Merge pull request #3 from dockstore/main

Update for Dockstore 1.16 and Java 17/21

Author: denis-yuen

.github/workflows/maven.yml

@@ -1,17 +1,19 @@
 name: Java CI
 
-on: [push]
+on: 
+  push:
 
 jobs:
   build:
 
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v1
-    - name: Set up JDK 11
-      uses: actions/setup-java@v1
+    - uses: actions/checkout@v4
+    - name: Set up JDK 21
+      uses: actions/setup-java@v4
       with:
-        java-version: 11.0.x
+        java-version: 21
+        distribution: 'adopt'
     - name: Build with Maven
       run: mvn -B package --file pom.xml

pom.xml

@@ -10,7 +10,7 @@
 
     <properties>
         <github.url>scm:git:git@github.com:dockstore/silly-workflow-language-interface.git</github.url>
-        <dockstore.version>1.9.0-alpha.0</dockstore.version>
+        <dockstore.version>1.16.0</dockstore.version>
         <plugin.id>${project.artifactId}</plugin.id>
         <plugin.class>io.dockstore.language.SillyWorkflowLanguagePlugin</plugin.class>
         <plugin.version>${project.version}</plugin.version>
@@ -67,7 +67,7 @@
                     <artifactId>maven-compiler-plugin</artifactId>
                     <version>3.8.0</version>
                     <configuration>
-                        <release>11</release>
+                        <release>17</release>
                         <showDeprecation>true</showDeprecation>
                     </configuration>
                 </plugin>
@@ -174,7 +174,7 @@
         <dependency>
             <groupId>com.google.guava</groupId>
             <artifactId>guava</artifactId>
-            <version>24.1.1-jre</version>
+            <version>32.0.0-jre</version>
         </dependency>
     </dependencies>
 </project>

src/main/java/io/dockstore/language/SillyWorkflowLanguagePlugin.java

@@ -16,14 +16,11 @@
 package io.dockstore.language;
 
 import java.util.HashMap;
-import java.util.List;
 import java.util.Map;
 import java.util.regex.Pattern;
 
 import io.dockstore.common.DescriptorLanguage;
 import io.dockstore.common.VersionTypeValidation;
-import org.apache.commons.lang3.tuple.ImmutablePair;
-import org.apache.commons.lang3.tuple.Pair;
 import org.pf4j.Extension;
 import org.pf4j.Plugin;
 import org.pf4j.PluginWrapper;
@@ -56,8 +53,9 @@ public String launchInstructions(String trsID) {
             return null;
         }
 
+
         @Override
-        public VersionTypeValidation validateWorkflowSet(String initialPath, String contents, Map<String, Pair<String, GenericFileType>> indexedFiles) {
+        public VersionTypeValidation validateWorkflowSet(String initialPath, String contents, Map<String, FileMetadata> indexedFiles) {
             VersionTypeValidation validation = new VersionTypeValidation(true, new HashMap<>());
             for (String line : contents.split("\\r?\\n")) {
                 if (!line.startsWith("import") && !line.startsWith("author") && !line.startsWith("description")) {
@@ -69,13 +67,14 @@ public VersionTypeValidation validateWorkflowSet(String initialPath, String cont
         }
 
         @Override
-        public VersionTypeValidation validateTestParameterSet(Map<String, Pair<String, GenericFileType>> indexedFiles) {
+        public VersionTypeValidation validateTestParameterSet(Map<String, FileMetadata> indexedFiles) {
             return new VersionTypeValidation(true, new HashMap<>());
         }
 
+
         @Override
-        public DescriptorLanguage getDescriptorLanguage() {
-            return DescriptorLanguage.SWL;
+        public io.dockstore.common.DescriptorLanguage getDescriptorLanguage() {
+            return null;
         }
 
         @Override
@@ -84,20 +83,21 @@ public Pattern initialPathPattern() {
         }
 
         @Override
-        public Map<String, Pair<String, GenericFileType>> indexWorkflowFiles(String initialPath, String contents, FileReader reader) {
-            Map<String, Pair<String, GenericFileType>> results = new HashMap<>();
+        public Map<String, FileMetadata> indexWorkflowFiles(String initialPath, String contents, FileReader reader) {
+            Map<String, FileMetadata> results = new HashMap<>();
             for (String line : contents.split("\\r?\\n")) {
                 if (line.startsWith("import")) {
                     final String[] s = line.split(":");
                     final String importedFile = reader.readFile(s[1].trim());
-                    results.put(s[1].trim(), new ImmutablePair<>(importedFile, GenericFileType.IMPORTED_DESCRIPTOR));
+                    // use real language version
+                    results.put(s[1].trim(), new FileMetadata(importedFile, GenericFileType.IMPORTED_DESCRIPTOR, "1.0"));
                 }
             }
             return results;
         }
 
         @Override
-        public WorkflowMetadata parseWorkflowForMetadata(String initialPath, String contents, Map<String, Pair<String, GenericFileType>> indexedFiles) {
+        public WorkflowMetadata parseWorkflowForMetadata(String initialPath, String contents, Map<String, FileMetadata> indexedFiles) {
             WorkflowMetadata metadata = new WorkflowMetadata();
             for (String line : contents.split("\\r?\\n")) {
                 if (line.startsWith("author")) {

src/test/java/io/dockstore/language/SillyWorkflowLanguagePluginTest.java

@@ -1,5 +1,6 @@
 package io.dockstore.language;
 
+import io.dockstore.language.MinimalLanguageInterface.FileMetadata;
 import java.io.IOException;
 import java.net.URL;
 import java.nio.charset.StandardCharsets;
@@ -18,7 +19,7 @@ public class SillyWorkflowLanguagePluginTest {
     public void testWorkflowParsing() {
         SillyWorkflowLanguagePlugin.SillyWorkflowLanguagePluginImpl plugin = new SillyWorkflowLanguagePlugin.SillyWorkflowLanguagePluginImpl();
         HttpFileReader reader = new HttpFileReader();
-        final Map<String, Pair<String, MinimalLanguageInterface.GenericFileType>> fileMap = plugin
+        final Map<String, FileMetadata> fileMap = plugin
             .indexWorkflowFiles("/Dockstore.swl", reader.readFile("Dockstore.swl"), reader);
         Assert.assertEquals(1, fileMap.size());
         Assert.assertTrue(fileMap.containsKey("foo.swl"));