Add ability to get workflow overviews for packed CWL file

Author: MarkRobbo

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

@@ -110,6 +110,51 @@ public CWLService(RDFService rdfService,
         this.singleFileSizeLimit = singleFileSizeLimit;
     }
 
+    /**
+     * Gets whether a file is packed using schema salad
+     * @param workflowFile The file to be parsed
+     * @return Whether the file is packed
+     */
+    public boolean isPacked(File workflowFile) throws IOException {
+        if (workflowFile.length() > singleFileSizeLimit) {
+            return false;
+        }
+        String fileContent = readFileToString(workflowFile);
+        return fileContent.contains("$graph");
+    }
+
+    /**
+     * Gets a list of workflows from a packed CWL file
+     * @param packedFile The packed CWL file
+     * @return The list of workflow overviews
+     */
+    public List<WorkflowOverview> getWorkflowOverviewsFromPacked(File packedFile) throws IOException {
+        if (packedFile.length() <= singleFileSizeLimit) {
+            List<WorkflowOverview> overviews = new ArrayList<>();
+
+            JsonNode packedJson = yamlStringToJson(readFileToString(packedFile));
+
+            if (packedJson.has(DOC_GRAPH)) {
+                for (JsonNode jsonNode : packedJson.get(DOC_GRAPH)) {
+                    if (extractProcess(jsonNode) == CWLProcess.WORKFLOW) {
+                        WorkflowOverview overview = new WorkflowOverview(jsonNode.get(ID).asText(),
+                                extractLabel(jsonNode), extractDoc(jsonNode));
+                        overviews.add(overview);
+                    }
+                }
+            } else {
+                throw new IOException("The file given was not recognised as a packed CWL file");
+            }
+
+            return overviews;
+
+        } else {
+            throw new IOException("File '" + packedFile.getName() +  "' is over singleFileSizeLimit - " +
+                    FileUtils.byteCountToDisplaySize(packedFile.length()) + "/" +
+                    FileUtils.byteCountToDisplaySize(singleFileSizeLimit));
+        }
+    }
+
     /**
      * Gets the Workflow object from internal parsing
      * @param workflowFile The workflow file to be parsed

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

@@ -39,6 +39,7 @@
 import java.io.ByteArrayInputStream;
 import java.io.File;
 import java.io.IOException;
+import java.util.List;
 import java.util.Map;
 
 import static org.apache.commons.io.FileUtils.readFileToString;
@@ -202,6 +203,23 @@ public void workflowOverviewOverSingleFileSizeLimitThrowsIOException() throws Ex
 
     }
 
+    /**
+     * Get workflow overviews from a packed file
+     * TODO: Get better example with multiple workflows with label/doc
+     */
+    @Test
+    public void workflowOverviewsFromPackedFile() throws Exception {
+        CWLService cwlService = new CWLService(Mockito.mock(RDFService.class),
+                Mockito.mock(CWLTool.class), 5242880);
+        File packedFile = new File("src/test/resources/cwl/make_to_cwl/dna.cwl");
+        assertTrue(cwlService.isPacked(packedFile));
+        List<WorkflowOverview> overviews = cwlService.getWorkflowOverviewsFromPacked(packedFile);
+        assertEquals(1, overviews.size());
+        assertEquals("main", overviews.get(0).getFileName());
+        assertNull(overviews.get(0).getLabel());
+        assertNull(overviews.get(0).getDoc());
+    }
+
     /**
      * Validate a LobSTR workflow
      * See: https://github.com/common-workflow-language/workflows/tree/master/workflows/lobSTR