Fix 282 ghost procedures (#295)

* returns none if no mapped procedures

* adds test case for no mapped las procs

src/aind_metadata_service/sharepoint/las2020/mapping.py

@@ -2094,7 +2094,7 @@ def map_viral_materials(injectable_materials: List[InjectableMaterial]):
             )
         return viral_materials
 
-    def get_procedure(self, subject_id) -> Surgery:
+    def get_procedure(self, subject_id) -> Optional[Surgery]:
         """Return Surgery as best as possible from a record."""
         subject_procedures = []
         if self.has_ip_injection():
@@ -2118,10 +2118,13 @@ def get_procedure(self, subject_id) -> Surgery:
                         injection_materials=injection_materials,
                     )
                     subject_procedures.append(ro_injection)
-        return Surgery.model_construct(
-            experimenter_full_name=self.aind_author_id,
-            iacuc_protocol=self.aind_protocol,
-            start_date=self.aind_n_start_date,
-            end_date=self.aind_n_end_date,
-            procedures=subject_procedures,
-        )
+        if subject_procedures:
+            return Surgery.model_construct(
+                experimenter_full_name=self.aind_author_id,
+                iacuc_protocol=self.aind_protocol,
+                start_date=self.aind_n_start_date,
+                end_date=self.aind_n_end_date,
+                procedures=subject_procedures,
+            )
+        else:
+            return None

src/aind_metadata_service/sharepoint/las2020/procedures.py

@@ -49,5 +49,6 @@ def get_procedures_from_sharepoint(
                 las_model = LASList.model_validate(list_item.to_json())
                 mapped_model = MappedLASList(las=las_model)
                 procedure = mapped_model.get_procedure(subject_id=subject_id)
-                list_of_procedures.append(procedure)
+                if procedure:
+                    list_of_procedures.append(procedure)
         return list_of_procedures

tests/resources/sharepoint/las2020/mapped/mapped_list_item4.json

@@ -0,0 +1 @@
+null

tests/resources/sharepoint/las2020/raw/list_item4.json

@@ -0,0 +1,250 @@
+{
+  "FileSystemObjectType": 0,
+  "Id": 6709,
+  "ServerRedirectedEmbedUri": null,
+  "ServerRedirectedEmbedUrl": "",
+  "ContentTypeId": "0x01005C6009AF417C4948814EADD3589ACE13",
+  "Title": "000000 000001",
+  "ComplianceAssetId": null,
+  "AuthorId": 5358,
+  "RequestStatus2": "New",
+  "Protocol": "2212 - Investigating Brain States",
+  "ProjectID": "AAV production 102-88-004-10",
+  "AccommodationComment": "This animal will be used for an acute ephys experiment on Friday morning.",
+  "ACSFID1": null,
+  "ACSFID2": null,
+  "ACSFID3": null,
+  "ACSFID4": null,
+  "ACSFID5": null,
+  "ACSFTime1": null,
+  "ACSFTime2": null,
+  "ACSFTime3": null,
+  "ACSFTime4": null,
+  "ACSFTime5": null,
+  "custcontact": null,
+  "CustomCom1": "Recover headpost, if possible.",
+  "CustomCom2": null,
+  "custpresent": false,
+  "doseduration": "30",
+  "doseRoute": "Intraperitoneal (IP)",
+  "doseSub": null,
+  "dosevolume": "70.4",
+  "doseWhere": null,
+  "Doxycycline": false,
+  "LTaID1": null,
+  "LTaID2": null,
+  "LTaID3": null,
+  "LTaID4": null,
+  "LTaID5": null,
+  "LTdate1": null,
+  "LTdate2": null,
+  "LTdate3": null,
+  "LTdate4": null,
+  "LTdate5": null,
+  "LTTask1": null,
+  "LTTask2": null,
+  "LTTask3": null,
+  "LTTask4": null,
+  "LTTask5": null,
+  "nEnd_x0020_Date": null,
+  "nROID1": "000000",
+  "nROID2": "000000",
+  "nROID3": "000001",
+  "nROID4": "000001",
+  "nROID5": "000001",
+  "nStart_x0020_Date": "2024-06-21T07:00:00Z",
+  "OCT": false,
+  "PostFix": "1xPBS+ 0.01%Azide",
+  "ReqAge1": null,
+  "ReqAge2": null,
+  "ReqAge3": null,
+  "Reqdate1": "2024-06-21T07:00:00Z",
+  "Reqdate2": null,
+  "Reqdate3": null,
+  "ReqPro1": "Tissue Collection",
+  "ReqPro2": null,
+  "ReqPro3": null,
+  "roEye1": "Behind Left",
+  "roEye2": "Behind Right",
+  "roEye3": "Behind Either",
+  "roEye4": null,
+  "roEye5": null,
+  "roSpinDown": "Yes",
+  "roSub1": "AiP12017",
+  "roSub2": "AiP1586",
+  "roSub3": "AiP12017",
+  "roSub4": "AiP12017",
+  "roSub5": "AiP1586",
+  "roVol1": "90",
+  "roVol2": "90 uL",
+  "roVol3": "89.9",
+  "roVol4": "90",
+  "roVol5": "90",
+  "roWhere": null,
+  "SpecDeliLoc": "Tissuecyte",
+  "TAM": false,
+  "TAMAge": null,
+  "TAMFreq": null,
+  "TCPrep": {
+    "0": "Mouse Cardiac Perfusion (SOP AF0075)"
+  },
+  "TCTiss": {
+    "0": "Brain"
+  },
+  "TMP": false,
+  "TMPAge": null,
+  "TMPFreq": null,
+  "LASComments": null,
+  "LIMSEntry": true,
+  "LIMSProject": "TempletonPsychedelics",
+  "LIMSWorkflow": "2p serial Imaging",
+  "roComment": null,
+  "ProjectLead2Id": 3212,
+  "ProjectLead2StringId": "3212",
+  "WellnessReport_x0028_No_x002F_Ye": false,
+  "QCDoorSheet": false,
+  "roIce": false,
+  "roSOP": null,
+  "roDiscard": true,
+  "roLIMS": null,
+  "icvID1": null,
+  "icvID2": null,
+  "icvID3": null,
+  "icvID4": null,
+  "icvID5": null,
+  "icvRoute1": null,
+  "icvRoute2": null,
+  "icvRoute3": null,
+  "icvRoute4": null,
+  "icvRoute5": null,
+  "icvSub1": null,
+  "icvSub2": null,
+  "icvSub3": null,
+  "icvSub4": null,
+  "icvSub5": null,
+  "WheretoObtainsubstance_x0028_ICV": null,
+  "Species": "Mouse",
+  "icvComment": null,
+  "Modified": "2024-05-20T18:28:26Z",
+  "icvLIMS": null,
+  "Created": "2024-05-13T17:59:22Z",
+  "LIMSWorkflow_x0020_2": null,
+  "OData__ColorTag": null,
+  "AfternoonPF": false,
+  "roSub1b": "AiP12017",
+  "roSub1c": "AiP12017",
+  "roSub1d": "AiP12017",
+  "roSub2b": null,
+  "roSub2c": null,
+  "roSub2d": null,
+  "roSub3b": null,
+  "roSub3c": null,
+  "roSub3d": null,
+  "roSub4b": null,
+  "roSub4c": null,
+  "roSub4d": null,
+  "roSub5b": null,
+  "roSub5c": null,
+  "roSub5d": null,
+  "roVolV1": null,
+  "roVolV1b": null,
+  "roVolV1c": null,
+  "roVolV1d": null,
+  "roVolV2": null,
+  "roVolV2b": null,
+  "roVolV2c": null,
+  "roVolV2d": null,
+  "roVolV3": null,
+  "roVolV3b": null,
+  "roVolV3c": null,
+  "roVolV3d": null,
+  "roVolV4": null,
+  "roVolV4b": null,
+  "roVolV4c": null,
+  "roVolV4d": null,
+  "roVolV5": null,
+  "roVolV5b": null,
+  "roVolV5c": null,
+  "roVolV5d": null,
+  "roTite1": "50",
+  "roTite1b": "50 gc/mL",
+  "roTite1c": null,
+  "roTite1d": null,
+  "roTite2": null,
+  "roTite2b": null,
+  "roTite2c": null,
+  "roTite2d": null,
+  "roTite3": null,
+  "roTite3b": null,
+  "roTite3c": null,
+  "roTite3d": null,
+  "roTite4": null,
+  "roTite4b": null,
+  "roTite4c": null,
+  "roTite4d": null,
+  "roTite5": null,
+  "roTite5b": null,
+  "roTite5c": null,
+  "roTite5d": null,
+  "roGC1": null,
+  "roGC1b": null,
+  "roGC1c": null,
+  "roGC1d": null,
+  "roGC2": null,
+  "roGC2b": null,
+  "roGC2c": null,
+  "roGC2d": null,
+  "roGC3": null,
+  "roGC3b": null,
+  "roGC3c": null,
+  "roGC3d": null,
+  "roGC4": null,
+  "roGC4b": null,
+  "roGC4c": null,
+  "roGC4d": null,
+  "roGC5": null,
+  "roGC5b": null,
+  "roGC5c": null,
+  "roGC5d": null,
+  "roLot1": "GT340C",
+  "roLot1b": null,
+  "roLot1c": null,
+  "roLot1d": null,
+  "roLot2": null,
+  "roLot2b": null,
+  "roLot2c": null,
+  "roLot2d": null,
+  "roLot3": null,
+  "roLot3b": null,
+  "roLot3c": null,
+  "roLot3d": null,
+  "roLot4": null,
+  "roLot4b": null,
+  "roLot4c": null,
+  "roLot4d": null,
+  "roLot5": null,
+  "roLot5b": null,
+  "roLot5c": null,
+  "roLot5d": null,
+  "roBox1": null,
+  "roBox2": null,
+  "roBox3": null,
+  "roBox4": null,
+  "roBox5": null,
+  "roTube1": "1",
+  "roTube2": "tube",
+  "roTube3": null,
+  "roTube4": null,
+  "roTube5": null,
+  "BCAge": null,
+  "BCGenotypes": null,
+  "BCType": null,
+  "BCVolume": null,
+  "BCTube": null,
+  "BCLocation": null,
+  "ID": 6709,
+  "EditorId": 538,
+  "OData__UIVersionString": "1.0",
+  "Attachments": false,
+  "GUID": "cd8a888b-4462-47e8-ba04-61e35515c697"
+}

tests/sharepoint/las2020/test_mapping.py

@@ -64,8 +64,16 @@ def test_parser(self):
             las_model = LASList.model_validate(raw_data)
             mapper = MappedLASList(las=las_model)
             mapped_procedure = mapper.get_procedure(subject_id="000000")
-            mapped_procedure_json = mapped_procedure.model_dump_json()
-            mapped_procedure_json_parsed = json.loads(mapped_procedure_json)
+            mapped_procedure_json = (
+                mapped_procedure.model_dump_json()
+                if mapped_procedure
+                else None
+            )
+            mapped_procedure_json_parsed = (
+                json.loads(mapped_procedure_json)
+                if mapped_procedure_json
+                else None
+            )
             self.assertEqual(
                 expected_mapped_data, mapped_procedure_json_parsed
             )

tests/test_response_handler.py

@@ -212,7 +212,7 @@ def test_multiple_items_response(self):
             content=(
                 {
                     "message": f"Multiple Items Found. Validation Errors:"
-                               f" {validation_error}, {validation_error}",
+                    f" {validation_error}, {validation_error}",
                     "data": models_json,
                 }
             ),
@@ -239,7 +239,7 @@ def test_multiple_items_response_no_validation(self):
             content=(
                 {
                     "message": "Multiple Items Found."
-                               " Models have not been validated.",
+                    " Models have not been validated.",
                     "data": models_json,
                 }
             ),