skip null config

quiltdata · Nov 5, 2024 · 1bf0225 · 1bf0225
1 parent 0ceff17
commit 1bf0225
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Showing 2 changed files with 30 additions and 8 deletions.
diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/QuiltProduct.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/QuiltProduct.groovy
@@ -170,20 +170,25 @@ ${nextflow}
     }
 
     boolean addSessionMeta() {
+        println("addSessionMeta: ${session}")
         if (shouldSkip(KEY_META)) {
             return false
         }
+
         Map<String, Map<String,Object>> cf = session.config
         println("addSessionMeta.cf: ${cf}")
-        Map qf = cf.navigate('quilt') as Map<String, Object>
-        qf['package_id'] = pkg.toString()
-        qf['uri'] = path.toUriString()
-        println("addSessionMeta.qf: ${qf}")
-        Map<String, Object> cmeta = qf.navigate('meta') as Map<String, Object>
-        qf.remove('meta')
-        println("addSessionMeta.cmeta: ${cmeta}")
-
+        if (cf == null) {
+            log.error("addSessionMeta: no config found", pkg.meta)
+            return false
+        }
         try {
+            Map qf = cf.navigate('quilt') as Map<String, Object>
+            qf['package_id'] = pkg.toString()
+            qf['uri'] = path.toUriString()
+            println("addSessionMeta.qf: ${qf}")
+            Map<String, Object> cmeta = qf.navigate('meta') as Map<String, Object>
+            qf.remove('meta')
+            println("addSessionMeta.cmeta: ${cmeta}")
             Map smeta = getMetadata(cf)
             // println("addSessionMeta.smeta: ${smeta}")
             smeta['quilt'] = qf

diff --git a/plugins/nf-quilt/src/test/nextflow/quilt/QuiltProductTest.groovy b/plugins/nf-quilt/src/test/nextflow/quilt/QuiltProductTest.groovy
@@ -62,6 +62,15 @@ class QuiltProductTest extends QuiltSpecification {
         return makeProductFromUrl(subURL, success)
     }
 
+    QuiltProduct makeConfigProduct(Map config = null) {
+        QuiltPath path = QuiltPathFactory.parse(testURI)
+        QuiltPathify pathify = new QuiltPathify(path)
+        Session session = GroovyMock(Session)
+        session.config >> config
+        QuiltProduct product = new QuiltProduct(pathify, session)
+
+    }
+
     QuiltProduct makeWriteProduct(Map meta = [:]) {
         String subURL = writeableURI('quilt_product_test') // + '&workflow=universal'
         if (meta) {
@@ -109,6 +118,7 @@ class QuiltProductTest extends QuiltSpecification {
     void 'shouldSkip is true if key=SKIP'() {
         given:
         QuiltProduct product = makeProduct('readme=SKIP')
+        Session 
         expect:
         !product.shouldSkip(QuiltProduct.KEY_SKIP)
         !product.shouldSkip(QuiltProduct.KEY_META)
@@ -117,6 +127,13 @@ class QuiltProductTest extends QuiltSpecification {
         !makeProduct('?readme=now').shouldSkip()
     }
 
+    void 'addSessionMeta is false if no config'() {
+        given:
+        QuiltProduct product = makeConfigProduct()
+        expect:
+        product.addSessionMeta() == false
+    }
+
     @IgnoreIf({ System.getProperty('os.name').toLowerCase().contains('windows') })
     void 'does not create README if readme=SKIP'() {
         given: