{ "version": "https://jsonfeed.org/version/1.1", "title": "chem-bla-ics", "description": "Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.", "home_page_url": "https://chem-bla-ics.linkedchemistry.info/", "feed_url": "https://chem-bla-ics.linkedchemistry.info/2008/11/04/next-generation-asynchronous.json", "icon": "https://chem-bla-ics.linkedchemistry.info/assets/images/chem-bla-ics_logo.png", "language": "en", "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286", "_orcid": "0000-0001-7542-0286" } ], "items": [ { "id": "https://doi.org/10.59350/esdth-ef628", "url": "https://chem-bla-ics.linkedchemistry.info/2008/11/04/next-generation-asynchronous.html", "title": "Next generation asynchronous webservices #2", "content_html": "

Getting back to some webservice stuff (see part #1 of this series )…\nactually, I’ll use cloud service from now on, since web service is reserved for SOAP/WSDL (see\nmy EMBRACE presentation ).\nLet me present this bit of JavaScript I just ran in Bioclipse2:

\n\n
xws.connect();\nservice = xws.getService(\"cdk.ws1.bmc.uu.se\");\nservice.discoverSync(9000);\nservice.getFunctions();\nf = service.getFunction(\"calculateMass\");\nios = f.getIoSchemataSync(9000);\niof = xws.getIoFactory(ios);\nsmiDoc = iof.createSmilesDocument();\nsmiDoc.setSmiles(\"CCC\");\nresult = f.invokeSync(smiDoc.toString(), 9000);\nobj = iof.getOutputObject(result);\nprint(\"Mass: \" +  obj.getStringValue())\n
\n\n

At first, it might look a bit verbose to just calculate the mass of a molecule, and it is, and it is not even written in XML. Hahahaha

\n\n

Anyway, the code rocks, thanx to Johannes’ great work on his xws4j library! I’ll explain\nthe script. The first line gets Bioclipse online using a Jabber account, which you set via Bioclipse’ preferences pages. The next few\nlines allows you to connect to a cloud service, this one running on ws1.bmc.uu.se and called cdk. With the getFunctions() method\nwe query which functions are available, called ports in WDSL if not mistaken, from which we pick the calculateMass one.

\n\n

And then the action joins in. One nice feature of the IO-DATA proposal is that the function\nitself defines the XML Schema it uses for input and output, and does not rely on WDSL to do that (or maybe recent SOAP specs allows that\ntoo). So, we query the function for its schemata, and the xws4j library then something funky happens: we order the library to create a\ndata model on the fly for this service! From this we get a Java data model for the service. This allows us to use createSmilesDocument()\nand setSmiles(). That’s function-specific stuff!

\n\n

Of course, we do not have to do that. For example, the second function I wrote (generate3Dcoordinates) eats and spits CML, and I’d\nrather rely on CMLDOM or CDK as data model then. But more on that later…

\n\n

The Bioclipse xws4j plugin actually puts the data model in my workspace, so that I can easily introspect the API:

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\"\"

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The last three lines invoke the function (synchronously, as it’s cheap), and get the mass from the function output. BTW, I should\nstress that a function does not require any specific implementation regarding synchronous or asynchronous calls. You write one\nfunction, and can call it in either way you like. The library hides all IO-DATA details around that.

", "summary": "Getting back to some webservice stuff (see part #1 of this series )… actually, I’ll use cloud service from now on, since web service is reserved for SOAP/WSDL (see my EMBRACE presentation ). Let me present this bit of JavaScript I just ran in Bioclipse2:", "image": "https://chem-bla-ics.linkedchemistry.info/assets/images/autogeneration.png", "date_published": "2008-11-04T00:00:00+00:00", "date_modified": "2025-10-11T00:00:00+00:00", "tags": ["xmpp","java","bioclipse","web"], "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ] } ] }