Untangle dependencies between CLI and runtime code

Signed-off-by: Ben Sherman <[email protected]>

Author: bentsherman

modules/nextflow/src/main/groovy/nextflow/cli/CmdClone.groovy

@@ -30,7 +30,7 @@ import nextflow.scm.AssetManager
 @Slf4j
 @CompileStatic
 @Parameters(commandDescription = "Clone a project into a folder")
-class CmdClone extends CmdBase implements HubOptions {
+class CmdClone extends CmdBase implements HubAware {
 
     static final public NAME = 'clone'
 
@@ -52,7 +52,7 @@ class CmdClone extends CmdBase implements HubOptions {
         Plugins.init()
         // the pipeline name
         String pipeline = args[0]
-        final manager = new AssetManager(pipeline, this)
+        final manager = new AssetManager(pipeline, toHubOptions())
 
         // the target directory is the second parameter
         // otherwise default the current pipeline name

modules/nextflow/src/main/groovy/nextflow/cli/CmdLint.groovy

@@ -25,7 +25,6 @@ import com.beust.jcommander.Parameters
 import com.beust.jcommander.ParameterException
 import groovy.json.JsonOutput
 import groovy.transform.CompileStatic
-import groovy.transform.Memoized
 import groovy.util.logging.Slf4j
 import nextflow.config.control.ConfigParser
 import nextflow.config.formatter.ConfigFormattingVisitor
@@ -35,13 +34,14 @@ import nextflow.script.control.ParanoidWarning
 import nextflow.script.control.ScriptParser
 import nextflow.script.formatter.FormattingOptions
 import nextflow.script.formatter.ScriptFormattingVisitor
+import nextflow.script.parser.v2.ErrorListener
+import nextflow.script.parser.v2.ErrorSummary
+import nextflow.script.parser.v2.StandardErrorListener
 import nextflow.util.PathUtils
 import org.codehaus.groovy.control.SourceUnit
 import org.codehaus.groovy.control.messages.SyntaxErrorMessage
 import org.codehaus.groovy.control.messages.WarningMessage
 import org.codehaus.groovy.syntax.SyntaxException
-import org.fusesource.jansi.Ansi
-import org.fusesource.jansi.AnsiConsole
 /**
  * CLI sub-command LINT
  *
@@ -266,248 +266,6 @@ class CmdLint extends CmdBase {
 }
 
 
-class ErrorSummary {
-    int errors = 0
-    int filesWithErrors = 0
-    int filesWithoutErrors = 0
-    int filesFormatted = 0
-}
-
-
-interface ErrorListener {
-    void beforeAll()
-    void beforeFile(File file)
-    void beforeErrors()
-    void onError(SyntaxException error, String filename, SourceUnit source)
-    void onWarning(WarningMessage warning, String filename, SourceUnit source)
-    void afterErrors()
-    void beforeFormat(File file)
-    void afterAll(ErrorSummary summary)
-}
-
-
-@CompileStatic
-class StandardErrorListener implements ErrorListener {
-    private String mode
-    private boolean ansiLog
-
-    StandardErrorListener(String mode, boolean ansiLog) {
-        this.mode = mode
-        this.ansiLog = ansiLog
-    }
-
-    private Ansi ansi() {
-        final ansi = Ansi.ansi()
-        ansi.setEnabled(ansiLog)
-        return ansi
-    }
-
-    @Override
-    void beforeAll() {
-        final line = ansi().a("Linting Nextflow code..").newline()
-        AnsiConsole.out.print(line)
-        AnsiConsole.out.flush()
-    }
-
-    @Override
-    void beforeFile(File file) {
-        final line = ansi()
-            .cursorUp(1).eraseLine()
-            .a(Ansi.Attribute.INTENSITY_FAINT).a("Linting: ${file}")
-            .reset().newline().toString()
-        AnsiConsole.out.print(line)
-        AnsiConsole.out.flush()
-    }
-
-    private Ansi term
-
-    @Override
-    void beforeErrors() {
-        term = ansi().cursorUp(1).eraseLine()
-    }
-
-    @Override
-    void onError(SyntaxException error, String filename, SourceUnit source) {
-        term.bold().a(filename).reset()
-        term.a(":${error.getStartLine()}:${error.getStartColumn()}: ")
-        term = highlightString(error.getOriginalMessage(), term)
-        if( mode != 'concise' ) {
-            term.newline()
-            term = printCodeBlock(source, Range.of(error), term, Ansi.Color.RED)
-        }
-        term.newline()
-    }
-
-    @Override
-    void onWarning(WarningMessage warning, String filename, SourceUnit source) {
-        final token = warning.getContext().getRoot()
-        term.bold().a(filename).reset()
-        term.a(":${token.getStartLine()}:${token.getStartColumn()}: ")
-        term.fg(Ansi.Color.YELLOW).a(warning.getMessage()).fg(Ansi.Color.DEFAULT)
-        if( mode != 'concise' ) {
-            term.newline()
-            term = printCodeBlock(source, Range.of(warning), term, Ansi.Color.YELLOW)
-        }
-        term.newline()
-    }
-
-    private Ansi highlightString(String str, Ansi term) {
-        final matcher = str =~ /^(.*)([`'][^`']+[`'])(.*)$/
-        if( matcher.find() ) {
-            term.a(matcher.group(1))
-                .fg(Ansi.Color.CYAN).a(matcher.group(2)).fg(Ansi.Color.DEFAULT)
-                .a(matcher.group(3))
-        }
-        else {
-            term.a(str)
-        }
-        return term
-    }
-
-    private Ansi printCodeBlock(SourceUnit source, Range range, Ansi term, Ansi.Color color) {
-        final startLine = range.startLine()
-        final startColumn = range.startColumn()
-        final endLine = range.endLine()
-        final endColumn = range.endColumn()
-        final lines = getSourceText(source)
-
-        // get context window (up to 5 lines)
-        int padding = mode == 'extended' ? 2 : 0
-        int fromLine = Math.max(1, startLine - padding)
-        int toLine = Math.min(lines.size(), endLine + padding)
-        if( toLine - fromLine + 1 > 5 ) {
-            if( startLine <= 3 ) {
-                toLine = fromLine + 4
-            }
-            else if( endLine >= lines.size() - 2 ) {
-                fromLine = toLine - 4
-            }
-            else {
-                fromLine = startLine - 2
-                toLine = startLine + 2
-            }
-        }
-
-        for( int i = fromLine; i <= toLine; i++ ) {
-            String fullLine = lines[i - 1]
-            int start = (i == startLine) ? startColumn - 1 : 0
-            int end = (i == endLine) ? endColumn - 1 : fullLine.length()
-
-            // Truncate to max 70 characters
-            int maxLen = 70
-            int lineLen = fullLine.length()
-            int windowStart = 0
-            if( lineLen > maxLen ) {
-                if( start < maxLen - 10 )
-                    windowStart = 0
-                else if( end > lineLen - 10 )
-                    windowStart = lineLen - maxLen
-                else
-                    windowStart = start - 30
-            }
-
-            String line = fullLine.substring(windowStart, Math.min(lineLen, windowStart + maxLen))
-            int adjStart = Math.max(0, start - windowStart)
-            int adjEnd = Math.max(adjStart + 1, Math.min(end - windowStart, line.length()))
-
-            // Line number
-            term.fg(Ansi.Color.BLUE).a(String.format("%3d | ", i)).reset()
-
-            if( i == startLine ) {
-                // Print line with range highlighted
-                term.a(Ansi.Attribute.INTENSITY_FAINT).a(line.substring(0, adjStart)).reset()
-                term.fg(color).a(line.substring(adjStart, adjEnd)).reset()
-                term.a(Ansi.Attribute.INTENSITY_FAINT).a(line.substring(adjEnd)).reset().newline()
-
-                // Print carets underneath the range
-                String marker = ' ' * adjStart
-                String carets = '^' * Math.max(1, adjEnd - adjStart)
-                term.a("    | ")
-                    .fg(color).bold().a(marker + carets).reset().newline()
-            }
-            else {
-                term.a(Ansi.Attribute.INTENSITY_FAINT).a(line).reset().newline()
-            }
-        }
-
-        return term
-    }
-
-    @Memoized
-    private List<String> getSourceText(SourceUnit source) {
-        return source.getSource().getReader().readLines()
-    }
-
-    @Override
-    void afterErrors() {
-        // print extra newline since next file status will chomp back one
-        term.fg(Ansi.Color.DEFAULT).newline()
-        AnsiConsole.out.print(term)
-        AnsiConsole.out.flush()
-    }
-
-    @Override
-    void beforeFormat(File file) {
-        final line = ansi()
-            .cursorUp(1).eraseLine()
-            .a(Ansi.Attribute.INTENSITY_FAINT).a("Formatting: ${file}")
-            .reset().newline().toString()
-        AnsiConsole.out.print(line)
-        AnsiConsole.out.flush()
-    }
-
-    @Override
-    void afterAll(ErrorSummary summary) {
-        final term = ansi()
-        term.cursorUp(1).eraseLine().cursorUp(1).eraseLine()
-        // print extra newline if no code is being shown
-        if( mode == 'concise' )
-            term.newline()
-        term.bold().a("Nextflow linting complete!").reset().newline()
-        if( summary.filesWithErrors > 0 ) {
-            term.fg(Ansi.Color.RED).a(" ❌ ${summary.filesWithErrors} file${summary.filesWithErrors==1 ? '' : 's'} had ${summary.errors} error${summary.errors==1 ? '' : 's'}").newline()
-        }
-        if( summary.filesWithoutErrors > 0 ) {
-            term.fg(Ansi.Color.GREEN).a(" ✅ ${summary.filesWithoutErrors} file${summary.filesWithoutErrors==1 ? '' : 's'} had no errors")
-            if( summary.filesFormatted > 0 )
-                term.fg(Ansi.Color.BLUE).a(" (${summary.filesFormatted} formatted)")
-            term.newline()
-        }
-        if( summary.filesWithErrors == 0 && summary.filesWithoutErrors == 0 ) {
-            term.a(" No files found to process").newline()
-        }
-        AnsiConsole.out.print(term)
-        AnsiConsole.out.flush()
-    }
-
-    private static record Range(
-        int startLine,
-        int startColumn,
-        int endLine,
-        int endColumn
-    ) {
-        public static Range of(SyntaxException error) {
-            return new Range(
-                error.getStartLine(),
-                error.getStartColumn(),
-                error.getEndLine(),
-                error.getEndColumn(),
-            )
-        }
-
-        public static Range of(WarningMessage warning) {
-            final token = warning.getContext().getRoot()
-            return new Range(
-                token.getStartLine(),
-                token.getStartColumn(),
-                token.getStartLine(),
-                token.getStartColumn() + token.getText().length(),
-            )
-        }
-    }
-}
-
-
 @CompileStatic
 class JsonErrorListener implements ErrorListener {
 

modules/nextflow/src/main/groovy/nextflow/cli/CmdPull.groovy

@@ -30,7 +30,7 @@ import nextflow.scm.AssetManager
 @Slf4j
 @CompileStatic
 @Parameters(commandDescription = "Download or update a project")
-class CmdPull extends CmdBase implements HubOptions {
+class CmdPull extends CmdBase implements HubAware {
 
     static final public NAME = 'pull'
 
@@ -74,7 +74,7 @@ class CmdPull extends CmdBase implements HubOptions {
 
         list.each {
             log.info "Checking $it ..."
-            def manager = new AssetManager(it, this)
+            def manager = new AssetManager(it, toHubOptions())
 
             def result = manager.download(revision,deep)
             manager.updateModules()

modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy

@@ -58,7 +58,7 @@ import org.yaml.snakeyaml.Yaml
 @Slf4j
 @CompileStatic
 @Parameters(commandDescription = "Execute a pipeline project")
-class CmdRun extends CmdBase implements HubOptions {
+class CmdRun extends CmdBase implements HubAware {
 
     static final public Pattern RUN_NAME_PATTERN = Pattern.compile(/^[a-z](?:[a-z\d]|[-_](?=[a-z\d])){0,79}$/, Pattern.CASE_INSENSITIVE)
 
@@ -579,7 +579,7 @@ class CmdRun extends CmdBase implements HubOptions {
         /*
          * try to look for a pipeline in the repository
          */
-        def manager = new AssetManager(pipelineName, this)
+        def manager = new AssetManager(pipelineName, toHubOptions())
         def repo = manager.getProject()
 
         boolean checkForUpdate = true

modules/nextflow/src/main/groovy/nextflow/cli/HubOptions.groovy renamed to modules/nextflow/src/main/groovy/nextflow/cli/HubAware.groovy

@@ -18,51 +18,22 @@ package nextflow.cli
 
 import com.beust.jcommander.Parameter
 import groovy.transform.CompileStatic
+import nextflow.scm.HubOptions
 /**
-  * Defines the command line parameters for command that need to interact with a pipeline service hub i.e. GitHub or BitBucket
+  * Command line parameters for commands that interact with a git repository provider i.e. GitHub or BitBucket
   *
   * @author Paolo Di Tommaso <[email protected]>
   */
-
 @CompileStatic
-trait HubOptions {
+interface HubAware {
 
     @Parameter(names=['-hub'], description = "Service hub where the project is hosted")
     String hubProvider
 
     @Parameter(names='-user', description = 'Private repository user name')
     String hubUser
 
-    /**
-     * Return the password provided on the command line or stop allowing the user to enter it on the console
-     *
-     * @return The password entered or {@code null} if no user has been entered
-     */
-    String getHubPassword() {
-
-        if( !hubUser )
-            return null
-
-        def p = hubUser.indexOf(':')
-        if( p != -1 )
-            return hubUser.substring(p+1)
-
-        def console = System.console()
-        if( !console )
-            return null
-
-        print "Enter your $hubProvider password: "
-        char[] pwd = console.readPassword()
-        new String(pwd)
+    default HubOptions toHubOptions() {
+        return new HubOptions(hubProvider, hubUser)
     }
-
-    String getHubUser() {
-        if(!hubUser) {
-            return hubUser
-        }
-
-        def p = hubUser.indexOf(':')
-        return p != -1 ? hubUser.substring(0,p) : hubUser
-    }
-
 }