Update to backbone v3.0.0 api

pom.xml

@@ -6,7 +6,7 @@
 
     <groupId>org.ohnlp.medtagger</groupId>
     <artifactId>medtagger</artifactId>
-    <version>1.0.55</version>
+    <version>1.0.56</version>
     <description>The MedTagger biomedical information extraction pipeline</description>
 
 
@@ -141,7 +141,7 @@
     <properties>
         <uimaj.version>2.10.0</uimaj.version>
         <uimafit.version>2.5.0</uimafit.version>
-        <backbone.version>2.0.0</backbone.version>
+        <backbone.version>3.0.0</backbone.version>
     </properties>
 
     <dependencies>

src/main/java/org/ohnlp/medtagger/backbone/MedTaggerBackboneTransform.java

@@ -1,8 +1,5 @@
 package org.ohnlp.medtagger.backbone;
 
-import com.fasterxml.jackson.databind.JsonNode;
-import com.fasterxml.jackson.databind.node.JsonNodeFactory;
-import com.fasterxml.jackson.databind.node.ObjectNode;
 import org.apache.beam.sdk.schemas.Schema;
 import org.apache.beam.sdk.transforms.DoFn;
 import org.apache.beam.sdk.transforms.ParDo;
@@ -24,7 +21,9 @@
 import org.apache.uima.util.CasCreationUtils;
 import org.apache.uima.util.InvalidXMLException;
 import org.joda.time.Instant;
-import org.ohnlp.backbone.api.Transform;
+import org.ohnlp.backbone.api.annotations.ComponentDescription;
+import org.ohnlp.backbone.api.annotations.ConfigurationProperty;
+import org.ohnlp.backbone.api.components.OneToOneTransform;
 import org.ohnlp.backbone.api.exceptions.ComponentInitializationException;
 import org.ohnlp.medtagger.context.RuleContextAnnotator;
 import org.ohnlp.medtagger.type.ConceptMention;
@@ -48,25 +47,54 @@
 /**
  * An implementation of a MedTagger pipeline as an OHNLP Backbone Transform component
  */
-public class MedTaggerBackboneTransform extends Transform {
+@ComponentDescription(
+        name = "MedTagger NLP",
+        desc = "Executes a MedTagger IE or Dictionary-Based Ruleset as a Backbone Component"
+)
+public class MedTaggerBackboneTransform extends OneToOneTransform {
 
+    @ConfigurationProperty(
+            path = "input",
+            desc = "Column to use as input"
+    )
     private String inputField;
+
+    @ConfigurationProperty(
+            path = "mode",
+            desc = "Whether to use IE or dictionary-based rulesets, or both, or retrieve from web. Defaults to STANDALONE_IE_ONLY",
+            required = false
+    )
+    private RunMode mode = RunMode.STANDALONE_IE_ONLY;
+    @ConfigurationProperty(
+            path = "ruleset",
+            desc = "The ruleset definition as located within the resources folder, or the dictionary name, " +
+                    "or resources folder|dictionary name if both, or URL if in web mode"
+    )
     private String resources;
-    private RunMode mode;
-    private String noteIdField;
+    @ConfigurationProperty(
+            path = "identifier_col",
+            desc = "The column to use as a note identifier. Defaults to note_id",
+            required = false
+    )
+    private String noteIdField = "note_id";
     private Schema outputSchema;
     private boolean outputJSON;
 
     @Override
-    public void initFromConfig(JsonNode config) throws ComponentInitializationException {
-        try {
-            this.inputField = config.get("input").asText();
-            this.mode = config.has("mode") ? RunMode.valueOf(config.get("mode").textValue().toUpperCase(Locale.ROOT)) : RunMode.STANDALONE;
-            this.resources = config.get("ruleset").asText();
-            this.noteIdField = config.has("identifier_col") ? config.get("identifier_col").asText() : "note_id";
-        } catch (Throwable t) {
-            throw new ComponentInitializationException(t);
-        }
+    public void init() throws ComponentInitializationException {
+    }
+
+    @Override
+    public boolean hasRequiredColumns() {
+        return true;
+    }
+
+    @Override
+    public Schema getRequiredColumns() {
+        return Schema.of(
+                Schema.Field.of(this.noteIdField, Schema.FieldType.STRING),
+                Schema.Field.of(this.inputField, Schema.FieldType.STRING)
+        );
     }
 
     @Override

src/main/java/org/ohnlp/medtagger/backbone/MedTaggerOutputToOHDSIFormatTransform.java

@@ -10,6 +10,9 @@
 import org.apache.beam.sdk.values.Row;
 import org.joda.time.Instant;
 import org.ohnlp.backbone.api.Transform;
+import org.ohnlp.backbone.api.annotations.ComponentDescription;
+import org.ohnlp.backbone.api.annotations.ConfigurationProperty;
+import org.ohnlp.backbone.api.components.OneToOneTransform;
 import org.ohnlp.backbone.api.exceptions.ComponentInitializationException;
 
 import java.io.BufferedReader;
@@ -27,17 +30,21 @@
  * <p>
  * Note: Assumes that rulesets supply a concept normalization -> OHDSI concept id mapping in ohdsi_mappings.txt
  */
-public class MedTaggerOutputToOHDSIFormatTransform extends Transform {
+@ComponentDescription(
+        name = "MedTagger to OHDSI CDM Format Transform",
+        desc = "Converts MedTagger Output into one complaint with the OHDSI OMOP CDM note_nlp table",
+        requires = {"org.ohnlp.medtagger.backbone.MedTaggerBackboneTransform"}
+)
+public class MedTaggerOutputToOHDSIFormatTransform extends OneToOneTransform {
     private static ThreadLocal<SimpleDateFormat> sdf = ThreadLocal.withInitial(() -> new SimpleDateFormat("yyy-MM-dd'T'HH:mm:ssXXX"));
+
+    @ConfigurationProperty(
+            path = "ruleset",
+            desc = "The ruleset folder containing a ohdsi_mappings.txt to map output concepts to OHDSI Athena concept codes, or NONE if output already in Athena concept code format"
+    )
     private String resources;
     private Schema schema;
 
-
-    @Override
-    public void initFromConfig(JsonNode config) throws ComponentInitializationException {
-        this.resources = config.get("ruleset").asText();
-    }
-
     @Override
     public Schema calculateOutputSchema(Schema schema) {
         List<Schema.Field> fields = new LinkedList<>(schema.getFields());
@@ -144,4 +151,8 @@ public void processElement(@Element Row input, OutputReceiver<Row> output) throw
     }
 
 
+    @Override
+    public void init() throws ComponentInitializationException {
+
+    }
 }