copyFile rather than writeString

quiltdata · Sep 6, 2024 · efc2392 · efc2392
1 parent fc0f41f
commit efc2392
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Showing 4 changed files with 40 additions and 22 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,9 @@
 # Changelog
 
+## [0.8.2] 2024-09-05
+
+- Use copyFile rather than writeString for overlay files
+
 ## [0.8.1] 2024-09-05
 
 - Get output URI directly from params

diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/QuiltObserver.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/QuiltObserver.groovy
@@ -117,7 +117,7 @@ class QuiltObserver implements TraceObserver {
     }
 
     boolean confirmPath(QuiltPath path) {
-        log.debug("checkPath[$path]")
+        log.debug("confirmPath[$path]")
         String key = pkgKey(path)
         if (!outputURIs.containsKey(key)) {
             log.warn("Output URI not found for key[$key] from path[$path]")
@@ -153,12 +153,11 @@ class QuiltObserver implements TraceObserver {
         // Path source may be null, won't work with older versions of Nextflow
         log.debug("onFilePublish.Path[$destination] <- $source")
         QuiltPath qPath = asQuiltPath(destination)
-        if (qPath) {
+        if (qPath != null) {
             confirmPath(qPath)
         } else {
             matchPath(destination.toString())
         }
-        confirmPath(qPath)
     }
 
     @Override

diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/QuiltProduct.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/QuiltProduct.groovy
@@ -106,6 +106,18 @@ ${nextflow}
         }
     }
 
+    static void copyFile(Path source, QuiltPackage pkg, String filepath) {
+        String dir = pkg.packageDest()
+        Path dest  = Paths.get(dir, filepath.split('/') as String[])
+        try {
+            dest.getParent().toFile().mkdirs() // ensure directories exist first
+            Files.copy(source, dest)
+        }
+        catch (Exception e) {
+            log.error("writeString: cannot write `$source` to `$dest` for `${pkg}`")
+        }
+    }
+
     static String now() {
         LocalDateTime time = LocalDateTime.now()
         return time.toString()
@@ -139,9 +151,12 @@ ${nextflow}
     }
 
     void publishOverlays(Map<String, Path> overlays) {
-        overlays.each { key, overlay ->
-            log.info("publishing overlay[$key]: ${overlay}")
-            writeString(overlay.text, pkg, key)
+        /// Copying working files to local package directory
+        /// for (re)upload to the package
+        /// FIXME: Replace this with in-place packaging
+        overlays.each { key, source ->
+            log.info("publishing overlay[$key]: ${source}")
+            copyFile(source, pkg, key)
         }
     }
 

diff --git a/plugins/nf-quilt/src/test/nextflow/quilt/nio/QuiltPathTest.groovy b/plugins/nf-quilt/src/test/nextflow/quilt/nio/QuiltPathTest.groovy
@@ -191,10 +191,10 @@ class QuiltPathTest extends QuiltSpecification {
         thrown ProviderMismatchException
     }
 
-    @Ignore('FIXME: subpath not yet implemented')
+    @Ignore('FIXME: test subpath in QuiltParser first')
     void 'should validate subpath: #expected'() {
         expect:
-        pathify(path).subpath(from, to) == pathify(expected)
+        pathify(path).subpath(from, to).getPath() == expected
         where:
         path                                             | from  | to    | expected
         'bucket#package=some%2fbig%2fdata%2ffile.txt'    | 0     | 1     | 'data'
@@ -209,13 +209,13 @@ class QuiltPathTest extends QuiltSpecification {
         pathify(path).startsWith(pathify(prefix)) == expected
 
         where:
-        path                         | prefix                | expected
+        path                          | prefix                | expected
         'bucket#package=s/d/file.txt' | 'bucket#package=s%2fd' | true
         'bucket#package=s/d/file.txt' | 'bucket#package=s' | true
         'bucket#package=s/d/file.txt' | 'bucket' | true
         'bucket#package=s/d/file.txt' | 'file.txt' | false
-        'data%2ffile.txt'            | 'data'              | true
-        'data%2ffile.txt'            | 'file.txt'          | false
+        'data%2ffile.txt'             | 'data'              | true
+        'data%2ffile.txt'             | 'file.txt'          | false
     }
 
     @Unroll
@@ -225,24 +225,24 @@ class QuiltPathTest extends QuiltSpecification {
         //pathify(path).endsWith(pathify(suffix)) == expected
 
         where:
-        path             | suffix            | expected
-        SUB_PATH         | 'file.txt'        | true
-        SUB_PATH         | 'f%2ffile.txt'    | true
-        SUB_PATH         | '/f%2ffile.txt'   | false
-        SUB_PATH         | 'bucket'          | false
-        'data%2ffile.txt' | 'data' | false
-        'data%2ffile.txt' | 'file.txt' | true
+        path              | suffix            | expected
+        SUB_PATH          | 'file.txt'        | true
+        SUB_PATH          | 'f%2ffile.txt'    | true
+        SUB_PATH          | '/f%2ffile.txt'   | false
+        SUB_PATH          | 'bucket'          | false
+        'data%2ffile.txt' | 'data'            | false
+        'data%2ffile.txt' | 'file.txt'        | true
     }
 
     @Unroll
     void 'should validate normalise'() {
         expect:
         pathify(path).normalize() == pathify(expected)
         where:
-        path                              | expected
-        'bucket#path=s/d/file.txt'        | 'bucket#path=s/d/file.txt'
+        path                               | expected
+        'bucket#path=s/d/file.txt'         | 'bucket#path=s/d/file.txt'
         'bucket#path=some%2f..%2ffile.txt' | 'bucket#path=file.txt'
-        'file.txt'                        | 'file.txt'
+        'file.txt'                         | 'file.txt'
     }
 
     @Unroll
@@ -272,7 +272,7 @@ class QuiltPathTest extends QuiltSpecification {
         expect:
         pathify(path).relativize(pathify(other)).toString() == pathify(expected).toString()
         where:
-        path               | other                                      | expected
+        path               | other                       | expected
         based()            | based('%2fdata%2ffile.txt') | sepJoin('data', 'file.txt')
         based('%2fdata')   | based('%2fdata%2ffile.txt') | 'file.txt'
         based('&path=foo') | based('&path=foo%2fbar')    | 'bar'