getRootPackage

From strings with more than one

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

@@ -41,6 +41,9 @@ class QuiltPathify  {
     QuiltPackage pkg
     String uri
 
+    /*
+     * Copy a file from source to destRoot/relpath
+     */
     static void copyFile(Path source, String destRoot, String relpath) {
         Path dest  = Paths.get(destRoot, relpath.split('/') as String[])
         try {
@@ -95,43 +98,59 @@ class QuiltPathify  {
 
     // Constructor takes a Path and finds QuiltPath and QuiltPackage
     QuiltPathify(Path path) {
+        println("QuiltPathify: $path")
         if (path in QuiltPath) {
             this.path = (QuiltPath) path
+            println("\tQuiltPathify.QuiltPath: $this.path")
             this.uri = this.path.toUriString()
+            println("\t\tQuiltPathify.QuiltPath.uri: $this.uri")
             this.pkg = this.path.pkg()
+            println("\t\tQuiltPathify.QuiltPath.pkg: $this.pkg")
         } else if (!findQuiltPath(path.getFileName().toString())) {
-            makeQuiltPath(path)
+            makeQuiltPath(path.toString())
             this.isOverlay = true
         }
     }
 
     boolean findQuiltPath(String filename) {
-        // check for '#package' in filename
-        if (!filename.toString().contains('#package')) {
+        println("findQuiltPath: $filename")
+        String base = QuiltPath.getRootPackage(filename)
+        if (base == null) {
             return false
         }
 
-        uri = "${QuiltParser.SCHEME}://${filename}"
+        uri = "${QuiltParser.SCHEME}://${base}"
+        println("\tfindQuiltPath.uri: $uri")
         path = QuiltPathFactory.parse(this.uri)
+        println("\tfindQuiltPath.path: $path")
         pkg = path.pkg()
+        println("\tfindQuiltPath.pkg: $pkg")
         return true
     }
 
-    boolean makeQuiltPath(Path path) {
-        String quiltURI = uriFromS3File(path.toString())
+    boolean makeQuiltPath(String s3File) {
+        println("makeQuiltPath: $s3File")
+        String quiltURI = uriFromS3File(s3File)
+        println("\tmakeQuiltPath.quiltURI: $quiltURI")
         this.path = QuiltPathFactory.parse(quiltURI)
+        println("\tmakeQuiltPath.path: $path")
         this.uri = this.path.toUriString()
+        println("\tmakeQuiltPath.uri: $uri")
         this.pkg = this.path.pkg()
+        println("\tmakeQuiltPath.pkg: $pkg")
         return true
     }
 
-    boolean copyToPackage(Path source) {
+    boolean copyToCache(Path source) {
+        println("copyToCache: $source -> $path")
         if (!this.isOverlay) {
             return false
         }
-        String localPath = path.sub_paths()
+        String localPath = source.getFileName() // FIXME: should be relative to workdir
+        println("\tcopyToCache.localPath: $localPath")
         Path destDir = pkg.packageDest()
-        log.debug("copyToPackage: $source -> $destDir / $localPath")
+        println("\tcopyToCache.destDir: $destDir")
+        println("copyToCache: $source -> $destDir / $localPath")
         copyFile(source, destDir.toString(), localPath)
         return true
     }

plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltPath.groovy

@@ -17,6 +17,7 @@ package nextflow.quilt.nio
 
 import nextflow.quilt.jep.QuiltPackage
 import nextflow.quilt.jep.QuiltParser
+
 import java.nio.file.Files
 import java.nio.file.FileSystem
 import java.nio.file.LinkOption
@@ -26,6 +27,7 @@ import java.nio.file.ProviderMismatchException
 import java.nio.file.WatchEvent
 import java.nio.file.WatchKey
 import java.nio.file.WatchService
+import java.util.regex.Matcher
 
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
@@ -45,6 +47,30 @@ final class QuiltPath implements Path, Comparable {
     private final String[] paths
     private final boolean isFileName
 
+    static String getRootPackage(String filename) {
+        int n_package = filename.count('#package')
+        if (n_package < 1) {
+            return null
+        }
+        String base = filename
+        if (n_package > 1) {
+            log.info("\tfindQuiltPath: multiple '#package' in $base")
+            println('\t\tTO MATCH')
+            Matcher matches = (filename =~ /^([^#]+#package=.*)?(?:(?!%2f).)*#package=/)
+            if (!matches) {
+                log.error("findQuiltPath: no match found for $filename")
+                return null
+            }
+            println('\t\tDID MATCH')
+            println("\tfindQuiltPath.matches: $matches")
+            List<String> parts = matches[0] as List<String>
+            println("\tfindQuiltPath.parts: $parts")
+            base = parts[1]
+            log.info("\tfindQuiltPath: trimmed to $base")
+        }
+        return base
+    }
+
     QuiltPath(QuiltFileSystem filesystem, QuiltParser parsed, boolean isFileName = false) {
         this.filesystem = filesystem
         this.parsed = parsed
@@ -239,7 +265,8 @@ final class QuiltPath implements Path, Comparable {
     }
 
     String toUriString() {
-        return parsed.toUriString()
+        String rawString = parsed.toUriString()
+        return getRootPackage(rawString) ?: rawString
     }
 
     @Override

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

@@ -20,8 +20,9 @@ import nextflow.quilt.jep.QuiltParser
 import nextflow.quilt.nio.QuiltPath
 import nextflow.quilt.nio.QuiltPathFactory
 
-// import java.nio.file.Path
-// import java.nio.file.Paths
+import java.nio.file.Files
+import java.nio.file.Paths
+import java.nio.file.Path
 //import spock.lang.Ignore
 import groovy.transform.CompileDynamic
 
@@ -82,9 +83,9 @@ class QuiltPathifyTest extends QuiltSpecification {
         rc    | path
         false | 'FILE.md'
         true  | 'bucket#package=prefix%2fsuffix&path=FILE.md'
+        true  | 'bkt#package=pre%2fsuffix&path=inputs%2fbkt#package=pre%2fsuffix@af541d2%2fdata.tsv'
     }
 
-    // Test findQuiltPath updates uri/path/pkg
     void 'test findQuiltPath overrides attributes'() {
         when:
         QuiltPathify pathify = getPathify()
@@ -119,8 +120,49 @@ class QuiltPathifyTest extends QuiltSpecification {
         pathify2.pkg.toUriString() == uriWith
     }
 
-    // Test makeQuiltPath creates new uri/path/pkg
-    // Test makeQuiltPath sets isOverlay
-    // Test copyToPackage copies overly file to package folder
+    // TODO: Test findQuiltPath works for dynamic URIs
+
+    void 'test makeQuiltPath'() {
+        when:
+        QuiltPathify pathify = getPathify()
+        pathify.makeQuiltPath(s3File)
+
+        then:
+        pathify.isOverlay == false
+        pathify.uri == "quilt+s3://${uri}"
+        pathify.path.toString() == uri
+        pathify.pkg.toUriString() == "quilt+s3://${uri}"
+
+        where:
+        s3File                      | uri
+        '/bkt/pre/suf/fold/FILE.md' | 'bkt#package=pre%2fsuf&path=fold%2fFILE.md'
+    }
+
+    void 'test copyToCache copies overlay file to package folder'() {
+        when:
+        Path tempFolder = Files.createTempDirectory('bkt')
+        Path source = Paths.get(tempFolder.toString(), sub_path)
+        Files.createDirectories(source.getParent())
+        Files.createFile(source)
+
+        then:
+        Files.exists(source)
+
+        when:
+        QuiltPathify pathify = new QuiltPathify(source)
+        Path destFolder = pathify.pkg.packageDest()
+        String file = source.getFileName()
+        Path dest = Paths.get(destFolder.toString(), file)
+        pathify.copyToCache(source)
+
+        then:
+        pathify.isOverlay == true
+        Files.exists(dest)
+        Files.delete(dest)
+        Files.delete(source)
+
+        where:
+        sub_path  << ['FILE.md']
+    }
 
 }

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: [meta: [cfkey: 'cfval']], runName: 'my-run', publishing: false]
+            config >> [quilt: [meta: [cfkey: 'cfval']]]
         }
         return new QuiltProduct(pathify, session)
     }