sapiopycommons 2024.10.25a345__tar.gz → 2024.10.29a346__tar.gz

{sapiopycommons-2024.10.25a345 → sapiopycommons-2024.10.29a346}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: sapiopycommons
-Version: 2024.10.25a345
+Version: 2024.10.29a346
 Summary: Official Sapio Python API Utilities Package
 Project-URL: Homepage, https://github.com/sapiosciences
 Author-email: Jonathan Steck <jsteck@sapiosciences.com>, Yechen Qiao <yqiao@sapiosciences.com>

{sapiopycommons-2024.10.25a345 → sapiopycommons-2024.10.29a346}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "sapiopycommons"
-version='2024.10.25a345'
+version='2024.10.29a346'
 authors = [
     { name="Jonathan Steck", email="jsteck@sapiosciences.com" },
     { name="Yechen Qiao", email="yqiao@sapiosciences.com" },

{sapiopycommons-2024.10.25a345 → sapiopycommons-2024.10.29a346}/src/sapiopycommons/chem/IndigoMolecules.py

@@ -9,7 +9,6 @@ indigo.setOption("ignore-stereochemistry-errors", True)
 indigo.setOption("render-stereo-style", "ext")
 indigo.setOption("aromaticity-model", "generic")
 indigo.setOption("render-coloring", True)
-indigo.setOption("molfile-saving-mode", "3000")
 indigo_inchi = IndigoInchi(indigo);
 
 

{sapiopycommons-2024.10.25a345 → sapiopycommons-2024.10.29a346}/src/sapiopycommons/chem/Molecules.py

@@ -1,6 +1,5 @@
 # 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
@@ -21,25 +20,6 @@ tautomer_params.tautomerReassignStereo = False
 tautomer_params.tautomerRemoveIsotopicHs = True
 enumerator = rdMolStandardize.TautomerEnumerator(tautomer_params)
 
-
-def get_enhanced_stereo_reg_hash(mol: Mol, enhanced_stereo: bool) -> str:
-    """
-    Get the Registration Hash for the molecule by the current registration configuration.
-    When we are running if we are canonicalization of tautomers or cleaning up any other way, do they first before calling.
-    :param mol: The molecule to obtain hash for.
-    :param canonical_tautomer: Whether the registry system canonicalize the tautomers.
-    :param enhanced_stereo: Whether we are computing enhanced stereo at all.
-    :return: The enhanced stereo hash.
-    """
-    if enhanced_stereo:
-        from rdkit.Chem.RegistrationHash import GetMolLayers, GetMolHash, HashScheme
-        layers = GetMolLayers(mol, enable_tautomer_hash_v2=True)
-        hash_scheme: HashScheme = HashScheme.TAUTOMER_INSENSITIVE_LAYERS
-        return GetMolHash(layers, hash_scheme=hash_scheme)
-    else:
-        return ""
-
-
 def neutralize_atoms(mol) -> Mol:
     """
     Neutralize atoms per https://baoilleach.blogspot.com/2019/12/no-charge-simple-approach-to.html
@@ -106,6 +86,7 @@ def mol_to_img(mol_str: str) -> str:
     return renderer.renderToString(mol)
 
 
+
 def mol_to_sapio_partial_pojo(mol: Mol):
     """
     Get the minimum information about molecule to Sapio, just its SMILES, V3000, and image data.
@@ -115,7 +96,7 @@ def mol_to_sapio_partial_pojo(mol: Mol):
     Chem.SanitizeMol(mol)
     mol.UpdatePropertyCache()
     smiles = Chem.MolToSmiles(mol)
-    molBlock = Chem.MolToMolBlock(mol, forceV3000=True)
+    molBlock = Chem.MolToMolBlock(mol)
     img = mol_to_img(mol)
     molecule = dict()
     molecule["smiles"] = smiles
@@ -124,52 +105,23 @@ def mol_to_sapio_partial_pojo(mol: Mol):
     return molecule
 
 
-def get_cxs_smiles_hash(mol: Mol, enhanced_stereo: bool) -> str:
-    """
-    Return the SHA1 CXS Smiles hash for the canonical, isomeric CXS SMILES of the molecule.
-    """
-    if not enhanced_stereo:
-        return ""
-    import hashlib
-    return hashlib.sha1(Chem.MolToCXSmiles(mol, canonical=True, isomericSmiles=True).encode()).hexdigest()
-
-
-def get_has_or_group(mol: Mol, enhanced_stereo: bool) -> bool:
-    """
-    Return true if and only if: enhanced stereochemistry is enabled and there is at least one OR group in mol.
-    """
-    if not enhanced_stereo:
-        return False
-    from rdkit.Chem import StereoGroup_vect, STEREO_OR
-    stereo_groups: StereoGroup_vect = mol.GetStereoGroups()
-    for stereo_group in stereo_groups:
-        if stereo_group.GetGroupType() == STEREO_OR:
-            return True
-    return False
-
-
-def mol_to_sapio_substance(mol: Mol, include_stereoisomers=False,
+def mol_to_sapio_substance(mol: Mol, include_stereoisomers: bool = False,
                            normalize: bool = False, remove_salt: bool = False, make_images: bool = False,
-                           salt_def: str | None = None, canonical_tautomer: bool = True,
-                           enhanced_stereo: bool = False, remove_atom_map: bool = True):
+                           salt_def: str | None = None, canonical_tautomer: bool = True):
     """
     Convert a molecule in RDKit to a molecule POJO in Sapio.
 
     :param mol: The molecule in RDKit.
+    :param include_stereoisomers: If true, will compute all stereoisomer permutations of this molecule.
     :param normalize If true, will normalize the functional groups and return normalized result.
     :param remove_salt If true, we will remove salts iteratively from the molecule before returning their data.
     We will also populate desaltedList with molecules we deleted.
-    :param make_images Whether to make images as part of the result without having another script to resolve it.
     :param salt_def: if not none, specifies custom salt to be used during the desalt process.
     :param canonical_tautomer: if True, we will attempt to compute canonical tautomer for the molecule. Slow!
     This is needed for a registry. Note it stops after enumeration of 1000.
-    :param enhanced_stereo: If enabled, enhanced stereo hash will be produced.
-    :param remove_atom_map: When set, clear all atom AAM maps that were set had it been merged into some reactions earlier.
     :return: The molecule POJO for Sapio.
     """
     molecule = dict()
-    if remove_atom_map:
-        [a.SetAtomMapNum(0) for a in mol.GetAtoms()]
     Chem.SanitizeMol(mol)
     mol.UpdatePropertyCache()
     Chem.GetSymmSSSR(mol)
@@ -205,7 +157,7 @@ def mol_to_sapio_substance(mol: Mol, include_stereoisomers=False,
     exactMass = Descriptors.ExactMolWt(mol)
     molFormula = rdMolDescriptors.CalcMolFormula(mol)
     charge = Chem.GetFormalCharge(mol)
-    molBlock = Chem.MolToMolBlock(mol, forceV3000=True)
+    molBlock = Chem.MolToMolBlock(mol)
 
     molecule["cLogP"] = cLogP
     molecule["tpsa"] = tpsa
@@ -229,38 +181,28 @@ def mol_to_sapio_substance(mol: Mol, include_stereoisomers=False,
     # We need to test the INCHI can be loaded back to indigo.
     indigo_mol = indigo.loadMolecule(molBlock)
     indigo_mol.aromatize()
-    if enhanced_stereo:
-        # Remove enhanced stereo layer when generating InChI as the stereo hash is generated separately for reg.
-        mol_copy: Mol = Chem.Mol(mol)
-        Chem.CanonicalizeEnhancedStereo(mol_copy)
-        molecule["inchi"] = Chem.MolToInchi(mol_copy)
-        molecule["inchiKey"] = Chem.MolToInchiKey(mol_copy)
-    else:
-        indigo_inchi.resetOptions()
-        indigo_inchi_str = indigo_inchi.getInchi(indigo_mol)
-        molecule["inchi"] = indigo_inchi_str
-        indigo_inchi_key_str = indigo_inchi.getInchiKey(indigo_inchi_str)
-        molecule["inchiKey"] = indigo_inchi_key_str
+    indigo_inchi.resetOptions()
+    indigo_inchi_str = indigo_inchi.getInchi(indigo_mol)
+    molecule["inchi"] = indigo_inchi_str
+    indigo_inchi_key_str = indigo_inchi.getInchiKey(indigo_inchi_str)
+    molecule["inchiKey"] = indigo_inchi_key_str
     molecule["smiles"] = indigo_mol.smiles()
-    molecule["reg_hash"] = get_enhanced_stereo_reg_hash(mol, enhanced_stereo=enhanced_stereo)
-    molecule["cxsmiles_hash"] = get_cxs_smiles_hash(mol, enhanced_stereo=enhanced_stereo)
-    molecule["has_or_group"] = get_has_or_group(mol, enhanced_stereo=enhanced_stereo)
 
+    if include_stereoisomers and has_chiral_centers(mol):
+        stereoisomers = find_all_possible_stereoisomers(mol, only_unassigned=False, try_embedding=False, unique=True)
+        molecule["stereoisomers"] = [mol_to_sapio_partial_pojo(x) for x in stereoisomers]
     return molecule
 
 
-def mol_to_sapio_compound(mol: Mol, include_stereoisomers=False, enhanced_stereo: bool = False,
+def mol_to_sapio_compound(mol: Mol, include_stereoisomers: bool = False,
                           salt_def: str | None = None, resolve_canonical: bool = True,
-                          make_images: bool = False, canonical_tautomer: bool = True,
-                          remove_atom_map: bool = True):
+                          make_images: bool = False, canonical_tautomer: bool = True):
     ret = dict()
-    ret['originalMol'] = mol_to_sapio_substance(mol, include_stereoisomers=False,
+    ret['originalMol'] = mol_to_sapio_substance(mol, include_stereoisomers,
                                                 normalize=False, remove_salt=False, make_images=make_images,
-                                                canonical_tautomer=canonical_tautomer,
-                                                enhanced_stereo=enhanced_stereo, remove_atom_map=remove_atom_map)
+                                                canonical_tautomer=canonical_tautomer)
     if resolve_canonical:
         ret['canonicalMol'] = mol_to_sapio_substance(mol, include_stereoisomers=False,
                                                      normalize=True, remove_salt=True, make_images=make_images,
-                                                     salt_def=salt_def, canonical_tautomer=canonical_tautomer,
-                                                     enhanced_stereo=enhanced_stereo, remove_atom_map=remove_atom_map)
+                                                     salt_def=salt_def, canonical_tautomer=canonical_tautomer)
     return ret

{sapiopycommons-2024.10.25a345 → sapiopycommons-2024.10.29a346}/src/sapiopycommons/customreport/custom_report_builder.py

@@ -96,14 +96,19 @@ class CustomReportBuilder:
                                                      AliasUtil.to_record_id(base_record),
                                                      AliasUtil.to_data_type_name(base_record))
 
-    def add_join(self, comparison_term: FieldCompareReportTerm) -> None:
+    def add_join(self, comparison_term: FieldCompareReportTerm, data_type: DataTypeIdentifier | None = None) -> None:
         """
         Add a join statement to this report builder.
 
-        :param comparison_term: The field comparison term to join with. The left side data type name of this term will
-            be the data type that is joined against.
+        :param comparison_term: The field comparison term to join with.
+        :param data_type: The data type name that this join is on. If not provided, then the left side data type name
+            of the comparison term will be the data type that is joined against.
         """
-        self.join_list.append(ExplicitJoinDefinition(comparison_term.left_data_type_name, comparison_term))
+        if data_type is None:
+            data_type: str = comparison_term.left_data_type_name
+        else:
+            data_type: str = AliasUtil.to_data_type_name(data_type)
+        self.join_list.append(ExplicitJoinDefinition(data_type, comparison_term))
 
     def build_report_criteria(self, page_size: int = 0, page_number: int = -1, case_sensitive: bool = False,
                               owner_restriction_set: list[str] = None) -> CustomReportCriteria:

sapiopycommons-2024.10.29a346/src/sapiopycommons/datatype/data_fields.py

@@ -0,0 +1,61 @@
+from sapiopylib.rest.pojo.datatype.FieldDefinition import FieldType
+from sapiopylib.rest.utils.recordmodel.RecordModelWrapper import WrapperField
+
+
+class SystemFields:
+    RECORD_ID__FIELD = WrapperField("RecordId", FieldType.LONG)
+    DATA_RECORD_NAME__FIELD = WrapperField("DataRecordName", FieldType.IDENTIFIER)
+    CREATED_BY__FIELD = WrapperField("CreatedBy", FieldType.STRING)
+    DATE_CREATED__FIELD = WrapperField("DateCreated", FieldType.DATE)
+    LAST_MODIFIED_BY__FIELD = WrapperField("VeloxLastModifiedBy", FieldType.STRING)
+    LAST_MODIFIED_DATE__FIELD = WrapperField("VeloxLastModifiedDate", FieldType.DATE)
+
+
+class ProcessQueueItemFields:
+    DATA_TYPE_NAME: str = 'ProcessQueueItem'
+    ASSIGNED_TO__FIELD = WrapperField('AssignedTo', FieldType.SELECTION)
+    DATA_RECORD_ID__FIELD = WrapperField('DataRecordId', FieldType.LONG)
+    DATA_TYPE_NAME__FIELD = WrapperField('DataTypeName', FieldType.STRING)
+    DURATION_IN_QUEUE__FIELD = WrapperField('DurationInQueue', FieldType.LONG)
+    EXPERIMENT__FIELD = WrapperField('Experiment', FieldType.SIDE_LINK)
+    LAUNCHED_DATE__FIELD = WrapperField('LaunchedDate', FieldType.DATE)
+    PROCESS_HEADER_NAME__FIELD = WrapperField('ProcessHeaderName', FieldType.STRING)
+    SCHEDULED_DATE__FIELD = WrapperField('ScheduledDate', FieldType.DATE)
+    SHOW_IN_QUEUE__FIELD = WrapperField('ShowInQueue', FieldType.BOOLEAN)
+    WORKFLOW_HEADER_NAME__FIELD = WrapperField('WorkflowHeaderName', FieldType.STRING)
+
+
+class ProcessWorkflowTrackingFields:
+    DATA_TYPE_NAME: str = 'ProcessWorkflowTracking'
+    ACTIVE_WORKFLOW_ID__FIELD = WrapperField("ActiveWorkflowId", FieldType.LONG)
+    BRANCH_LONG_ID__FIELD = WrapperField("BranchLongId", FieldType.LONG)
+    END_DATE__FIELD = WrapperField("EndDate", FieldType.DATE)
+    END_HOUR__FIELD = WrapperField("EndHour", FieldType.LONG)
+    END_MINUTE_TIME__FIELD = WrapperField("EndMinuteTime", FieldType.LONG)
+    EXPECTED_QUEUE_TIME__FIELD = WrapperField("ExpectedQueueTime", FieldType.DOUBLE)
+    EXPECTED_TAT__FIELD = WrapperField("ExpectedTAT", FieldType.DOUBLE)
+    PROCESS_QUEUE_ITEM__FIELD = WrapperField("ProcessQueueItem", FieldType.SIDE_LINK)
+    PROCESS_STEP_NUMBER__FIELD = WrapperField("ProcessStepNumber", FieldType.LONG)
+    QUEUED_HOURS__FIELD = WrapperField("QueuedHours", FieldType.LONG)
+    QUEUED_MINUTES__FIELD = WrapperField("QueuedMinutes", FieldType.LONG)
+    QUEUED_TIME__FIELD = WrapperField("QueuedTime", FieldType.DOUBLE)
+    QUEUE_START_DATE__FIELD = WrapperField("QueueStartDate", FieldType.DATE)
+    QUEUE_START_HOUR__FIELD = WrapperField("QueueStartHour", FieldType.LONG)
+    QUEUE_START_MINUTE_TIME__FIELD = WrapperField("QueueStartMinuteTime", FieldType.LONG)
+    SAMPLE_RECORD_ID__FIELD = WrapperField("SampleRecordId", FieldType.LONG)
+    START_DATE__FIELD = WrapperField("StartDate", FieldType.DATE)
+    START_HOUR__FIELD = WrapperField("StartHour", FieldType.LONG)
+    START_MINUTE_TIME__FIELD = WrapperField("StartMinuteTime", FieldType.LONG)
+    STATUS__FIELD = WrapperField("Status", FieldType.PICKLIST)
+    TURN_AROUND_HOURS__FIELD = WrapperField("TurnAroundHours", FieldType.LONG)
+    TURN_AROUND_MINUTES__FIELD = WrapperField("TurnAroundMinutes", FieldType.LONG)
+    WORKFLOW_END_USER_ID__FIELD = WrapperField("WorkflowEndUserId", FieldType.STRING)
+    WORKFLOW_EXPECTED_QUEUE_TIME__FIELD = WrapperField("WorkflowExpectedQueueTime", FieldType.STRING)
+    WORKFLOW_EXPECTED_TAT__FIELD = WrapperField("WorkflowExpectedTAT", FieldType.STRING)
+    WORKFLOW_EXPECTED_TOTAL_TAT__FIELD = WrapperField("WorkflowExpectedTotalTAT", FieldType.DOUBLE)
+    WORKFLOW_ID_NUMBER__FIELD = WrapperField("WorkflowIdNumber", FieldType.LONG)
+    WORKFLOW_NAME__FIELD = WrapperField("WorkflowName", FieldType.STRING)
+    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)

{sapiopycommons-2024.10.25a345 → sapiopycommons-2024.10.29a346}/src/sapiopycommons/eln/experiment_handler.py

@@ -57,9 +57,9 @@ class ExperimentHandler:
     # additional queries to obtain, but may also be repeatedly accessed. In such cases, cache the information after it
     # has been requested so that the user doesn't need to worry about caching it themselves.
     # CR-46341: Replace class variables with instance variables.
-    __exp_record: DataRecord
+    __exp_record: DataRecord | None
     """The data record for this experiment. Only cached when first accessed."""
-    __exp_template: ElnTemplate
+    __exp_template: ElnTemplate | None
     """The template for this experiment. Only cached when first accessed."""
     __exp_options: dict[str, str]
     """Experiment options for this experiment. Only cached when first accessed."""
@@ -277,6 +277,7 @@ class ExperimentHandler:
         """
         template_id: int | None = self.__eln_exp.template_id
         if template_id is None:
+            self.__exp_template = None
             if exception_on_none:
                 raise SapioException(f"Experiment with ID {self.__exp_id} has no template ID.")
             return None
@@ -635,6 +636,9 @@ class ExperimentHandler:
         if not records:
             return
         dt: str = AliasUtil.to_singular_data_type_name(records)
+        if ElnBaseDataType.is_base_data_type(dt):
+            raise SapioException(f"{dt} is an ELN data type. This function call has no effect on ELN data types. "
+                                 f"Use add_eln_rows or add_sample_details instead.")
         if dt != step.get_data_type_names()[0]:
             raise SapioException(f"Cannot add {dt} records to entry {step.get_name()} of type "
                                  f"{step.get_data_type_names()[0]}.")
@@ -659,6 +663,9 @@ class ExperimentHandler:
         if not records:
             return
         dt: str = AliasUtil.to_singular_data_type_name(records)
+        if ElnBaseDataType.is_base_data_type(dt):
+            raise SapioException(f"{dt} is an ELN data type. This function call has no effect on ELN data types. "
+                                 f"Use remove_eln_rows or remove_sample_details instead.")
         if dt != step.get_data_type_names()[0]:
             raise SapioException(f"Cannot remove {dt} records from entry {step.get_name()} of type "
                                  f"{step.get_data_type_names()[0]}.")
@@ -687,6 +694,9 @@ class ExperimentHandler:
         step = self.__to_eln_step(step)
         if records:
             dt: str = AliasUtil.to_singular_data_type_name(records)
+            if ElnBaseDataType.is_base_data_type(dt):
+                raise SapioException(f"{dt} is an ELN data type. This function call has no effect on ELN data types. "
+                                     f"Use add_eln_rows or add_sample_details instead.")
             if dt != step.get_data_type_names()[0]:
                 raise SapioException(f"Cannot set {dt} records for entry {step.get_name()} of type "
                                      f"{step.get_data_type_names()[0]}.")
@@ -779,7 +789,7 @@ class ExperimentHandler:
             raise SapioException("The provided step is not an ELN data type entry.")
         if not records:
             return
-        record_dt: str = AliasUtil.to_singular_data_type_name(records)
+        record_dt: str = AliasUtil.to_singular_data_type_name(records, False)
         if record_dt != dt:
             raise SapioException(f"Cannot remove {dt} records from entry {step.get_name()} of type "
                                  f"{step.get_data_type_names()[0]}.")