sapiopycommons 2024.10.1a338__py3-none-any.whl → 2024.10.8a340__py3-none-any.whl

sapiopycommons/callbacks/callback_util.py

@@ -3,6 +3,7 @@ from __future__ import annotations
 import io
 from weakref import WeakValueDictionary
 
+from requests import ReadTimeout
 from sapiopylib.rest.ClientCallbackService import ClientCallback
 from sapiopylib.rest.DataMgmtService import DataMgmtServer
 from sapiopylib.rest.User import SapioUser
@@ -27,7 +28,8 @@ from sapiopycommons.files.file_util import FileUtil
 from sapiopycommons.general.aliases import FieldMap, SapioRecord, AliasUtil, RecordIdentifier, FieldValue, \
     UserIdentifier
 from sapiopycommons.general.custom_report_util import CustomReportUtil
-from sapiopycommons.general.exceptions import SapioUserCancelledException, SapioException, SapioUserErrorException
+from sapiopycommons.general.exceptions import SapioUserCancelledException, SapioException, SapioUserErrorException, \
+    SapioDialogTimeoutException
 from sapiopycommons.recordmodel.record_handler import RecordHandler
 
 
@@ -35,6 +37,8 @@ class CallbackUtil:
     user: SapioUser
     callback: ClientCallback
     dt_cache: DataTypeCacheManager
+    _original_timeout: int
+    timeout_seconds: int
     width_pixels: int | None
     width_percent: float | None
 
@@ -64,6 +68,8 @@ class CallbackUtil:
         self.user = AliasUtil.to_sapio_user(context)
         self.callback = DataMgmtServer.get_client_callback(self.user)
         self.dt_cache = DataTypeCacheManager(self.user)
+        self._original_timeout = self.user.timeout_seconds
+        self.timeout_seconds = self.user.timeout_seconds
         self.width_pixels = None
         self.width_percent = None
 
@@ -80,6 +86,17 @@ class CallbackUtil:
         self.width_pixels = width_pixels
         self.width_percent = width_percent
 
+    def set_dialog_timeout(self, timeout: int):
+        """
+        Alter the timeout time used for callback requests that create dialogs for the user to interact with. By default,
+        a CallbackUtil will use the timeout time of the SapioUser provided to it. By altering this, a different timeout
+        time is used.
+
+        :param timeout: The number of seconds that must elapse before a SapioDialogTimeoutException is thrown by
+            any callback that creates a dialog for the user to interact with.
+        """
+        self.timeout_seconds = timeout
+
     def toaster_popup(self, message: str, title: str = "", popup_type: PopupType = PopupType.Info) -> None:
         """
         Display a toaster popup in the bottom right corner of the user's screen.
@@ -134,7 +151,13 @@ class CallbackUtil:
         """
         request = OptionDialogRequest(title, msg, options, default_option, user_can_cancel,
                                       width_in_pixels=self.width_pixels, width_percentage=self.width_percent)
-        response: int | None = self.callback.show_option_dialog(request)
+        try:
+            self.user.timeout_seconds = self.timeout_seconds
+            response: int | None = self.callback.show_option_dialog(request)
+        except ReadTimeout:
+            raise SapioDialogTimeoutException()
+        finally:
+            self.user.timeout_seconds = self._original_timeout
         if response is None:
             raise SapioUserCancelledException()
         return options[response]
@@ -187,7 +210,13 @@ class CallbackUtil:
         """
         request = ListDialogRequest(title, multi_select, options, preselected_values,
                                     width_in_pixels=self.width_pixels, width_percentage=self.width_percent)
-        response: list[str] | None = self.callback.show_list_dialog(request)
+        try:
+            self.user.timeout_seconds = self.timeout_seconds
+            response: list[str] | None = self.callback.show_list_dialog(request)
+        except ReadTimeout:
+            raise SapioDialogTimeoutException()
+        finally:
+            self.user.timeout_seconds = self._original_timeout
         if response is None:
             raise SapioUserCancelledException()
         return response
@@ -239,7 +268,13 @@ class CallbackUtil:
 
         request = FormEntryDialogRequest(title, msg, builder.get_temporary_data_type(), values,
                                          width_in_pixels=self.width_pixels, width_percentage=self.width_percent)
-        response: FieldMap | None = self.callback.show_form_entry_dialog(request)
+        try:
+            self.user.timeout_seconds = self.timeout_seconds
+            response: FieldMap | None = self.callback.show_form_entry_dialog(request)
+        except ReadTimeout:
+            raise SapioDialogTimeoutException()
+        finally:
+            self.user.timeout_seconds = self._original_timeout
         if response is None:
             raise SapioUserCancelledException()
         return response
@@ -297,7 +332,13 @@ class CallbackUtil:
 
         request = FormEntryDialogRequest(title, msg, builder.get_temporary_data_type(), values,
                                          width_in_pixels=self.width_pixels, width_percentage=self.width_percent)
-        response: FieldMap | None = self.callback.show_form_entry_dialog(request)
+        try:
+            self.user.timeout_seconds = self.timeout_seconds
+            response: FieldMap | None = self.callback.show_form_entry_dialog(request)
+        except ReadTimeout:
+            raise SapioDialogTimeoutException()
+        finally:
+            self.user.timeout_seconds = self._original_timeout
         if response is None:
             raise SapioUserCancelledException()
         return response
@@ -313,7 +354,13 @@ class CallbackUtil:
         """
         request = InputDialogCriteria(title, msg, field,
                                       width_in_pixels=self.width_pixels, width_percentage=self.width_percent)
-        response: FieldValue | None = self.callback.show_input_dialog(request)
+        try:
+            self.user.timeout_seconds = self.timeout_seconds
+            response: FieldValue | None = self.callback.show_input_dialog(request)
+        except ReadTimeout:
+            raise SapioDialogTimeoutException()
+        finally:
+            self.user.timeout_seconds = self._original_timeout
         if response is None:
             raise SapioUserCancelledException()
         return response
@@ -432,7 +479,13 @@ class CallbackUtil:
         request = TableEntryDialogRequest(title, msg, builder.get_temporary_data_type(), values,
                                           record_image_data_list=image_data, group_by_field=group_by,
                                           width_in_pixels=self.width_pixels, width_percentage=self.width_percent)
-        response: list[FieldMap] | None = self.callback.show_table_entry_dialog(request)
+        try:
+            self.user.timeout_seconds = self.timeout_seconds
+            response: list[FieldMap] | None = self.callback.show_table_entry_dialog(request)
+        except ReadTimeout:
+            raise SapioDialogTimeoutException()
+        finally:
+            self.user.timeout_seconds = self._original_timeout
         if response is None:
             raise SapioUserCancelledException()
         return response
@@ -496,7 +549,13 @@ class CallbackUtil:
         request = TableEntryDialogRequest(title, msg, builder.get_temporary_data_type(), field_map_list,
                                           record_image_data_list=image_data, group_by_field=group_by,
                                           width_in_pixels=self.width_pixels, width_percentage=self.width_percent)
-        response: list[FieldMap] | None = self.callback.show_table_entry_dialog(request)
+        try:
+            self.user.timeout_seconds = self.timeout_seconds
+            response: list[FieldMap] | None = self.callback.show_table_entry_dialog(request)
+        except ReadTimeout:
+            raise SapioDialogTimeoutException()
+        finally:
+            self.user.timeout_seconds = self._original_timeout
         if response is None:
             raise SapioUserCancelledException()
         return response
@@ -654,7 +713,13 @@ class CallbackUtil:
 
         request = TableEntryDialogRequest(title, msg, builder.get_temporary_data_type(), values,
                                           width_in_pixels=self.width_pixels, width_percentage=self.width_percent)
-        response: list[FieldMap] | None = self.callback.show_table_entry_dialog(request)
+        try:
+            self.user.timeout_seconds = self.timeout_seconds
+            response: list[FieldMap] | None = self.callback.show_table_entry_dialog(request)
+        except ReadTimeout:
+            raise SapioDialogTimeoutException()
+        finally:
+            self.user.timeout_seconds = self._original_timeout
         if response is None:
             raise SapioUserCancelledException()
         return response
@@ -704,7 +769,13 @@ class CallbackUtil:
 
         request = DataRecordDialogRequest(title, record, layout, minimized, access_level, plugin_path_list,
                                           width_in_pixels=self.width_pixels, width_percentage=self.width_percent)
-        response: bool = self.callback.data_record_form_view_dialog(request)
+        try:
+            self.user.timeout_seconds = self.timeout_seconds
+            response: bool = self.callback.data_record_form_view_dialog(request)
+        except ReadTimeout:
+            raise SapioDialogTimeoutException()
+        finally:
+            self.user.timeout_seconds = self._original_timeout
         if not response:
             raise SapioUserCancelledException()
     
@@ -744,7 +815,13 @@ class CallbackUtil:
 
         request = TempTableSelectionRequest(builder.get_temporary_data_type(), msg, values,
                                             multi_select=multi_select)
-        response: list[FieldMap] | None = self.callback.show_temp_table_selection_dialog(request)
+        try:
+            self.user.timeout_seconds = self.timeout_seconds
+            response: list[FieldMap] | None = self.callback.show_temp_table_selection_dialog(request)
+        except ReadTimeout:
+            raise SapioDialogTimeoutException()
+        finally:
+            self.user.timeout_seconds = self._original_timeout
         if response is None:
             raise SapioUserCancelledException()
         return response
@@ -796,7 +873,13 @@ class CallbackUtil:
 
         request = TempTableSelectionRequest(builder.get_temporary_data_type(), msg, field_map_list,
                                             multi_select=multi_select)
-        response: list[FieldMap] | None = self.callback.show_temp_table_selection_dialog(request)
+        try:
+            self.user.timeout_seconds = self.timeout_seconds
+            response: list[FieldMap] | None = self.callback.show_temp_table_selection_dialog(request)
+        except ReadTimeout:
+            raise SapioDialogTimeoutException()
+        finally:
+            self.user.timeout_seconds = self._original_timeout
         if response is None:
             raise SapioUserCancelledException()
         # Map the field maps in the response back to the record they come from, returning the chosen record instead of
@@ -872,7 +955,13 @@ class CallbackUtil:
         request = InputSelectionRequest(data_type, msg, search_types, only_key_fields, record_blacklist,
                                         record_whitelist, preselected_records, custom_search, scan_criteria,
                                         multi_select)
-        response: list[DataRecord] | None = self.callback.show_input_selection_dialog(request)
+        try:
+            self.user.timeout_seconds = self.timeout_seconds
+            response: list[DataRecord] | None = self.callback.show_input_selection_dialog(request)
+        except ReadTimeout:
+            raise SapioDialogTimeoutException()
+        finally:
+            self.user.timeout_seconds = self._original_timeout
         if response is None:
             raise SapioUserCancelledException()
         return RecordHandler(self.user).wrap_models(response, wrapper_type)
@@ -898,7 +987,13 @@ class CallbackUtil:
             temp_dt = builder.get_temporary_data_type()
         request = ESigningRequestPojo(title, msg, show_comment, temp_dt,
                                       width_in_pixels=self.width_pixels, width_percentage=self.width_percent)
-        response: ESigningResponsePojo | None = self.callback.show_esign_dialog(request)
+        try:
+            self.user.timeout_seconds = self.timeout_seconds
+            response: ESigningResponsePojo | None = self.callback.show_esign_dialog(request)
+        except ReadTimeout:
+            raise SapioDialogTimeoutException()
+        finally:
+            self.user.timeout_seconds = self._original_timeout
         if response is None:
             raise SapioUserCancelledException()
         return response
@@ -929,7 +1024,13 @@ class CallbackUtil:
                 return sink.consume_data(chunk, io_obj)
 
             request = FilePromptRequest(title, show_image_editor, ",".join(exts), show_camera_button)
-            file_path: str | None = self.callback.show_file_dialog(request, do_consume)
+            try:
+                self.user.timeout_seconds = self.timeout_seconds
+                file_path: str | None = self.callback.show_file_dialog(request, do_consume)
+            except ReadTimeout:
+                raise SapioDialogTimeoutException()
+            finally:
+                self.user.timeout_seconds = self._original_timeout
         if file_path is None:
             raise SapioUserCancelledException()
 
@@ -954,7 +1055,13 @@ class CallbackUtil:
             exts: list[str] = []
 
         request = MultiFilePromptRequest(title, show_image_editor, ",".join(exts), show_camera_button)
-        file_paths: list[str] | None = self.callback.show_multi_file_dialog(request)
+        try:
+            self.user.timeout_seconds = self.timeout_seconds
+            file_paths: list[str] | None = self.callback.show_multi_file_dialog(request)
+        except ReadTimeout:
+            raise SapioDialogTimeoutException()
+        finally:
+            self.user.timeout_seconds = self._original_timeout
         if not file_paths:
             raise SapioUserCancelledException()
 

sapiopycommons/chem/IndigoMolecules.py

@@ -9,6 +9,7 @@ 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/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
@@ -20,6 +21,25 @@ 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
@@ -86,7 +106,6 @@ 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.
@@ -96,7 +115,7 @@ def mol_to_sapio_partial_pojo(mol: Mol):
     Chem.SanitizeMol(mol)
     mol.UpdatePropertyCache()
     smiles = Chem.MolToSmiles(mol)
-    molBlock = Chem.MolToMolBlock(mol)
+    molBlock = Chem.MolToMolBlock(mol, forceV3000=True)
     img = mol_to_img(mol)
     molecule = dict()
     molecule["smiles"] = smiles
@@ -105,23 +124,52 @@ def mol_to_sapio_partial_pojo(mol: Mol):
     return molecule
 
 
-def mol_to_sapio_substance(mol: Mol, include_stereoisomers: bool = False,
+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,
                            normalize: bool = False, remove_salt: bool = False, make_images: bool = False,
-                           salt_def: str | None = None, canonical_tautomer: bool = True):
+                           salt_def: str | None = None, canonical_tautomer: bool = True,
+                           enhanced_stereo: bool = False, remove_atom_map: 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)
@@ -157,7 +205,7 @@ def mol_to_sapio_substance(mol: Mol, include_stereoisomers: bool = False,
     exactMass = Descriptors.ExactMolWt(mol)
     molFormula = rdMolDescriptors.CalcMolFormula(mol)
     charge = Chem.GetFormalCharge(mol)
-    molBlock = Chem.MolToMolBlock(mol)
+    molBlock = Chem.MolToMolBlock(mol, forceV3000=True)
 
     molecule["cLogP"] = cLogP
     molecule["tpsa"] = tpsa
@@ -181,28 +229,38 @@ def mol_to_sapio_substance(mol: Mol, include_stereoisomers: bool = False,
     # We need to test the INCHI can be loaded back to indigo.
     indigo_mol = indigo.loadMolecule(molBlock)
     indigo_mol.aromatize()
-    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
+    if enhanced_stereo:
+        # Remove enhanced stereo layer when generating InChI as the stereo hash is generated separately for reg.
+        mol_copy: Mol = Chem.MolFromMolBlock(Chem.MolToMolBlock(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
     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: bool = False,
+def mol_to_sapio_compound(mol: Mol, include_stereoisomers=False, enhanced_stereo: bool = False,
                           salt_def: str | None = None, resolve_canonical: bool = True,
-                          make_images: bool = False, canonical_tautomer: bool = True):
+                          make_images: bool = False, canonical_tautomer: bool = True,
+                          remove_atom_map: bool = True):
     ret = dict()
-    ret['originalMol'] = mol_to_sapio_substance(mol, include_stereoisomers,
+    ret['originalMol'] = mol_to_sapio_substance(mol, include_stereoisomers=False,
                                                 normalize=False, remove_salt=False, make_images=make_images,
-                                                canonical_tautomer=canonical_tautomer)
+                                                canonical_tautomer=canonical_tautomer,
+                                                enhanced_stereo=enhanced_stereo, remove_atom_map=remove_atom_map)
     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)
+                                                     salt_def=salt_def, canonical_tautomer=canonical_tautomer,
+                                                     enhanced_stereo=enhanced_stereo, remove_atom_map=remove_atom_map)
     return ret

sapiopycommons/eln/experiment_handler.py

@@ -806,7 +806,7 @@ class ExperimentHandler:
         for sample in samples:
             if sample.data_type_name != "Sample":
                 raise SapioException(f"Received a {sample.data_type_name} record when Sample records were expected.")
-            detail: PyRecordModel = sample.add(Child.of_type_name(dt))
+            detail: PyRecordModel = sample.add(Child.create_by_name(dt))
             detail.set_field_values({
                 "SampleId": sample.get_field_value("SampleId"),
                 "OtherSampleId": sample.get_field_value("OtherSampleId")

sapiopycommons/flowcyto/flow_cyto.py

@@ -0,0 +1,77 @@
+from __future__ import annotations
+
+from weakref import WeakValueDictionary
+
+from sapiopylib.rest.User import SapioUser
+from databind.json import dumps
+
+from sapiopycommons.flowcyto.flowcyto_data import FlowJoWorkspaceInputJson, UploadFCSInputJson, \
+    ComputeFlowStatisticsInputJson
+
+
+class FlowCytoManager:
+    """
+    This manager includes flow cytometry analysis tools that would require FlowCyto license to use.
+    """
+    _user: SapioUser
+
+    __instances: WeakValueDictionary[SapioUser, FlowCytoManager] = WeakValueDictionary()
+    __initialized: bool
+
+    def __new__(cls, user: SapioUser):
+        """
+        Observes singleton pattern per record model manager object.
+
+        :param user: The user that will make the webservice request to the application.
+        """
+        obj = cls.__instances.get(user)
+        if not obj:
+            obj = object.__new__(cls)
+            obj.__initialized = False
+            cls.__instances[user] = obj
+        return obj
+
+    def __init__(self, user: SapioUser):
+        if self.__initialized:
+            return
+        self._user = user
+        self.__initialized = True
+
+    def create_flowjo_workspace(self, workspace_input: FlowJoWorkspaceInputJson) -> int:
+        """
+        Create FlowJo Workspace and return the workspace record ID of workspace root record,
+        after successful creation.
+        :param workspace_input: the request data payload.
+        :return: The new workspace record ID.
+        """
+        payload = dumps(workspace_input, FlowJoWorkspaceInputJson)
+        response = self._user.plugin_post("flowcyto/workspace", payload=payload, is_payload_plain_text=True)
+        self._user.raise_for_status(response)
+        return int(response.json())
+
+    def upload_fcs_for_sample(self, upload_input: UploadFCSInputJson) -> int:
+        """
+        Upload FCS file as root of the sample FCS.
+        :param upload_input: The request data payload
+        :return: The root FCS file uploaded under sample.
+        """
+        payload = dumps(upload_input, UploadFCSInputJson)
+        response = self._user.plugin_post("flowcyto/fcs", payload=payload, is_payload_plain_text=True)
+        self._user.raise_for_status(response)
+        return int(response.json())
+
+    def compute_statistics(self, stat_compute_input: ComputeFlowStatisticsInputJson) -> list[int]:
+        """
+        Requests to compute flow cytometry statistics.
+        The children are of type FCSStatistic.
+        If the FCS files have not been evaluated yet,
+        then the lazy evaluation will be performed immediately prior to computing statistics, which can take longer.
+        If any new statistics are computed as children of FCS, they will be returned in the result record id list.
+        Note: if input has multiple FCS files, the client should try to get parent FCS file from each record to figure out which one is for which FCS.
+        :param stat_compute_input:
+        :return:
+        """
+        payload = dumps(stat_compute_input, ComputeFlowStatisticsInputJson)
+        response = self._user.plugin_post("flowcyto/statistics", payload=payload, is_payload_plain_text=True)
+        self._user.raise_for_status(response)
+        return list(response.json())

sapiopycommons/flowcyto/flowcyto_data.py

@@ -0,0 +1,75 @@
+import base64
+from enum import Enum
+
+from databind.core.dataclasses import dataclass
+
+
+class ChannelStatisticType(Enum):
+    """
+    All supported channel statistics type.
+    """
+    MEAN = "(Mean) MFI"
+    MEDIAN = "(Median) MFI"
+    STD_EV = "Std. Dev."
+    COEFFICIENT_OF_VARIATION = "CV"
+
+    display_name: str
+
+    def __init__(self, display_name: str):
+        self.display_name = display_name
+
+
+@dataclass
+class ChannelStatisticsParameterJSON:
+    channelNameList: list[str]
+    statisticsType: ChannelStatisticType
+
+    def __init__(self, channel_name_list: list[str], stat_type: ChannelStatisticType):
+        self.channelNameList = channel_name_list
+        self.statisticsType = stat_type
+
+
+@dataclass
+class ComputeFlowStatisticsInputJson:
+    fcsFileRecordIdList: list[int]
+    statisticsParameterList: list[ChannelStatisticsParameterJSON]
+
+    def __init__(self, fcs_file_record_id_list: list[int], statistics_parameter_list: list[ChannelStatisticsParameterJSON]):
+        self.fcsFileRecordIdList = fcs_file_record_id_list
+        self.statisticsParameterList = statistics_parameter_list
+
+
+@dataclass
+class FlowJoWorkspaceInputJson:
+    filePath: str
+    base64Data: str
+
+    def __init__(self, filePath: str, file_data: bytes):
+        self.filePath = filePath
+        self.base64Data = base64.b64encode(file_data).decode('utf-8')
+
+
+@dataclass
+class UploadFCSInputJson:
+    """
+    Request to upload new FCS file
+    Attributes:
+        filePath: The file name of the FCS file to be uploaded. For FlowJo workspace, this is important to match the file in group (via file names).
+        attachmentDataType: the attachment data type that contains already-uploaded FCS data.
+        attachmentRecordId: the attachment record ID that contains already-uploaded FCS data.
+        associatedRecordDataType: the "parent" association for the FCS. Can either be a workspace or a sample record.
+        associatedRecordId: the "parent" association for the FCS. Can either be a workspace or a sample record.
+    """
+    filePath: str
+    attachmentDataType: str
+    attachmentRecordId: int
+    associatedRecordDataType: str
+    associatedRecordId: int
+
+    def __init__(self, associated_record_data_type: str, associated_record_id: int,
+                 file_path: str, attachment_data_type: str, attachment_record_id: int):
+        self.filePath = file_path
+        self.attachmentDataType = attachment_data_type
+        self.attachmentRecordId = attachment_record_id
+        self.associatedRecordDataType = associated_record_data_type
+        self.associatedRecordId = associated_record_id

sapiopycommons/general/exceptions.py

@@ -3,34 +3,47 @@ class SapioException(Exception):
     """
     A generic exception thrown by sapiopycommons methods. Typically caused by programmer error, but may also be from
     extremely edge case user errors. For expected user errors, use SapioUserErrorException.
+
+    CommonsWebhookHandler's default behavior for this and any other exception that doesn't extend SapioException is
+    to return a generic toaster message saying that an unexpected error has occurred.
     """
     pass
 
 
-# CommonsWebhookHandler catches this exception and returns "User Cancelled."
 class SapioUserCancelledException(SapioException):
     """
     An exception thrown when the user cancels a client callback.
+
+    CommonsWebhookHandler's default behavior is to simply end the webhook session with a true result without logging
+    the exception.
+    """
+    pass
+
+
+class SapioDialogTimeoutException(SapioException):
+    """
+    An exception thrown when the user leaves a client callback open for too long.
+
+    CommonsWebhookHandler's default behavior is to display an OK popup notifying the user that the dialog has timed out.
     """
     pass
 
 
-# CommonsWebhookHandler catches this exception and returns the text to the user as display text in a webhook result.
 class SapioUserErrorException(SapioException):
     """
     An exception caused by user error (e.g. user provided a CSV when an XLSX was expected), which promises to return a
-    user-friendly message explaining the error that should be displayed to the user. It is the responsibility of the
-    programmer to catch any such exceptions and return the value in e.args[0] as text for the user to see (such as
-    through the display text of a webhook result).
+    user-friendly message explaining the error that should be displayed to the user.
+
+    CommonsWebhookHandler's default behavior is to return the error message in a toaster popup.
     """
     pass
 
 
-# CommonsWebhookHandler catches this exception and returns the text in a display_error client callback.
 class SapioCriticalErrorException(SapioException):
     """
     A critical exception caused by user error, which promises to return a user-friendly message explaining the error
-    that should be displayed to the user. It is the responsibility of the programmer to catch any such exceptions and
-    return the value in e.args[0] as text for the user to see (such as through a dialog form client callback request).
+    that should be displayed to the user.
+
+    CommonsWebhookHandler's default behavior is to return the error message in a display_error callback.
     """
     pass

sapiopycommons/multimodal/multimodal_data.py

@@ -38,6 +38,9 @@ class PyMolecule:
     normError: str | None
     desaltError: str | None
     desaltedList: list[str] | None
+    registrationHash: str | None
+    hasOrGroup: bool
+    CXSMILESHash: str | None
 
 
 @dataclass
@@ -100,9 +103,9 @@ class PyMoleculeLoaderResult:
         compoundList: the compounds successfully loaded.
         errorList: an error record is added here for each one we failed to load in Sapio.
     """
-    compoundByStr: dict[str, PyCompound]
-    compoundList: list[PyCompound]
-    errorList: list[ChemLoadingError]
+    compoundByStr: dict[str, PyCompound] | None
+    compoundList: list[PyCompound] | None
+    errorList: list[ChemLoadingError] | None
 
 
 @dataclass

sapiopycommons/webhook/webhook_handlers.py

@@ -18,7 +18,7 @@ from sapiopylib.rest.utils.recordmodel.ancestry import RecordModelAncestorManage
 from sapiopycommons.callbacks.callback_util import CallbackUtil
 from sapiopycommons.eln.experiment_handler import ExperimentHandler
 from sapiopycommons.general.exceptions import SapioUserErrorException, SapioCriticalErrorException, \
-    SapioUserCancelledException, SapioException
+    SapioUserCancelledException, SapioException, SapioDialogTimeoutException
 from sapiopycommons.general.sapio_links import SapioNavigationLinker
 from sapiopycommons.recordmodel.record_handler import RecordHandler
 from sapiopycommons.rules.eln_rule_handler import ElnRuleHandler
@@ -90,6 +90,8 @@ class CommonsWebhookHandler(AbstractWebhookHandler):
             return self.handle_critical_error_exception(e)
         except SapioUserCancelledException as e:
             return self.handle_user_cancelled_exception(e)
+        except SapioDialogTimeoutException as e:
+            return self.handle_dialog_timeout_exception(e)
         except Exception as e:
             return self.handle_unexpected_exception(e)
 
@@ -111,11 +113,12 @@ class CommonsWebhookHandler(AbstractWebhookHandler):
     # the run method and into their own functions.
     def handle_user_error_exception(self, e: SapioUserErrorException) -> SapioWebhookResult:
         """
-        Handle a SapioUserErrorException. Default behavior returns the error message as display text in a webhook
-        result.
+        Handle a SapioUserErrorException.
+
+        Default behavior returns a false result and the error message as display text in a webhook result.
 
         :param e: The exception that was raised.
-        :return: A SapioWebhookResult reporting the exception to the user.
+        :return: A SapioWebhookResult to end the webhook session with.
         """
         result: SapioWebhookResult | None = self.handle_any_exception(e)
         if result is not None:
@@ -125,50 +128,84 @@ class CommonsWebhookHandler(AbstractWebhookHandler):
 
     def handle_critical_error_exception(self, e: SapioCriticalErrorException) -> SapioWebhookResult:
         """
-        Handle a SapioCriticalErrorException. Default behavior makes a display_error client callback.
+        Handle a SapioCriticalErrorException.
+
+        Default behavior makes a display_error client callback with the error message and returns a false result.
 
         :param e: The exception that was raised.
-        :return: A SapioWebhookResult reporting the exception to the user.
+        :return: A SapioWebhookResult to end the webhook session with.
         """
         result: SapioWebhookResult | None = self.handle_any_exception(e)
         if result is not None:
             return result
         self.log_error(traceback.format_exc())
+        # This error can be thrown by endpoints that can't send client callbacks. If that happens, fall back onto
+        # sending display text instead.
         if self.can_send_client_callback():
-            DataMgmtServer.get_client_callback(self.user).display_error(e.args[0])
+            self.callback.display_error(e.args[0])
+        else:
+            return SapioWebhookResult(False, e.args[0])
         return SapioWebhookResult(False)
 
-    def handle_unexpected_exception(self, e: Exception) -> SapioWebhookResult:
+    def handle_user_cancelled_exception(self, e: SapioUserCancelledException) -> SapioWebhookResult:
         """
-        Handle a generic exception which isn't a SapioUserErrorException or SapioCriticalErrorException. Default
-        behavior returns a generic error message as display text informing the user to contact Sapio support.
+        Handle a SapioUserCancelledException.
+
+        Default behavior simply ends the webhook session with a true result (since the user cancelling is a valid
+        action).
 
         :param e: The exception that was raised.
-        :return: A SapioWebhookResult reporting the exception to the user.
+        :return: A SapioWebhookResult to end the webhook session with.
         """
         result: SapioWebhookResult | None = self.handle_any_exception(e)
         if result is not None:
             return result
-        msg: str = traceback.format_exc()
-        self.log_error(msg)
-        # FR-47079: Also log all unexpected exception messages to the webhook execution log within the platform.
-        self.log_error_to_webhook_execution_log(msg)
-        return SapioWebhookResult(False, display_text="Unexpected error occurred during webhook execution. "
-                                                      "Please contact Sapio support.")
+        return SapioWebhookResult(True)
 
-    def handle_user_cancelled_exception(self, e: SapioUserCancelledException) -> SapioWebhookResult:
+    def handle_dialog_timeout_exception(self, e: SapioDialogTimeoutException) -> SapioWebhookResult:
         """
-        Handle a SapioUserCancelledException. Default behavior returns "User Cancelled" as display text in a webhook
-        result.
+        Handle a SapioDialogTimeoutException.
+
+        Default behavior displays an OK popup notifying the user that the dialog has timed out and returns a false
+        webhook result.
 
         :param e: The exception that was raised.
-        :return: A SapioWebhookResult with display text saying the user cancelled the request.
+        :return: A SapioWebhookResult to end the webhook session with.
         """
         result: SapioWebhookResult | None = self.handle_any_exception(e)
         if result is not None:
             return result
+        # This dialog could time out too! Ignore it if it does.
+        # No need to check can_send_client_callback() here, as this exception should only be thrown by endpoints that
+        # are capable of sending callbacks.
+        try:
+            self.callback.ok_dialog("Notice", "You have remained idle for too long and this dialog has timed out. "
+                                              "Close and re-initiate it to continue.")
+        except SapioDialogTimeoutException:
+            pass
         return SapioWebhookResult(False)
 
+    def handle_unexpected_exception(self, e: Exception) -> SapioWebhookResult:
+        """
+        Handle a generic exception which isn't one of the handled Sapio exceptions.
+
+        Default behavior returns a false webhook result with a generic error message as display text informing the user
+        to contact Sapio support. Additionally, the stace trace of the exception that was thrown is logged to the
+        execution log for the webhook call in the system.
+
+        :param e: The exception that was raised.
+        :return: A SapioWebhookResult to end the webhook session with.
+        """
+        result: SapioWebhookResult | None = self.handle_any_exception(e)
+        if result is not None:
+            return result
+        msg: str = traceback.format_exc()
+        self.log_error(msg)
+        # FR-47079: Also log all unexpected exception messages to the webhook execution log within the platform.
+        self.log_error_to_webhook_execution_log(msg)
+        return SapioWebhookResult(False, display_text="Unexpected error occurred during webhook execution. "
+                                                      "Please contact Sapio support.")
+
     # noinspection PyMethodMayBeStatic,PyUnusedLocal
     def handle_any_exception(self, e: Exception) -> SapioWebhookResult | None:
         """
@@ -177,7 +214,8 @@ class CommonsWebhookHandler(AbstractWebhookHandler):
 
         :param e: The exception that was raised.
         :return: An optional SapioWebhookResult. May return a custom message to the client that wouldn't have been
-            sent by one of the normal exception handlers, or may return None if no result needs returned.
+            sent by one of the normal exception handlers, or may return None if no result needs returned. It a result is
+            returned, then the default behavior of other exception handlers is skipped.
         """
         return None
 

{sapiopycommons-2024.10.1a338.dist-info → sapiopycommons-2024.10.8a340.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: sapiopycommons
-Version: 2024.10.1a338
+Version: 2024.10.8a340
 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-2024.10.1a338.dist-info → sapiopycommons-2024.10.8a340.dist-info}/RECORD

@@ -1,8 +1,8 @@
 sapiopycommons/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 sapiopycommons/callbacks/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-sapiopycommons/callbacks/callback_util.py,sha256=7gUyJ-i3Owdy9bdQSOYKX_AgNRaT0PTbdhulA59tNys,63616
-sapiopycommons/chem/IndigoMolecules.py,sha256=QqFDi9CKERj6sn_ZwVcS2xZq4imlkaTeCrpq1iNcEJA,1992
-sapiopycommons/chem/Molecules.py,sha256=t80IsQBPJ9mwE8ZxnWomAGrZDhdsOuPvLaTPb_N6jGU,8639
+sapiopycommons/callbacks/callback_util.py,sha256=nb6cXK8yFq96gtG0Z2NiK-qdNaRh88bavUH-ZoBjh18,67953
+sapiopycommons/chem/IndigoMolecules.py,sha256=3f-aig3AJkKJhRmhlQ0cI-5G8oeaQk_3foJTDZCvoko,2040
+sapiopycommons/chem/Molecules.py,sha256=0B_SsXB2swg2DiP50p0tcNOVO1ajlxumSI42YyDiSHI,11517
 sapiopycommons/chem/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 sapiopycommons/customreport/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 sapiopycommons/customreport/column_builder.py,sha256=sS_wZYOR72rs3syTNjwCVP4h8M8N0b0burkTxFQItVU,3019
@@ -11,7 +11,7 @@ sapiopycommons/customreport/term_builder.py,sha256=oVsr7iFPnug2TrZUCcAMhyps-b62k
 sapiopycommons/datatype/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 sapiopycommons/datatype/attachment_util.py,sha256=_l2swuP8noIGAl4bwzBUEhr6YlN_OVZl3-gi1XqFHYA,3364
 sapiopycommons/eln/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-sapiopycommons/eln/experiment_handler.py,sha256=PdphawD0ZoSljxJpo3PjDQ1mA8FtZSUts57m_zFKkw4,66848
+sapiopycommons/eln/experiment_handler.py,sha256=eUVKHmgd4oowWg37mBnp4Ag_NsXBkDhm6mV4j36HhKs,66850
 sapiopycommons/eln/experiment_report_util.py,sha256=B55hXbTGndCEI19LiqhjvO46_chujZUK0qDTWHjzfcU,6398
 sapiopycommons/eln/plate_designer.py,sha256=FYJfhhNq8hdfuXgDYOYHy6g0m2zNwQXZWF_MTPzElDg,7184
 sapiopycommons/files/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -22,18 +22,20 @@ sapiopycommons/files/file_data_handler.py,sha256=SCsjODMJIPEBSsahzXUeOM7CfSCmYwP
 sapiopycommons/files/file_util.py,sha256=wbL3rxcFc-t2mXaPWWkoFWYGopvTcQts9Wf-L5GkhT8,29498
 sapiopycommons/files/file_validator.py,sha256=4OvY98ueJWPJdpndwnKv2nqVvLP9S2W7Il_dM0Y0ojo,28709
 sapiopycommons/files/file_writer.py,sha256=96Xl8TTT46Krxe_J8rmmlEMtel4nzZB961f5Yqtl1-I,17616
+sapiopycommons/flowcyto/flow_cyto.py,sha256=YlkKJR_zEHYRuNW0bnTqlTyZeXs0lOaeSCfG2fnfD7E,3227
+sapiopycommons/flowcyto/flowcyto_data.py,sha256=mYKFuLbtpJ-EsQxLGtu4tNHVlygTxKixgJxJqD68F58,2596
 sapiopycommons/general/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 sapiopycommons/general/accession_service.py,sha256=HYgyOsH_UaoRnoury-c2yTW8SeG4OtjLemdpCzoV4R8,13484
 sapiopycommons/general/aliases.py,sha256=Gih9shHsj765q4HimfFTTI7wWDPAtXjoqCgHisyIQZY,10409
 sapiopycommons/general/audit_log.py,sha256=tJi4uU4qRY2WWcK4ItkjRvoCHCwwiU9LwCNv4lP5-QQ,8713
 sapiopycommons/general/custom_report_util.py,sha256=BGu9Ki0wn3m4Nk-LKM6inDSfe8ULUSG9d-HJJNOTtGc,15653
-sapiopycommons/general/exceptions.py,sha256=DOlLKnpCatxQF-lVCToa8ryJgusWLvip6N_1ALN00QE,1679
+sapiopycommons/general/exceptions.py,sha256=GY7fe0qOgoy4kQVn_Pn3tdzHsJZyNIpa6VCChg6tzuM,1813
 sapiopycommons/general/popup_util.py,sha256=L-4qpTemSZdlD6_6oEsDYIzLOCiZgDK6wC6DqUwzOYA,31925
 sapiopycommons/general/sapio_links.py,sha256=o9Z-8y2rz6AI0Cy6tq58ElPge9RBnisGc9NyccbaJxs,2610
 sapiopycommons/general/storage_util.py,sha256=ovmK_jN7v09BoX07XxwShpBUC5WYQOM7dbKV_VeLXJU,8892
 sapiopycommons/general/time_util.py,sha256=sXThADCRAQDWYDD9C5CdhcKYIt3qOaVNyZfGBR7HW9A,8701
 sapiopycommons/multimodal/multimodal.py,sha256=A1QsC8QTPmgZyPr7KtMbPRedn2Ie4WIErodUvQ9otgU,6724
-sapiopycommons/multimodal/multimodal_data.py,sha256=p_caXW0vrURkzDHHspUptEI7lVFpZUrmyF7foz2fAvA,14983
+sapiopycommons/multimodal/multimodal_data.py,sha256=t-0uY4cVgm88uXaSOL4ZeB6zmdHufowXuLFlMk61wFg,15087
 sapiopycommons/processtracking/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 sapiopycommons/processtracking/endpoints.py,sha256=w5bziI2xC7450M95rCF8JpRwkoni1kEDibyAux9B12Q,10848
 sapiopycommons/recordmodel/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -42,9 +44,9 @@ sapiopycommons/rules/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hS
 sapiopycommons/rules/eln_rule_handler.py,sha256=JYzDA_14D2nLnlqwbpIxVOrfKWzbOS27AYf4TQfGr4Q,10469
 sapiopycommons/rules/on_save_rule_handler.py,sha256=Rkqvph20RbNq6m-RF4fbvCP-YfD2CZYBM2iTr3nl0eY,10236
 sapiopycommons/webhook/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-sapiopycommons/webhook/webhook_handlers.py,sha256=jwc4xu-wwl8haS5k1dENZ1UIYK9GQk74TAo3CGxMW9U,16583
+sapiopycommons/webhook/webhook_handlers.py,sha256=JTquLBln49L1pJ9txJ4oc4Hpzy9kYtMKs0m4SLaFx78,18363
 sapiopycommons/webhook/webservice_handlers.py,sha256=1J56zFI0pWl5MHoNTznvcZumITXgAHJMluj8-2BqYEw,3315
-sapiopycommons-2024.10.1a338.dist-info/METADATA,sha256=WIoAas-Q73shhg1LUx--YyRKafyn0mQjwZhbJ5dhL-g,3176
-sapiopycommons-2024.10.1a338.dist-info/WHEEL,sha256=1yFddiXMmvYK7QYTqtRNtX66WJ0Mz8PYEiEUoOUUxRY,87
-sapiopycommons-2024.10.1a338.dist-info/licenses/LICENSE,sha256=HyVuytGSiAUQ6ErWBHTqt1iSGHhLmlC8fO7jTCuR8dU,16725
-sapiopycommons-2024.10.1a338.dist-info/RECORD,,
+sapiopycommons-2024.10.8a340.dist-info/METADATA,sha256=hUyMLJOeFecV_gjXhZxYralqHgHZudCGTKbZbq3mUbI,3176
+sapiopycommons-2024.10.8a340.dist-info/WHEEL,sha256=1yFddiXMmvYK7QYTqtRNtX66WJ0Mz8PYEiEUoOUUxRY,87
+sapiopycommons-2024.10.8a340.dist-info/licenses/LICENSE,sha256=HyVuytGSiAUQ6ErWBHTqt1iSGHhLmlC8fO7jTCuR8dU,16725
+sapiopycommons-2024.10.8a340.dist-info/RECORD,,