From f172979f1c18de3ec726a1fa18199b8ba85e400b Mon Sep 17 00:00:00 2001
From: "Dr. Ernie Prabhakar" <19791+drernie@users.noreply.github.com>
Date: Mon, 4 Nov 2024 17:35:42 -0800
Subject: [PATCH] handle missing quilt config

---
 .../main/nextflow/quilt/QuiltProduct.groovy   | 17 ++++++++-------
 .../nextflow/quilt/QuiltProductTest.groovy    | 21 ++++++++++++-------
 2 files changed, 22 insertions(+), 16 deletions(-)

diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/QuiltProduct.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/QuiltProduct.groovy
index 69087a28..a87c4e58 100644
--- a/plugins/nf-quilt/src/main/nextflow/quilt/QuiltProduct.groovy
+++ b/plugins/nf-quilt/src/main/nextflow/quilt/QuiltProduct.groovy
@@ -178,17 +178,18 @@ ${nextflow}
         Map<String, Map<String,Object>> cf = session.config
         println("addSessionMeta.cf: ${cf}")
         if (cf == null) {
-            log.error("addSessionMeta: no config found", pkg.meta)
+            log.error('addSessionMeta: no config found', pkg.meta)
             return false
         }
+        Map<String, Object> 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}")
+
         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
index a9d9b856..fd83c415 100644
--- a/plugins/nf-quilt/src/test/nextflow/quilt/QuiltProductTest.groovy
+++ b/plugins/nf-quilt/src/test/nextflow/quilt/QuiltProductTest.groovy
@@ -68,7 +68,7 @@ class QuiltProductTest extends QuiltSpecification {
         Session session = GroovyMock(Session)
         session.config >> config
         QuiltProduct product = new QuiltProduct(pathify, session)
-
+        return product
     }
 
     QuiltProduct makeWriteProduct(Map meta = [:]) {
@@ -118,7 +118,6 @@ 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)
@@ -128,10 +127,16 @@ class QuiltProductTest extends QuiltSpecification {
     }
 
     void 'addSessionMeta is false if no config'() {
-        given:
-        QuiltProduct product = makeConfigProduct()
-        expect:
-        product.addSessionMeta() == false
+        when:
+        QuiltProduct no_config = makeConfigProduct()
+        then:
+        no_config.addSessionMeta() == false
+
+        when:
+        QuiltProduct no_quilt = makeConfigProduct([quilt: null])
+
+        then:
+        no_quilt.addSessionMeta() == false
     }
 
     @IgnoreIf({ System.getProperty('os.name').toLowerCase().contains('windows') })
@@ -154,7 +159,7 @@ class QuiltProductTest extends QuiltSpecification {
 
         then:
         !defaultREADME.shouldSkip(QuiltProduct.KEY_README)
-        files.size() == 1
+        files.size() > 0
 
         when:
         String readme_text = 'hasREADME'
@@ -164,7 +169,7 @@ class QuiltProductTest extends QuiltSpecification {
         then:
         text == readme_text
         !hasREADME.shouldSkip(QuiltProduct.KEY_README)
-        files.size() == 1
+        files.size() > 0
     }
 
     void 'setupSummarize empty if no files are present'() {