Add version, kind, and spec to lineage schema

modules/nf-commons/src/main/nextflow/serde/gson/RuntimeTypeAdapterFactory.java

@@ -251,6 +251,18 @@ public RuntimeTypeAdapterFactory<T> registerSubtype(Class<? extends T> type) {
         return registerSubtype(type, type.getSimpleName());
     }
 
+    protected Class<?> getSubTypeFromLabel(String label){
+        return labelToSubtype.get(label);
+    }
+
+    protected String getLabelFromSubtype(Class<?> subType){
+        return subtypeToLabel.get(subType);
+    }
+
+    protected String getTypeFieldName(){
+        return typeFieldName;
+    }
+
     @Override
     public <R> TypeAdapter<R> create(Gson gson, TypeToken<R> type) {
         if (type == null) {

modules/nf-lineage/src/main/nextflow/lineage/serde/LinTypeAdapterFactory.groovy

@@ -16,15 +16,13 @@
 package nextflow.lineage.serde
 
 import com.google.gson.Gson
-import com.google.gson.JsonElement
 import com.google.gson.JsonObject
 import com.google.gson.JsonParseException
 import com.google.gson.JsonParser
 import com.google.gson.TypeAdapter
 import com.google.gson.reflect.TypeToken
 import com.google.gson.stream.JsonReader
 import com.google.gson.stream.JsonWriter
-
 import groovy.transform.CompileStatic
 import nextflow.lineage.model.v1beta1.FileOutput
 import nextflow.lineage.model.v1beta1.LinModel
@@ -34,15 +32,16 @@ import nextflow.lineage.model.v1beta1.Workflow
 import nextflow.lineage.model.v1beta1.WorkflowOutput
 import nextflow.lineage.model.v1beta1.WorkflowRun
 import nextflow.serde.gson.RuntimeTypeAdapterFactory
-
 /**
  * Class to serialize LiSerializable objects including the Lineage model version.
  *
  * @author Jorge Ejarque <jorge.ejarque@seqera.io>
  */
 @CompileStatic
 class LinTypeAdapterFactory<T> extends RuntimeTypeAdapterFactory<T> {
+
     public static final String VERSION_FIELD = 'version'
+    public static final String SPEC_FIELD = 'spec'
     public static final String CURRENT_VERSION = LinModel.VERSION
 
     LinTypeAdapterFactory() {
@@ -53,7 +52,6 @@ class LinTypeAdapterFactory<T> extends RuntimeTypeAdapterFactory<T> {
             .registerSubtype(TaskRun, TaskRun.simpleName)
             .registerSubtype(TaskOutput, TaskOutput.simpleName)
             .registerSubtype(FileOutput, FileOutput.simpleName)
-
     }
 
     @Override
@@ -70,39 +68,43 @@ class LinTypeAdapterFactory<T> extends RuntimeTypeAdapterFactory<T> {
         return new TypeAdapter<R>() {
             @Override
             void write(JsonWriter out, R value) throws IOException {
-                def json = delegate.toJsonTree(value)
-                if (json instanceof JsonObject) {
-                    json = addVersion(json)
-                }
-                gson.toJson(json, out)
+                final object = new JsonObject()
+                object.addProperty(VERSION_FIELD, CURRENT_VERSION)
+                String label = getLabelFromSubtype(value.class)
+                if (!label)
+                     throw new JsonParseException("Not registered class ${value.class}")
+                object.addProperty(getTypeFieldName(), label)
+                def json = gson.toJsonTree(value)
+                object.add(SPEC_FIELD, json)
+                gson.toJson(object, out)
             }
 
             @Override
             R read(JsonReader reader) throws IOException {
-                def json = JsonParser.parseReader(reader)
-                if (json instanceof JsonObject) {
-                    def obj = (JsonObject) json
-                    def versionEl = obj.get(VERSION_FIELD)
-                    if (versionEl == null || versionEl.asString != CURRENT_VERSION) {
-                        throw new JsonParseException("Invalid or missing version")
-                    }
+                final obj = JsonParser.parseReader(reader)?.getAsJsonObject()
+                if( obj==null )
+                    throw new JsonParseException("Parsed JSON object is null")
+                final versionEl = obj.get(VERSION_FIELD)
+                if (versionEl == null || versionEl.asString != CURRENT_VERSION) {
+                    throw new JsonParseException("Invalid or missing '${VERSION_FIELD}' JSON property")
+                }
+                final typeEl = obj.get(getTypeFieldName())
+                if( typeEl==null )
+                    throw new JsonParseException("JSON property '${getTypeFieldName()}' not found")
+
+                // Check if this is the new format (has 'spec' field) or old format (data at root level)
+                final specEl = obj.get(SPEC_FIELD)?.asJsonObject
+                if ( specEl != null ) {
+                    // New format: data is wrapped in 'spec' field
+                    specEl.add(getTypeFieldName(), typeEl)
+                    return (R) delegate.fromJsonTree(specEl)
+                } else {
+                    // Old format: data is at root level, just remove version field
                     obj.remove(VERSION_FIELD)
+                    return (R) delegate.fromJsonTree(obj)
                 }
-                return delegate.fromJsonTree(json)
             }
         }
     }
 
-    private static JsonObject addVersion(JsonObject json){
-        if( json.has(VERSION_FIELD) )
-            throw new JsonParseException("object already defines a field named ${VERSION_FIELD}")
-
-        JsonObject clone = new JsonObject();
-        clone.addProperty(VERSION_FIELD, CURRENT_VERSION)
-        for (Map.Entry<String, JsonElement> e : json.entrySet()) {
-            clone.add(e.getKey(), e.getValue());
-        }
-        return clone
-    }
-
 }

modules/nf-lineage/src/test/nextflow/lineage/cli/LinCommandImplTest.groovy

@@ -387,27 +387,27 @@ class LinCommandImplTest extends Specification{
         def expectedOutput = '''diff --git 12345 67890
 --- 12345
 +++ 67890
-@@ -1,16 +1,16 @@
- {
+@@ -2,16 +2,16 @@
    "version": "lineage/v1beta1",
    "kind": "FileOutput",
--  "path": "path/to/file",
-+  "path": "path/to/file2",
-   "checksum": {
--    "value": "45372qe",
-+    "value": "42472qet",
-     "algorithm": "nextflow",
-     "mode": "standard"
-   },
--  "source": "lid://123987/file.bam",
-+  "source": "lid://123987/file2.bam",
-   "workflowRun": "lid://123987/",
-   "taskRun": null,
--  "size": 1234,
-+  "size": 1235,
-   "createdAt": "1970-01-02T10:17:36.789Z",
-   "modifiedAt": "1970-01-02T10:17:36.789Z",
-   "labels": null
+   "spec": {
+-    "path": "path/to/file",
++    "path": "path/to/file2",
+     "checksum": {
+-      "value": "45372qe",
++      "value": "42472qet",
+       "algorithm": "nextflow",
+       "mode": "standard"
+     },
+-    "source": "lid://123987/file.bam",
++    "source": "lid://123987/file2.bam",
+     "workflowRun": "lid://123987/",
+     "taskRun": null,
+-    "size": 1234,
++    "size": 1235,
+     "createdAt": "1970-01-02T10:17:36.789Z",
+     "modifiedAt": "1970-01-02T10:17:36.789Z",
+     "labels": null
 '''
 
         when:

modules/nf-lineage/src/test/nextflow/lineage/fs/LinFileSystemProviderTest.groovy

@@ -123,7 +123,7 @@ class LinFileSystemProviderTest extends Specification {
         def output = data.resolve("output.txt")
         output.text = "Hello, World!"
         outputMeta.mkdirs()
-        outputMeta.resolve(".data.json").text = '{"version":"lineage/v1beta1","kind":"FileOutput","path":"'+output.toString()+'"}'
+        outputMeta.resolve(".data.json").text = '{"version":"lineage/v1beta1","kind":"FileOutput","spec":{"path":"'+output.toString()+'"}}'
 
         Global.session = Mock(Session) { getConfig()>>config }
         and:
@@ -179,7 +179,7 @@ class LinFileSystemProviderTest extends Specification {
         def config = [lineage:[store:[location:wdir.toString()]]]
         def outputMeta = wdir.resolve("12345")
         outputMeta.mkdirs()
-        outputMeta.resolve(".data.json").text = '{"version":"lineage/v1beta1","kind":"WorkflowRun","sessionId":"session","name":"run_name","params":[{"type":"String","name":"param1","value":"value1"}]}'
+        outputMeta.resolve(".data.json").text = '{"version":"lineage/v1beta1","kind":"WorkflowRun","spec":{"sessionId":"session","name":"run_name","params":[{"type":"String","name":"param1","value":"value1"}]}}'
 
         Global.session = Mock(Session) { getConfig()>>config }
         and:
@@ -238,7 +238,7 @@ class LinFileSystemProviderTest extends Specification {
         def output = data.resolve("output.txt")
         output.text = "Hello, World!"
         outputMeta.mkdirs()
-        outputMeta.resolve(".data.json").text = '{"version":"lineage/v1beta1","kind":"FileOutput","path":"'+output.toString()+'"}'
+        outputMeta.resolve(".data.json").text = '{"version":"lineage/v1beta1","kind":"FileOutput","spec":{"path":"'+output.toString()+'"}}'
 
         Global.session = Mock(Session) { getConfig()>>config }
         and:
@@ -278,8 +278,8 @@ class LinFileSystemProviderTest extends Specification {
         output1.resolve('file3.txt').text = 'file3'
         wdir.resolve('12345/output1').mkdirs()
         wdir.resolve('12345/output2').mkdirs()
-        wdir.resolve('12345/.data.json').text = '{"version":"lineage/v1beta1","kind":"TaskRun"}'
-        wdir.resolve('12345/output1/.data.json').text = '{"version":"lineage/v1beta1","kind":"FileOutput", "path": "' + output1.toString() + '"}'
+        wdir.resolve('12345/.data.json').text = '{"version":"lineage/v1beta1","kind":"TaskRun","spec":{"name":"dummy"}}'
+        wdir.resolve('12345/output1/.data.json').text = '{"version":"lineage/v1beta1","kind":"FileOutput","spec":{"path": "' + output1.toString() + '"}}'
 
         and:
         def config = [lineage:[store:[location:wdir.toString()]]]
@@ -403,7 +403,7 @@ class LinFileSystemProviderTest extends Specification {
         output.resolve('abc').text = 'file1'
         output.resolve('.foo').text = 'file2'
         wdir.resolve('12345/output').mkdirs()
-        wdir.resolve('12345/output/.data.json').text = '{"version":"lineage/v1beta1","kind":"FileOutput", "path": "' + output.toString() + '"}'
+        wdir.resolve('12345/output/.data.json').text = '{"version":"lineage/v1beta1","kind":"FileOutput","spec":{"path": "' + output.toString() + '"}}'
         and:
         def provider = new LinFileSystemProvider()
         def lid1 = provider.getPath(LinPath.asUri('lid://12345/output/abc'))
@@ -423,7 +423,7 @@ class LinFileSystemProviderTest extends Specification {
         def file = data.resolve('abc')
         file.text = 'Hello'
         wdir.resolve('12345/abc').mkdirs()
-        wdir.resolve('12345/abc/.data.json').text = '{"version":"lineage/v1beta1","kind":"FileOutput", "path":"' + file.toString() + '"}'
+        wdir.resolve('12345/abc/.data.json').text = '{"version":"lineage/v1beta1","kind":"FileOutput","spec":{"path":"' + file.toString() + '"}}'
         and:
         Global.session = Mock(Session) { getConfig()>>config }
         and:

modules/nf-lineage/src/test/nextflow/lineage/fs/LinPathTest.groovy

@@ -161,9 +161,9 @@ class LinPathTest extends Specification {
 
         wdir.resolve('12345/output1').mkdirs()
         wdir.resolve('12345/path/to/file2.txt').mkdirs()
-        wdir.resolve('12345/.data.json').text = '{"version":"lineage/v1beta1","kind":"TaskRun"}'
-        wdir.resolve('12345/output1/.data.json').text = '{"version":"lineage/v1beta1","kind":"FileOutput", "path": "' + outputFolder.toString() + '"}'
-        wdir.resolve('12345/path/to/file2.txt/.data.json').text = '{"version":"lineage/v1beta1","kind":"FileOutput", "path": "' + outputFile.toString() + '"}'
+        wdir.resolve('12345/.data.json').text = '{"version":"lineage/v1beta1","kind":"TaskRun","spec":{"name":"test"}}'
+        wdir.resolve('12345/output1/.data.json').text = '{"version":"lineage/v1beta1","kind":"FileOutput","spec":{"path": "' + outputFolder.toString() + '"}}'
+        wdir.resolve('12345/path/to/file2.txt/.data.json').text = '{"version":"lineage/v1beta1","kind":"FileOutput","spec":{"path": "' + outputFile.toString() + '"}}'
         def time = OffsetDateTime.now()
         def wfResultsMetadata = new LinEncoder().withPrettyPrint(true).encode(new WorkflowOutput(time, "lid://1234", [new Parameter( "Path", "a", "lid://1234/a.txt")]))
         wdir.resolve('5678/').mkdirs()

modules/nf-lineage/src/test/nextflow/lineage/serde/LinEncoderTest.groovy

@@ -167,7 +167,7 @@ class LinEncoderTest extends Specification{
         def encoded = encoder.encode(wfResults)
         def object = encoder.decode(encoded)
         then:
-        encoded == '{"version":"lineage/v1beta1","kind":"WorkflowOutput","createdAt":null,"workflowRun":"lid://1234","output":null}'
+        encoded == '{"version":"lineage/v1beta1","kind":"WorkflowOutput","spec":{"createdAt":null,"workflowRun":"lid://1234","output":null}}'
         def result = object as WorkflowOutput
         result.createdAt == null