145 quilt sumarize.json wrong path for child html files

CHANGELOG.md

@@ -1,5 +1,10 @@
 # Changelog
 
+## [0.7.1] 2023-10-15
+
+- Fix [quiltdata/nf-quilt#145](https://github.com/quiltdata/nf-quilt/issues/145)
+- Remove automatic pre-install of packages
+
 ## [0.7.0] 2023-10-05
 
 - Officially QuiltCore 0.1.0 instead of Python

README.md

@@ -75,8 +75,8 @@ From the command-line, do, e.g.:
 
 ```bash
 # export NXF_VER=23.04.3
-export NXF_PLUGINS_TEST_REPOSITORY=https://github.com/quiltdata/nf-quilt/releases/download/0.7.0/nf-quilt-0.7.0-meta.json
-nextflow run main.nf -plugins [email protected].0
+export NXF_PLUGINS_TEST_REPOSITORY=https://github.com/quiltdata/nf-quilt/releases/download/0.7.1/nf-quilt-0.7.1-meta.json
+nextflow run main.nf -plugins [email protected].1
 ```
 
 For Tower, you can use the "Pre-run script" to set the environment variables.

plugins/nf-quilt/build.gradle

@@ -54,8 +54,8 @@ sourceSets {
     test.resources.srcDirs = ['src/testResources']
 }
 
-ext{
-    nextflowVersion = '23.04.3'
+ext {
+    nextflowVersion = rootProject.file('VERSION').text.trim()
 }
 
 dependencies {

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

@@ -98,6 +98,8 @@ ${nextflow}
         String dir = pkg.packageDest()
         Path path  = Paths.get(dir, filename.split('/') as String[])
         try {
+            // ensure directories exist first
+            path.getParent().toFile().mkdirs()
             Files.write(path, text.bytes)
         }
         catch (Exception e) {
@@ -141,7 +143,7 @@ ${nextflow}
         meta = setupMeta()
         String text = setupReadme()
         log.debug("setupReadme: $text")
-        Map quilt_summarize = setupSummarize()
+        List<Map> quilt_summarize = setupSummarize()
         log.debug("setupSummarize: $quilt_summarize")
         int rc = pkg.push(msg, meta)
         log.info("$rc: pushed package[$pkg] $msg")
@@ -289,8 +291,8 @@ ${nextflow}
         return matches
     }
 
-    Map setupSummarize() {
-        Map quilt_summarize = [:]
+    List<Map> setupSummarize() {
+        List<Map> quilt_summarize = []
         if (shouldSkip(KEY_SUMMARIZE)) {
             return quilt_summarize
         }
@@ -300,11 +302,12 @@ ${nextflow}
             List<Path> paths = match(wildcard)
             paths.each { path ->
                 String filename = path.getFileName()
-                quilt_summarize[filename] = path
+                Map entry = ["path": path.toString(), "title": filename]
+                quilt_summarize.add(entry)
             }
         }
 
-        String qs_json = JsonOutput.toJson(quilt_summarize.keySet() as String[])
+        String qs_json = JsonOutput.toJson(quilt_summarize)
         writeString(qs_json, pkg, SUMMARY_FILE)
         return quilt_summarize
     }

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

@@ -87,18 +87,6 @@ class QuiltPackage {
 
         pkg = new QuiltPackage(parsed)
         PKGS[pkgKey] = pkg
-        if (pkg.is_force()) {
-            //log.debug("Do not install `${pkg}` if force-overwriting output")
-            return pkg
-        }
-
-        try {
-            log.debug("${pkg}: attempting install for.pkgKey $pkgKey (okay if fails)")
-            pkg.install()
-        }
-        catch (IOException e) {
-            log.warn("Package `${parsed.toUriString()}` does not yet exist")
-        }
         return pkg
     }
 

plugins/nf-quilt/src/resources/META-INF/MANIFEST.MF

@@ -1,7 +1,7 @@
 Manifest-Version: 1.0
 Plugin-Class: nextflow.quilt.QuiltPlugin
 Plugin-Id: nf-quilt
-Plugin-Version: 0.7.0
+Plugin-Version: 0.7.1
 Plugin-Provider: Quilt Data
 Plugin-Requires: >=22.10.6
 

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

@@ -115,16 +115,18 @@ class QuiltProductTest extends QuiltSpecification {
         product.pkg.reset()
         expect:
         !product.match('*.md')
-        product.setupSummarize() == [:]
+        product.setupSummarize() == []
     }
 
     void 'should create summarize if files are present'() {
         String readme_text = 'hasREADME'
         QuiltProduct product = makeProduct("readme=${readme_text}")
         product.setupReadme()
-        expect:
         product.match('*.md')
-        product.setupSummarize()
+        List<Map> quilt_summarize = product.setupSummarize()
+        expect:
+        quilt_summarize
+        quilt_summarize.size() == 1
     }
 
     @IgnoreIf({ env.WRITE_BUCKET == 'quilt-example' || env.WRITE_BUCKET ==  null })

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

@@ -68,7 +68,10 @@ class QuiltNioTest extends QuiltSpecification {
     @IgnoreIf({ System.getProperty('os.name').contains('indows') })
     void 'should read from a path'() {
         given:
-        Path path = Paths.get(new URI(READ_URL))
+        QuiltPath path = Paths.get(new URI(READ_URL)) as QuiltPath
+        path.pkg().install()
+
+        when:
 
         when:
         String text = readObject(path)