sapiopycommons 2025.4.8a473__py3-none-any.whl → 2025.4.9a150__py3-none-any.whl

sapiopycommons/callbacks/field_builder.py

@@ -443,8 +443,6 @@ class FieldBuilder:
                 raise SapioException("Unable to set multiple list modes at once for a selection list.")
             # Static values don't have a list mode. Evaluate this last so that the multiple list modes check doesn't
             # need to be more complex.
-            # PR-47531: Even though static values don't use an existing list mode, a list mode must still be set.
-            list_mode = ListMode.USER
 
         if not list_mode and static_values is None:
             raise SapioException("A list mode must be chosen for selection list fields.")

sapiopycommons/chem/Molecules.py

@@ -1,5 +1,6 @@
 # Author Yechen Qiao
 # Common Molecule Utilities for Molecule Transfers with Sapio
+from typing import cast
 
 from rdkit import Chem
 from rdkit.Chem import Crippen, MolToInchi
@@ -8,6 +9,7 @@ from rdkit.Chem import rdMolDescriptors
 from rdkit.Chem.EnumerateStereoisomers import StereoEnumerationOptions, EnumerateStereoisomers
 from rdkit.Chem.MolStandardize import rdMolStandardize
 from rdkit.Chem.SaltRemover import SaltRemover
+from rdkit.Chem.rdChemReactions import ChemicalReaction
 from rdkit.Chem.rdchem import Mol, RWMol, Bond
 
 from sapiopycommons.chem.IndigoMolecules import indigo, renderer, indigo_inchi

sapiopycommons/customreport/term_builder.py

@@ -279,7 +279,7 @@ class TermBuilder:
 
         :param a: The first term in the operation.
         :param b: The second term in the operation.
-        :param is_negated: Whether the returned term should be negated (i.e. turn this into an XNOR operation).
+        :param is_negated: Whether the returned term should be negated (i.e. turn this into an xnor operation).
         :return: A composite report term for "A xor B".
         """
         return TermBuilder.and_terms(TermBuilder.or_terms(a, b),

sapiopycommons/datatype/attachment_util.py

@@ -1,7 +1,6 @@
 import io
 
 from sapiopylib.rest.DataMgmtService import DataMgmtServer
-from sapiopylib.rest.utils.recordmodel.PyRecordModel import PyRecordModel
 from sapiopylib.rest.utils.recordmodel.RecordModelWrapper import WrappedType
 
 from sapiopycommons.general.aliases import AliasUtil, SapioRecord, UserIdentifier
@@ -50,10 +49,9 @@ class AttachmentUtil:
         with io.BytesIO(file_bytes) as stream:
             dr_man.set_attachment_data(attachment, file_name, stream)
 
-    # CR-47491: Support providing a data type name string to receive PyRecordModels instead of requiring a WrapperType.
     @staticmethod
     def create_attachment(context: UserIdentifier, file_name: str, file_bytes: bytes,
-                          wrapper_type: type[WrappedType] | str) -> WrappedType | PyRecordModel:
+                          wrapper_type: type[WrappedType]) -> WrappedType:
         """
         Create an attachment data type and initialize its attachment bytes at the same time.
         Makes a webservice call to create the attachment record and a second to set its bytes.
@@ -64,6 +62,6 @@ class AttachmentUtil:
         :param wrapper_type: The attachment type to create.
         :return: A record model for the newly created attachment.
         """
-        attachment: WrappedType | PyRecordModel = RecordHandler(context).create_models(wrapper_type, 1)[0]
+        attachment: WrappedType = RecordHandler(context).create_models(wrapper_type, 1)[0]
         AttachmentUtil.set_attachment_bytes(context, attachment, file_name, file_bytes)
         return attachment

sapiopycommons/datatype/data_fields.py

@@ -58,26 +58,4 @@ class ProcessWorkflowTrackingFields:
     WORKFLOW_PROCESS_TAT__FIELD = WrapperField("WorkflowProcessTAT", FieldType.DOUBLE)
     WORKFLOW_START_USER_ID__FIELD = WrapperField("WorkflowStartUserId", FieldType.STRING)
     WORKFLOW_TAT__FIELD = WrapperField("WorkflowTAT", FieldType.DOUBLE)
-    WORKFLOW_VERSION__FIELD = WrapperField("WorkflowVersion", FieldType.LONG)
-
-class PlateDesignerWellElementFields:
-    DATA_TYPE_NAME = 'PlateDesignerWellElement'
-    ACTUAL_VOLUME_REMOVED__FIELD = WrapperField("ActualVolumeRemoved", FieldType.DOUBLE)
-    ALIQUOT_SAMPLE_RECORD_ID__FIELD = WrapperField("AliquotSampleRecordId", FieldType.LONG)
-    COL_POSITION__FIELD = WrapperField("ColPosition", FieldType.SELECTION)
-    CONCENTRATION__FIELD = WrapperField("Concentration", FieldType.DOUBLE)
-    CONCENTRATION_UNITS__FIELD = WrapperField("ConcentrationUnits", FieldType.STRING)
-    CONTROL_TYPE__FIELD = WrapperField("ControlType", FieldType.STRING)
-    DILUTION_SCHEME__FIELD = WrapperField("DilutionScheme", FieldType.DOUBLE)
-    IS_CONTROL__FIELD = WrapperField("IsControl", FieldType.BOOLEAN)
-    LAYER__FIELD = WrapperField("Layer", FieldType.INTEGER)
-    PLATE_RECORD_ID__FIELD = WrapperField("PlateRecordId", FieldType.LONG)
-    ROW_POSITION__FIELD = WrapperField("RowPosition", FieldType.SELECTION)
-    SOURCE_DATA_TYPE_NAME__FIELD = WrapperField("SourceDataTypeName", FieldType.STRING)
-    SOURCE_RECORD_ID__FIELD = WrapperField("SourceRecordId", FieldType.LONG)
-    SOURCE_SAMPLE_CONCENTRATION__FIELD = WrapperField("SourceSampleConcentration", FieldType.DOUBLE)
-    SOURCE_SAMPLE_MASS__FIELD = WrapperField("SourceSampleMass", FieldType.DOUBLE)
-    SOURCE_SAMPLE_VOLUME__FIELD = WrapperField("SourceSampleVolume", FieldType.DOUBLE)
-    SOURCE_VOLUME_TO_REMOVE__FIELD = WrapperField("SourceVolumeToRemove", FieldType.DOUBLE)
-    TARGET_MASS__FIELD = WrapperField("TargetMass", FieldType.DOUBLE)
-    VOLUME__FIELD = WrapperField("Volume", FieldType.DOUBLE)
+    WORKFLOW_VERSION__FIELD = WrapperField("WorkflowVersion", FieldType.LONG)