Parse helix messages

.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

.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 }}

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)

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.

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;

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");

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