Generate alternatives

pom.xml

@@ -127,6 +127,12 @@
 			<version>3.1.0</version>
 		</dependency>
 
+		<!-- snakeyaml: CWL-Parsing für POST /alternatives/parse -->
+		<dependency>
+			<groupId>org.yaml</groupId>
+			<artifactId>snakeyaml</artifactId>
+		</dependency>
+
 	</dependencies>
 
 	<build>

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

@@ -0,0 +1,71 @@
+package nl.esciencecenter.controller;
+
+import java.io.IOException;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.MediaType;
+import org.springframework.http.ResponseEntity;
+import org.springframework.web.bind.annotation.ExceptionHandler;
+import org.springframework.web.bind.annotation.PostMapping;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestParam;
+import org.springframework.web.bind.annotation.RestController;
+import org.springframework.web.multipart.MultipartFile;
+
+import io.swagger.v3.oas.annotations.Operation;
+import io.swagger.v3.oas.annotations.media.Content;
+import io.swagger.v3.oas.annotations.media.Schema;
+import io.swagger.v3.oas.annotations.responses.ApiResponse;
+import nl.esciencecenter.controller.dto.ParseResponse;
+import nl.esciencecenter.restape.CwlParser;
+import nl.esciencecenter.restape.EdamLabels;
+
+@RestController
+@RequestMapping("/alternatives")
+public class AlternativesController {
+
+    @Autowired
+    private EdamLabels edamLabels;
+
+    /**
+     * Parses a CWL v1.2 workflow and returns its DAG representation plus
+     * workflow-level I/O terms for use as APE synthesis constraints.
+     */
+    @PostMapping(value = "/parse", consumes = MediaType.MULTIPART_FORM_DATA_VALUE)
+    @Operation(
+            summary = "Parse a CWL workflow file",
+            description = "Accepts a CWL v1.2 Workflow file as multipart/form-data and returns a " +
+                    "graph-optimised representation: tool nodes, data-flow edges, and the " +
+                    "workflow-level input/output EDAM terms.",
+            tags = {"Alternatives"},
+            responses = {
+                    @ApiResponse(responseCode = "200",
+                            description = "Successful operation. Graph representation of the CWL workflow is returned.",
+                            content = @Content(
+                                    schema = @Schema(implementation = ParseResponse.class),
+                                    mediaType = MediaType.APPLICATION_JSON_VALUE)),
+                    @ApiResponse(responseCode = "400", description = "Invalid or unsupported CWL file")
+            })
+    public ResponseEntity<ParseResponse> parseCwl(
+            @RequestParam("cwl_file") MultipartFile cwlFile) throws IOException {
+        edamLabels.ensureLoaded();
+        ParseResponse response = CwlParser.parse(cwlFile.getInputStream(), edamLabels::resolve);
+        return ResponseEntity.ok().contentType(MediaType.APPLICATION_JSON).body(response);
+    }
+
+    @ExceptionHandler(IllegalArgumentException.class)
+    public ResponseEntity<String> handleIllegalArgument(IllegalArgumentException e) {
+        return ResponseEntity.badRequest().body(e.getMessage());
+    }
+
+    @ExceptionHandler(IOException.class)
+    public ResponseEntity<String> handleIOException(IOException e) {
+        return ResponseEntity.badRequest().body(e.getMessage());
+    }
+
+    @ExceptionHandler(Exception.class)
+    public ResponseEntity<String> handleAny(Exception e) {
+        return ResponseEntity.internalServerError()
+                .body(e.getClass().getSimpleName() + ": " + e.getMessage());
+    }
+}

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

@@ -0,0 +1,11 @@
+package nl.esciencecenter.controller.dto;
+
+import lombok.AllArgsConstructor;
+import lombok.Getter;
+
+@Getter
+@AllArgsConstructor
+public class GraphEdge {
+    private final String source;
+    private final String target;
+}

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

@@ -0,0 +1,21 @@
+package nl.esciencecenter.controller.dto;
+
+import lombok.AllArgsConstructor;
+import lombok.Getter;
+
+@Getter
+@AllArgsConstructor
+public class GraphNode {
+    private final String id;
+    private final String label;
+    private final NodeType type;
+
+    /**
+     * Kind of node in the workflow graph. Constants are lowercase so Jackson
+     * serialises them as {@code "input"}/{@code "tool"}/{@code "output"} for the
+     * frontend (matching the existing {@code ImageFormat} enum convention).
+     */
+    public enum NodeType {
+        input, tool, output
+    }
+}

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

@@ -0,0 +1,15 @@
+package nl.esciencecenter.controller.dto;
+
+import java.util.List;
+
+import lombok.AllArgsConstructor;
+import lombok.Getter;
+
+@Getter
+@AllArgsConstructor
+public class ParseResponse {
+    private final List<GraphNode> nodes;
+    private final List<GraphEdge> edges;
+    private final List<TaxonomyElem> inputs;
+    private final List<TaxonomyElem> outputs;
+}

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

@@ -1,16 +1,18 @@
 package nl.esciencecenter.controller.dto;
 
+import com.fasterxml.jackson.annotation.JsonInclude;
+
 import lombok.AllArgsConstructor;
 import lombok.NoArgsConstructor;
 
 /**
  * This class represents a single element of the taxonomy.
- * TODO: This class is not used at the moment, but it is a good idea to use it
- * in the future.
- * 
+ * Used for taxonomy tree responses as well as for the flat input/output EDAM
+ * terms of a parsed workflow, where only {@code id} and {@code label} are set.
  */
 @NoArgsConstructor
 @AllArgsConstructor
+@JsonInclude(JsonInclude.Include.NON_NULL)
 public class TaxonomyElem {
     public String id;
     public String label;

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

@@ -0,0 +1,178 @@
+package nl.esciencecenter.restape;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.ArrayList;
+import java.util.LinkedHashMap;
+import java.util.LinkedHashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.function.UnaryOperator;
+
+import org.yaml.snakeyaml.LoaderOptions;
+import org.yaml.snakeyaml.Yaml;
+import org.yaml.snakeyaml.constructor.SafeConstructor;
+
+import nl.esciencecenter.controller.dto.GraphEdge;
+import nl.esciencecenter.controller.dto.GraphNode;
+import nl.esciencecenter.controller.dto.ParseResponse;
+import nl.esciencecenter.controller.dto.TaxonomyElem;
+
+/**
+ * Transforms a CWL v1.2 Workflow document into the graph-optimised ParseResponse.
+ */
+public class CwlParser {
+
+    private CwlParser() {}
+
+    /**
+     * Parses a CWL v1.2 Workflow from the given stream and returns the full DAG
+     * including input and output data nodes.
+     *
+     * @throws IllegalArgumentException if the document fails validation or is structurally incomplete
+     * @throws IOException              if the stream cannot be read
+     */
+    @SuppressWarnings("unchecked")
+    public static ParseResponse parse(InputStream inputStream, UnaryOperator<String> labelResolver) throws IOException {
+        Yaml yaml = new Yaml(new SafeConstructor(new LoaderOptions()));
+        Map<String, Object> cwl;
+        try {
+            cwl = yaml.load(inputStream);
+        } catch (Exception e) {
+            throw new IllegalArgumentException("CWL file could not be parsed as YAML: " + e.getMessage());
+        }
+        if (cwl == null) {
+            throw new IllegalArgumentException("CWL file is empty.");
+        }
+
+        // Step 1 – Validate
+        validateMetadata(cwl);
+
+        Map<String, Object> inputsSection  = (Map<String, Object>) cwl.get("inputs");
+        Map<String, Object> stepsSection   = (Map<String, Object>) cwl.get("steps");
+        Map<String, Object> outputsSection = (Map<String, Object>) cwl.get("outputs");
+
+        if (stepsSection == null || stepsSection.isEmpty()) {
+            throw new IllegalArgumentException("CWL Workflow must contain a non-empty 'steps' section.");
+        }
+
+        List<GraphNode> nodes = new ArrayList<>();
+        List<GraphEdge> edges = new ArrayList<>();
+        Set<String> seen     = new LinkedHashSet<>();
+
+        // Step 2a – Input nodes (dagre places them at the top in TB layout)
+        Set<String> inputIds = new LinkedHashSet<>();
+        if (inputsSection != null) {
+            for (Map.Entry<String, Object> entry : inputsSection.entrySet()) {
+                String id    = entry.getKey();
+                String label = formatLabel(entry.getValue(), id, labelResolver);
+                nodes.add(new GraphNode(id, label, GraphNode.NodeType.input));
+                inputIds.add(id);
+            }
+        }
+
+        // Step 2b – Tool nodes
+        Set<String> stepIds = stepsSection.keySet();
+        for (String stepId : stepIds) {
+            nodes.add(new GraphNode(stepId, toolLabel(stepId), GraphNode.NodeType.tool));
+        }
+
+        // Step 2c – Output nodes + remember which step feeds each output
+        Map<String, String> outputSources = new LinkedHashMap<>();
+        if (outputsSection != null) {
+            for (Map.Entry<String, Object> entry : outputsSection.entrySet()) {
+                String id    = entry.getKey();
+                String label = formatLabel(entry.getValue(), id, labelResolver);
+                nodes.add(new GraphNode(id, label, GraphNode.NodeType.output));
+
+                if (entry.getValue() instanceof Map<?, ?> def) {
+                    String src = (String) ((Map<String, Object>) def).get("outputSource");
+                    if (src != null && src.contains("/")) {
+                        String sourceStepId = src.substring(0, src.indexOf('/'));
+                        if (stepIds.contains(sourceStepId)) {
+                            outputSources.put(id, sourceStepId);
+                        }
+                    }
+                }
+            }
+        }
+
+        // Step 3 – Edges
+        for (String targetId : stepIds) {
+            Object inField = ((Map<String, Object>) stepsSection.get(targetId)).get("in");
+            if (!(inField instanceof Map<?, ?> rawIn)) continue;
+
+            for (Object sourceRef : ((Map<String, Object>) rawIn).values()) {
+                if (!(sourceRef instanceof String ref)) continue;
+
+                if (ref.contains("/")) {
+                    // Tool → Tool
+                    String sourceId = ref.substring(0, ref.indexOf('/'));
+                    if (stepIds.contains(sourceId) && seen.add(sourceId + "->" + targetId)) {
+                        edges.add(new GraphEdge(sourceId, targetId));
+                    }
+                } else if (inputIds.contains(ref) && seen.add(ref + "->" + targetId)) {
+                    // Input → Tool
+                    edges.add(new GraphEdge(ref, targetId));
+                }
+            }
+        }
+
+        // Tool → Output
+        outputSources.forEach((outputId, sourceId) ->
+            edges.add(new GraphEdge(sourceId, outputId)));
+
+        // Step 4 – EDAM tuples for APE synthesis constraints
+        List<TaxonomyElem> inputs  = extractTuples(inputsSection,  labelResolver);
+        List<TaxonomyElem> outputs = extractTuples(outputsSection, labelResolver);
+
+        return new ParseResponse(nodes, edges, inputs, outputs);
+    }
+
+    private static void validateMetadata(Map<String, Object> cwl) {
+        String cwlClass   = (String) cwl.get("class");
+        String cwlVersion = (String) cwl.get("cwlVersion");
+        if (!"Workflow".equals(cwlClass)) {
+            throw new IllegalArgumentException(
+                    "CWL file must declare 'class: Workflow', found: " + cwlClass);
+        }
+        if (!"v1.2".equals(cwlVersion)) {
+            throw new IllegalArgumentException(
+                    "CWL file must declare 'cwlVersion: v1.2', found: " + cwlVersion);
+        }
+    }
+
+    /** Strips the APE-generated numeric suffix (e.g. MSFragger_01 → MSFragger). */
+    private static String toolLabel(String stepId) {
+        return stepId.replaceAll("_\\d+$", "");
+    }
+
+    /**
+     * Resolves the EDAM format URI from an inputs/outputs entry to a human-readable label.
+     * Falls back to the port ID when no format is declared.
+     */
+    @SuppressWarnings("unchecked")
+    private static String formatLabel(Object entry, String fallbackId, UnaryOperator<String> resolver) {
+        if (entry instanceof Map<?, ?> def) {
+            String uri = (String) ((Map<String, Object>) def).get("format");
+            if (uri != null && !uri.isBlank()) {
+                return resolver.apply(uri);
+            }
+        }
+        return fallbackId;
+    }
+
+    @SuppressWarnings("unchecked")
+    private static List<TaxonomyElem> extractTuples(Map<String, Object> section, UnaryOperator<String> resolver) {
+        List<TaxonomyElem> tuples = new ArrayList<>();
+        if (section == null) return tuples;
+        for (Map.Entry<String, Object> entry : section.entrySet()) {
+            if (!(entry.getValue() instanceof Map<?, ?> def)) continue;
+            String uri = (String) ((Map<String, Object>) def).get("format");
+            if (uri == null) continue;
+            tuples.add(new TaxonomyElem(uri, resolver.apply(uri), null, null));
+        }
+        return tuples;
+    }
+}

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

@@ -0,0 +1,54 @@
+package nl.esciencecenter.restape;
+
+import com.fasterxml.jackson.core.type.TypeReference;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import org.springframework.stereotype.Component;
+
+import java.io.InputStream;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.Map;
+
+/**
+ * Resolves EDAM URIs to human-readable labels via a pre-generated static index.
+ *
+ * The index (edam_labels.json) is bundled as a classpath resource and was generated
+ * once from the EDAM OWL file. Lookups are O(1) after the first call to
+ * {@link #ensureLoaded()}.
+ */
+@Component
+public class EdamLabels {
+
+    private volatile Map<String, String> labels = null;
+
+    /**
+     * Loads the static label index if not already done. Thread-safe; subsequent
+     * calls return immediately.
+     */
+    public synchronized void ensureLoaded() {
+        if (labels != null) return;
+        try (InputStream is = getClass().getClassLoader()
+                .getResourceAsStream("edam_labels.json")) {
+            if (is == null) throw new IllegalStateException("edam_labels.json not found on classpath");
+            Map<String, String> map = new ObjectMapper()
+                    .readValue(is, new TypeReference<HashMap<String, String>>() {});
+            labels = Collections.unmodifiableMap(map);
+        } catch (Exception e) {
+            throw new IllegalStateException("Failed to load edam_labels.json: " + e.getMessage(), e);
+        }
+    }
+
+    public String resolve(String uri) {
+        if (uri == null || uri.isBlank()) return "";
+        Map<String, String> map = labels;
+        if (map == null) return shortForm(uri);
+        return map.getOrDefault(uri, shortForm(uri));
+    }
+
+    static String shortForm(String uri) {
+        if (uri == null || uri.isBlank()) return "";
+        int slash = uri.lastIndexOf('/');
+        int hash  = uri.lastIndexOf('#');
+        return uri.substring(Math.max(slash, hash) + 1);
+    }
+}