[Esciencecentral-users] FW: FW: Adding blocks and libraries [was: RE: Error in installing source co

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Hi Abhik,

Sorry to hear it’s complicated for you. Anyway, I’m forwarding your e-mail to our users’ list. I guess, one of my colleagues will be able to help you with the development materials.

  Cheers,
  Jacek /yatsek/

From: Abhik Seal [mailto:ab...@um...]
Sent: 08 November 2014 04:18
To: Jacek Cala
Subject: Re: FW: [Esciencecentral-users] Adding blocks and libraries [was: RE: Error in installing source code.]

Hi Jacek,

I find the system very complicated not like pipeline pilot and Knime . I can easily R scripts and other languages easily and even see whats going on on each nodes . But in this case its hard to see whats going on. Also if possible  please send me materials how to use scripting languages like R and how to connect the csv import data to R dataframe and plot simple plots and visualize it . Let me know how its is done. Once i get the idea i can create several Cheminformatics workflows using these platform.

On Fri, Nov 7, 2014 at 4:07 AM, Jacek Cala <jac...@ne...<mailto:jac...@ne...>> wrote:
Great to hear you’ve managed to setup everything correctly. Will get back to you with the QSAR stuff at some point. But it won’t be too soon.

  Cheers,
  Jacek /yatsek/

From: Abhik Seal [mailto:ab...@um...<mailto:ab...@um...>]
Sent: 07 November 2014 04:26

To: Jacek Cala
Subject: Re: FW: [Esciencecentral-users] Adding blocks and libraries [was: RE: Error in installing source code.]

Hi Jacek,

Finally i figured it out i had a problem with username i was using vm username but it would be escience central registered username and password .

Thanks If you have some QSAR Workflow let me know no hurry please.

On Thu, Nov 6, 2014 at 11:02 PM, Abhik Seal <ab...@um...<mailto:ab...@um...>> wrote:
Hi,

I think some problem with the maven.props file as 401 == Unauthorized, which means username/password combo are incorrect but i am using the same password for login in .

On Thu, Nov 6, 2014 at 10:56 PM, Abhik Seal <ab...@um...<mailto:ab...@um...>> wrote:
Hi Jacek,

Still the same error i created a directory under home ~/.inkspot and saved maven.props. I found the server returning

java.io.IOException: Server returned HTTP response code: 401 for URL: http://149.165.158.49:8080/api/public/rest/v1/storage/timestamp

for which 401 means unauthorised. Well i am not sure how come the main program is running not the webflow sections.

If you want to access my desktop let me know i can setup team viewer for you.

On Thu, Nov 6, 2014 at 4:29 PM, Jacek Cala <jac...@ne...<mailto:jac...@ne...>> wrote:
  Hi Abhik,

One cause might be improperly set maven.props. Looking into what I sent you couple of days ago, it seems I made a mistake in the serverURL.
If your server runs on port 8080, the server url property should be:

serverURL=http://<SERVER_ADDR>:8080/APIServer

Notice the port number after the server address. if after changing it you still cannot use the upload plugin, please double check that you set all other details correctly and get back to me if it fails.

  Cheers,
  Jacek /yatsek/

From: Abhik Seal [mailto:ab...@um...<mailto:ab...@um...>]
Sent: 06 November 2014 01:38

To: Jacek Cala
Subject: Re: FW: [Esciencecentral-users] Adding blocks and libraries [was: RE: Error in installing source code.]

Here is the log file looks like it cannot connect to the server .

On Wed, Nov 5, 2014 at 3:04 AM, Jacek Cala <jac...@ne...<mailto:jac...@ne...>> wrote:
Hi Abhik,

Sorry, in my last e-mail I meant blocks/misc/GenerateRandomData. So please run ‘mvn clean install > genrand.log’ and send me the log file.

  Cheers,
  Jacek /yatsek/

From: Abhik Seal [mailto:ab...@um...<mailto:ab...@um...>]
Sent: 05 November 2014 00:38
To: Jacek Cala
Subject: Re: FW: [Esciencecentral-users] Adding blocks and libraries [was: RE: Error in installing source code.]

All of the methods got compiled with maven with success but when i start the server i cannot see the workflows. Am i missing some thing on my steps.

I rebuild the code and also created folders and then did mvn clean install on those three directories and then use ansible-playbook command. Also i made a /.inkspot/maven.props file too.

On Tue, Nov 4, 2014 at 4:29 AM, Jacek Cala <jac...@ne...<mailto:jac...@ne...>> wrote:
Hi Abhik,

I’ve got info that the relevant fixes have been checked out. Have a go, checkout the latest version, rebuild the code and run the standalone playbook to update your server instance. Then do all three steps related to building libraries and blocks, as mentioned yesterday.

  Cheers,
  Jacek /yatsek/

From: Hugo Hiden
Sent: 04 November 2014 08:53
To: Jacek Cala
Subject: Re: [Esciencecentral-users] Adding blocks and libraries [was: RE: Error in installing source code.]

Hi,

Fixes now checked in – he will need to do a checkout and rebuild I’m afraid. There were some changes to the API server to support uploading workflows. Alternatively, he can comment out the upload-workflow plugin because I don’t think he actually needs to upload any workflows.

H.

From: Jacek Cala <jac...@ne...<mailto:jac...@ne...>>
Date: Tuesday, 4 November 2014 07:17
To: Hugo Hiden <hug...@ne...<mailto:hug...@ne...>>, Simon Woodman <sim...@ne...<mailto:sim...@ne...>>
Subject: FW: [Esciencecentral-users] Adding blocks and libraries [was: RE: Error in installing source code.]

Hi,

Abhik has faced some issue with the upload workflow plugin. This is related to the recent changes in the API re stream lengths.

Could you please have a look at that, fix where appropriate and get back to him. I guess, maven tools were not tested/compiled after the change.

  Cheers,
  Jacek /yatsek/

From: Abhik Seal [mailto:ab...@um...]
Sent: 04 November 2014 05:30

To: Jacek Cala
Subject: Re: [Esciencecentral-users] Adding blocks and libraries [was: RE: Error in installing source code.]

Thanks for this

I am getting an error in the first mvn installation like given below

[INFO] --- maven-compiler-plugin:3.1:compile (default-compile) @ upload-workflow-plugin ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 1 source file to /Users/abhikseal/esciencecentral-code/code/tools/maven/upload-workflow-plugin/target/classes
[INFO] -------------------------------------------------------------
[ERROR] COMPILATION ERROR :
[INFO] -------------------------------------------------------------
[ERROR] /Users/abhikseal/esciencecentral-code/code/tools/maven/upload-workflow-plugin/src/main/java/com/connexience/UploadWorkflowMojo.java:[206,24] method upload in interface com.connexience.server.workflow.api.API cannot be applied to given types;
  required: com.connexience.server.model.document.DocumentRecord,java.io.InputStream,long
  found: com.connexience.server.model.workflow.WorkflowDocument,java.io.FileInputStream
  reason: actual and formal argument lists differ in length
[INFO] 1 error
[INFO] upload-plugin ...................................... SUCCESS [  4.382 s]
[INFO] upload-workflow-plugin ............................. FAILURE [  0.468 s]
ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.1:compile (default-compile) on project upload-workflow-plugin: Compilation failure
[ERROR] /Users/abhikseal/esciencecentral-code/code/tools/maven/upload-workflow-plugin/src/main/java/com/connexience/UploadWorkflowMojo.java:[206,24] method upload in interface com.connexience.server.workflow.api.API cannot be applied to given types;
[ERROR] required: com.connexience.server.model.document.DocumentRecord,java.io.InputStream,long
[ERROR] found: com.connexience.server.model.workflow.WorkflowDocument,java.io.FileInputStream
[ERROR] reason: actual and formal argument lists differ in length
[ERROR] -> [Help 1]
[ERROR]
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR]
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException
[ERROR]
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR]   mvn <goals> -rf :upload-workflow-plugin

On Mon, Nov 3, 2014 at 7:59 PM, Jacek Cala <jac...@ne...<mailto:jac...@ne...>> wrote:
Hmmm, with the QSAR scenario (as described in one of our papers) it’s tricky right now. Last time it was used a few years ago and to make it running I’ll need to dig it out from some old e-SC version. More and more people are interested though, so I’m going to work on it soon. Still, however, it’ll take me some time.

BTW, after you build blocks there will be some simple workflows uploaded, too. A bit simplistic but you can see the principle, run and edit them as well.

It’s late here in the UK, so in case you have some other issues, I’ll be back tomorrow.

  Cheers,
  Jacek /yatsek/

From: Abhik Seal [mailto:ab...@um...<mailto:ab...@um...>]
Sent: 04 November 2014 00:50
To: Jacek Cala
Subject: Re: [Esciencecentral-users] Adding blocks and libraries [was: RE: Error in installing source code.]

Can you give me a full example workflow on QSAR i want to run it on the main escience server with all the files? Just try to see how does it work. I am well accustomed with pipeline pilot and Knime . But when i have a new system just wanted to make sure how the system works.

Thanks will work on the blocks palettes .

On Mon, Nov 3, 2014 at 7:23 PM, Jacek Cala <jac...@ne...<mailto:jac...@ne...>> wrote:
Hi Abhik,

Glad to hear that you’ve managed to use our ansible playbook on MacOS. You’re the first one! ☺

Regarding the block palette, to make it full of blocks you need to build and upload libraries and blocks to your server. Currently, it’s still only semi-automated process. First, you need to create file ~/.inkspot/maven.props with contents:

serverURL=http://<SERVER_ADDRESS>/APIServer<http://%3cSERVER_ADDRESS%3e/APIServer>
hostname=<SERVER_ADDRESS>
port=8080
username=<USERNAME>
password=<PASSWORD>

Then log in to the server and create folder “Services” and “Libraries” in your home folder.

Finally, build maven tools, libraries and blocks:

1.       Run ‘mvn clean install’ in the ‘code/tools/maven’ directory

2.       Run ‘mvn clean install’ in ‘code/webflow/WorkflowItems/libraries’.

3.       Run ‘mvn clean install’ in ‘code/webflow/WorkflowItems/blocks’.

Note that the order of the build is important. If you set maven.props properly, libraries and blocks should be successfully built and uploaded to your instance.

  Cheers,
  Jacek /yatsek/

From: Abhik Seal [mailto:ab...@um...<mailto:ab...@um...>]
Sent: 04 November 2014 00:07
To: Jacek Cala
Subject: Re: [Esciencecentral-users] Error in installing source code.

Yes I used ansible. Now attaching a figure i couldnt found the nodes in analyse with workflows tab. Do i need to write my own binaries or you need to download it from somewhere . If i want to make a QSAR workflow how do i create it ?

On Mon, Nov 3, 2014 at 6:45 PM, Jacek Cala <jac...@ne...<mailto:jac...@ne...>> wrote:
Hi Abhik,

Did you get it running via ansible? If yes, the basic setup can be eSC server + db engine on one node and a number of engines on the rest of your nodes in the cluster. Just edit inventory.ini and set addresses accordingly. Alternatively, for very high demanding setups you may run db engine and eSC server separately but that shouldn’t be needed before you reach about 100-200 engine nodes.

  Cheers,
  Jacek /yatsek/

From: Abhik Seal [mailto:ab...@um...<mailto:ab...@um...>]
Sent: 03 November 2014 23:04

To: Jacek Cala
Subject: Re: [Esciencecentral-users] Error in installing source code.

Great works now thanks.  So do you have any links or docs to install it on multinode cluster ??

On Mon, Nov 3, 2014 at 8:16 AM, Jacek Cala <jac...@ne...<mailto:jac...@ne...>> wrote:
Hi Abhik,

I assume you’ve checked out the sources to your mac.

Yes, you need to build the sources with maven. You have to have code/server/Ear/target/inkspot.ear and code/webflow/WorkflowEngine/target/ engine-package.zip. They are automatically installed by the ansible playbook.

Then to use ansible deployment you will need:

-          install ansible on your mac – hope the blog info I sent you will help with that.

-          edit inventory.ini and set your target Ubuntu machine(s) instead of the default example addresses.

-          preferably exchange keys between the mac and target machine(s), e.g. with ssh-copy-id but you can run ansible with the --ask-pass option.

-          run from your mac ansible-playbook standalone.yml -i inventory.ini

You don’t need to install db, roles nor jBoss, the ansible playbook takes care of it.

  Jacek /yatsek/

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[Esciencecentral-users] FW: FW: Adding blocks and libraries [was: RE: Error in installing source code.]