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Marvin JS in Pipeline Pilot
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Warren

Joined: 13 Jun 2016
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Link to postPosted: Thu Aug 04, 2016 12:19 amPost subject: Marvin JS in Pipeline Pilot Reply with quote

I have the Marvin JS component in PP2017. How do I configure it to run in a web protocol?

 

Thanks,

Warren

Szilard
ChemAxon personnel
Joined: 21 May 2004
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Link to postPosted: Thu Aug 04, 2016 3:42 pmPost subject: Reply with quote

Hi Warren,

Under

Protocols -> ChemAxon -> Examples -> Marvin JS

there is an example form and work protocol.

They also run from the GUI, but you can also copy them to the Web Port, e.g. under Protocols -> Web Services.

In this case you need to adjust the "Protocol Form" parameter to point to the actual location of the form protocol.

Of course you can copy the form under a "Utilities" sub folder to hide it as usual.

So far we have only tested on 2016, testing on 2017 is scheduled very soon.

Since 2017 is a minor release, I do not expect any surprises.

Nevertheless if you encounter any problems, please let us know.

Best regards,

Szilard

Warren

Joined: 13 Jun 2016
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Link to postPosted: Thu Aug 04, 2016 3:51 pmPost subject: Marvin JS, Pipeline Pilot Reply with quote

Hi Szilard,

When we try to run the example, we get this message:

The requested URL /marvinjs/editor.html was not found on this server.

Thanks,

Warren

Hi Warren,

Under

Protocols -> ChemAxon -> Examples -> Marvin JS

there is an example form and work protocol.

They also run from the GUI, but you can also copy them to the Web Port, e.g. under Protocols -> Web Services.

In this case you need to adjust the "Protocol Form" parameter to point to the actual location of the form protocol.

Of course you can copy the form under a "Utilities" sub folder to hide it as usual.

So far we have only tested on 2016, testing on 2017 is scheduled very soon.

Since 2017 is a minor release, I do not expect any surprises.

Nevertheless if you encounter any problems, please let us know.

Best regards,

Szilard

Szilard
ChemAxon personnel
Joined: 21 May 2004
Posts: 1668

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Link to postPosted: Thu Aug 04, 2016 3:59 pmPost subject: Reply with quote

Hi,

Have you followed the installation instructions in the README.txt below ?

Also what is your component collection version ?

Please run "ChemAxon" -> "Utilities" -> "Show ChemAxon Environment" to obtain the version information, and send us the output.

Best regards,

Szilard


6. (Optional) Install Marvin JS

Needed for the "Marvin JS" component.
Please see APPENDIX B.
APPENDIX B. INSTALLING MARVIN JS

1. Download the appropriate Marvin JS package from ChemAxon:
https://www.chemaxon.com/download/marvin-suite/#mjs
This package is tested against version @REQUIRED_MARVINJS_VERSION@.
(Later versions may also work, but it is not guaranteed.)
Make sure to select the full package (not the "core"), e.g. "marvinjs-@REQUIRED_MARVINJS_VERSION@-all.zip".

2. Create a "marvinjs" directory under <pipeline_pilot_home>/apps/scitegic/core/web

3. Extract the contents of the downloaded Marvin JS package to
<pipeline_pilot_home>/apps/scitegic/core/web/marvinjs

4. Copy your Marvin JS license ("marvin4js-license.cxl") under

<pipeline_pilot_home>/apps/scitegic/core/web

5. Enable Web Services functionality (optional, strongly recommended for full functionality):

- Download and install the latest version of JChem Web Services.
(In case of an existing JChem Web Services installation
make sure the version matches the current requirement for Marvin JS)

https://www.chemaxon.com/download/jchem-suite/#jcws

https://restdemo.chemaxon.com/docs/installationguide.html

- Install the Marvin JS license for the Web Service.
(If you have a Web Services license installed you may skip this step)

Navigate to the home folder of the user that is running the Web Services container.
(running the service as a named user is recommended under Windows for this approach)
Create a "chemaxon" or (".chemaxon") directory under this folder, with also write permissions to this user.
Create a "licenses" subfolder below this.
Copy your Marvin JS license file ("marvin4js-license.cxl") to the "licenses" folder.

As an alternative to using the home folder, the license file may also be listed in the
CHEMAXON_LICENSE_URL or via a Java property. More information:
https://docs.chemaxon.com/display/docs/Installing+to+servers+LIC

Restart the servlet container after installing the icense.

- Define a reverse proxy, so the JChem Web Services will be accessible as part of the Apache URL.
This is needed because of the "same-origin policy" restriction.

Locate the "httpd.conf" file for the Apache configuration inside Pipeline Pilot, for example:

"c:\Program Files\Accelrys\AEP\apps\scitegic\core\packages_win64\apache\httpd-2.2.22\conf\httpd.conf"

Make a copy of it (just in case).
Add these lines at the bottom, substitute <web_services_url> for the URL of the Web Services:

ProxyPass /webservices <web_services_url>
ProxyPassReverse /webservices <web_services_url>

For example if Web Services are running on the default port of Tomcat, installed on the same host:

ProxyPass /webservices http://localhost:8080/webservices
ProxyPassReverse /webservices http://localhost:8080/webservices

- Restart the Pipeline Pilot Apache (httpd) daemon.

Now you should see the Web Services via the Apache, for example, if your web port URL is
http://myppserver:9944/webport/main.htm
then go to
http://myppserver:9944/webservices

- Edit the file "<pipeline_pilot_home>/apps/chemaxon/toolkit/chemaxon.conf"
Set the "chemaxon.pp.mjs.ws.url" variable to point to the web service, e.g.:

chemaxon.pp.mjs.ws.url = http://myppserver:9944/webservices

After saving the file all Marvin JS components will utilize this URL (no restart needed).

[...]

Szilard
ChemAxon personnel
Joined: 21 May 2004
Posts: 1668

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Link to postPosted: Fri Aug 05, 2016 3:14 pmPost subject: Reply with quote

Update:

Meanwhile we have started testing with 2017, and the MJS component works for us in 2017 as expected.

We have tested with the latest version of our component collection, but there were no significant changes to this component since February 5 (version 16.1.25.0).

Best,

Szilard

Szilard
ChemAxon personnel
Joined: 21 May 2004
Posts: 1668

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Link to postPosted: Mon Aug 15, 2016 6:55 amPost subject: Reply with quote

Hi Warren,

Could you make it work ?

Let us know if you have any further difficulties.

On a related note we choose to make Marvin JS an integral part of the package, simplifying the installation somewhat.

We will also update and streamline the installation instructions.

Best regards,

Szilard

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