Move test-like functions to test folder
diff --git a/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/CWLParser.java b/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/CWLParser.java
index 9e764e0..63e70d1 100644
--- a/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/CWLParser.java
+++ b/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/CWLParser.java
@@ -39,7 +39,6 @@
public CWLParser(JsonNode cwlFile) {
this.cwlFile = cwlFile;
- this.yamlHelper;
}
public Set<Step> parseSteps() {
diff --git a/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/Main.java b/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/Main.java
deleted file mode 100644
index d4fa6b8..0000000
--- a/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/Main.java
+++ /dev/null
@@ -1,46 +0,0 @@
-/*
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License. You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing,
- * software distributed under the License is distributed on an
- * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- * KIND, either express or implied. See the License for the
- * specific language governing permissions and limitations
- * under the License.
- */
-package org.apache.taverna.scufl2.cwl;
-
-import org.yaml.snakeyaml.Yaml;
-
-import com.fasterxml.jackson.databind.JsonNode;
-import com.fasterxml.jackson.databind.ObjectMapper;
-
-public class Main {
-
- private static final String HELLO_WORLD_CWL = "/hello_world.cwl";
- private static final String WORKFLOW_WITH_COMMAND = "/workflow_with_command.cwl";
- private static JsonNode cwlFile;
-
- public static void main(String[] args) {
-
- Yaml reader = new Yaml();
- ObjectMapper mapper = new ObjectMapper();
- cwlFile = mapper.valueToTree(reader.load(Main.class.getResourceAsStream(WORKFLOW_WITH_COMMAND)));
- System.out.println(cwlFile);
-
- Process workflow = ProcessFactory.createProcess(cwlFile);
- workflow.parse();
- Converter converter = new Converter();
- JsonNode node = converter.convertWorkflowProcessToJsonNode((WorkflowProcess) workflow);
- System.out.println("NODE");
- System.out.println(node);
- }
-}
\ No newline at end of file
diff --git a/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/components/CommandLineTool.java b/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/components/CommandLineTool.java
index db954aa..ca551fa 100644
--- a/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/components/CommandLineTool.java
+++ b/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/components/CommandLineTool.java
@@ -46,8 +46,6 @@
this.node = node;
this.cwlParser = new CWLParser(node);
this.parse();
- this.receiverPorts = new HashSet(processorInputs.values());
- this.senderPorts = new HashSet(processorOutputs.values());
}
public void parse() {
@@ -57,6 +55,7 @@
}
public void parseInputs() {
+ // TODO: Set the processor port depth from the CWL type
Set<PortDetail> cwlInputs = cwlParser.parseInputs();
for(PortDetail detail: cwlInputs) {
String portId = detail.getId();
diff --git a/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/components/Process.java b/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/components/Process.java
index 342864a..70e3669 100644
--- a/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/components/Process.java
+++ b/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/components/Process.java
@@ -28,9 +28,6 @@
public interface Process {
- Set<ReceiverPort> receiverPorts;
- Set<SenderPort> senderPorts;
-
public void parse();
}
\ No newline at end of file
diff --git a/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/components/WorkflowProcess.java b/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/components/WorkflowProcess.java
index afee5da..b8902e7 100644
--- a/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/components/WorkflowProcess.java
+++ b/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/components/WorkflowProcess.java
@@ -19,8 +19,6 @@
package org.apache.taverna.scufl2.cwl;
-import java.io.File;
-import java.io.IOException;
import java.util.Set;
import java.util.HashSet;
import java.util.Map;
@@ -31,8 +29,6 @@
import org.apache.taverna.scufl2.api.core.DataLink;
import org.apache.taverna.scufl2.api.core.Workflow;
-import org.apache.taverna.scufl2.api.container.WorkflowBundle;
-
import org.apache.taverna.scufl2.api.port.InputWorkflowPort;
import org.apache.taverna.scufl2.api.port.OutputWorkflowPort;
import org.apache.taverna.scufl2.api.port.InputProcessorPort;
@@ -40,9 +36,6 @@
import org.apache.taverna.scufl2.api.port.SenderPort;
import org.apache.taverna.scufl2.api.port.ReceiverPort;
-import org.apache.taverna.scufl2.api.io.WorkflowBundleIO;
-import org.apache.taverna.scufl2.api.io.WriterException;
-
import com.fasterxml.jackson.databind.JsonNode;
public class WorkflowProcess implements Process {
@@ -61,8 +54,6 @@
public WorkflowProcess(JsonNode node) {
cwlParser = new CWLParser(node);
this.parse();
- this.receiverPorts = new HashSet(workflowInputs.values());
- this.senderPorts = new HashSet(workflowOutputs.values());
}
public void parse() {
@@ -82,9 +73,6 @@
workflow.setProcessors(processors);
workflow.setDataLinks(dataLinks);
-// System.out.println(workflow);
-// writeWorkflowToFile(workflow);
-//
// System.out.println("DEBUG WORKFLOW");
// System.out.println(workflow.getInputPorts());
// System.out.println(workflow.getOutputPorts());
@@ -92,23 +80,6 @@
}
- public void writeWorkflowToFile(Workflow workflow) {
- try {
- WorkflowBundleIO io = new WorkflowBundleIO();
- File scufl2File = new File("workflow.wfbundle");
- WorkflowBundle bundle = io.createBundle();
- Set<Workflow> workflowSet = new HashSet<>();
- workflowSet.add(workflow);
- bundle.setWorkflows(workflowSet);
- bundle.setMainWorkflow(workflow);
- io.writeBundle(bundle, scufl2File, "text/vnd.taverna.scufl2.structure");
- } catch(WriterException e) {
- System.out.println("Exception writing the workflow bundle");
- } catch(IOException e) {
- System.out.println("IOException");
- }
- }
-
public void parseInputs() {
Set<PortDetail> cwlInputs = cwlParser.parseInputs();
for (PortDetail port: cwlInputs) {
diff --git a/taverna-scufl2-cwl/src/test/java/org/apache/taverna/scufl2/cwl/TestWorkflowProcess.java b/taverna-scufl2-cwl/src/test/java/org/apache/taverna/scufl2/cwl/TestWorkflowProcess.java
index 015ded4..10604b1 100644
--- a/taverna-scufl2-cwl/src/test/java/org/apache/taverna/scufl2/cwl/TestWorkflowProcess.java
+++ b/taverna-scufl2-cwl/src/test/java/org/apache/taverna/scufl2/cwl/TestWorkflowProcess.java
@@ -18,7 +18,8 @@
*/
package org.apache.taverna.scufl2.cwl;
-
+import java.io.File;
+import java.io.IOException;
import java.util.Set;
import java.util.HashSet;
import java.util.Map;
@@ -45,6 +46,11 @@
import org.apache.taverna.scufl2.api.port.OutputWorkflowPort;
import org.apache.taverna.scufl2.api.port.InputProcessorPort;
+import org.apache.taverna.scufl2.api.io.WorkflowBundleIO;
+import org.apache.taverna.scufl2.api.io.WriterException;
+
+import org.apache.taverna.scufl2.api.container.WorkflowBundle;
+
public class TestWorkflowProcess {
private static final String HELLO_WORLD_CWL = "/hello_world.cwl";
@@ -92,8 +98,26 @@
@Test
public void testWorkflowSteps() {
cwlFile = loadYamlFile(WORKFLOW_WITH_COMMAND);
- WorkflowProcess workflow = new WorkflowProcess(cwlFile);
+ Process workflow = ProcessFactory.createProcess(cwlFile);
+ assert(workflow instanceof WorkflowProcess);
+ }
+
+ public void writeWorkflowToFile(Workflow workflow) {
+ try {
+ WorkflowBundleIO io = new WorkflowBundleIO();
+ File scufl2File = new File("workflow.wfbundle");
+ WorkflowBundle bundle = io.createBundle();
+ Set<Workflow> workflowSet = new HashSet<>();
+ workflowSet.add(workflow);
+ bundle.setWorkflows(workflowSet);
+ bundle.setMainWorkflow(workflow);
+ io.writeBundle(bundle, scufl2File, "text/vnd.taverna.scufl2.structure");
+ } catch(WriterException e) {
+ System.out.println("Exception writing the workflow bundle");
+ } catch(IOException e) {
+ System.out.println("IOException");
+ }
}
}
