Merge pull request #276 from dgasmith/mol

Database updates

.codecov.yml

@@ -1,6 +1,8 @@
 coverage:
   ignore:
     - */tests/*
+    - qcfractal/dashboard/* # early state
+    - qcfractal/migrations/* # difficult to test
     - qcfractal/_version.py
     - setup.py
   status:

qcfractal/interface/collections/reaction_dataset.py

@@ -8,7 +8,6 @@
 import numpy as np
 import pandas as pd
 from pydantic import BaseModel
-import qcelemental as qcel
 
 from .collection_utils import nCr, register_collection
 from .dataset import Dataset
@@ -487,10 +486,6 @@ def parse_stoichiometry(self, stoichiometry):
             # What kind of molecule is it?
             mol = line[0]
 
-            # This is a molecule hash, should be in the database
-            if isinstance(mol, qcel.models.Molecule):
-                mol = Molecule(**mol.dict())
-
             if isinstance(mol, str) and (len(mol) == 40):
                 molecule_hash = mol
 

qcfractal/interface/models/common_models.py

@@ -6,8 +6,7 @@
 from typing import Any, Dict, Optional, Union, List, Tuple
 
 from pydantic import BaseModel, validator
-from qcelemental.models import Provenance
-import qcelemental as qcel
+from qcelemental.models import Molecule, Provenance
 
 from .model_utils import hash_dictionary, prepare_basis, recursive_normalizer
 
@@ -36,19 +35,6 @@ def validate(cls, v):
             raise TypeError("The string {} is not a valid 24-character hexadecimal or integer ObjectId!".format(v))
 
 
-class Molecule(qcel.models.Molecule):
-
-    id: Optional[ObjectId] = None
-    connectivity: List[Tuple[int, int, float]] = None
-
-    def __init__(self, **kwargs):
-        # print(kwargs.get("connectivity", None))
-        if ("connectivity" in kwargs) and (len(kwargs["connectivity"]) == 0):
-            del kwargs["connectivity"]
-        # print(kwargs.get("id", None), type(kwargs.get("id", None)))
-        super().__init__(**kwargs)
-
-
 class DriverEnum(str, Enum):
     energy = 'energy'
     gradient = 'gradient'
@@ -82,7 +68,7 @@ class Config:
         extra = "forbid"
         allow_mutation = False
 
-    def form_schema_object(self, keywords: Optional['KeywordSet']=None, checks=True) -> Dict[str, Any]:
+    def form_schema_object(self, keywords: Optional['KeywordSet'] = None, checks=True) -> Dict[str, Any]:
         if checks and self.keywords:
             assert keywords.id == self.keywords
 

qcfractal/interface/models/task_models.py

@@ -44,7 +44,7 @@ class PythonComputeSpec(BaseModel):
 
 class TaskRecord(BaseModel):
 
-    id: Union[ObjectId, int] = None
+    id: ObjectId = None
 
     spec: PythonComputeSpec
     parser: str

qcfractal/interface/models/torsiondrive.py

@@ -47,7 +47,7 @@ class TorsionDriveInput(BaseModel):
 
     program: _td_constr = "torsiondrive"
     procedure: _td_constr = "torsiondrive"
-    initial_molecule: List[Union[ObjectId, Molecule, int]]
+    initial_molecule: List[Union[ObjectId, Molecule]]
     keywords: TDKeywords
     optimization_spec: OptimizationSpecification
     qc_spec: QCSpecification
@@ -78,15 +78,15 @@ class TorsionDriveRecord(RecordBase):
     program: _td_constr = "torsiondrive"
 
     # Input data
-    initial_molecule: List[Union[ObjectId, int]]
+    initial_molecule: List[ObjectId]
     keywords: TDKeywords
     optimization_spec: OptimizationSpecification
     qc_spec: QCSpecification
 
     # Output data
     final_energy_dict: Dict[str, float]
 
-    optimization_history: Dict[str, List[Union[ObjectId, int]]]
+    optimization_history: Dict[str, List[ObjectId]]
     minimum_positions: Dict[str, int]
 
     class Config(RecordBase.Config):

qcfractal/storage_sockets/sqlalchemy_socket.py

@@ -477,10 +477,6 @@ def get_molecules(self, id=None, molecule_hash=None, molecular_formula=None, lim
 
         # ret["meta"]["errors"].extend(errors)
 
-        # Todo: tobe removed after bug is fixed in elemental
-        for d in rdata:
-            if d['connectivity'] is None:
-                d['connectivity'] = []
         data = [Molecule(**d, validate=False) for d in rdata]
 
         return {'meta': meta, 'data': data}

qcfractal/tests/test_procedures.py

@@ -109,7 +109,7 @@ def test_procedure_optimization(fractal_compute_server):
 
     for results in [results1, results2]:
         assert len(results) == 1
-        assert isinstance(results[0].provenance.creator, str) # TODO: Bug in QCEngine, see molssi/qcengine#42
+        assert isinstance(results[0].provenance.creator, str)
         assert isinstance(str(results[0]), str)  # Check that repr runs
         assert pytest.approx(-1.117530188962681, 1e-5) == results[0].get_final_energy()