add a method that vallidate the cwl tool for Taverna
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/repo Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/commit/18c5155f Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/18c5155f Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/18c5155f Branch: refs/heads/cwl-browse Commit: 18c5155f380bc1e6e7d92b5b9dcadacff6f9da13 Parents: 6bb504e Author: ThilinaManamgoda <maanafun...@gmail.com> Authored: Sun May 29 03:23:35 2016 +0530 Committer: ThilinaManamgoda <maanafun...@gmail.com> Committed: Sun May 29 03:23:35 2016 +0530 ---------------------------------------------------------------------- .../CWLFiles/binding-test.cwl | 1 - .../java/org/apache/taverna/cwl/ui/App.java | 29 ------ .../org/apache/taverna/cwl/ui/CWLParser.java | 93 ----------------- .../ui/serviceprovider/CwlServiceProvider.java | 101 ++++++++++++++++++- .../taverna/cwl/ui/serviceprovider/Testing.java | 88 +++++++++++++--- .../org/apache/taverna/cwl/CwlDumyActivity.java | 15 ++- 6 files changed, 186 insertions(+), 141 deletions(-) ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/18c5155f/taverna-cwl-activity-ui/CWLFiles/binding-test.cwl ---------------------------------------------------------------------- diff --git a/taverna-cwl-activity-ui/CWLFiles/binding-test.cwl b/taverna-cwl-activity-ui/CWLFiles/binding-test.cwl index 2905c51..6906d71 100644 --- a/taverna-cwl-activity-ui/CWLFiles/binding-test.cwl +++ b/taverna-cwl-activity-ui/CWLFiles/binding-test.cwl @@ -5,7 +5,6 @@ cwlVersion: cwl:draft-3 inputs: - id: reference - type: File inputBinding: { position: 2 } - id: reads http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/18c5155f/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/App.java ---------------------------------------------------------------------- diff --git a/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/App.java b/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/App.java deleted file mode 100644 index 4abf19f..0000000 --- a/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/App.java +++ /dev/null @@ -1,29 +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.cwl.ui; - -/** - * Hello world! - * - */ -public class App -{ - public static void main( String[] args ) - { - System.out.println( "Hello World!" ); - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/18c5155f/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/CWLParser.java ---------------------------------------------------------------------- diff --git a/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/CWLParser.java b/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/CWLParser.java deleted file mode 100644 index 1badefd..0000000 --- a/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/CWLParser.java +++ /dev/null @@ -1,93 +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.cwl.ui; - -import java.io.File; -import java.io.FileInputStream; -import java.io.FileNotFoundException; -import java.util.ArrayList; -import java.util.Map; - -import org.yaml.snakeyaml.Yaml; - - -public class CWLParser { - - private File cwlFile; - - private void setUpFile(File cwlFile) { - - this.cwlFile = cwlFile; - } - - private void readKeyWords() throws FileNotFoundException { - - Yaml yaml = new Yaml(); - Map contents = (Map) yaml.load(new FileInputStream(cwlFile)); - - for (Object key : contents.keySet()) { - if (key.equals("inputs")) - for (Object inputPairs : (ArrayList<String>) contents.get(key)) { - Map test = (Map) inputPairs; - System.out.println(inputPairs); - - for (Object inputKey : test.keySet()) { - if (inputKey.equals("id")) - System.out.println(test.get(inputKey)); - else if (inputKey.equals("type")) { - try { - Map inputType = (Map) test.get(inputKey); - for (Object inputTypekey : inputType.keySet()) { - if (inputTypekey.equals("inputBinding")) { - Map typeInputBinding = (Map) inputType.get(inputTypekey); - for (Object inputBindingKey : typeInputBinding.keySet()) { - - System.out.println( - inputBindingKey + " " + typeInputBinding.get(inputBindingKey)); - } - } else { - System.out.println(inputTypekey + " " + inputType.get(inputTypekey)); - } - } - } catch (ClassCastException e) { - System.out.println(inputKey + " " + test.get(inputKey)); - } - } else { - System.out.println(inputKey + " " + test.get(inputKey)); - } - - } - - } - } - - } - - public static void main(String[] args) { - CWLParser cwlParser = new CWLParser(); - - cwlParser.setUpFile(new File("CWLFiles/binding-test.cwl")); - - try { - cwlParser.readKeyWords(); - } catch (FileNotFoundException e) { - e.printStackTrace(); - } - - } - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/18c5155f/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/serviceprovider/CwlServiceProvider.java ---------------------------------------------------------------------- diff --git a/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/serviceprovider/CwlServiceProvider.java b/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/serviceprovider/CwlServiceProvider.java index 44cdbdc..ec82630 100644 --- a/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/serviceprovider/CwlServiceProvider.java +++ b/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/serviceprovider/CwlServiceProvider.java @@ -21,11 +21,13 @@ import java.io.FileInputStream; import java.io.FileNotFoundException; import java.io.FilenameFilter; import java.util.ArrayList; +import java.util.HashMap; import java.util.List; import java.util.Map; import javax.swing.Icon; +import org.apache.taverna.cwl.Type; import org.yaml.snakeyaml.Yaml; import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider; @@ -33,6 +35,18 @@ import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider; public class CwlServiceProvider implements ServiceDescriptionProvider { private static final File cwlFilesLocation = new File("CWLFiles"); + // CWLTYPES + private static final String FILE = "File"; + private static final String INTEGER = "int"; + private static final String DOUBLE = "double"; + private static final String FLOAT = "float"; + private static final String STRING = "string"; + + private static final String ITEMS = "items"; + private static final String TYPE = "type"; + private static final String ID = "id"; + private static final String INPUTS = "inputs"; + private static final String ARRAY = "array"; @Override public void findServiceDescriptionsAsync(FindServiceDescriptionsCallBack callBack) { @@ -41,10 +55,10 @@ public class CwlServiceProvider implements ServiceDescriptionProvider { List<CwlServiceDesc> result = new ArrayList<CwlServiceDesc>(); File[] cwlFiles = getCwlFiles(); - + // Load the CWL file using SnakeYaml lib Yaml cwlReader = new Yaml(); - + for (File file : cwlFiles) { Map cwlFile = null; @@ -68,6 +82,89 @@ public class CwlServiceProvider implements ServiceDescriptionProvider { } + private HashMap<String, Type> processInputs(ArrayList<Map> inputs) { + + HashMap<String, Type> result = new HashMap<>(); + + for (Map input : inputs) { + + String Id = (String) input.get(ID); + // This require for nested type definitions + Map typeConfigurations; + // this object holds the type and if it's an array then type of the + // elements in the array + Type type = null; + try { + /* + * This part will go through nested type definitions + * + * type : type : array items : boolean + * + */ + + typeConfigurations = (Map) input.get(TYPE); + + // Check type is defined or not + if (typeConfigurations != null) { + type = new Type(); + type.setType((String) typeConfigurations.get(TYPE)); + type.setItems((String) typeConfigurations.get(ITEMS)); + + } + + } catch (ClassCastException e) { + /* + * This exception means type is described as single argument ex: + * type : File + */ + type = new Type(); + type.setType((String) input.get(TYPE)); + type.setItems(null); + } + //when processing the inputs from the HashMap type should be checked for is it null or not + result.put(Id, type); + } + return result; + } + + public boolean isTavernaCompatible(Map cwlFile) { + + + /* + * in this method cwl tool is verified whether it's compatible with + * Taverna or not + */ + ArrayList<Map> inputs = (ArrayList<Map>) cwlFile.get(INPUTS); + + if (inputs != null) { + + HashMap<String, Type> processedinputs = processInputs(inputs); + + for (String inputId : processedinputs.keySet()) { + Type type = processedinputs.get(inputId); + if (type != null) + if (type.getItems() == null) { + String inputType = type.getType(); + if (!(inputType.equals(DOUBLE) || inputType.equals(FILE) || inputType.equals(FLOAT) + || inputType.equals(INTEGER) || inputType.equals(STRING))) + return false; + + } else { + if (type.getType().equals(ARRAY)) { + String inputType = type.getItems(); + if (!(inputType.equals(DOUBLE) || inputType.equals(FILE) || inputType.equals(FLOAT) + || inputType.equals(INTEGER) || inputType.equals(STRING))) + return false; + + } + } + else return false; + } + } + return true; + + } + @Override public Icon getIcon() { // TODO Auto-generated method stub http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/18c5155f/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/serviceprovider/Testing.java ---------------------------------------------------------------------- diff --git a/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/serviceprovider/Testing.java b/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/serviceprovider/Testing.java index 9a7a015..d6baf60 100644 --- a/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/serviceprovider/Testing.java +++ b/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/serviceprovider/Testing.java @@ -18,13 +18,21 @@ public class Testing { private static final String ID = "id"; private static final String TYPE = "type"; private static final String ARRAY = "array"; - private static final String FILE = "File"; private static final String ITEMS = "items"; - static int i=0; + static int i = 0; + + // CWLTYPES + private static final String FILE = "File"; + private static final String INTEGER = "int"; + private static final String DOUBLE = "double"; + private static final String FLOAT = "float"; + private static final String STRING = "string"; + public static void main(String[] args) { File[] cwlFiles = getCwlFiles(); for (File file : cwlFiles) { + Map cwlFile = null; // Load the CWL file using SnakeYaml lib Yaml cwlReader = new Yaml(); @@ -37,14 +45,53 @@ public class Testing { // Creating the CWL configuration bean CwlActivityConfigurationBean configurationBean = new CwlActivityConfigurationBean(); configurationBean.setCwlConfigurations(cwlFile); - getInputs(configurationBean); + // getInputs(configurationBean); + if (isTavernaCompatible(cwlFile)) + System.out.println(file.getName().split("\\.")[0]); } } } + public static boolean isTavernaCompatible(Map cwlFile) { + + /* + * in this method cwl tool is verified whether it's compatible with + * Taverna or not + */ + ArrayList<Map> inputs = (ArrayList<Map>) cwlFile.get(INPUTS); + + if (inputs != null) { + + HashMap<String, Type> processedinputs = processInputs(inputs); + + for (String inputId : processedinputs.keySet()) { + Type type = processedinputs.get(inputId); + if (type != null) + if (type.getItems() == null) { + String inputType = type.getType(); + if (!(inputType.equals(DOUBLE) || inputType.equals(FILE) || inputType.equals(FLOAT) + || inputType.equals(INTEGER) || inputType.equals(STRING))) + return false; + + } else { + if (type.getType().equals(ARRAY)) { + String inputType = type.getItems(); + if (!(inputType.equals(DOUBLE) || inputType.equals(FILE) || inputType.equals(FLOAT) + || inputType.equals(INTEGER) || inputType.equals(STRING))) + return false; + + } + } + else return false; + } + } + return true; + + } + private static void getInputs(CwlActivityConfigurationBean configurationBean) { - + System.out.println(i); i++; Map cwlFile = configurationBean.getCwlConfigurations(); @@ -53,12 +100,14 @@ public class Testing { if (mainKey.equals(INPUTS)) { ArrayList<Map> arrayList = (ArrayList<Map>) cwlFile.get(mainKey); - + HashMap<String, Type> map = processInputs(arrayList); - for (String s:map.keySet() ) { - if(map.get(s).getType().equals(FILE)) System.out.println("ID: "+s+" type : File"); - - if(map.get(s).getType().equals(ARRAY)) System.out.println("ID :"+s+" type: Array items: "+map.get(s).getItems()); + for (String s : map.keySet()) { + if (map.get(s).getType().equals(FILE)) + System.out.println("ID: " + s + " type : File"); + + if (map.get(s).getType().equals(ARRAY)) + System.out.println("ID :" + s + " type: Array items: " + map.get(s).getItems()); } } } @@ -71,18 +120,31 @@ public class Testing { for (Map input : inputs) { String currentInputId = (String) input.get(ID); Map typeConfigurations; - Type type = new Type(); + Type type = null; + try { + typeConfigurations = (Map) input.get(TYPE); - type.setType((String) typeConfigurations.get(TYPE)); - type.setItems((String) typeConfigurations.get(ITEMS)); + + if (typeConfigurations != null) { + type = new Type(); + type.setType((String) typeConfigurations.get(TYPE)); + type.setItems((String) typeConfigurations.get(ITEMS)); + } } catch (ClassCastException e) { // This exception means type is described as single argument ex: // type : File - type.setType((String)input.get(TYPE)); + + type = new Type(); + type.setType((String) input.get(TYPE)); type.setItems(null); + } catch (NullPointerException e) { + + System.out.println("No type is defined"); } + result.put(currentInputId, type); + } return result; } http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/18c5155f/taverna-cwl-activity/src/main/java/org/apache/taverna/cwl/CwlDumyActivity.java ---------------------------------------------------------------------- diff --git a/taverna-cwl-activity/src/main/java/org/apache/taverna/cwl/CwlDumyActivity.java b/taverna-cwl-activity/src/main/java/org/apache/taverna/cwl/CwlDumyActivity.java index d7147cc..03944e0 100644 --- a/taverna-cwl-activity/src/main/java/org/apache/taverna/cwl/CwlDumyActivity.java +++ b/taverna-cwl-activity/src/main/java/org/apache/taverna/cwl/CwlDumyActivity.java @@ -33,15 +33,24 @@ public class CwlDumyActivity extends AbstractAsynchronousActivity<CwlActivityCon private static final String ID = "id"; private static final String TYPE = "type"; private static final String ARRAY = "array"; - private static final String FILE = "File"; - private static final String ITEMS = "items"; + private static final String ITEMS = "items"; + + //CWLTYPES + private static final String FILE = "File"; + private static final String INTEGER="int"; + private static final String DOUBLE="double"; + private static final String FLOAT="float"; + private static final String STRING="string"; + @Override public void configure(CwlActivityConfigurationBean arg0) throws ActivityConfigurationException { removeInputs(); removeOutputs(); } + + private void getInputs(CwlActivityConfigurationBean configurationBean) { @@ -58,6 +67,7 @@ public class CwlDumyActivity extends AbstractAsynchronousActivity<CwlActivityCon for (String inputId : processedInputs.keySet()) { if (processedInputs.get(inputId).getType().equals(FILE)) System.out.println("ID: " + inputId + " type : File"); + if (processedInputs.get(inputId).getType().equals(ARRAY)) System.out.println( @@ -106,7 +116,6 @@ public class CwlDumyActivity extends AbstractAsynchronousActivity<CwlActivityCon @Override public void executeAsynch(Map<String, T2Reference> arg0, AsynchronousActivityCallback arg1) { - } @Override
