Add component descriptions and required columns

OHNLP · Mar 9, 2023 · 664ea2d · 664ea2d
1 parent 8312ecf
commit 664ea2d
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diff --git a/src/main/java/org/ohnlp/familyhistory/FHPostProcessingTransform.java b/src/main/java/org/ohnlp/familyhistory/FHPostProcessingTransform.java
@@ -6,6 +6,7 @@
 import org.apache.beam.sdk.values.PCollectionRowTuple;
 import org.apache.beam.sdk.values.PCollectionTuple;
 import org.apache.beam.sdk.values.Row;
+import org.ohnlp.backbone.api.annotations.ComponentDescription;
 import org.ohnlp.backbone.api.components.OneToManyTransform;
 import org.ohnlp.backbone.api.exceptions.ComponentInitializationException;
 import org.ohnlp.familyhistory.tasks.*;
@@ -14,7 +15,27 @@
 import java.util.List;
 import java.util.Map;
 
+@ComponentDescription(
+        name = "Family History Postprocessing",
+        desc = "Extracts and Creates Family History Relations",
+        requires = {"org.ohnlp.medtagger.backbone.MedTaggerBackboneTransform"}
+)
 public class FHPostProcessingTransform extends OneToManyTransform {
+
+    public Schema getRequiredColumns(String inputTag) {
+        return Schema.of(
+                Schema.Field.of("note_id", Schema.FieldType.STRING),
+                Schema.Field.of("sentid", Schema.FieldType.STRING),
+                Schema.Field.of("concept_code", Schema.FieldType.STRING),
+                Schema.Field.of("matched_sentence", Schema.FieldType.STRING),
+                Schema.Field.of("certainty", Schema.FieldType.STRING),
+                Schema.Field.of("offset", Schema.FieldType.INT32),
+                Schema.Field.of("sent_offset", Schema.FieldType.INT32),
+                Schema.Field.of("semgroups", Schema.FieldType.STRING)
+        );
+    }
+
+
     @Override
     public Map<String, Schema> calculateOutputSchema(Schema schema) {
         return Map.of(

diff --git a/src/main/java/org/ohnlp/familyhistory/GenerateFHIRFamilyHistoryResources.java b/src/main/java/org/ohnlp/familyhistory/GenerateFHIRFamilyHistoryResources.java
@@ -1,11 +1,13 @@
 package org.ohnlp.familyhistory;
 
+import org.apache.beam.sdk.schemas.Schema;
 import org.apache.beam.sdk.transforms.DoFn;
 import org.apache.beam.sdk.transforms.ParDo;
 import org.apache.beam.sdk.values.KV;
 import org.apache.beam.sdk.values.PCollection;
 import org.apache.beam.sdk.values.PDone;
 import org.apache.beam.sdk.values.Row;
+import org.ohnlp.backbone.api.annotations.ComponentDescription;
 import org.ohnlp.backbone.api.annotations.ConfigurationProperty;
 import org.ohnlp.backbone.api.components.LoadFromOne;
 import org.ohnlp.familyhistory.tasks.CreateFHIRResources;
@@ -14,13 +16,32 @@
 import java.io.FileWriter;
 import java.io.IOException;
 
+@ComponentDescription(
+        name = "Generate Family History FHIR Resources",
+        desc = "Generates FamilyMemberHistory FHIR R4 resources embedded within a DocumentReference and outputs as " +
+                "JSON to a specified folder. Note that no patient linkage is performed and as such cross-reference of " +
+                "document to patient IDs may be desirable as a post-processing step.",
+        requires = {"org.ohnlp.familyhistory.FHPostProcessingTransform"}
+)
 public class GenerateFHIRFamilyHistoryResources extends LoadFromOne {
     @ConfigurationProperty(
             path = "fileSystemPath",
             desc = "The path into which to write generated FHIR resources"
     )
     private String workingDir;
 
+    public Schema getRequiredColumns(String inputTag) {
+        return Schema.of(
+                Schema.Field.of("document_id", Schema.FieldType.STRING),
+                Schema.Field.of("family_member", Schema.FieldType.STRING),
+                Schema.Field.of("side", Schema.FieldType.STRING),
+                Schema.Field.of("clinical_entity", Schema.FieldType.STRING),
+                Schema.Field.of("concept_codes", Schema.FieldType.STRING),
+                Schema.Field.of("certainty", Schema.FieldType.STRING)
+        );
+    }
+
+
     @Override
     public void init() {
         this.workingDir = this.workingDir + File.separator + "DocumentReference";