Merge branch 'develop' into stefpiatek/admission_discharge_indexes

stefpiatek · web-flow · commit 8a2696ca8dfc · 2025-08-27T18:40:54.000+01:00
diff --git a/.github/ISSUE_TEMPLATE/issue.yml b/.github/ISSUE_TEMPLATE/issue.yml
@@ -0,0 +1,61 @@
+#  Copyright (c) University College London Hospitals NHS Foundation Trust
+#
+#  Licensed under the Apache License, Version 2.0 (the "License");
+#  you may not use this file except in compliance with the License.
+#  You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+#  Unless required by applicable law or agreed to in writing, software
+#  distributed under the License is distributed on an "AS IS" BASIS,
+#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#  See the License for the specific language governing permissions and
+#  limitations under the License.
+name: Story/Task
+description: Create a new story or task
+projects: ["UCLH-DHCT/4"]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Let's add a new task/story to the project
+  - type: textarea
+    id: definition_of_done
+    attributes:
+      label: Definition of Done / Acceptance Criteria
+      description: What can someone see/do when this task is done.
+      placeholder: "- [ ] The export data is available in the xxx format, including age of the patient at the time of imaging..."
+    validations:
+      required: true
+  - type: textarea
+    id: testing
+    attributes:
+      label: Testing
+      description: Specific testing considerations for this task to be done
+      placeholder: "- [ ] Passed integration testing that uses the correct modality..."
+    validations:
+      required: false
+  - type: textarea
+    id: documentation
+    attributes:
+      label: Documentation
+      description: Documentation to be completed along with this task
+      placeholder: "- [ ] Update module README and user guide..."
+    validations:
+      required: false
+  - type: textarea
+    id: dependencies
+    attributes:
+      label: Dependencies
+      description: Enter the github issue number that the requirement is dependent on, in the form `- [ ] #1` to make a checklist
+      placeholder: "- [ ] #1"
+    validations:
+      required: false
+  - type: textarea
+    id: details
+    attributes:
+      label: Details and Comments
+      description: Other details or comments
+      placeholder: The algorithm used is based on...
+    validations:
+      required: false
diff --git a/.github/workflows/comment.yaml b/.github/workflows/comment.yaml
@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout documentation
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           repository: SAFEHR-data/internal_emap_documentation
           token: ${{ secrets.GH_PAT_READ_AND_COMMENT }}
diff --git a/README.md b/README.md
@@ -1,6 +1,19 @@
 # Emap
 
-A monorepo for all core Emap functions
+Experimental Medicine Application Platform (EMAP) produces a near real-time database 
+containing clinical data for research and dashboard development within UCLH. 
+
+This is a non-operational “mirror” of a subset of UCLH data (historical and live). 
+The underpinning aim is to ensure that no clinical data are corrupted or destroyed during the interaction 
+between the research process and the hospital’s systems and that the systems are not compromised 
+(for instance, that they are not interrupted or slowed down by research enquiries).
+
+For more information about EMAP, please see the [docs](https://github.com/SAFEHR-data/emap/tree/main/docs)
+
+## Developer onboarding
+
+- How to [configure IntelliJ](docs/dev/intellij.md) to build emap and run tests.
+- [Onboarding](docs/dev/onboarding.md) gives details on how data items are processed and the test strategies used.
 
 # Setup
 
@@ -20,12 +33,6 @@ EMAP [your root emap directory]
 │   ├── [etc.]
 ```
 
-## Developer onboarding
-
-- How to [configure IntelliJ](docs/dev/intellij.md) to build emap and run tests.
-- [Onboarding](docs/dev/onboarding.md) gives details on how data items are processed and the test strategies used.
-
-
 # Monorepo migration
 
 How were [old repos migrated into this repo?](docs/dev/migration.md)
diff --git a/core/src/main/java/uk/ac/ucl/rits/inform/datasinks/emapstar/controllers/PendingAdtController.java b/core/src/main/java/uk/ac/ucl/rits/inform/datasinks/emapstar/controllers/PendingAdtController.java
@@ -75,6 +75,7 @@ public void processMsg(HospitalVisit visit, PendingTransfer msg, Instant validFr
         RowState<PlannedMovement, PlannedMovementAudit> plannedState = getOrCreate(
                 allFromRequest, visit, plannedLocation, msg.getPendingEventType().toString(), msg.getEventOccurredDateTime(), validFrom, storedFrom
         );
+        addHospitalService(msg, plannedState);
         PlannedMovement plannedMovement = plannedState.getEntity();
         // If we receive a cancelled message before the original request then add it in
         if (plannedMovement.getEventDatetime() == null) {
@@ -159,6 +160,16 @@ private void deletePlannedMovement(PlannedMovement plannedMovement, Instant dele
         plannedMovementAuditRepo.save(plannedMovement.createAuditEntity(deletionTime, storedUntil));
         plannedMovementRepo.delete(plannedMovement);
     }
+
+    /**
+     * Add hospital service.
+     * @param msg           PendingTransfer
+     * @param movementState movement wrapped in state class
+     */
+    private void addHospitalService(final PendingTransfer msg, RowState<PlannedMovement, PlannedMovementAudit> movementState) {
+        PlannedMovement movement = movementState.getEntity();
+        movementState.assignInterchangeValue(msg.getHospitalService(), movement.getHospitalService(), movement::setHospitalService);
+    }
 }
 
 /**
diff --git a/core/src/test/java/uk/ac/ucl/rits/inform/datasinks/emapstar/adt/TestPendingAdt.java b/core/src/test/java/uk/ac/ucl/rits/inform/datasinks/emapstar/adt/TestPendingAdt.java
@@ -96,6 +96,7 @@ void testPendingCreatesPlannedMovement() throws Exception {
         assertEquals(EVENT_TIME, plannedMovement.getEventDatetime());
         assertEquals(PendingType.TRANSFER.toString(), plannedMovement.getEventType());
         assertNull(plannedMovement.getCancelledDatetime());
+        assertEquals("Head and Neck - OMFS", plannedMovement.getHospitalService());
     }
 
     /**
diff --git a/docs/Glossary.md b/docs/Glossary.md
@@ -324,6 +324,10 @@
 
 ## T
 
+- <a id="tdl">**TCI**</a>
+
+	To Come In (a patient is TCI for ward X if they are on the way to the ward but not admitted).
+
 - <a id="tdl">**TDL**</a>
 
 	The Doctors Laboratory provide the biochemistry and microbiology analysis for the hospital.
diff --git a/emap-interchange/src/main/java/uk/ac/ucl/rits/inform/interchange/adt/CancelPendingTransfer.java b/emap-interchange/src/main/java/uk/ac/ucl/rits/inform/interchange/adt/CancelPendingTransfer.java
@@ -21,6 +21,7 @@
 public class CancelPendingTransfer extends AdtMessage implements PendingEvent, AdtCancellation {
     private PendingType pendingEventType = PendingType.TRANSFER;
     private InterchangeValue<String> pendingDestination = InterchangeValue.unknown();
+    private InterchangeValue<String> hospitalService = InterchangeValue.unknown();
     private Instant cancelledDateTime;
 
 
diff --git a/emap-interchange/src/main/java/uk/ac/ucl/rits/inform/interchange/adt/PendingEvent.java b/emap-interchange/src/main/java/uk/ac/ucl/rits/inform/interchange/adt/PendingEvent.java
@@ -21,4 +21,16 @@ public interface PendingEvent {
      * @param location Concatenated location string
      */
     void setPendingDestination(InterchangeValue<String> location);
+
+
+    /**
+     * @return Hospital service from PV1-10.
+     */
+    InterchangeValue<String> getHospitalService();
+
+    /**
+     * @param hospitalService
+     */
+    void  setHospitalService(InterchangeValue<String> hospitalService);
+
 }
diff --git a/emap-interchange/src/main/java/uk/ac/ucl/rits/inform/interchange/adt/PendingTransfer.java b/emap-interchange/src/main/java/uk/ac/ucl/rits/inform/interchange/adt/PendingTransfer.java
@@ -19,6 +19,7 @@
 public class PendingTransfer extends AdtMessage implements PendingEvent {
     private PendingType pendingEventType = PendingType.TRANSFER;
     private InterchangeValue<String> pendingDestination = InterchangeValue.unknown();
+    private InterchangeValue<String> hospitalService = InterchangeValue.unknown();
 
     @Override
     public void processMessage(EmapOperationMessageProcessor processor) throws EmapOperationMessageProcessingException {
diff --git a/emap-interchange/src/test/resources/AdtMessages/pending/A15.yaml b/emap-interchange/src/test/resources/AdtMessages/pending/A15.yaml
@@ -54,4 +54,7 @@ modeOfArrival:
   "@class": "uk.ac.ucl.rits.inform.interchange.InterchangeValue"
   status: "SAVE"
   value: "Walk-in"
-
+hospitalService:
+  "@class": "uk.ac.ucl.rits.inform.interchange.InterchangeValue"
+  status: "SAVE"
+  value: "Head and Neck - OMFS"
diff --git a/emap-star/emap-star/src/main/java/uk/ac/ucl/rits/inform/informdb/movement/PlannedMovement.java b/emap-star/emap-star/src/main/java/uk/ac/ucl/rits/inform/informdb/movement/PlannedMovement.java
@@ -84,6 +84,13 @@ public class PlannedMovement extends TemporalCore<PlannedMovement, PlannedMoveme
     @Column(columnDefinition = "timestamp with time zone")
     private Instant cancelledDatetime;
 
+    /**
+     * \brief The hospital service associated with this planned movement.
+     *
+     * Also known as the subspeciality.
+     */
+    private String hospitalService;
+
     /**
      * Minimal constructor.
      * @param hospitalVisitId associated hospital visit
@@ -109,6 +116,7 @@ private PlannedMovement(PlannedMovement other) {
         eventDatetime = other.eventDatetime;
         cancelled = other.cancelled;
         cancelledDatetime = other.cancelledDatetime;
+        hospitalService = other.hospitalService;
     }
 
     @Override
diff --git a/hl7-reader/src/main/java/uk/ac/ucl/rits/inform/datasources/ids/AdtMessageFactory.java b/hl7-reader/src/main/java/uk/ac/ucl/rits/inform/datasources/ids/AdtMessageFactory.java
@@ -251,6 +251,7 @@ private AdtMessage buildAdtMessageSubclass(final PV1Wrap pv1Wrap, final Message
             case "A15":
                 PendingTransfer pendingTransfer = new PendingTransfer();
                 setPendingDestination(pv1Wrap, pendingTransfer);
+                setHospitalService(pv1Wrap, pendingTransfer);
                 msg = pendingTransfer;
                 break;
             case "A17":
@@ -448,4 +449,9 @@ private void setPendingDestination(PV1Wrap pv1Wrap, PendingEvent pendingEvent) {
         String pendingLocation = pv1Wrap.getPendingLocation();
         pendingEvent.setPendingDestination(InterchangeValue.buildFromHl7(pendingLocation));
     }
+
+    private void setHospitalService(PV1Wrap pv1Wrap, PendingEvent pendingEvent) throws HL7Exception {
+        String hospitalService = pv1Wrap.getHospitalService();
+        pendingEvent.setHospitalService(InterchangeValue.buildFromHl7(hospitalService));
+    }
 }
diff --git a/hl7-reader/src/main/java/uk/ac/ucl/rits/inform/datasources/ids/OrderAndResultService.java b/hl7-reader/src/main/java/uk/ac/ucl/rits/inform/datasources/ids/OrderAndResultService.java
@@ -173,7 +173,7 @@ private OrderCodingSystem determineCodingSystem(OBR obr, String sendingApplicati
         String codingSystem = obr.getObr4_UniversalServiceIdentifier().getCwe3_NameOfCodingSystem().getValueOrEmpty();
         String alternativeIdentifier = obr.getObr4_UniversalServiceIdentifier().getCwe4_AlternateIdentifier().getValueOrEmpty();
 
-        if ("WinPath".equals(codingSystem)) {
+        if ("WinPath".equals(codingSystem) || (codingSystem.isBlank() && "WinPath".equals(sendingApplication))) {
             return OrderCodingSystem.WIN_PATH;
         } else if ("CoPathPlus".equals(fillerNamespace) || "CPEAP".equals(codingSystem)) {
             return OrderCodingSystem.CO_PATH;
diff --git a/hl7-reader/src/test/java/uk/ac/ucl/rits/inform/datasources/ids/adt/TestPendingAdt.java b/hl7-reader/src/test/java/uk/ac/ucl/rits/inform/datasources/ids/adt/TestPendingAdt.java
@@ -33,6 +33,7 @@ void testPendingTransferSpecificFields() throws Exception {
 
         assertEquals(PendingType.TRANSFER, msg.getPendingEventType());
         assertEquals(InterchangeValue.buildFromHl7("1020100166^SDEC BY02^11 SDEC"), msg.getPendingDestination());
+        assertEquals(InterchangeValue.buildFromHl7("Head and Neck - OMFS"), msg.getHospitalService());
     }
 
     /**
@@ -48,6 +49,18 @@ void testPendingLocationUnknown() throws Exception {
         assertTrue(msg.getPendingDestination().isUnknown());
     }
 
+    /**
+     * Given a pending transfer message with no hospital service (PV1-10)
+     * When processed into an interchange message
+     * The hospital service should be unknown
+     * @throws Exception
+     */
+    @Test
+    void testNoHospitalService() throws Exception {
+        PendingEvent msg = (PendingEvent) processSingleAdtMessage("Adt/pending/A15_no_hospital_service.txt");
+        assertTrue(msg.getHospitalService().isUnknown());
+    }
+
     /**
      * Given a cancel pending transfer message
      * When processed
diff --git a/hl7-reader/src/test/java/uk/ac/ucl/rits/inform/datasources/ids/labs/TestWinPathLabOruR01Results.java b/hl7-reader/src/test/java/uk/ac/ucl/rits/inform/datasources/ids/labs/TestWinPathLabOruR01Results.java
@@ -362,6 +362,18 @@ void testIsolateSensitivities() throws Exception {
         assertEquals(LabResultStatus.FINAL, sensitivity.getResultStatus());
     }
 
+    /**
+     * GIVEN a helix message (has WinPath as sending application and no coding system
+     * WHEN this HL7 message is processed
+     * THEN the message should be processed successfully with an isolate
+     * @throws Exception shouldn't happen
+     */
+    @Test
+    void testIsolateFromHelix() throws Exception {
+        LabIsolateMsg isolate = getFirstLabIsolate("isolate_helix");
+        assertEquals("KLEOXY", isolate.getIsolateCode());
+    }
+
     @Test
     void testClinicalInformationIsAddedToSensitivity() throws Exception {
         LabOrderMsg orderMsg = labReader.getFirstOrder(FILE_TEMPLATE, "isolate_clinical_notes");
diff --git a/hl7-reader/src/test/resources/Adt/pending/A15.txt b/hl7-reader/src/test/resources/Adt/pending/A15.txt
@@ -4,6 +4,6 @@ PID|1||40800000^^^MRENTR^MEDREC~9999999999^^^NHS^HN||AGBTESTD^Satesta^^^MRS||198
 ZPD||Email~MYCH||ACTIVATED|||N||N|||||||||||||||F
 PD1|||GP AT HAND^^E85124~~
 NTE|1||EP34C Patient|PatComments
-PV1|1|E|ED^COVID MAJORS 16^16-COVID MAJORS^U^R^^^^^^DEPID|Emergency|||1236^BEAR^BLACK^^^^^^PROVID^^^^PROVID|||A\T\E|||||||||123412341234|SELF|||||||||||||||||||||Adm*Conf|1020100166^SDEC BY02^11 SDEC^U^D^^^^^^DEPID||20220421195000||||||123412341234
+PV1|1|E|ED^COVID MAJORS 16^16-COVID MAJORS^U^R^^^^^^DEPID|Emergency|||1236^BEAR^BLACK^^^^^^PROVID^^^^PROVID|||Head and Neck - OMFS|||||||||123412341234|SELF|||||||||||||||||||||Adm*Conf|1020100166^SDEC BY02^11 SDEC^U^D^^^^^^DEPID||20220421195000||||||123412341234
 PV2|||||||||||||||||||||n|N||||||||||||||||Walk-in
 OBX|1|TX|AdminCode^ADMINISTRATIVE CATEGORY CODE|1|1|||||||||20220422
diff --git a/hl7-reader/src/test/resources/Adt/pending/A15_no_hospital_service.txt b/hl7-reader/src/test/resources/Adt/pending/A15_no_hospital_service.txt
@@ -0,0 +1,9 @@
+MSH|^~\&|EPIC|UCLH|||20220422002300|10018372|ADT^A15|39278859|P|2.4|||AL|NE
+EVN|A15|20220422002300||PNDTRANSFER|10018372^GIANT^PANDA^^^^^^UCLHS^^^^^UCHC|20220422002258
+PID|1||40800000^^^MRENTR^MEDREC~9999999999^^^NHS^HN||AGBTESTD^Satesta^^^MRS||19800601|F||N|^^London^^T5 1TT||0200 000 0000~07777 000 000||BG|N||123412341234||||||||||||N
+ZPD||Email~MYCH||ACTIVATED|||N||N|||||||||||||||F
+PD1|||GP AT HAND^^E85124~~
+NTE|1||EP34C Patient|PatComments
+PV1|1|E|ED^COVID MAJORS 16^16-COVID MAJORS^U^R^^^^^^DEPID|Emergency|||1236^BEAR^BLACK^^^^^^PROVID^^^^PROVID||||||||||||123412341234|SELF|||||||||||||||||||||Adm*Conf|1020100166^SDEC BY02^11 SDEC^U^D^^^^^^DEPID||20220421195000||||||123412341234
+PV2|||||||||||||||||||||n|N||||||||||||||||Walk-in
+OBX|1|TX|AdminCode^ADMINISTRATIVE CATEGORY CODE|1|1|||||||||20220422
diff --git a/hl7-reader/src/test/resources/LabOrders/winpath/isolate_helix.txt b/hl7-reader/src/test/resources/LabOrders/winpath/isolate_helix.txt
@@ -0,0 +1,16 @@
+MSH|^~\&|WinPath|UCH|EPIC|UCH|20190715094018||ORU^R01|12345678-1234-1234-1234-123456789012|P|2.3
+PID|||44444444^^^MRENTR^MEDREC|
+PV1||NH|MMCHCA^MCC H05 HCA||||^Unknown Clinician|||||||||||NH|123412341234^^^VISITID
+ORC|RE|93939393|20V042424|20V0424245|CM
+OBR|1|93939393|20V042424|URNC^URINE CULTURE|UCUL|201907101232|201907101106||||||:-UTI??||MSU^Mid Stream Urine (MSU)|||||||201907150937||MC|F
+OBX|1|FT|URNC^URINE CULTURE^Winpath||URINE CULTURE REPORT||||||F
+OBX|2|ST|ISOLATE^ISOLATE^Winpath|1|10,000 - 100,000 CFU/mL|||A|||F
+OBX|3|CE|ISOLATE^ISOLATE^Winpath|1|KLEOXY^Klebsiella oxytoca|||A|||F
+OBX|4|FT|URST^STATUS^Winpath||COMPLETE: 14/07/19||||||F
+ORC|RE|93939393|20V042424|20V0424245
+OBR|2|93939393|20V042424|Micro^Sensitivities^WinPath||201907101232|201907101106||||||Gentamicin resistant||MSU^Mid Stream Urine (MSU)|||||||||MC|F|ISOLATE&&Winpath^1|||93939393&&URNC^20V042424&&URNC
+OBX|1|ST|VAK^Amikacin^Winpath||VAK|||S|||F
+OBX|2|ST|VAC^Amoxi/Clav.acid^Winpath||VAC|||S|||F
+OBX|3|ST|VM^Amoxicillin^Winpath||VM|||R|||F
+OBX|4|ST|VCN^Gentamicin^Winpath||VCN|||R|||F
+OBX|5|ST|VF^Nitrofurantoin^Winpath||VF|||R|||F

Original file line number	Diff line number	Diff line change
`@@ -96,6 +96,7 @@ void testPendingCreatesPlannedMovement() throws Exception {`
`96`	`96`	`assertEquals(EVENT_TIME, plannedMovement.getEventDatetime());`
`97`	`97`	`assertEquals(PendingType.TRANSFER.toString(), plannedMovement.getEventType());`
`98`	`98`	`assertNull(plannedMovement.getCancelledDatetime());`
	`99`	`+ assertEquals("Head and Neck - OMFS", plannedMovement.getHospitalService());`
`99`	`100`	`}`
`100`	`101`
`101`	`102`	`/**`