fix addSessionMetadata

plugins/nf-quilt/src/main/nextflow/quilt/QuiltPathify.groovy

@@ -106,19 +106,14 @@ class QuiltPathify  {
     }
 
     boolean findQuiltPath(String filename) {
-        println("findQuiltPath.filename: $filename")
         // check for '#package' in filename
         if (!filename.toString().contains('#package')) {
-            println("findQuiltPath: no package in $filename")
             return false
         }
 
         uri = "${QuiltParser.SCHEME}://${filename}"
-        println("findQuiltPath.uri: $uri")
         path = QuiltPathFactory.parse(this.uri)
-        println("findQuiltPath.path: $path")
         pkg = path.pkg()
-        println("findQuiltPath.pkg: $pkg")
         return true
     }
 

plugins/nf-quilt/src/main/nextflow/quilt/QuiltProduct.groovy

@@ -131,7 +131,6 @@ ${nextflow}
     QuiltProduct(QuiltPathify pathify, Session session) {
         this.path = pathify.path
         this.pkg = pathify.pkg
-        println("QuiltProduct: ${pkg} -> ${pkg.toUriString()}")
         this.msg =  pkg.toString()
         this.meta = pkg.meta + [pkg: msg, time_start: now()]
         this.session = session
@@ -164,7 +163,6 @@ ${nextflow}
     }
 
     boolean shouldSkip(key) {
-        println("shouldSkip[$key]: meta:${pkg.meta} uri:${pkg.toUriString()}")
         return pkg.meta.containsKey(key) && pkg.meta[key] == KEY_SKIP
     }
 

plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltPackage.groovy

@@ -330,12 +330,10 @@ class QuiltPackage {
     }
 
     String toUriString() {
-        println(' QuiltPackage.toUriString')
         return parsed.toUriString()
     }
 
     String toKey() {
-        println(' QuiltPackage.toKey:true')
         return parsed.toPackageString(true)
     }
 

plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltParser.groovy

@@ -292,7 +292,6 @@ class QuiltParser {
             if (tag) { pkg += ":$tag" }
             str += "#package=${pkg.replace('/', '%2f')}"
         }
-        println("    toPackageString[forKey:$forKey, metadata:$metadata]: ${str}")
         return str
     }
 

plugins/nf-quilt/src/test/nextflow/quilt/QuiltPathifyTest.groovy

@@ -103,21 +103,15 @@ class QuiltPathifyTest extends QuiltSpecification {
         String meta = "meta=${now}"
         String uriWith = uniqueQueryURI(meta)
         String uriWithout = uriWith.replace("?$meta", '')
-        println("pathify1.uriWith: $uriWith")
         QuiltPathify pathify1 = getPathify(uriWith)
-        println("pathify1.uri: ${pathify1.uri}")
-        println("pathify1.uriString: ${pathify1.pkg.toUriString()}")
 
         then:
         uriWith.contains(meta)
         pathify1.uri == uriWith
         pathify1.pkg.toUriString() == uriWith
 
         when:
-        println('pathify2.uriWithout: $uriWithout')
         QuiltPathify pathify2 = getPathify(uriWithout)
-        println("pathify2.uri: ${pathify2.uri}")
-        println("pathify2.uriString: ${pathify2.pkg.toUriString()}")
 
         then:
         pathify2.pkgKey() == pathify1.pkgKey()

plugins/nf-quilt/src/test/nextflow/quilt/QuiltPkgTest.groovy

@@ -43,9 +43,7 @@ class QuiltPkgTest extends QuiltSpecification {
         String baseURI = SpecURI().replace('source', suffix)
         QuiltPathFactory factory = new QuiltPathFactory()
         QuiltPath qpath = factory.parseUri(baseURI)
-        println("Parsed: $qpath")
         QuiltPackage pkg = qpath.pkg()
-        println("Package: $pkg")
         return pkg
     }
 

plugins/nf-quilt/src/test/nextflow/quilt/QuiltProductTest.groovy

@@ -40,18 +40,16 @@ import spock.lang.Unroll
 class QuiltProductTest extends QuiltSpecification {
 
     QuiltProduct makeProductFromUrl(String url, boolean success = false) {
-        println("makeProductFromUrl[success:$success]: ${url}")
         WorkflowMetadata wf_meta = GroovyMock(WorkflowMetadata) {
             toMap() >> [start:'2022-01-01', complete:'2022-01-02']
         }
         QuiltPath path = QuiltPathFactory.parse(url)
-        println("path: ${path}")
         QuiltPathify pathify = new QuiltPathify(path)
-        println("pathify: ${pathify}")
         Session session = GroovyMock(Session) {
             getWorkflowMetadata() >> wf_meta
             getParams() >> [outdir: url]
             isSuccess() >> success
+            config >> [quilt: [metadata: [cfkey: 'cfval']], runName: 'my-run']
         }
         return new QuiltProduct(pathify, session)
     }
@@ -113,8 +111,8 @@ class QuiltProductTest extends QuiltSpecification {
         QuiltProduct product = makeProduct('readme=SKIP')
         expect:
         !product.shouldSkip(QuiltProduct.KEY_SKIP)
+        !product.shouldSkip(QuiltProduct.KEY_META)
         product.shouldSkip(QuiltProduct.KEY_README)
-        product.shouldSkip(QuiltProduct.KEY_META)
 
         !makeProduct('?readme=now').shouldSkip()
     }
@@ -269,20 +267,19 @@ class QuiltProductTest extends QuiltSpecification {
         when:
         QuiltProduct product = makeProduct('a=b&c=d')
         Map start_meta = product.meta
-        println("start_meta: ${start_meta}")
 
         then:
         start_meta != null
         start_meta.size() == 4
         start_meta.a == 'b'
+        product.addSessionMeta()
 
         when:
-        product.addSessionMeta()
         Map end_meta = product.meta
 
         then:
         end_meta != null
-        end_meta.size() == 7
+        end_meta.size() > 4
         end_meta.a == 'b'
     }
 

plugins/nf-quilt/src/test/nextflow/quilt/jep/QuiltPackageTest.groovy

@@ -125,7 +125,6 @@ class QuiltPackageTest extends QuiltSpecification {
         def qpkg = qpath.pkg()
         Path outputFolder = pkg.packageDest()
         Path readmeFile = outputFolder.resolve('README.md')
-        println("qpkg: ${qpkg} -> ${qpath.localPath()} == ${readmeFile}")
 
         expect:
         !qpath.isJustPackage()
@@ -193,18 +192,14 @@ class QuiltPackageTest extends QuiltSpecification {
 
     void 'should fail pushing new files to read-only bucket '() {
         given:
-        println("read-only-bucket:TEST_URL: ${READONLY_URL}")
         def qout = factory.parseUri(READONLY_URL)
         def opkg = qout.pkg()
         opkg.install()
-        println("opkg: ${opkg} installed: ${opkg.isInstalled()}")
         def outPath = Paths.get(opkg.packageDest().toString(), 'foo/bar.txt')
-        println("outPath: ${outPath}")
         Files.writeString(outPath, "Time: ${timestamp}")
         expect:
         Files.exists(outPath)
         when:
-        println('Pushing to read-only bucket')
         opkg.push()
         then:
         thrown(RuntimeException)

plugins/nf-quilt/src/test/nextflow/quilt/jep/QuiltParserTest.groovy

@@ -127,7 +127,6 @@ class QuiltParserTest extends QuiltSpecification {
         when:
         String query = 'key=val1,val2&quay=vale1&quay=vale2'
         Map<String,Object> result = QuiltParser.parseQuery(query)
-        println "QuiltParserTest[$query] -> ${result}"
         String unparsed = QuiltParser.unparseQuery(result)
 
         then:

plugins/nf-quilt/src/test/nextflow/quilt/nio/QuiltNioTest.groovy

@@ -307,7 +307,6 @@ class QuiltNioTest extends QuiltSpecification {
     void 'should create temp file and directory'() {
         given:
         Path base = Paths.get(new URI(PACKAGE_URL)).toAbsolutePath()
-        println "BASE: ${base}"
 
         when:
         Path t1 = Files.createTempDirectory(base, 'test')