sapiopycommons 2024.10.24a342__tar.gz → 2024.10.25a345__tar.gz

{sapiopycommons-2024.10.24a342 → sapiopycommons-2024.10.25a345}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: sapiopycommons
-Version: 2024.10.24a342
+Version: 2024.10.25a345
 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-2024.10.24a342 → sapiopycommons-2024.10.25a345}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "sapiopycommons"
-version='2024.10.24a342'
+version='2024.10.25a345'
 authors = [
     { name="Jonathan Steck", email="jsteck@sapiosciences.com" },
     { name="Yechen Qiao", email="yqiao@sapiosciences.com" },

{sapiopycommons-2024.10.24a342 → sapiopycommons-2024.10.25a345}/src/sapiopycommons/chem/Molecules.py

@@ -231,7 +231,7 @@ def mol_to_sapio_substance(mol: Mol, include_stereoisomers=False,
     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.MolFromMolBlock(Chem.MolToMolBlock(mol))
+        mol_copy: Mol = Chem.Mol(mol)
         Chem.CanonicalizeEnhancedStereo(mol_copy)
         molecule["inchi"] = Chem.MolToInchi(mol_copy)
         molecule["inchiKey"] = Chem.MolToInchiKey(mol_copy)

{sapiopycommons-2024.10.24a342 → sapiopycommons-2024.10.25a345}/src/sapiopycommons/customreport/column_builder.py

@@ -52,9 +52,9 @@ class ColumnBuilder:
         :param field: The field name to return the type of.
         :return: The field type of the given field name.
         """
-        # Check if the field name is a system field. If it us, use the field type defined in this file.
+        # Check if the field name is a system field. If it is, use the field type defined in this file.
         field_name: str = AliasUtil.to_data_field_name(field)
         if field_name in SYSTEM_FIELDS:
             return SYSTEM_FIELDS.get(field_name)
         # Otherwise, check if the field type can be found from the wrapper.
-        return AliasUtil.to_field_type(field_name, data_type)
+        return AliasUtil.to_field_type(field, data_type)

sapiopycommons-2024.10.25a345/src/sapiopycommons/datatype/pseudo_data_types.py

@@ -0,0 +1,440 @@
+from sapiopylib.rest.pojo.datatype.FieldDefinition import FieldType
+from sapiopylib.rest.utils.recordmodel.RecordModelWrapper import WrapperField
+
+
+class ActiveTaskPseudoDef:
+    DATA_TYPE_NAME: str = "ActiveTask"
+    ACTIVE_TASK_ID__FIELD_NAME = WrapperField("ActiveTaskId", FieldType.LONG)
+    ACTIVE_WORKFLOW_ID__FIELD_NAME = WrapperField("ActiveWorkflowId", FieldType.LONG)
+    DATE_EDITED__FIELD_NAME = WrapperField("DateEdited", FieldType.DATE)
+    EDITED_BY__FIELD_NAME = WrapperField("EditedBy", FieldType.STRING)
+    STATUS__FIELD_NAME = WrapperField("Status", FieldType.ENUM)
+    TASK_USAGE_ID__FIELD_NAME = WrapperField("TaskUsageId", FieldType.LONG)
+
+
+class ActiveWorkflowPseudoDef:
+    DATA_TYPE_NAME: str = "ActiveWorkflow"
+    ACTIVE_WORKFLOW_ID__FIELD_NAME = WrapperField("ActiveWorkflowId", FieldType.LONG)
+    CREATED_BY__FIELD_NAME = WrapperField("CreatedBy", FieldType.STRING)
+    DATE_CREATED__FIELD_NAME = WrapperField("DateCreated", FieldType.DATE)
+    DATE_EDITED__FIELD_NAME = WrapperField("DateEdited", FieldType.STRING)
+    EDITED_BY__FIELD_NAME = WrapperField("EditedBy", FieldType.STRING)
+    ESTIMATED_ATTACHMENTS__FIELD_NAME = WrapperField("EstimatedAttachments", FieldType.LONG)
+    NAME__FIELD_NAME = WrapperField("Name", FieldType.STRING)
+    RELATED_RECORD_ID__FIELD_NAME = WrapperField("RelatedRecordId", FieldType.LONG)
+    STATUS__FIELD_NAME = WrapperField("Status", FieldType.ENUM)
+    WORKFLOW_ID__FIELD_NAME = WrapperField("WorkflowId", FieldType.LONG)
+
+
+class AuditLogPseudoDef:
+    DATA_TYPE_NAME: str = "AuditLog"
+    DATA_FIELD_NAME__FIELD_NAME = WrapperField("DataFieldName", FieldType.STRING)
+    DATA_TYPE_NAME__FIELD_NAME = WrapperField("DataTypeName", FieldType.STRING)
+    DESCRIPTION__FIELD_NAME = WrapperField("Description", FieldType.STRING)
+    EVENT_TYPE__FIELD_NAME = WrapperField("EventType", FieldType.ENUM)
+    FULL_NAME__FIELD_NAME = WrapperField("FullName", FieldType.STRING)
+    NEW_VALUE__FIELD_NAME = WrapperField("NewValue", FieldType.STRING)
+    ORIGINAL_VALUE__FIELD_NAME = WrapperField("OriginalValue", FieldType.STRING)
+    RECORD_ID__FIELD_NAME = WrapperField("RecordId", FieldType.LONG)
+    RECORD_NAME__FIELD_NAME = WrapperField("RecordName", FieldType.STRING)
+    TIME_STAMP__FIELD_NAME = WrapperField("TimeStamp", FieldType.DATE)
+    USER_COMMENT__FIELD_NAME = WrapperField("UserComment", FieldType.STRING)
+    USER_NAME__FIELD_NAME = WrapperField("UserName", FieldType.STRING)
+
+
+class DataFieldDefinitionPseudoDef:
+    DATA_TYPE_NAME: str = "DataFieldDefinition"
+    APPROVE_EDIT__FIELD_NAME = WrapperField("ApproveEdit", FieldType.BOOLEAN)
+    AUTO_CLEAR_FIELD_LIST__FIELD_NAME = WrapperField("AutoClearFieldList", FieldType.STRING)
+    AUTO_SORT__FIELD_NAME = WrapperField("AutoSort", FieldType.BOOLEAN)
+    COLOR_MAPPING_ID__FIELD_NAME = WrapperField("ColorMappingId", FieldType.LONG)
+    DATA_FIELD_NAME__FIELD_NAME = WrapperField("DataFieldName", FieldType.STRING)
+    DATA_FIELD_TAG__FIELD_NAME = WrapperField("DataFieldTag", FieldType.STRING)
+    DATA_FIELD_TYPE__FIELD_NAME = WrapperField("DataFieldType", FieldType.STRING)
+    DATA_TYPE_NAME__FIELD_NAME = WrapperField("DataTypeName", FieldType.STRING)
+    DECIMAL_DIGITS__FIELD_NAME = WrapperField("DecimalDigits", FieldType.INTEGER)
+    DEFAULT_VALUE__FIELD_NAME = WrapperField("DefaultValue", FieldType.STRING)
+    DEPENDENT_FIELDS__FIELD_NAME = WrapperField("Dependent_Fields", FieldType.STRING)
+    DESCRIPTION__FIELD_NAME = WrapperField("Description", FieldType.STRING)
+    DIRECT_EDIT__FIELD_NAME = WrapperField("DirectEdit", FieldType.BOOLEAN)
+    DISPLAY_NAME__FIELD_NAME = WrapperField("DisplayName", FieldType.STRING)
+    EDITABLE__FIELD_NAME = WrapperField("Editable", FieldType.BOOLEAN)
+    ENUM_VALUES__FIELD_NAME = WrapperField("EnumValues", FieldType.STRING)
+    FORM_COL__FIELD_NAME = WrapperField("FormCol", FieldType.SHORT)
+    FORM_COL_SPAN__FIELD_NAME = WrapperField("FormColSpan", FieldType.SHORT)
+    FORM_NAME__FIELD_NAME = WrapperField("FormName", FieldType.STRING)
+    HTML_EDITOR__FIELD_NAME = WrapperField("HtmlEditor", FieldType.BOOLEAN)
+    IDENTIFIER__FIELD_NAME = WrapperField("Identifier", FieldType.BOOLEAN)
+    INDEX_FOR_SEARCH__FIELD_NAME = WrapperField("IndexForSearch", FieldType.BOOLEAN)
+    LINK_OUT__FIELD_NAME = WrapperField("LinkOut", FieldType.BOOLEAN)
+    LINK_OUT_URL__FIELD_NAME = WrapperField("LinkOutUrl", FieldType.BOOLEAN)
+    MAX_LENGTH__FIELD_NAME = WrapperField("MaxLength", FieldType.INTEGER)
+    MAXIMUM_VALUE__FIELD_NAME = WrapperField("MaximumValue", FieldType.DOUBLE)
+    MINIMUM_VALUE__FIELD_NAME = WrapperField("MinimumValue", FieldType.DOUBLE)
+    MULT_SELECT__FIELD_NAME = WrapperField("MultSelect", FieldType.BOOLEAN)
+    NUM_LINES__FIELD_NAME = WrapperField("NumLines", FieldType.INTEGER)
+    REQUIRED__FIELD_NAME = WrapperField("Required", FieldType.BOOLEAN)
+    SORT_KEY__FIELD_NAME = WrapperField("SortKey", FieldType.BOOLEAN)
+    STATIC_DATE__FIELD_NAME = WrapperField("StaticDate", FieldType.BOOLEAN)
+    UNIQUE_VALUE__FIELD_NAME = WrapperField("UniqueValue", FieldType.BOOLEAN)
+    VISIBLE__FIELD_NAME = WrapperField("Visible", FieldType.BOOLEAN)
+    WORKFLOW_ONLY_EDITING__FIELD_NAME = WrapperField("WorkflowOnlyEditing", FieldType.BOOLEAN)
+
+
+class DataTypeDefinitionPseudoDef:
+    DATA_TYPE_NAME: str = "DataTypeDefinition"
+    ADDABLE__FIELD_NAME = WrapperField("Addable", FieldType.BOOLEAN)
+    ATTACHMENT__FIELD_NAME = WrapperField("Attachment", FieldType.BOOLEAN)
+    ATTACHMENT_TYPE__FIELD_NAME = WrapperField("AttachmentType", FieldType.STRING)
+    DATA_TYPE_TAG__FIELD_NAME = WrapperField("DATA_TYPE_TAG", FieldType.STRING)
+    DATA_TYPE_ID__FIELD_NAME = WrapperField("DataTypeId", FieldType.LONG)
+    DATA_TYPE_NAME__FIELD_NAME = WrapperField("DataTypeName", FieldType.STRING)
+    DELETABLE__FIELD_NAME = WrapperField("Deletable", FieldType.BOOLEAN)
+    DESCRIPTION__FIELD_NAME = WrapperField("Description", FieldType.STRING)
+    DISPLAY_NAME__FIELD_NAME = WrapperField("DisplayName", FieldType.STRING)
+    EXTENSION_TYPE__FIELD_NAME = WrapperField("ExtensionType", FieldType.BOOLEAN)
+    GROUP_ADDABLE__FIELD_NAME = WrapperField("GroupAddable", FieldType.BOOLEAN)
+    HIDE_DATA_RECORDS__FIELD_NAME = WrapperField("HideDataRecords", FieldType.BOOLEAN)
+    HIGH_VOLUME__FIELD_NAME = WrapperField("HighVolume", FieldType.BOOLEAN)
+    IS_HIDE_IN_MOBILE__FIELD_NAME = WrapperField("IS_HIDE_IN_MOBILE", FieldType.BOOLEAN)
+    IS_HVDT_ON_SAVE_ENABLED__FIELD_NAME = WrapperField("IS_HVDT_ON_SAVE_ENABLED", FieldType.BOOLEAN)
+    IS_PUBLIC_ATTACHMENT__FIELD_NAME = WrapperField("IS_PUBLIC_ATTACHMENT", FieldType.BOOLEAN)
+    ICON_COLOR__FIELD_NAME = WrapperField("IconColor", FieldType.STRING)
+    ICON_NAME__FIELD_NAME = WrapperField("IconName", FieldType.STRING)
+    IMPORTABLE__FIELD_NAME = WrapperField("Importable", FieldType.BOOLEAN)
+    IS_ACTIVE__FIELD_NAME = WrapperField("IsActive", FieldType.BOOLEAN)
+    IS_HIDDEN__FIELD_NAME = WrapperField("IsHidden", FieldType.BOOLEAN)
+    MAX_TABLE_ROW_COUNT__FIELD_NAME = WrapperField("MaxTableRowCount", FieldType.LONG)
+    PLURAL_DISPLAY_NAME__FIELD_NAME = WrapperField("PluralDisplayName", FieldType.STRING)
+    RECORD_ASSIGNABLE__FIELD_NAME = WrapperField("RecordAssignable", FieldType.BOOLEAN)
+    RECORD_IMAGE_ASSIGNABLE__FIELD_NAME = WrapperField("RecordImageAssignable", FieldType.BOOLEAN)
+    RECORD_IMAGE_MANUALLY_ADDABLE__FIELD_NAME = WrapperField("RecordImageManuallyAddable", FieldType.BOOLEAN)
+    REMOVABLE__FIELD_NAME = WrapperField("Removable", FieldType.BOOLEAN)
+    RESTRICTED__FIELD_NAME = WrapperField("Restricted", FieldType.BOOLEAN)
+    SHOW_ON_HOME_SCREEN__FIELD_NAME = WrapperField("ShowOnHomeScreen", FieldType.BOOLEAN)
+    SHOW_SUB_TABLES__FIELD_NAME = WrapperField("ShowSubTables", FieldType.BOOLEAN)
+    SHOW_TABS__FIELD_NAME = WrapperField("ShowTabs", FieldType.BOOLEAN)
+    SINGLE_PARENT__FIELD_NAME = WrapperField("SingleParent", FieldType.BOOLEAN)
+    UNDER_CONTAINER__FIELD_NAME = WrapperField("UnderContainer", FieldType.BOOLEAN)
+
+
+class EnbDataTypeDefinitionPseudoDef:
+    DATA_TYPE_NAME: str = "EnbDataTypeDefinition"
+    DATA_TYPE_ID__FIELD_NAME = WrapperField("DataTypeId", FieldType.LONG)
+    DATA_TYPE_NAME__FIELD_NAME = WrapperField("DataTypeName", FieldType.STRING)
+    DESCRIPTION__FIELD_NAME = WrapperField("Description", FieldType.STRING)
+    DISPLAY_NAME__FIELD_NAME = WrapperField("DisplayName", FieldType.STRING)
+    ENB_DATA_TYPE_NAME__FIELD_NAME = WrapperField("EnbDataTypeName", FieldType.STRING)
+    ICON_COLOR__FIELD_NAME = WrapperField("IconColor", FieldType.STRING)
+    ICON_NAME__FIELD_NAME = WrapperField("IconName", FieldType.STRING)
+    NOTEBOOK_EXPERIMENT_ID__FIELD_NAME = WrapperField("Notebook_Experiment_ID", FieldType.LONG)
+    PLURAL_DISPLAY_NAME__FIELD_NAME = WrapperField("PluralDisplayName", FieldType.STRING)
+
+
+class EnbEntryPseudoDef:
+    DATA_TYPE_NAME: str = "EnbEntry"
+    APPROVAL_DUE_DATE__FIELD_NAME = WrapperField("ApprovalDueDate", FieldType.DATE)
+    COLUMN_ORDER__FIELD_NAME = WrapperField("ColumnOrder", FieldType.INTEGER)
+    COLUMN_SPAN__FIELD_NAME = WrapperField("ColumnSpan", FieldType.INTEGER)
+    CREATED_BY__FIELD_NAME = WrapperField("CreatedBy", FieldType.STRING)
+    DATA_TYPE_NAME__FIELD_NAME = WrapperField("DataTypeName", FieldType.STRING)
+    DATE_CREATED__FIELD_NAME = WrapperField("DateCreated", FieldType.DATE)
+    DEPENDENT_ENTRY_ID_LIST__FIELD_NAME = WrapperField("DependentEntryIdList", FieldType.STRING)
+    ENTRY_DESCRIPTION__FIELD_NAME = WrapperField("EntryDescription", FieldType.STRING)
+    ENTRY_HEIGHT__FIELD_NAME = WrapperField("EntryHeight", FieldType.INTEGER)
+    ENTRY_ID__FIELD_NAME = WrapperField("EntryId", FieldType.LONG)
+    ENTRY_NAME__FIELD_NAME = WrapperField("EntryName", FieldType.STRING)
+    ENTRY_ORDER__FIELD_NAME = WrapperField("EntryOrder", FieldType.INTEGER)
+    ENTRY_REQUIRES_E_SIGN__FIELD_NAME = WrapperField("EntryRequiresESign", FieldType.BOOLEAN)
+    ENTRY_SINGLETON_ID__FIELD_NAME = WrapperField("EntrySingletonId", FieldType.STRING)
+    ENTRY_STATUS__FIELD_NAME = WrapperField("EntryStatus", FieldType.STRING)
+    ENTRY_TYPE__FIELD_NAME = WrapperField("EntryType", FieldType.STRING)
+    EXPERIMENT_ID__FIELD_NAME = WrapperField("ExperimentId", FieldType.LONG)
+    HAS_COMMENTS__FIELD_NAME = WrapperField("HasComments", FieldType.BOOLEAN)
+    IS_CREATED_FROM_TEMPLATE__FIELD_NAME = WrapperField("IsCreatedFromTemplate", FieldType.BOOLEAN)
+    IS_REQUIRED_ENTRY__FIELD_NAME = WrapperField("IsRequiredEntry", FieldType.BOOLEAN)
+    IS_SHOWN_IN_TEMPLATE__FIELD_NAME = WrapperField("IsShownInTemplate", FieldType.BOOLEAN)
+    LAST_MODIFIED_BY__FIELD_NAME = WrapperField("LastModifiedBy", FieldType.STRING)
+    LAST_MODIFIED_DATE__FIELD_NAME = WrapperField("LastModifiedDate", FieldType.DATE)
+    RELATED_ENTRY_ID_LIST__FIELD_NAME = WrapperField("RelatedEntryIdList", FieldType.STRING)
+    REQUIRES_GRABBER_PLUGIN__FIELD_NAME = WrapperField("RequriesGrabberPlugin", FieldType.BOOLEAN)
+    SOURCE_ENTRY_ID__FIELD_NAME = WrapperField("SourceEntryId", FieldType.LONG)
+    SUBMITTED_BY__FIELD_NAME = WrapperField("SubmittedBy", FieldType.STRING)
+    SUBMITTED_DATE__FIELD_NAME = WrapperField("SubmittedDate", FieldType.DATE)
+    TAB_ID__FIELD_NAME = WrapperField("TabId", FieldType.LONG)
+    TEMPLATE_ITEM_FULFILLED_TIME_STAMP__FIELD_NAME = WrapperField("TemplateItemFulfilledTimeStamp", FieldType.LONG)
+
+
+class EnbEntryOptionsPseudoDef:
+    DATA_TYPE_NAME: str = "EnbEntryOptions"
+    ENTRY_ID__FIELD_NAME = WrapperField("EntryId", FieldType.LONG)
+    ENTRY_OPTION_VALUE__FIELD_NAME = WrapperField("EntryOptionValue", FieldType.STRING)
+    ENTRY_OPTION_KEY__FIELD_NAME = WrapperField("EntryOptionkey", FieldType.STRING)
+
+
+class ExperimentEntryRecordPseudoDef:
+    DATA_TYPE_NAME: str = "ExperimentEntryRecord"
+    ENTRY_ID__FIELD_NAME = WrapperField("EntryId", FieldType.LONG)
+    RECORD_ID__FIELD_NAME = WrapperField("RecordId", FieldType.LONG)
+
+
+class LimsUserPseudoDef:
+    DATA_TYPE_NAME: str = "LimsUser"
+    API_USER__FIELD_NAME = WrapperField("ApiUser", FieldType.BOOLEAN)
+    EMAIL_ADDRESS__FIELD_NAME = WrapperField("EmailAddress", FieldType.STRING)
+    FIRST_NAME__FIELD_NAME = WrapperField("FirstName", FieldType.STRING)
+    LAST_NAME__FIELD_NAME = WrapperField("LastName", FieldType.STRING)
+    MIDDLE_NAME__FIELD_NAME = WrapperField("MiddleName", FieldType.STRING)
+    PWD_EXPIRE_DATE__FIELD_NAME = WrapperField("PwdExpireDate", FieldType.DATE)
+    PWD_EXPIRE_INTERVAL__FIELD_NAME = WrapperField("PwdExpireInterval", FieldType.INTEGER)
+    USER_NAME__FIELD_NAME = WrapperField("UserName", FieldType.STRING)
+
+
+class NotebookExperimentPseudoDef:
+    DATA_TYPE_NAME: str = "NotebookExperiment"
+    ACCESS_LEVEL__FIELD_NAME = WrapperField("AccessLevel", FieldType.STRING)
+    APPROVAL_DUE_DATE__FIELD_NAME = WrapperField("ApprovalDueDate", FieldType.DATE)
+    CREATED_BY__FIELD_NAME = WrapperField("CreatedBy", FieldType.STRING)
+    DATE_CREATED__FIELD_NAME = WrapperField("DateCreated", FieldType.DATE)
+    DESCRIPTION__FIELD_NAME = WrapperField("Description", FieldType.STRING)
+    EXPERIMENT_ID__FIELD_NAME = WrapperField("ExperimentId", FieldType.LONG)
+    EXPERIMENT_NAME__FIELD_NAME = WrapperField("ExperimentName", FieldType.STRING)
+    EXPERIMENT_OWNER__FIELD_NAME = WrapperField("ExperimentOwner", FieldType.STRING)
+    EXPERIMENT_RECORD_ID__FIELD_NAME = WrapperField("ExperimentRecordId", FieldType.LONG)
+    EXPERIMENT_TYPE_NAME__FIELD_NAME = WrapperField("ExperimentTypeName", FieldType.STRING)
+    IS_ACTIVE__FIELD_NAME = WrapperField("IsActive", FieldType.BOOLEAN)
+    IS_MODIFIABLE__FIELD_NAME = WrapperField("IsModifiable", FieldType.BOOLEAN)
+    IS_TEMPLATE__FIELD_NAME = WrapperField("IsTemplate", FieldType.BOOLEAN)
+    IS_PROTOCOL_TEMPLATE__FIELD_NAME = WrapperField("Is_Protocol_Template", FieldType.BOOLEAN)
+    LAST_MODIFIED_BY__FIELD_NAME = WrapperField("LastModifiedBy", FieldType.STRING)
+    LAST_MODIFIED_DATE__FIELD_NAME = WrapperField("LastModifiedDate", FieldType.DATE)
+    SOURCE_TEMPLATE_ID__FIELD_NAME = WrapperField("SourceTemplateId", FieldType.LONG)
+    STATUS__FIELD_NAME = WrapperField("Status", FieldType.STRING)
+
+
+class NotebookExperimentOptionPseudoDef:
+    DATA_TYPE_NAME: str = "NotebookExperimentOption"
+    EXPERIMENT_ID__FIELD_NAME = WrapperField("ExperimentId", FieldType.LONG)
+    OPTION_KEY__FIELD_NAME = WrapperField("OptionKey", FieldType.STRING)
+    OPTION_VALUE__FIELD_NAME = WrapperField("OptionValue", FieldType.STRING)
+
+
+class SystemLogPseudoDef:
+    DATA_TYPE_NAME: str = "SystemLog"
+    DATA_FIELD_NAME__FIELD_NAME = WrapperField("DataFieldName", FieldType.STRING)
+    DATA_TYPE_NAME__FIELD_NAME = WrapperField("DataTypeName", FieldType.STRING)
+    DESCRIPTION__FIELD_NAME = WrapperField("Description", FieldType.STRING)
+    EVENT_ID__FIELD_NAME = WrapperField("EventId", FieldType.LONG)
+    EVENT_TYPE__FIELD_NAME = WrapperField("EventType", FieldType.STRING)
+    FULL_NAME__FIELD_NAME = WrapperField("FullName", FieldType.STRING)
+    NEW_VALUE__FIELD_NAME = WrapperField("NewValue", FieldType.STRING)
+    ORIGINAL_VALUE__FIELD_NAME = WrapperField("OriginalValue", FieldType.STRING)
+    RECORD_ID__FIELD_NAME = WrapperField("RecordId", FieldType.LONG)
+    RECORD_NAME__FIELD_NAME = WrapperField("RecordName", FieldType.STRING)
+    TIMESTAMP__FIELD_NAME = WrapperField("Timestamp", FieldType.DATE)
+    USER_COMMENT__FIELD_NAME = WrapperField("UserComment", FieldType.STRING)
+    USERNAME__FIELD_NAME = WrapperField("Username", FieldType.STRING)
+
+
+class SystemObjectChangeLogPseudoDef:
+    DATA_TYPE_NAME: str = "System_Object_Change_Log"
+    ALT_ID__FIELD_NAME = WrapperField("Alt_Id", FieldType.STRING)
+    ATTRIBUTE_NAME__FIELD_NAME = WrapperField("Attribute_Name", FieldType.STRING)
+    CHANGE_TYPE__FIELD_NAME = WrapperField("Change_Type", FieldType.STRING)
+    DATA_FIELD_NAME__FIELD_NAME = WrapperField("Data_Field_Name", FieldType.STRING)
+    DATA_TYPE_NAME__FIELD_NAME = WrapperField("Data_Type_Name", FieldType.STRING)
+    EVENT_ID__FIELD_NAME = WrapperField("Event_Id", FieldType.STRING)
+    NEW_VALUE__FIELD_NAME = WrapperField("New_Value", FieldType.STRING)
+    OBJECT_ID__FIELD_NAME = WrapperField("Object_Id", FieldType.STRING)
+    OBJECT_TYPE__FIELD_NAME = WrapperField("Object_Type", FieldType.STRING)
+    OLD_VALUE__FIELD_NAME = WrapperField("Old_Value", FieldType.STRING)
+    TIMESTAMP__FIELD_NAME = WrapperField("Timestamp", FieldType.DATE)
+    USERNAME__FIELD_NAME = WrapperField("Username", FieldType.STRING)
+
+
+class TaskPseudoDef:
+    DATA_TYPE_NAME: str = "Task"
+    ATTACHMENT_REQUIRED__FIELD_NAME = WrapperField("AttachmentRequired", FieldType.BOOLEAN)
+    CREATED_BY__FIELD_NAME = WrapperField("CreatedBy", FieldType.STRING)
+    CUSTOM_ACTION__FIELD_NAME = WrapperField("CustomAction", FieldType.STRING)
+    DATA_TYPE_NAME_LIST__FIELD_NAME = WrapperField("DataTypeNameList", FieldType.STRING)
+    DATE_CREATED__FIELD_NAME = WrapperField("DateCreated", FieldType.DATE)
+    DATE_EDITED__FIELD_NAME = WrapperField("DateEdited", FieldType.DATE)
+    DISPLAY_TYPE__FIELD_NAME = WrapperField("DisplayType", FieldType.ENUM)
+    EDITED_BY__FIELD_NAME = WrapperField("EditedBy", FieldType.STRING)
+    INPUT_DATA_TYPE_NAME__FIELD_NAME = WrapperField("InputDataTypeName", FieldType.STRING)
+    IS_TEMPLATE__FIELD_NAME = WrapperField("IsTemplate", FieldType.BOOLEAN)
+    LONG_DESC__FIELD_NAME = WrapperField("LongDesc", FieldType.STRING)
+    MENU_TASK_ID__FIELD_NAME = WrapperField("MenuTaskId", FieldType.ENUM)
+    NAME__FIELD_NAME = WrapperField("Name", FieldType.STRING)
+    SHORT_DESC__FIELD_NAME = WrapperField("ShortDesc", FieldType.STRING)
+    TASK_ID__FIELD_NAME = WrapperField("TaskId", FieldType.LONG)
+    TASK_VERSION__FIELD_NAME = WrapperField("TaskVersion", FieldType.LONG)
+    TEMPLATE_TASK_ID__FIELD_NAME = WrapperField("TemplateTaskId", FieldType.LONG)
+    TYPE__FIELD_NAME = WrapperField("Type", FieldType.ENUM)
+
+
+class TaskAttachmentPseudoDef:
+    DATA_TYPE_NAME: str = "TaskAttachment"
+    ACTIVE_TASK_ID__FIELD_NAME = WrapperField("ActiveTaskId", FieldType.LONG)
+    RECORD_ID__FIELD_NAME = WrapperField("RecordId", FieldType.LONG)
+
+
+class TaskOptionPseudoDef:
+    DATA_TYPE_NAME: str = "TaskOption"
+    OPTION_KEY__FIELD_NAME = WrapperField("OptionKey", FieldType.STRING)
+    OPTION_VALUE__FIELD_NAME = WrapperField("OptionValue", FieldType.STRING)
+    TASK_ID__FIELD_NAME = WrapperField("TaskId", FieldType.LONG)
+
+
+class TaskUsagePseudoDef:
+    DATA_TYPE_NAME: str = "TaskUsage"
+    FORCE_ATTACH__FIELD_NAME = WrapperField("ForceAttach", FieldType.BOOLEAN)
+    IS_TEMPLATE__FIELD_NAME = WrapperField("IsTemplate", FieldType.BOOLEAN)
+    TASK_ID__FIELD_NAME = WrapperField("TaskId", FieldType.LONG)
+    TASK_ORDER__FIELD_NAME = WrapperField("TaskOrder", FieldType.INTEGER)
+    TASK_USAGE_ID__FIELD_NAME = WrapperField("TaskUsageId", FieldType.LONG)
+    WORKFLOW_ID__FIELD_NAME = WrapperField("WorkflowId", FieldType.LONG)
+
+
+class VeloxWebhookPseudoDef:
+    DATA_TYPE_NAME: str = "VELOXWEBHOOK"
+    CUSTOM_PLUGIN_POINT__FIELD_NAME = WrapperField("CUSTOM_PLUGIN_POINT", FieldType.STRING)
+    DATA_TYPE_NAME_SET__FIELD_NAME = WrapperField("DATA_TYPE_NAME_SET", FieldType.STRING)
+    DESCRIPTION__FIELD_NAME = WrapperField("DESCRIPTION", FieldType.STRING)
+    ENB_ENTRY_TYPE__FIELD_NAME = WrapperField("ENB_ENTRY_TYPE", FieldType.STRING)
+    EXPERIMENT_ENTRY_NAME__FIELD_NAME = WrapperField("EXPERIMENT_ENTRY_NAME", FieldType.STRING)
+    GUID__FIELD_NAME = WrapperField("GUID", FieldType.STRING)
+    ICON_COLOR__FIELD_NAME = WrapperField("ICON_COLOR", FieldType.STRING)
+    ICON_GUID__FIELD_NAME = WrapperField("ICON_GUID", FieldType.STRING)
+    IS_RETRY_ON_FAILURE__FIELD_NAME = WrapperField("IS_RETRY_ON_FAILURE", FieldType.BOOLEAN)
+    IS_TRANSACTIONAL__FIELD_NAME = WrapperField("IS_TRANSACTIONAL", FieldType.BOOLEAN)
+    LINE_1_TEXT__FIELD_NAME = WrapperField("LINE_1_TEXT", FieldType.STRING)
+    LINE_2_TEXT__FIELD_NAME = WrapperField("LINE_2_TEXT", FieldType.STRING)
+    PLUGIN_ORDER__FIELD_NAME = WrapperField("PLUGIN_ORDER", FieldType.INTEGER)
+    PLUGIN_POINT__FIELD_NAME = WrapperField("PLUGIN_POINT", FieldType.STRING)
+    SECTION_NAME_PATH__FIELD_NAME = WrapperField("SECTION_NAME_PATH", FieldType.STRING)
+    TEMPLATE_NAME__FIELD_NAME = WrapperField("TEMPLATE_NAME", FieldType.STRING)
+    WEBHOOK_URL__FIELD_NAME = WrapperField("WEBHOOK_URL", FieldType.STRING)
+
+
+class VeloxWebhookExecutionPseudoDef:
+    DATA_TYPE_NAME: str = "VELOXWEBHOOK_EXECUTION"
+    EXECUTION_TIMESTAMP__FIELD_NAME = WrapperField("EXECUTION_TIMESTAMP", FieldType.DATE)
+    EXECUTION_USERNAME__FIELD_NAME = WrapperField("EXECUTION_USERNAME", FieldType.STRING)
+    GUID__FIELD_NAME = WrapperField("GUID", FieldType.STRING)
+    LAST_ATTEMPT_NUMBER__FIELD_NAME = WrapperField("LAST_ATTEMPT_NUMBER", FieldType.INTEGER)
+    LAST_ATTEMPT_RESULT__FIELD_NAME = WrapperField("LAST_ATTEMPT_RESULT", FieldType.STRING)
+    REQUEST_BODY__FIELD_NAME = WrapperField("REQUEST_BODY", FieldType.STRING)
+    WEBHOOK_GUID__FIELD_NAME = WrapperField("WEBHOOK_GUID", FieldType.STRING)
+    WEBHOOK_URL__FIELD_NAME = WrapperField("WEBHOOK_URL", FieldType.STRING)
+
+
+class VeloxWebhookExecutionAttemptPseudoDef:
+    DATA_TYPE_NAME: str = "VELOXWEBHOOK_EXECUTION_ATTEMPT"
+    ATTEMPT_DURATION__FIELD_NAME = WrapperField("ATTEMPT_DURATION", FieldType.INTEGER)
+    ATTEMPT_NUMBER__FIELD_NAME = WrapperField("ATTEMPT_NUMBER", FieldType.INTEGER)
+    ATTEMPT_RESULT__FIELD_NAME = WrapperField("ATTEMPT_RESULT", FieldType.STRING)
+    ATTEMPT_TIMESTAMP__FIELD_NAME = WrapperField("ATTEMPT_TIMESTAMP", FieldType.DATE)
+    EXECUTION_GUID__FIELD_NAME = WrapperField("EXECUTION_GUID", FieldType.STRING)
+    GUID__FIELD_NAME = WrapperField("GUID", FieldType.STRING)
+    RESPONSE_BODY__FIELD_NAME = WrapperField("RESPONSE_BODY", FieldType.STRING)
+    RESPONSE_CODE__FIELD_NAME = WrapperField("RESPONSE_CODE", FieldType.INTEGER)
+    WEBHOOK_GUID__FIELD_NAME = WrapperField("WEBHOOK_GUID", FieldType.STRING)
+    WEBHOOK_URL__FIELD_NAME = WrapperField("WEBHOOK_URL", FieldType.STRING)
+
+
+class VeloxWebhookExecutionLogPseudoDef:
+    DATA_TYPE_NAME: str = "VELOXWEBHOOK_EXECUTION_LOG"
+    ATTEMPT_GUID__FIELD_NAME = WrapperField("ATTEMPT_GUID", FieldType.STRING)
+    LOG_LEVEL__FIELD_NAME = WrapperField("LOG_LEVEL", FieldType.STRING)
+    LOG_LINE_NUM__FIELD_NAME = WrapperField("LOG_LINE_NUM", FieldType.INTEGER)
+    LOG_MESSAGE__FIELD_NAME = WrapperField("LOG_MESSAGE", FieldType.STRING)
+    LOG_TIMESTAMP__FIELD_NAME = WrapperField("LOG_TIMESTAMP", FieldType.DATE)
+
+
+class VeloxRuleCostPseudoDef:
+    DATA_TYPE_NAME: str = "VELOX_RULE_COST"
+    ACTION_COST__FIELD_NAME = WrapperField("ACTION_COST", FieldType.LONG)
+    ACTION_COUNT__FIELD_NAME = WrapperField("ACTION_COUNT", FieldType.LONG)
+    ANCESTOR_DESCENDANT_COUNT__FIELD_NAME = WrapperField("ANCESTOR_DESCENDANT_COUNT", FieldType.LONG)
+    PARENT_CHILD_COUNT__FIELD_NAME = WrapperField("PARENT_CHILD_COUNT", FieldType.LONG)
+    PROCESSING_TIME__FIELD_NAME = WrapperField("PROCESSING_TIME", FieldType.LONG)
+    RULE_GUID__FIELD_NAME = WrapperField("RULE_GUID", FieldType.STRING)
+    SOURCE_RECORD_COUNT__FIELD_NAME = WrapperField("SOURCE_RECORD_COUNT", FieldType.LONG)
+    TIMESTAMP__FIELD_NAME = WrapperField("TIMESTAMP", FieldType.DATE)
+    TOTAL_COST__FIELD_NAME = WrapperField("TOTAL_COST", FieldType.LONG)
+    TRANSACTION_GUID__FIELD_NAME = WrapperField("TRANSACTION_GUID", FieldType.STRING)
+    USERNAME__FIELD_NAME = WrapperField("USERNAME", FieldType.STRING)
+
+
+class VeloxConversationPseudoDef:
+    DATA_TYPE_NAME: str = "VeloxConversation"
+    CONVERSATION_DESCRIPTION__FIELD_NAME = WrapperField("ConversationDescription", FieldType.STRING)
+    CONVERSATION_GUID__FIELD_NAME = WrapperField("ConversationGuid", FieldType.STRING)
+    CONVERSATION_NAME__FIELD_NAME = WrapperField("ConversationName", FieldType.STRING)
+    CREATED_BY__FIELD_NAME = WrapperField("CreatedBy", FieldType.STRING)
+    DATE_CREATED__FIELD_NAME = WrapperField("DateCreated", FieldType.DATE)
+    SERVER_PLUGIN_PATH__FIELD_NAME = WrapperField("Server_Plugin_Path", FieldType.STRING)
+
+
+class VeloxConversationMessagePseudoDef:
+    DATA_TYPE_NAME: str = "VeloxConversationMessage"
+    CONVERSATION_GUID__FIELD_NAME = WrapperField("ConversationGuid", FieldType.STRING)
+    MESSAGE__FIELD_NAME = WrapperField("Message", FieldType.STRING)
+    MESSAGE_GUID__FIELD_NAME = WrapperField("MessageGuid", FieldType.STRING)
+    MESSAGE_SENDER__FIELD_NAME = WrapperField("MessageSender", FieldType.STRING)
+    MESSAGE_TIMESTAMP__FIELD_NAME = WrapperField("MessageTimestamp", FieldType.DATE)
+
+
+class VeloxScriptPseudoDef:
+    DATA_TYPE_NAME: str = "VeloxScript"
+    CODE__FIELD_NAME = WrapperField("Code", FieldType.STRING)
+    CREATED_BY__FIELD_NAME = WrapperField("CreatedBy", FieldType.STRING)
+    DATE_CREATED__FIELD_NAME = WrapperField("DateCreated", FieldType.LONG)
+    LAST_MODIFIED_BY__FIELD_NAME = WrapperField("LastModifiedBy", FieldType.STRING)
+    LAST_MODIFIED_DATE__FIELD_NAME = WrapperField("LastModifiedDate", FieldType.LONG)
+    PATH__FIELD_NAME = WrapperField("Path", FieldType.STRING)
+    PLUGIN_DESCRIPTION__FIELD_NAME = WrapperField("PluginDescription", FieldType.STRING)
+    PLUGIN_LINE1_TEXT__FIELD_NAME = WrapperField("PluginLine1Text", FieldType.STRING)
+    PLUGIN_LINE2_TEXT__FIELD_NAME = WrapperField("PluginLine2Text", FieldType.STRING)
+    PLUGIN_ORDER__FIELD_NAME = WrapperField("PluginOrder", FieldType.INTEGER)
+    PLUGIN_POINT__FIELD_NAME = WrapperField("PluginPoint", FieldType.STRING)
+    PROJECT_GUID__FIELD_NAME = WrapperField("ProjectGuid", FieldType.STRING)
+    SCRIPT_GUID__FIELD_NAME = WrapperField("ScriptGuid", FieldType.STRING)
+
+
+class VeloxScriptProjectPseudoDef:
+    DATA_TYPE_NAME: str = "VeloxScriptProject"
+    CLASS_PATH__FIELD_NAME = WrapperField("ClassPath", FieldType.STRING)
+    CREATED_BY__FIELD_NAME = WrapperField("CreatedBy", FieldType.STRING)
+    DATE_CREATED__FIELD_NAME = WrapperField("DateCreated", FieldType.LONG)
+    DEPLOYMENT_OUT_OF_DATE__FIELD_NAME = WrapperField("DeploymentOutOfDate", FieldType.BOOLEAN)
+    DESCRIPTION__FIELD_NAME = WrapperField("Description", FieldType.STRING)
+    PROJECT_GUID__FIELD_NAME = WrapperField("ProjectGuid", FieldType.STRING)
+    PROJECT_NAME__FIELD_NAME = WrapperField("ProjectName", FieldType.STRING)
+    SCRIPT_LANGUAGE__FIELD_NAME = WrapperField("ScriptLanguage", FieldType.STRING)
+
+
+class WorkflowPseudoDef:
+    DATA_TYPE_NAME: str = "Workflow"
+    ALL_ACCESS__FIELD_NAME = WrapperField("AllAccess", FieldType.BOOLEAN)
+    CATEGORY__FIELD_NAME = WrapperField("Category", FieldType.STRING)
+    CREATED_BY__FIELD_NAME = WrapperField("CreatedBy", FieldType.STRING)
+    DATE_CREATED__FIELD_NAME = WrapperField("DateCreated", FieldType.DATE)
+    DATE_EDITED__FIELD_NAME = WrapperField("DateEdited", FieldType.DATE)
+    DIRECT_LAUNCH__FIELD_NAME = WrapperField("DirectLaunch", FieldType.BOOLEAN)
+    EDITED_BY__FIELD_NAME = WrapperField("EditedBy", FieldType.STRING)
+    IS_TEMPLATE__FIELD_NAME = WrapperField("IsTemplate", FieldType.BOOLEAN)
+    LONG_DESC__FIELD_NAME = WrapperField("LongDesc", FieldType.STRING)
+    NAME__FIELD_NAME = WrapperField("Name", FieldType.STRING)
+    SHORT_DESC__FIELD_NAME = WrapperField("ShortDesc", FieldType.STRING)
+    WORKFLOW_ID__FIELD_NAME = WrapperField("WorkflowId", FieldType.LONG)
+    WORKFLOW_VERSION__FIELD_NAME = WrapperField("WorkflowVersion", FieldType.LONG)
+
+
+class WorkflowOptionPseudoDef:
+    DATA_TYPE_NAME: str = "WorkflowOption"
+    OPTION_KEY__FIELD_NAME = WrapperField("OptionKey", FieldType.STRING)
+    OPTION_VALUE__FIELD_NAME = WrapperField("OptionValue", FieldType.STRING)
+    WORKFLOW_ID__FIELD_NAME = WrapperField("WorkflowId", FieldType.LONG)

{sapiopycommons-2024.10.24a342 → sapiopycommons-2024.10.25a345}/src/sapiopycommons/eln/experiment_handler.py

@@ -23,6 +23,7 @@ from sapiopylib.rest.utils.recordmodel.RecordModelManager import RecordModelInst
 from sapiopylib.rest.utils.recordmodel.RecordModelWrapper import WrappedType
 from sapiopylib.rest.utils.recordmodel.properties import Child
 
+from sapiopycommons.eln.experiment_report_util import ExperimentReportUtil
 from sapiopycommons.general.aliases import AliasUtil, SapioRecord, ExperimentIdentifier, UserIdentifier, \
     DataTypeIdentifier, RecordModel
 from sapiopycommons.general.exceptions import SapioException
@@ -67,9 +68,9 @@ class ExperimentHandler:
     """Whether this ExperimentHandler has queried the system for all steps in the experiment."""
     __steps: dict[str, ElnEntryStep]
     """Steps from this experiment. All steps are cached the first time any individual step is accessed."""
-    __step_options: dict[ElnEntryStep, dict[str, str]]
-    """Entry options for each step in this experiment. Only cached for each individual step when they are first accessed.
-    The cache is updated whenever the entry options for a step are changed by this handler."""
+    __step_options: dict[int, dict[str, str]]
+    """Entry options for each step in this experiment. All entry options are cached the first time any individual step's
+    options are queried. The cache is updated whenever the entry options for a step are changed by this handler."""
 
     # Constants
     __ENTRY_COMPLETE_STATUSES = [ExperimentEntryStatus.Completed, ExperimentEntryStatus.CompletedApproved]
@@ -549,6 +550,39 @@ class ExperimentHandler:
         data_type: str = AliasUtil.to_data_type_name(data_type)
         return [x for x in all_steps if data_type in x.get_data_type_names()]
 
+    def get_step_by_option(self, key: str, value: str | None = None) -> ElnEntryStep:
+        """
+        Retrieve the step in this experiment that contains an entry option with the provided key and value.
+        Throws an exception if no entries or multiple entries in the experiment match.
+
+        :param key: The key of the entry option to match on.
+        :param value: The value of the entry option to match on. If not provided, then only matches on key.
+        :return: The entry in this experiment that matches the provided entry option key and value.
+        """
+        steps: list[ElnEntryStep] = self.get_steps_by_option(key, value)
+        count: int = len(steps)
+        if count != 1:
+            option = key + ("::" + value if value is not None else "")
+            raise SapioException(f"{('No' if count == 0 else 'Multiple')} entries in this experiment match the "
+                                 f"provided option: {option}")
+        return steps[0]
+
+    def get_steps_by_option(self, key: str, value: str | None = None) -> list[ElnEntryStep]:
+        """
+        Retrieve every step in this experiment that contains an entry option with the provided key and value.
+
+        :param key: The key of the entry option to match on.
+        :param value: The value of the entry option to match on. If not provided, then only matches on key.
+        :return: The entries in this experiment that match the provided entry option key and value.
+        """
+        ret_list: list[ElnEntryStep] = []
+        for step in self.get_all_steps():
+            options: dict[str, str] = self.get_step_options(step)
+            if key in options:
+                if value is None or options[key] == value:
+                    ret_list.append(step)
+        return ret_list
+
     def get_step_records(self, step: Step) -> list[DataRecord]:
         """
         Query for the data records for the given step. The returned records are not cached by the ExperimentHandler.
@@ -966,7 +1000,7 @@ class ExperimentHandler:
         if clear_template_item_fulfilled_timestamp is True:
             entry.template_item_fulfilled_timestamp = None
         if entry_options_map is not None:
-            self.__step_options.update({step: entry_options_map})
+            self.__step_options.update({step.get_id(): entry_options_map})
 
     def get_step_option(self, step: Step, option: str) -> str:
         """
@@ -996,8 +1030,8 @@ class ExperimentHandler:
         list of steps in the experiment and caches them.
 
         Getting the step options requires a webservice query, which is made the first time any step option
-        method is called for a specific step. The step options are cached so that subsequent calls of this
-        method for that step don't make a webservice call.
+        method is called for any step in this experiment. The step options are cached so that subsequent calls of this
+        method don't make a webservice call.
 
         :param step:
             The step to get the options of.
@@ -1005,7 +1039,10 @@ class ExperimentHandler:
             If given a name, throws an exception if no step of the given name exists in the experiment.
         :return: The map of options for the input step.
         """
-        return self.__get_step_options(step)
+        step = self.__to_eln_step(step)
+        if step not in self.__step_options:
+            self.__step_options.update(ExperimentReportUtil.get_experiment_entry_options(self.user, self.get_all_steps()))
+        return self.__step_options[step.get_id()]
 
     def add_step_options(self, step: Step, mapping: Mapping[str, str]):
         """
@@ -1175,16 +1212,3 @@ class ExperimentHandler:
             return self.__exp_options
         self.__exp_options = self.__eln_man.get_notebook_experiment_options(self.__exp_id)
         return self.__exp_options
-
-    def __get_step_options(self, step: Step) -> dict[str, str]:
-        """
-        Cache the options for the input step if they haven't been cached yet.
-
-        :return: The entry options for the input step.
-        """
-        step = self.__to_eln_step(step)
-        if step in self.__step_options:
-            return self.__step_options.get(step)
-        options: dict[str, str] = step.get_options()
-        self.__step_options.update({step: options})
-        return options