Merge branch 'main' of https://github.com/quiltdata/nf-quilt

quiltdata · Oct 16, 2023 · 055adb5 · 055adb5
2 parents f4e751d + d22cff6
commit 055adb5
Show file tree

Hide file tree

Showing 4 changed files with 57 additions and 42 deletions.
diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/QuiltProduct.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/QuiltProduct.groovy
@@ -117,43 +117,29 @@ ${nextflow}
     private final Session session
     private String msg
     private Map meta
-    final Integer pubStatus
 
     QuiltProduct(QuiltPath path, Session session) {
         this.path = path
         this.pkg = path.pkg()
         this.msg =  pkg.toString()
         this.meta = [pkg: msg, time_start: now()]
         this.session = session
-        this.pubStatus = -1
         if (session.isSuccess() || pkg.is_force()) {
-            try {
-                this.pubStatus = publish()
-            }
-            catch (Exception e) {
-                log.error("publish failed: ${e.getMessage()}", pkg.meta)
-            }
+            publish()
         } else {
             log.info("not publishing: ${pkg} [unsuccessful session]")
         }
     }
 
-    int publish() {
+    void publish() {
         log.debug("publish($msg)")
         meta = setupMeta()
         String text = setupReadme()
         log.debug("setupReadme: $text")
         List<Map> quilt_summarize = setupSummarize()
         log.debug("setupSummarize: $quilt_summarize")
-        int rc = pkg.push(msg, meta)
-        log.info("$rc: pushed package[$pkg] $msg")
-        if (rc > 0) {
-            print("ERROR[package push failed]: $pkg\n")
-        } else {
-            print("SUCCESS: $pkg\n")
-        }
-
-        return rc
+        pkg.push(msg, meta)
+        print("SUCCESS: $pkg\n")
     }
 
     boolean shouldSkip(key) {

diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltPackage.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltPackage.groovy
@@ -221,7 +221,7 @@ class QuiltPackage {
         })
     }
     // https://docs.quiltdata.com/v/version-5.0.x/examples/gitlike#install-a-package
-    int push(String msg = 'update', Map meta = [:]) {
+    void push(String msg = 'update', Map meta = [:]) {
         S3PhysicalKey registryPath = new S3PhysicalKey(bucket, '', null)
         Registry registry = new Registry(registryPath)
         Namespace namespace = registry.getNamespace(packageName)
@@ -245,14 +245,7 @@ class QuiltPackage {
 
         Manifest m = builder.build()
 
-        try {
-            m.push(namespace, "nf-quilt:${today()}-${msg}", parsed.workflowName)
-        } catch (WorkflowException e) {
-            return 1
-        } catch (IOException e) {
-            return 1
-        }
-        return 0
+        m.push(namespace, "nf-quilt:${today()}-${msg}", parsed.workflowName)
     }
 
     @Override

diff --git a/plugins/nf-quilt/src/test/nextflow/quilt/QuiltProductTest.groovy b/plugins/nf-quilt/src/test/nextflow/quilt/QuiltProductTest.groovy
@@ -141,15 +141,37 @@ class QuiltProductTest extends QuiltSpecification {
         Map bad_meta = meta + ['Type': 'Workflow']
         Map skip_meta = ['metadata': 'SKIP']
 
+        when:
+        makeWriteProduct() // no metadata
+        then:
+        thrown(com.quiltdata.quiltcore.workflows.WorkflowException)
+
         expect:
-        makeWriteProduct().pubStatus == 1 // no metadata
-        makeWriteProduct(meta).pubStatus == 0 // valid metadata
-        makeWriteProduct().pubStatus == 1 // invalid default metadata
-        makeWriteProduct(bad_meta).pubStatus == 1 // invalid explicit metadata
-        makeWriteProduct(skip_meta).pubStatus == 1 // no default metadata
+        makeWriteProduct(meta) // valid metadata
+
+        when:
+        makeWriteProduct() // invalid default metadata
+        then:
+        thrown(com.quiltdata.quiltcore.workflows.WorkflowException)
+
+        when:
+        makeWriteProduct(bad_meta) // invalid explicit metadata
+        then:
+        thrown(com.quiltdata.quiltcore.workflows.WorkflowException)
+
+        when:
+        makeWriteProduct(skip_meta) // no default metadata
+        then:
+        thrown(com.quiltdata.quiltcore.workflows.WorkflowException)
+
         // NOTE: push does NOT update local registry
+        expect:
         makeWriteProduct().pkg.install() // try to merge existing metadata
-        makeWriteProduct(skip_meta).pubStatus == 1 // still fails on implicit metadata
+
+        when:
+        makeWriteProduct(skip_meta) // still fails on implicit metadata
+        then:
+        thrown(com.quiltdata.quiltcore.workflows.WorkflowException)
     }
 
     void writeFile(root, filename) {
@@ -188,7 +210,7 @@ class QuiltProductTest extends QuiltSpecification {
         QuiltProduct product = new QuiltProduct(path, session)
 
         expect:
-        product.publish() == 0
+        product.publish()
         sumPkg.install()
         Files.exists(Paths.get(sumPkg.packageDest().toString(), QuiltProduct.SUMMARY_FILE))
     }

diff --git a/plugins/nf-quilt/src/test/nextflow/quilt/jep/QuiltPackageTest.groovy b/plugins/nf-quilt/src/test/nextflow/quilt/jep/QuiltPackageTest.groovy
@@ -154,7 +154,10 @@ class QuiltPackageTest extends QuiltSpecification {
         Files.writeString(outPath, "Time: ${timestamp}")
         expect:
         Files.exists(outPath)
-        opkg.push() != 0
+        when:
+        opkg.push()
+        then:
+        thrown(java.io.IOException)
     }
 
     @IgnoreIf({ env.WRITE_BUCKET == 'quilt-example' || env.WRITE_BUCKET ==  null })
@@ -176,7 +179,7 @@ class QuiltPackageTest extends QuiltSpecification {
         Files.writeString(outPath, "Time: ${timestamp}")
         expect:
         Files.exists(outPath)
-        opkg.push() == 0
+        opkg.push()
         opkg.reset()
         !Files.exists(outPath)
         opkg.install() // returns Path
@@ -190,16 +193,18 @@ class QuiltPackageTest extends QuiltSpecification {
         QuiltPackage opkg = writeablePackage('observer')
         Map meta =  ['key': "val=\'(key)\'"]
         expect:
-        opkg.push('msg', meta) == 0
+        opkg.push('msg', meta)
     }
 
     @IgnoreIf({ env.WRITE_BUCKET == 'quilt-example' || env.WRITE_BUCKET ==  null })
     void 'should fail if invalid workflow'() {
         given:
         String pkgName = "workflow-bad-${timestamp}"
         QuiltPackage bad_wf = writeablePackage(pkgName, 'missing-workflow')
-        expect:
-        bad_wf.push('missing-workflow first time', [:]) == 1
+        when:
+        bad_wf.push('missing-workflow first time', [:])
+        then:
+        thrown(com.quiltdata.quiltcore.workflows.WorkflowException)
     }
 
     @IgnoreIf({ env.WRITE_BUCKET == 'quilt-example' || env.WRITE_BUCKET ==  null })
@@ -213,10 +218,19 @@ class QuiltPackageTest extends QuiltSpecification {
         ]
         Map bad_meta = meta + ['Type': 'Workflow']
         QuiltPackage good_wf = writeablePackage('workflow-good', 'my-workflow')
+
+        when:
+        good_wf.push('empty meta', [:])
+        then:
+        thrown(com.quiltdata.quiltcore.workflows.WorkflowException)
+
+        when:
+        good_wf.push('bad_meta', bad_meta)
+        then:
+        thrown(com.quiltdata.quiltcore.workflows.WorkflowException)
+
         expect:
-        good_wf.push('empty meta', [:]) == 1
-        good_wf.push('bad_meta', bad_meta) == 1
-        good_wf.push('my-workflow', meta) == 0
+        good_wf.push('my-workflow', meta)
     }
 
 }