How to use MarvinSketch for input on WebPortal

Hi,

I would ike to use MarvinSketch in a workflow distributed through the WebPortal, so that users can draw a molecule as input. How do I set this up? Do I need to attach a Quickform to the marvinSketch node?

Any tips appreciated!

Hi Evert,

you would need the Molecule String Input node.

Best, Iris

Thanks for your pointer. I hooked this node up to the variable port of the MarvinSketch node, but now get an error in the WebPortal:

Path to sketcher needs to be relative and start with '/'.

See atached pictures of my workflow (unfinished) and the error message.

In the end, I would the user to be able to choose between drawing a structure or providing and SD file as input mfor this workflow. How would I do that?

Thanks,

Evert

cas_workflow_error.png

cas_workflow.png

Molecule sketcher configuration is described in the server installation manual on pages 19ff ("Installing a sketcher").

Looks like ChemAxon changed their web site, so the links in the 4.1 server installation manual to the Marvin applet files are no longer accurate.

Could you point me to the correct download links for the Marvin Sketcher and Marvin JS Sketcher applet?

Much appreciated,

Evert

The link still works for me. You get automatically redirected to the new page.

I used the Marvin Sketcher applet enclosed in the server installation package, configured it according to the manual p. 19, and made some progress. I don't get any error messages, but the sketcher doesn't show up...(see image).

The plan is to be able to sketch a structure, convert to SDF with RDKit node, then use the CIR node to fetch the CAS number, which is then to be reported together with the structure. It works perfectly in the Knime Desktop, but I would like to put this on the WebPortal...

Kind regards,

Evert

marvin_0.png

Hi again,

I have gone over the installation instructions several times and checked the configuration, but cannot get the Marvin Sketch applet to show up on the WebPortal (same behaviour as earlier).

Please advice!

What browser are you using?

Firefox 43.0 on Ubuntu 14.04. Same problem with FireFox 42.0 on Windows 7. Java applications work fine on both machines, both have Java 8 update 60, if that's any help.

Hi,

do you see any error messages in the console if you open the developer tools in your browser?

Hi,

I am trying to show the Marvin Sketch JS when invoking the workflow at the web portal.

I hooked up Molecule String Input - > Marvin Sketch.

Published to the webportal. Got this error message:

2017-07-19 18:29:00,974 : DEBUG : KNIME-Worker-12 : WorkflowManager : Molecule String Input : 6:10 : Molecule String Input 6:10 doBeforePreExecution
2017-07-19 18:29:00,974 : DEBUG : KNIME-Worker-12 : NodeContainer : Molecule String Input : 6:10 : Molecule String Input 6:10 has new state: PREEXECUTE
2017-07-19 18:29:00,975 : DEBUG : KNIME-Worker-12 : WorkflowManager : Molecule String Input : 6:10 : Molecule String Input 6:10 doBeforeExecution
2017-07-19 18:29:00,975 : DEBUG : KNIME-Worker-12 : NodeContainer : Molecule String Input : 6:10 : Molecule String Input 6:10 has new state: EXECUTING
2017-07-19 18:29:00,975 : DEBUG : KNIME-Worker-12 : WorkflowFileStoreHandlerRepository : Molecule String Input : 6:10 : Adding handler 2d15d34b-de36-4d14-b64c-89d3548e3118 (Molecule String Input 6:10:  ) - 1 in total
2017-07-19 18:29:00,975 : DEBUG : KNIME-Worker-12 : LocalNodeExecutionJob : Molecule String Input : 6:10 : Molecule String Input 6:10 Start execute
2017-07-19 18:29:04,243 : ERROR : KNIME-Worker-12 : MoleculeStringInputQuickFormNodeModel : Molecule String Input : 6:10 : Retrieving SVG from view failed: Error executing JavaScript: Can't find variable: org_knime_js_base_node_quickform_input_molecule
2017-07-19 18:29:04,243 : DEBUG : KNIME-Worker-12 : MoleculeStringInputQuickFormNodeModel : Molecule String Input : 6:10 : Retrieving SVG from view failed: Error executing JavaScript: Can't find variable: org_knime_js_base_node_quickform_input_molecule
java.io.IOException: Error executing JavaScript: Can't find variable: org_knime_js_base_node_quickform_input_molecule
        at org.knime.ext.phantomjs.PhantomJSImageGenerator.executeScript(PhantomJSImageGenerator.java:155)
        at org.knime.ext.js.node.quickform.input.molecule.MoleculeStringInputQuickFormNodeModel.createSVGImagePortObjectFromView(MoleculeStringInputQuickFormNodeModel.java:171)
        at org.knime.ext.js.node.quickform.input.molecule.MoleculeStringInputQuickFormNodeModel.execute(MoleculeStringInputQuickFormNodeModel.java:125)
        at org.knime.core.node.NodeModel.executeModel(NodeModel.java:566)
        at org.knime.core.node.Node.invokeFullyNodeModelExecute(Node.java:1128)
        at org.knime.core.node.Node.execute(Node.java:915)
        at org.knime.core.node.workflow.NativeNodeContainer.performExecuteNode(NativeNodeContainer.java:561)
        at org.knime.core.node.exec.LocalNodeExecutionJob.mainExecute(LocalNodeExecutionJob.java:95)
        at org.knime.core.node.workflow.NodeExecutionJob.internalRun(NodeExecutionJob.java:179)
        at org.knime.core.node.workflow.NodeExecutionJob.run(NodeExecutionJob.java:110)
        at org.knime.core.util.ThreadUtils$RunnableWithContextImpl.runWithContext(ThreadUtils.java:328)
        at org.knime.core.util.ThreadUtils$RunnableWithContext.run(ThreadUtils.java:204)
        at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
        at java.util.concurrent.FutureTask.run(FutureTask.java:266)
        at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:123)
        at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:246)
Caused by: org.openqa.selenium.WebDriverException: {"errorMessage":"Can't find variable: org_knime_js_base_node_quickform_input_molecule","request":{"headers":{"Accept-Encoding":"gzip,deflate","Connection":"Keep-Alive","Content-Length":"87","Content-Type":"application/json; charset=utf-8","Host":"localhost:11688","User-Agent":"Apache-HttpClient/4.5.2 (Java/1.8.0_60)"},"httpVersion":"1.1","method":"POST","post":"{\"script\":\"return org_knime_js_base_node_quickform_input_molecule.getSVG();\",\"args\":[]}","url":"/execute","urlParsed":{"anchor":"","query":"","file":"execute","directory":"/","path":"/execute","relative":"/execute","port":"","host":"","password":"","user":"","userInfo":"","authority":"","protocol":"","source":"/execute","queryKey":{},"chunks":["execute"]},"urlOriginal":"/session/cf685dc0-6cea-11e7-aaa6-d3bb9978ee64/execute"}}

I don't think the installation instruction addressed the issue.

It doesn't seem to be as simple as connecting two nodes together.

I have installed the chemaxon plugin on both the

Really appreciate if anyone can share, how they get it to work.

Thanks,
Simon