sapiopycommons 2025.3.6a454__py3-none-any.whl → 2025.3.10a455__py3-none-any.whl

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/datatype/data_fields.py

@@ -58,4 +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)
+    WORKFLOW_VERSION__FIELD = WrapperField("WorkflowVersion", FieldType.LONG)

sapiopycommons/eln/experiment_handler.py

@@ -2,7 +2,6 @@ from __future__ import annotations
 
 import time
 from collections.abc import Mapping, Iterable
-from typing import TypeAlias
 from weakref import WeakValueDictionary
 
 from sapiopylib.rest.DataMgmtService import DataMgmtServer
@@ -29,7 +28,7 @@ from sapiopycommons.general.aliases import AliasUtil, SapioRecord, ExperimentIde
     DataTypeIdentifier, RecordModel
 from sapiopycommons.general.exceptions import SapioException
 
-Step: TypeAlias = str | ElnEntryStep
+Step = str | ElnEntryStep
 """An object representing an identifier to an ElnEntryStep. May be either the name of the step or the ElnEntryStep
 itself."""
 

sapiopycommons/eln/experiment_report_util.py

@@ -6,13 +6,13 @@ from sapiopylib.rest.pojo.eln.ElnExperiment import ElnExperiment, ElnExperimentQ
 from sapiopylib.rest.pojo.eln.SapioELNEnums import ElnExperimentStatus, ElnBaseDataType
 from sapiopylib.rest.utils.recordmodel.RecordModelWrapper import WrappedType
 
-from sapiopycommons.customreport.auto_pagers import CustomReportDictAutoPager
 from sapiopycommons.customreport.custom_report_builder import CustomReportBuilder
 from sapiopycommons.customreport.term_builder import TermBuilder
 from sapiopycommons.datatype.pseudo_data_types import EnbEntryOptionsPseudoDef, NotebookExperimentOptionPseudoDef, \
     NotebookExperimentPseudoDef, ExperimentEntryRecordPseudoDef, EnbEntryPseudoDef
 from sapiopycommons.general.aliases import SapioRecord, UserIdentifier, AliasUtil, FieldValue, \
     ExperimentEntryIdentifier, ExperimentIdentifier
+from sapiopycommons.general.custom_report_util import CustomReportUtil
 from sapiopycommons.general.exceptions import SapioException
 from sapiopycommons.recordmodel.record_handler import RecordHandler
 
@@ -201,7 +201,7 @@ class ExperimentReportUtil:
         criteria = report_builder.build_report_criteria()
 
         ret_val: dict[SapioRecord, int] = {}
-        rows: list[dict[str, FieldValue]] = CustomReportDictAutoPager(context, criteria).get_all_at_once()
+        rows: list[dict[str, FieldValue]] = CustomReportUtil.run_custom_report(context, criteria)
         for row in rows:
             dt: str = row[EnbEntryPseudoDef.DATA_TYPE_NAME__FIELD_NAME.field_name]
             exp_id: int = row[EnbEntryPseudoDef.EXPERIMENT_ID__FIELD_NAME.field_name]
@@ -268,7 +268,7 @@ class ExperimentReportUtil:
 
         # Ensure that each experiment appears in the dictionary, even if it has no experiment options.
         options: dict[int, dict[str, str]] = {x: {} for x in exp_ids}
-        results: list[dict[str, FieldValue]] = CustomReportDictAutoPager(context, report).get_all_at_once()
+        results: list[dict[str, FieldValue]] = CustomReportUtil.run_custom_report(context, report)
         for row in results:
             exp_id: int = row[NotebookExperimentOptionPseudoDef.EXPERIMENT_ID__FIELD_NAME.field_name]
             key: str = row[NotebookExperimentOptionPseudoDef.OPTION_KEY__FIELD_NAME.field_name]
@@ -299,7 +299,7 @@ class ExperimentReportUtil:
 
         # Ensure that each entry appears in the dictionary, even if it has no entry options.
         options: dict[int, dict[str, str]] = {x: {} for x in entries}
-        results: list[dict[str, FieldValue]] = CustomReportDictAutoPager(context, report).get_all_at_once()
+        results: list[dict[str, FieldValue]] = CustomReportUtil.run_custom_report(context, report)
         for row in results:
             entry_id: int = row[EnbEntryOptionsPseudoDef.ENTRY_ID__FIELD_NAME.field_name]
             key: str = row[EnbEntryOptionsPseudoDef.ENTRY_OPTION_KEY__FIELD_NAME.field_name]
@@ -332,7 +332,7 @@ class ExperimentReportUtil:
         report = report_builder.build_report_criteria()
 
         ret_val: dict[int, str] = {}
-        results: list[dict[str, FieldValue]] = CustomReportDictAutoPager(context, report).get_all_at_once()
+        results: list[dict[str, FieldValue]] = CustomReportUtil.run_custom_report(context, report)
         for row in results:
             exp_id: int = row[NotebookExperimentPseudoDef.EXPERIMENT_ID__FIELD_NAME.field_name]
             name: str = row["TemplateExperimentName"]
@@ -581,7 +581,7 @@ class ExperimentReportUtil:
         """
         user = AliasUtil.to_sapio_user(context)
         exp_ids: list[int] = []
-        for row in CustomReportDictAutoPager(user, report):
+        for row in CustomReportUtil.run_custom_report(user, report):
             exp_ids.append(row[NotebookExperimentPseudoDef.EXPERIMENT_ID__FIELD_NAME.field_name])
         if not exp_ids:
             return []
@@ -646,4 +646,4 @@ class ExperimentReportUtil:
         report_builder.add_join(records_entry_join, ExperimentEntryRecordPseudoDef.DATA_TYPE_NAME)
         report_builder.add_join(experiment_entry_enb_entry_join, EnbEntryPseudoDef.DATA_TYPE_NAME)
         report_builder.add_join(enb_entry_experiment_join, NotebookExperimentPseudoDef.DATA_TYPE_NAME)
-        return CustomReportDictAutoPager(user, report_builder.build_report_criteria()).get_all_at_once()
+        return CustomReportUtil.run_custom_report(user, report_builder.build_report_criteria())

sapiopycommons/files/file_bridge.py

@@ -1,7 +1,6 @@
 import base64
 import io
 import urllib.parse
-from typing import Any
 
 from requests import Response
 from sapiopylib.rest.User import SapioUser
@@ -9,36 +8,6 @@ from sapiopylib.rest.User import SapioUser
 from sapiopycommons.general.aliases import UserIdentifier, AliasUtil
 
 
-# FR-47387: Add support for the metadata endpoints in FileBridge.
-class FileBridgeMetadata:
-    """
-    Metadata for a file or directory in FileBridge.
-    """
-    file_name: str
-    """The name of the file or directory."""
-    is_file: bool
-    """True if the metadata is for a file, False if it is for a directory."""
-    is_directory: bool
-    """True if the metadata is for a directory, False if it is for a file."""
-    size: int
-    """The size of the file in bytes. For directories, this value will always be zero."""
-    creation_time: int
-    """The time the file or directory was created, in milliseconds since the epoch."""
-    last_accessed_time: int
-    """The time the file or directory was last accessed, in milliseconds since the epoch."""
-    last_modified_time: int
-    """The time the file or directory was last modified, in milliseconds since the epoch."""
-
-    def __init__(self, json_dict: dict[str, Any]):
-        self.file_name = json_dict['fileName']
-        self.is_file = json_dict['isFile']
-        self.is_directory = json_dict['isDirectory']
-        self.size = json_dict['size']
-        self.creation_time = json_dict['creationTime']
-        self.last_accessed_time = json_dict['lastAccessTime']
-        self.last_modified_time = json_dict['lastModifiedTime']
-
-
 # FR-46064 - Initial port of PyWebhookUtils to sapiopycommons.
 class FileBridge:
     @staticmethod
@@ -168,48 +137,3 @@ class FileBridge:
         user: SapioUser = AliasUtil.to_sapio_user(context)
         response = user.delete(sub_path, params=params)
         user.raise_for_status(response)
-
-    @staticmethod
-    def file_metadata(context: UserIdentifier, bridge_name: str, file_path: str) -> FileBridgeMetadata:
-        """
-        Get metadata for a file or directory in FileBridge.
-
-        The file path may be to a directory, in which case only the metadata for that directory will be returned. If you
-        want the metadata for the contents of a directory, then use the directory_metadata function.
-
-        :param context: The current webhook context or a user object to send requests from.
-        :param bridge_name: The name of the bridge to use. This is the "connection name" in the
-            file bridge configurations.
-        :param file_path: The path to the file to retrieve the metadata from.
-        :return: The metadata for the file.
-        """
-        sub_path = '/ext/filebridge/file/metadata'
-        params = {
-            'Filepath': f"bridge://{bridge_name}/{file_path}"
-        }
-        user: SapioUser = AliasUtil.to_sapio_user(context)
-        response = user.get(sub_path, params=params)
-        user.raise_for_status(response)
-        response_body: dict[str, Any] = response.json()
-        return FileBridgeMetadata(response_body)
-
-    @staticmethod
-    def directory_metadata(context: UserIdentifier, bridge_name: str, file_path: str) -> list[FileBridgeMetadata]:
-        """
-        Get metadata for every file or nested directory in a directory in FileBridge.
-
-        :param context: The current webhook context or a user object to send requests from.
-        :param bridge_name: The name of the bridge to use. This is the "connection name" in the
-            file bridge configurations.
-        :param file_path: The path to the directory to retrieve the metadata of the contents.
-        :return: A list of the metadata for the contents of the directory.
-        """
-        sub_path = '/ext/filebridge/directory/metadata'
-        params = {
-            'Filepath': f"bridge://{bridge_name}/{file_path}"
-        }
-        user: SapioUser = AliasUtil.to_sapio_user(context)
-        response = user.get(sub_path, params=params)
-        user.raise_for_status(response)
-        response_body: list[dict[str, Any]] = response.json()
-        return [FileBridgeMetadata(x) for x in response_body]