Intellij code cleanup (#263)

linter and permission fixes --------- Co-authored-by: Dr. Ernie Prabhakar <[email protected]>
quiltdata · Nov 13, 2024 · 88b3f50 · 88b3f50
1 parent bd70b45
commit 88b3f50
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Showing 10 changed files with 122 additions and 112 deletions.
diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/QuiltObserverFactory.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/QuiltObserverFactory.groovy
@@ -33,7 +33,10 @@ class QuiltObserverFactory implements TraceObserverFactory {
     @Override
     Collection<TraceObserver> create(Session session) {
         //log.debug("`create` ${this}")
-        return (Collection<TraceObserver>) [new QuiltObserver()]
+        Collection<QuiltObserver> quiltObservers = new ArrayList<>()
+        quiltObservers.add(new QuiltObserver())
+
+        return quiltObservers as Collection<TraceObserver>
     }
 
 }
diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/QuiltPathify.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/QuiltPathify.groovy
@@ -51,7 +51,7 @@ class QuiltPathify  {
             Files.copy(source, dest)
         }
         catch (Exception e) {
-            log.error("writeString: cannot write `$source` to `$dest` in `${destRoot}`")
+            log.error("writeString: cannot write `$source` to `$dest` in `${destRoot}`\n$e")
         }
     }
 

diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/QuiltProduct.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/QuiltProduct.groovy
@@ -16,6 +16,7 @@
 package nextflow.quilt
 
 import nextflow.quilt.jep.QuiltPackage
+import nextflow.quilt.jep.QuiltParser
 import nextflow.quilt.nio.QuiltPath
 import nextflow.Session
 
@@ -47,14 +48,11 @@ class QuiltProduct {
     public final static String README_FILE = 'README_NF_QUILT.md'
     public final static String SUMMARY_FILE = 'quilt_summarize.json'
 
-    private final static String KEY_CATALOG = 'catalog'
-    private final static String KEY_FORCE = 'force'
-    private final static String KEY_META = 'meta'
-    private final static String KEY_MSG = 'message'
-    private final static String KEY_PKG = 'package'
-    private final static String KEY_QUILT = 'quilt'
-    private final static String KEY_README = 'readme'
-    private final static String KEY_SUMMARIZE = 'summarize'
+    public final static String KEY_META = 'meta'
+    public final static String KEY_MSG = 'message'
+    public final static String KEY_QUILT = 'quilt'
+    public final static String KEY_README = 'readme'
+    public final static String KEY_SUMMARIZE = 'summarize'
 
 /* groovylint-disable-next-line GStringExpressionWithinString */
     private final static String DEFAULT_MSG = '''
@@ -112,7 +110,7 @@ ${nextflow}
             Files.write(path, text.bytes)
         }
         catch (Exception e) {
-            log.error("writeString: cannot write `$text` to `$path` for `${pkg}`")
+            log.error("writeString: cannot write `$text` to `$path` for `${pkg}`\n$e")
         }
     }
 
@@ -123,7 +121,7 @@ ${nextflow}
             Files.copy(source, dest)
         }
         catch (Exception e) {
-            log.error("writeString: cannot write `$source` to `$dest` in `${destRoot}`")
+            log.error("writeString: cannot write `$source` to `$dest` in `${destRoot}`\n$e.message()")
         }
     }
 
@@ -148,15 +146,17 @@ ${nextflow}
     ])
 
     QuiltProduct(QuiltPathify pathify, Session session) {
+        println("Creating QuiltProduct: ${pathify}")
         this.session = session
         this.config = session.config ?: [:]
         this.path = pathify.path
+        println('QuiltProduct.path')
         this.pkg = pathify.pkg
-        println("QuiltProduct.pkg: ${pkg.toUriString()}")
+        println('QuiltProduct.pkg')
         this.metadata = getMetadata()
-        println("QuiltProduct.metadata: ${metadata}")
-        println("QuiltProduct.flags: ${flags}")
-        if (session.isSuccess() || flags.getProperty(KEY_FORCE)) {
+        println('QuiltProduct.metadata')
+        // println("QuiltProduct.flags: ${flags}")
+        if (session.isSuccess() || flags.getProperty(QuiltParser.P_FORCE) == true) {
             publish()
         } else {
             log.info("not publishing: ${pkg} [unsuccessful session]")
@@ -168,7 +168,7 @@ ${nextflow}
             log.info("SKIP: metadata for ${pkg}")
             return [:]
         }
-        println("getMetadata.config: ${config}")
+        // println("getMetadata.config: ${config}")
         config.remove('executor')
         config.remove('params')
         config.remove('session')
@@ -181,19 +181,20 @@ ${nextflow}
 
         Map<String, Object> cf_meta = quilt_cf.navigate(KEY_META) as Map<String, Object> ?: [:]
         quilt_cf.remove(KEY_META)
-        Map pkg_meta = pkg.meta
+        // println("getMetadata.cf_meta: ${cf_meta}")
+        Map pkg_meta = pkg.getMetadata()
         updateFlags(pkg_meta, quilt_cf)
 
         Map params = session.getParams()
-        println("getMetadata.params: ${params}")
+        // println("getMetadata.params: ${params}")
         if (params != null) {
             writeMapToPackage(params, 'params')
             params.remove('genomes')
             params.remove('test_data')
             printMap(params, 'params')
         }
         Map wf = session.getWorkflowMetadata()?.toMap()
-        println("getMetadata.wf: ${wf}")
+        // println("getMetadata.wf: ${wf}")
         String start = wf?.get('start')
         String complete = wf?.get('complete')
         String cmd = wf?.get('commandLine')
@@ -209,8 +210,9 @@ ${nextflow}
             log.info("\npublishing: ${wf['runName']}")
         }
 
+        println("getMetadata.pkg_meta: ${pkg_meta}")
         Map base_meta = cf_meta + pkg_meta
-        log.debug("getMetadata.base_meta: ${base_meta}")
+        log.info("getMetadata.base_meta: ${base_meta}")
         return base_meta + [
             cmd: cmd,
             now: now(),
@@ -228,7 +230,7 @@ ${nextflow}
             cmd: metadata.get('cmd'),
             meta: metadata,
             now: metadata.get('now'),
-            pkg: flags.getProperty(KEY_PKG)
+            pkg: flags.getProperty(QuiltParser.P_PKG)
         ]
         return params
     }
@@ -245,16 +247,17 @@ ${nextflow}
         * @param cf Map of config (from nextflow.config)
      */
     void updateFlags(Map meta, Map cf) {
-        for (String key : flags.properties.keySet()) {
+        //println("updateFlags.meta: ${meta}")
+        for (String key : flags.getProperties().keySet()) {
             if (meta.containsKey(key)) {
                 flags.setProperty(key, meta[key])
             } else if (cf.containsKey(key)) {
                 flags.setProperty(key, cf[key])
             }
         }
         // FIXME: should this only work for names inferred from S3 URIs?
-        String pkgName = cf.containsKey(KEY_PKG) ? cf[KEY_PKG] : pkg.packageName
-        flags.setProperty(KEY_PKG, pkgName)
+        String pkgName = cf.containsKey(QuiltParser.P_PKG) ? cf[QuiltParser.P_PKG] : pkg.packageName
+        flags.setProperty(QuiltParser.P_PKG, pkgName)
     }
 
     String writeMapToPackage(Map map, String prefix) {
@@ -291,16 +294,23 @@ ${nextflow}
     }
 
     String displayName() {
-        Object catalog = flags.getProperty(KEY_CATALOG)
+        Object catalog = flags.getProperty(QuiltParser.P_CAT)
         return catalog ? pkg.toCatalogURL(catalog.toString()) : pkg.toUriString()
     }
 
     String compileMessage() {
         String msg = flags.getProperty(KEY_MSG)
         GStringTemplateEngine engine = new GStringTemplateEngine()
-        String output = engine.createTemplate(msg).make(getParams())
-        log.debug("compileMessage.output: ${output}")
-        return output
+        println("compileMessage: ${msg}")
+        try {
+            String output = engine.createTemplate(msg).make(getParams())
+            log.debug("compileMessage.output: ${output}")
+            return output
+        }
+        catch (Exception e) {
+            log.error("compileMessage failed: ${e.getMessage()}\n{$e}", flags)
+        }
+        return "compileMessage.FAILED\n$msg"
     }
 
     String compileReadme(String msg) {
@@ -320,10 +330,16 @@ ${nextflow}
             nextflow: nextflow,
         ]
         log.debug("compileReadme.params: ${params}")
-        GStringTemplateEngine engine = new GStringTemplateEngine()
-        String output = engine.createTemplate(raw_readme).make(params)
-        log.debug("compileReadme.output: ${output}")
-        return output
+        try {
+            GStringTemplateEngine engine = new GStringTemplateEngine()
+            String output = engine.createTemplate(raw_readme).make(params)
+            log.debug("compileReadme.output: ${output}")
+            return output
+        }
+        catch (Exception e) {
+            log.error("compileReadme failed: ${e.getMessage()}\n{$e}", flags)
+        }
+        return "compileReadme.FAILED\n$raw_readme"
     }
 
     String writeReadme(String message) {
@@ -373,12 +389,14 @@ ${nextflow}
     List<Map> writeSummarize() {
         List<Map> quilt_summarize = []
         if (shouldSkip(KEY_SUMMARIZE)) {
+            log.info("SKIP: summarize for ${flags}")
             return quilt_summarize
         }
         String summarize = flags.getProperty(KEY_SUMMARIZE)
         String[] wildcards = summarize.split(',')
         wildcards.each { wildcard ->
             List<Path> paths = match(wildcard)
+            println("writeSummarize: ${paths.size()} matches for ${wildcard}")
             paths.each { path ->
                 String filename = path.getFileName()
                 Map entry = ['path': path.toString(), 'title': filename]

diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltID.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltID.groovy
@@ -15,9 +15,6 @@
  */
 package nextflow.quilt.jep
 
-/* groovylint-disable-next-line ImportFromSamePackage */
-import nextflow.quilt.jep.QuiltParser
-
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
 

diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltPackage.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltPackage.groovy
@@ -22,6 +22,7 @@ import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
 import java.nio.file.FileSystems
 import java.nio.file.Files
+import java.nio.file.NoSuchFileException
 import java.nio.file.Path
 import java.nio.file.Paths
 import java.nio.file.SimpleFileVisitor
@@ -48,8 +49,8 @@ class QuiltPackage {
     private static final String INSTALL_PREFIX = 'QuiltPackage'
     static final Path INSTALL_ROOT = Files.createTempDirectory(INSTALL_PREFIX)
 
+    public final String packageName
     private final String bucket
-    private final String packageName
     private final QuiltParser parsed
     private final String hash
     private final Path folder
@@ -97,11 +98,6 @@ class QuiltPackage {
         PKGS.clear()
     }
 
-    static QuiltPackage forUriString(String uri) {
-        QuiltParser parsed = QuiltParser.forUriString(uri)
-        return forParsed(parsed)
-    }
-
     static QuiltPackage forParsed(QuiltParser parsed) {
         println("QuiltPackage.forParsed: $parsed")
         boolean isNull = parsed.hasNullBucket()
@@ -123,13 +119,6 @@ class QuiltPackage {
         return PKGS.containsKey(pkgKey)
     }
 
-    static QuiltPackage forKey(String pkgKey) {
-        if (hasKey(pkgKey)) {
-            return PKGS.get(pkgKey)
-        }
-        return null
-    }
-
     static List<Path> listDirectory(Path rootPath) {
         return Files.walk(rootPath).sorted(Comparator.reverseOrder()).collect(Collectors.toList())
     }
@@ -147,8 +136,8 @@ class QuiltPackage {
                 Files.deleteIfExists(path)
             }
         }
-        catch (java.nio.file.NoSuchFileException e) {
-            log.debug 'deleteDirectory: ignore non-existent files'
+        catch (NoSuchFileException e) {
+            log.debug "deleteDirectory: ignore non-existent files\n$e"
         }
         return true
     }
@@ -205,7 +194,7 @@ class QuiltPackage {
     }
 
     boolean is_force() {
-        return parsed.options[QuiltParser.P_FORCE]
+        return parsed.getOptions(QuiltParser.P_FORCE)
     }
 
     boolean isNull() {
@@ -231,6 +220,10 @@ class QuiltPackage {
         return folder
     }
 
+    Map getMetadata() {
+        return this.meta
+    }
+
     /*
      * Package methods
      */
@@ -315,7 +308,7 @@ class QuiltPackage {
             LocalPhysicalKey physicalKey = new LocalPhysicalKey(f)
             long size = Files.size(f)
             builder.addEntry(logicalKey, new Entry(physicalKey, size, null, null))
-        });
+        })
 
         Map<String, Object> fullMeta = [
             'version': Manifest.VERSION,
@@ -337,7 +330,7 @@ class QuiltPackage {
             /* groovylint-disable-next-line ThrowRuntimeException */
             throw new RuntimeException(e)
         }
-        return m
+        // return m
     }
 
     @Override
@@ -357,9 +350,4 @@ class QuiltPackage {
         return parsed.toPackageString(true)
     }
 
-    String meta_overrides(String key, Serializable baseline = null) {
-        Object temp = meta[key] ? meta[key] : baseline
-        return temp.toString()
-    }
-
 }