XNAT gateway problems: XML search request returned null

[John McLean]

Dear all,

I am trying to link up a dicom viewer (ginkgo on Ubunutu) to my XNAT database such that I can query the data in the database and view the output in the dicom viewer. I installed the XNAT gateway on the client computer, adjacent to ginkgo. 

I followed the instructions in the documentation. On completing the configuration, ginkgo can 'see' the XNAT gateway as a dicom node once the gateway is running, however, the queries to the main server xnat continually fail. See the output from the XNAT GATEWAY log below.

-----------------------

INFO - handle - Socket[addr=/172.31.171.167,port=33049,localport=4006]

INFO - Socket[addr=/172.31.171.167,port=33049,localport=4006]

INFO - received AAssociateRQ

appCtxName: 1.2.840.10008.3.1.1.1/DICOM Application Context Name

implClass: 1.2.276.0.7230010.3.0.3.6.0

implVersion: OFFIS_DCMTK_360

calledAET: XNATGATEWAY

callingAET: JM_PC1

maxPDULen: 16384

asyncOpsWindow:

pc-1: as=1.2.840.10008.5.1.4.1.2.2.1/Study Root Query/Retrieve Information Model - FIND

ts=1.2.840.10008.1.2/Implicit VR Little Endian

ts=1.2.840.10008.1.2.1/Explicit VR Little Endian

ts=1.2.840.10008.1.2.2/Explicit VR Big Endian

INFO - sending AAssociateAC

appCtxName: 1.2.840.10008.3.1.1.1/DICOM Application Context Name

implClass: 1.2.40.0.13.1.1

implVersion: dcm4che-1.4.27

calledAET: XNATGATEWAY

callingAET: JM_PC1

maxPDULen: 16352

asyncOpsWindow:

pc-1: 0 - acceptance

ts=1.2.840.10008.1.2/Implicit VR Little Endian

INFO - received [pc-1] 1:C_FIND_RQ with Dataset

class: 1.2.840.10008.5.1.4.1.2.2.1/Study Root Query/Retrieve Information Model - FIND

INFO - Jan 14, 2014 9:51:11 AM: REST query string:

/experiments?project=CBT&xnat:imagesessiondata/date=20131114-20140114&columns=xnat:experimentdata/label,xnat:subjectdata/label,xnat:subjectdata/demographics[@xsi:type=xnat:demographicdata]/gender,xnat:subjectdata/demographics[@xsi:type=xnat:demographicdata]/dob,xnat:subjectdata/demographics[@xsi:type=xnat:demographicdata]/age,xnat:subjectdata/demographics[@xsi:type=xnat:demographicdata]/height,xnat:subjectdata/demographics[@xsi:type=xnat:demographicdata]/weight,xnat:subjectdata/demographics[@xsi:type=xnat:demographicdata]/ethnicity,xnat:experimentdata/visit_id,xnat:imagesessiondata/uid,project,xnat:experimentdata/project,xsitype,xnat:imagesessiondata/date,xnat:imagesessiondata/time

INFO - Jan 14, 2014 9:51:11 AM: XML search request returned null

INFO - sending [pc-1] 1:C_FIND_RSP

class: 1.2.840.10008.5.1.4.1.2.2.1/Study Root Query/Retrieve Information Model - FIND

status: 0

INFO - received A-RELEASE-RQ

INFO - sending A-RELEASE-RP

INFO - finished - Socket[addr=/172.31.171.167,port=33049,localport=4006]

INFO - closing connection - Socket[addr=/172.31.171.167,port=33049,localport=4006]

----------------------------------------------

I've tried a few variation in the query i.e. trying different projects , different subject id's , dates etc, nothing seems to work.

Is there something on XNAT I need to do i.e. enable the Rest API (i think i'm right in saying xnat gateway uses Rest calls?) or is that done by default during installation.

Any help appreciated as always

Thanks

John

[John McLean]

Update....

I am now able to connect to my server. The error was in the AET path title. I needed to include the port and the /'database_name' as per my web browser to enable to correct connection.

Haven't been able to download a scan yet, but information is passing between the different programs which is a step forward.

John

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[Gerardo Sanchez]

Hi, I have similar problems
I am using Slicer / xnat gateway / xnat

Checking packets with wireshark (old ethereal), i guess a posible error: gateway is waiting for xml responses and xnat reply with json responses. Gateway log report a exception: Content is not allowed in prolog (see log details below) but this error could raizes if you try to use xml parser with json (or any other) text

I tried with gateway's older version and i could receive study sinopsis in Slicer, but i could not download any images

My gateway, xnat and slicer are running in the same pc, and xnat is working great

Some suggestions? Thanks in advance

Gateway error log reports this:
INFO - 06/02/2014 09:11:29 PM: REST query string:
/experiments?&columns=xnat:experimentdata/label,xnat:subjectdata/label,xnat:subjectdata/demographics[@xsi:type=xnat:demographicdata]/gender,xnat:subjectdata/demographics[@xsi:type=xnat:demographicdata]/dob,xnat:subjectdata/demographics[@xsi:type=xnat:demographicdata]/age,xnat:subjectdata/demographics[@xsi:type=xnat:demographicdata]/height,xnat:subjectdata/demographics[@xsi:type=xnat:demographicdata]/weight,xnat:subjectdata/demographics[@xsi:type=xnat:demographicdata]/ethnicity,xnat:experimentdata/visit_id,xnat:imagesessiondata/uid,project,xnat:experimentdata/project,xsitype,xnat:imagesessiondata/date,xnat:imagesessiondata/time
ERROR - 06/02/2014 09:11:29 PM: Error parsing the response to REST query
org.dom4j.DocumentException: Error on line 1 of document  : Content is not allowed in prolog. Nested exception: Content is not allowed in prolog.
    at org.dom4j.io.SAXReader.read(SAXReader.java:482)
    at org.dom4j.io.SAXReader.read(SAXReader.java:343)
    at org.nrg.xnat.gateway.XNATCFindRsp.executeQuery(XNATCFindRsp.java:77)
    at org.nrg.xnat.gateway.XNATGatewayServer.getMultiCFindRsp(XNATGatewayServer.java:137)
    at org.dcm4chex.archive.dcm.qrscp.FindScp.newMultiCFindRsp(FindScp.java:374)
    at org.dcm4chex.archive.dcm.qrscp.FindScp.doCFind(FindScp.java:180)
    at org.dcm4che.net.DcmServiceBase.c_find(DcmServiceBase.java:154)
    at org.dcm4cheri.net.ActiveAssociationImpl.run(ActiveAssociationImpl.java:231)
    at org.dcm4cheri.util.LF_ThreadPool.join(LF_ThreadPool.java:174)
    at org.dcm4cheri.net.ActiveAssociationImpl.run(ActiveAssociationImpl.java:157)
    at org.dcm4cheri.server.DcmHandlerImpl.handle(DcmHandlerImpl.java:249)
    at org.dcm4cheri.server.ServerImpl.run(ServerImpl.java:279)
    at org.dcm4cheri.util.LF_ThreadPool.join(LF_ThreadPool.java:174)
    at org.dcm4cheri.util.LF_ThreadPool$1.run(LF_ThreadPool.java:221)
    at java.lang.Thread.run(Thread.java:744)
Nested exception:
org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.
    at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:198)
    at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.fatalError(ErrorHandlerWrapper.java:177)
    at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:441)
    at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:368)
    at com.sun.org.apache.xerces.internal.impl.XMLScanner.reportFatalError(XMLScanner.java:1436)
    at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$PrologDriver.next(XMLDocumentScannerImpl.java:999)
    at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:606)
    at com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(XMLNSDocumentScannerImpl.java:117)
    at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:510)
    at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:848)
    at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:777)
    at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:141)
    at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1213)
    at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:649)
    at org.dom4j.io.SAXReader.read(SAXReader.java:465)
    at org.dom4j.io.SAXReader.read(SAXReader.java:343)
    at org.nrg.xnat.gateway.XNATCFindRsp.executeQuery(XNATCFindRsp.java:77)
    at org.nrg.xnat.gateway.XNATGatewayServer.getMultiCFindRsp(XNATGatewayServer.java:137)
    at org.dcm4chex.archive.dcm.qrscp.FindScp.newMultiCFindRsp(FindScp.java:374)
    at org.dcm4chex.archive.dcm.qrscp.FindScp.doCFind(FindScp.java:180)
    at org.dcm4che.net.DcmServiceBase.c_find(DcmServiceBase.java:154)
    at org.dcm4cheri.net.ActiveAssociationImpl.run(ActiveAssociationImpl.java:231)
    at org.dcm4cheri.util.LF_ThreadPool.join(LF_ThreadPool.java:174)
    at org.dcm4cheri.net.ActiveAssociationImpl.run(ActiveAssociationImpl.java:157)
    at org.dcm4cheri.server.DcmHandlerImpl.handle(DcmHandlerImpl.java:249)
    at org.dcm4cheri.server.ServerImpl.run(ServerImpl.java:279)
    at org.dcm4cheri.util.LF_ThreadPool.join(LF_ThreadPool.java:174)
    at org.dcm4cheri.util.LF_ThreadPool$1.run(LF_ThreadPool.java:221)
    at java.lang.Thread.run(Thread.java:744)

[Mikhail Milchenko]

John and Gerardo,

Unfortunately we don't have manpower to debug Gateway against DICOM clients that you use. But, given that there are several possible problematic areas,  it is helpful to isolate where the problem originates and compare your configuration against configurations that are known to work. Gateway is tested to work solidly with K-PACS on Windows and Osirix on Mac. So, if you cannot get it to work with those with your XNAT instance, this might indicate Gateway or XNAT configuration problem.

-Misha

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