Expose Snakemake generation of APE to RestfulAPE

CITATION.cff

@@ -9,8 +9,8 @@ type: software
 authors:
   - given-names: Vedran
     family-names: Kasalica
-    email: v.kasalica@esciencecenter.nl
-    affiliation: Netherlands eScience Center, Netherlands
+    email: vedran.kasalica@health-ri.nl
+    affiliation: Health-RI, Netherlands
     orcid: 'https://orcid.org/0000-0002-0097-1056'
   - given-names: Peter
     family-names: Kok

pom.xml

@@ -8,9 +8,9 @@
 		<version>3.0.4</version>
 		<relativePath/> <!-- lookup parent from repository -->
 	</parent>
-	<groupId>nl.esciencecenter</groupId>
+	<groupId>org.workflomics</groupId>
 	<artifactId>restape</artifactId>
-	<version>1.0.0</version>
+	<version>1.1.0</version>
 	<name>restape</name>
 	<description>RESTful API for the APE library</description>
 	<licenses>
@@ -23,10 +23,16 @@
 	<developers>
 		<developer>
 			<name>Vedran Kasalica</name>
-			<email>v.kasalica@esciencecenter.nl</email>
-			<organization>Netherlands eScience Center</organization>
-			<organizationUrl>https://www.esciencecenter.nl/</organizationUrl>
+			<email>vedran.kasalica@health-ri.nl</email>
+			<organization>Health-RI</organization>
+			<organizationUrl>https://www.health-ri.nl/</organizationUrl>
 		</developer>
+        <developer>
+            <name>Mario Frank</name>
+            <email>mario.frank@uni-potsdam.de</email>
+            <organization>University of Potsdam</organization>
+            <organizationUrl>https://www.uni-potsdam.de</organizationUrl>
+        </developer>
 	</developers>
 	<scm>
 		<connection>scm:git:git://github.com/workflomics/restape.git</connection>
@@ -86,11 +92,11 @@
 			<scope>runtime</scope>
 		</dependency>
 
-		<!-- https://mvnrepository.com/artifact/io.github.sanctuuary/APE -->
+		<!-- https://mvnrepository.com/artifact/org.workflomics/APE -->
 		<dependency>
-			<groupId>io.github.sanctuuary</groupId>
+			<groupId>org.workflomics</groupId>
 			<artifactId>APE</artifactId>
-			<version>2.5.3</version>
+			<version>2.6.1</version>
 		</dependency>
 
 		<!-- https://mvnrepository.com/artifact/org.springdoc/springdoc-openapi-starter-webmvc-ui -->

src/main/java/nl/esciencecenter/controller/RestApeController.java

@@ -29,7 +29,8 @@
 import io.swagger.v3.oas.annotations.Parameter;
 import nl.esciencecenter.controller.dto.APEConfig;
 import nl.esciencecenter.controller.dto.CWLFileInfo;
-import nl.esciencecenter.controller.dto.CWLZip;
+import nl.esciencecenter.controller.dto.SnakeFileInfo;
+import nl.esciencecenter.controller.dto.WorkflowsZip;
 import nl.esciencecenter.controller.dto.ConstraintElem;
 import nl.esciencecenter.controller.dto.ImgFileInfo;
 import nl.esciencecenter.controller.dto.TaxonomyElem;
@@ -349,7 +350,7 @@ public ResponseEntity<?> postImage(
                 description = "Retrieve a cwl file from the file system, describing the workflow.",
                 tags = {"Download"},
                 requestBody = @io.swagger.v3.oas.annotations.parameters.RequestBody(
-                        description = "JSON object containing the information for retrieving the CWL file, including the name of the CWL file (as 'figure_name') and the ID of the corresponding synthesis run.",
+                        description = "JSON object containing the information for retrieving the CWL file, including the name of the CWL file (as 'cwl_name') and the ID of the corresponding synthesis run.",
                         required = true,
                         content = @Content(
                                 mediaType = "application/json",
@@ -368,6 +369,40 @@ public ResponseEntity<String> postCwl(
                                 .body(IOUtils.getLocalCwlFile(path));
         }
 
+        /**
+         * Retrieve the solution CWL workflow based on the provided run ID and a
+         * candidate solution.
+         *
+         * @param fileName Name of the Snakemake file (provided under 'name' after the
+         *                 synthesis run).
+         * @param runID    ID of the corresponding synthesis run (provided under
+         *                 'run_id' after the synthesis run).
+         * @return Snakemake file representing the workflow.
+         */
+        @PostMapping("/snakemake")
+        @Operation(summary = "Retrieve a Snakemake file",
+                description = "Retrieve a Snakemake file from the file system, describing the workflow.",
+                tags = {"Download"},
+                requestBody = @io.swagger.v3.oas.annotations.parameters.RequestBody(
+                        description = "JSON object containing the information for retrieving the Snakemake file, including the name of the Snakemake file (as 'snakemake_name') and the ID of the corresponding synthesis run.",
+                        required = true,
+                        content = @Content(
+                                mediaType = "application/json",
+                                schema = @Schema(implementation = SnakeFileInfo.class))
+                ),
+                responses = {
+                        @ApiResponse(responseCode = "200", description = "Successful operation. Snakemake file describing the workflow is provided.", content = @Content(mediaType = "application/x-yaml")),
+                        @ApiResponse(responseCode = "400", description = "Invalid input"),
+                        @ApiResponse(responseCode = "404", description = "Not found")
+                })
+        public ResponseEntity<String> postSnakemake(
+                @RequestBody(required = true) SnakeFileInfo snakeInfoJson) throws IOException {
+
+            Path path = snakeInfoJson.calculatePath();
+            return ResponseEntity.ok().contentType(MediaType.parseMediaType("application/x-yaml"))
+                    .body(IOUtils.getLocalSnakemakeFile(path));
+        }
+
         /**
          * Retrieve the CWL input file based on the provided run ID.
          * 
@@ -461,26 +496,26 @@ public ResponseEntity<String> getBenchmarks(
          * @return CWL file representing the workflow.
          */
         @PostMapping("/cwl_zip")
-        @Operation(summary = "Retrieve the zip of cwl files.",
-                description = "Retrieve the zip comprising CWL files specified in the request body. The request body should be a JSON object with the following fields: 'run_id' and 'workflows'. The 'run_id' field specifies the ID of the synthesis run, while the 'workflows' field is a list of CWL file names.",
+        @Operation(summary = "Retrieve the zip of cwl and Snakemake files.",
+                description = "Retrieve the zip comprising CWL and Snakemake files specified in the request body. The request body should be a JSON object with the following fields: 'run_id' and 'workflows'. The 'run_id' field specifies the ID of the synthesis run, while the 'workflows' field is a list of CWL and Snakemake file names.",
                 tags = {"Download"},
                 requestBody = @io.swagger.v3.oas.annotations.parameters.RequestBody(
                 description = "JSON object containing the following fields: 'run_id' and 'workflows'.",
                 required = true,
-                content = @Content(schema = @Schema(implementation = CWLZip.class))
+                content = @Content(schema = @Schema(implementation = WorkflowsZip.class))
                 ),
                 responses = {
                         @ApiResponse(responseCode = "200", 
-                                description = "Successful operation. A zip file comprising specified CWL files is returned.",
+                                description = "Successful operation. A zip file comprising specified CWL and Snakemake files is returned.",
                                 content = @Content(mediaType = "application/zip")),
                         @ApiResponse(responseCode = "400", description = "Invalid input"),
                         @ApiResponse(responseCode = "404", description = "Not found"),
                         @ApiResponse(responseCode = "500", description = "Internal server error")
                 })
         public ResponseEntity<?> postZipCWLs(
-                        @RequestBody(required = true) CWLZip cwlZipInfo) {
+                        @RequestBody(required = true) WorkflowsZip workflowsZipInfo) {
                 try {
-                        Path zipPath = IOUtils.zipFilesForLocalExecution(cwlZipInfo);
+                        Path zipPath = IOUtils.zipFilesForLocalExecution(workflowsZipInfo);
 
                         Resource zipResource = new UrlResource(zipPath.toUri());
                         String zipContentType = Files.probeContentType(zipPath);

src/main/java/nl/esciencecenter/controller/dto/APEConfig.java

@@ -50,6 +50,9 @@ public class APEConfig {
     @JsonProperty("number_of_cwl_files")
     private int numberOfCwlFiles;
 
+    @JsonProperty("number_of_snakemake_files")
+    private int numberOfSnakemakeFiles;
+
     @JsonProperty("tool_seq_repeat")
     private boolean toolSeqRepeat;
 

src/main/java/nl/esciencecenter/controller/dto/SnakeFileInfo.java

@@ -0,0 +1,63 @@
+package nl.esciencecenter.controller.dto;
+
+import java.nio.file.Files;
+import java.nio.file.Path;
+
+import com.fasterxml.jackson.annotation.JsonProperty;
+
+import lombok.Getter;
+import lombok.NoArgsConstructor;
+import nl.esciencecenter.restape.RestApeUtils;
+
+@Getter
+@NoArgsConstructor
+public class SnakeFileInfo {
+    @JsonProperty("run_id")
+    private String runID;
+
+    @JsonProperty("file_name")
+    private String fileName;
+    static final String snakemakeExtension = "smk";
+
+
+    /**
+     * Set the runID in case it is valid, i.e., corresponds to runID formatting defined within RESTful APE. If the runID is not valid, an exception is thrown.
+     *
+     * @throws IllegalArgumentException If the structure is not valid.
+     */
+    public void setRunID(String runID) throws IllegalArgumentException {
+        if (!RestApeUtils.isValidRunID(runID)) {
+            throw new IllegalArgumentException("The runID format '" + runID + "' is invalid.");
+        }
+        this.runID = runID;
+    }
+
+    /**
+     * Set the file name in case it is valid, i.e., corresponds to file name formatting defined within APE and includes the supported Snakemake extension.
+     * If the file name is not valid, an exception is thrown.
+     *
+     * @throws IllegalArgumentException If the structure is not valid.
+     */
+    public void setFileName(String fileName) throws IllegalArgumentException {
+        if (!RestApeUtils.isValidAPEFileName(fileName, snakemakeExtension)) {
+            throw new IllegalArgumentException("The Snakemake file_name format '" + fileName + "' is invalid.");
+        }
+        this.fileName = fileName;
+    }
+
+    /**
+     * Get the path to the Snakemake file. If the file does not exist or is not accessible, an exception is thrown.
+     *
+     * @return Path to the Snakemake file.
+     */
+    public Path calculatePath() {
+        Path path = RestApeUtils.calculatePath(runID, "Snakemake", fileName);
+        if(Files.notExists(path)) {
+            throw new IllegalArgumentException("The specified Snakemake file does not exist: " + path.toString());
+        } else if (!Files.isReadable(path)) {
+            throw new IllegalArgumentException("The Snakemake file cannot be accessed: " + path.toString());
+        }
+        return path;
+    }
+
+}

src/main/java/nl/esciencecenter/controller/dto/CWLZip.java → src/main/java/nl/esciencecenter/controller/dto/WorkflowsZip.java

@@ -19,7 +19,7 @@
 @Getter
 @Setter
 @NoArgsConstructor
-public class CWLZip {
+public class WorkflowsZip {
     @JsonProperty("run_id")
     private String runID;
     private List<String> workflows;
@@ -51,7 +51,7 @@ public void setWorkflows(List<String> workflows) throws IllegalArgumentException
 
     /**
      * Check whether all the workflows are valid CWL file names.
-     * @param workflows2 
+     * @param workflows The workflows to verify
      * 
      * @return true if all the workflows are valid CWL file names, false otherwise.
      */
@@ -71,14 +71,26 @@ public List<Path> getCWLPaths() {
     }
 
     /**
-     * Get the paths to the CWL files and the SVG files.
+     * Get the paths to the Snakemake files.
+     *
+     * @return List of paths to the Snakemake files.
+     */
+    public List<Path> getSnakemakePaths() {
+        return workflows.stream()
+                .map(fileName -> RestApeUtils.calculatePath(runID, "Snakemake", fileName))
+                .collect(Collectors.toList());
+    }
+
+    /**
+     * Get the paths to the CWL, Snakemake and the SVG files.
      * 
-     * @return List of paths to the CWL files and the SVG files.
+     * @return List of paths to the CWL, Snakemake and the SVG files.
      */
-    public List<Path> getCWLandSVGPaths() {
+    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")));
             paths.add(RestApeUtils.calculatePath(runID, "Figures", fileName.replace(".cwl", ".svg")));
         }
         return paths;

src/main/java/nl/esciencecenter/models/Workflow.java

@@ -30,6 +30,9 @@ public class Workflow {
     @Column
     private String cwlFilePath;
 
+    @Column
+    private String snakemakeFilePath;
+
     @Column
     private String pngFilePath;
 

src/main/java/nl/esciencecenter/restape/APEWorkflowMetadata.java

@@ -30,6 +30,8 @@ public class APEWorkflowMetadata {
     private String runId;
     @JsonProperty("cwl_name")
     private String cwlName;
+    @JsonProperty("snakemake_name")
+    private String snakemakeName;
     @JsonProperty("figure_name")
     private String figureName;
     @JsonProperty("benchmark_file")
@@ -49,6 +51,7 @@ public APEWorkflowMetadata(SolutionWorkflow sol, String runID, boolean benchmark
         this.workflowLength = sol.getSolutionLength();
         this.runId = runID;
         this.cwlName = sol.getFileName() + ".cwl";
+        this.snakemakeName = sol.getFileName() + ".smk";
         this.figureName = sol.getFileName();
         if (benchmark) {
             this.benchmarkFile = sol.getFileName() + ".json";
@@ -70,6 +73,7 @@ public JSONObject toJSONObject() {
         json.put("workflow_length", this.workflowLength);
         json.put("run_id", this.runId);
         json.put("cwl_name", this.cwlName);
+        json.put("snakemake_name", this.snakemakeName);
         json.put("figure_name", this.figureName);
         if (this.benchmarkFile != null) {
             json.put("benchmark_file", this.benchmarkFile);

src/main/java/nl/esciencecenter/restape/ApeAPI.java

@@ -248,8 +248,9 @@ public static List<APEWorkflowMetadata> runSynthesis(JSONObject configJson, bool
 
         SolutionsList candidateSolutions = executeSynthesis(configJson, runID);
 
-        // Write solutions (as CWL files and figures) to the file system.
-        APE.writeCWLWorkflows(candidateSolutions);
+        // Write solutions (as CWL and Snakemake files and figures) to the file system.
+        APE.writeCWLWorkflows(candidateSolutions, true);
+        APE.writeSnakemakeWorkflows(candidateSolutions, true);
         APE.writeTavernaDesignGraphs(candidateSolutions, Format.SVG);
         APE.writeTavernaDesignGraphs(candidateSolutions, Format.PNG);
 
@@ -287,6 +288,7 @@ private static SolutionsList executeSynthesis(JSONObject configJson, String runI
         runConfig.setSolutionPath(solutionPath);
         int maxSol = runConfig.getMaxNoSolutions();
         runConfig.setNoCWL(maxSol);
+        runConfig.setNoSnakemake(maxSol);
         runConfig.setNoGraphs(maxSol);
         runConfig.setDebugMode(true);
         // run the synthesis and retrieve the solutions

src/main/java/nl/esciencecenter/restape/IOUtils.java

@@ -18,7 +18,7 @@
 
 import lombok.AccessLevel;
 import lombok.NoArgsConstructor;
-import nl.esciencecenter.controller.dto.CWLZip;
+import nl.esciencecenter.controller.dto.WorkflowsZip;
 
 /**
  * The {@code IOUtils} class provides static methods to read the input files.
@@ -42,6 +42,17 @@ public static String getLocalCwlFile(Path filePath) throws IOException, NoSuchFi
                 return FileUtils.readFileToString(filePath.toFile(), StandardCharsets.UTF_8);
         }
 
+        /**
+         * Get the Snakemake content of the file at the given path.
+         *
+         * @param filePath - path to the Snakemake file
+         * @return Snakemake content of the file representing a workflow
+         * @throws IOException - if the file cannot be read
+         */
+        public static String getLocalSnakemakeFile(Path filePath) throws IOException, NoSuchFileException {
+            return FileUtils.readFileToString(filePath.toFile(), StandardCharsets.UTF_8);
+        }
+
         /**
          * Get the JSON content of the file at the given path.
          * 
@@ -58,24 +69,24 @@ public static String getLocalBenchmarkFile(Path filePath) throws IOException {
          * a single zip file. In addition, a `readme.txt` file with instructions on how
          * to run the workflows is added to the zip.
          * 
-         * @param cwlZipInfo - the CWL zip information, containing the runID and the list of workflow file names.
+         * @param workflowsZipInfo - the CWL zip information, containing the runID and the list of workflow file names.
          * 
          * @return Path to the created zip file.
          * @throws IOException Error is thrown if the zip file cannot be created or
          *                     written to.
          */
-        public static Path zipFilesForLocalExecution(CWLZip cwlZipInfo) throws IOException {
+        public static Path zipFilesForLocalExecution(WorkflowsZip workflowsZipInfo) throws IOException {
 
-                List<Path> cwlFilePaths = cwlZipInfo.getCWLandSVGPaths();
+                List<Path> filePaths = workflowsZipInfo.getAllPaths();
 
                 // Add the CWL input file to the zip
-                Path cwlInputPath = RestApeUtils.calculatePath(cwlZipInfo.getRunID(), "CWL", "input.yml");
-                cwlFilePaths.add(cwlInputPath);
+                Path cwlInputPath = RestApeUtils.calculatePath(workflowsZipInfo.getRunID(), "CWL", "input.yml");
+                filePaths.add(cwlInputPath);
 
                 Path zipPath = cwlInputPath.getParent().resolve("workflows.zip");
                 try (FileOutputStream fos = new FileOutputStream(zipPath.toFile());
                                 ZipOutputStream zipOut = new ZipOutputStream(fos)) {
-                        for (Path file : cwlFilePaths) {
+                        for (Path file : filePaths) {
                                 zipOut.putNextEntry(new ZipEntry(file.getFileName().toString()));
                                 Files.copy(file, zipOut);
                                 zipOut.closeEntry();