require that the initial path point at a Snakefile

Author: svonworl

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

@@ -40,6 +40,7 @@ public class SnakemakeWorkflowPlugin extends Plugin {
 
     public static final Logger LOG = LoggerFactory.getLogger(SnakemakeWorkflowPlugin.class);
     public static final String SNAKEMAKE_WORKFLOW_CATALOG_YML = "/.snakemake-workflow-catalog.yml";
+    public static final String INVALID_INITIAL_PATH_MESSAGE = "the primary descriptor path must be the Snakefile";
 
 
     /**
@@ -63,6 +64,10 @@ public String launchInstructions(String trsID) {
 
         @Override
         public VersionTypeValidation validateWorkflowSet(String initialPath, String contents, Map<String, FileMetadata> indexedFiles) {
+            // if the initial path doesn't point at the Snakefile, the version is invalid
+            if (!initialPathPattern().matcher(initialPath).matches()) {
+                return new VersionTypeValidation(false, Map.of(initialPath, INVALID_INITIAL_PATH_MESSAGE));
+            }
             VersionTypeValidation validation = new VersionTypeValidation(indexedFiles.containsKey(SNAKEMAKE_WORKFLOW_CATALOG_YML), new HashMap<>());
             // TODO hook up some real validation
             return validation;
@@ -86,7 +91,7 @@ public DescriptorLanguage getDescriptorLanguage() {
          */
         @Override
         public Pattern initialPathPattern() {
-            return Pattern.compile("workflow/Snakefile");
+            return Pattern.compile("(/.*)?/[Ss]nakefile");
         }
 
         @Override

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

@@ -7,6 +7,8 @@
 
 import com.google.common.io.Resources;
 import io.dockstore.common.VersionTypeValidation;
+import io.dockstore.language.MinimalLanguageInterface.FileMetadata;
+import io.dockstore.language.MinimalLanguageInterface.GenericFileType;
 import java.io.File;
 import java.io.IOException;
 import java.net.URL;
@@ -70,6 +72,28 @@ public void testWorkflowParsingComplex() {
         assertTrue(plugin.validateWorkflowSet(initialPath, contents,fileMap).isValid());
     }
 
+    private static Map<String, FileMetadata> createDummyFileMap(String initialPath) {
+        return Map.of(
+            initialPath, new FileMetadata("dummy snakefile content", GenericFileType.IMPORTED_DESCRIPTOR, "1.0"),
+            SnakemakeWorkflowPlugin.SNAKEMAKE_WORKFLOW_CATALOG_YML, new FileMetadata("dummy workflow catalog content", GenericFileType.IMPORTED_DESCRIPTOR, "1.0")
+        );
+    }
+
+    @Test
+    public void testWorkflowPrimaryDescriptorMustBeSnakefile() {
+        final SnakemakeWorkflowPlugin.SnakemakeWorkflowPluginImpl plugin =
+            new SnakemakeWorkflowPlugin.SnakemakeWorkflowPluginImpl();
+        for (String validPath: List.of("/Snakefile", "/workflow/Snakefile", "/snakefile", "/workflow/snakefile")) {
+            VersionTypeValidation validation = plugin.validateWorkflowSet(validPath, "", createDummyFileMap(validPath));
+            assertTrue(validation.isValid());
+        }
+        for (String invalidPath: List.of("/workflow.wdl", "/data.txt")) {
+            VersionTypeValidation validation = plugin.validateWorkflowSet(invalidPath, "", createDummyFileMap(invalidPath));
+            assertFalse(validation.isValid());
+            assertEquals(validation.getMessage().get(invalidPath), SnakemakeWorkflowPlugin.INVALID_INITIAL_PATH_MESSAGE);
+        }
+    }
+
     abstract static class URLFileReader implements MinimalLanguageInterface.FileReader {
         // URL to repo
         protected final String repo;