stub dynamic URIs

quiltdata · Oct 14, 2024 · ef67536 · ef67536
1 parent 2a8738b
commit ef67536
Show file tree

Hide file tree

Showing 6 changed files with 38 additions and 24 deletions.
diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/QuiltPathify.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/QuiltPathify.groovy
@@ -87,7 +87,7 @@ class QuiltPathify  {
         String folder = parts.join('/')
         String sub_path = folder.length() > 0 ? folder + '/' + file : file
 
-        println("uriFromS3File: $bucket/$prefix/$suffix/$sub_path")
+        log.debug("uriFromS3File: $bucket/$prefix/$suffix/$sub_path")
         String base = "quilt+s3://${bucket}#package=${prefix}%2f${suffix}"
         String uri = base + '&path=' + sub_path
         return uri
@@ -119,7 +119,6 @@ class QuiltPathify  {
         println("findQuiltPath.path: $path")
         pkg = path.pkg()
         println("findQuiltPath.pkg: $pkg")
-        println("findQuiltPath.uri2: $uri")
         return true
     }
 
@@ -146,15 +145,8 @@ class QuiltPathify  {
         return pkg.toKey()
     }
 
-    boolean hasRoot() {
-        return (QuiltPackage.hasKey(pkgKey()))
-    }
-
-    QuiltPackage getRoot() {
-        if (hasRoot()) {
-            return QuiltPackage.forKey(pkgKey())
-        }
-        return null
+    String toString() {
+        return "QuiltPathify[${uri}]"
     }
 
 }
diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/QuiltProduct.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/QuiltProduct.groovy
@@ -132,7 +132,7 @@ ${nextflow}
         this.path = pathify.path
         this.pkg = pathify.pkg
         this.msg =  pkg.toString()
-        this.meta = [pkg: msg, time_start: now()]
+        this.meta = pkg.meta + [pkg: msg, time_start: now()]
         this.session = session
 
         if (session.isSuccess() || pkg.is_force()) {
@@ -163,6 +163,7 @@ ${nextflow}
     }
 
     boolean shouldSkip(key) {
+        println("shouldSkip[$key]: ${pkg.meta}")
         return pkg.meta.containsKey(key) && pkg.meta[key] == KEY_SKIP
     }
 
@@ -188,6 +189,7 @@ ${nextflow}
     }
 
     Map getMetadata(Map cf) {
+        // add metadata from quilt and URI
         if (cf != null) {
             cf.remove('executor')
             cf.remove('params')

diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltPackage.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltPackage.groovy
@@ -108,7 +108,7 @@ class QuiltPackage {
             return PKGS.values().last()
         }
 
-        String pkgKey = parsed.toPackageString()
+        String pkgKey = parsed.toPackageString(true) // ignore metadata for Key
         log.debug("QuiltPackage.forParsed[${pkgKey}]")
         def pkg = PKGS.get(pkgKey)
         if (pkg) { return pkg }
@@ -330,11 +330,13 @@ class QuiltPackage {
     }
 
     String toUriString() {
+        println(' QuiltPackage.toUriString')
         return parsed.toUriString()
     }
 
     String toKey() {
-        return parsed.toPackageString()
+        println(' QuiltPackage.toKey:true')
+        return parsed.toPackageString(true)
     }
 
     String meta_overrides(String key, Serializable baseline = null) {

diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltParser.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltParser.groovy
@@ -281,9 +281,9 @@ class QuiltParser {
         return options?.get(key)
     }
 
-    String toPackageString() {
+    String toPackageString(boolean forKey = false) {
         String str = "${getBucket()}"
-        if (metadata) {
+        if (metadata && !forKey) {
             str += "?${unparseQuery(metadata)}"
         }
         if (packageName) {
@@ -292,11 +292,12 @@ class QuiltParser {
             if (tag) { pkg += ":$tag" }
             str += "#package=${pkg.replace('/', '%2f')}"
         }
-        // log.debug("toPackageString: ${str}")
+        println("    toPackageString[forKey:$forKey, metdata:$metadata]: ${str}")
         return str
     }
 
     String toString() {
+        println('  QuiltParser.toString')
         String str = toPackageString()
         if (!hasPath()) { return str }
         str += (packageName) ? '&' : '#'
@@ -314,6 +315,7 @@ class QuiltParser {
     }
 
     String toUriString() {
+        println('  QuiltParser.toUriString')
         return PREFIX + toString()
     }
 

diff --git a/plugins/nf-quilt/src/test/nextflow/quilt/QuiltPathifyTest.groovy b/plugins/nf-quilt/src/test/nextflow/quilt/QuiltPathifyTest.groovy
@@ -88,30 +88,43 @@ class QuiltPathifyTest extends QuiltSpecification {
     void 'test findQuiltPath overrides attributes'() {
         when:
         QuiltPathify pathify = getPathify()
-        println("pathify1: ${pathify.uri}")
         pathify.findQuiltPath('buck#package=prefix%2fsuffix&path=.%2fFILE.md')
-        println("pathify2: ${pathify.uri}")
 
         then:
         pathify.isOverlay == false
         pathify.uri == 'quilt+s3://buck#package=prefix%2fsuffix&path=.%2fFILE.md'
         pathify.path.toString() == 'buck#package=prefix%2fsuffix&path=.%2fFILE.md'
         pathify.pkg.toUriString() == 'quilt+s3://buck#package=prefix%2fsuffix&path=.%2fFILE.md'
-        pathify.pkgKey() == 'buck#package=prefix%2fsuffix'
     }
 
     void 'test findQuiltPath preserves metadata'() {
         when:
-        String pathWithout = 'bucket#package=prefix%2fsuffix&path=FILE.md'
-        String pathWith = pathWithout.replace('#', '?key=value#')
-        String uriWith = "quilt+s3://${pathWith}"
+        println('\nMETADATA: findQuiltPath preserves metadata\n')
+        String meta = '?key=value'
+        String uriWithout = 'quilt+s3://bucket#package=prefix%2fsuffix&path=FILE.md'
+        String uriWith = uriWithout.replace('#', meta + '#')
+        println("pathify1.uriWith: $uriWith")
         QuiltPathify pathify = getPathify(uriWith)
+        println("pathify1.uri: ${pathify.uri}")
+        println("pathify1.uriString: ${pathify.pkg.toUriString()}")
 
         then:
+        uriWith.contains(meta)
         pathify.uri == uriWith
+        pathify.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() == pathify.pkgKey()
+        pathify2.uri == uriWithout
+        pathify2.pkg.toUriString() == uriWith
     }
 
-    // Test findQuiltPath.getRoot() retrieves metadata from prior package
     // Test makeQuiltPath creates new uri/path/pkg
     // Test makeQuiltPath sets isOverlay
     // Test copyToPackage copies overly file to package folder

diff --git a/plugins/nf-quilt/src/test/nextflow/quilt/QuiltProductTest.groovy b/plugins/nf-quilt/src/test/nextflow/quilt/QuiltProductTest.groovy
@@ -74,6 +74,9 @@ class QuiltProductTest extends QuiltSpecification {
         product.pkg
         product.session != null
         product.session.getWorkflowMetadata() != null
+        product.meta != null
+        product.meta.size() == 4
+        product.meta.key == 'val'
     }
 
     void 'should generate solid string for timestamp from now'() {