Creates CgaPipelineCommand and refactors Clustal Omega module

This commit creates the CLI command for the CGA pipeline operation. In doing so, the Clustal Omega module was slightly refactored to rearrange some classes (e.g. move the TransformationProvider into its own package).
sing-group · May 16, 2023 · dcf9571 · dcf9571
1 parent ec25845
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diff --git a/seda-plugin-cga/README.md b/seda-plugin-cga/README.md
@@ -10,7 +10,7 @@ By default, the intermediate files generated by this operation in temporary dire
 For developers
 --------------
 
-The CGA pipeline involes a series of steps implemented in the `CgaPipeline` class. In order to programmatically test this pipeline, the following code can be used with the test data available [here](https://www.sing-group.org/seda/downloads/data/test-data-splign-compart.zip). It tooks about 21 minutes to complete using a workstation with Ubuntu 18.04.6 LTS, 8 CPUs (Intel(R) Core(TM) i7-8565U CPU @ 1.80GHz), 16GB of RAM and SSD disk
+The CGA pipeline involes a series of steps implemented in the `CgaPipeline` class. In order to programmatically test this pipeline, the following code can be used with the test data available [here](https://github.com/pegi3s/cga/raw/master/resources/test-data/cga-test-data.zip). It tooks about 21 minutes to complete using a workstation with Ubuntu 18.04.6 LTS, 8 CPUs (Intel(R) Core(TM) i7-8565U CPU @ 1.80GHz), 16GB of RAM and SSD disk
 
 ```java
   public static void main(String[] args) throws IOException, InterruptedException {
@@ -31,3 +31,8 @@ The CGA pipeline involes a series of steps implemented in the `CgaPipeline` clas
     ).run();
   }
 ```
+
+Using the same test data, the CLI command can be tested as follows:
+```
+cga --reference-fasta /path/to/cga/ref.fasta --results predicted_cds --max-dist 10000 --intron-bp 500 --min-full-nucleotide-size 200 --selection-criterion criterion_1 -selection-correction 10 --input-file /path/to/cga/input.fasta --output-directory /path/to/cga/output --save-parameters-file /path/to/cga/seda-cga.params
+```
diff --git a/seda-plugin-cga/src/main/java/org/sing_group/seda/cga/cli/CgaPipelineCommand.java b/seda-plugin-cga/src/main/java/org/sing_group/seda/cga/cli/CgaPipelineCommand.java
@@ -0,0 +1,268 @@
+/*
+ * #%L
+ * SEquence DAtaset builder CGA plugin
+ * %%
+ * Copyright (C) 2017 - 2022 Jorge Vieira, Cristina Vieira, Noé Vázquez, Miguel Reboiro-Jato and Hugo López-Fernández
+ * %%
+ * This program 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.
+ * 
+ * This program 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 this program.  If not, see
+ * <http://www.gnu.org/licenses/gpl-3.0.html>.
+ * #L%
+ */
+package org.sing_group.seda.cga.cli;
+
+import static java.util.Arrays.asList;
+import static java.util.Collections.emptyList;
+import static org.sing_group.seda.cga.plugin.core.CgaPipelineSedaPluginInfo.DESCRIPTION;
+import static org.sing_group.seda.cga.plugin.core.CgaPipelineSedaPluginInfo.NAME;
+import static org.sing_group.seda.cga.plugin.core.CgaPipelineSedaPluginInfo.PARAM_CGA_RESULTS_HELP;
+import static org.sing_group.seda.cga.plugin.core.CgaPipelineSedaPluginInfo.PARAM_CGA_RESULTS_NAME;
+import static org.sing_group.seda.cga.plugin.core.CgaPipelineSedaPluginInfo.PARAM_CGA_RESULTS_SHORT_NAME;
+import static org.sing_group.seda.cga.plugin.core.CgaPipelineSedaPluginInfo.PARAM_COMPI_TASKS_HELP;
+import static org.sing_group.seda.cga.plugin.core.CgaPipelineSedaPluginInfo.PARAM_COMPI_TASKS_NAME;
+import static org.sing_group.seda.cga.plugin.core.CgaPipelineSedaPluginInfo.PARAM_COMPI_TASKS_SHORT_NAME;
+import static org.sing_group.seda.cga.plugin.core.CgaPipelineSedaPluginInfo.PARAM_DOCKER_MODE_HELP;
+import static org.sing_group.seda.cga.plugin.core.CgaPipelineSedaPluginInfo.PARAM_INTRON_BP_HELP;
+import static org.sing_group.seda.cga.plugin.core.CgaPipelineSedaPluginInfo.PARAM_INTRON_BP_NAME;
+import static org.sing_group.seda.cga.plugin.core.CgaPipelineSedaPluginInfo.PARAM_INTRON_BP_SHORT_NAME;
+import static org.sing_group.seda.cga.plugin.core.CgaPipelineSedaPluginInfo.PARAM_MAX_DIST_HELP;
+import static org.sing_group.seda.cga.plugin.core.CgaPipelineSedaPluginInfo.PARAM_MAX_DIST_NAME;
+import static org.sing_group.seda.cga.plugin.core.CgaPipelineSedaPluginInfo.PARAM_MAX_DIST_SHORT_NAME;
+import static org.sing_group.seda.cga.plugin.core.CgaPipelineSedaPluginInfo.PARAM_MIN_FULL_NUCLEOTIDE_SIZE_HELP;
+import static org.sing_group.seda.cga.plugin.core.CgaPipelineSedaPluginInfo.PARAM_MIN_FULL_NUCLEOTIDE_SIZE_NAME;
+import static org.sing_group.seda.cga.plugin.core.CgaPipelineSedaPluginInfo.PARAM_MIN_FULL_NUCLEOTIDE_SIZE_SHORT_NAME;
+import static org.sing_group.seda.cga.plugin.core.CgaPipelineSedaPluginInfo.PARAM_MIN_SELECTION_CRITERION_HELP;
+import static org.sing_group.seda.cga.plugin.core.CgaPipelineSedaPluginInfo.PARAM_REFERENCE_FASTA_HELP;
+import static org.sing_group.seda.cga.plugin.core.CgaPipelineSedaPluginInfo.PARAM_REFERENCE_FASTA_NAME;
+import static org.sing_group.seda.cga.plugin.core.CgaPipelineSedaPluginInfo.PARAM_REFERENCE_FASTA_SHORT_NAME;
+import static org.sing_group.seda.cga.plugin.core.CgaPipelineSedaPluginInfo.PARAM_SELECTION_CORRECTION_HELP;
+import static org.sing_group.seda.cga.plugin.core.CgaPipelineSedaPluginInfo.PARAM_SELECTION_CORRECTION_NAME;
+import static org.sing_group.seda.cga.plugin.core.CgaPipelineSedaPluginInfo.PARAM_SELECTION_CORRECTION_SHORT_NAME;
+import static org.sing_group.seda.cga.plugin.core.CgaPipelineSedaPluginInfo.PARAM_SELECTION_CRITERION_NAME;
+import static org.sing_group.seda.cga.plugin.core.CgaPipelineSedaPluginInfo.PARAM_SELECTION_CRITERION_SHORT_NAME;
+import static org.sing_group.seda.cga.plugin.core.CgaPipelineSedaPluginInfo.PARAM_SKIP_PULL_DOCKER_IMAGES_HELP;
+import static org.sing_group.seda.cga.plugin.core.CgaPipelineSedaPluginInfo.PARAM_SKIP_PULL_DOCKER_IMAGES_NAME;
+import static org.sing_group.seda.cga.plugin.core.CgaPipelineSedaPluginInfo.PARAM_SKIP_PULL_DOCKER_IMAGES_SHORT_NAME;
+import static org.sing_group.seda.cga.plugin.core.CgaPipelineSedaPluginInfo.PROPERTY_ENABLE_LOCAL_EXECUTION_CGA;
+import static org.sing_group.seda.cga.plugin.core.CgaPipelineSedaPluginInfo.SHORT_NAME;
+import static org.sing_group.seda.plugin.core.info.AbstractInfo.PARAM_DOCKER_MODE_NAME;
+import static org.sing_group.seda.plugin.core.info.AbstractInfo.PARAM_DOCKER_MODE_SHORT_NAME;
+
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.List;
+import java.util.Optional;
+
+import org.sing_group.seda.cga.execution.CgaBinariesExecutor;
+import org.sing_group.seda.cga.execution.CgaCompiPipelineConfiguration;
+import org.sing_group.seda.cga.execution.DefaultDockerCgaBinariesExecutor;
+import org.sing_group.seda.cga.plugin.core.CgaPipelineSedaPluginInfo;
+import org.sing_group.seda.cga.transformation.dataset.CgaResults;
+import org.sing_group.seda.cga.transformation.provider.CgaPipelineTransformationProvider;
+import org.sing_group.seda.cli.ExternalSoftwareExecutionCommand;
+import org.sing_group.seda.core.io.JsonObjectReader;
+import org.sing_group.seda.plugin.spi.TransformationProvider;
+
+import es.uvigo.ei.sing.yacli.command.option.BooleanOption;
+import es.uvigo.ei.sing.yacli.command.option.DefaultValuedStringOption;
+import es.uvigo.ei.sing.yacli.command.option.FileOption;
+import es.uvigo.ei.sing.yacli.command.option.IntegerDefaultValuedStringConstructedOption;
+import es.uvigo.ei.sing.yacli.command.option.Option;
+import es.uvigo.ei.sing.yacli.command.option.StringOption;
+import es.uvigo.ei.sing.yacli.command.parameter.Parameters;
+
+public class CgaPipelineCommand extends ExternalSoftwareExecutionCommand {
+
+  private static final CgaCompiPipelineConfiguration DEFAULT_CGA_PARAMETERS = 
+    new CgaCompiPipelineConfiguration();
+
+  public static final FileOption OPTION_REFERENCE_FASTA =
+    new FileOption(
+      PARAM_REFERENCE_FASTA_NAME, PARAM_REFERENCE_FASTA_SHORT_NAME, 
+      PARAM_REFERENCE_FASTA_HELP, false, true
+    );
+
+  public static final DefaultValuedStringOption OPTION_CGA_RESULTS =
+    new DefaultValuedStringOption(
+      PARAM_CGA_RESULTS_NAME, PARAM_CGA_RESULTS_SHORT_NAME,
+      PARAM_CGA_RESULTS_HELP, CgaResults.PREDICTED_CDS.name().toLowerCase()
+    );
+
+  public static final IntegerDefaultValuedStringConstructedOption OPTION_NUM_TASKS =
+    new IntegerDefaultValuedStringConstructedOption(
+      PARAM_COMPI_TASKS_NAME, PARAM_COMPI_TASKS_SHORT_NAME,
+      PARAM_COMPI_TASKS_HELP, 4
+    );
+
+  public static final IntegerDefaultValuedStringConstructedOption OPTION_MAX_DIST =
+    new IntegerDefaultValuedStringConstructedOption(
+      PARAM_MAX_DIST_NAME, PARAM_MAX_DIST_SHORT_NAME, 
+      PARAM_MAX_DIST_HELP, DEFAULT_CGA_PARAMETERS.getMaxDist()
+    );
+
+  public static final IntegerDefaultValuedStringConstructedOption OPTION_MIN_FULL_NUCLEOTIDE_SIZE =
+    new IntegerDefaultValuedStringConstructedOption(
+      PARAM_MIN_FULL_NUCLEOTIDE_SIZE_NAME, PARAM_MIN_FULL_NUCLEOTIDE_SIZE_SHORT_NAME, 
+      PARAM_MIN_FULL_NUCLEOTIDE_SIZE_HELP, DEFAULT_CGA_PARAMETERS.getMinFullNucleotideSize() 
+    );
+
+  public static final IntegerDefaultValuedStringConstructedOption OPTION_INTRON_BP =
+    new IntegerDefaultValuedStringConstructedOption(
+      PARAM_INTRON_BP_NAME, PARAM_INTRON_BP_SHORT_NAME, 
+      PARAM_INTRON_BP_HELP, DEFAULT_CGA_PARAMETERS.getIntronBp()
+    );
+
+  public static final DefaultValuedStringOption OPTION_SELECTION_CRITERION =
+    new DefaultValuedStringOption(
+      PARAM_SELECTION_CRITERION_NAME, PARAM_SELECTION_CRITERION_SHORT_NAME, 
+      PARAM_MIN_SELECTION_CRITERION_HELP, DEFAULT_CGA_PARAMETERS.getSelectionCriterion().name().toLowerCase()
+    );
+
+
+  public static final IntegerDefaultValuedStringConstructedOption OPTION_SELECTION_CORRECTION =
+    new IntegerDefaultValuedStringConstructedOption(
+      PARAM_SELECTION_CORRECTION_NAME, PARAM_SELECTION_CORRECTION_SHORT_NAME, 
+      PARAM_SELECTION_CORRECTION_HELP, DEFAULT_CGA_PARAMETERS.getSelectionCorrection()
+    );
+
+  public static final BooleanOption OPTION_SKIP_PULL_DOCKER_IMAGES_NAME =
+    new BooleanOption(
+      PARAM_SKIP_PULL_DOCKER_IMAGES_NAME, PARAM_SKIP_PULL_DOCKER_IMAGES_SHORT_NAME, 
+      PARAM_SKIP_PULL_DOCKER_IMAGES_HELP, true, false
+    );
+
+  public static final StringOption OPTION_DOCKER_MODE =
+    new StringOption(
+      PARAM_DOCKER_MODE_NAME, PARAM_DOCKER_MODE_SHORT_NAME, PARAM_DOCKER_MODE_HELP, true, true
+    );
+
+  @Override
+  public String getName() {
+    return SHORT_NAME;
+  }
+
+  @Override
+  public String getDescriptiveName() {
+    return NAME;
+  }
+
+  @Override
+  public String getDescription() {
+    return DESCRIPTION;
+  }
+
+  @Override
+  protected String getSedaGroup() {
+    return CgaPipelineSedaPluginInfo.GROUP;
+  }
+
+  @Override
+  protected String getPropertyEnableLocalExecution() {
+    return PROPERTY_ENABLE_LOCAL_EXECUTION_CGA;
+  }
+
+  @Override
+  protected List<Option<?>> getLocalOptionsList() {
+    return emptyList();
+  }
+
+  @Override
+  protected List<Option<?>> createExternalSedaOptions() {
+    return asList(
+      OPTION_REFERENCE_FASTA,
+      OPTION_CGA_RESULTS,
+      OPTION_NUM_TASKS,
+      OPTION_MAX_DIST,
+      OPTION_INTRON_BP,
+      OPTION_MIN_FULL_NUCLEOTIDE_SIZE,
+      OPTION_SELECTION_CRITERION,
+      OPTION_SELECTION_CORRECTION,
+      OPTION_SKIP_PULL_DOCKER_IMAGES_NAME,
+      OPTION_DOCKER_MODE
+     );
+  }
+
+  @Override
+  protected TransformationProvider getTransformation(Parameters parameters) {
+    CgaPipelineTransformationProvider provider = new CgaPipelineTransformationProvider();
+
+    if(!parameters.hasOption(OPTION_REFERENCE_FASTA)) {
+      formattedValidationError("The reference fasta file is mandatory.");
+    }
+
+    Path referenceFasta = parameters.getSingleValue(OPTION_REFERENCE_FASTA).toPath();
+
+    if (!Files.exists(referenceFasta)) {
+      formattedValidationError("Invalid path. The path to the reference fasta file must be valid and exist.");
+    }
+    provider.setReferenceFasta(referenceFasta.toFile());
+
+    CgaResults cgaResults = null;
+
+    try {
+      cgaResults = CgaResults.valueOf(parameters.getSingleValueString(OPTION_CGA_RESULTS).toUpperCase());
+      provider.setCgaResults(cgaResults);
+    } catch (IllegalArgumentException e) {
+      invalidEnumValue(OPTION_CGA_RESULTS);
+    }
+
+    if (parameters.hasOption(OPTION_NUM_TASKS)) {
+      provider.setCompiTasks(parameters.getSingleValue(OPTION_NUM_TASKS));
+    }
+
+
+    int maxDist = parameters.getSingleValue(OPTION_MAX_DIST);
+
+    int intronBp = parameters.getSingleValue(OPTION_INTRON_BP);
+
+    int minFullNucleotideSize = parameters.getSingleValue(OPTION_MIN_FULL_NUCLEOTIDE_SIZE);
+
+    CgaCompiPipelineConfiguration.SelectionCriterion selectionCriterion = null;
+
+    try {
+      selectionCriterion = CgaCompiPipelineConfiguration.SelectionCriterion.valueOf(parameters.getSingleValueString(OPTION_SELECTION_CRITERION).toUpperCase());
+    } catch (IllegalArgumentException e) {
+      invalidEnumValue(OPTION_SELECTION_CRITERION);
+    }
+
+    int selectionCorrection = parameters.getSingleValue(OPTION_SELECTION_CORRECTION);
+
+    boolean skipPullDockerImages = parameters.hasOption(OPTION_SKIP_PULL_DOCKER_IMAGES_NAME);
+
+    provider.setCgaCompiPipelineConfiguration(
+      new CgaCompiPipelineConfiguration(
+        maxDist, intronBp, minFullNucleotideSize, selectionCriterion, 
+        selectionCorrection, skipPullDockerImages
+      )
+    );
+
+    CgaBinariesExecutor executor = null;
+    if (parameters.hasOption(OPTION_DOCKER_MODE)) {
+      executor = new DefaultDockerCgaBinariesExecutor(parameters.getSingleValue(OPTION_DOCKER_MODE));
+    } else {
+      executor = new DefaultDockerCgaBinariesExecutor();
+    }
+
+    provider.setCgaBinariesExecutor(Optional.of(executor));
+
+    return provider;
+  }
+
+  @Override
+  protected TransformationProvider getTransformation(File parametersFile) throws IOException {
+    return new JsonObjectReader<CgaPipelineTransformationProvider>()
+      .read(parametersFile, CgaPipelineTransformationProvider.class);
+  }
+}
diff --git a/...cga/src/main/java/org/sing_group/seda/cga/execution/DefaultDockerCgaBinariesExecutor.java b/...cga/src/main/java/org/sing_group/seda/cga/execution/DefaultDockerCgaBinariesExecutor.java
@@ -118,11 +118,4 @@ public void checkBinary() throws BinaryCheckException {
   public String getDockerImage() {
     return dockerImage;
   }
-
-  public static void main(String[] args) throws IOException, InterruptedException, BinaryCheckException {
-    // new DefaultDockerCgaBinariesExecutor().checkBinary();
-//      new DefaultDockerCgaBinariesExecutor().initWorkingDir(new File("/tmp/seda_cga2"));
-    System.setProperty(SEDA_EXECUTION_SHOW_COMMANDS, "true");
-     new DefaultDockerCgaBinariesExecutor().run(new File("/tmp/seda_cga2"), "--until split-reference");
-  }
 }