Moving to singleton design.

phac-nml · Jan 31, 2025 · ea4271c · ea4271c
1 parent 60263fc
commit ea4271c
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Showing 3 changed files with 38 additions and 7 deletions.
diff --git a/plugins/nf-iridanext/src/main/nextflow/iridanext/IridaNextJSONOutput.groovy b/plugins/nf-iridanext/src/main/nextflow/iridanext/IridaNextJSONOutput.groovy
@@ -31,6 +31,7 @@ import net.jimblackler.jsonschemafriend.ValidationException
 import nextflow.iridanext.MetadataPostProcessor
 
 import groovy.transform.CompileStatic
+import groovy.transform.Synchronized
 import groovy.json.JsonOutput
 import groovy.util.logging.Slf4j
 
@@ -40,24 +41,35 @@ class IridaNextJSONOutput {
     public static final Schema defaultSchema = loadDefaultOutputSchema()
     public static final String SAMPLES = "samples"
 
+    private static IridaNextJSONOutput instance;
+
     private Map files = ["global": [], (SAMPLES): [:]]
     private Map metadata = [(SAMPLES): [:]]
-    private static Map<String,Set<String>> scopeIds = [(SAMPLES): [] as Set<String>]
+    private Map<String,Set<String>> scopeIds = [(SAMPLES): [] as Set<String>]
     private Path relativizePath
     private Boolean shouldRelativize
     private Schema jsonSchema
     private Boolean validate
     private MetadataPostProcessor metadataPostProcessor
 
 
-    public IridaNextJSONOutput(Path relativizePath = null,
+    private IridaNextJSONOutput(Path relativizePath = null,
         Schema jsonSchema = null, Boolean validate = false) {
         this.relativizePath = relativizePath
         this.shouldRelativize = (this.relativizePath != null)
         this.jsonSchema = jsonSchema
         this.validate = validate
     }
 
+    @Synchronized
+    public static IridaNextJSONOutput getInstance() {
+        if(this.instance == null) {
+            this.instance = new IridaNextJSONOutput()
+        }
+
+        return this.instance
+    }
+
     public void setMetadataPostProcessor(MetadataPostProcessor processor) {
         this.metadataPostProcessor = processor
     }
@@ -75,10 +87,18 @@ class IridaNextJSONOutput {
         return validate
     }
 
+    public void setValidate(Boolean validate) {
+        this.validate = validate
+    }
+
     public Schema getOutputSchema() {
         return jsonSchema
     }
 
+    public void setOutputSchema(Schema jsonSchema) {
+        this.jsonSchema = jsonSchema
+    }
+
     public Boolean getShouldRelativize() {
         return shouldRelativize
     }
@@ -87,6 +107,10 @@ class IridaNextJSONOutput {
         return relativizePath
     }
 
+    public void setRelativizePath(Path relativizePath) {
+        this.relativizePath = relativizePath
+    }
+
     public void appendMetadata(String scope, Map data) {
         if (scope in metadata.keySet()) {
             Map validMetadata = data.collectEntries { k, v ->
@@ -101,7 +125,8 @@ class IridaNextJSONOutput {
         }
     }
 
-    public static void addId(String scope, String id) {
+    @Synchronized
+    public void addId(String scope, String id) {
         log.trace "Adding scope=${scope} id=${id}"
         scopeIds[scope].add(id)
     }

diff --git a/plugins/nf-iridanext/src/main/nextflow/iridanext/IridaNextObserver.groovy b/plugins/nf-iridanext/src/main/nextflow/iridanext/IridaNextObserver.groovy
@@ -211,7 +211,11 @@ class IridaNextObserver implements TraceObserver {
             this.samplesMetadataParsers = this.samplesMetadataParsers.findAll()
         }
 
-        iridaNextJSONOutput = new IridaNextJSONOutput(relativizePath, jsonSchema, validate)
+        iridaNextJSONOutput = IridaNextJSONOutput.getInstance()
+        iridaNextJSONOutput.setRelativizePath(relativizePath)
+        iridaNextJSONOutput.setOutputSchema(jsonSchema)
+        iridaNextJSONOutput.setValidate(validate)
+
         iridaNextJSONOutput.setMetadataPostProcessor(metadataPostProcessor)
     }
 

diff --git a/plugins/nf-iridanext/src/main/nextflow/iridanext/SamplesheetParser.groovy b/plugins/nf-iridanext/src/main/nextflow/iridanext/SamplesheetParser.groovy
@@ -20,15 +20,17 @@ class SamplesheetParser extends PluginExtensionPoint {
     }
 
     @Operator
-    DataflowWriteChannel parseSamplesheet( DataflowReadChannel source ) {
+    DataflowWriteChannel loadIridaSampleIds( DataflowReadChannel source ) {
         final target = CH.createBy(source)
         final String scope = IridaNextJSONOutput.SAMPLES
+        final IridaNextJSONOutput iridaNextJSONOutput = IridaNextJSONOutput.getInstance()
 
         final next = { it ->
-            def meta = it[0]
+            // Check that it's a map and the id_key exists, ignore and warn otherwise / trace
+            def meta = it[0] // TODO: Check with workflow that's not just metadata
             def id = meta[this.id_key]
 
-            IridaNextJSONOutput.addId(scope, id)
+            iridaNextJSONOutput.addId(scope, id)
             target.bind(it)
         }