sapiopycommons 2025.7.9a582__py3-none-any.whl → 2025.7.9a583__py3-none-any.whl

sapiopycommons/callbacks/field_builder.py

@@ -443,6 +443,8 @@ 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/IndigoMolecules.py

@@ -10,9 +10,36 @@ indigo.setOption("render-stereo-style", "ext")
 indigo.setOption("aromaticity-model", "generic")
 indigo.setOption("render-coloring", True)
 indigo.setOption("molfile-saving-mode", "3000")
+indigo.setOption("dearomatize-verification", False)
 indigo_inchi = IndigoInchi(indigo)
 
 
+def get_aromatic_dearomatic_forms(m: IndigoObject):
+    """
+    Get the aromatic and dearomatic forms of the molecule. Retain the original form if it's not inversible.
+    Inversible: after aromatic-dearomatic-aromatic transformation, the molecule is the same as the first aromatic transformation.
+    :param m: molecule from indigo.
+    :return: pair of indigo objects, first is aromatic, second is dearomatic.
+    """
+    try:
+        aromatic_reaction = m.clone()
+        aromatic_reaction.aromatize()
+        dearomatic_reaction = aromatic_reaction.clone()
+        dearomatic_reaction.dearomatize()
+        second_aromatic_reaction = dearomatic_reaction.clone()
+        second_aromatic_reaction.aromatize()
+        match = indigo.exactMatch(aromatic_reaction, second_aromatic_reaction)
+        if match:
+            return aromatic_reaction, dearomatic_reaction
+        else:
+            return m, dearomatic_reaction
+    except (Exception):
+        # If aromatization then following deromatization fails, we just skip it.
+        dearomatic_reaction = m.clone()
+        dearomatic_reaction.dearomatize()
+        return m, dearomatic_reaction
+
+
 # Function to process dative bonds in a molecule
 # Returns True if at least one dative bond (_BOND_COORDINATION) was removed
 def remove_dative_bonds_in_mol(molecule: IndigoObject) -> bool:
@@ -51,7 +78,8 @@ def remove_dative_in_reaction(reaction: IndigoObject) -> bool:
     :param reaction: The reaction to remove dative bonds.
     :return: Whether there are any dative bonds in the reaction that were removed.
     """
-    reactant_dative_removed: bool = any(remove_dative_bonds_in_mol(reactant) for reactant in reaction.iterateReactants())
+    reactant_dative_removed: bool = any(
+        remove_dative_bonds_in_mol(reactant) for reactant in reaction.iterateReactants())
     product_dative_removed: bool = any(remove_dative_bonds_in_mol(product) for product in reaction.iterateProducts())
     return reactant_dative_removed or product_dative_removed
 

sapiopycommons/chem/Molecules.py

@@ -1,6 +1,6 @@
 # Author Yechen Qiao
 # Common Molecule Utilities for Molecule Transfers with Sapio
-
+from indigo import IndigoObject
 from rdkit import Chem
 from rdkit.Chem import Crippen, MolToInchi
 from rdkit.Chem import Descriptors
@@ -10,7 +10,7 @@ from rdkit.Chem.MolStandardize import rdMolStandardize
 from rdkit.Chem.SaltRemover import SaltRemover
 from rdkit.Chem.rdchem import Mol, RWMol, Bond
 
-from sapiopycommons.chem.IndigoMolecules import indigo, renderer, indigo_inchi
+from sapiopycommons.chem.IndigoMolecules import indigo, renderer, indigo_inchi, get_aromatic_dearomatic_forms
 
 metal_disconnector = rdMolStandardize.MetalDisconnector()
 tautomer_params = Chem.MolStandardize.rdMolStandardize.CleanupParameters()
@@ -247,7 +247,7 @@ def mol_to_sapio_substance(mol: Mol, include_stereoisomers=False,
         molecule["image"] = None
     # We need to test the INCHI can be loaded back to indigo.
     indigo_mol = indigo.loadMolecule(molBlock)
-    indigo_mol.aromatize()
+    indigo_mol = get_aromatic_dearomatic_forms(indigo_mol)[0]  # Get the aromatic form of the molecule.
     if enhanced_stereo:
         # Remove enhanced stereo layer when generating InChI as the stereo hash is generated separately for reg.
         Chem.CanonicalizeEnhancedStereo(inchi_mol)

sapiopycommons/customreport/auto_pagers.py

@@ -6,6 +6,7 @@ from sapiopylib.rest.CustomReportService import CustomReportManager
 from sapiopylib.rest.DataMgmtService import DataMgmtServer
 from sapiopylib.rest.pojo.CustomReport import CustomReportCriteria, CustomReport, RawReportTerm, ReportColumn
 from sapiopylib.rest.pojo.datatype.FieldDefinition import FieldType
+# noinspection PyProtectedMember
 from sapiopylib.rest.utils.autopaging import SapioPyAutoPager, PagerResultCriteriaType, _default_report_page_size, \
     _default_record_page_size
 from sapiopylib.rest.utils.recordmodel.PyRecordModel import PyRecordModel
@@ -61,6 +62,12 @@ class CustomReportDictAutoPager(_DictReportPagerBase):
     def __init__(self, user: UserIdentifier, report_criteria: CustomReportCriteria,
                  page_number: int = 0, page_size: int = _default_report_page_size):
         """
+        IMPORTANT NOTICE: Custom reports that are not single data type (i.e. they have terms or columns from multiple
+        data types) may not be 100% time accurate. Such reports use the system's ancestor table to retrieve the
+        relationships, and this table takes some time to update after relationships are updated, especially for more
+        populous data types. If you need 100% time accurate results to the current state of the records and
+        relationships in the database, you should query for the records directly instead of using a custom report.
+
         :param user: The current webhook context or a user object to send requests from.
         :param report_criteria: The custom report criteria to run.
         :param page_number: The page number to start on. The first page is page 0.
@@ -82,6 +89,12 @@ class SystemReportDictAutoPager(_DictReportPagerBase):
     def __init__(self, user: UserIdentifier, report_name: str,
                  page_number: int = 0, page_size: int = _default_report_page_size):
         """
+        IMPORTANT NOTICE: Custom reports that are not single data type (i.e. they have terms or columns from multiple
+        data types) may not be 100% time accurate. Such reports use the system's ancestor table to retrieve the
+        relationships, and this table takes some time to update after relationships are updated, especially for more
+        populous data types. If you need 100% time accurate results to the current state of the records and
+        relationships in the database, you should query for the records directly instead of using a custom report.
+
         :param user: The current webhook context or a user object to send requests from.
         :param report_name: The name of the system report to run.
         :param page_number: The page number to start on. The first page is page 0.
@@ -153,7 +166,7 @@ class _RecordReportPagerBase(SapioPyAutoPager[CustomReportCriteria, WrappedType
         if id_index == -1:
             raise SapioException(f"This report does not contain a Record ID column for the given record model type "
                                  f"{self._data_type}.")
-        ids: list[int] = [row[id_index] for row in report.result_table]
+        ids: set[int] = {row[id_index] for row in report.result_table}
         for row in self._rec_handler.query_models_by_id(self._query_type, ids, page_size=report.page_size):
             queue.put(row)
         if report.has_next_page:
@@ -172,6 +185,12 @@ class CustomReportRecordAutoPager(_RecordReportPagerBase):
                  wrapper_type: type[WrappedType] | str, page_number: int = 0,
                  page_size: int = _default_record_page_size):
         """
+        IMPORTANT NOTICE: Custom reports that are not single data type (i.e. they have terms or columns from multiple
+        data types) may not be 100% time accurate. Such reports use the system's ancestor table to retrieve the
+        relationships, and this table takes some time to update after relationships are updated, especially for more
+        populous data types. If you need 100% time accurate results to the current state of the records and
+        relationships in the database, you should query for the records directly instead of using a custom report.
+
         :param user: The current webhook context or a user object to send requests from.
         :param report_criteria: The custom report criteria to run.
         :param wrapper_type: The record model wrapper type or data type name of the records being searched for.
@@ -197,6 +216,12 @@ class SystemReportRecordAutoPager(_RecordReportPagerBase):
     def __init__(self, user: UserIdentifier, report_name: str, wrapper_type: type[WrappedType] | str,
                  page_number: int = 0, page_size: int = _default_record_page_size):
         """
+        IMPORTANT NOTICE: Custom reports that are not single data type (i.e. they have terms or columns from multiple
+        data types) may not be 100% time accurate. Such reports use the system's ancestor table to retrieve the
+        relationships, and this table takes some time to update after relationships are updated, especially for more
+        populous data types. If you need 100% time accurate results to the current state of the records and
+        relationships in the database, you should query for the records directly instead of using a custom report.
+
         :param user: The current webhook context or a user object to send requests from.
         :param report_name: The name of the system report to run.
         :param wrapper_type: The record model wrapper type or data type name of the records being searched for.

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),