Web UI first commit #88

build.gradle

@@ -104,6 +104,7 @@ configurations {
     dnanexus.extendsFrom runtime
     ignite.extendsFrom runtime
     console.extendsFrom runtime
+    webui.extendsFrom runtime
     gdocLibs.extendsFrom runtime
 }
 
@@ -158,6 +159,10 @@ dependencies {
         exclude module: 'nextflow'
     }
 
+    webui(project(':nxf-webui')) {
+        exclude module: 'nextflow'
+    }
+
     drmaa(project(':nxf-drmaa')) {
         exclude module: 'nextflow'
     }
@@ -279,6 +284,7 @@ ext.deployable << project(':nxf-commons')
 ext.deployable << project(':nxf-ignite')
 ext.deployable << project(':nxf-console')
 ext.deployable << project(':nxf-drmaa')
+ext.deployable << project(':nxf-webui')
 
 protected error(String message) {
     logger.error message
@@ -353,6 +359,13 @@ task packOne(type: Jar) {
     manifest.attributes('Application-Class' : 'nextflow.ui.console.Nextflow', 'console' )
     manifest.attributes('Dependencies': deps, 'console')
 
+    /*
+     * `webui` dependencies
+     */
+    deps = resolveDeps('webui')
+    manifest.attributes('Application-Class' : 'nextflow.ui.web.Main', 'webui' )
+    manifest.attributes('Dependencies': deps, 'webui')
+
     /*
      * `ignite` dependencies
      */
@@ -567,10 +580,10 @@ task dnanexus(dependsOn: packDx) {
  * Save the runtime classpath
  */
 task exportClasspath {
-    dependsOn configurations.ignite, configurations.console
+    dependsOn configurations.ignite, configurations.console, configurations.webui
 
     def home = System.getProperty('user.home')
-    def all = configurations.ignite + configurations.console
+    def all = configurations.ignite + configurations.console + configurations.webui
     def libs = all.collect { File file -> /* println file.canonicalPath.replace(home, '$HOME'); */ file.canonicalPath;  }
     new File('.launch.classpath').text = libs.join(':')
 }

nextflow

@@ -151,7 +151,7 @@ export NXF_HOME
 bg=''
 declare -a jvmopts=()
 declare -a args=("$@")
-declare -a cli=(clone config drop help history info ls pull run view node console)
+declare -a cli=(clone config drop help history info ls pull run view node console webui)
 cmd=''
 while [[ $# != 0 ]]; do
     case $1 in
@@ -281,12 +281,15 @@ elif [[ "$NXF_DRMAA" ]]; then
   exit 1
 fi
 
+[[ "$cmd" == "webui" ]] && NXF_MODE='webui'
 [[ "$cmd" == "console" ]] && NXF_MODE='console'
 [[ "$cmd" == "node" && ! "$NXF_MODE" ]] && NXF_MODE='ignite'
 
 COLUMNS=${COLUMNS:-`tty -s && tput cols 2>/dev/null || true`}
 JAVA_OPTS="-Dfile.encoding=UTF-8 -noverify -Dcapsule.trampoline -Dcapsule.java.cmd=$JAVA_CMD"
 if [[ $cmd == console ]]; then bg=1;
+if [[ $cmd == webui ]]; then bg=1;
+elif [[ $cmd == console ]]; then bg=1;
 else JAVA_OPTS+=" -Djava.awt.headless=true"
 fi
 

settings.gradle

@@ -24,6 +24,7 @@ include 'nxf-dnanexus'
 include 'nxf-console'
 include 'nxf-drmaa'
 include 'nxf-ignite'
+include 'nxf-webui'
 
 rootProject.children.each { prj ->
     prj.projectDir = new File("$rootDir/subprojects/$prj.name")

src/main/groovy/nextflow/config/ComposedConfigScript.groovy

@@ -109,4 +109,18 @@ abstract class ComposedConfigScript extends Script {
         this.configStack.pop()
     }
 
+    /**
+     * Create an workflow input field
+     */
+    def field( value ) {
+        new InputField((Object)value)
+    }
+
+    def field( Map opts, value ) {
+        new InputField(opts,value)
+    }
+
+    def field( Map opts ) {
+        new InputField(opts)
+    }
 }

src/main/groovy/nextflow/config/InputField.groovy

@@ -0,0 +1,89 @@
+package nextflow.config
+
+import groovy.transform.CompileStatic
+import groovy.transform.EqualsAndHashCode
+
+/**
+ * Models a workflow input field parameter rendered in workflow webui
+ *
+ * @author Paolo Di Tommaso <[email protected]>
+ */
+@EqualsAndHashCode
+@CompileStatic
+class InputField {
+
+    /**
+     * The field name
+     */
+    String name
+
+    /**
+     * Descriptive name
+     */
+    String label
+
+    /**
+     * Descriptive text
+     */
+    String hint
+
+    /**
+     * Field type
+     */
+    String type
+
+
+    /**
+     * default value to show when the field is rendered and
+     * the actual value entered by the user when submit
+     */
+    def value
+
+    /**
+     * Creates an empty field
+     */
+    InputField() { }
+
+    /**
+     * Creates a field and set the value attribute
+     *
+     * @param value
+     */
+    InputField( def value ) {
+        this.value = value
+    }
+
+    /**
+     * Creates a field and assign the attributes specified as a map object
+     *
+     * @param opts
+     */
+    InputField( Map opts ) {
+        if( opts.containsKey('name') )
+            this.name = opts.name
+
+        if( opts.containsKey('label') )
+            this.label = opts.label
+
+        if( opts.containsKey('hint'))
+            this.hint = opts.hint
+
+        if( opts.containsKey('type') )
+            this.type = opts.type
+
+        if( opts.containsKey('value') )
+            this.value = opts.value
+    }
+
+    /**
+     * Creates a field and assigned the attributes specified
+     *
+     * @param opts
+     * @param value
+     */
+    InputField( Map opts, def value )  {
+        this(opts)
+        this.value = value
+    }
+
+}

src/test/groovy/nextflow/config/ComposedConfigSlurperTest.groovy

@@ -417,4 +417,25 @@ class ComposedConfigSlurperTest extends Specification {
         cleanup:
         folder?.deleteDir()
     }
+
+    def 'should create a form field parameters' () {
+
+        given:
+        def text = '''
+        params {
+          alpha = 'one'
+          beta = field 'two', type: 'file'
+          gamma = field type: 'text', label: 'Gamma value'
+          delta = field 'hello'
+        }
+        '''
+
+        when:
+        def config = new ComposedConfigSlurper().parse(text)
+        then:
+        config.params.alpha == 'one'
+        config.params.beta == new InputField('two', type: 'file')
+        config.params.gamma == new InputField(type: 'text', label: 'Gamma value')
+        config.params.delta == new InputField('hello')
+    }
 }

subprojects/nxf-webui/build.gradle

@@ -0,0 +1,34 @@
+/*
+ * Copyright (c) 2013-2015, Centre for Genomic Regulation (CRG).
+ * Copyright (c) 2013-2015, Paolo Di Tommaso and the respective authors.
+ *
+ *   This file is part of 'Nextflow'.
+ *
+ *   Nextflow is free software: you can redistribute it and/or modify
+ *   it under the terms of the GNU General Public License as published by
+ *   the Free Software Foundation, either version 3 of the License, or
+ *   (at your option) any later version.
+ *
+ *   Nextflow is distributed in the hope that it will be useful,
+ *   but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *   GNU General Public License for more details.
+ *
+ *   You should have received a copy of the GNU General Public License
+ *   along with Nextflow.  If not, see <http://www.gnu.org/licenses/>.
+ */
+apply plugin: 'groovy'
+
+sourceSets {
+    main.java.srcDirs = []
+    main.groovy.srcDirs = ['src/main']
+    main.resources.srcDirs = ['src/resources']
+    test.groovy.srcDirs = ['src/test']
+    test.java.srcDirs = []
+    test.resources.srcDirs = []
+}
+
+dependencies {
+    compile project(':')
+}
+

subprojects/nxf-webui/src/main/nextflow/ui/web/Main.groovy

@@ -0,0 +1,19 @@
+package nextflow.ui.web
+
+import groovy.transform.CompileStatic
+
+/**
+ * Web UI entry point
+ *
+ * @author Paolo Di Tommaso <[email protected]>
+ */
+@CompileStatic
+class Main {
+
+    static void main(String... args) {
+
+        println "The web UI starts here!"
+
+    }
+
+}