Merge branch 'release_19.09' into release_20.01

lib/galaxy/managers/context.py

@@ -180,12 +180,24 @@ class ProvidesHistoryContext(object):
             # The API presents a Bunch for a history.  Until the API is
             # more fully featured for handling this, also return None.
             return None
-        datasets = self.sa_session.query(self.app.model.HistoryDatasetAssociation) \
-                                  .filter_by(deleted=False, history_id=self.history.id, extension="len")
+        non_ready_or_ok = set(self.app.model.Dataset.non_ready_states)
+        non_ready_or_ok.add(self.app.model.HistoryDatasetAssociation.states.OK)
+        datasets = self.sa_session.query(
+            self.app.model.HistoryDatasetAssociation
+        ).filter_by(
+            deleted=False,
+            history_id=self.history.id,
+            extension="len"
+        ).filter(
+            self.app.model.HistoryDatasetAssociation._state.in_(non_ready_or_ok),
+        )
+        valid_ds = None
         for ds in datasets:
-            if dbkey == ds.dbkey:
-                return ds
-        return None
+            if ds.dbkey == dbkey:
+                if ds.state == self.app.model.HistoryDatasetAssociation.states.OK:
+                    return ds
+                valid_ds = ds
+        return valid_ds
 
     @property
     def db_builds(self):

lib/galaxy/tools/cache.py

@@ -149,16 +149,20 @@ class ToolShedRepositoryCache(object):
         self.repos_by_tuple[(repository.tool_shed, repository.owner, repository.name)].append(repository)
 
     def rebuild(self):
-        self.repositories = self.app.install_model.context.current.query(self.app.install_model.ToolShedRepository).options(
-            defer(self.app.install_model.ToolShedRepository.metadata),
-            joinedload('tool_dependencies').subqueryload('tool_shed_repository').options(
-                defer(self.app.install_model.ToolShedRepository.metadata)
-            ),
-        ).all()
-        repos_by_tuple = defaultdict(list)
-        for repository in self.repositories + self.local_repositories:
-            repos_by_tuple[(repository.tool_shed, repository.owner, repository.name)].append(repository)
-        self.repos_by_tuple = repos_by_tuple
+        try:
+            session = self.app.install_model.context.current.session_factory()
+            self.repositories = session.query(self.app.install_model.ToolShedRepository).options(
+                defer(self.app.install_model.ToolShedRepository.metadata),
+                joinedload('tool_dependencies').subqueryload('tool_shed_repository').options(
+                    defer(self.app.install_model.ToolShedRepository.metadata)
+                ),
+            ).all()
+            repos_by_tuple = defaultdict(list)
+            for repository in self.repositories + self.local_repositories:
+                repos_by_tuple[(repository.tool_shed, repository.owner, repository.name)].append(repository)
+            self.repos_by_tuple = repos_by_tuple
+        finally:
+            session.close()
 
     def get_installed_repository(self, tool_shed=None, name=None, owner=None, installed_changeset_revision=None, changeset_revision=None, repository_id=None):
         if repository_id:

test/unit/tools/conftest.py

@@ -65,4 +65,13 @@ def create_repo(app, changeset, installed_changeset, config_filename=None):
     repository.deleted = False
     repository.uninstalled = False
     app.install_model.context.add(repository)
+    app.install_model.context.flush()
+    tool_dependency = tool_shed_install.ToolDependency(
+        name='Name',
+        version='100',
+        type='package',
+        status='ok',
+        tool_shed_repository_id=repository.id,
+    )
+    app.install_model.context.add(tool_dependency)
     return repository

test/unit/tools/test_tool_shed_repository_cache.py

@@ -1,4 +1,5 @@
 import pytest
+from sqlalchemy.orm.exc import DetachedInstanceError
 
 from .conftest import create_repo
 
@@ -54,3 +55,20 @@ def test_get_installed_repository(tool_shed_repository_cache, repos, tool_conf_r
         assert repo
     else:
         assert repo is None
+
+
+def test_repo_cache_expunge(tool_shed_repository_cache, repos):
+    tool_shed_repository_cache.rebuild()
+    assert len(tool_shed_repository_cache.repositories) == 10
+    # Modify and commit a repo, will expire in memory attributes of orm objects (unless using a different session)
+    repo = tool_shed_repository_cache.repositories[0]
+    repo.name = 'new name'
+    tool_shed_repository_cache.app.install_model.session.flush()
+    # remove session, should demonstrate the separate session is in use
+    tool_shed_repository_cache.app.install_model.session.remove()
+    assert repo.changeset_revision == "1"
+    assert repo.tool_dependencies[0].name == 'Name'
+    with pytest.raises(DetachedInstanceError):
+        # Make sure this still raises DetachedInstanceError,
+        # keeping this in memory would be expensive
+        repo.metadata