Add CRAN package support for Wave container builds

build.gradle

@@ -39,8 +39,8 @@ dependencies {
     implementation 'io.seqera:lib-retry:1.1.0'
     implementation 'io.seqera:lib-random:1.0.0'
     implementation 'io.seqera:lib-activator:1.0.0'
-    implementation 'io.seqera:wave-api:0.16.0'
-    implementation 'io.seqera:wave-utils:1.0.0'
+    implementation 'io.seqera:wave-api:0.17.0-alpha.1'
+    implementation 'io.seqera:wave-utils:1.1.0-alpha.1'
     implementation 'io.seqera:lib-crypto:1.0.0'
     implementation 'io.seqera:jedis-lock:1.0.0'
     implementation 'io.seqera:lib-data-queue-redis:1.1.0'

src/main/groovy/io/seqera/wave/util/ContainerHelper.groovy

@@ -28,6 +28,7 @@ import io.seqera.wave.api.PackagesSpec
 import io.seqera.wave.api.SubmitContainerTokenRequest
 import io.seqera.wave.api.SubmitContainerTokenResponse
 import io.seqera.wave.config.CondaOpts
+import io.seqera.wave.config.CranOpts
 import io.seqera.wave.core.ContainerPlatform
 import io.seqera.wave.exception.BadRequestException
 import io.seqera.wave.service.builder.BuildFormat
@@ -41,6 +42,10 @@ import static io.seqera.wave.util.DockerHelper.condaFileToSingularityFile
 import static io.seqera.wave.util.DockerHelper.condaPackagesToCondaYaml
 import static io.seqera.wave.util.DockerHelper.condaPackagesToDockerFile
 import static io.seqera.wave.util.DockerHelper.condaPackagesToSingularityFile
+import static io.seqera.wave.util.CranHelper.cranPackagesToDockerFile
+import static io.seqera.wave.util.CranHelper.cranPackagesToSingularityFile
+import static io.seqera.wave.util.CranHelper.cranFileToDockerFile
+import static io.seqera.wave.util.CranHelper.cranFileToSingularityFile
 /**
  * Container helper methods
  *
@@ -78,6 +83,23 @@ class ContainerHelper {
             return result
         }
 
+        if( spec.type == PackagesSpec.Type.CRAN ) {
+            if( !spec.cranOpts )
+                spec.cranOpts = new CranOpts()
+            def result
+            if ( spec.entries ) {
+                final String packages = spec.entries.join(' ')
+                result = formatSingularity
+                        ? cranPackagesToSingularityFile(packages, spec.channels, spec.cranOpts)
+                        : cranPackagesToDockerFile(packages, spec.channels, spec.cranOpts)
+            } else {
+                result = formatSingularity
+                        ? cranFileToSingularityFile(spec.cranOpts)
+                        : cranFileToDockerFile(spec.cranOpts)
+            }
+            return result
+        }
+
         throw new BadRequestException("Unexpected packages spec type: $spec.type")
     }
 

src/test/groovy/io/seqera/wave/util/ContainerHelperTest.groovy

@@ -28,6 +28,7 @@ import io.seqera.wave.api.ImageNameStrategy
 import io.seqera.wave.api.PackagesSpec
 import io.seqera.wave.api.SubmitContainerTokenRequest
 import io.seqera.wave.config.CondaOpts
+import io.seqera.wave.config.CranOpts
 import io.seqera.wave.exception.BadRequestException
 import io.seqera.wave.service.request.ContainerRequest
 import io.seqera.wave.service.builder.BuildFormat
@@ -603,4 +604,73 @@ class ContainerHelperTest extends Specification {
 
     }
 
+    def 'should create cran docker file with packages'() {
+        given:
+        def REPOSITORIES = ['cran', 'bioconductor']
+        def CRAN_OPTS = new CranOpts([rImage: 'rocker/r-ver:4.4.1', basePackages: 'littler r-cran-docopt'])
+        def PACKAGES = ['dplyr', 'ggplot2', 'bioc::GenomicRanges']
+        def packages = new PackagesSpec(type: PackagesSpec.Type.CRAN, entries: PACKAGES, channels: REPOSITORIES, cranOpts: CRAN_OPTS)
+
+        when:
+        def result = ContainerHelper.containerFileFromPackages(packages, false)
+
+        then:
+        result.contains('FROM rocker/r-ver:4.4.1')
+        result.contains('install2.r')
+        result.contains('dplyr ggplot2 bioc::GenomicRanges')
+        result.contains('R_LIBS_USER="/usr/local/lib/R/site-library"')
+    }
+
+    def 'should create cran singularity file with packages'() {
+        given:
+        def REPOSITORIES = ['cran']
+        def CRAN_OPTS = new CranOpts([rImage: 'rocker/r-ver:4.4.1'])
+        def PACKAGES = ['tidyverse', 'data.table']
+        def packages = new PackagesSpec(type: PackagesSpec.Type.CRAN, entries: PACKAGES, channels: REPOSITORIES, cranOpts: CRAN_OPTS)
+
+        when:
+        def result = ContainerHelper.containerFileFromPackages(packages, true)
+
+        then:
+        result.contains('BootStrap: docker')
+        result.contains('From: rocker/r-ver:4.4.1')
+        result.contains('install2.r')
+        result.contains('tidyverse data.table')
+        result.contains('export R_LIBS_USER="/usr/local/lib/R/site-library"')
+    }
+
+    def 'should create cran docker file without packages (file mode)'() {
+        given:
+        def CRAN_OPTS = new CranOpts([rImage: 'rocker/r-ver:4.4.1'])
+        def packages = new PackagesSpec(type: PackagesSpec.Type.CRAN, cranOpts: CRAN_OPTS)
+
+        when:
+        def result = ContainerHelper.containerFileFromPackages(packages, false)
+
+        then:
+        result.contains('FROM rocker/r-ver:4.4.1')
+        result.contains('COPY --from=wave_context_dir . .')
+        result.contains('renv.lock')
+        result.contains('install.R')
+        result.contains('R_LIBS_USER="/usr/local/lib/R/site-library"')
+    }
+
+    def 'should create cran singularity file without packages (file mode)'() {
+        given:
+        def CRAN_OPTS = new CranOpts([rImage: 'rocker/r-ver:4.4.1', basePackages: 'build-essential'])
+        def packages = new PackagesSpec(type: PackagesSpec.Type.CRAN, cranOpts: CRAN_OPTS)
+
+        when:
+        def result = ContainerHelper.containerFileFromPackages(packages, true)
+
+        then:
+        result.contains('BootStrap: docker')
+        result.contains('From: rocker/r-ver:4.4.1')
+        result.contains('%files')
+        result.contains('/opt/wave_context_dir')
+        result.contains('build-essential')
+        result.contains('renv.lock')
+        result.contains('export R_LIBS_USER="/usr/local/lib/R/site-library"')
+    }
+
 }

typespec/models/ContainerRequest.tsp

@@ -1,5 +1,5 @@
 import "./ContainerConfig.tsp";
-import "./CondaPackages.tsp";
+import "./PackagesSpec.tsp";
 import "./ScanMode.tsp";
 import "./ScanLevel.tsp";
 
@@ -39,8 +39,8 @@ model ContainerRequest {
   @doc("The name strategy to be used to create the name of the container built by Wave. Its values can be `none`, `tagPrefix`, or `imageSuffix`. ")
   nameStrategy?: "none" | "tagPrefix" | "imageSuffix";
   mirror?: boolean;
-  @doc("Conda packages to be installed in the container.")
-  packages?: CondaPackages;
+  @doc("Packages to be installed in the container.")
+  packages?: PackagesSpec;
   scanMode?: ScanMode;
   scanLevels?: ScanLevel[];
   @doc("Request submission timestamp using ISO-8601.")