Make repository creation slightly safer

lib/tool_shed/util/hg_util.py

@@ -71,14 +71,13 @@ def get_hgrc_path(repo_path):
     return os.path.join(repo_path, ".hg", "hgrc")
 
 
-def create_hgrc_file(app, repository):
+def create_hgrc_file(app, repository, repo_path):
     # 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 = get_hgrc_path(repo_path)
     with open(hgrc_path, "w") as fp:
         fp.write("[paths]\n")

lib/tool_shed/util/hgweb_config.py

@@ -5,8 +5,6 @@ import shutil
 import threading
 from datetime import date
 
-from galaxy.util import unicodify
-
 log = logging.getLogger(__name__)
 
 new_hgweb_config_template = """
@@ -36,8 +34,8 @@ class HgWebConfigManager:
             self.in_memory_config.set("paths", lhs, rhs)
             # Persist our in-memory configuration.
             self.write_config()
-        except Exception as e:
-            log.debug("Exception in HgWebConfigManager.add_entry(): %s", unicodify(e))
+        except Exception:
+            log.exception("Exception in HgWebConfigManager.add_entry()")
         finally:
             self.lock.release()
 
@@ -52,8 +50,8 @@ class HgWebConfigManager:
             self.in_memory_config.set("paths", new_lhs, new_rhs)
             # Persist our in-memory configuration.
             self.write_config()
-        except Exception as e:
-            log.debug("Exception in HgWebConfigManager.change_entry(): %s", unicodify(e))
+        except Exception:
+            log.exception("Exception in HgWebConfigManager.change_entry()")
         finally:
             self.lock.release()
 

lib/tool_shed/util/repository_util.py

@@ -2,6 +2,7 @@ import configparser
 import logging
 import os
 import re
+import tempfile
 from typing import (
     Optional,
     Tuple,
@@ -154,23 +155,18 @@ def create_repo_info_dict(
 def create_repository_admin_role(app: "ToolShedApp", repository: "Repository"):
     """
     Create a new role with name-spaced name based on the repository name and its owner's public user
-    name.  This will ensure that the tole name is unique.
+    name.  This will ensure that the role name is unique.
     """
     sa_session = app.model.session
     name = get_repository_admin_role_name(str(repository.name), str(repository.user.username))
     description = "A user or group member with this role can administer this repository."
     role = app.model.Role(name=name, description=description, type=app.model.Role.types.SYSTEM)
     sa_session.add(role)
-    session = sa_session()
-    with transaction(session):
-        session.commit()
     # Associate the role with the repository owner.
     app.model.UserRoleAssociation(repository.user, role)
     # Associate the role with the repository.
     rra = app.model.RepositoryRoleAssociation(repository, role)
     sa_session.add(rra)
-    with transaction(session):
-        session.commit()
     return role
 
 
@@ -180,7 +176,7 @@ def create_repository(
     type: str,
     description,
     long_description,
-    user_id,
+    user,
     category_ids=None,
     remote_repository_url=None,
     homepage_url=None,
@@ -196,43 +192,39 @@ def create_repository(
         homepage_url=homepage_url,
         description=description,
         long_description=long_description,
-        user_id=user_id,
+        user=user,
     )
-    # Flush to get the id.
     sa_session.add(repository)
-    session = sa_session()
-    with transaction(session):
-        session.commit()
-    # Create an admin role for the repository.
-    create_repository_admin_role(app, repository)
-    # Determine the repository's repo_path on disk.
-    dir = os.path.join(app.config.file_path, *util.directory_hash_id(repository.id))
-    # Create directory if it does not exist.
-    if not os.path.exists(dir):
-        os.makedirs(dir)
-    # Define repo name inside hashed directory.
-    repository_path = os.path.join(dir, "repo_%d" % repository.id)
-    # Create local repository directory.
-    if not os.path.exists(repository_path):
-        os.makedirs(repository_path)
-    # Create the local repository.
-    init_repository(repo_path=repository_path)
-    # Add an entry in the hgweb.config file for the local repository.
-    lhs = f"{app.config.hgweb_repo_prefix}{repository.user.username}/{repository.name}"
-    app.hgweb_config_manager.add_entry(lhs, repository_path)
-    # Create a .hg/hgrc file for the local repository.
-    create_hgrc_file(app, repository)
-    flush_needed = False
     if category_ids:
         # Create category associations
         for category_id in category_ids:
             category = sa_session.query(app.model.Category).get(app.security.decode_id(category_id))
             rca = app.model.RepositoryCategoryAssociation(repository, category)
             sa_session.add(rca)
-            flush_needed = True
-    if flush_needed:
+    # Create an admin role for the repository.
+    create_repository_admin_role(app, repository)
+    # Create a temporary repo_path on disk.
+    with tempfile.TemporaryDirectory(
+        dir=app.config.file_path, prefix="f{repository.user.username}-{repository.name}"
+    ) as repository_path:
+        # Create the local repository.
+        init_repository(repo_path=repository_path)
+        # Create a .hg/hgrc file for the local repository.
+        create_hgrc_file(app, repository, repo_path=repository_path)
+        # Add an entry in the hgweb.config file for the local repository.
+        lhs = f"{app.config.hgweb_repo_prefix}{repository.user.username}/{repository.name}"
+        # Flush to get the id.
+        session = sa_session()
         with transaction(session):
             session.commit()
+        dir = os.path.join(app.config.file_path, *util.directory_hash_id(repository.id))
+        # Define repo name inside hashed directory.
+        final_repository_path = os.path.join(dir, "repo_%d" % repository.id)
+        # Create final repository directory.
+        if not os.path.exists(final_repository_path):
+            os.makedirs(final_repository_path)
+        os.rename(repository_path, final_repository_path)
+    app.hgweb_config_manager.add_entry(lhs, final_repository_path)
     # Update the repository registry.
     app.repository_registry.add_entry(repository)
     message = f"Repository <b>{escape(str(repository.name))}</b> has been created."

lib/tool_shed/webapp/api/repositories.py

@@ -986,7 +986,7 @@ class RepositoriesController(BaseAPIController):
             type=repo_type,
             description=synopsis,
             long_description=description,
-            user_id=trans.user.id,
+            user=trans.user,
             category_ids=category_ids,
             remote_repository_url=remote_repository_url,
             homepage_url=homepage_url,

lib/tool_shed/webapp/controllers/repository.py

@@ -759,7 +759,7 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
                     repository_type,
                     description,
                     long_description,
-                    user_id=trans.user.id,
+                    user=trans.user,
                     category_ids=category_ids,
                     remote_repository_url=remote_repository_url,
                     homepage_url=homepage_url,

lib/tool_shed/webapp/model/__init__.py

@@ -422,12 +422,13 @@ class Repository(Base, Dictifiable):
     ]
     file_states = Bunch(NORMAL="n", NEEDS_MERGING="m", MARKED_FOR_REMOVAL="r", MARKED_FOR_ADDITION="a", NOT_TRACKED="?")
 
-    def __init__(self, private=False, times_downloaded=0, deprecated=False, **kwd):
+    def __init__(self, private=False, times_downloaded=0, deprecated=False, user=None, **kwd):
         super().__init__(**kwd)
         self.private = private
         self.times_downloaded = times_downloaded
         self.deprecated = deprecated
         self.name = self.name or "Unnamed repository"
+        self.user = user
 
     @property
     def hg_repo(self):