Use hg id to map a changeset to a revision number

This allows removing a lot of calls to `hg_util.get_repo_for_repository()`, which uses the discouraged Mercurial API.
galaxyproject · Jun 8, 2018 · 4299995 · 4299995
1 parent 7c75c23
commit 4299995
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Showing 14 changed files with 72 additions and 95 deletions.
diff --git a/lib/galaxy/webapps/tool_shed/api/repositories.py b/lib/galaxy/webapps/tool_shed/api/repositories.py
@@ -216,8 +216,7 @@ def get_repository_revision_install_info(self, trans, name, owner, changeset_rev
             if repository_metadata is None:
                 # The changeset_revision column in the repository_metadata table has been updated with a new
                 # value value, so find the changeset_revision to which we need to update.
-                repo = hg_util.get_repo_for_repository(self.app, repository=repository)
-                new_changeset_revision = metadata_util.get_next_downloadable_changeset_revision(repository, repo, changeset_revision)
+                new_changeset_revision = metadata_util.get_next_downloadable_changeset_revision(self.app, repository, changeset_revision)
                 repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(self.app,
                                                                                                   encoded_repository_id,
                                                                                                   new_changeset_revision)
@@ -800,15 +799,14 @@ def updates(self, trans, **kwd):
             repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(trans.app,
                                                                                               trans.security.encode_id(repository.id),
                                                                                               changeset_revision)
-            repo = hg_util.get_repo_for_repository(trans.app, repository=repository)
             tool_shed_status_dict = {}
             # Handle repository deprecation.
             tool_shed_status_dict['repository_deprecated'] = str(repository.deprecated)
             # Handle latest installable revision.
             if changeset_revision == repository.tip(trans.app):
                 tool_shed_status_dict['latest_installable_revision'] = 'True'
             else:
-                next_installable_revision = metadata_util.get_next_downloadable_changeset_revision(repository, repo, changeset_revision)
+                next_installable_revision = metadata_util.get_next_downloadable_changeset_revision(trans.app, repository, changeset_revision)
                 if repository_metadata is None:
                     if next_installable_revision and next_installable_revision != changeset_revision:
                         tool_shed_status_dict['latest_installable_revision'] = 'True'
@@ -828,7 +826,7 @@ def updates(self, trans, **kwd):
                 else:
                     tool_shed_status_dict['revision_update'] = 'False'
             # Handle revision upgrades.
-            metadata_revisions = [revision[1] for revision in metadata_util.get_metadata_revisions(repository, repo)]
+            metadata_revisions = [revision[1] for revision in metadata_util.get_metadata_revisions(trans.app, repository)]
             num_metadata_revisions = len(metadata_revisions)
             for index, metadata_revision in enumerate(metadata_revisions):
                 if index == num_metadata_revisions:

diff --git a/lib/galaxy/webapps/tool_shed/api/repository_revisions.py b/lib/galaxy/webapps/tool_shed/api/repository_revisions.py
@@ -6,7 +6,6 @@
 from galaxy import web
 from galaxy.web.base.controller import BaseAPIController, HTTPBadRequest
 from tool_shed.capsule import capsule_manager
-from tool_shed.util import hg_util
 from tool_shed.util import metadata_util
 from tool_shed.util import repository_util
 
@@ -141,10 +140,7 @@ def repository_dependencies(self, trans, id, **kwd):
                 if repository_dependency_repository_metadata is None:
                     # The changeset_revision column in the repository_metadata table has been updated with a new
                     # value value, so find the changeset_revision to which we need to update.
-                    repo = hg_util.get_repo_for_repository(trans.app, repository=repository_dependency)
-                    new_changeset_revision = metadata_util.get_next_downloadable_changeset_revision(repository_dependency,
-                                                                                                    repo,
-                                                                                                    changeset_revision)
+                    new_changeset_revision = metadata_util.get_next_downloadable_changeset_revision(trans.app, repository_dependency, changeset_revision)
                     if new_changeset_revision != changeset_revision:
                         repository_dependency_repository_metadata = \
                             metadata_util.get_repository_metadata_by_changeset_revision(trans.app,

diff --git a/lib/galaxy/webapps/tool_shed/controllers/repository.py b/lib/galaxy/webapps/tool_shed/controllers/repository.py
@@ -1354,8 +1354,7 @@ def get_latest_downloadable_changeset_revision(self, trans, **kwd):
         if repository_name is not None and repository_owner is not None:
             repository = repository_util.get_repository_by_name_and_owner(trans.app, repository_name, repository_owner)
             if repository:
-                repo = hg_util.get_repo_for_repository(trans.app, repository=repository)
-                return metadata_util.get_latest_downloadable_changeset_revision(trans.app, repository, repo)
+                return metadata_util.get_latest_downloadable_changeset_revision(trans.app, repository)
         return hg_util.INITIAL_CHANGELOG_HASH
 
     @web.json
@@ -1565,20 +1564,18 @@ def get_updated_repository_information(self, trans, name, owner, changeset_revis
         repository = repository_util.get_repository_by_name_and_owner(trans.app, name, owner)
         repository_id = trans.security.encode_id(repository.id)
         repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed(trans.user, repository)
-        repo = hg_util.get_repo_for_repository(trans.app, repository=repository)
         repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(trans.app, repository_id, changeset_revision)
         if not repository_metadata:
             # The received changeset_revision is no longer associated with metadata, so get the next changeset_revision in the repository
             # changelog that is associated with metadata.
-            changeset_revision = metadata_util.get_next_downloadable_changeset_revision(repository,
-                                                                                        repo,
-                                                                                        after_changeset_revision=changeset_revision)
+            changeset_revision = metadata_util.get_next_downloadable_changeset_revision(trans.app, repository, after_changeset_revision=changeset_revision)
             repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(trans.app, repository_id, changeset_revision)
-        ctx = hg_util.get_changectx_for_changeset(repo, changeset_revision)
+        repo_path = repository.repo_path(trans.app)
+        ctx_rev = hg_util.changeset2rev(repo_path, changeset_revision)
         repo_info_dict = repository_util.create_repo_info_dict(app=trans.app,
                                                                repository_clone_url=repository_clone_url,
                                                                changeset_revision=changeset_revision,
-                                                               ctx_rev=str(ctx.rev()),
+                                                               ctx_rev=ctx_rev,
                                                                repository_owner=repository.user.username,
                                                                repository_name=repository.name,
                                                                repository=repository,
@@ -1979,7 +1976,7 @@ def manage_repository(self, trans, id, **kwd):
                 # There is no repository_metadata defined for the changeset_revision, so see if it was defined in a previous
                 # changeset in the changelog.
                 previous_changeset_revision = \
-                    metadata_util.get_previous_metadata_changeset_revision(repository, repo, changeset_revision, downloadable=False)
+                    metadata_util.get_previous_metadata_changeset_revision(trans.app, repository, changeset_revision, downloadable=False)
                 if previous_changeset_revision != hg_util.INITIAL_CHANGELOG_HASH:
                     repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(trans.app, id, previous_changeset_revision)
                     if repository_metadata:
@@ -2078,12 +2075,8 @@ def manage_repository_admins(self, trans, id, **kwd):
             else:
                 # There is no repository_metadata defined for the changeset_revision, so see if it was defined
                 # in a previous changeset in the changelog.
-                repo = hg_util.get_repo_for_repository(trans.app, repository=repository)
                 previous_changeset_revision = \
-                    metadata_util.get_previous_metadata_changeset_revision(repository,
-                                                                           repo,
-                                                                           changeset_revision,
-                                                                           downloadable=False)
+                    metadata_util.get_previous_metadata_changeset_revision(trans.app, repository, changeset_revision, downloadable=False)
                 if previous_changeset_revision != hg_util.INITIAL_CHANGELOG_HASH:
                     repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(trans.app,
                                                                                                       id,
@@ -2155,9 +2148,8 @@ def next_installable_changeset_revision(self, trans, **kwd):
         owner = kwd.get('owner', None)
         changeset_revision = kwd.get('changeset_revision', None)
         repository = repository_util.get_repository_by_name_and_owner(trans.app, name, owner)
-        repo = hg_util.get_repo_for_repository(trans.app, repository=repository)
         # Get the next installable changeset_revision beyond the received changeset_revision.
-        next_changeset_revision = metadata_util.get_next_downloadable_changeset_revision(repository, repo, changeset_revision)
+        next_changeset_revision = metadata_util.get_next_downloadable_changeset_revision(trans.app, repository, changeset_revision)
         if next_changeset_revision and next_changeset_revision != changeset_revision:
             return next_changeset_revision
         return ''
@@ -2259,10 +2251,8 @@ def previous_changeset_revisions(self, trans, from_tip=False, **kwd):
             if changeset_revision is not None:
                 repo = hg_util.get_repo_for_repository(trans.app, repository=repository)
                 # Get the lower bound changeset revision.
-                lower_bound_changeset_revision = metadata_util.get_previous_metadata_changeset_revision(repository,
-                                                                                                        repo,
-                                                                                                        changeset_revision,
-                                                                                                        downloadable=True)
+                lower_bound_changeset_revision = \
+                    metadata_util.get_previous_metadata_changeset_revision(trans.app, repository, changeset_revision, downloadable=True)
                 # Build the list of changeset revision hashes.
                 changeset_hashes = []
                 for changeset in hg_util.reversed_lower_upper_bounded_changelog(repo,
@@ -2604,8 +2594,7 @@ def sharable_repository_revision(self, trans, owner, name, changeset_revision):
                                                                                                             changeset_revision)
             if not repository_metadata:
                 # Get updates to the received changeset_revision if any exist.
-                repo = hg_util.get_repo_for_repository(trans.app, repository=repository)
-                upper_bound_changeset_revision = metadata_util.get_next_downloadable_changeset_revision(repository, repo, changeset_revision)
+                upper_bound_changeset_revision = metadata_util.get_next_downloadable_changeset_revision(trans.app, repository, changeset_revision)
                 if upper_bound_changeset_revision and upper_bound_changeset_revision != changeset_revision:
                     changeset_revision = upper_bound_changeset_revision
                     repository_metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision(trans.app,

diff --git a/lib/galaxy/webapps/tool_shed/model/__init__.py b/lib/galaxy/webapps/tool_shed/model/__init__.py
@@ -249,17 +249,14 @@ def get_type_class(self, app):
         return app.repository_types_registry.get_class_by_label(self.type)
 
     def get_tool_dependencies(self, app, changeset_revision):
-        repo = hg_util.get_repo_for_repository(app, repository=self)
-        changeset_revision = metadata_util.get_next_downloadable_changeset_revision(self, repo, changeset_revision)
+        changeset_revision = metadata_util.get_next_downloadable_changeset_revision(app, self, changeset_revision)
         for downloadable_revision in self.downloadable_revisions:
             if downloadable_revision.changeset_revision == changeset_revision:
                 return downloadable_revision.metadata.get('tool_dependencies', {})
         return {}
 
     def installable_revisions(self, app, sort_revisions=True):
-        return metadata_util.get_metadata_revisions(self,
-                                                    hg_util.get_repo_for_repository(app, repository=self),
-                                                    sort_revisions=sort_revisions)
+        return metadata_util.get_metadata_revisions(app, self, sort_revisions=sort_revisions)
 
     def is_new(self, app):
         repo = hg_util.get_repo_for_repository(app, repository=self)

diff --git a/lib/tool_shed/capsule/capsule_manager.py b/lib/tool_shed/capsule/capsule_manager.py
@@ -587,11 +587,8 @@ def get_dependent_downloadable_revisions(self, repository_metadata):
                                             # The defined changeset_revision is not associated with a repository_metadata
                                             # record, so updates must be necessary.
                                             defined_repository = repository_util.get_repository_by_name_and_owner(self.app, name, owner)
-                                            defined_repo = hg_util.get_repo_for_repository(self.app, repository=defined_repository)
                                             updated_changeset_revision = \
-                                                metadata_util.get_next_downloadable_changeset_revision(defined_repository,
-                                                                                                       defined_repo,
-                                                                                                       changeset_revision)
+                                                metadata_util.get_next_downloadable_changeset_revision(self.app, defined_repository, changeset_revision)
                                             if updated_changeset_revision == rm_changeset_revision and updated_changeset_revision != changeset_revision:
                                                 dependent_downloadable_revisions.append(downloadable_revision)
         return dependent_downloadable_revisions

diff --git a/lib/tool_shed/dependencies/attribute_handlers.py b/lib/tool_shed/dependencies/attribute_handlers.py
@@ -109,9 +109,8 @@ def handle_elem(self, elem):
             # revision to ensure that the contents of the revision are valid.
             repository = repository_util.get_repository_by_name_and_owner(self.app, name, owner)
             if repository:
-                repo = hg_util.get_repo_for_repository(self.app, repository=repository)
                 lastest_installable_changeset_revision = \
-                    metadata_util.get_latest_downloadable_changeset_revision(self.app, repository, repo)
+                    metadata_util.get_latest_downloadable_changeset_revision(self.app, repository)
                 if lastest_installable_changeset_revision != hg_util.INITIAL_CHANGELOG_HASH:
                     elem.attrib['changeset_revision'] = lastest_installable_changeset_revision
                     altered = True

diff --git a/lib/tool_shed/dependencies/repository/relation_builder.py b/lib/tool_shed/dependencies/repository/relation_builder.py
@@ -2,8 +2,12 @@
 
 import tool_shed.util.repository_util
 from galaxy.util import asbool, listify
-from tool_shed.util import (common_util, container_util, hg_util, metadata_util,
-    shed_util_common as suc)
+from tool_shed.util import (
+    common_util,
+    container_util,
+    metadata_util,
+    shed_util_common as suc
+)
 
 log = logging.getLogger(__name__)
 
@@ -195,8 +199,7 @@ def get_updated_changeset_revisions_for_repository_dependencies(self, key_rd_dic
                         updated_key_rd_dicts.append(key_rd_dict)
                     else:
                         # The repository changeset_revision is no longer installable, so see if there's been an update.
-                        repo = hg_util.get_repo_for_repository(self.app, repository=repository)
-                        changeset_revision = metadata_util.get_next_downloadable_changeset_revision(repository, repo, rd_changeset_revision)
+                        changeset_revision = metadata_util.get_next_downloadable_changeset_revision(self.app, repository, rd_changeset_revision)
                         if changeset_revision != rd_changeset_revision:
                             repository_metadata = \
                                 metadata_util.get_repository_metadata_by_repository_id_changeset_revision(self.app,

diff --git a/lib/tool_shed/grids/repository_grids.py b/lib/tool_shed/grids/repository_grids.py
@@ -1010,11 +1010,8 @@ def get_value(self, trans, grid, repository_metadata):
                                                                                                               required_repository_id,
                                                                                                               changeset_revision)
                                 if not required_repository_metadata:
-                                    repo = hg_util.get_repo_for_repository(trans.app, repository=required_repository)
                                     updated_changeset_revision = \
-                                        metadata_util.get_next_downloadable_changeset_revision(required_repository,
-                                                                                               repo,
-                                                                                               changeset_revision)
+                                        metadata_util.get_next_downloadable_changeset_revision(trans.app, required_repository, changeset_revision)
                                     required_repository_metadata = \
                                         metadata_util.get_repository_metadata_by_repository_id_changeset_revision(trans.app,
                                                                                                                   required_repository_id,