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Expose the functionality to suppress the creation of non-executable CWL and snakemake files. #104

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Merged
eladrion merged 4 commits into from
Sep 8, 2026
Merged

Expose the functionality to suppress the creation of non-executable CWL and snakemake files. #104

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e81652e
Expose the functionality to suppress the creation of non-executable C…
eladrion Jul 29, 2026
6e53bf8
Fixing typo
eladrion Jul 29, 2026
b759889
Leave CWL and SMK file name in metadata empty, if the files were not …
eladrion Jul 29, 2026
e8230d0
Fix metadata creation
eladrion Jul 29, 2026
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18 changes: 14 additions & 4 deletions src/main/java/nl/esciencecenter/controller/dto/WorkflowsZip.java
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
package nl.esciencecenter.controller.dto;

import java.nio.file.Files;
import java.nio.file.Path;
import java.util.ArrayList;
import java.util.List;
Expand Down Expand Up @@ -82,15 +83,24 @@ public List<Path> getSnakemakePaths() {
}

/**
* Get the paths to the CWL, Snakemake and the SVG files.
* Get the paths to the existing CWL, Snakemake and the SVG files.
*
* @return List of paths to the CWL, Snakemake and the SVG files.
* @return List of paths to the existing CWL, Snakemake and the SVG files.
*/
public List<Path> getAllPaths() {
List<Path> paths = new ArrayList<>();
for (String fileName : workflows) {
paths.add(RestApeUtils.calculatePath(runID, "CWL", fileName));
paths.add(RestApeUtils.calculatePath(runID, "Snakemake", fileName.replace(".cwl", ".smk")));

Path cwlPath = RestApeUtils.calculatePath(runID, "CWL", fileName);
if(Files.exists(cwlPath)) {
paths.add(cwlPath);
}

Path smkPath = RestApeUtils.calculatePath(runID, "Snakemake", fileName.replace(".cwl", ".smk"));
if(Files.exists(smkPath)) {
paths.add(smkPath);
}

paths.add(RestApeUtils.calculatePath(runID, "Figures", fileName.replace(".cwl", ".svg")));
}
return paths;
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26 changes: 22 additions & 4 deletions src/main/java/nl/esciencecenter/restape/APEWorkflowMetadata.java
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,9 @@
import lombok.NoArgsConstructor;
import nl.uu.cs.ape.solver.solutionStructure.SolutionWorkflow;

import java.nio.file.Files;
import java.nio.file.Path;

/**
* The {@link APEWorkflowMetadata} class represents metadata for a workflow solution from the APE solver.
* This class encapsulates the details and metadata of a workflow solution,
Expand Down Expand Up @@ -50,11 +53,26 @@ public APEWorkflowMetadata(SolutionWorkflow sol, String runID, boolean benchmark
this.description = sol.getDescription();
this.workflowLength = sol.getSolutionLength();
this.runId = runID;
this.cwlName = sol.getFileName() + ".cwl";
this.snakemakeName = sol.getFileName() + ".smk";
this.figureName = sol.getFileName();

String fileName = sol.getFileName();

Path cwlPath = RestApeUtils.calculatePath(runID, "CWL", fileName + ".cwl");
if(Files.notExists(cwlPath)) {
this.cwlName = "";
} else {
this.cwlName = fileName + ".cwl";
}

Path smkPath = RestApeUtils.calculatePath(runID, "Snakemake", fileName + ".smk");
if(Files.notExists(smkPath)) {
this.snakemakeName = "";
} else {
this.snakemakeName = fileName + ".smk";
}

this.figureName = fileName;
if (benchmark) {
this.benchmarkFile = sol.getFileName() + ".json";
this.benchmarkFile = fileName + ".json";
}
}

Expand Down
22 changes: 19 additions & 3 deletions src/main/java/nl/esciencecenter/restape/ApeAPI.java
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Expand Up @@ -246,11 +246,27 @@ public static List<APEWorkflowMetadata> runSynthesis(JSONObject configJson, bool
// Define the synthesis run ID
String runID = RestApeUtils.generateRunID(configJson.toString());

SolutionsList candidateSolutions = executeSynthesis(configJson, runID);
String solutionPath = RestApeUtils.createDirectory(runID);

APE apeFramework = new APE(configJson);

APERunConfig runConfig = new APERunConfig(configJson, apeFramework.getDomainSetup());

runConfig.setSolutionPath(solutionPath);
int maxSol = runConfig.getMaxNoSolutions();
runConfig.setNoCWL(maxSol);

@vedran-kasalica vedran-kasalica Sep 8, 2026

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It would be even better if Workflomics would provide these in the configJson, but not crucial atm

@eladrion eladrion Sep 8, 2026

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You mean that APERunConfig sets the count of CWL/SMK/Graphs based on what is written in the configJson or that configJson contains an attribute for count of CWL/SMK/Graphs?

@eladrion eladrion Sep 8, 2026

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Aah, I get it, @vedran-kasalica. You mean that workflomics-frontend sets the existing fields number_of_generated_graphs and number_of_cwl_files in configJson and RestAPE just collects the info from there. I will open an issue.

@eladrion eladrion Sep 8, 2026

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Issue opened.

runConfig.setNoSnakemake(maxSol);
runConfig.setNoGraphs(maxSol);
runConfig.setDebugMode(true);

boolean createPartialScripts = runConfig.getCreatePartialScripts();
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vedran-kasalica marked this conversation as resolved.

// run the synthesis and retrieve the solutions
SolutionsList candidateSolutions = apeFramework.runSynthesis(runConfig);

// Write solutions (as CWL and Snakemake files and figures) to the file system.
APE.writeCWLWorkflows(candidateSolutions, true);
APE.writeSnakemakeWorkflows(candidateSolutions, true);
APE.writeCWLWorkflows(candidateSolutions, createPartialScripts);

@vedran-kasalica vedran-kasalica Sep 8, 2026

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Totally unrelated, but I just looked up the original implementation and made an issue as this might be redundant to define as such. Workflomics/ape#158

@eladrion eladrion Sep 8, 2026

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Set myself as assignee, can refactor this.

APE.writeSnakemakeWorkflows(candidateSolutions, createPartialScripts);
APE.writeTavernaDesignGraphs(candidateSolutions, Format.SVG);
APE.writeTavernaDesignGraphs(candidateSolutions, Format.PNG);

Expand Down
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