Error & info messages, code comments language fixes (#3475)

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>

buildSrc/src/main/groovy/io/nextflow/gradle/tasks/GithubRepositoryPublisher.groovy

@@ -72,15 +72,15 @@ class GithubRepositoryPublisher extends DefaultTask {
             }
             else {
                 for (PluginRelease rel : pluginReleases) {
-                    // check if this version already exist in the index
+                    // check if this version already exists in the index
                     final index = indexEntry.releases.findIndexOf { PluginRelease it -> it.version == rel.version }
                     final indexRel = index!=-1 ? indexEntry.releases[index] : null as PluginRelease
 
-                    // if not exists, add to the index
+                    // if not, add to the index
                     if( !indexRel ) {
                         indexEntry.releases << rel
                     }
-                    // otherwise verify the checksum matches
+                    // otherwise, verify the checksum matches
                     else if( indexRel.sha512sum != rel.sha512sum ) {
                         if( overwrite ) {
                             indexEntry.releases[index] = rel
@@ -113,7 +113,7 @@ class GithubRepositoryPublisher extends DefaultTask {
 
 
     /*
-     * Traverse a S3 bucket and return a map given all releases for each
+     * Traverse an S3 bucket and return a map with all releases for each
      * plugin id
      *
      * @return The map holding the plugin releases for each plugin id
@@ -152,7 +152,7 @@ class GithubRepositoryPublisher extends DefaultTask {
         final metaFile = "${repo}-${version}-meta.json"
         final json = client.getReleaseAsset(version, metaFile)?.text
         if( !json )
-            throw new GradleException("Can't load plugin release metafile $metaFile")
+            throw new GradleException("Failed to load plugin release metafile $metaFile")
         return new Gson().fromJson(json, PluginRelease)
     }
 

buildSrc/src/main/groovy/io/nextflow/gradle/tasks/GithubUploader.groovy

@@ -84,19 +84,19 @@ class GithubUploader extends DefaultTask {
             return
 
         if( !sourceFile.exists() )
-            throw new GradleException("Github upload failed -- Source file does not exists: $sourceFile")
+            throw new GradleException("Github upload failed -- source file does not exist: $sourceFile")
 
         final fileName = sourceFile.name
         final asset = client.getReleaseAsset(release.get(), fileName)
         if ( asset ) {
             if( skipExisting && isSame(sourceFile, asset) ) {
-                logger.quiet("${owner}/${repo.get()}/${fileName} exists! -- Skipping it.")
+                logger.quiet("${owner}/${repo.get()}/${fileName} already exists -- skipping")
             }
             else if (overwrite) {
                 updateRelease(sourceFile)
             }
             else {
-                throw new GradleException("${owner}/${repo.get()}/${fileName} exists! -- Refuse to owerwrite it.")
+                throw new GradleException("${owner}/${repo.get()}/${fileName} already exists -- overwrite refused")
             }
         }
         else {
@@ -106,7 +106,7 @@ class GithubUploader extends DefaultTask {
 
     private void updateRelease(File sourceFile) {
         if( dryRun ) {
-            logger.quiet("Would update ${sourceFile} → github.com://$owner/${repo.get()}")
+            logger.quiet("Will update ${sourceFile} → github.com://$owner/${repo.get()}")
         }
         else {
             logger.quiet("Updating ${sourceFile} → github.com://$owner/${repo.get()}")
@@ -117,7 +117,7 @@ class GithubUploader extends DefaultTask {
 
     private void uploadRelease(File sourceFile) {
         if( dryRun ) {
-            logger.quiet("Would upload ${sourceFile} → github.com://$owner/${repo.get()}")
+            logger.quiet("Will upload ${sourceFile} → github.com://$owner/${repo.get()}")
         }
         else {
             logger.quiet("Uploading ${sourceFile} → github.com://$owner/${repo.get()}")
@@ -155,15 +155,15 @@ class GithubUploader extends DefaultTask {
         def j1 = gson.fromJson(sourceFile.text, Map)
         def j2 = gson.fromJson( new InputStreamReader(asset), Map)
         if( j1.version != j2.version ) {
-            logger.quiet("Plugin metafile $sourceFile not matching versions: local=$j1.version; remote: $j2.version")
+            logger.quiet("Plugin metafile $sourceFile does not match versions: local=$j1.version; remote: $j2.version")
             return false
         }
         if( j1.url != j2.url ) {
-            logger.quiet("Plugin metafile $sourceFile not matching urls: local=$j1.url; remote: $j2.url")
+            logger.quiet("Plugin metafile $sourceFile does not match urls: local=$j1.url; remote: $j2.url")
             return false
         }
         if( j1.sha512sum != j2.sha512sum ) {
-            logger.quiet("Plugin metafile $sourceFile not matching sha512sum: local=$j1.sha512sum; remote: $j2.sha512sum")
+            logger.quiet("Plugin metafile $sourceFile does not match sha512sum: local=$j1.sha512sum; remote: $j2.sha512sum")
             return false
         }
         return true

buildSrc/src/main/groovy/io/nextflow/gradle/tasks/S3Upload.groovy

@@ -49,25 +49,25 @@ class S3Upload extends AbstractS3Task {
         final targetUrl = target.get()
         final urlTokens = BucketTokenizer.from(targetUrl)
         if( urlTokens.scheme != 's3' )
-            throw new GradleException("S3 upload failed -- Invalid target s3 path: $targetUrl")
+            throw new GradleException("S3 upload failed -- invalid target s3 path: $targetUrl")
         final bucket = urlTokens.bucket
         final targetKey = urlTokens.key
 
         if( !sourceFile.exists() )
-            throw new GradleException("S3 upload failed -- Source file does not exists: $sourceFile")
+            throw new GradleException("S3 upload failed -- source file does not exist: $sourceFile")
 
         if (s3Client.doesObjectExist(bucket, targetKey)) {
             if( skipExisting ) {
-                logger.quiet("s3://${bucket}/${targetKey} exists. Skipping it!")
+                logger.quiet("s3://${bucket}/${targetKey} already exists -- skipping")
             }
             else if (overwrite) {
                 copy(sourceFile, bucket, targetKey, true)
             }
             else if( isSameContent(sourceFile, bucket, targetKey) ) {
-                logger.quiet("s3://${bucket}/${targetKey} exists!")
+                logger.quiet("s3://${bucket}/${targetKey} already exists")
             }
             else {
-                throw new GradleException("s3://${bucket}/${targetKey} exists! -- Refuse to owerwrite it.")
+                throw new GradleException("s3://${bucket}/${targetKey} already exists -- overwrite refused")
             }
         }
         else {
@@ -88,14 +88,14 @@ class S3Upload extends AbstractS3Task {
 
     void copy(File sourceFile, String bucket, String targetKey, boolean exists) {
         if( dryRun ) {
-            logger.quiet("S3 Would upload ${sourceFile} → s3://${bucket}/${targetKey} ${exists ? '[would overwrite existing]' : ''}")
+            logger.quiet("S3 will upload ${sourceFile} → s3://${bucket}/${targetKey} ${exists ? '[would overwrite existing]' : ''}")
         }
         else {
             final req = new PutObjectRequest(bucket, targetKey, sourceFile)
             if( publicRead )
                 req.withCannedAcl(CannedAccessControlList.PublicRead)
 
-            logger.quiet("S3 Upload ${sourceFile} → s3://${bucket}/${targetKey} ${exists ? '[overwrite existing]': ''}")
+            logger.quiet("S3 upload ${sourceFile} → s3://${bucket}/${targetKey} ${exists ? '[overwrite existing]': ''}")
             s3Client.putObject(req)
         }
     }

buildSrc/src/main/groovy/io/nextflow/gradle/util/BucketTokenizer.groovy

@@ -89,7 +89,7 @@ class BucketTokenizer {
     }
 
     /**
-     * @return The object key, essentially the same as {@link #path} stripping the leading slash character
+     * @return The object key, effectively the same as {@link #path} stripping the leading slash character
      */
     String getKey() {
         path?.startsWith('/') ? path.substring(1) : path

buildSrc/src/main/groovy/io/nextflow/gradle/util/GithubClient.groovy

@@ -81,7 +81,7 @@ class GithubClient {
     }
 
     /**
-     *  2. Create the blobs with the files content
+     *  2. Create the blobs with the file content
      *
      * @param file content
      * @return The SHA id of the uploaded content
@@ -93,7 +93,7 @@ class GithubClient {
     }
 
     /**
-     * 3. Create a tree which defines the file structure
+     * 3. Create a tree that defines the file structure
      *
      * @param fileName The name of the file changed
      * @param blobId The id of the changed content

modules/nextflow/src/main/groovy/nextflow/NextflowMeta.groovy

@@ -23,7 +23,7 @@ import static nextflow.extension.Bolts.DATETIME_FORMAT
 @EqualsAndHashCode
 class NextflowMeta {
 
-    private static final String DSL1_EOL_MESSAGE = "Nextflow DSL1 is no longer supported — Please update your script to DSL2 or use Nextflow 22.10.x or an earlier version"
+    private static final String DSL1_EOL_MESSAGE = "Nextflow DSL1 is no longer supported — Update your script to DSL2, or use Nextflow 22.10.x or earlier"
     private static final Pattern DSL_DECLARATION = ~/(?m)^\s*(nextflow\.(preview|enable)\.dsl\s*=\s*(\d))\s*(;?\s*)?(;?\/{2}.*)?$/
 
     private static final Pattern DSL1_INPUT = ~/(?m)input:\s*(tuple|file|path|val|env|stdin)\b.*\s.*\bfrom\b.+$/
@@ -50,13 +50,13 @@ class NextflowMeta {
             if( num != 2 )
                 throw new IllegalArgumentException("Not a valid DSL version number: $num")
             if( num == 2 && !ignoreWarnDsl2 )
-                log.warn1 "DSL 2 PREVIEW MODE IS DEPRECATED - USE THE STABLE VERSION INSTEAD -- Read more at https://www.nextflow.io/docs/latest/dsl2.html#dsl2-migration-notes"
+                log.warn1 "DSL 2 PREVIEW MODE IS DEPRECATED - USE THE STABLE VERSION INSTEAD. Read more at https://www.nextflow.io/docs/latest/dsl2.html#dsl2-migration-notes"
             dsl = num
         }
 
         void setRecursion(Boolean recurse) {
             if( recurse )
-                log.warn "NEXTFLOW RECURSION IS A PREVIEW FEATURE - SYNTAX AND FUNCTIONALITY CAN CHANGE IN FUTURE RELEASE"
+                log.warn "NEXTFLOW RECURSION IS A PREVIEW FEATURE - SYNTAX AND FUNCTIONALITY CAN CHANGE IN FUTURE RELEASES"
             this.recursion = recurse
         }
     }
@@ -174,7 +174,7 @@ class NextflowMeta {
             return ver
         }
         else if( mode == 'preview' )
-            throw new IllegalArgumentException("Preview nextflow mode 'preview' is not supported anymore -- Please use `nextflow.enable.dsl=2` instead")
+            throw new IllegalArgumentException("Preview nextflow mode ('preview') is no longer supported —- use `nextflow.enable.dsl=2` instead")
         else
             throw new IllegalArgumentException("Unknown nextflow mode=${matcher.group(1)}")
     }

modules/nextflow/src/main/groovy/nextflow/file/DirWatcherV2.groovy

@@ -114,7 +114,7 @@ class DirWatcherV2 implements DirListener, FileAlterationListener {
     void apply( Closure onNext ) {
         this.onNext = onNext
         if( !base.isDirectory() ) {
-            log.warn "Cannot watch a non-existent directory: $base -- Make sure that the path exists and is a directory"
+            log.warn "Cannot watch a non-existent directory: $base -- Ensure the path is a valid directory"
             onComplete?.call()
             return
         }

modules/nf-commons/src/main/nextflow/plugin/PluginsFacade.groovy

@@ -153,11 +153,11 @@ class PluginsFacade implements PluginStateListener {
             return env.NXF_PLUGINS_DEFAULT!='false'
         }
         else if( env.containsKey('NXF_HOME') ) {
-            log.trace "Detected NXF_HOME - Using plugins defaults"
+            log.trace "Detected NXF_HOME - Using plugin defaults"
             return true
         }
         else {
-            log.trace "Disabling plugins defaults"
+            log.trace "Disabling plugin defaults"
             return false
         }
     }
@@ -187,7 +187,7 @@ class PluginsFacade implements PluginStateListener {
 
     void init(boolean embedded=false) {
         if( manager )
-            throw new IllegalArgumentException("Plugin system was already setup")
+            throw new IllegalArgumentException("Plugin system already setup")
 
         log.debug "Setting up plugin manager > mode=${mode}; embedded=$embedded; plugins-dir=$root; core-plugins: ${defaultPlugins.toSortedString()}"
         // make sure plugins dir exists
@@ -205,7 +205,7 @@ class PluginsFacade implements PluginStateListener {
 
     void init(Path root, String mode, CustomPluginManager pluginManager) {
         if( manager )
-            throw new IllegalArgumentException("Plugin system was already setup")
+            throw new IllegalArgumentException("Plugin system already setup")
         this.root = root
         this.mode = mode
         // setup plugin manager
@@ -228,7 +228,7 @@ class PluginsFacade implements PluginStateListener {
 
     void load(Map config) {
         if( !manager )
-            throw new IllegalArgumentException("Plugin system has not been initialised yet")
+            throw new IllegalArgumentException("Plugin system has not been initialized")
         start(pluginsRequirement(config))
     }
 
@@ -255,7 +255,7 @@ class PluginsFacade implements PluginStateListener {
             // this should oly be used to load system extensions
             // i.e. included in the app class path not provided by
             // a plugin extension
-            log.debug "Using Default plugins manager"
+            log.debug "Using Default plugin manager"
             return defaultManager().getExtensions(type)
         }
     }
@@ -312,7 +312,7 @@ class PluginsFacade implements PluginStateListener {
 
     void start( String pluginId ) {
         if( isSelfContained() && defaultPlugins.hasPlugin(pluginId) ) {
-            log.debug "Plugin 'start' is not required in self-contained mode -- ignoring it for plugin: $pluginId"
+            log.debug "Plugin 'start' is not required in self-contained mode -- ignoring for plugin: $pluginId"
             return
         }
 
@@ -321,7 +321,7 @@ class PluginsFacade implements PluginStateListener {
 
     void start(PluginSpec plugin) {
         if( isSelfContained() && defaultPlugins.hasPlugin(plugin.id) ) {
-            log.debug "Plugin 'start' is not required in self-contained mode -- ignoring it for plugin: $plugin.id"
+            log.debug "Plugin 'start' is not required in self-contained mode -- ignoring for plugin: $plugin.id"
             return
         }
 
@@ -351,7 +351,7 @@ class PluginsFacade implements PluginStateListener {
         def specs = parseConf(config)
         if( isSelfContained() && specs ) {
             // custom plugins are not allowed for nextflow self-contained package
-            log.warn "Nextflow self-contained distribution only allows core plugins -- User config plugins will be ignored: ${specs.join(',')}"
+            log.warn "Nextflow self-contained distribution allows only core plugins -- User config plugins will be ignored: ${specs.join(',')}"
             return Collections.emptyList()
         }
         if( specs ) {
@@ -441,14 +441,14 @@ class PluginsFacade implements PluginStateListener {
     }
 
     /**
-     * Merge two list of plugins requirement
+     * Merge two lists of plugin requirements
      *
      * @param configPlugins
      *      The list of plugins specified via the configuration file. This has higher priority
      * @param defaultPlugins
      *      The list of plugins specified via the environment
      * @return
-     *      The list of plugins resulting from merging the twos
+     *      The list of plugins resulting from merging the two lists
      */
     protected List<PluginSpec> mergePluginSpecs(List<PluginSpec> configPlugins, List<PluginSpec> defaultPlugins) {
         final map = new LinkedHashMap<String,PluginSpec>(10)
@@ -457,7 +457,7 @@ class PluginsFacade implements PluginStateListener {
             map.put(plugin.id, plugin)
         }
         // add the plugin in the 'defaultPlugins' argument
-        // when the map contains already the plugin,
+        // if the map already contains the plugin,
         // override it only if it does not specify a version
         for( PluginSpec plugin : defaultPlugins ) {
             if( !map[plugin.id] || !map[plugin.id].version ) {

modules/nf-commons/src/main/nextflow/util/Base62.java

@@ -74,7 +74,7 @@ static BigInteger decode(final String string, int bitLimit) {
             int digit = DIGITS.indexOf(string.charAt(digits - index - 1));
             result = result.add(BigInteger.valueOf(digit).multiply(BASE.pow(index)));
             if (bitLimit > 0 && result.bitLength() > bitLimit) {
-                throwIllegalArgumentException("String contains '%s' more than 128bit information (%sbit)", string, result.bitLength());
+                throwIllegalArgumentException("String contains '%s' more than 128-bit information (%sbit)", string, result.bitLength());
             }
         }
         return result;

modules/nf-commons/src/main/nextflow/util/ServiceDiscover.groovy

@@ -69,7 +69,7 @@ class ServiceDiscover<S> {
 
         if (n != 0) {
             if ((ln.indexOf(' ') >= 0) || (ln.indexOf('\t') >= 0))
-                fail(service, u, lc, "Illegal configuration-file syntax")
+                fail(service, u, lc, "Illegal configuration file syntax")
 
             int cp = ln.codePointAt(0)
             if (!Character.isJavaIdentifierStart(cp))

modules/nf-httpfs/src/main/nextflow/file/http/XPath.groovy

@@ -273,7 +273,7 @@ class XPath implements Path {
     }
 
     /**
-     * @return The unique hash code for this pah
+     * @return The unique hash code for this path
      */
     @Override
     int hashCode() {
@@ -284,11 +284,11 @@ class XPath implements Path {
      * Path factory method.
      *
      * @param str
-     *      A fully qualified URI path string e.g. {@code http://www.host.name/data.file.txt}
+     *      A fully qualified URI path string, e.g. {@code http://www.host.name/data.file.txt}
      * @return
      *      The corresponding {@link XPath} object
      * @throws
-     *      ProviderMismatchException When the URI scheme does not match any supported protocol i.e. {@code ftp},
+     *      ProviderMismatchException When the URI scheme does not match any supported protocol, i.e. {@code ftp},
      *      {@code http}, {@code https}
      */
     static XPath get(String str) {