Load default CWL creator configuration dynamically from resources

src/main/java/nl/uu/cs/ape/solver/solutionStructure/cwl/DefaultCWLCreator.java

@@ -4,12 +4,17 @@
 import nl.uu.cs.ape.solver.solutionStructure.ModuleNode;
 import nl.uu.cs.ape.solver.solutionStructure.SolutionWorkflow;
 import nl.uu.cs.ape.solver.solutionStructure.TypeNode;
+import nl.uu.cs.ape.utils.APEResources;
+import nl.uu.cs.ape.utils.APEUtils;
 
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 import java.util.stream.IntStream;
 
+import org.json.JSONArray;
+import org.json.JSONObject;
+
 import lombok.extern.slf4j.Slf4j;
 
 /**
@@ -96,16 +101,17 @@ private String getInputsInCWL(boolean formatForCwlInputsYmlFile) {
                     .append(typeNode.getFormat())
                     .append("\n");
             if (formatForCwlInputsYmlFile) {
-                /* TODO: FIX THIS. IT CANNOT BE HARDCODED. */
+                // Load resources file
+                JSONObject availableDataJson = APEResources.getJSONResource("default_cwl_creator_data.json");
+
                 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");
+                for (JSONObject entry : APEUtils.getJSONListFromJson(availableDataJson, "inputs")) {
+                    String format = entry.getString("format");
+                    String data = entry.getString("data");
+
+                    availableData.put(format, data);
+                    log.trace("Read default CWL creator config format and data {} : {}", format, data);
+                }
                 String inputPath = availableData.containsKey(currTypeFormat) ? availableData.get(currTypeFormat)
                         : "set_full_path_to_the_file_with_extension_here";
                 inputsInCWL

src/test/java/nl/uu/cs/ape/sat/test/utils/TestResources.java → src/main/java/nl/uu/cs/ape/utils/APEResources.java

@@ -1,12 +1,10 @@
-package nl.uu.cs.ape.sat.test.utils;
+package nl.uu.cs.ape.utils;
 
 import org.apache.commons.io.IOUtils;
 import org.json.JSONObject;
 
 import lombok.extern.slf4j.Slf4j;
 
-import static nl.uu.cs.ape.sat.test.utils.Evaluation.fail;
-
 import java.io.File;
 import java.io.IOException;
 import java.net.URISyntaxException;
@@ -18,26 +16,26 @@
 import java.util.Objects;
 
 /**
- * The {@code TestUtil} class is used to read contents of resource files more
+ * The {@code APEResources} class is used to read contents of resource files more
  * easily, as functional tests will make use of json files in the test resource
  * folders.
  *
  * @author Maurin Voshol
  */
 @Slf4j
-public class TestResources {
+public class APEResources {
 
     /**
      * @param resource: relative path of a resource in the test resource folder
      * @return the absolute path of a resource that can be used by the library.
      */
     public static String getAbsoluteResourcePath(String resource) {
         try {
-            return Paths.get(Objects.requireNonNull(TestResources.class.getClassLoader().getResource(resource)).toURI())
+            return Paths.get(Objects.requireNonNull(APEResources.class.getClassLoader().getResource(resource)).toURI())
                     .toAbsolutePath().toString();
         } catch (URISyntaxException | NullPointerException e) {
             e.printStackTrace();
-            fail("Could not retrieve resource '%s'", resource);
+            log.error("Could not retrieve resource '{}'", resource);
             return null;
         }
     }
@@ -58,11 +56,11 @@ public static String getAbsoluteRoot() {
     public static String getTextResource(String resource, Charset charset) {
         try {
             return IOUtils.toString(
-                    Objects.requireNonNull(TestResources.class.getClassLoader().getResourceAsStream(resource)),
+                    Objects.requireNonNull(APEResources.class.getClassLoader().getResourceAsStream(resource)),
                     charset);
         } catch (IOException e) {
             e.printStackTrace();
-            fail("Could not retrieve %s resource '%s' ", charset, resource);
+            log.error("Could not retrieve {} resource '{}' ", charset, resource);
             return null;
         }
     }
@@ -84,7 +82,7 @@ public static JSONObject getJSONResource(String resource) {
     }
 
     public static String writeFile(String relativePath, String content) {
-        Path absolutePath = Paths.get(TestResources.getAbsoluteRoot()).resolve(relativePath).toAbsolutePath();
+        Path absolutePath = Paths.get(APEResources.getAbsoluteRoot()).resolve(relativePath).toAbsolutePath();
         Path absoluteParentPath = absolutePath.getParent();
         try {
             File folder = absoluteParentPath.toFile();
@@ -106,7 +104,7 @@ public static String writeFile(String relativePath, String content) {
     }
 
     public static JSONObject getConfigResource(String base_config_path, String ontology_path, String tools_path,
-            String constraints_path, String solution_dir_path) {
+                                               String constraints_path, String solution_dir_path) {
         return getJSONResource(base_config_path)
                 // add paths to the other files to the configuration
                 .put("ontology_path", getAbsoluteResourcePath(ontology_path))

src/main/resources/default_cwl_creator_data.json

@@ -0,0 +1,25 @@
+
+{
+  "inputs": [
+    {
+      "_comment" : "MZML format and data",
+      "format": "http://edamontology.org/format_3244",
+      "data" : "https://raw.githubusercontent.com/Workflomics/DemoKit/main/data/inputs/2021-10-8_Ecoli.mzML"
+    },
+    {
+      "_comment" : "FASTA format and data",
+      "format": "http://edamontology.org/format_1929",
+      "data" : "https://raw.githubusercontent.com/Workflomics/DemoKit/main/data/inputs/up00000062.fasta"
+    },
+    {
+      "_comment" : "plain OBO format and data (plain means any OBO variant)",
+      "format": "http://edamontology.org/format_2196_plain",
+      "data" : "https://raw.githubusercontent.com/Workflomics/DemoKit/main/data/inputs/go.obo"
+    },
+    {
+      "_comment" : "plain TSV format and data (plain means any TSV variant)",
+      "format": "http://edamontology.org/format_3475_plain",
+      "data" : "https://raw.githubusercontent.com/Workflomics/DemoKit/main/data/inputs/goa_human.gaf"
+    }
+  ]
+}

src/test/java/nl/uu/cs/ape/sat/test/configuration/APEConfigTagTest.java

@@ -6,7 +6,7 @@
 import nl.uu.cs.ape.configuration.tags.APEConfigTag;
 import nl.uu.cs.ape.configuration.tags.validation.ValidationResults;
 import nl.uu.cs.ape.domain.APEDomainSetup;
-import nl.uu.cs.ape.sat.test.utils.TestResources;
+import nl.uu.cs.ape.utils.APEResources;
 import nl.uu.cs.ape.utils.APEUtils;
 
 import org.json.JSONObject;
@@ -19,6 +19,7 @@
 import java.util.List;
 import java.util.stream.Collectors;
 
+import static nl.uu.cs.ape.sat.test.utils.Evaluation.fail;
 import static nl.uu.cs.ape.sat.test.utils.Evaluation.success;
 import static org.junit.jupiter.api.Assertions.assertFalse;
 import static org.junit.jupiter.api.Assertions.assertTrue;
@@ -50,12 +51,17 @@ public void infoOutputTest() {
 
     @Test
     public void coreValidationTest() {
-        final JSONObject correct_config = TestResources.getJSONResource("cli/gmt/base_config.json")
-                // add paths to the other files to the configuration
-                .put("ontology_path", TestResources.getAbsoluteResourcePath("cli/gmt/GMT_UseCase_taxonomy.owl"))
-                .put("tool_annotations_path", TestResources.getAbsoluteResourcePath("cli/gmt/tool_annotations.json"))
-                .put("constraints_path", TestResources.getAbsoluteResourcePath("cli/gmt/constraints_e0.json"))
-                .put("solutions_dir_path", TestResources.getAbsoluteResourcePath("cli/gmt"));
+        final JSONObject correct_config = APEResources.getJSONResource("cli/gmt/base_config.json");
+        if (correct_config.isEmpty())
+        {
+            fail("Could not retrieve resource '%s' ", "cli/gmt/base_config.json");
+        } else {
+            // add paths to the other files to the configuration
+            correct_config.put("ontology_path", APEResources.getAbsoluteResourcePath("cli/gmt/GMT_UseCase_taxonomy.owl"))
+                    .put("tool_annotations_path", APEResources.getAbsoluteResourcePath("cli/gmt/tool_annotations.json"))
+                    .put("constraints_path", APEResources.getAbsoluteResourcePath("cli/gmt/constraints_e0.json"))
+                    .put("solutions_dir_path", APEResources.getAbsoluteResourcePath("cli/gmt"));
+        }
 
         ValidationResults results = APECoreConfig.validate(correct_config);
 
@@ -107,12 +113,17 @@ public void coreValidationTest() {
 
     @Test
     public void runValidationTest() throws IOException, OWLOntologyCreationException {
-        final JSONObject correct_config = TestResources.getJSONResource("cli/gmt/base_config.json")
-                // add paths to the other files to the configuration
-                .put("ontology_path", TestResources.getAbsoluteResourcePath("cli/gmt/GMT_UseCase_taxonomy.owl"))
-                .put("tool_annotations_path", TestResources.getAbsoluteResourcePath("cli/gmt/tool_annotations.json"))
-                .put("constraints_path", TestResources.getAbsoluteResourcePath("cli/gmt/constraints_e0.json"))
-                .put("solutions_dir_path", TestResources.getAbsoluteResourcePath("cli/gmt"));
+        final JSONObject correct_config = APEResources.getJSONResource("cli/gmt/base_config.json");
+        if (correct_config.isEmpty())
+        {
+            fail("Could not retrieve resource '%s' ", "cli/gmt/base_config.json");
+        } else {
+            // add paths to the other files to the configuration
+            correct_config.put("ontology_path", APEResources.getAbsoluteResourcePath("cli/gmt/GMT_UseCase_taxonomy.owl"))
+                    .put("tool_annotations_path", APEResources.getAbsoluteResourcePath("cli/gmt/tool_annotations.json"))
+                    .put("constraints_path", APEResources.getAbsoluteResourcePath("cli/gmt/constraints_e0.json"))
+                    .put("solutions_dir_path", APEResources.getAbsoluteResourcePath("cli/gmt"));
+        }
 
         APEDomainSetup domainSetup = new APE(correct_config).getDomainSetup();
 

src/test/java/nl/uu/cs/ape/sat/test/configuration/APEConfigTest.java

@@ -8,7 +8,7 @@
 import nl.uu.cs.ape.models.Range;
 import nl.uu.cs.ape.models.enums.ConfigEnum;
 import nl.uu.cs.ape.sat.test.utils.Evaluation;
-import nl.uu.cs.ape.sat.test.utils.TestResources;
+import nl.uu.cs.ape.utils.APEResources;
 
 import org.json.JSONException;
 import org.json.JSONObject;
@@ -33,13 +33,13 @@ class APEConfigTest {
      * A correct template construct that is converted to a String at initialisation.
      */
     private static final String jsonTemplate = new JSONObject()
-            .put("ontology_path", TestResources.getAbsoluteResourcePath("template/ontology.owl"))
+            .put("ontology_path", APEResources.getAbsoluteResourcePath("template/ontology.owl"))
             .put("ontologyPrefixIRI", "http://www.co-ode.org/ontologies/ont.owl#")
             .put("toolsTaxonomyRoot", "ToolsTaxonomy")
             .put("dataDimensionsTaxonomyRoots", new String[] { "TypesTaxonomy" })
-            .put("tool_annotations_path", TestResources.getAbsoluteResourcePath("template/tool_annotations.json"))
-            .put("constraints_path", TestResources.getAbsoluteResourcePath("template/constraints.json"))
-            .put("solutions_dir_path", TestResources.getAbsoluteResourcePath("template"))
+            .put("tool_annotations_path", APEResources.getAbsoluteResourcePath("template/tool_annotations.json"))
+            .put("constraints_path", APEResources.getAbsoluteResourcePath("template/constraints.json"))
+            .put("solutions_dir_path", APEResources.getAbsoluteResourcePath("template"))
             .put("tool_seq_repeat", false)
             .put("solution_length", new JSONObject().put(Range.MIN_TAG, 1).put(Range.MAX_TAG, 5))
             .put("solutions", 5)
@@ -169,7 +169,7 @@ public void testIncorrectFilePaths() {
         final String[] pathTags = new String[] { "ontology_path", "tool_annotations_path" };
         final String[] wrongPaths = new String[] { null, "", "./does/not/exist.json", "does/not/exist.json",
                 "./does/not/exist/", "does/not/exist/",
-                TestResources.getAbsoluteResourcePath("") + "\\doesnotexist.json" };
+                APEResources.getAbsoluteResourcePath("") + "\\doesnotexist.json" };
 
         for (String tag : pathTags) {
             for (String path : wrongPaths) {
@@ -197,7 +197,7 @@ public void testIncorrectDirectoryPaths() {
 
         final String[] pathTags = new String[] { "solutions_dir_path" };
         final String[] wrongPaths = new String[] { "file.json",
-                TestResources.getAbsoluteResourcePath("") + "\\file.json" };
+                APEResources.getAbsoluteResourcePath("") + "\\file.json" };
 
         for (String tag : pathTags) {
             for (String path : wrongPaths) {

src/test/java/nl/uu/cs/ape/sat/test/utils/GitHubRepo.java

@@ -16,6 +16,7 @@
 import java.util.HashMap;
 import java.util.Objects;
 
+import nl.uu.cs.ape.utils.APEResources;
 import static nl.uu.cs.ape.sat.test.utils.Evaluation.fail;
 import static nl.uu.cs.ape.sat.test.utils.Evaluation.success;
 import static org.junit.jupiter.api.Assertions.assertFalse;
@@ -33,7 +34,7 @@ public class GitHubRepo {
     private HashMap<Integer, TempFile> files;
 
     public GitHubRepo(String repository, String commitOrBranch) {
-        this.absoluteLocalRoot = Paths.get(TestResources.getAbsoluteRoot(), "temp").toString();
+        this.absoluteLocalRoot = Paths.get(APEResources.getAbsoluteRoot(), "temp").toString();
         this.repository = repository;
         this.commit = commitOrBranch;
         this.files = new HashMap<>();

src/test/java/nl/uu/cs/ape/test/sat/ape/CLITest.java

@@ -2,7 +2,7 @@
 
 import nl.uu.cs.ape.Main;
 import nl.uu.cs.ape.configuration.APERunConfig;
-import nl.uu.cs.ape.sat.test.utils.TestResources;
+import nl.uu.cs.ape.utils.APEResources;
 
 import org.apache.commons.io.FileUtils;
 import org.json.JSONObject;
@@ -50,7 +50,7 @@ void run(String base_config_path, String ontology_path, String tools_path, Strin
 
         // absolute solution_dir_path
         final Path solution_path = Paths
-                .get(Objects.requireNonNull(TestResources.getAbsoluteResourcePath(solution_dir_path)));
+                .get(Objects.requireNonNull(APEResources.getAbsoluteResourcePath(solution_dir_path)));
 
         // absolute Figures and Executables directories
         final Path figures_path = solution_path.resolve(APERunConfig.FIGURES_FOLDER_NAME);
@@ -68,16 +68,16 @@ void run(String base_config_path, String ontology_path, String tools_path, Strin
         }
 
         // get the base configuration file
-        final JSONObject config_content = TestResources.getConfigResource(
+        final JSONObject config_content = APEResources.getConfigResource(
                 base_config_path,
                 ontology_path,
                 tools_path,
                 constraints_path,
                 solution_dir_path);
 
         // create a new configuration file
-        final String config_path = TestResources
-                .writeFile(Paths.get(Objects.requireNonNull(TestResources.getAbsoluteResourcePath(solution_dir_path)))
+        final String config_path = APEResources
+                .writeFile(Paths.get(Objects.requireNonNull(APEResources.getAbsoluteResourcePath(solution_dir_path)))
                         .resolve("config.json").toAbsolutePath().toString(), config_content.toString(2));
 
         Main.main(new String[] {
@@ -87,14 +87,14 @@ void run(String base_config_path, String ontology_path, String tools_path, Strin
         // check whether images are produced correctly
         assertTrue(Files.exists(figures_path));
         final int figures_amount_generated = Objects.requireNonNull(
-                Paths.get(Objects.requireNonNull(TestResources.getAbsoluteResourcePath(solution_dir_path)))
+                Paths.get(Objects.requireNonNull(APEResources.getAbsoluteResourcePath(solution_dir_path)))
                         .resolve(APERunConfig.FIGURES_FOLDER_NAME).toFile().list()).length;
         assertEquals(config_content.getInt("number_of_generated_graphs"), figures_amount_generated);
 
         // check whether scripts are produced correctly
         assertTrue(Files.exists(executables_path));
         final int executables_amount_generated = Objects.requireNonNull(
-                Paths.get(Objects.requireNonNull(TestResources.getAbsoluteResourcePath(solution_dir_path)))
+                Paths.get(Objects.requireNonNull(APEResources.getAbsoluteResourcePath(solution_dir_path)))
                         .resolve(APERunConfig.EXECUTABLES_FOLDER_NAME).toFile().list()).length;
         assertEquals(config_content.getInt("number_of_execution_scripts"), executables_amount_generated);
     }

src/test/java/nl/uu/cs/ape/test/sat/ape/UseCaseTest.java

@@ -3,7 +3,7 @@
 import nl.uu.cs.ape.APE;
 import nl.uu.cs.ape.configuration.APEConfigException;
 import nl.uu.cs.ape.sat.test.utils.GitHubRepo;
-import nl.uu.cs.ape.sat.test.utils.TestResources;
+import nl.uu.cs.ape.utils.APEResources;
 import nl.uu.cs.ape.utils.APEUtils;
 import nl.uu.cs.ape.solver.solutionStructure.SolutionsList;
 
@@ -173,7 +173,11 @@ private static class UseCase {
 
         public UseCase(String useCasePath, GitHubRepo repo) {
 
-            JSONObject useCase = TestResources.getJSONResource(useCasePath);
+            JSONObject useCase = APEResources.getJSONResource(useCasePath);
+            if (useCase.isEmpty())
+            {
+                fail("Could not retrieve resource '%s' ", useCasePath);
+            }
 
             // read name
             this.name = useCase.getString("name");