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Posted to commits@taverna.apache.org by st...@apache.org on 2018/08/06 15:22:54 UTC
[06/13] incubator-taverna-language git commit: Revert "Parse
workflows and command line tools recursively"
Revert "Parse workflows and command line tools recursively"
This reverts commit b56f451d2e5accb6ab602ec1155e17db6e969eaf.
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/e27be561
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/e27be561
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/e27be561
Branch: refs/heads/master
Commit: e27be561fa2414c2afaffde5561cde6173bc2a74
Parents: a4e79d4
Author: Majdi Haouech <m....@criteo.com>
Authored: Wed Jul 25 15:30:08 2018 +0200
Committer: Majdi Haouech <m....@criteo.com>
Committed: Wed Jul 25 15:39:49 2018 +0200
----------------------------------------------------------------------
.../main/resources/workflow_with_command.cwl | 45 -------------------
.../taverna/scufl2/cwl/TestWorkflowProcess.java | 44 +++++++++---------
.../test/resources/workflow_with_command.cwl | 45 +++++++++++++++++++
taverna-scufl2-cwl/taverna-scufl2-cwl.iml | 11 -----
taverna-scufl2-cwl/workflow.t2flow.txt | 10 -----
.../workflow.vnd.taverna.scufl2.structure.txt | Bin 2574 -> 0 bytes
taverna-scufl2-cwl/workflow.wfbundle | 10 -----
7 files changed, 69 insertions(+), 96 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/e27be561/taverna-scufl2-cwl/src/main/resources/workflow_with_command.cwl
----------------------------------------------------------------------
diff --git a/taverna-scufl2-cwl/src/main/resources/workflow_with_command.cwl b/taverna-scufl2-cwl/src/main/resources/workflow_with_command.cwl
deleted file mode 100644
index e640ecc..0000000
--- a/taverna-scufl2-cwl/src/main/resources/workflow_with_command.cwl
+++ /dev/null
@@ -1,45 +0,0 @@
-#!/usr/bin/env cwl-runner
-
-# 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.
-
-cwlVersion: v1.0
-class: Workflow
-
-inputs:
- name: string
-
-outputs: []
-
-steps:
- step1:
- run:
- class: CommandLineTool
- baseCommand: echo
- inputs:
- message:
- type: string
-
- inputBinding:
- position: 1
- outputs: []
-
- inputs:
- - id: text
- source: "#x/name"
-
- outputs: []
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/e27be561/taverna-scufl2-cwl/src/test/java/org/apache/taverna/scufl2/cwl/TestWorkflowProcess.java
----------------------------------------------------------------------
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 97d944f..fc386ac 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
@@ -18,47 +18,35 @@
*/
package org.apache.taverna.scufl2.cwl;
-<<<<<<< HEAD
-=======
import java.io.File;
import java.io.IOException;
->>>>>>> 87fa1c18d2b7aa210db3d238905234bf4f52b491
import java.util.Set;
import java.util.HashSet;
import java.util.Map;
import java.util.HashMap;
-import org.junit.Before;
import org.junit.Test;
import static org.junit.Assert.assertEquals;
import org.yaml.snakeyaml.Yaml;
-import com.fasterxml.jackson.core.type.TypeReference;
import com.fasterxml.jackson.databind.JsonNode;
import com.fasterxml.jackson.databind.ObjectMapper;
-import com.fasterxml.jackson.databind.node.ArrayNode;
+import com.fasterxml.jackson.dataformat.yaml.YAMLMapper;
-import org.apache.taverna.scufl2.api.core.Workflow;
-import org.apache.taverna.scufl2.api.core.Processor;
-import org.apache.taverna.scufl2.api.core.DataLink;
+import com.fasterxml.jackson.core.JsonProcessingException;
-import org.apache.taverna.scufl2.api.common.NamedSet;
+import org.apache.taverna.scufl2.api.core.Workflow;
import org.apache.taverna.scufl2.api.port.InputWorkflowPort;
import org.apache.taverna.scufl2.api.port.OutputWorkflowPort;
-import org.apache.taverna.scufl2.api.port.InputProcessorPort;
-<<<<<<< HEAD
-=======
import org.apache.taverna.scufl2.api.io.WorkflowBundleIO;
import org.apache.taverna.scufl2.api.io.WriterException;
import org.apache.taverna.scufl2.api.container.WorkflowBundle;
->>>>>>> 87fa1c18d2b7aa210db3d238905234bf4f52b491
-
public class TestWorkflowProcess {
private static final String HELLO_WORLD_CWL = "/hello_world.cwl";
private static final String WORKFLOW_WITH_COMMAND = "/workflow_with_command.cwl";
@@ -105,15 +93,32 @@ public class TestWorkflowProcess {
@Test
public void testWorkflowSteps() {
cwlFile = loadYamlFile(WORKFLOW_WITH_COMMAND);
-<<<<<<< HEAD
- WorkflowProcess workflow = new WorkflowProcess(cwlFile);
-
-=======
Process workflow = ProcessFactory.createProcess(cwlFile);
assert(workflow instanceof WorkflowProcess);
}
+ @Test
+ public void testConvertWorkflowProcess() {
+ cwlFile = loadYamlFile(WORKFLOW_WITH_COMMAND);
+
+ Process workflow = ProcessFactory.createProcess(cwlFile);
+ workflow.parse();
+ Converter converter = new Converter();
+ JsonNode node = converter.convertWorkflowProcessToJsonNode((WorkflowProcess) workflow);
+ printAsYaml(node);
+ }
+
+ private static void printAsYaml(JsonNode node) {
+ try {
+ String yaml = new YAMLMapper().writeValueAsString(node);
+ System.out.println("YAML DATA");
+ System.out.println(yaml);
+ } catch (JsonProcessingException e) {
+ System.err.println("Error writing JsonNode to YAML");
+ }
+ }
+
public void writeWorkflowToFile(Workflow workflow) {
try {
WorkflowBundleIO io = new WorkflowBundleIO();
@@ -129,7 +134,6 @@ public class TestWorkflowProcess {
} catch(IOException e) {
System.out.println("IOException");
}
->>>>>>> 87fa1c18d2b7aa210db3d238905234bf4f52b491
}
}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/e27be561/taverna-scufl2-cwl/src/test/resources/workflow_with_command.cwl
----------------------------------------------------------------------
diff --git a/taverna-scufl2-cwl/src/test/resources/workflow_with_command.cwl b/taverna-scufl2-cwl/src/test/resources/workflow_with_command.cwl
new file mode 100644
index 0000000..e640ecc
--- /dev/null
+++ b/taverna-scufl2-cwl/src/test/resources/workflow_with_command.cwl
@@ -0,0 +1,45 @@
+#!/usr/bin/env cwl-runner
+
+# 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.
+
+cwlVersion: v1.0
+class: Workflow
+
+inputs:
+ name: string
+
+outputs: []
+
+steps:
+ step1:
+ run:
+ class: CommandLineTool
+ baseCommand: echo
+ inputs:
+ message:
+ type: string
+
+ inputBinding:
+ position: 1
+ outputs: []
+
+ inputs:
+ - id: text
+ source: "#x/name"
+
+ outputs: []
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/e27be561/taverna-scufl2-cwl/taverna-scufl2-cwl.iml
----------------------------------------------------------------------
diff --git a/taverna-scufl2-cwl/taverna-scufl2-cwl.iml b/taverna-scufl2-cwl/taverna-scufl2-cwl.iml
deleted file mode 100644
index 788bb17..0000000
--- a/taverna-scufl2-cwl/taverna-scufl2-cwl.iml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<module type="JAVA_MODULE" version="4">
- <component name="NewModuleRootManager" inherit-compiler-output="true">
- <exclude-output />
- <content url="file://$MODULE_DIR$">
- <sourceFolder url="file://$MODULE_DIR$/src2" isTestSource="false" />
- </content>
- <orderEntry type="jdk" jdkName="1.8" jdkType="JavaSDK" />
- <orderEntry type="sourceFolder" forTests="false" />
- </component>
-</module>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/e27be561/taverna-scufl2-cwl/workflow.t2flow.txt
----------------------------------------------------------------------
diff --git a/taverna-scufl2-cwl/workflow.t2flow.txt b/taverna-scufl2-cwl/workflow.t2flow.txt
deleted file mode 100644
index 59ce3fb..0000000
--- a/taverna-scufl2-cwl/workflow.t2flow.txt
+++ /dev/null
@@ -1,10 +0,0 @@
-WorkflowBundle 'bundle1'
- MainWorkflow 'cdba0a80-366b-4f66-8f26-85e882d41eed'
- Workflow 'cdba0a80-366b-4f66-8f26-85e882d41eed'
- In 'name'
- Processor 'step1'
- In 'text'
- Links
- 'name' -> 'step1:text'
- MainProfile 'profile1'
- Profile 'profile1'
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/e27be561/taverna-scufl2-cwl/workflow.vnd.taverna.scufl2.structure.txt
----------------------------------------------------------------------
diff --git a/taverna-scufl2-cwl/workflow.vnd.taverna.scufl2.structure.txt b/taverna-scufl2-cwl/workflow.vnd.taverna.scufl2.structure.txt
deleted file mode 100644
index e8b6430..0000000
Binary files a/taverna-scufl2-cwl/workflow.vnd.taverna.scufl2.structure.txt and /dev/null differ
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/e27be561/taverna-scufl2-cwl/workflow.wfbundle
----------------------------------------------------------------------
diff --git a/taverna-scufl2-cwl/workflow.wfbundle b/taverna-scufl2-cwl/workflow.wfbundle
deleted file mode 100644
index e2c6d40..0000000
--- a/taverna-scufl2-cwl/workflow.wfbundle
+++ /dev/null
@@ -1,10 +0,0 @@
-WorkflowBundle 'bundle1'
- MainWorkflow '6ce2e3b6-39b1-4773-8aee-e74cccb7ca7d'
- Workflow '6ce2e3b6-39b1-4773-8aee-e74cccb7ca7d'
- In 'name'
- Processor 'step1'
- In 'text'
- Links
- 'name' -> 'step1:text'
- MainProfile 'profile1'
- Profile 'profile1'