feat: implant part mapping (#216)

AllenNeuralDynamics · Apr 4, 2024 · 149ced3 · 149ced3
1 parent 8b085f3
commit 149ced3
Show file tree

Hide file tree

Showing 8 changed files with 17 additions and 37 deletions.
diff --git a/src/aind_metadata_service/sharepoint/client.py b/src/aind_metadata_service/sharepoint/client.py
@@ -240,9 +240,9 @@ def _merge_two_responses(
             )
         else:
             left_procedures: List[Procedures] = left_model_response.aind_models
-            right_procedures: List[Procedures] = (
-                right_model_response.aind_models
-            )
+            right_procedures: List[
+                Procedures
+            ] = right_model_response.aind_models
             procedures = self._merge_procedures(
                 left_procedures=left_procedures,
                 right_procedures=right_procedures,

diff --git a/src/aind_metadata_service/sharepoint/nsb2023/mapping.py b/src/aind_metadata_service/sharepoint/nsb2023/mapping.py
@@ -1983,29 +1983,7 @@ def aind_implant_id_coverslip_type(self) -> Optional[Any]:
         return (
             None
             if self._nsb.implant_id_coverslip_type is None
-            else {
-                self._nsb.implant_id_coverslip_type.SELECT: None,
-                self._nsb.implant_id_coverslip_type.N_2001: None,
-                self._nsb.implant_id_coverslip_type.N_2002: None,
-                self._nsb.implant_id_coverslip_type.N_2004: None,
-                self._nsb.implant_id_coverslip_type.N_2005: None,
-                self._nsb.implant_id_coverslip_type.N_2006: None,
-                self._nsb.implant_id_coverslip_type.N_2007: None,
-                self._nsb.implant_id_coverslip_type.N_2008: None,
-                self._nsb.implant_id_coverslip_type.N_2009: None,
-                self._nsb.implant_id_coverslip_type.N_2010: None,
-                self._nsb.implant_id_coverslip_type.N_2011: None,
-                self._nsb.implant_id_coverslip_type.N_3001: None,
-                self._nsb.implant_id_coverslip_type.N_3002: None,
-                self._nsb.implant_id_coverslip_type.N_3003: None,
-                self._nsb.implant_id_coverslip_type.N_3004: None,
-                self._nsb.implant_id_coverslip_type.N_3004_25_PURALUBESYSTANE: None,
-                self._nsb.implant_id_coverslip_type.N_3005: None,
-                self._nsb.implant_id_coverslip_type.WHC_2_P_CURVED_GLASS_WITH: None,
-                self._nsb.implant_id_coverslip_type.N_3MM_STACKED_COVERSLIP: None,
-                self._nsb.implant_id_coverslip_type.N_5MM_STACKED_COVERSLIP: None,
-                self._nsb.implant_id_coverslip_type.N_5MM_STACKED_COVERSLIP_W: None,
-            }.get(self._nsb.implant_id_coverslip_type, None)
+            else self._nsb.implant_id_coverslip_type
         )
 
     @property
@@ -3627,6 +3605,7 @@ def get_procedure(self) -> List[Surgery]:
             cran_during = self.aind_craniotomy_perform_d
             cran_during_info = self.surgery_during_info(cran_during)
             bregma_to_lambda_distance = self.aind_breg2_lamb
+            implant_part_number = self.aind_implant_id_coverslip_type
             if craniotomy_type == CraniotomyType.FIVE_MM:
                 craniotomy_coordinates_reference = (
                     CoordinateReferenceLocation.LAMBDA
@@ -3647,6 +3626,7 @@ def get_procedure(self) -> List[Surgery]:
                 craniotomy_coordinates_reference=(
                     craniotomy_coordinates_reference
                 ),
+                implant_part_number=implant_part_number,
             )
             headpost_info = HeadPostInfo.from_hp_and_hp_type(
                 hp=self.aind_headpost, hp_type=self.aind_headpost_type

diff --git a/src/aind_metadata_service/smartsheet/protocols/mapping.py b/src/aind_metadata_service/smartsheet/protocols/mapping.py
@@ -81,10 +81,10 @@ def _get_protocol_list(
         """
         rows_associated_with_protocol_name: List[ProtocolInformation] = []
         for row in self.model.rows:
-            opt_protocol: Optional[ProtocolInformation] = (
-                self._map_row_to_protocol(
-                    row=row, input_protocol_name=protocol_name
-                )
+            opt_protocol: Optional[
+                ProtocolInformation
+            ] = self._map_row_to_protocol(
+                row=row, input_protocol_name=protocol_name
             )
             if opt_protocol is not None:
                 rows_associated_with_protocol_name.append(opt_protocol)

diff --git a/src/aind_metadata_service/tars/mapping.py b/src/aind_metadata_service/tars/mapping.py
@@ -265,9 +265,9 @@ def integrate_injection_materials(
                                     new_material.titer = (
                                         injection_material.titer
                                     )
-                                    procedure.injection_materials[idx] = (
-                                        new_material
-                                    )
+                                    procedure.injection_materials[
+                                        idx
+                                    ] = new_material
                                 elif (
                                     tars_response.status_code
                                     == StatusCodes.NO_DATA_FOUND.value

diff --git a/tests/resources/sharepoint/nsb2023/mapped/mapped_list_item10.json b/tests/resources/sharepoint/nsb2023/mapped/mapped_list_item10.json
@@ -26,7 +26,7 @@
         "craniotomy_coordinates_unit": "millimeter",
         "bregma_to_lambda_unit": "millimeter",
         "craniotomy_size_unit": "millimeter",
-        "implant_part_number": null,
+        "implant_part_number": "3mm stacked coverslip",
         "dura_removed": null,
         "protective_material": null,
         "recovery_time_unit": "minute"

diff --git a/tests/resources/sharepoint/nsb2023/mapped/mapped_list_item22.json b/tests/resources/sharepoint/nsb2023/mapped/mapped_list_item22.json
@@ -21,7 +21,7 @@
         "craniotomy_coordinates_unit": "millimeter",
         "bregma_to_lambda_unit": "millimeter",
         "craniotomy_size_unit": "millimeter",
-        "implant_part_number": null,
+        "implant_part_number": "2006",
         "dura_removed": null,
         "protective_material": null,
         "recovery_time_unit": "minute"

diff --git a/tests/resources/sharepoint/nsb2023/mapped/mapped_list_item9.json b/tests/resources/sharepoint/nsb2023/mapped/mapped_list_item9.json
@@ -26,7 +26,7 @@
         "craniotomy_coordinates_unit": "millimeter",
         "bregma_to_lambda_unit": "millimeter",
         "craniotomy_size_unit": "millimeter",
-        "implant_part_number": null,
+        "implant_part_number": "5mm stacked coverslip",
         "dura_removed": null,
         "protective_material": null,
         "recovery_time_unit": "minute"

diff --git a/tests/resources/sharepoint/nsb2023/raw/list_item22.json b/tests/resources/sharepoint/nsb2023/raw/list_item22.json
@@ -47,7 +47,7 @@
   "Headpost": "Visual Ctx",
   "HeadpostType": "Mesoscope",
   "CraniotomyType": "5mm",
-  "ImplantIDCoverslipType": "5mm stacked coverslip",
+  "ImplantIDCoverslipType": "2006",
   "Burr_x0020_hole_x0020_1": null,
   "Inj1VirusStrain_rt": "Select...",
   "Burr1_x0020_Virus_x0020_Biosafte": null,