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Refactor Conda and Spack support for Wave to Java
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
1 parent f6e4b9b commit 36b9e22

23 files changed

Lines changed: 985 additions & 516 deletions

‎plugins/nf-wave/build.gradle‎

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@@ -33,6 +33,7 @@ dependencies {
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compileOnly 'org.slf4j:slf4j-api:2.0.7'
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compileOnly 'org.pf4j:pf4j:3.4.1'
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api 'org.apache.commons:commons-compress:1.21'
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api 'org.apache.commons:commons-lang3:3.12.0'
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api 'com.google.code.gson:gson:2.10.1'
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testImplementation(testFixtures(project(":nextflow")))

plugins/nf-wave/src/main/io/seqera/wave/plugin/config/CondaOpts.groovy renamed to plugins/nf-wave/src/main/io/seqera/wave/config/CondaOpts.java

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@@ -15,25 +15,27 @@
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*
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*/
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package io.seqera.wave.plugin.config
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package io.seqera.wave.config;
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import java.util.List;
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import java.util.Map;
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/**
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* Conda build options
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*
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* @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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*/
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class CondaOpts {
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final public static String DEFAULT_MAMBA_IMAGE = 'mambaorg/micromamba:1.4.2'
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public class CondaOpts {
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final public static String DEFAULT_MAMBA_IMAGE = "mambaorg/micromamba:1.4.2";
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final String mambaImage
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final List<String> commands
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final String basePackages
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final public String mambaImage;
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final public List<String> commands;
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final public String basePackages;
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CondaOpts(Map opts) {
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this.mambaImage = opts.mambaImage ?: DEFAULT_MAMBA_IMAGE
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this.commands = opts.commands as List<String>
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this.basePackages = opts.basePackages
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public CondaOpts(Map<String,?> opts) {
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this.mambaImage = opts.containsKey("mambaImage") ? opts.get("mambaImage").toString(): DEFAULT_MAMBA_IMAGE;
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this.commands = opts.containsKey("commands") ? (List<String>)opts.get("commands") : null;
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this.basePackages = (String)opts.get("basePackages");
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}
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}

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

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@@ -0,0 +1,58 @@
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/*
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* Copyright 2013-2023, Seqera Labs
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*
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* Licensed under the Apache License, Version 2.0 (the "License");
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* you may not use this file except in compliance with the License.
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* You may obtain a copy of the License at
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*
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* http://www.apache.org/licenses/LICENSE-2.0
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*
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* Unless required by applicable law or agreed to in writing, software
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* distributed under the License is distributed on an "AS IS" BASIS,
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* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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* See the License for the specific language governing permissions and
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* limitations under the License.
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*
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*/
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package io.seqera.wave.config;
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import java.util.List;
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import java.util.Map;
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/**
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* Spack build options
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*
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* @author Marco De La Pierre <marco.delapierre@gmail.com>
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*/
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public class SpackOpts {
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final static public String DEFAULT_SPACK_BUILDER_IMAGE = "spack/ubuntu-jammy:v0.19.2";
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final static public String DEFAULT_SPACK_RUNNER_IMAGE = "ubuntu:22.04";
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final static public String DEFAULT_SPACK_OSPACKAGES = "";
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final static public String DEFAULT_SPACK_FLAGS = "-O3";
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public final Boolean checksum;
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public final String builderImage;
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public final String runnerImage;
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public final String osPackages;
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public final String cFlags;
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public final String cxxFlags;
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public final String fFlags;
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public final List<String> commands;
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public SpackOpts() {
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this(Map.of());
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}
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public SpackOpts(Map<String,?> opts) {
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this.checksum = opts.get("checksum") == null || Boolean.parseBoolean(opts.get("checksum").toString());
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this.builderImage = opts.containsKey("builderImage") ? opts.get("builderImage").toString() : DEFAULT_SPACK_BUILDER_IMAGE;
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this.runnerImage = opts.containsKey("runnerImage") ? opts.get("runnerImage").toString() : DEFAULT_SPACK_RUNNER_IMAGE;
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this.osPackages = opts.containsKey("osPackages") ? opts.get("osPackages").toString() : DEFAULT_SPACK_OSPACKAGES;
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this.cFlags = opts.containsKey("cFlags") ? opts.get("cFlags").toString() : DEFAULT_SPACK_FLAGS;
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this.cxxFlags = opts.containsKey("cxxFlags") ? opts.get("cxxFlags").toString() : DEFAULT_SPACK_FLAGS;
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this.fFlags = opts.containsKey("fFlags") ? opts.get("fFlags").toString() : DEFAULT_SPACK_FLAGS;
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this.commands = opts.containsKey("commands") ? (List<String>)opts.get("commands") : null;
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}
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}

‎plugins/nf-wave/src/main/io/seqera/wave/plugin/DescribeContainerResponse.groovy‎

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@@ -1,3 +1,20 @@
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/*
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* Copyright 2013-2023, Seqera Labs
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*
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* Licensed under the Apache License, Version 2.0 (the "License");
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* you may not use this file except in compliance with the License.
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* You may obtain a copy of the License at
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*
8+
* http://www.apache.org/licenses/LICENSE-2.0
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*
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* Unless required by applicable law or agreed to in writing, software
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* distributed under the License is distributed on an "AS IS" BASIS,
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* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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* See the License for the specific language governing permissions and
14+
* limitations under the License.
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*
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*/
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package io.seqera.wave.plugin
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import java.time.Instant

‎plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy‎

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@@ -17,6 +17,7 @@
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package io.seqera.wave.plugin
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import static io.seqera.wave.util.DockerHelper.*
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import java.net.http.HttpClient
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import java.net.http.HttpRequest
@@ -54,12 +55,10 @@ import io.seqera.wave.plugin.packer.Packer
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import nextflow.Session
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import nextflow.SysEnv
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import nextflow.container.resolver.ContainerInfo
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import nextflow.executor.BashTemplateEngine
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import nextflow.fusion.FusionConfig
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import nextflow.processor.Architecture
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import nextflow.processor.TaskRun
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import nextflow.script.bundle.ResourcesBundle
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import nextflow.util.MustacheTemplateEngine
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import nextflow.util.SysHelper
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import org.slf4j.Logger
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import org.slf4j.LoggerFactory
@@ -380,10 +379,11 @@ class WaveClient {
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// map the recipe to a dockerfile
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if( isCondaLocalFile(attrs.conda) ) {
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condaFile = Path.of(attrs.conda)
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dockerScript = condaFileToDockerFile()
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dockerScript = condaFileToDockerFile(config.condaOpts())
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}
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// 'conda' attributes is resolved as the conda packages to be used
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else {
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dockerScript = condaRecipeToDockerFile(attrs.conda)
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dockerScript = condaPackagesToDockerFile(attrs.conda, condaChannels, config.condaOpts())
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}
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}
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@@ -399,10 +399,10 @@ class WaveClient {
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// map the recipe to a dockerfile
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if( isSpackFile(attrs.spack) ) {
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spackFile = Path.of(attrs.spack)
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dockerScript = spackFileToDockerFile(spackArch)
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dockerScript = spackFileToDockerFile(spackArch, config.spackOpts())
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}
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else {
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dockerScript = spackRecipeToDockerFile(attrs.spack, spackArch)
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dockerScript = spackPackagesToDockerFile(attrs.spack, spackArch, config.spackOpts())
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}
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}
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@@ -464,105 +464,7 @@ class WaveClient {
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}
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}
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protected String condaFileToDockerFile() {
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final template = """\
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FROM {{base_image}}
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COPY --chown=\$MAMBA_USER:\$MAMBA_USER conda.yml /tmp/conda.yml
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RUN micromamba install -y -n base -f /tmp/conda.yml && \\
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{{base_packages}}
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micromamba clean -a -y
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""".stripIndent(true)
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final image = config.condaOpts().mambaImage
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477-
final basePackage = config.condaOpts().basePackages ? "micromamba install -y -n base ${config.condaOpts().basePackages} && \\".toString() : null
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final binding = ['base_image': image, 'base_packages': basePackage]
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final result = new MustacheTemplateEngine().render(template, binding)
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return addCommands(result)
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}
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// Dockerfile template adpated from the Spack package manager
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// https://github.com/spack/spack/blob/develop/share/spack/templates/container/Dockerfile
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// LICENSE APACHE 2.0
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protected String spackFileToDockerFile(String spackArch) {
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String cmd_template = ''
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final binding = [
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'builder_image': config.spackOpts().builderImage,
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'c_flags': config.spackOpts().cFlags,
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'cxx_flags': config.spackOpts().cxxFlags,
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'f_flags': config.spackOpts().fFlags,
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'spack_arch': spackArch,
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'checksum_string': config.spackOpts().checksum ? '' : '-n ',
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'runner_image': config.spackOpts().runnerImage,
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'os_packages': config.spackOpts().osPackages,
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'add_commands': addCommands(cmd_template),
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]
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final template = WaveClient.class.getResource('/templates/spack/dockerfile-spack-file.txt')
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try(final reader = template.newReader()) {
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final result = new BashTemplateEngine().render(reader, binding)
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return result
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}
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}
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protected String addCommands(String result) {
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if( config.condaOpts().commands )
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for( String cmd : config.condaOpts().commands ) {
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result += cmd + "\n"
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}
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if( config.spackOpts().commands )
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for( String cmd : config.spackOpts().commands ) {
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result += cmd + "\n"
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}
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return result
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}
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protected String condaRecipeToDockerFile(String recipe) {
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final template = """\
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FROM {{base_image}}
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RUN \\
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micromamba install -y -n base {{channel_opts}} \\
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{{target}} \\
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{{base_packages}}
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&& micromamba clean -a -y
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""".stripIndent(true)
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final channelsOpts = condaChannels.collect(it -> "-c $it").join(' ')
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final image = config.condaOpts().mambaImage
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final target = recipe.startsWith('http://') || recipe.startsWith('https://')
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? "-f $recipe".toString()
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: recipe
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final basePackage = config.condaOpts().basePackages ? "&& micromamba install -y -n base ${config.condaOpts().basePackages} \\".toString() : null
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final binding = [base_image: image, channel_opts: channelsOpts, target:target, base_packages: basePackage]
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final result = new MustacheTemplateEngine().render(template, binding)
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return addCommands(result)
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}
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// Dockerfile template adpated from the Spack package manager
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// https://github.com/spack/spack/blob/develop/share/spack/templates/container/Dockerfile
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// LICENSE APACHE 2.0
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protected String spackRecipeToDockerFile(String recipe, String spackArch) {
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546-
String cmd_template = ''
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final binding = [
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'recipe': recipe,
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'builder_image': config.spackOpts().builderImage,
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'c_flags': config.spackOpts().cFlags,
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'cxx_flags': config.spackOpts().cxxFlags,
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'f_flags': config.spackOpts().fFlags,
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'spack_arch': spackArch,
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'checksum_string': config.spackOpts().checksum ? '' : '-n ',
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'runner_image': config.spackOpts().runnerImage,
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'os_packages': config.spackOpts().osPackages,
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'add_commands': addCommands(cmd_template),
558-
]
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final template = WaveClient.class.getResource('/templates/spack/dockerfile-spack-recipe.txt')
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561-
try(final reader = template.newReader()) {
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final result = new BashTemplateEngine().render(reader, binding)
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return result
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}
565-
}
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567469
static protected boolean isCondaLocalFile(String value) {
568470
if( value.contains('\n') )

‎plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveObserver.groovy‎

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/*
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* Copyright 2020-2022, Seqera Labs
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* Copyright 2013-2023, Seqera Labs
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*
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* Licensed under the Apache License, Version 2.0 (the "License");
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* you may not use this file except in compliance with the License.

‎plugins/nf-wave/src/main/io/seqera/wave/plugin/adapter/InstantAdapter.groovy‎

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/*
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* Copyright 2020-2022, Seqera Labs
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* Copyright 2013-2023, Seqera Labs
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*
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* Licensed under the Apache License, Version 2.0 (the "License");
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* you may not use this file except in compliance with the License.

‎plugins/nf-wave/src/main/io/seqera/wave/plugin/config/ReportOpts.groovy‎

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/*
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* Copyright 2020-2022, Seqera Labs
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* Copyright 2013-2023, Seqera Labs
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*
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* Licensed under the Apache License, Version 2.0 (the "License");
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* you may not use this file except in compliance with the License.

‎plugins/nf-wave/src/main/io/seqera/wave/plugin/config/RetryOpts.groovy‎

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/*
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* Copyright 2020-2022, Seqera Labs
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* Copyright 2013-2023, Seqera Labs
33
*
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* Licensed under the Apache License, Version 2.0 (the "License");
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* you may not use this file except in compliance with the License.

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

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