Reset, small fixes, test when no loading.

phac-nml · Feb 10, 2025 · ff3d000 · ff3d000
1 parent 307ca6d
commit ff3d000
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Showing 3 changed files with 47 additions and 6 deletions.
diff --git a/plugins/nf-iridanext/src/main/nextflow/iridanext/IridaNextJSONOutput.groovy b/plugins/nf-iridanext/src/main/nextflow/iridanext/IridaNextJSONOutput.groovy
@@ -70,6 +70,13 @@ class IridaNextJSONOutput {
         return this.instance
     }
 
+    @Synchronized
+    public void reset() {
+        this.files = ["global": [], (SAMPLES): [:]]
+        this.metadata = [(SAMPLES): [:]]
+        this.scopeIds = [(SAMPLES): [] as Set<String>]
+    }
+
     public void setMetadataPostProcessor(MetadataPostProcessor processor) {
         this.metadataPostProcessor = processor
     }

diff --git a/plugins/nf-iridanext/src/main/nextflow/iridanext/SamplesheetParser.groovy b/plugins/nf-iridanext/src/main/nextflow/iridanext/SamplesheetParser.groovy
@@ -9,8 +9,9 @@ import nextflow.Session
 import nextflow.plugin.extension.Operator
 import nextflow.plugin.extension.PluginExtensionPoint
 import nextflow.iridanext.IridaNextJSONOutput
+import groovy.util.logging.Slf4j
 
-
+@Slf4j
 class SamplesheetParser extends PluginExtensionPoint {
     private String id_key
 
@@ -27,21 +28,21 @@ class SamplesheetParser extends PluginExtensionPoint {
 
         final next = { it ->
             def meta = it[0]
-            def id = meta[this.id_key]
 
             if(meta instanceof Map<String,Object>)
             {
                 if(meta.containsKey(this.id_key))
                 {
+                    def id = meta[this.id_key]
                     iridaNextJSONOutput.addId(scope, id)
                 }
                 else {
-                    throw new Exception("The expected key (${this.id_key}) was not found in the meta map.")
+                    log.warn("The expected key (${this.id_key}) was not found in the meta map (${meta}).")
                 }
 
             }
             else {
-                throw new Exception("Expected a Map object in channel, but found ${meta}.")
+                log.warn("Expected a Map object in channel, but found ${meta}.")
             }
 
             target.bind(it)

diff --git a/plugins/nf-iridanext/src/test/nextflow/iridanext/SamplesheetParserTest.groovy b/plugins/nf-iridanext/src/test/nextflow/iridanext/SamplesheetParserTest.groovy
@@ -84,8 +84,9 @@ class SamplesheetParserTest extends Dsl2Spec {
                 .of([["id":"sample1"]], [["id":"sample2"]], [["id":"sample3"]])
                 .loadIridaSampleIds()
             '''
-        
+
         final IridaNextJSONOutput iridaNextJSONOutput = IridaNextJSONOutput.getInstance()
+        iridaNextJSONOutput.reset() // Otherwise singleton class attributes persist across tests.
 
         and:
         def result = new MockScriptRunner([:]).setScript(SCRIPT).execute()
@@ -118,6 +119,7 @@ class SamplesheetParserTest extends Dsl2Spec {
             '''
 
         final IridaNextJSONOutput iridaNextJSONOutput = IridaNextJSONOutput.getInstance()
+        iridaNextJSONOutput.reset() // Otherwise singleton class attributes persist across tests.
 
         and:
         def result = new MockScriptRunner([:]).setScript(SCRIPT).execute()
@@ -128,4 +130,35 @@ class SamplesheetParserTest extends Dsl2Spec {
         iridaNextJSONOutput.isValidId(iridaNextJSONOutput.SAMPLES, "sample3")
         iridaNextJSONOutput.isValidId(iridaNextJSONOutput.SAMPLES, "sample4") == false
     }
-}
+
+    def 'Test no loadIridaSampleIds' () {
+        when:
+        def config = [
+            iridanext: [
+                enabled: true,
+                output: [
+                    path: "/tmp/output/output.json.gz"
+                ]
+            ]
+        ]
+        def session = Spy(Session) {
+            getConfig() >> config
+        }
+        def SCRIPT = '''
+            include { loadIridaSampleIds } from 'plugin/nf-iridanext'
+            channel.of([["id":"sample1"], "data1"], [["id":"sample2"], "data2"], [["id":"sample3"], "data3"])
+            '''
+
+        final IridaNextJSONOutput iridaNextJSONOutput = IridaNextJSONOutput.getInstance()
+        iridaNextJSONOutput.reset() // Otherwise singleton class attributes persist across tests.
+
+        and:
+        def result = new MockScriptRunner([:]).setScript(SCRIPT).execute()
+
+        then:
+        iridaNextJSONOutput.isValidId(iridaNextJSONOutput.SAMPLES, "sample1") == false
+        iridaNextJSONOutput.isValidId(iridaNextJSONOutput.SAMPLES, "sample2") == false
+        iridaNextJSONOutput.isValidId(iridaNextJSONOutput.SAMPLES, "sample3") == false
+        iridaNextJSONOutput.isValidId(iridaNextJSONOutput.SAMPLES, "sample4") == false
+    }
+}