Merge pull request #135 from CGru21/main

Add functionality to generate Snakemake files.

Author: eladrion

CITATION.cff

@@ -24,8 +24,13 @@ authors:
     family-names: Haverkort
     affiliation: Utrecht University, Netherlands
     orcid: 'https://orcid.org/0009-0005-4904-0868'
-  - given-names: Maurin
-    family-names: Voshol
+  - family-names: Maurin
+    given-names: Voshol
+  - given-names: Charlotte
+    family-names: Grunert
+    email: [email protected]
+    affiliation: University of Potsdam, Germany
+    orcid: 'https://orcid.org/0009-0007-1871-5409'
 identifiers:
   - type: doi
     value: 10.5281/zenodo.5638988

src/main/java/nl/uu/cs/ape/APE.java

@@ -31,6 +31,7 @@
 import nl.uu.cs.ape.solver.solutionStructure.SolutionWorkflow;
 import nl.uu.cs.ape.solver.solutionStructure.SolutionsList;
 import nl.uu.cs.ape.solver.solutionStructure.cwl.DefaultCWLCreator;
+import nl.uu.cs.ape.solver.solutionStructure.snakemake.SnakemakeCreator;
 import nl.uu.cs.ape.utils.APEFiles;
 import nl.uu.cs.ape.utils.APEUtils;
 
@@ -666,6 +667,47 @@ public static boolean writeCWLWorkflows(SolutionsList allSolutions) {
 		return true;
 	}
 
+	public static boolean writeSnakemakeWorkflows(SolutionsList allSolutions) {
+        if (allSolutions.isEmpty()) {
+            return false;
+        }
+        Path snakemakeFolder = allSolutions.getRunConfiguration().getSolutionDirPath2Snakemake();
+        int noSnakemakeFiles = allSolutions.getRunConfiguration().getNoSnakemake();
+        if (snakemakeFolder == null || noSnakemakeFiles == 0) {
+            return false;
+        }
+
+        final String timerID = "writingSnakemake";
+        APEUtils.printHeader(null, String.format("Writing the first %d solution(s) to Snakemake files", noSnakemakeFiles));
+        APEUtils.timerStart(timerID, true);
+
+        final File snakemakeDir = snakemakeFolder.toFile();
+        if (snakemakeDir.isDirectory()) {
+            // If the directory already exists, empty it first
+            deleteExistingFiles(snakemakeDir, SolutionWorkflow.getFileNamePrefix(), "snakefile");
+        } else {
+            // Create the Snakemake directory if it does not already exist
+            snakemakeDir.mkdir();
+        }
+        log.debug("Generating Snakemake files.");
+
+        allSolutions.getParallelStream().filter(solution -> solution.getIndex() < noSnakemakeFiles).forEach(solution -> {
+            try {
+				String titleSnakefile= solution.getFileName() + "_snakefile";
+				File script = snakemakeFolder.resolve(titleSnakefile).toFile();
+				SnakemakeCreator snakemakeCreator = new SnakemakeCreator(solution);
+				APEFiles.write2file(snakemakeCreator.generateSnakemakeRepresentation(), script, false);
+
+            } catch (IOException e) {
+                log.error("Error occurred while writing a Snakemake file to the file system.");
+                e.printStackTrace();
+            }
+        });
+
+        APEUtils.timerPrintText(timerID, "Snakemake files have been generated.");
+        return true;
+    }
+
 	/**
 	 * Delete all files in the given directory that start with the given prefix and
 	 * have the given extension.

src/main/java/nl/uu/cs/ape/Main.java

@@ -238,6 +238,7 @@ public static void executeSynthesis(String[] args) {
                 APE.writeTavernaDesignGraphs(solutions);
                 APE.writeExecutableWorkflows(solutions);
                 APE.writeCWLWorkflows(solutions);
+                APE.writeSnakemakeWorkflows(solutions);
             } catch (IOException e) {
                 log.error("Error in writing the solutions. to the file system.");
                 e.printStackTrace();

src/main/java/nl/uu/cs/ape/configuration/APERunConfig.java

@@ -66,6 +66,11 @@ public class APERunConfig {
      * Default is 0.
      */
     private final APEConfigTag<Integer> NO_CWL = new APEConfigTagFactory.TAGS.NO_CWL();
+    /**
+     * Number of Snakemake files that should be generated from candidate workflows.
+     * Default is 0.
+     */
+    private final APEConfigTag<Integer> NO_SNAKEMAKE = new APEConfigTagFactory.TAGS.NO_SNAKEMAKE();
     /**
      * Determines the required usage for the data instances that are given as
      * workflow input:<br>
@@ -119,6 +124,7 @@ public class APERunConfig {
             this.NO_EXECUTIONS,
             this.NO_GRAPHS,
             this.NO_CWL,
+            this.NO_SNAKEMAKE,
             this.USE_WORKFLOW_INPUT,
             this.USE_ALL_GENERATED_DATA,
             this.DEBUG_MODE,
@@ -141,6 +147,7 @@ public class APERunConfig {
             new NO_EXECUTIONS(),
             new NO_GRAPHS(),
             new NO_CWL(),
+            new NO_SNAKEMAKE(),
             new USE_WORKFLOW_INPUT(),
             new USE_ALL_GENERATED_DATA(),
             new DEBUG_MODE(),
@@ -366,6 +373,20 @@ public Path getSolutionDirPath2CWL() {
         return getSolutionDirPath2(CWL_FOLDER_NAME);
     }
 
+    /** Tag value. */
+    public static final String SNAKEMAKE_FOLDER_NAME = "Snakemake";
+
+    /**
+     * Get the path to the directory where the snakemake scripts corresponding the given
+     * solutions should be stored.
+     *
+     * @return the path to the directory where the snakemake scripts corresponding to the
+     *         given solutions should be stored
+     */
+    public Path getSolutionDirPath2Snakemake() {
+        return getSolutionDirPath2(SNAKEMAKE_FOLDER_NAME);
+    }
+
     /** Tag value. */
     public static final String EXECUTABLE_CWL_FOLDER_NAME = "CWL_executables";
 
@@ -462,6 +483,24 @@ public void setNoCWL(int noCWL) {
         NO_CWL.setValue(noCWL);
     }
 
+    /**
+     * Gets number of Snakemake files.
+     * 
+     * @return The value of {@link #NO_SNAKEMAKE}
+     */
+    public int getNoSnakemake() {
+        return NO_SNAKEMAKE.getValue();
+    }
+
+    /**
+     * Set the number of Snakemake files.
+     * 
+     * @param noSnakemake The number to set.
+     */
+    public void setNoSnakemake(int noSnakemake) {
+        NO_SNAKEMAKE.setValue(noSnakemake);
+    }
+
     /**
      * Gets program inputs.
      *

src/main/java/nl/uu/cs/ape/configuration/tags/APEConfigTagFactory.java

@@ -919,6 +919,40 @@ protected ValidationResults validate(Integer value, ValidationResults results) {
             }
         }
 
+        /**
+         * Configuration field.
+         */
+        public static class NO_SNAKEMAKE extends TYPES.Int {
+            public NO_SNAKEMAKE() {
+                super(Range.of(0, Integer.MAX_VALUE));
+            }
+
+            @Override
+            public APEConfigDefaultValue<Integer> getDefault() {
+                return APEConfigDefaultValue.withDefault(0);
+            }
+
+            @Override
+            public String getTagName() {
+                return "number_of_snakemake_files";
+            }
+
+            @Override
+            public String getLabel() {
+                return "Number of Snakemake files";
+            }
+
+            @Override
+            public String getDescription() {
+                return "The number of Snakemake representations of solutions that should be generated.";
+            }
+
+            @Override
+            protected ValidationResults validate(Integer value, ValidationResults results) {
+                return results;
+            }
+        }
+
         /**
          * Configuration field.
          */