CWL fixes and dependencies update

.github/workflows/mvnbuild.yml

@@ -36,9 +36,9 @@ jobs:
     - name: Test CWL generation
       run: |
         git clone https://github.com/Workflomics/domain-annotations
-        cd domain-annotations
-        java -jar ../target/APE-*-executable.jar ./WombatP_tools/config_local.json
-        cd ./WombatP_tools/CWL
+        cd domain-annotations/WombatP_tools
+        java -jar ../../target/APE-*-executable.jar ./config.json
+        cd ./CWL
         cwltool --enable-dev --validate workflowSolution_0.cwl
 
     # Optional: Uploads the full dependency graph to GitHub to improve the quality of Dependabot alerts this repository can receive

pom.xml

@@ -4,7 +4,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>io.github.sanctuuary</groupId>
 	<artifactId>APE</artifactId>
-	<version>2.1.7</version>
+	<version>2.1.8</version>
 	<packaging>jar</packaging>
 	<name>io.github.sanctuuary:APE</name>
 	<description>APE is a command line tool and an API for the automated exploration of possible computational pipelines (workflows) from large collections of computational tools.</description>
@@ -162,7 +162,7 @@
 		<dependency>
 			<groupId>org.json</groupId>
 			<artifactId>json</artifactId>
-			<version>20230618</version>
+			<version>20231013</version>
 		</dependency>
 		<!-- https://mvnrepository.com/artifact/org.junit.jupiter/junit-jupiter-api -->
 		<dependency>
@@ -174,28 +174,29 @@
 		<dependency>
 			<groupId>org.slf4j</groupId>
 			<artifactId>slf4j-api</artifactId>
-			<version>2.0.7</version>
+			<version>2.0.9</version>
 		</dependency>
 		<dependency>
 			<groupId>org.slf4j</groupId>
 			<artifactId>slf4j-simple</artifactId>
-			<version>2.0.7</version>
+			<version>2.0.9</version>
 		</dependency>
 		<!-- https://mvnrepository.com/artifact/org.antlr/antlr4-runtime -->
 		<dependency>
 		    <groupId>org.antlr</groupId>
 		    <artifactId>antlr4-runtime</artifactId>
-		    <version>4.13.0</version>
+		    <version>4.13.1</version>
 		</dependency>
 		<dependency>
 			<groupId>org.yaml</groupId>
 			<artifactId>snakeyaml</artifactId>
-			<version>2.0</version>
+			<version>2.2</version>
 		</dependency>
+		<!-- https://mvnrepository.com/artifact/commons-io/commons-io -->
 		<dependency>
 			<groupId>commons-io</groupId>
 			<artifactId>commons-io</artifactId>
-			<version>2.11.0</version>
+			<version>2.14.0</version>
 		</dependency>
 		<!-- https://mvnrepository.com/artifact/com.squareup.okhttp3/okhttp -->
 		<dependency>

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

@@ -8,7 +8,6 @@
 import nl.uu.cs.ape.core.SynthesisEngine;
 import nl.uu.cs.ape.core.implSAT.SATSynthesisEngine;
 import nl.uu.cs.ape.core.solutionStructure.DefaultCWLCreator;
-import nl.uu.cs.ape.core.solutionStructure.ExecutableCWLCreator;
 import nl.uu.cs.ape.core.solutionStructure.SolutionWorkflow;
 import nl.uu.cs.ape.core.solutionStructure.SolutionsList;
 import nl.uu.cs.ape.io.APEFiles;

src/main/java/nl/uu/cs/ape/core/solutionStructure/AbstractCWLCreator.java

@@ -67,7 +67,7 @@ private void generateWorkflowInputs() {
                     // Format
                     .append(ind(2))
                     .append("format: ")
-                    .append(typeNode.getNodeID())
+                    .append(typeNode.getFormat())
                     .append("\n");
         }
     }
@@ -92,7 +92,7 @@ private void generateWorkflowOutputs() {
                     // Format
                     .append(ind(2))
                     .append("format: ")
-                    .append(typeNode.getNodeID())
+                    .append(typeNode.getFormat())
                     .append("\n")
                     // outputSource
                     .append(ind(2))
@@ -323,7 +323,7 @@ private void generateTypeNodes(ModuleNode moduleNode, List<TypeNode> typeNodeLis
                     // Format
                     .append(ind(baseInd + 1))
                     .append("format: ")
-                    .append(typeNode.getNodeID())
+                    .append(typeNode.getFormat())
                     .append("\n");
         }
     }

src/main/java/nl/uu/cs/ape/core/solutionStructure/DefaultCWLCreator.java

@@ -1,9 +1,11 @@
 package nl.uu.cs.ape.core.solutionStructure;
 
+import nl.uu.cs.ape.models.Type;
 import nl.uu.cs.ape.models.logic.constructs.TaxonomyPredicate;
 
 import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
 import java.util.stream.IntStream;
 
 import lombok.extern.slf4j.Slf4j;
@@ -62,6 +64,19 @@ private void generateWorkflowInputs() {
      * @return The CWL representation of the workflow outputs.
      */
     private String getInputsInCWL(boolean formatForCwlInputsYmlFile) {
+
+        Map<String, String> availableData = new HashMap<>();
+        availableData.put("http://edamontology.org/format_3244",// mzML
+                "https://raw.githubusercontent.com/Workflomics/DemoKit/main/data/inputs/2021-10-8_Ecoli.mzML");
+        availableData.put("http://edamontology.org/format_1929",// FASTA
+                "https://raw.githubusercontent.com/Workflomics/DemoKit/main/data/inputs/up00000062.fasta");
+        availableData.put("http://edamontology.org/format_2196_plain",// OBO format_p
+                "https://raw.githubusercontent.com/Workflomics/DemoKit/main/data/inputs/go.obo");
+        availableData.put("http://edamontology.org/format_3475_plain",// TSV_p
+                "https://raw.githubusercontent.com/Workflomics/DemoKit/main/data/inputs/goa_human_smaller.gaf");
+
+
+
         StringBuilder inputsInCWL = new StringBuilder();
 
         int indentLevel = 1;
@@ -72,6 +87,13 @@ private String getInputsInCWL(boolean formatForCwlInputsYmlFile) {
         }
         int i = 1;
         for (TypeNode typeNode : solution.getWorkflowInputTypeStates()) {
+            String currTypeFormat = "";
+            for (Type type : typeNode.getTypes()) {
+                if (type.getRootNodeID().equals("http://edamontology.org/format_1915")) {
+                    currTypeFormat = type.getPredicateID();
+                }
+            }
+            String inputPath = availableData.containsKey(currTypeFormat) ? availableData.get(currTypeFormat) : "set_full_path_to_the_file_with_extension_here";
             String inputName = String.format("input%o", i++);
             addNewParameterToMap(typeNode, inputName);
             inputsInCWL
@@ -92,7 +114,7 @@ private String getInputsInCWL(boolean formatForCwlInputsYmlFile) {
                 inputsInCWL
                         .append(ind(indentLevel + 1))
                         .append("path: ")
-                        .append("set_full_path_to_the_file_with_extension_here")
+                        .append(inputPath)
                         .append("\n");
             }
         }
@@ -234,7 +256,7 @@ private void generateDefaultStepRun(ModuleNode moduleNode) {
         cwlRepresentation
                 // Main key
                 .append(ind(baseInd))
-                .append("run: https://raw.githubusercontent.com/Workflomics/containers/main/cwl/tools/" + moduleName
+                .append("run: https://raw.githubusercontent.com/Workflomics/containers/docker/cwl/tools/" + moduleName
                         + "/" + moduleName + ".cwl")
                 .append("\n");
         /*

src/main/java/nl/uu/cs/ape/core/solutionStructure/TypeNode.java

@@ -251,14 +251,14 @@ public String getNodeID() {
     }
 
     /**
-     * Get the unique ID of the current workflow node in .dot representation.
+     * Get the format of the current workflow node and a label for the CWL file.
      */
     public String getFormat() {
         StringBuilder printString = new StringBuilder();
 
         for (Type type : this.usedTypes) {
             if (type.getRootNodeID().equals("http://edamontology.org/format_1915")) {
-                printString.append("\"").append(type.getPredicateID()).append("\" # ").append(type.getPredicateLabel());
+                printString.append("\"").append(type.getPredicateLongLabel()).append("\" # ").append(type.getPredicateLabel());
             }
         }
         if (printString.length() == 0) {

src/main/java/nl/uu/cs/ape/utils/BioToolsAPI.java

@@ -9,6 +9,8 @@
 import org.json.JSONException;
 import org.json.JSONObject;
 
+import lombok.AccessLevel;
+import lombok.NoArgsConstructor;
 import lombok.extern.slf4j.Slf4j;
 import nl.uu.cs.ape.configuration.ToolAnnotationTag;
 import nl.uu.cs.ape.io.APEFiles;
@@ -21,6 +23,7 @@
  * from bio.tools API.
  */
 @Slf4j
+@NoArgsConstructor(access = AccessLevel.PRIVATE)
 public class BioToolsAPI {
 
 	/** Http-Client */