Merge pull request #757 from MolSSI/next

A few miscellaneous tweaks

docs/source/user_guide/connecting_qcportal.rst

@@ -7,16 +7,15 @@ This class handles connecting to the server and exposing all the functionality o
 Connecting to the server is handled by the constructor of the :class:`~qcportal.client.PortalClient` class.
 
 The first parameter is the address or URI of the server you with to connect to (including ``http``/``https``).
-If no address is given, then by default the client will connect to the public, MolSSI-hosted server.
 
 .. tab-set::
 
  .. tab-item:: PYTHON
 
  >>> from qcportal import PortalClient
- >>> client = PortalClient()
+ >>> client = PortalClient("https://ml.qcarchive.molssi.org")
  >>> print(client.server_name)
- MolSSI Public QCArchive Server
+ The MolSSI ML QCFractal Server
 
 However, you can specify the address of another server. Here we connect to the MolSSI-hosted
 public demonstration server

qcfractal/qcfractal/components/auth/routes.py

@@ -2,9 +2,9 @@
 
 from flask import current_app, g
 
-from qcfractal.api_v1.blueprint import api_v1
-from qcfractal.api_v1.helpers import wrap_route
 from qcfractal.flask_app import storage_socket
+from qcfractal.flask_app.api_v1.blueprint import api_v1
+from qcfractal.flask_app.api_v1.helpers import wrap_route
 from qcportal.auth import UserInfo, RoleInfo, GroupInfo
 from qcportal.exceptions import (
  InconsistentUpdateError,

qcfractal/qcfractal/components/dataset_routes.py

@@ -2,9 +2,9 @@
 
 from flask import current_app, g
 
-from qcfractal.api_v1.blueprint import api_v1
-from qcfractal.api_v1.helpers import wrap_route
 from qcfractal.flask_app import storage_socket
+from qcfractal.flask_app.api_v1.blueprint import api_v1
+from qcfractal.flask_app.api_v1.helpers import wrap_route
 from qcportal.base_models import ProjURLParameters
 from qcportal.dataset_models import (
  DatasetAddBody,

qcfractal/qcfractal/components/dataset_socket.py

@@ -361,13 +361,18 @@ def update_metadata(
  raise MissingDataError(f"Could not find dataset with type={self.dataset_type} and {dataset_id}")
 
  if ds.name != new_metadata.name:
- stmt2 = select(self.dataset_orm.id)
- stmt2 = stmt2.where(self.dataset_orm.dataset_type == self.dataset_type)
- stmt2 = stmt2.where(self.dataset_orm.lname == new_metadata.name.lower())
- existing = session.execute(stmt2).scalar_one_or_none()
 
- if existing:
- raise AlreadyExistsError(f"{self.dataset_type} dataset named '{new_metadata.name}' already exists")
+ # If only change in case, no need to check if it already exists
+ if ds.name.lower() != new_metadata.name.lower():
+ stmt2 = select(self.dataset_orm.id)
+ stmt2 = stmt2.where(self.dataset_orm.dataset_type == self.dataset_type)
+ stmt2 = stmt2.where(self.dataset_orm.lname == new_metadata.name.lower())
+ existing = session.execute(stmt2).scalar_one_or_none()
+
+ if existing:
+ raise AlreadyExistsError(
+ f"{self.dataset_type} dataset named '{new_metadata.name}' already exists"
+ )
 
  ds.name = new_metadata.name
 
@@ -571,6 +576,10 @@ def rename_specifications(
  is used, it will be flushed (but not committed) before returning from this function.
  """
 
+ specification_name_map = {k: v for k, v in specification_name_map.items() if k != v}
+ if not specification_name_map:
+ return
+
  stmt = select(self.specification_orm)
  stmt = stmt.where(self.specification_orm.dataset_id == dataset_id)
  stmt = stmt.where(self.specification_orm.name.in_(specification_name_map.keys()))
@@ -805,6 +814,11 @@ def rename_entries(self, dataset_id: int, entry_name_map: Dict[str, str], *, ses
  is used, it will be flushed (but not committed) before returning from this function.
  """
 
+ # strip out any renames that don't rename
+ entry_name_map = {k: v for k, v in entry_name_map.items() if k != v}
+ if not entry_name_map:
+ return
+
  stmt = select(self.entry_orm)
  stmt = stmt.where(self.entry_orm.dataset_id == dataset_id)
  stmt = stmt.where(self.entry_orm.name.in_(entry_name_map.keys()))

qcfractal/qcfractal/components/gridoptimization/routes.py

@@ -2,9 +2,9 @@
 
 from flask import current_app, g
 
-from qcfractal.api_v1.blueprint import api_v1
-from qcfractal.api_v1.helpers import wrap_route
 from qcfractal.flask_app import storage_socket
+from qcfractal.flask_app.api_v1.blueprint import api_v1
+from qcfractal.flask_app.api_v1.helpers import wrap_route
 from qcportal.exceptions import LimitExceededError
 from qcportal.gridoptimization import (
  GridoptimizationDatasetSpecification,

qcfractal/qcfractal/components/internal_jobs/routes.py

@@ -1,8 +1,8 @@
 from flask import current_app
 
-from qcfractal.api_v1.blueprint import api_v1
-from qcfractal.api_v1.helpers import wrap_route
 from qcfractal.flask_app import storage_socket
+from qcfractal.flask_app.api_v1.blueprint import api_v1
+from qcfractal.flask_app.api_v1.helpers import wrap_route
 from qcportal.exceptions import InvalidUpdateError
 from qcportal.internal_jobs import InternalJobQueryFilters, InternalJobStatusEnum
 from qcportal.utils import calculate_limit

qcfractal/qcfractal/components/managers/routes.py

@@ -1,9 +1,9 @@
 from flask import current_app
 
-from qcfractal.api_v1.blueprint import api_v1
-from qcfractal.api_v1.helpers import wrap_route
-from qcfractal.compute_v1.blueprint import compute_v1
 from qcfractal.flask_app import storage_socket
+from qcfractal.flask_app.api_v1.blueprint import api_v1
+from qcfractal.flask_app.api_v1.helpers import wrap_route
+from qcfractal.flask_app.compute_v1.blueprint import compute_v1
 from qcportal.base_models import CommonBulkGetNamesBody
 from qcportal.exceptions import LimitExceededError
 from qcportal.managers import (

qcfractal/qcfractal/components/manybody/routes.py

@@ -2,9 +2,9 @@
 
 from flask import current_app, g
 
-from qcfractal.api_v1.blueprint import api_v1
-from qcfractal.api_v1.helpers import wrap_route
 from qcfractal.flask_app import storage_socket
+from qcfractal.flask_app.api_v1.blueprint import api_v1
+from qcfractal.flask_app.api_v1.helpers import wrap_route
 from qcportal.exceptions import LimitExceededError
 from qcportal.manybody import (
  ManybodyDatasetSpecification,

qcfractal/qcfractal/components/molecules/routes.py

@@ -2,9 +2,9 @@
 
 from flask import current_app
 
-from qcfractal.api_v1.blueprint import api_v1
-from qcfractal.api_v1.helpers import wrap_route
 from qcfractal.flask_app import storage_socket
+from qcfractal.flask_app.api_v1.blueprint import api_v1
+from qcfractal.flask_app.api_v1.helpers import wrap_route
 from qcportal.base_models import CommonBulkGetBody, ProjURLParameters
 from qcportal.exceptions import LimitExceededError
 from qcportal.molecules import Molecule, MoleculeQueryFilters, MoleculeModifyBody

qcfractal/qcfractal/components/neb/routes.py

@@ -2,9 +2,9 @@
 
 from flask import current_app, g
 
-from qcfractal.api_v1.blueprint import api_v1
-from qcfractal.api_v1.helpers import wrap_route
 from qcfractal.flask_app import storage_socket
+from qcfractal.flask_app.api_v1.blueprint import api_v1
+from qcfractal.flask_app.api_v1.helpers import wrap_route
 from qcportal.exceptions import LimitExceededError
 from qcportal.neb import NEBDatasetSpecification, NEBDatasetNewEntry, NEBAddBody, NEBQueryFilters
 from qcportal.utils import calculate_limit

qcfractal/qcfractal/components/optimization/routes.py

@@ -2,9 +2,9 @@
 
 from flask import current_app, g
 
-from qcfractal.api_v1.blueprint import api_v1
-from qcfractal.api_v1.helpers import wrap_route
 from qcfractal.flask_app import storage_socket
+from qcfractal.flask_app.api_v1.blueprint import api_v1
+from qcfractal.flask_app.api_v1.helpers import wrap_route
 from qcportal.exceptions import LimitExceededError
 from qcportal.optimization import (
  OptimizationDatasetSpecification,

qcfractal/qcfractal/components/reaction/routes.py

@@ -2,9 +2,9 @@
 
 from flask import current_app, g
 
-from qcfractal.api_v1.blueprint import api_v1
-from qcfractal.api_v1.helpers import wrap_route
 from qcfractal.flask_app import storage_socket
+from qcfractal.flask_app.api_v1.blueprint import api_v1
+from qcfractal.flask_app.api_v1.helpers import wrap_route
 from qcportal.exceptions import LimitExceededError
 from qcportal.reaction import (
  ReactionDatasetSpecification,

qcfractal/qcfractal/components/record_routes.py

@@ -2,9 +2,9 @@
 
 from flask import current_app, g
 
-from qcfractal.api_v1.blueprint import api_v1
-from qcfractal.api_v1.helpers import wrap_route
 from qcfractal.flask_app import storage_socket
+from qcfractal.flask_app.api_v1.blueprint import api_v1
+from qcfractal.flask_app.api_v1.helpers import wrap_route
 from qcportal.base_models import ProjURLParameters, CommonBulkGetBody
 from qcportal.exceptions import LimitExceededError
 from qcportal.record_models import (

qcfractal/qcfractal/components/serverinfo/routes.py

@@ -1,15 +1,15 @@
 from flask import current_app
 
 from qcfractal import __version__ as qcfractal_version
-from qcfractal.api_v1.blueprint import api_v1
-from qcfractal.api_v1.helpers import wrap_route
 from qcfractal.client_versions import (
  client_version_lower_limit,
  client_version_upper_limit,
  manager_version_lower_limit,
  manager_version_upper_limit,
 )
 from qcfractal.flask_app import storage_socket
+from qcfractal.flask_app.api_v1.blueprint import api_v1
+from qcfractal.flask_app.api_v1.helpers import wrap_route
 from qcportal.serverinfo import (
  AccessLogSummaryFilters,
  AccessLogQueryFilters,

qcfractal/qcfractal/components/singlepoint/routes.py

@@ -2,9 +2,9 @@
 
 from flask import current_app, g
 
-from qcfractal.api_v1.blueprint import api_v1
-from qcfractal.api_v1.helpers import wrap_route
 from qcfractal.flask_app import storage_socket
+from qcfractal.flask_app.api_v1.blueprint import api_v1
+from qcfractal.flask_app.api_v1.helpers import wrap_route
 from qcportal.exceptions import LimitExceededError
 from qcportal.singlepoint import (
  SinglepointDatasetSpecification,

qcfractal/qcfractal/components/tasks/routes.py

@@ -1,8 +1,8 @@
 from flask import current_app
 
-from qcfractal.api_v1.helpers import wrap_route # uses the same wrap_route as the user api
-from qcfractal.compute_v1.blueprint import compute_v1
 from qcfractal.flask_app import storage_socket
+from qcfractal.flask_app.api_v1.helpers import wrap_route # uses the same wrap_route as the user api
+from qcfractal.flask_app.compute_v1.blueprint import compute_v1
 from qcportal.exceptions import LimitExceededError
 from qcportal.tasks import TaskClaimBody, TaskReturnBody
 from qcportal.utils import calculate_limit