sapiopycommons 2024.6.24a263__tar.gz → 2024.6.24a265__tar.gz

{sapiopycommons-2024.6.24a263 → sapiopycommons-2024.6.24a265}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: sapiopycommons
-Version: 2024.6.24a263
+Version: 2024.6.24a265
 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-2024.6.24a263 → sapiopycommons-2024.6.24a265}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "sapiopycommons"
-version='2024.06.24a263'
+version='2024.06.24a265'
 authors = [
     { name="Jonathan Steck", email="jsteck@sapiosciences.com" },
     { name="Yechen Qiao", email="yqiao@sapiosciences.com" },

{sapiopycommons-2024.6.24a263 → sapiopycommons-2024.6.24a265}/src/sapiopycommons/callbacks/callback_util.py

@@ -14,8 +14,8 @@ from sapiopylib.rest.pojo.datatype.FieldDefinition import AbstractVeloxFieldDefi
     VeloxIntegerFieldDefinition, VeloxDoubleFieldDefinition, FieldDefinitionParser
 from sapiopylib.rest.pojo.webhook.ClientCallbackRequest import OptionDialogRequest, ListDialogRequest, \
     FormEntryDialogRequest, InputDialogCriteria, TableEntryDialogRequest, ESigningRequestPojo, \
-    DataRecordSelectionRequest, DataRecordDialogRequest, InputSelectionRequest, FilePromptRequest, \
-    MultiFilePromptRequest
+    DataRecordDialogRequest, InputSelectionRequest, FilePromptRequest, MultiFilePromptRequest, \
+    TempTableSelectionRequest
 from sapiopylib.rest.pojo.webhook.ClientCallbackResult import ESigningResponsePojo
 from sapiopylib.rest.pojo.webhook.WebhookContext import SapioWebhookContext
 from sapiopylib.rest.pojo.webhook.WebhookEnums import FormAccessLevel, ScanToSelectCriteria, SearchType
@@ -627,7 +627,8 @@ class CallbackUtil:
                          values: list[FieldMap],
                          multi_select: bool = True,
                          *,
-                         display_name: str = "Default",
+                         data_type: str = "Default",
+                         display_name: str | None = None,
                          plural_display_name: str | None = None) -> list[FieldMap]:
         """
         Create a selection dialog for a list of field maps for the user to choose from. Requires that the caller
@@ -638,18 +639,25 @@ class CallbackUtil:
             they are provided in this list.
         :param values: The values to set for each row of the table.
         :param multi_select: Whether the user is able to select multiple rows from the list.
-        :param display_name: The display name for the temporary data type that will be created.
+        :param data_type: The data type name for the temporary data type that will be created for this table.
+        :param display_name: The display name for the temporary data type. If not provided, defaults to the data type
+            name.
         :param plural_display_name: The plural display name for the temporary data type. If not provided, defaults to
             the display name + "s".
         :return: A list of field maps corresponding to the chosen input field maps.
         """
+        if display_name is None:
+            display_name = data_type
         if plural_display_name is None:
             plural_display_name = display_name + "s"
 
-        # Build the form using only those fields that are desired.
-        request = DataRecordSelectionRequest(display_name, plural_display_name,
-                                             fields, values, msg, multi_select)
-        response: list[FieldMap] | None = self.callback.show_data_record_selection_dialog(request)
+        builder = FormBuilder(data_type, display_name, plural_display_name)
+        for field in fields:
+            builder.add_field(field)
+
+        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)
         if response is None:
             raise SapioUserCancelledException()
         return response
@@ -690,16 +698,16 @@ class CallbackUtil:
         modifier = FieldModifier(visible=True, key_field=False)
 
         # Build the form using only those fields that are desired.
-        field_def_list: list = []
+        builder = FormBuilder(data_type, type_def.display_name, type_def.plural_display_name)
         for field_name in fields:
             field_def = field_defs.get(field_name)
             if field_def is None:
                 raise SapioException(f"No field of name \"{field_name}\" in field definitions of type \"{data_type}\"")
-            field_def_list.append(modifier.modify_field(field_def))
+            builder.add_field(modifier.modify_field(field_def))
 
-        request = DataRecordSelectionRequest(type_def.display_name, type_def.plural_display_name,
-                                             field_def_list, field_map_list, msg, multi_select)
-        response: list[FieldMap] | None = self.callback.show_data_record_selection_dialog(request)
+        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)
         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

{sapiopycommons-2024.6.24a263 → sapiopycommons-2024.6.24a265}/src/sapiopycommons/multimodal/multimodal_data.py

@@ -251,11 +251,11 @@ class ChemSearchRequestPojo:
     contextData: ChemQuickSearchContextData | None
     simSearchUpperLimit: float | None
 
-    def __init__(self, search_str: str, search_type: ChemSearchType, join_method: str | None = None,
+    def __init__(self, search_str: str, search_type: ChemSearchType, join_sapio_type: str | None = None,
                  context_data: ChemQuickSearchContextData | None = None, sim_search_upper: float | None = None):
         self.searchStr = search_str
         self.searchType = search_type
-        self.joinMethod = join_method
+        self.joinSapioType = join_sapio_type
         self.contextData = context_data
         self.simSearchUpperLimit = sim_search_upper
 

{sapiopycommons-2024.6.24a263 → sapiopycommons-2024.6.24a265}/tests/chem_test.py

@@ -1,6 +1,6 @@
 # Add facilities to test chemistry endpoints. This will run its own webserver.
 # These testing will require working with a server with chemistry license and is set up with chemistry correctly.
-from io import StringIO, BytesIO
+from io import BytesIO
 
 from sapiopylib.rest.ClientCallbackService import ClientCallback
 from sapiopylib.rest.DataMgmtService import DataMgmtServer
@@ -11,31 +11,30 @@ from sapiopylib.rest.pojo.webhook.ClientCallbackRequest import *
 from sapiopylib.rest.pojo.webhook.WebhookContext import SapioWebhookContext
 from sapiopylib.rest.pojo.webhook.WebhookResult import SapioWebhookResult
 from sapiopylib.rest.utils.autopaging import QueryDataRecordByIdListAutoPager
-from sapiopylib.rest.utils.recorddatasinks import InMemoryRecordDataSink
 
 from data_type_models import *
 from sapiopycommons.multimodal.multimodal import MultiModalManager
 from sapiopycommons.multimodal.multimodal_data import *
 
 
-def __select_type_and_item_to_load(client_callback: ClientCallback) -> tuple[ChemDataType, bool]:
+def __select_type_and_item_to_load(client_callback: ClientCallback) -> tuple[str, bool]:
     options = ["Compound Parts", "Compound Samples", "Chem Reagent Parts", "Chem Reagent Samples"]
     selected = client_callback.show_option_dialog(OptionDialogRequest(
         "Select Item Type", "Select one of the following item types that correspond to what you are registering",
         options))
-    data_type: ChemDataType
+    data_type: str
     is_adding_items: bool
     if selected == 0:
-        data_type = ChemDataType.CompoundPart
+        data_type = CompoundPartModel.DATA_TYPE_NAME
         is_adding_items = False
     elif selected == 1:
-        data_type = ChemDataType.CompoundPart
+        data_type = CompoundPartModel.DATA_TYPE_NAME
         is_adding_items = True
     elif selected == 2:
-        data_type = ChemDataType.ChemicalReagentPart
+        data_type = ChemicalReagentPartModel.DATA_TYPE_NAME
         is_adding_items = False
     elif selected == 3:
-        data_type = ChemDataType.ChemicalReagentPart
+        data_type = ChemicalReagentPartModel.DATA_TYPE_NAME
         is_adding_items = True
     else:
         raise ValueError("Invalid selection index: " + str(selected))
@@ -61,34 +60,6 @@ def download_chem_image(context: SapioWebhookContext) -> SapioWebhookResult:
     return SapioWebhookResult(True)
 
 
-def register_interactively(context: SapioWebhookContext) -> SapioWebhookResult:
-    """
-    Load an SDF file, provide error report back to the caller, and then let user pick the field mapping like loading from material management.
-    """
-    # TODO pending client_callback enablement on the webhook => webservice endpoint route.
-    user = context.user
-    client_callback = DataMgmtServer.get_client_callback(user)
-    data_type, is_adding_items = __select_type_and_item_to_load(client_callback)
-
-    data_sink = InMemoryRecordDataSink(user)
-    data_sink.upload_single_file_to_webhook_server(FilePromptRequest("Upload SDF File Data", file_extension=".sdf"))
-
-    reg_man = MultiModalManager(user)
-    reg_result: ChemCompleteImportPojo = reg_man.register_interactively(
-        ChemInteractiveRegisterRequestPojo(data_type, ChemFileType.SDF, is_adding_items, data_sink.data))
-    if not reg_result:
-        client_callback.display_warning("Registration incomplete.")
-        return SapioWebhookResult(False)
-    if reg_result.errors:
-        for error in reg_result.errors:
-            client_callback.display_warning(
-                "Item with properties " + str(error.properties) + "cannot be registered: " + str(error.errorMsg))
-    client_callback.display_info(
-        "Successfully registered " + str(len(reg_result.newPartList)) + " new parts and used " + str(
-            reg_result.numOldParts) + " old parts in this registration.")
-    return SapioWebhookResult(True)
-
-
 def register_non_interactively(context: SapioWebhookContext) -> SapioWebhookResult:
     """
     Without asking user for anything in between the registration,
@@ -152,17 +123,19 @@ def structure_search(context: SapioWebhookContext) -> SapioWebhookResult:
         "Enter the SMARTS for compound substructure search or SMILES for compound similarity search, "
         "or rSMARTS for reaction substructure search."))
 
-    join_method: CartridgeMolJoinMethod | None = None
+    join_sapio_type: str
     if search_type is ChemSearchType.COMPOUND_SUBSTRUCTURE or search_type is ChemSearchType.COMPOUND_SIMILARITY:
         option = client_callback.show_option_dialog(OptionDialogRequest(
             "Select Join Type", "Select a Sapio registry type you are joining result with.",
             ["Compounds", "Chemical Reagants", "HELM Chemical Properties"]))
         if option == 0:
-            join_method = CartridgeMolJoinMethod.COMPOUND_REGISTRY
+            join_sapio_type = CompoundPartModel.DATA_TYPE_NAME
         elif option == 1:
-            join_method = CartridgeMolJoinMethod.REAGENT_REGISTRY
+            join_sapio_type = ChemicalReagentPartModel.DATA_TYPE_NAME
         else:
-            join_method = CartridgeMolJoinMethod.HELM_STRUCTURE
+            join_sapio_type = HelmChemPropertyModel.DATA_TYPE_NAME
+    else:
+        join_sapio_type = ReactionModel.DATA_TYPE_NAME
     sim_search_upper: float | None = None
     if search_type is ChemSearchType.COMPOUND_SIMILARITY:
         field_def = VeloxDoubleFieldDefinition("Upper", "Upper", "Upper",
@@ -177,24 +150,10 @@ def structure_search(context: SapioWebhookContext) -> SapioWebhookResult:
         return SapioWebhookResult(False)
     reg_man = MultiModalManager(user)
     dt_man = DataTypeManager(user)
-    temp_dt: TemporaryDataType
-    if search_type is ChemSearchType.REACTION_SUBSTRUCTURE:
-        temp_dt: TemporaryDataType = dt_man.get_temporary_data_type(ReactionModel.DATA_TYPE_NAME)
-    elif join_method is CartridgeMolJoinMethod.COMPOUND_REGISTRY:
-        temp_dt: TemporaryDataType = dt_man.get_temporary_data_type(CompoundPartModel.DATA_TYPE_NAME)
-    elif join_method is CartridgeMolJoinMethod.REAGENT_REGISTRY:
-        temp_dt: TemporaryDataType = dt_man.get_temporary_data_type(ChemicalReagentPartModel.DATA_TYPE_NAME)
-    elif join_method is CartridgeMolJoinMethod.HELM_STRUCTURE:
-        temp_dt: TemporaryDataType = dt_man.get_temporary_data_type(HelmChemPropertyModel.DATA_TYPE_NAME)
-    else:
-        raise ValueError("Unable to obtain temp type to display???")
+    temp_dt: TemporaryDataType = dt_man.get_temporary_data_type(join_sapio_type)
     while True:
         search_result = reg_man.search_structures(
-            ChemSearchRequestPojo(query, search_type, join_method, next_page_context, sim_search_upper))
-        if not search_result.nextPageAvailable:
-            client_callback.display_info("Hit End of Results. No further pages available.")
-            return SapioWebhookResult(True)
-        next_page_context = search_result.nextPageContext
+            ChemSearchRequestPojo(query, search_type, join_sapio_type, next_page_context, sim_search_upper))
         if search_result.recordIdListOfPage:
             records: list[DataRecord] = QueryDataRecordByIdListAutoPager(
                 temp_dt.data_type_name, search_result.recordIdListOfPage, user).get_all_at_once()
@@ -204,6 +163,11 @@ def structure_search(context: SapioWebhookContext) -> SapioWebhookResult:
             client_callback.display_popup(DisplayPopupRequest(
                 "No Results in Page", "This page may not contain any results. Good luck next time!",
                 PopupType.Info))
+        if not search_result.nextPageAvailable:
+            client_callback.display_info("Hit End of Results. No further pages available.")
+            return SapioWebhookResult(True)
+        next_page_context = search_result.nextPageContext
+
         selected = client_callback.show_option_dialog(OptionDialogRequest("Continue?", "Continue to next page?", ["Yes", "No"]))
         if selected is None or selected != 0:
             return SapioWebhookResult(True)
@@ -215,7 +179,7 @@ class ChemistryRegistrationTestHandler(AbstractWebhookHandler):
     """
 
     def run(self, context: SapioWebhookContext) -> SapioWebhookResult:
-        options = ['Download Image', 'Register Interactively', 'Register Non-Interactively', 'Structure Search',
+        options = ['Download Image', 'Register Non-Interactively', 'Structure Search',
                    'Register Reaction']
         user = context.user
         client_callback = DataMgmtServer.get_client_callback(user)
@@ -226,12 +190,10 @@ class ChemistryRegistrationTestHandler(AbstractWebhookHandler):
         if selected == 0:
             return download_chem_image(context)
         elif selected == 1:
-            return register_interactively(context)
-        elif selected == 2:
             return register_non_interactively(context)
-        elif selected == 3:
+        elif selected == 2:
             return structure_search(context)
-        elif selected == 4:
+        elif selected == 3:
             return register_reaction(context)
         return SapioWebhookResult(False)