Hi Donal,
Many thanks for your prompt reply. I tried your suggestion in point#2 - trying
to retrieve the run directory of a completed workflow run using both the
getRunDirectoryContents and getRunDirectoryAsZip APIs however I'm getting the
same unmarshalling error (see the requests/responses below). Could you please
help in this regard?
listRuns:
Request:
<soapenv:Envelope xmlns:soapenv="http://schemas.xmlsoap.org/soap/envelope/";
xmlns:soap="http://ns.taverna.org.uk/2010/xml/server/soap/";>
<soapenv:Header/>
<soapenv:Body>
<soap:listRuns/>
</soapenv:Body>
</soapenv:Envelope>
Response:
<soap:Envelope xmlns:soap="http://schemas.xmlsoap.org/soap/envelope/";>
<soap:Body>
<ns3:listRunsResponse xmlns:xlink="http://www.w3.org/1999/xlink";
xmlns:ns3="http://ns.taverna.org.uk/2010/xml/server/soap/";
xmlns:ns4="http://ns.taverna.org.uk/2010/xml/server/";>
<Run
xlink:href="/taverna-server/rest/runs/0e15a376-e349-4fe3-9563-5acd5bdc829c">0e15a376-e349-4fe3-9563-5acd5bdc829c</Run>
<Run
xlink:href="/taverna-server/rest/runs/491bcc2c-0129-4c23-bbbe-e9f76bc6aa83">491bcc2c-0129-4c23-bbbe-e9f76bc6aa83</Run>
<Run
xlink:href="/taverna-server/rest/runs/1ecc43bf-be63-4ad0-9ccd-3dffb2ee7c89">1ecc43bf-be63-4ad0-9ccd-3dffb2ee7c89</Run>
</ns3:listRunsResponse>
</soap:Body>
</soap:Envelope>
getRunStatus:
Request:
<soapenv:Envelope xmlns:soapenv="http://schemas.xmlsoap.org/soap/envelope/";
xmlns:soap="http://ns.taverna.org.uk/2010/xml/server/soap/";>
<soapenv:Header/>
<soapenv:Body>
<soap:getRunStatus>
<!--Optional:-->
<runName>491bcc2c-0129-4c23-bbbe-e9f76bc6aa83</runName>
</soap:getRunStatus>
</soapenv:Body>
</soapenv:Envelope>
Response:
<soap:Envelope xmlns:soap="http://schemas.xmlsoap.org/soap/envelope/";>
<soap:Body>
<ns3:getRunStatusResponse xmlns:xlink="http://www.w3.org/1999/xlink";
xmlns:ns3="http://ns.taverna.org.uk/2010/xml/server/soap/";
xmlns:ns4="http://ns.taverna.org.uk/2010/xml/server/";>
<Status>Finished</Status>
</ns3:getRunStatusResponse>
</soap:Body>
</soap:Envelope>
getRunDirectoryContents:
Request:
<soapenv:Envelope xmlns:soapenv="http://schemas.xmlsoap.org/soap/envelope/";
xmlns:soap="http://ns.taverna.org.uk/2010/xml/server/soap/";
xmlns:xlin="http://www.w3.org/1999/xlink";
xmlns:ser="http://ns.taverna.org.uk/2010/xml/server/";>
<soapenv:Header/>
<soapenv:Body>
<soap:getRunDirectoryContents>
<!--Optional:-->
<runName>491bcc2c-0129-4c23-bbbe-e9f76bc6aa83</runName>
<!--Optional:-->
<directory xlin:href="?" ser:name="?">out</directory>
</soap:getRunDirectoryContents>
</soapenv:Body>
</soapenv:Envelope>
Response:
<soap:Envelope xmlns:soap="http://schemas.xmlsoap.org/soap/envelope/";>
<soap:Body>
<soap:Fault>
<faultcode>soap:Client</faultcode>
<faultstring>Unmarshalling Error: Unable to create an instance of
org.taverna.server.master.common.DirEntryReference</faultstring>
</soap:Fault>
</soap:Body>
</soap:Envelope>
getRunDirectoryAsZip:
Request:
<soapenv:Envelope xmlns:soapenv="http://schemas.xmlsoap.org/soap/envelope/";
xmlns:soap="http://ns.taverna.org.uk/2010/xml/server/soap/";
xmlns:xlin="http://www.w3.org/1999/xlink";
xmlns:ser="http://ns.taverna.org.uk/2010/xml/server/";>
<soapenv:Header/>
<soapenv:Body>
<soap:getRunDirectoryAsZip>
<!--Optional:-->
<runName>491bcc2c-0129-4c23-bbbe-e9f76bc6aa83</runName>
<!--Optional:-->
<directory xlin:href="?" ser:name="?">out</directory>
</soap:getRunDirectoryAsZip>
</soapenv:Body>
</soapenv:Envelope>
Response:
<soap:Envelope xmlns:soap="http://schemas.xmlsoap.org/soap/envelope/";>
<soap:Body>
<soap:Fault>
<faultcode>soap:Client</faultcode>
<faultstring>Unmarshalling Error: Unable to create an instance of
org.taverna.server.master.common.DirEntryReference</faultstring>
</soap:Fault>
</soap:Body>
</soap:Envelope>
Regards,
Ali
-----Original Message-----
From: Donal K. Fellows [mailto:[email protected]]
Sent: Monday, January 17, 2011 9:35 PM
To: Ali Ranalvi
Cc: [email protected]
Subject: Re: [Taverna-users] Problem with retrieving output of workflow run
using SOAP in TavernaServer-2.2a1
On 17/01/2011 14:01, Ali Ranalvi wrote:
> My questions are:
>
> 1.Do I explicitly need to create a run directory before executing
> workflow by using makeRunDirectory?
No. You might want to, but you don't *need* to. You have a per-run directory
created for you automatically. That will go away when the run is deleted. You
can make extra directories though, if it helps with organizing your inputs or
auxiliary files.
> What do the parentDirectory (path on
> server where workflow run outputs/errors will be stored?) and
> directoryName parameters signify? When I try to this request with
> parentDirectory set to /tmp and directoryName set to the runName, it
> gives me this error:
>
> <soap:Envelope xmlns:soap="http://schemas.xmlsoap.org/soap/envelope/";>
> <soap:Body>
> <soap:Fault>
> <faultcode>soap:Client</faultcode>
> <faultstring>Unmarshalling Error: Unable to create an instance of
> org.taverna.server.master.common.DirEntryReference</faultstring>
> </soap:Fault>
> </soap:Body>
> </soap:Envelope>
Hmm, it (JAXB) is not extracting the description of the directory to create.
The content of the directory parameter should be:
<dir></dir>
(That is, nothing between the tags.) Well, I think it should. JAXB is a bit
opaque at times, and there's a number of bits and pieces in here that are
rather complex since there's a sharing of much of the Taverna Server machinery
with the REST API. If we still can't make it work (and I'll need to see the
whole request message in that case) then I'll see what I can do to fix it for
2.2b1 (I'm currently working on the last major feature that's been blocking
that; then it's a round of bugfixing before doing the release).
> 2.How does one retrieve the output of a workflow execution? I think
> getRunDirectoryContents and getRunDirectoryAsZip are the required
> functions but they too require a directory parameter. What value
> should be passed there?
I think you'll find that:
<dir>out</dir>
works for that.
Donal.
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