Merge pull request #177 from microsoft/dotliquid

Upgrade DotLiquid converter to v3.2
microsoft · Jan 13, 2021 · cbe5eab · cbe5eab
2 parents 6f106e9 + 3376786
commit cbe5eab
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Showing 42 changed files with 731 additions and 254 deletions.
diff --git a/data/Templates/Hl7v2/ADT_A01.liquid b/data/Templates/Hl7v2/ADT_A01.liquid
@@ -1,8 +1,8 @@
 {
     "resourceType": "Bundle",
-    "type": "transaction",
+    "type": "batch",
     "entry": [
-        {% assign firstSegments = hl7v2Data | get_first_segments: 'PID|PD1|PV1|PV2|PR1|AVR|MSH' -%}
+        {% assign firstSegments = hl7v2Data | get_first_segments: 'PID|PD1|PV1|PV2|AVR|MSH' -%}
 
         {% evaluate messageHeaderId using 'ID/MessageHeader' MSH: firstSegments.MSH -%}
         {% if messageHeaderId -%}
@@ -15,7 +15,7 @@
             {% include 'Resource/Patient' PID: firstSegments.PID, PD1: firstSegments.PD1, ID: patientId -%}
         {% endif -%}
 
-        {% evaluate provenanceId using 'ID/Provenance' MSH: firstSegments.MSH, baseID: patientId -%}
+        {% evaluate provenanceId using 'ID/Provenance' MSH: firstSegments.MSH, baseId: patientId -%}
         {% if provenanceId -%}
             {% include 'Resource/Provenance' MSH: firstSegments.MSH, ORC: firstSegments.ORC, ID: provenanceId -%}
         {% endif -%}
@@ -34,34 +34,39 @@
         {% if encounterId -%}
             {% include 'Resource/Encounter' PV1: firstSegments.PV1, PV2: firstSegments.PV2, ID: encounterId -%}
 
-            {% evaluate locationId using 'ID/Location' PL: firstSegments.PV1.3 -%}
-            {% if locationId -%}
-                {% include 'Resource/Location' PL: firstSegments.PV1.3, ID: locationId -%}
+            {% evaluate locationId3 using 'ID/Location' PL: firstSegments.PV1.3 -%}
+            {% if locationId3 -%}
+                {% include 'Resource/Location' PL: firstSegments.PV1.3, ID: locationId3 -%}
             {% endif -%}
 
-            {% evaluate locationId using 'ID/Location' PL: firstSegments.PV1.6 -%}
-            {% if locationId -%}
-                {% include 'Resource/Location' PL: firstSegments.PV1.6, ID: locationId -%}
+            {% evaluate locationId6 using 'ID/Location' PL: firstSegments.PV1.6 -%}
+            {% if locationId6 -%}
+                {% include 'Resource/Location' PL: firstSegments.PV1.6, ID: locationId6 -%}
             {% endif -%}
 
+            {% include 'Resource/Encounter' PV1: firstSegments.PV1, Location_ID_PV1_3: locationId3, Location_ID_PV1_6: locationId6, ID: encounterId -%}
+
             {% if patientId -%}
                 {% include 'Reference/Encounter/Subject' ID: encounterId, REF: fullPatientId -%}
             {% endif -%}
         {% endif -%}
 
-        {% evaluate procedureId using 'ID/Procedure' PR1: firstSegments.PR1, baseId: patientId -%}
-        {% if procedureId -%}
-            {% include 'Resource/Procedure' PR1: firstSegments.PR1, ID: procedureId -%}
+        {% assign pr1SegmentLists = hl7v2Data | get_segment_lists: 'PR1' -%}
+        {% for pr1Segment in pr1SegmentLists.PR1 -%}
+            {% evaluate procedureId using 'ID/Procedure' PR1: pr1Segment, baseId: patientId -%}
+            {% if procedureId -%}
+                {% include 'Resource/Procedure' PR1: pr1Segment, ID: procedureId -%}
 
-            {% evaluate locationId using 'ID/Location' PL: firstSegments.PR1.23 -%}
-            {% if locationId -%}
-                {% include 'Resource/Location' PL: firstSegments.PR1.23, ID: locationId -%}
-            {% endif -%}
+                {% evaluate locationId using 'ID/Location' PL: pr1Segment.23 -%}
+                {% if locationId -%}
+                    {% include 'Resource/Location' PL: pr1Segment.23, ID: locationId -%}
+                {% endif -%}
 
-            {% if patientId -%}
-                {% include 'Reference/Procedure/Subject' ID: procedureId, REF: fullPatientId -%}
+                {% if patientId -%}
+                    {% include 'Reference/Procedure/Subject' ID: procedureId, REF: fullPatientId -%}
+                {% endif -%}
             {% endif -%}
-        {% endif -%}
+        {% endfor -%}
 
         {% assign nk1SegmentLists = hl7v2Data | get_segment_lists: 'NK1' -%}
         {% for nk1Segment in nk1SegmentLists.NK1 -%}

diff --git a/data/Templates/Hl7v2/OML_O21.liquid b/data/Templates/Hl7v2/OML_O21.liquid
@@ -1,6 +1,6 @@
 {
     "resourceType": "Bundle",
-    "type": "transaction",
+    "type": "batch",
     "entry": [
         {% assign firstSegments = hl7v2Data | get_first_segments: 'PID|PD1|PV1|PV2|ORC|MSH' -%}
 
@@ -15,7 +15,7 @@
             {% include 'Resource/Patient' PID: firstSegments.PID, PD1: firstSegments.PD1, ID: patientId -%}
         {% endif -%}
 
-        {% evaluate provenanceId using 'ID/Provenance' MSH: firstSegments.MSH, baseID: patientId -%}
+        {% evaluate provenanceId using 'ID/Provenance' MSH: firstSegments.MSH, baseId: patientId -%}
         {% if provenanceId -%}
             {% include 'Resource/Provenance' MSH: firstSegments.MSH, ORC: firstSegments.ORC, ID: provenanceId -%}
         {% endif -%}
@@ -35,16 +35,18 @@
             {% assign fullEncounterId = encounterId | prepend: 'Encounter/' -%}
             {% include 'Resource/Encounter' PV1: firstSegments.PV1, PV2: firstSegments.PV2, ID: encounterId -%}
 
-            {% evaluate locationId using 'ID/Location' PL: firstSegments.PV1.3 -%}
-            {% if locationId -%}
-                {% include 'Resource/Location' PL: firstSegments.PV1.3, ID: locationId -%}
+            {% evaluate locationId3 using 'ID/Location' PL: firstSegments.PV1.3 -%}
+            {% if locationId3 -%}
+                {% include 'Resource/Location' PL: firstSegments.PV1.3, ID: locationId3 -%}
             {% endif -%}
 
-            {% evaluate locationId using 'ID/Location' PL: firstSegments.PV1.6 -%}
-            {% if locationId -%}
-                {% include 'Resource/Location' PL: firstSegments.PV1.6, ID: locationId -%}
+            {% evaluate locationId6 using 'ID/Location' PL: firstSegments.PV1.6 -%}
+            {% if locationId6 -%}
+                {% include 'Resource/Location' PL: firstSegments.PV1.6, ID: locationId6 -%}
             {% endif -%}
 
+            {% include 'Resource/Encounter' PV1: firstSegments.PV1, Location_ID_PV1_3: locationId3, Location_ID_PV1_6: locationId6, ID: encounterId -%}
+
             {% if patientId -%}
                 {% include 'Reference/Encounter/Subject' ID: encounterId, REF: fullPatientId -%}
             {% endif -%}

diff --git a/data/Templates/Hl7v2/ORU_R01.liquid b/data/Templates/Hl7v2/ORU_R01.liquid
@@ -1,6 +1,6 @@
 {
     "resourceType": "Bundle",
-    "type": "transaction",
+    "type": "batch",
     "entry": [
         {% assign firstSegments = hl7v2Data | get_first_segments: 'PID|PD1|NK1|PV1|PV2|MSH' -%}
 
@@ -15,7 +15,7 @@
             {% include 'Resource/Patient' PID: firstSegments.PID, PD1: firstSegments.PD1, ID: patientId -%}
         {% endif -%}
 
-        {% evaluate provenanceId using 'ID/Provenance' MSH: firstSegments.MSH, baseID: patientId -%}
+        {% evaluate provenanceId using 'ID/Provenance' MSH: firstSegments.MSH, baseId: patientId -%}
         {% if provenanceId -%}
             {% include 'Resource/Provenance' MSH: firstSegments.MSH, ORC: firstSegments.ORC, ID: provenanceId -%}
         {% endif -%}
@@ -35,16 +35,18 @@
             {% assign fullEncounterId = encounterId | prepend: 'Encounter/' -%}
             {% include 'Resource/Encounter' PV1: firstSegments.PV1, PV2: firstSegments.PV2, ID: encounterId -%}
 
-            {% evaluate locationId using 'ID/Location' PL: firstSegments.PV1.3 -%}
-            {% if locationId -%}
-                {% include 'Resource/Location' PL: firstSegments.PV1.3, ID: locationId -%}
+            {% evaluate locationId3 using 'ID/Location' PL: firstSegments.PV1.3 -%}
+            {% if locationId3 -%}
+                {% include 'Resource/Location' PL: firstSegments.PV1.3, ID: locationId3 -%}
             {% endif -%}
 
-            {% evaluate locationId using 'ID/Location' PL: firstSegments.PV1.6 -%}
-            {% if locationId -%}
-                {% include 'Resource/Location' PL: firstSegments.PV1.6, ID: locationId -%}
+            {% evaluate locationId6 using 'ID/Location' PL: firstSegments.PV1.6 -%}
+            {% if locationId6 -%}
+                {% include 'Resource/Location' PL: firstSegments.PV1.6, ID: locationId6 -%}
             {% endif -%}
-
+
+            {% include 'Resource/Encounter' PV1: firstSegments.PV1, Location_ID_PV1_3: locationId3, Location_ID_PV1_6: locationId6, ID: encounterId -%}
+
             {% if patientId -%}
                 {% include 'Reference/Encounter/Subject' ID: encounterId, REF: fullPatientId -%}
             {% endif -%}

diff --git a/data/Templates/Hl7v2/Resource/_Encounter.liquid b/data/Templates/Hl7v2/Resource/_Encounter.liquid
@@ -18,25 +18,25 @@
             {
                 "location":
                 {
-                    {% if PV1.3 -%}
-                    "reference":"Location/{{generateUUID PV1-3}}",
+                    {% if Location_ID_PV1_3 -%}
+                    "reference":"Location/{{ Location_ID_PV1_3 }}",
                     {% endif -%}
                 },
-                {% if PV1.2.1.Value != "P" -%}
+                {% if PV1.2.1.Value != "P" and Location_ID_PV1_3 -%}
                 "status":"active",
                 {% endif -%}
-                {% if PV1.2.1.Value == "P" -%}
+                {% if PV1.2.1.Value == "P" and Location_ID_PV1_3 -%}
                 "status":"planned",
                 {% endif -%}
             },
             {
                 "location":
                 {
-                    {% if PV1.6 -%}
-                    "reference":"Location/{{generateUUID PV1-6}}",
+                    {% if Location_ID_PV1_6 -%}
+                    "reference":"Location/{{ Location_ID_PV1_6 }}",
                     {% endif -%}
                 },
-                {% if PV1.6 -%}
+                {% if PV1.6 and Location_ID_PV1_6 -%}
                 "status":"completed",
                 {% endif -%}
             },

diff --git a/data/Templates/Hl7v2/Resource/_Patient.liquid b/data/Templates/Hl7v2/Resource/_Patient.liquid
@@ -42,9 +42,11 @@
         ],
         "name":
         [
+            {% for p in PID.5.Repeats -%}
             {
-                {% include 'DataType/XPN' XPN: PID.5 -%}
+                {% include 'DataType/XPN' XPN: p -%}
             },
+            {% endfor -%}
             {
                 {% include 'DataType/XPN' XPN: PID.9 -%}
             },
@@ -53,9 +55,11 @@
         "gender":"{{ PID.8.Value | get_property: 'CodeSystem/Gender', 'code' }}",
         "address":
         [
+            {% for p in PID.11.Repeats -%}
             {
-                {% include 'DataType/XAD' XAD: PID.11 -%}
+                {% include 'DataType/XAD' XAD: p -%}
             },
+            {% endfor -%}
             {
                 "district":"{{ PID.12.Value }}",
             },

diff --git a/data/Templates/Hl7v2/Resource/_PractitionerRole.liquid b/data/Templates/Hl7v2/Resource/_PractitionerRole.liquid
@@ -33,8 +33,8 @@
         "location":
         [
             {
-                {% if ROL.13 -%}
-                "reference":"Location/{{generateUUID ROL-13}}",
+                {% if Location_ID_ROL_13 -%}
+                "reference":"Location/{{ Location_ID_ROL_13 }}",
                 {% endif -%}
             },
         ],

diff --git a/data/Templates/Hl7v2/Resource/_Procedure.liquid b/data/Templates/Hl7v2/Resource/_Procedure.liquid
@@ -38,8 +38,8 @@
         ],
         "location":
         {
-            {% if PR1.23 -%}
-            "reference":"Location/{{generateUUID PR1-23}}",
+            {% if Location_ID_PR1_23 -%}
+            "reference":"Location/{{ Location_ID_PR1_23 }}",
             {% endif -%}
         },
     },

diff --git a/data/Templates/Hl7v2/VXU_V04.liquid b/data/Templates/Hl7v2/VXU_V04.liquid
@@ -1,6 +1,6 @@
 {
     "resourceType": "Bundle",
-    "type": "transaction",
+    "type": "batch",
     "entry": [
         {% assign firstSegments = hl7v2Data | get_first_segments: 'PID|PD1|PV1|ORC|MSH' -%}
 
@@ -15,7 +15,7 @@
             {% include 'Resource/Patient' PID: firstSegments.PID, PD1: firstSegments.PD1, ID: patientId -%}
         {% endif -%}
 
-        {% evaluate provenanceId using 'ID/Provenance' MSH: firstSegments.MSH, baseID: patientId -%}
+        {% evaluate provenanceId using 'ID/Provenance' MSH: firstSegments.MSH, baseId: patientId -%}
         {% if provenanceId -%}
             {% include 'Resource/Provenance' MSH: firstSegments.MSH, ORC: firstSegments.ORC, ID: provenanceId -%}
         {% endif -%}
@@ -34,15 +34,17 @@
         {% if encounterId -%}
             {% include 'Resource/Encounter' PV1: firstSegments.PV1, ID: encounterId -%}
 
-            {% evaluate locationId using 'ID/Location' PL: firstSegments.PV1.3 -%}
-            {% if locationId -%}
-                {% include 'Resource/Location' PL: firstSegments.PV1.3, ID: locationId -%}
+            {% evaluate locationId3 using 'ID/Location' PL: firstSegments.PV1.3 -%}
+            {% if locationId3 -%}
+                {% include 'Resource/Location' PL: firstSegments.PV1.3, ID: locationId3 -%}
             {% endif -%}
 
-            {% evaluate locationId using 'ID/Location' PL: firstSegments.PV1.6 -%}
-            {% if locationId -%}
-                {% include 'Resource/Location' PL: firstSegments.PV1.6, ID: locationId -%}
+            {% evaluate locationId6 using 'ID/Location' PL: firstSegments.PV1.6 -%}
+            {% if locationId6 -%}
+                {% include 'Resource/Location' PL: firstSegments.PV1.6, ID: locationId6 -%}
             {% endif -%}
+
+            {% include 'Resource/Encounter' PV1: firstSegments.PV1, Location_ID_PV1_3: locationId3, Location_ID_PV1_6: locationId6, ID: encounterId -%}
 
             {% if patientId -%}
                 {% include 'Reference/Encounter/Subject' ID: encounterId, REF: fullPatientId -%}

diff --git a/release.yml b/release.yml
@@ -16,7 +16,7 @@ variables:
   functionalTests: "**/*FunctionalTests/*.csproj"
   buildConfiguration: 'Release'
   major: 3
-  minor: 1
+  minor: 2
   bulidnum: $[counter(format('{0}.{1}',variables['major'],variables['minor']), 100)]
   revision: $[counter(format('{0:yyyyMMdd}', pipeline.startTime), 1)]
   version: $(major).$(minor).$(bulidnum).$(revision)
@@ -29,6 +29,16 @@ stages:
   - job: Build
     steps:
     - script: echo $(version)
+
+    - task: DotNetCoreCLI@2
+      displayName: 'dotnet restore'
+      inputs:
+        command: 'restore'
+        projects: '$(solution)'
+        arguments: '--configuration $(buildConfiguration)'
+        feedsToUse: 'select'
+        vstsFeed: '7621b231-1a7d-4364-935b-2f72b911c43d/a60b7c8b-c6ae-4a8e-bd15-a526b603a1f2'
+
     - task: DotNetCoreCLI@2
       displayName: 'dotnet build'
       inputs:
@@ -81,7 +91,7 @@ stages:
         includeRootFolder: false
         archiveType: 'tar'
         tarCompression: 'gz'
-        archiveFile: '$(Build.SourcesDirectory)/data/Templates/DefaultTemplates.tar.gz'
+        archiveFile: '$(Build.SourcesDirectory)/data/Templates/Hl7v2DefaultTemplates.tar.gz'
 
     - task: CopyFiles@2
       displayName: 'copy DefaultTemplates to artifacts'
@@ -127,7 +137,10 @@ stages:
         artifactName: FhirConverterBuild
         downloadPath: $(System.DefaultWorkingDirectory)
     - script: |
-        docker run --rm -d -p 5000:5000 --name registry stefanscherer/registry-windows:2.6.2
+        git clone -q https://github.com/sowu880/dockerfiles-windows.git
+        cd dockerfiles-windows/registry/
+        docker build -t registry-windows:2.7.1 .
+        docker run --rm -d -p 5000:5000 --name registry registry-windows:2.7.1
       displayName: start registry
 
     # - script: |
@@ -158,6 +171,11 @@ stages:
         artifactName: FhirConverterBuild
         downloadPath: $(System.DefaultWorkingDirectory)
     - script: |
+        curl -LO https://github.com/deislabs/oras/releases/download/v0.8.1/oras_0.8.1_linux_amd64.tar.gz
+        mkdir -p oras-install/
+        tar -zxf oras_0.8.1_*.tar.gz -C oras-install/
+        mv oras-install/oras /usr/local/bin/
+        rm -rf oras_0.8.1_*.tar.gz oras-install/
         docker run --rm -d -p 5000:5000 --name registry registry:2
       displayName: start registry
     - script: |
@@ -194,7 +212,7 @@ stages:
         tag: v$(major).$(minor).$(bulidnum)      
         assets: |
           $(System.DefaultWorkingDirectory)/FhirConverterBuild/bin/**
-          $(System.DefaultWorkingDirectory)/FhirConverterBuild/data/Templates/DefaultTemplates.tar.gz
+          $(System.DefaultWorkingDirectory)/FhirConverterBuild/data/Templates/Hl7v2DefaultTemplates.tar.gz
 
 
 

diff --git a/src/Microsoft.Health.Fhir.Liquid.Converter.FunctionalTests/FunctionalTests.cs b/src/Microsoft.Health.Fhir.Liquid.Converter.FunctionalTests/FunctionalTests.cs
@@ -86,5 +86,22 @@ public void GivenAnInvalidTemplate_WhenConverting_ExceptionsShouldBeThrown()
             var exception = Assert.Throws<RenderException>(() => hl7v2Processor.Convert(@"MSH|^~\&|", "template", new Hl7v2TemplateProvider(templateCollection)));
             Assert.True(exception.InnerException is DotLiquid.Exceptions.StackLevelException);
         }
+
+        [Fact]
+        public void GivenEscapedMessage_WhenConverting_ExpectedCharacterShouldbeReturned()
+        {
+            var hl7v2Processor = new Hl7v2Processor();
+            var templateDirectory = Path.Join(AppDomain.CurrentDomain.BaseDirectory, Constants.TemplateDirectory, "Hl7v2");
+            var inputContent = string.Join("\n", new List<string>
+            {
+                @"MSH|^~\&|FOO|BAR|FOO|BAR|20201225000000|FOO|ADT^A01|123456|P|2.3|||||||||||",
+                @"PR1|1|FOO|FOO^ESCAPED ONE \T\ ESCAPED TWO^BAR|ESCAPED THREE \T\ ESCAPED FOUR|20201225000000||||||||||",
+            });
+            var result = JObject.Parse(hl7v2Processor.Convert(inputContent, "ADT_A01", new Hl7v2TemplateProvider(templateDirectory)));
+
+            var texts = result.SelectTokens("$.entry[?(@.resource.resourceType == 'Procedure')].resource.code.text").Select(Convert.ToString);
+            var expected = new List<string> { "ESCAPED ONE & ESCAPED TWO", "ESCAPED THREE & ESCAPED FOUR" };
+            Assert.NotEmpty(texts.Intersect(expected));
+        }
     }
 }