Add support for Wave native build for singularity

Signed-off-by: Paolo Di Tommaso <[email protected]>

Author: pditommaso

build.gradle

@@ -82,6 +82,8 @@ allprojects {
         mavenCentral()
         maven { url 'https://repo.eclipse.org/content/groups/releases' }
         maven { url 'https://oss.sonatype.org/content/repositories/snapshots' }
+        maven { url = "https://s3-eu-west-1.amazonaws.com/maven.seqera.io/releases" }
+        maven { url = "https://s3-eu-west-1.amazonaws.com/maven.seqera.io/snapshots" }
     }
 
     configurations {

modules/nextflow/src/main/groovy/nextflow/script/bundle/ResourcesBundle.groovy

@@ -45,13 +45,15 @@ class ResourcesBundle {
     private Path root
     private LinkedHashMap<String,Path> content = new LinkedHashMap<>(100)
     private Path dockerfile
+    private Path singularityfile
     private MemoryUnit maxFileSize = MAX_FILE_SIZE
     private MemoryUnit maxBundleSize = MAX_BUNDLE_SIZE
     private String baseDirectory
 
     ResourcesBundle(Path root) {
         this.root = root
-        this.dockerfile = dockefile0(root.resolveSibling('Dockerfile'))
+        this.dockerfile = pathIfExists0(root.resolveSibling('Dockerfile'))
+        this.singularityfile = pathIfExists0(root.resolveSibling('Singularityfile'))
     }
 
     ResourcesBundle withMaxFileSize(MemoryUnit mem) {
@@ -68,7 +70,7 @@ class ResourcesBundle {
 
     Map<String,Path> content() { content }
 
-    static private Path dockefile0(Path path) {
+    static private Path pathIfExists0(Path path) {
         return path?.exists() ? path : null
     }
 
@@ -100,6 +102,10 @@ class ResourcesBundle {
         return dockerfile
     }
 
+    Path getSingularityfile() {
+        return singularityfile
+    }
+
     Set<Path> getPaths() {
         return new HashSet<Path>(content.values())
     }
@@ -125,7 +131,7 @@ class ResourcesBundle {
     }
 
     boolean asBoolean() {
-        return content.size() || dockerfile
+        return content.size() || dockerfile || singularityfile
     }
 
     /**
@@ -189,6 +195,9 @@ class ResourcesBundle {
         if( dockerfile ) {
             allMeta.add(fileMeta(dockerfile.name, dockerfile))
         }
+        if( singularityfile ) {
+            allMeta.add(fileMeta(singularityfile.name, singularityfile))
+        }
 
         return CacheHelper.hasher(allMeta).hash().toString()
     }

modules/nextflow/src/test/groovy/nextflow/script/bundle/ResourcesBundleTest.groovy

@@ -106,12 +106,31 @@ class ResourcesBundleTest extends Specification {
         then:
         bundle.fingerprint() == '7b2200ff24230f76cea22e5eb15b1701'
 
+    }
+
+    def 'should get singularityfile' () {
+        given:
+        def singularPath = folder.resolve('Singularityfile'); singularPath.text = "I'm the main file"
+        def bundlePath = folder.resolve('bundle')
+        and:
+        singularPath.setLastModified(LAST_MODIFIED)
+        singularPath.setPermissions(6,4,4)
         when:
-        // changing the last modified time, change the fingerprint
-        dockerPath.setLastModified(LAST_MODIFIED +100)
+        def bundle = ResourcesBundle.scan(bundlePath)
         then:
-        bundle.fingerprint() == '7b2200ff24230f76cea22e5eb15b1701'
-        
+        bundle.getSingularityfile() == singularPath
+        and:
+        bundle
+        !bundle.hasEntries()
+        and:
+        bundle.fingerprint() == '6933e9238f3363c8e013a35715fa0540'
+
+        when:
+        // changing file permissions, change the fingerprint
+        singularPath.setPermissions(6,0,0)
+        then:
+        bundle.fingerprint() == '3ffe7f16cd5ae17e6ba7485e01972b20'
+
     }
 
     def 'should check max file size'() {

plugins/nf-wave/build.gradle

@@ -36,6 +36,8 @@ dependencies {
     api 'org.apache.commons:commons-lang3:3.12.0'
     api 'com.google.code.gson:gson:2.10.1'
     api 'org.yaml:snakeyaml:2.0'
+    api 'io.seqera:wave-api:0.4.0'
+    api 'io.seqera:wave-utils:0.6.2'
 
     testImplementation(testFixtures(project(":nextflow")))
     testImplementation "org.codehaus.groovy:groovy:3.0.18"

plugins/nf-wave/src/main/io/seqera/wave/config/CondaOpts.java

@@ -111,4 +111,9 @@ class SubmitContainerTokenRequest {
      */
     boolean freeze
 
+    /**
+     * Specify the format of the container file
+     */
+    String format
+
 }

plugins/nf-wave/src/main/io/seqera/wave/config/SpackOpts.java

@@ -36,10 +36,11 @@ class WaveAssets {
     final String containerPlatform
     final ResourcesBundle moduleResources
     final ContainerConfig containerConfig
-    final String dockerFileContent
+    final String containerFile
     final Path condaFile
     final Path spackFile
     final ResourcesBundle projectResources
+    final boolean singularity
 
     static fromImage(String containerImage,String containerPlatform=null) {
         new WaveAssets(containerImage, containerPlatform)
@@ -50,8 +51,8 @@ class WaveAssets {
     }
 
     String dockerFileEncoded() {
-        return dockerFileContent
-                ? dockerFileContent.bytes.encodeBase64()
+        return containerFile
+                ? containerFile.bytes.encodeBase64()
                 : null
     }
 
@@ -73,7 +74,7 @@ class WaveAssets {
         allMeta.add( this.containerImage )
         allMeta.add( this.moduleResources?.fingerprint() )
         allMeta.add( this.containerConfig?.fingerprint() )
-        allMeta.add( this.dockerFileContent )
+        allMeta.add( this.containerFile )
         allMeta.add( this.condaFile?.text )
         allMeta.add( this.spackFile?.text )
         allMeta.add( this.projectResources?.fingerprint() )