@ -1066,7 +1066,7 @@ def create_changeset_revision(self, trans, id, payload, **kwd):
                 "err_msg": "You do not have permission to update this repository.",
             }
 
-        repo = hg_util.get_repo_for_repository(self.app, repository=repository)
+        repo_dir = repository.repo_path(self.app)
 
         upload_point = commit_util.get_upload_point(repository, **kwd)
         tip = repository.tip(self.app)
@@ -1117,7 +1117,7 @@ def create_changeset_revision(self, trans, id, payload, **kwd):
             )
         if ok:
             # Update the repository files for browsing.
-            hg_util.update_repository(repo)
+            hg_util.update_repository(repo_dir)
             # Get the new repository tip.
             if tip == repository.tip(self.app):
                 trans.response.status = 400

lib/galaxy/webapps/tool_shed/controllers/repository.py

@@ -435,9 +435,9 @@ def browse_repository(self, trans, id, **kwd):
         status = kwd.get('status', 'done')
         commit_message = escape(kwd.get('commit_message', 'Deleted selected files'))
         repository = repository_util.get_repository_in_tool_shed(trans.app, id)
-        repo = hg_util.get_repo_for_repository(trans.app, repository=repository)
+        repo_path = repository.repo_path(trans.app)
         # Update repository files for browsing.
-        hg_util.update_repository(repo)
+        hg_util.update_repository(repo_path)
         changeset_revision = repository.tip(trans.app)
         metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision(trans.app,
                                                                                              id,
@@ -2410,7 +2410,7 @@ def select_files_to_delete(self, trans, id, **kwd):
                                          message=commit_message)
                 suc.handle_email_alerts(trans.app, trans.request.host, repository)
                 # Update the repository files for browsing.
-                hg_util.update_repository(repo)
+                hg_util.update_repository(repo_dir)
                 # Get the new repository tip.
                 if tip == repository.tip(trans.app):
                     message += 'No changes to repository.  '

lib/galaxy/webapps/tool_shed/controllers/upload.py

@@ -42,7 +42,6 @@ def upload(self, trans, **kwd):
         repository_id = kwd.get('repository_id', '')
         repository = repository_util.get_repository_in_tool_shed(trans.app, repository_id)
         repo_dir = repository.repo_path(trans.app)
-        repo = hg_util.get_repo_for_repository(trans.app, repo_path=repo_dir)
         uncompress_file = util.string_as_bool(kwd.get('uncompress_file', 'true'))
         remove_repo_files_not_in_tar = util.string_as_bool(kwd.get('remove_repo_files_not_in_tar', 'true'))
         uploaded_file = None
@@ -230,7 +229,7 @@ def upload(self, trans, **kwd):
                                                     admin_only=admin_only)
                 if ok:
                     # Update the repository files for browsing.
-                    hg_util.update_repository(repo)
+                    hg_util.update_repository(repo_dir)
                     # Get the new repository tip.
                     if tip == repository.tip(trans.app):
                         message = 'No changes to repository.  '

lib/tool_shed/galaxy_install/install_manager.py

@@ -880,9 +880,8 @@ def install_tool_shed_repository(self, tool_shed_repository, repo_info_dict, too
                 current_ctx_rev = changeset_revision_dict.get('ctx_rev', None)
                 if current_ctx_rev != ctx_rev:
                     repo_path = os.path.abspath(install_dir)
-                    repo = hg_util.get_repo_for_repository(self.app, repo_path=repo_path)
                     hg_util.pull_repository(repo_path, repository_clone_url, current_changeset_revision)
-                    hg_util.update_repository(repo, ctx_rev=current_ctx_rev)
+                    hg_util.update_repository(repo_path, ctx_rev=current_ctx_rev)
             self.__handle_repository_contents(tool_shed_repository=tool_shed_repository,
                                               tool_path=tool_path,
                                               repository_clone_url=repository_clone_url,

lib/tool_shed/util/hg_util.py

@@ -29,9 +29,9 @@ def add_changeset(repo_path, path_to_filename_in_archive):
 
 def archive_repository_revision(app, repository, archive_dir, changeset_revision):
     '''Create an un-versioned archive of a repository.'''
-    repo = get_repo_for_repository(app, repository=repository)
+    repo_path = repository.repo_path(app)
     try:
-        subprocess.check_output(['hg', 'archive', '-r', changeset_revision, archive_dir], stderr=subprocess.STDOUT, cwd=repo.root)
+        subprocess.check_output(['hg', 'archive', '-r', changeset_revision, archive_dir], stderr=subprocess.STDOUT, cwd=repo_path)
     except Exception as e:
         error_message = "Error attempting to archive revision '%s' of repository '%s': %s" % (changeset_revision, repository.name, e)
         if isinstance(e, subprocess.CalledProcessError):
@@ -88,25 +88,24 @@ def copy_file_from_manifest(repo, ctx, filename, dir):
 
 
 def create_hgrc_file(app, repository):
-    # At this point, an entry for the repository is required to be in the hgweb.config
-    # file so we can call repository.repo_path( trans.app ).  Since we support both
-    # http and https, we set push_ssl to False to override the default (which is True)
-    # in the mercurial api.  The hg purge extension purges all files and directories
-    # not being tracked by mercurial in the current repository.  It'll remove unknown
-    # files and empty directories.  This is not currently used because it is not supported
-    # in the mercurial API.
-    repo = get_repo_for_repository(app, repository=repository)
-    fp = repo.opener('hgrc', 'wb')
-    fp.write('[paths]\n')
-    fp.write('default = .\n')
-    fp.write('default-push = .\n')
-    fp.write('[web]\n')
-    fp.write('allow_push = %s\n' % repository.user.username)
-    fp.write('name = %s\n' % repository.name)
-    fp.write('push_ssl = false\n')
-    fp.write('[extensions]\n')
-    fp.write('hgext.purge=')
-    fp.close()
+    # Since we support both http and https, we set `push_ssl` to False to
+    # override the default (which is True) in the Mercurial API.
+    # The hg purge extension purges all files and directories not being tracked
+    # by Mercurial in the current repository. It will remove unknown files and
+    # empty directories. This is not currently used because it is not supported
+    # in the Mercurial API.
+    repo_path = repository.repo_path(app)
+    hgrc_path = os.path.join(repo_path, '.hg', 'hgrc')
+    with open(hgrc_path, 'wb') as fp:
+        fp.write('[paths]\n')
+        fp.write('default = .\n')
+        fp.write('default-push = .\n')
+        fp.write('[web]\n')
+        fp.write('allow_push = %s\n' % repository.user.username)
+        fp.write('name = %s\n' % repository.name)
+        fp.write('push_ssl = false\n')
+        fp.write('[extensions]\n')
+        fp.write('hgext.purge=')
 
 
 def get_changectx_for_changeset(repo, changeset_revision, **kwd):
@@ -356,7 +355,7 @@ def reversed_upper_bounded_changelog(repo, included_upper_bounds_changeset_revis
     return reversed_lower_upper_bounded_changelog(repo, INITIAL_CHANGELOG_HASH, included_upper_bounds_changeset_revision)
 
 
-def update_repository(repo, ctx_rev=None):
+def update_repository(repo_path, ctx_rev=None):
     """
     Update the cloned repository to changeset_revision.  It is critical that the installed repository is updated to the desired
     changeset_revision before metadata is set because the process for setting metadata uses the repository files on disk.
@@ -376,7 +375,7 @@ def update_repository(repo, ctx_rev=None):
     if ctx_rev:
         cmd.extend(['-r', ctx_rev])
     try:
-        subprocess.check_output(cmd, stderr=subprocess.STDOUT, cwd=repo.root)
+        subprocess.check_output(cmd, stderr=subprocess.STDOUT, cwd=repo_path)
     except Exception as e:
         error_message = 'Error updating repository: %s' % e
         if isinstance(e, subprocess.CalledProcessError):