258 handle null configs (#259)

Co-authored-by: Dr. Ernie Prabhakar <[email protected]>
quiltdata · Nov 5, 2024 · 81f4083 · 81f4083
1 parent c973252
commit 81f4083
Show file tree

Hide file tree

Showing 5 changed files with 42 additions and 4 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -8,6 +8,11 @@
 - Improve handling of dynamically-specified URIs
 - Rewrite README.md, splitting out developer documentation to README_DEV.md
 
+## [0.8.10] 2024-11-4 UNPUBLISHED
+
+- Ignore publish to 'home'
+- Fix: Cannot set property 'package_id' on null object
+
 ## [0.8.9] 2024-10-31 UNPUBLISHED
 
 - Handle multiple/internal publishDir calls

diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/QuiltPathify.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/QuiltPathify.groovy
@@ -156,6 +156,11 @@ class QuiltPathify  {
     }
 
     boolean isBucketAccessible() {
+        // ignore internal publishing from work dir
+        if (path.getBucket() == 'home') {
+            log.warn('isBucketAccessible: ignoring `home` bucket')
+            return false
+        }
         return pkg.isBucketAccessible()
     }
 

diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/QuiltProduct.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/QuiltProduct.groovy
@@ -170,12 +170,18 @@ ${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>
+        if (cf == null) {
+            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}")

diff --git a/plugins/nf-quilt/src/resources/META-INF/MANIFEST.MF b/plugins/nf-quilt/src/resources/META-INF/MANIFEST.MF
@@ -1,7 +1,7 @@
 Manifest-Version: 1.0
 Plugin-Class: nextflow.quilt.QuiltPlugin
 Plugin-Id: nf-quilt
-Plugin-Version: 0.8.9
+Plugin-Version: 0.8.10
 Plugin-Provider: Quilt Data
 Plugin-Requires: >=22.10.6
 
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)
+        return product
+    }
+
     QuiltProduct makeWriteProduct(Map meta = [:]) {
         String subURL = writeableURI('quilt_product_test') // + '&workflow=universal'
         if (meta) {
@@ -117,6 +126,19 @@ class QuiltProductTest extends QuiltSpecification {
         !makeProduct('?readme=now').shouldSkip()
     }
 
+    void 'addSessionMeta is false if no config'() {
+        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') })
     void 'does not create README if readme=SKIP'() {
         given:
@@ -137,7 +159,7 @@ class QuiltProductTest extends QuiltSpecification {
 
         then:
         !defaultREADME.shouldSkip(QuiltProduct.KEY_README)
-        files.size() == 1
+        files.size() > 0
 
         when:
         String readme_text = 'hasREADME'
@@ -147,7 +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'() {