pass unit tests

quiltdata · Oct 30, 2024 · 666f80a · 666f80a
1 parent bdbb79c
commit 666f80a
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Showing 4 changed files with 16 additions and 13 deletions.
diff --git a/README.md b/README.md
@@ -142,7 +142,7 @@ keys to extract only the metadata you need, if present. For example:
 ```groovy
 quilt {
     meta = [pipeline: 'nf-core/rnaseq']
-    msg = "${meta['config']['runName']}: ${meta['cmd']}"
+    msg = "${meta['config']?.get('runName')}: ${meta['cmd']}"
     readme = '''
 # ${pkg}
 

diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/QuiltProduct.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/QuiltProduct.groovy
@@ -173,20 +173,23 @@ ${nextflow}
         }
         Map<String, Map<String,Object>> cf = session.config
         println("addSessionMeta.cf: ${cf}")
-        Map qf = cf.navigate('quilt') as Map<String, Map<String, Object>>
+        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>
         println("addSessionMeta.cmeta: ${cmeta}")
 
         try {
             Map smeta = getMetadata(cf)
             // println("addSessionMeta.smeta: ${smeta}")
-            smeta['quilt'] = [package_id: pkg.toString(), uri: path.toUriString()]
-            msg = "${smeta['config']['runName']}: ${smeta['cmd']}"
+            smeta['quilt'] = qf
             smeta.remove('config')
             meta += smeta + cmeta
+            msg = "${cf.get('runName')}: ${meta['cmd']}"
         } catch (Exception e) {
-            log.error("addSessionMeta.getMetadata failed: ${e.getMessage()}\n{$e}", pkg.meta)
+            println("addSessionMeta.getMetadata failed: $e")
+            log.error("addSessionMeta.getMetadata failed: ${e.getMessage()}", pkg.meta)
             return false
         }
         writeNextflowMetadata(meta, 'metadata')

diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltPackage.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltPackage.groovy
@@ -281,15 +281,15 @@ class QuiltPackage {
         })
     }
     // https://docs.quiltdata.com/v/version-5.0.x/examples/gitlike#install-a-package
-    Manifest push(String msg = 'update', Map meta = [:]) {
+    Manifest push(String msg = 'update', Map meta = [:], String pkg = null) {
         if (isNull()) {
             log.debug('null bucket: no need to push')
             return null
         }
-
+        String pkgName = pkg ?: packageName
         S3PhysicalKey registryPath = new S3PhysicalKey(bucket, '', null)
         Registry registry = new Registry(registryPath)
-        Namespace namespace = registry.getNamespace(packageName)
+        Namespace namespace = registry.getNamespace(pkgName)
 
         Manifest.Builder builder = Manifest.builder()
 
@@ -309,10 +309,10 @@ class QuiltPackage {
         builder.setMetadata((ObjectNode)mapper.valueToTree(fullMeta))
 
         Manifest m = builder.build()
-        log.debug("push[${this.parsed}]: ${m}")
+        log.debug("push[${pkgName}]: ${m}")
         try {
             Manifest manifest = m.push(namespace, "nf-quilt:${today()}-${msg}", parsed.workflowName)
-            log.debug("pushed[${this.parsed}]: ${manifest}")
+            log.debug("pushed[${pkgName}]: ${manifest}")
             return manifest
         } catch (Exception e) {
             log.error('ERROR: Failed to push manifest', e)

diff --git a/plugins/nf-quilt/src/test/nextflow/quilt/QuiltProductTest.groovy b/plugins/nf-quilt/src/test/nextflow/quilt/QuiltProductTest.groovy
@@ -49,7 +49,7 @@ class QuiltProductTest extends QuiltSpecification {
             getWorkflowMetadata() >> wf_meta
             getParams() >> [outdir: url]
             isSuccess() >> success
-            config >> [quilt: [metadata: [cfkey: 'cfval']], runName: 'my-run', publishing: false]
+            config >> [quilt: [meta: [cfkey: 'cfval']], runName: 'my-run', publishing: false]
         }
         return new QuiltProduct(pathify, session)
     }
@@ -187,7 +187,7 @@ class QuiltProductTest extends QuiltSpecification {
     }
 
     @Ignore('Not implemented yet: pushes previous metadata')
-    void 'pushes previous metadata if metadata=SKIP'() {
+    void 'pushes previous metadata if meta=SKIP'() {
         given:
         Map meta = [
             'Name': 'QuiltPackageTest',
@@ -196,7 +196,7 @@ class QuiltProductTest extends QuiltSpecification {
             'Type': 'NGS'
         ]
         Map bad_meta = meta + ['Type': 'Workflow']
-        Map skip_meta = ['metadata': 'SKIP']
+        Map skip_meta = ['meta': 'SKIP']
 
         when:
         makeWriteProduct() // no metadata