allow some CWL extensions that we know about

Author: mr-c

src/main/java/org/commonwl/view/cwl/CWLTool.java

@@ -107,6 +107,8 @@ private String runCwltoolOnWorkflow(String argument, String workflowUrl)
         "--disable-color",
         "--non-strict",
         "--quiet",
+        "--enable-dev",
+        "--enable-ext",
         "--skip-schemas",
         argument,
         workflowUrl

src/main/java/org/commonwl/view/git/GitConfig.java

@@ -4,7 +4,6 @@
 import com.fasterxml.jackson.databind.node.ObjectNode;
 import java.util.HashMap;
 import java.util.Map;
-
 import org.apache.commons.lang3.StringUtils;
 import org.commonwl.view.util.LicenseUtils;
 import org.springframework.context.annotation.Bean;
@@ -24,7 +23,7 @@ public Map<String, String> licenseVocab() {
         restTemplate.getForObject(LicenseUtils.SPDX_LICENSES_JSON_URL, ObjectNode.class);
     if (jsonLicenses == null) {
       throw new GitLicenseException(
-              "Failed to load SPDX licenses from " + LicenseUtils.SPDX_LICENSES_JSON_URL);
+          "Failed to load SPDX licenses from " + LicenseUtils.SPDX_LICENSES_JSON_URL);
     }
     Map<String, String> licenseMap = new HashMap<>();
     for (JsonNode license : jsonLicenses.withArray("licenses")) {

src/main/java/org/commonwl/view/util/FileUtils.java

@@ -4,7 +4,6 @@
 import java.io.IOException;
 import java.nio.file.Path;
 import java.util.regex.Pattern;
-
 import org.apache.taverna.robundle.Bundle;
 import org.apache.taverna.robundle.fs.BundleFileSystem;
 import org.eclipse.jgit.api.Git;
@@ -75,8 +74,9 @@ public static void deleteTemporaryGitRepository(Git repo) throws IOException {
         && repo.getRepository() != null
         && repo.getRepository().getDirectory() != null
         && repo.getRepository().getDirectory().getParentFile() != null) {
-      if (UUID_REGEX_PATTERN.matcher(
-          repo.getRepository().getDirectory().getParentFile().getName()).matches()) {
+      if (UUID_REGEX_PATTERN
+          .matcher(repo.getRepository().getDirectory().getParentFile().getName())
+          .matches()) {
         deleteGitRepository(repo);
       }
     }

src/test/java/org/commonwl/view/cwl/CWLServiceTest.java

@@ -19,6 +19,20 @@
 
 package org.commonwl.view.cwl;
 
+import static org.apache.commons.io.FileUtils.readFileToString;
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertNotNull;
+import static org.junit.jupiter.api.Assertions.assertNull;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+import static org.mockito.ArgumentMatchers.any;
+import static org.mockito.Mockito.when;
+
+import java.io.ByteArrayInputStream;
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.Paths;
+import java.util.List;
+import java.util.Map;
 import org.apache.jena.query.Dataset;
 import org.apache.jena.query.DatasetFactory;
 import org.apache.jena.query.Query;
@@ -43,21 +57,6 @@
 import org.mockito.stubbing.Answer;
 import org.springframework.test.context.ContextConfiguration;
 
-import java.io.ByteArrayInputStream;
-import java.io.File;
-import java.io.IOException;
-import java.nio.file.Paths;
-import java.util.List;
-import java.util.Map;
-
-import static org.apache.commons.io.FileUtils.readFileToString;
-import static org.junit.jupiter.api.Assertions.assertEquals;
-import static org.junit.jupiter.api.Assertions.assertNotNull;
-import static org.junit.jupiter.api.Assertions.assertNull;
-import static org.junit.jupiter.api.Assertions.assertTrue;
-import static org.mockito.ArgumentMatchers.any;
-import static org.mockito.Mockito.when;
-
 @ContextConfiguration(classes = {GitConfig.class})
 public class CWLServiceTest {