Merge pull request #108 from sanctuuary/cwl_output

Improve CWL support + refactor

Author: kretep

.github/workflows/mvnbuild.yml

@@ -39,7 +39,7 @@ jobs:
         cd domain-annotations/WombatP_tools
         java -jar ../../target/APE-*-executable.jar ./config.json
         cd ./CWL
-        cwltool --enable-dev --validate candidate_solution_1.cwl
+        cwltool --enable-dev --validate candidate_workflow_1.cwl
 
     # Optional: Uploads the full dependency graph to GitHub to improve the quality of Dependabot alerts this repository can receive
     - name: Update dependency graph

.gitignore

@@ -84,3 +84,6 @@ nb-configuration.xml
 ##############################
 .DS_Store
 /lib/
+solutions.txt
+CWL/*
+Figures/*

pom.xml

@@ -4,7 +4,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>io.github.sanctuuary</groupId>
 	<artifactId>APE</artifactId>
-	<version>2.2.6</version>
+	<version>2.3.0</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>
@@ -164,12 +164,12 @@
 		<dependency>
 			<groupId>org.apache.commons</groupId>
 			<artifactId>commons-lang3</artifactId>
-			<version>3.13.0</version>
+			<version>3.14.0</version>
 		</dependency>
 		<dependency>
 			<groupId>org.apache.logging.log4j</groupId>
 			<artifactId>log4j-core</artifactId>
-			<version>2.20.0</version>
+			<version>2.22.1</version>
 		</dependency>
 		<dependency>
 			<groupId>guru.nidi</groupId>
@@ -180,7 +180,7 @@
 		<dependency>
 			<groupId>org.json</groupId>
 			<artifactId>json</artifactId>
-			<version>20231013</version>
+			<version>20240205</version>
 		</dependency>
 		<!-- https://mvnrepository.com/artifact/org.junit.jupiter/junit-jupiter-api -->
 		<dependency>
@@ -192,12 +192,12 @@
 		<dependency>
 			<groupId>org.slf4j</groupId>
 			<artifactId>slf4j-api</artifactId>
-			<version>2.0.9</version>
+			<version>2.0.12</version>
 		</dependency>
 		<dependency>
 			<groupId>org.slf4j</groupId>
 			<artifactId>slf4j-simple</artifactId>
-			<version>2.0.9</version>
+			<version>2.0.12</version>
 		</dependency>
 		<!-- https://mvnrepository.com/artifact/org.antlr/antlr4-runtime -->
 		<dependency>
@@ -214,7 +214,7 @@
 		<dependency>
 			<groupId>commons-io</groupId>
 			<artifactId>commons-io</artifactId>
-			<version>2.14.0</version>
+			<version>2.15.1</version>
 		</dependency>
 		<!-- https://mvnrepository.com/artifact/com.squareup.okhttp3/okhttp -->
 		<dependency>

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

@@ -137,21 +137,7 @@ private boolean setupDomain() throws APEDimensionsException, IOException, OWLOnt
 
 		// Update allModules and allTypes sets based on the tool annotations
 		succRun &= apeDomainSetup
-				.updateToolAnnotationsFromJson(APEFiles.readFileToJSONObject(config.getToolAnnotationsFile()));
-
-		// Update allModules with CWL annotations, if CWL annotations file is given
-		if (config.getCwlAnnotationsFile().isPresent()) {
-			try {
-				Yaml yaml = new Yaml();
-				File file = config.getCwlAnnotationsFile().get();
-				Map<String, Object> cwlAnnotations = yaml.load(new FileInputStream(file));
-				succRun &= apeDomainSetup
-						.updateCWLAnnotationsFromYaml(cwlAnnotations);
-			} catch (FileNotFoundException e) {
-				log.error("Could not find CWL yaml configuration file!");
-				e.printStackTrace();
-			}
-		}
+				.annotateToolFromJson(APEFiles.readFileToJSONObject(config.getToolAnnotationsFile()));
 
 		succRun &= apeDomainSetup.trimTaxonomy();
 

src/main/java/nl/uu/cs/ape/automaton/Block.java

@@ -27,7 +27,7 @@ public class Block {
      * @param blockNumber The block number.
      */
     public Block(int blockNumber) {
-        typeStates = new ArrayList<State>();
+        typeStates = new ArrayList<>();
         this.blockNumber = blockNumber;
     }
 

src/main/java/nl/uu/cs/ape/automaton/ModuleAutomaton.java

@@ -31,7 +31,7 @@ public class ModuleAutomaton implements Automaton {
      *                        modules).
      */
     public ModuleAutomaton(int automataBound, int inputBranching, int outputBranching) {
-        moduleStates = new ArrayList<State>();
+        moduleStates = new ArrayList<>();
         automataBound = Math.max(automataBound, 1);
 
         for (int i = 1; i <= automataBound; i++) {

src/main/java/nl/uu/cs/ape/automaton/TypeAutomaton.java

@@ -54,8 +54,8 @@ public class TypeAutomaton implements Automaton {
      *                        modules)
      */
     public TypeAutomaton(int automataBound, int inputBranching, int outputBranching) {
-        memoryTypesAutomaton = new ArrayList<Block>();
-        usedTypesAutomaton = new ArrayList<Block>();
+        memoryTypesAutomaton = new ArrayList<>();
+        usedTypesAutomaton = new ArrayList<>();
         nullState = new State(null, null, -1, inputBranching, outputBranching);
 
         automataBound = automataBound < 1 ? 1 : automataBound;
@@ -105,7 +105,7 @@ public List<Block> getMemoryTypesBlocks() {
      * @return Blocks of data types used by tools.
      */
     public List<Block> getAllBlocks() {
-        List<Block> allBlocks = new ArrayList<Block>(usedTypesAutomaton);
+        List<Block> allBlocks = new ArrayList<>(usedTypesAutomaton);
         allBlocks.addAll(memoryTypesAutomaton);
         return allBlocks;
     }
@@ -224,7 +224,7 @@ public Block getMemoryTypesBlock(int i) {
      * @return List of memory States.
      */
     public List<State> getMemoryStatesUntilBlockNo(int maxBlockNo) {
-        List<State> untilStates = new ArrayList<State>();
+        List<State> untilStates = new ArrayList<>();
         for (int i = 0; i <= maxBlockNo && i < this.usedTypesAutomaton.size(); i++) {
             Block currBlock = this.getMemoryTypesBlock(i);
             for (State currState : currBlock.getStates()) {
@@ -244,7 +244,7 @@ public List<State> getMemoryStatesUntilBlockNo(int maxBlockNo) {
      * @return List of Type States.
      */
     public List<State> getAllStatesUntilBlockNo(int maxBlockNo) {
-        List<State> untilStates = new ArrayList<State>();
+        List<State> untilStates = new ArrayList<>();
         for (int i = 0; i <= maxBlockNo && i < this.usedTypesAutomaton.size(); i++) {
             Block currBlock = this.usedTypesAutomaton.get(i);
             for (State currState : currBlock.getStates()) {
@@ -268,7 +268,7 @@ public List<State> getAllStatesUntilBlockNo(int maxBlockNo) {
      * @return List of Memory Type States.
      */
     public List<State> getAllMemoryStatesUntilBlockNo(int maxBlockNo) {
-        List<State> untilStates = new ArrayList<State>();
+        List<State> untilStates = new ArrayList<>();
         for (int i = 0; i <= maxBlockNo && i < this.usedTypesAutomaton.size(); i++) {
             Block currBlock = this.memoryTypesAutomaton.get(i);
             for (State currState : currBlock.getStates()) {
@@ -287,7 +287,7 @@ public List<State> getAllMemoryStatesUntilBlockNo(int maxBlockNo) {
      * @return List of memory States.
      */
     public List<State> getMemoryStatesAfterBlockNo(int minBlockNo) {
-        List<State> afterStates = new ArrayList<State>();
+        List<State> afterStates = new ArrayList<>();
         for (int i = minBlockNo + 1; i < this.memoryTypesAutomaton.size(); i++) {
             Block currBlock = this.getMemoryTypesBlock(i);
             for (State currState : currBlock.getStates()) {
@@ -307,7 +307,7 @@ public List<State> getMemoryStatesAfterBlockNo(int minBlockNo) {
      * @return List of Used States.
      */
     public List<State> getUsedStatesAfterBlockNo(int minBlockNo) {
-        List<State> afterStates = new ArrayList<State>();
+        List<State> afterStates = new ArrayList<>();
         for (int i = minBlockNo + 1; i < this.usedTypesAutomaton.size(); i++) {
             Block currBlock = this.usedTypesAutomaton.get(i);
             for (State currState : currBlock.getStates()) {
@@ -324,7 +324,7 @@ public List<State> getUsedStatesAfterBlockNo(int minBlockNo) {
      */
     @Override
     public List<State> getAllStates() {
-        List<State> allStates = new ArrayList<State>();
+        List<State> allStates = new ArrayList<>();
         for (Block currBlock : getAllBlocks()) {
             for (State currState : currBlock.getStates()) {
                 allStates.add(currState);
@@ -339,7 +339,7 @@ public List<State> getAllStates() {
      * @return List of memory type states.
      */
     public List<State> getAllMemoryTypesStates() {
-        List<State> allMemoryStates = new ArrayList<State>();
+        List<State> allMemoryStates = new ArrayList<>();
         for (Block currBlock : getMemoryTypesBlocks()) {
             for (State currState : currBlock.getStates()) {
                 allMemoryStates.add(currState);
@@ -354,7 +354,7 @@ public List<State> getAllMemoryTypesStates() {
      * @return List of used type states.
      */
     public List<State> getAllUsedTypesStates() {
-        List<State> allUsedStates = new ArrayList<State>();
+        List<State> allUsedStates = new ArrayList<>();
         for (Block currBlock : getUsedTypesBlocks()) {
             for (State currState : currBlock.getStates()) {
                 allUsedStates.add(currState);

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

@@ -60,10 +60,6 @@ public class APECoreConfig {
      * restrictive message passing structure.
      */
     public final APEConfigTag<Boolean> STRICT_TOOL_ANNOTATIONS = new APEConfigTagFactory.TAGS.STRICT_TOOL_ANNOTATIONS();
-    /**
-     * The CWL file with all CWL annotations.
-     */
-    public final APEConfigTag<File> CWL_ANNOTATIONS = new APEConfigTagFactory.TAGS.CWL_ANNOTATIONS();
 
     /**
      * All the Tags specified in this class. Should be in correct order of
@@ -75,8 +71,7 @@ public class APECoreConfig {
             this.TOOL_ONTOLOGY_ROOT,
             this.DIMENSIONS_ONTOLOGY,
             this.TOOL_ANNOTATIONS,
-            this.STRICT_TOOL_ANNOTATIONS,
-            this.CWL_ANNOTATIONS
+            this.STRICT_TOOL_ANNOTATIONS
     };
 
     /**
@@ -89,8 +84,7 @@ public class APECoreConfig {
             new TOOL_ONTOLOGY_ROOT(null),
             new DIMENSIONS_ONTOLOGY(null),
             new TOOL_ANNOTATIONS(),
-            new STRICT_TOOL_ANNOTATIONS(),
-            new CWL_ANNOTATIONS());
+            new STRICT_TOOL_ANNOTATIONS());
 
     /**
      * Initialize the configuration of the project.
@@ -317,19 +311,6 @@ public void setToolAnnotationsFile(File toolAnnotations) {
         TOOL_ANNOTATIONS.setValue(toolAnnotations);
     }
 
-    /**
-     * Gets CWL annotations path.
-     *
-     * @return the value of tag {@link #TOOL_ANNOTATIONS}
-     */
-    public Optional<File> getCwlAnnotationsFile() {
-        if (CWL_ANNOTATIONS.getValue() == null) {
-            return Optional.empty();
-        } else {
-            return Optional.of(CWL_ANNOTATIONS.getValue());
-        }
-    }
-
     /**
      * Get information whether the domain was annotated under the strict rules of
      * the output dependency.

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

@@ -35,6 +35,12 @@ public enum ToolAnnotationTag {
      */
     OUTPUTS("outputs"),
 
+    /**
+     * Represents the implementation details of a tool.
+     */
+    CWL_REFERENCE("cwl_reference"),
+
+
     /**
      * Represents the implementation details of a tool.
      */

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

@@ -656,37 +656,6 @@ public APEConfigDefaultValue<File> getDefault() {
             }
         }
 
-        /**
-         * Configuration field.
-         */
-        public static class CWL_ANNOTATIONS extends TYPES.ExistingFile {
-
-            @Override
-            protected APEFiles.Permission[] getRequiredPermissions() {
-                return new APEFiles.Permission[] { APEFiles.Permission.READ };
-            }
-
-            @Override
-            public String getTagName() {
-                return "cwl_annotations_path";
-            }
-
-            @Override
-            public String getLabel() {
-                return "CWL annotations";
-            }
-
-            @Override
-            public String getDescription() {
-                return "This tag should be a path to an existing .yaml file.";
-            }
-
-            @Override
-            public APEConfigDefaultValue<File> getDefault() {
-                return APEConfigDefaultValue.withDefault(null);
-            }
-        }
-
         /**
          * Configuration field.
          */