sapiopycommons 2024.6.11a252__tar.gz → 2024.6.18a254__tar.gz

{sapiopycommons-2024.6.11a252 → sapiopycommons-2024.6.18a254}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: sapiopycommons
-Version: 2024.6.11a252
+Version: 2024.6.18a254
 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-2024.6.11a252 → sapiopycommons-2024.6.18a254}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "sapiopycommons"
-version='2024.06.11a252'
+version='2024.06.18a254'
 authors = [
     { name="Jonathan Steck", email="jsteck@sapiosciences.com" },
     { name="Yechen Qiao", email="yqiao@sapiosciences.com" },

{sapiopycommons-2024.6.11a252 → sapiopycommons-2024.6.18a254}/src/sapiopycommons/multimodal/multimodal.py

@@ -46,19 +46,6 @@ class MultiModalManager:
         self._user.raise_for_status(response)
         return response.json()
 
-    def register_interactively(self, request: ChemInteractiveRegisterRequestPojo):
-        """
-        Prompt user interactively to load the provided file data.
-        User will be able to select or define a field map for the assay data included.
-        User will also be able to define which one is the SMILES column if csv.
-        """
-        # TODO pending client_callback enablement on the webhook => webservice endpoint route.
-        payload = dumps(request, ChemInteractiveRegisterRequestPojo)
-        response = self._user.plugin_post("chemistry/register_interactively",
-                                          payload=payload, is_payload_plain_text=True)
-        self._user.raise_for_status(response)
-        return loads(response.text, ChemCompleteImportPojo)
-
     def load_compounds(self, request: CompoundLoadRequestPojo):
         """
         Load compounds from the provided data here.

{sapiopycommons-2024.6.11a252 → sapiopycommons-2024.6.18a254}/src/sapiopycommons/multimodal/multimodal_data.py

@@ -56,18 +56,6 @@ class PyCompound:
     props: dict[str, object] | None
 
 
-class ChemDataType(Enum):
-    CompoundPart = 'CompoundPart'
-    ChemicalReagentPart = 'ChemicalReagentPart'
-
-    def __init__(self, data_type_name: str):
-        self._data_type_name = data_type_name
-
-    @property
-    def data_type_name(self):
-        return self._data_type_name
-
-
 class ChemFileType(Enum):
     CSV = 0
     SDF = 1
@@ -133,12 +121,12 @@ class ChemCompleteImportPojo:
 
 @dataclass
 class ChemInteractiveRegisterRequestPojo:
-    dataType: ChemDataType
+    dataType: str
     fileType: ChemFileType
     fileDataEncodedBase64: str | None
     addingItems: bool
 
-    def __init__(self, data_type: ChemDataType, file_type: ChemFileType, is_adding_items: bool, file_data: bytes):
+    def __init__(self, data_type: str, file_type: ChemFileType, is_adding_items: bool, file_data: bytes):
         self.dataType = data_type
         self.fileType = file_type
         self.addingItems = is_adding_items
@@ -156,12 +144,12 @@ class CompoundLoadRequestPojo:
         dataList: If the source data is not a file, here you specify a list of string describing molecule for that src.
         fileDataBase64: If the source data is a file, the file's base64 data content.
     """
-    dataType: ChemDataType
+    dataType: str
     loadType: ChemLoadType
     dataList: list[str] | None
     fileDataBase64: str | None
 
-    def __init__(self, data_type: ChemDataType, load_type: ChemLoadType, data_list: list[str] | None = None,
+    def __init__(self, data_type: str, load_type: ChemLoadType, data_list: list[str] | None = None,
                  file_data: bytes | None = None):
         self.dataType = data_type
         self.loadType = load_type
@@ -184,10 +172,10 @@ class ChemRegisterRequestPojo:
         dataType: The data type of records to be registered in Sapio.
         registrationList: This list must be of correct data structure suitable for the type. For example, for CompoundPart data type the canonical form must be resolved by earlier call.
     """
-    dataType: ChemDataType
+    dataType: str
     registrationList: list[PyCompound]
 
-    def __init__(self, data_type: ChemDataType, registration_list: list[PyCompound]):
+    def __init__(self, data_type: str, registration_list: list[PyCompound]):
         self.dataType = data_type
         self.registrationList = registration_list
 
@@ -228,16 +216,6 @@ class PyIndigoReactionPojo:
     reactionRenderRxn: str
 
 
-class CartridgeMolJoinMethod(Enum):
-    """
-    The structure search join method to filter results against Sapio registry.
-    Since we have multiple registries in Sapio, you will need to specify which one to join against.
-    """
-    COMPOUND_REGISTRY = 0
-    REAGENT_REGISTRY = 1
-    HELM_STRUCTURE = 2
-
-
 @dataclass
 class ChemQuickSearchContextData:
     """
@@ -250,7 +228,7 @@ class ChemQuickSearchContextData:
     nextPageSearchAfter: str | None
     pitId: str | None
     query: str | None
-    joinMethod: CartridgeMolJoinMethod | None
+    joinSapioPartType: str | None
     simUpperLimit: float | None
 
 
@@ -269,11 +247,11 @@ class ChemSearchRequestPojo:
     """
     searchStr: str
     searchType: ChemSearchType
-    joinMethod: CartridgeMolJoinMethod | None
+    joinSapioType: str | None
     contextData: ChemQuickSearchContextData | None
     simSearchUpperLimit: float | None
 
-    def __init__(self, search_str: str, search_type: ChemSearchType, join_method: CartridgeMolJoinMethod | None = None,
+    def __init__(self, search_str: str, search_type: ChemSearchType, join_method: str | None = None,
                  context_data: ChemQuickSearchContextData | None = None, sim_search_upper: float | None = None):
         self.searchStr = search_str
         self.searchType = search_type