support multi-source-inputs

CHANGELOG.md

@@ -4,6 +4,7 @@
 ## v1.4.5 [unreleased]
 
 Switch to snakeyaml-engine (YAML 1.2) from snakeyaml (YAML 1.1)
+Support workflows using `MultipleInputFeatureRequirement`
 
 ## v1.4.4 [2022-06-08]
 

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

@@ -758,7 +758,14 @@ private Map<String, CWLElement> getStepInputsOutputs(Object inOut) {
 				if (Map.class.isAssignableFrom(inOutNode.getClass())) {
 					Map<String, Object> properties = (Map<String, Object>) inOutNode;
 					if (properties.containsKey(SOURCE)) {
-						inputOutput.addSourceID(stepIDFromSource((String) properties.get(SOURCE)));
+						Object source = properties.get(SOURCE);
+						if (List.class.isAssignableFrom(source.getClass())) {
+							for (String sourceEntry : (List<String>) source) {
+								inputOutput.addSourceID(stepIDFromSource(sourceEntry));
+							}
+						} else {
+							inputOutput.addSourceID(stepIDFromSource((String) source));
+						}
 					} else {
 						inputOutput.setDefaultVal(extractDefault(properties));
 					}

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

@@ -19,6 +19,23 @@
 
 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.io.InputStream;
+import java.net.URI;
+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;
@@ -39,25 +56,6 @@
 import org.mockito.invocation.InvocationOnMock;
 import org.mockito.stubbing.Answer;
 
-import java.io.ByteArrayInputStream;
-import java.io.File;
-import java.io.IOException;
-import java.io.InputStream;
-import java.net.URI;
-import java.net.URL;
-import java.nio.file.Path;
-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;
-
 public class CWLServiceTest {
 
     /**
@@ -156,6 +154,18 @@ public void parseWorkflowInlineOptionalTypesNative() throws Exception {
 		assertEquals(wkflow.getInputs().get("rfam_models").getType(), "{type=array, items=[string, File]}");
 
 	}
+
+	/**
+	 * Test native loading parsing of MultipleInputFeatureRequirement using workflows
+	 */
+	@Test
+	public void parseWorkflowMultiInboundLins() throws Exception {
+		CWLService cwlService = new CWLService(rdfService, new CWLTool(), 5242880);
+        Workflow wkflow = cwlService.parseWorkflowNative(Paths.get("src/test/resources/cwl/complex-workflow/complex-workflow-1.cwl"),
+				null);
+		assertEquals(wkflow.getSteps().get("re_tar_step").getSources().get("file_list").getSourceIDs().get(0), "touch_step");
+		assertEquals(wkflow.getSteps().get("re_tar_step").getSources().get("file_list").getSourceIDs().get(1), "files");
+	}
 
 	/**
 	 * Test native loading parsing of nested array types

src/test/resources/cwl/complex-workflow/complex-workflow-1.cwl

@@ -0,0 +1,123 @@
+# Source: https://github.com/heliumdatacommons/TOPMed_RNAseq_CWL/tree/578066ec5d6847892528f973b22531d4c8487280/workflows/complex-workflow
+
+# BSD 3-Clause License
+# 
+# Copyright (c) 2018, RTI International
+# All rights reserved.
+# 
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+# 
+# * Redistributions of source code must retain the above copyright notice, this
+#   list of conditions and the following disclaimer.
+# 
+# * Redistributions in binary form must reproduce the above copyright notice,
+#   this list of conditions and the following disclaimer in the documentation
+#   and/or other materials provided with the distribution.
+# 
+# * Neither the name of the copyright holder nor the names of its
+#   contributors may be used to endorse or promote products derived from
+#   this software without specific prior written permission.
+# 
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+# FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+cwlVersion: v1.0
+class: Workflow
+id: complex-workflow
+inputs:
+  archive:
+    type: string
+  files:
+    type:
+      type: array
+      items: File
+  new_archive:
+    type: string
+  touch_files:
+    type:
+      type: array
+      items: string
+  echo_message:
+    type: string
+  echo_output_location:
+    type: string
+
+outputs:
+  archive_out:
+    type: File
+    outputSource: tar_step/archive_out
+  touch_out:
+    type:
+      type: array
+      items: File
+    outputSource: touch_step/file_out
+  echo_out:
+    type: File
+    outputSource: echo_step/echo_output
+  re_tar_out:
+    type: File
+    outputSource: re_tar_step/archive_out
+
+steps:
+  tar_step:
+    run: tar.cwl
+    in:
+      archive_file:
+        source: "#archive"
+      file_list:
+        source: "#files"
+    out: [archive_out]
+
+  touch_step:
+    run: touch.cwl
+    scatter: filename
+    scatterMethod: dotproduct
+    in:
+      waitfor:
+        source: "#tar_step/archive_out"
+      filename:
+        source: "#touch_files"
+    out: [file_out]
+
+  echo_step:
+    run: echo.cwl
+    in:
+      message: "#echo_message"
+      output_location: "#echo_output_location"
+    out: [echo_output]
+
+  re_tar_step:
+    run: tar.cwl
+    in:
+      archive_file:
+        source: "#archive"
+      file_list:
+        source: ["#touch_step/file_out", "#files"]
+        linkMerge: merge_flattened
+    out: [archive_out]
+
+  # rm_step:
+  #   run: rm.cwl
+  #   scatter: filename
+  #   scatterMethod: dotproduct
+  #   in:
+  #     waitfor:
+  #       source: "#re_tar_step/archive_out"
+  #     filename:
+  #       source: ["#files", "#touch_step/file_out", "#echo_step/echo_output"]
+  #       linkMerge: merge_flattened
+  #   out: [standard_out]
+
+requirements:
+  - class: StepInputExpressionRequirement
+  - class: ScatterFeatureRequirement
+  - class: MultipleInputFeatureRequirement