Re: Website Updates

[Gale Naylor]

Sounds good, thanks! I'll try to remember the magic words, "silent
consensus in 48h." :)

On Tue, Jul 12, 2016 at 1:35 PM Stian Soiland-Reyes 
wrote:

> "Silent consensus in 48h" is often a good option :-)
>
> I think you can update at will right away if you want - the 'embargo'
> was because of the download pages before the release was public.
>
> On 12 July 2016 at 19:24, Gale Naylor  wrote:
> > If there is a need NOT to publish changes to web pages, please let me
> know.
> > Otherwise, I will start publishing changes in 48 hours.
> >
> > Thanks!
> >
> > Gale
> >
> > On Mon, Jul 11, 2016 at 5:31 PM Gale Naylor  >
> > wrote:
> >
> >> I know for a while we were not publishing website updates because we had
> >> pages that needed to stay "staged."
> >>
> >> Is it okay to publish pages now? I've made a few minor corrections.
> >>
> >> Thanks,
> >>
> >> Gale
> >>
>
>
>
> --
> Stian Soiland-Reyes
> Apache Taverna (incubating), Apache Commons
> http://orcid.org/-0001-9842-9718
>

Re: Website Updates

[Stian Soiland-Reyes]

"Silent consensus in 48h" is often a good option :-)

I think you can update at will right away if you want - the 'embargo'
was because of the download pages before the release was public.

On 12 July 2016 at 19:24, Gale Naylor  wrote:
> If there is a need NOT to publish changes to web pages, please let me know.
> Otherwise, I will start publishing changes in 48 hours.
>
> Thanks!
>
> Gale
>
> On Mon, Jul 11, 2016 at 5:31 PM Gale Naylor 
> wrote:
>
>> I know for a while we were not publishing website updates because we had
>> pages that needed to stay "staged."
>>
>> Is it okay to publish pages now? I've made a few minor corrections.
>>
>> Thanks,
>>
>> Gale
>>



-- 
Stian Soiland-Reyes
Apache Taverna (incubating), Apache Commons
http://orcid.org/-0001-9842-9718

[GitHub] incubator-taverna-common-activities issue #12: Docker activity start contain...

[stain]

Github user stain commented on the issue:

https://github.com/apache/incubator-taverna-common-activities/pull/12
  
As this pull request seems to be a smaller part of #9, see my comments 
there.


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[GitHub] incubator-taverna-common-activities issue #11: Docker activity list containe...

[stain]

Github user stain commented on the issue:

https://github.com/apache/incubator-taverna-common-activities/pull/11
  
As this pull request seems to be a smaller part of #9, see my comments 
there.


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[GitHub] incubator-taverna-common-activities issue #10: Docker activity create contai...

[stain]

Github user stain commented on the issue:

https://github.com/apache/incubator-taverna-common-activities/pull/10
  
As this pull request seems to be a smaller part of #9, see my comments 
there.


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[GitHub] incubator-taverna-common-activities issue #13: Taverna 3

[stain]

Github user stain commented on the issue:

https://github.com/apache/incubator-taverna-common-activities/pull/13
  
Thank you for showing your progress!

I've left lots of comments under "Files changed" in the  pull request - 
don't be discouraged! Sorry I hadn't reviewed many of the files in this detail 
before.

As for the Taverna 3 upgrade your activity is almost there - but the 
activity-ui is still using the old imports, which means it's now kind of "in 
between". :-)  I think once you get the right `` and `import`s 
added it would show up better in Eclipse what needs to be changed - but I guess 
you will have more questions after that.

Just yesterday I helped our local student @edikaradumi in updating 
https://github.com/apache/incubator-taverna-plugin-gis/tree/master/taverna-gis-activity-ui/src/main/java/org/apache/taverna/gis/ui/serviceprovider
 to Taverna 3 - I must admit we didn't get to tested it in the T3 workbench 
yet, but  it should compile. :)


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[GitHub] incubator-taverna-common-activities pull request #13: Taverna 3

[stain]

Github user stain commented on a diff in the pull request:


https://github.com/apache/incubator-taverna-common-activities/pull/13#discussion_r70513304
  
--- Diff: 
taverna-cwl-utilities/src/test/java/org/apache/taverna/cwl/utilities/CWLUtilTest.java
 ---
@@ -0,0 +1,122 @@

+/***
+ *  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.utilities;
+
+import static org.junit.Assert.*;
+
+import java.io.FileInputStream;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.LinkedHashMap;
+import java.util.Map;
+
+import org.junit.Before;
+import org.junit.Test;
+import org.yaml.snakeyaml.Yaml;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+public class CWLUtilTest {
+   JsonNode cwlFile;
+   CWLUtil cwlUtil;
+   JsonNode input;
+
+   @Before
+   public void setUp() throws Exception {
+   Yaml reader = new Yaml();
+   Path path = Paths.get("CWLFiles", "customtool1.cwl");
+   ObjectMapper mapper = new  ObjectMapper();
+   cwlFile = mapper.valueToTree(reader.load(new 
FileInputStream(path.toFile(; 
+
+   cwlUtil = new CWLUtil(cwlFile);
+   input =  cwlFile.get("inputs").get(0);
+   }
+
+   @Test
+   public void processNameSpaceTest() {
+   JsonNode nameSpace = cwlUtil.getNameSpace();
+
+   assertEquals(1, nameSpace.size());
+   assertTrue(nameSpace.has("edam"));
+   assertEquals("http://edamontology.org/;, 
nameSpace.get("edam").asText());
+   }
+
+   @Test
+   public void extractLabelTest() {
+   PortDetail detail = new PortDetail();
+
+   cwlUtil.extractLabel(null, detail);
+   assertEquals(null, detail.getLabel());
+
+   cwlUtil.extractLabel(input, detail);
+   assertEquals("input 1 testing label", detail.getLabel());
+
+   }
+
+   @Test
+   public void extractDescriptionTest() {
+   PortDetail detail = new PortDetail();
+
+   cwlUtil.extractDescription(null, detail);
+   assertEquals(null, detail.getDescription());
+
+   cwlUtil.extractDescription(input, detail);
+   assertEquals("this is a short description of input 1", 
detail.getDescription());
+
+   }
+
+   @Test
+   public void figureOutFormatsTest() {
+   PortDetail detail = new PortDetail();
+   detail.setFormat(new ArrayList());
+   cwlUtil.figureOutFormats("edam:1245", detail);
+   assertEquals("http://edamontology.org/1245;, 
detail.getFormat().get(0));
+
+   cwlUtil.figureOutFormats("$formatExpression", detail);
+   assertEquals("$formatExpression", detail.getFormat().get(1));
+
+   // format that doesn't defined in the name space
+
+   cwlUtil.figureOutFormats("formatkey: not Defined", detail);
+   assertEquals("formatkey: not Defined", 
detail.getFormat().get(2));
+   }
+
+   @Test
+   public void processTest() {
--- End diff --

Great!


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[GitHub] incubator-taverna-common-activities pull request #13: Taverna 3

[stain]

Github user stain commented on a diff in the pull request:


https://github.com/apache/incubator-taverna-common-activities/pull/13#discussion_r70512965
  
--- Diff: 
taverna-cwl-utilities/src/main/java/org/apache/taverna/cwl/utilities/CWLUtil.java
 ---
@@ -0,0 +1,216 @@
+package org.apache.taverna.cwl.utilities;
--- End diff --

Could you add the ASF header..? Thanks! :-)


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[GitHub] incubator-taverna-common-activities pull request #13: Taverna 3

[stain]

Github user stain commented on a diff in the pull request:


https://github.com/apache/incubator-taverna-common-activities/pull/13#discussion_r70512846
  
--- Diff: taverna-cwl-utilities/CWLFiles/customtool1.cwl ---
@@ -0,0 +1,67 @@

+
--- End diff --

Could we move `CWLFiles/` to `src/test/resources` to avoid dependency on 
correct relative paths?  (E.g. so it works in both the IDE and Maven).

Then within the test you can try to use `getClass().getResource()` to 
retrieve it.. or perhaps that is awkward for methods that need a `Path`?


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[GitHub] incubator-taverna-common-activities pull request #13: Taverna 3

[stain]

Github user stain commented on a diff in the pull request:


https://github.com/apache/incubator-taverna-common-activities/pull/13#discussion_r70512633
  
--- Diff: 
taverna-cwl-activity/src/main/resources/META-INF/spring/cwl-activity-context.xml
 ---
@@ -0,0 +1,29 @@
+
+
+http://www.springframework.org/schema/beans; 
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance;
+   xsi:schemaLocation="http://www.springframework.org/schema/beans
+  
http://www.springframework.org/schema/beans/spring-beans.xsd;>
+
+
+   
--- End diff --

+1, this looks correct to me


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[GitHub] incubator-taverna-common-activities pull request #13: Taverna 3

[stain]

Github user stain commented on a diff in the pull request:


https://github.com/apache/incubator-taverna-common-activities/pull/13#discussion_r70512455
  
--- Diff: 
taverna-cwl-activity/src/main/java/org/apache/taverna/cwl/CwlActivityFactory.java
 ---
@@ -0,0 +1,102 @@
+/*
+* 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;
+
+import java.net.URI;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Set;
+
+import org.apache.log4j.Logger;
+import org.apache.taverna.cwl.utilities.CWLUtil;
+import org.apache.taverna.workflowmodel.Edits;
+import org.apache.taverna.workflowmodel.processor.activity.Activity;
+import 
org.apache.taverna.workflowmodel.processor.activity.ActivityConfigurationException;
+import org.apache.taverna.workflowmodel.processor.activity.ActivityFactory;
+import 
org.apache.taverna.workflowmodel.processor.activity.ActivityInputPort;
+import 
org.apache.taverna.workflowmodel.processor.activity.ActivityOutputPort;
+
+import com.fasterxml.jackson.databind.JsonNode;
+
+public class CwlActivityFactory implements ActivityFactory {
+   private static Logger logger = 
Logger.getLogger(CwlActivityFactory.class);
+   private static final int DEPTH_0 = 0;
+   private static final int DEPTH_1 = 1;
+   private Edits edits;
+
+   @Override
+   public Activity createActivity() {
+   CwlDumyActivity activity = new CwlDumyActivity();
+   activity.setEdits(edits);
+   return activity;
+   }
+
+   @Override
+   public URI getActivityType() {
+   return null;
+   }
+
+   @Override
+   public JsonNode getActivityConfigurationSchema() {
+   return null;
+   }
+
+   @Override
+   public Set getInputPorts(JsonNode configuration) 
throws ActivityConfigurationException {
+   CWLUtil cwlUtil = new CWLUtil(configuration.path("map"));
+
+   Set inputs = new HashSet<>();
+   
+   
+   //get the processed data
+   HashMap  processedInputs= 
cwlUtil.processInputDepths();
--- End diff --

It's not common for API methods in Java to be so specific about which 
implementation they return, but rather use the interface. Perhaps change 
`processInputDepths()` and friends to return/accept `Map`  
rather than `HashMap`?

Similar for `ArrayList` -> `List`.


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[GitHub] incubator-taverna-common-activities pull request #13: Taverna 3

[stain]

Github user stain commented on a diff in the pull request:


https://github.com/apache/incubator-taverna-common-activities/pull/13#discussion_r70512153
  
--- Diff: 
taverna-cwl-activity/src/main/java/org/apache/taverna/cwl/CwlActivityFactory.java
 ---
@@ -0,0 +1,102 @@
+/*
+* 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;
+
+import java.net.URI;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Set;
+
+import org.apache.log4j.Logger;
+import org.apache.taverna.cwl.utilities.CWLUtil;
+import org.apache.taverna.workflowmodel.Edits;
+import org.apache.taverna.workflowmodel.processor.activity.Activity;
+import 
org.apache.taverna.workflowmodel.processor.activity.ActivityConfigurationException;
+import org.apache.taverna.workflowmodel.processor.activity.ActivityFactory;
+import 
org.apache.taverna.workflowmodel.processor.activity.ActivityInputPort;
+import 
org.apache.taverna.workflowmodel.processor.activity.ActivityOutputPort;
+
+import com.fasterxml.jackson.databind.JsonNode;
+
+public class CwlActivityFactory implements ActivityFactory {
+   private static Logger logger = 
Logger.getLogger(CwlActivityFactory.class);
+   private static final int DEPTH_0 = 0;
+   private static final int DEPTH_1 = 1;
+   private Edits edits;
+
+   @Override
+   public Activity createActivity() {
+   CwlDumyActivity activity = new CwlDumyActivity();
+   activity.setEdits(edits);
+   return activity;
+   }
+
+   @Override
+   public URI getActivityType() {
+   return null;
+   }
+
+   @Override
+   public JsonNode getActivityConfigurationSchema() {
+   return null;
+   }
+
+   @Override
+   public Set getInputPorts(JsonNode configuration) 
throws ActivityConfigurationException {
--- End diff --

Yes, great! This also uses CWLUtil, so that is nice.


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[GitHub] incubator-taverna-common-activities pull request #13: Taverna 3

[stain]

Github user stain commented on a diff in the pull request:


https://github.com/apache/incubator-taverna-common-activities/pull/13#discussion_r70511985
  
--- Diff: 
taverna-cwl-activity/src/main/java/org/apache/taverna/cwl/CwlActivityFactory.java
 ---
@@ -0,0 +1,102 @@
+/*
+* 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;
+
+import java.net.URI;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Set;
+
+import org.apache.log4j.Logger;
+import org.apache.taverna.cwl.utilities.CWLUtil;
+import org.apache.taverna.workflowmodel.Edits;
+import org.apache.taverna.workflowmodel.processor.activity.Activity;
+import 
org.apache.taverna.workflowmodel.processor.activity.ActivityConfigurationException;
+import org.apache.taverna.workflowmodel.processor.activity.ActivityFactory;
+import 
org.apache.taverna.workflowmodel.processor.activity.ActivityInputPort;
+import 
org.apache.taverna.workflowmodel.processor.activity.ActivityOutputPort;
+
+import com.fasterxml.jackson.databind.JsonNode;
+
+public class CwlActivityFactory implements ActivityFactory {
+   private static Logger logger = 
Logger.getLogger(CwlActivityFactory.class);
+   private static final int DEPTH_0 = 0;
+   private static final int DEPTH_1 = 1;
+   private Edits edits;
+
+   @Override
+   public Activity createActivity() {
+   CwlDumyActivity activity = new CwlDumyActivity();
+   activity.setEdits(edits);
+   return activity;
+   }
+
+   @Override
+   public URI getActivityType() {
+   return null;
+   }
+
+   @Override
+   public JsonNode getActivityConfigurationSchema() {
+   return null;
--- End diff --

I'm not sure if this would pass with `null`. An example minimal schema 
which you could potentially adapt:


https://github.com/apache/incubator-taverna-plugin-gis/blob/master/taverna-gis-activity/src/main/resources/schema.json

returned as:


https://github.com/apache/incubator-taverna-plugin-gis/blob/master/taverna-gis-activity/src/main/java/org/apache/taverna/gis/GisActivityFactory.java#L55

```java

/*
 *
 * 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.gis;

import static org.apache.taverna.gis.GisActivity.*;

import java.io.IOException;
import java.net.URI;
import java.util.HashSet;
import java.util.Set;

import com.fasterxml.jackson.databind.JsonNode;
import com.fasterxml.jackson.databind.ObjectMapper;

import org.apache.taverna.workflowmodel.Edits;
import org.apache.taverna.workflowmodel.processor.activity.ActivityFactory;
import 
org.apache.taverna.workflowmodel.processor.activity.ActivityInputPort;
import 
org.apache.taverna.workflowmodel.processor.activity.ActivityOutputPort;

/**
 * Gis ActivityFactory.
 */
public class GisActivityFactory implements ActivityFactory {

private Edits edits;

@Override
public GisActivity createActivity() {
return new GisActivity();
}

@Override
public URI getActivityType() {

[GitHub] incubator-taverna-common-activities pull request #13: Taverna 3

[stain]

Github user stain commented on a diff in the pull request:


https://github.com/apache/incubator-taverna-common-activities/pull/13#discussion_r70511457
  
--- Diff: 
taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/serviceprovider/Testing.java
 ---
@@ -18,141 +18,63 @@
 
 import java.io.File;
 import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.FilenameFilter;
-import java.util.ArrayList;
-import java.util.HashMap;
+import java.io.IOException;
+import java.io.Writer;
+import java.util.Arrays;
+import java.util.Iterator;
 import java.util.LinkedHashMap;
 import java.util.Map;
 
-import org.apache.taverna.cwl.CwlActivityConfigurationBean;
+import org.apache.jena.atlas.iterator.Iter;
+import org.openjena.atlas.json.JsonObject;
+import org.springframework.util.SystemPropertyUtils;
 import org.yaml.snakeyaml.Yaml;
 
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.core.type.TypeReference;
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.ObjectWriter;
+import com.fasterxml.jackson.databind.node.ObjectNode;
+
 public class Testing {
--- End diff --

If this class is for testing, can we move it to same package, but under 
`src/test/java` ? 

I'm not sure what it is testing.. is it more for experimenting?  If it can 
be rewritten to a junit test with `@Test` methods, that would be ideal.


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[GitHub] incubator-taverna-common-activities pull request #13: Taverna 3

[stain]

Github user stain commented on a diff in the pull request:


https://github.com/apache/incubator-taverna-common-activities/pull/13#discussion_r70511075
  
--- Diff: 
taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/serviceprovider/CwlServiceProvider.java
 ---
@@ -16,72 +16,103 @@
  
***/
 package org.apache.taverna.cwl.ui.serviceprovider;
 
-import java.io.File;
 import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.FilenameFilter;
+import java.io.IOException;
 import java.net.URI;
-import java.util.ArrayList;
+import java.nio.file.DirectoryStream;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.Arrays;
 import java.util.List;
 import java.util.Map;
+import java.util.stream.Stream;
+import java.util.stream.StreamSupport;
 
 import javax.swing.Icon;
 
+import org.apache.log4j.Logger;
 import org.yaml.snakeyaml.Yaml;
 
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.node.ObjectNode;
+
 import 
net.sf.taverna.t2.servicedescriptions.AbstractConfigurableServiceProvider;
 import net.sf.taverna.t2.servicedescriptions.ConfigurableServiceProvider;
 
 public class CwlServiceProvider extends 
AbstractConfigurableServiceProvider
implements 
ConfigurableServiceProvider {
-
+   
+   public static final String  TOOL_NAME="toolName";
+   public static final String  MAP ="map";
+   private static Logger logger = 
Logger.getLogger(CwlServiceProvider.class);
+   
CwlServiceProvider() {
super(new CwlServiceProviderConfig());
}
-   private static final String providerName ="CWL Services";
-   private static final URI providerId = URI
-   
.create("http://cwl.com/2016/service-provider/cwlcommandlinetools;);
-   private File cwlFilesLocation;
+
+   private static final String providerName = "CWL Services";
+   private static final URI providerId = 
URI.create("http://cwl.com/2016/service-provider/cwlcommandlinetools;);
 
@Override
public void 
findServiceDescriptionsAsync(FindServiceDescriptionsCallBack callBack) {
 
// get the location of the cwl tool from the workbench
-   cwlFilesLocation = new File(getConfiguration().getPath());
-   // This is holding the CWL configuration beans
-   List result = new ArrayList();
-
-   File[] cwlFiles = getCwlFiles();
-
-   // Load the CWL file using SnakeYaml lib
-   Yaml cwlReader = new Yaml();
-
-   for (File file : cwlFiles) {
-   Map cwlFile = null;
-
-   try {
-   cwlFile = (Map) cwlReader.load(new 
FileInputStream(file));
-   } catch (FileNotFoundException e) {
-   e.printStackTrace();
-   }
-   if (cwlFile != null) {
-   // Creating CWl service Description
-   CwlServiceDesc cwlServiceDesc = new 
CwlServiceDesc();
-   cwlServiceDesc.setCwlConfiguration(cwlFile);
-   
cwlServiceDesc.setToolName(file.getName().split("\\.")[0]);
-
-   // add to the result
-   result.add(cwlServiceDesc);
-   // return the service description
-   callBack.partialResults(result);
-   }
-
+   Path path = Paths.get(getConfiguration().getPath());
+   //figure out the dots in the path ex: /maanadev/../cwltools
+   Path normalizedPath = path.normalize();
+
+   DirectoryStream stream = null;
+   try {
+   stream = Files.newDirectoryStream(normalizedPath, 
"*.cwl");
+   } catch (IOException e) {
+   logger.warn("Path is not correct !");
+   return;
}
+   //create stream with parallel capabilities 
+   Stream paralleStream = 
StreamSupport.stream(stream.spliterator(), true);
+   
+   paralleStream.forEach(p -> {
+   Yaml reader = getYamlReader();
+   
+   Map cwlFile;
+   try {
+   cwlFile = (Map) reader.load(new 
FileInputStream(path.toFile()));
+   JsonNode config = 
createJsonNode(p,cwlFile);
+

[GitHub] incubator-taverna-common-activities pull request #13: Taverna 3

[stain]

Github user stain commented on a diff in the pull request:


https://github.com/apache/incubator-taverna-common-activities/pull/13#discussion_r70509966
  
--- Diff: 
taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/serviceprovider/CwlServiceDesc.java
 ---
@@ -16,79 +16,67 @@
  
***/
 package org.apache.taverna.cwl.ui.serviceprovider;
 
-import java.util.Arrays;
 import java.util.List;
-import java.util.Map;
 
 import javax.swing.Icon;
 
-import org.apache.taverna.cwl.CwlActivityConfigurationBean;
 import org.apache.taverna.cwl.CwlDumyActivity;
 
+import com.fasterxml.jackson.databind.JsonNode;
+
 import net.sf.taverna.t2.servicedescriptions.ServiceDescription;
 import net.sf.taverna.t2.workflowmodel.processor.activity.Activity;
 
-public class CwlServiceDesc extends 
ServiceDescription {
+public class CwlServiceDesc extends ServiceDescription {
 
private static final String DESCRIPTION = "description";
 
@Override
public String getDescription() {
-   String description = (String) cwlConfiguration.get(DESCRIPTION);
+   
//see  whether description is too long
-   if (description == null || (description.length()>40))
-   return "";
+   if (cwlConfiguration.has(DESCRIPTION)){
+   String description = 
cwlConfiguration.path(DESCRIPTION).asText();
+   if((description.length()<40))return description;
+   else return "";
+   }
else
-   return description;
+   return "";
}
 
-   private Map cwlConfiguration;
-   private String toolName;
+   private JsonNode cwlConfiguration;
 
-   @Override
-   public Class> 
getActivityClass() {
-   return (Class>) CwlDumyActivity.class;
+   public void setCwlConfiguration(JsonNode cwlConfiguration) {
+   //set yaml parse CWL tool content
+   this.cwlConfiguration = cwlConfiguration;
}
 
+   private String toolName;
+
@Override
-   public CwlActivityConfigurationBean getActivityConfiguration() {
-   // Creating the CWL configuration bean
-   CwlActivityConfigurationBean configurationBean = new 
CwlActivityConfigurationBean();
-   configurationBean.setCwlConfigurations(cwlConfiguration);
-   configurationBean.setToolName(toolName);
-   return configurationBean;
+   public Class> getActivityClass() {
--- End diff --

This should be replaced in Taverna 3 with the 
[`getActivityType()`](https://github.com/apache/incubator-taverna-workbench/blob/master/taverna-activity-palette-api/src/main/java/org/apache/taverna/servicedescriptions/ServiceDescription.java#L45)
 method returning an URI which must match the `CWLActivityFactory` URI.   (This 
URI is used to match up the corresponding `ActivityFactory`)

I would suggest an URI like https://taverna.apache.org/ns/2016/activity/cwl 
for both.


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[GitHub] incubator-taverna-common-activities pull request #13: Taverna 3

[stain]

Github user stain commented on a diff in the pull request:


https://github.com/apache/incubator-taverna-common-activities/pull/13#discussion_r70509151
  
--- Diff: 
taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/serviceprovider/CwlServiceDesc.java
 ---
@@ -16,79 +16,67 @@
  
***/
 package org.apache.taverna.cwl.ui.serviceprovider;
 
-import java.util.Arrays;
 import java.util.List;
-import java.util.Map;
 
 import javax.swing.Icon;
 
-import org.apache.taverna.cwl.CwlActivityConfigurationBean;
 import org.apache.taverna.cwl.CwlDumyActivity;
 
+import com.fasterxml.jackson.databind.JsonNode;
+
 import net.sf.taverna.t2.servicedescriptions.ServiceDescription;
--- End diff --

These `import`s need to be updated to their `org.apache.taverna` 
equivalents.


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[GitHub] incubator-taverna-common-activities pull request #13: Taverna 3

[stain]

Github user stain commented on a diff in the pull request:


https://github.com/apache/incubator-taverna-common-activities/pull/13#discussion_r70508895
  
--- Diff: taverna-cwl-activity-ui/pom.xml ---
@@ -65,27 +60,45 @@


+

-   org.yaml
-   snakeyaml
-   1.17
+   org.apache.taverna.commonactivities
+   taverna-cwl-utilities
+   ${project.version}
+   bundle


+   taverna-cwl-activity
+   ${project.groupId}
+   ${project.version}
+   
+   
+   
net.sf.taverna.t2.ui-api
activity-palette-api
${t2.ui.api.version}

-

-   taverna-cwl-activity
-   ${project.groupId}
-   ${project.version}
+   net.sf.taverna.t2.ui-api
+   menu-api
+   ${t2.ui.api.version}
+   
+   
+   net.sf.taverna.t2.ui-api
+   contextual-views-api
+   ${t2.ui.api.version}


+   net.sf.taverna.t2.ui-impl
+   activity-tools
+   ${t2.ui.impl.version}
+   
+   
+   
net.sf.taverna.t2.taverna-workbench
workbench-dev
${t2.workbench.version}
-   test
--- End diff --

`workbench-dev` must be commented out as it does not exist in Taverna 3 :-( 
 -- and anyway it should stay in `test`






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College Internship Evaluation Form

[Sagar]

Hi Folks,

Stain, Ian, and Alan,  As Rajan Maurya said during introducing me to the
community. It will be my internship project. I will continue this project
after my two-month internship also.

In my college, we have to evaluate our self by his mentor, In which mentor
have to fill some question related to internship and give us marks
accordingly.
The evaluation form has been provided from the college.

But I am confused, by whom I will be evaluated.

I talk to Rajan Maurya, He told me to ask you first.

-- 

*With warm regards  *
*Sincerely yours*
Sagar


*Student ,(6th Semester )B.Tech IT and mathematical innovation*
*Cluster Innovation Centre*
*University of Delhi *

[GitHub] incubator-taverna-mobile pull request #22: Redesigning Favourite Workflow Li...

[sagar15795]

Github user sagar15795 commented on a diff in the pull request:


https://github.com/apache/incubator-taverna-mobile/pull/22#discussion_r70439444
  
--- Diff: 
app/src/main/java/org/apache/taverna/mobile/data/local/DBHelper.java ---
@@ -184,6 +186,24 @@ public boolean updateFavouriteWorkflow(String id) {
 return false;
 }
 
+public Observable getFavouriteWorkflow() {
+return Observable.create(new 
Observable.OnSubscribe() {
+@Override
+public void call(Subscriber> 
subscriber) {
+if (subscriber.isUnsubscribed()) return;
--- End diff --

This is necessary if we use create operator. 
For further info please refer issue [#12 
](https://github.com/ribot/ribot-app-android/issues/12) at ribot android app


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