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tomcat severe error

Hi ,

I installed jdk 7u51, postresql 9.3,tomcat 7.0.52 in Ubuntu 14.04 os with openclinica 3.9. As for the first time i installed its run well but the next i seen tomcat is stop and openclinica is unable to stat with the following errors:

Mar 07, 2016 12:41:44 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: Error listenerStart
Mar 07, 2016 12:41:44 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: Context [/OpenClinica] startup failed due to previous errors
Mar 07, 2016 12:41:44 PM org.apache.catalina.loader.WebappClassLoader clearReferencesJdbc
SEVERE: The web application [/OpenClinica] registered the JDBC driver [net.sf.log4jdbc.DriverSpy] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
Mar 07, 2016 12:41:44 PM org.apache.catalina.loader.WebappClassLoader clearReferencesJdbc
SEVERE: The web application [/OpenClinica] registered the JDBC driver [oracle.jdbc.driver.OracleDriver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
Mar 07, 2016 12:41:44 PM org.apache.catalina.loader.WebappClassLoader clearReferencesJdbc
SEVERE: The web application [/OpenClinica] registered the JDBC driver [org.postgresql.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
Mar 07, 2016 12:41:44 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/OpenClinica] appears to have started a thread named [[email protected]] but has failed to stop it. This is very likely to create a memory leak.
Mar 07, 2016 12:41:44 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/OpenClinica] appears to have started a thread named [Timer-0] but has failed to stop it. This is very likely to create a memory leak.

how could i resolve this issue .please respond soon..

gmahankali

OpenClinica 3.15 now available

Hello Everyone!

We've just released OpenClinica 3.15! This release includes numerous bug fixes and minor enhancements.

Download the community edition and check out the release notes at https://docs.openclinica.com/downloads.

Best Regards,
Cal

ccollins

Re: Webservice to retrieve CRF data? (version 3.14)

one approach with curl you can find in that other post, otherwise with python request library it is straightforward as well:

method = "S_DEFAULTS1/SS_01/*/*"

dataFormat = "json"
ocUrl = "http://localhost:8080/OpenClinica/"

s = requests.Session()
loginCredentials = {"j_username": "root", "j_password": "12345678"}

r = s.post(ocUrl + "j_spring_security_check", loginCredentials)
r = s.get(ocUrl + "rest/clinicaldata/" + dataFormat + "/view/" + method)

toskrip

Re: Webservice to retrieve CRF data? (version 3.14)

Hi,

regarding the order of ItemGroups when importing complex eCRF data (my notes):

- first is the un-grouped (not named) ItemGroup (UNGRUPED keyword in OID)
- then named non-repeating ItemGroup(s)
- then repeating ItemGroup(s) (ordered by repeatKey) with less repeating rows
- then repeating ItemGroup(s) (ordered by repeatKey) with more repeating rows

Note: there is no hard rule that would require this but in my testing I was able to create and import some invalid ODM when not following those rules. This means the data was stored in DB and also visible in audit trail but e.g. was not loadable in eCRF (user interface).

The other advice if you are planning to import a lot of data for many subjects you may want to limit the number of subjects that you put in one ODM file. Personally I usually just include one patient into ODM and trigger the import as many times as many patients I need to import.

best

Tomas

toskrip

Re: Multiple sites for a study

Hi Ravi,
Re-assigning subjects is done in the subject-matrix, using the icon that is at the right of the row of a subject, next to view and remove.
Kind regards,
Gerben Rienk

GerbenRienk

Re: How to fill CRFs in OpenClinica OpenSource/Community Edition EDC using SOAP/REST?

Hi Ravi,
For 3.14 you would need the web-servcies to import data, see for example http://www.trialdatasolutions.com/tds/howto/wssetup.jsp
For retrieving data you could use rest and you would authenticate using j_spring_security_check It depends on your programming environment how you would do that, but for vba, have a look at http://www.trialdatasolutions.com/tds/howto/scripttorunarule.jsp
If you would like use the same construct to download clinical data, the vbs-script would be something like:

Option explicit
Dim objIEDebugWindow
Dim objHTTP
Dim strURLStart
Dim strURL
Dim strReq
Dim objFSO
Dim objFile
Dim fileName

Set objFSO=CreateObject("Scripting.FileSystemObject")

If WScript.Arguments.Count <> 3 then
WScript.Echo "Missing parameters. This script needs: "_
& VbNewLine & "username, password and StudyOID"_
& VbNewLine & "to run correctly."
Else
'build the file name
fileName = "d:\temp\" & WScript.Arguments(2) & ".json"
Set objFile=objFSO.CreateTextFile(fileName,2,true)
Set objHTTP = CreateObject("MSXML2.XMLHTTP")
'change this to match your situation
strURLStart = "https://trialdatasolutions.com/OpenClinica/"
'j_spring_security_check
strURL = strURLStart & "j_spring_security_check?j_username=" & WScript.Arguments(0)
strURL = strURL & "&j_password=" & WScript.Arguments(1)
objHTTP.Open "POST", strURL, False
objHTTP.send
'uncomment the next line if you want to check if the authorization went OK
'debug (objHTTP.responseText)

'request the data in json
strURL = strURLStart & "rest/clinicaldata/json/view/" & WScript.Arguments(2) & "/*/*/*"
'WScript.Echo strURL
objHTTP.Open "GET", strURL, False
objHTTP.send
'write the result to disk
objFile.Write(objHTTP.responseText)

'uncomment the next line if you want to check if the request went OK
'debug (objHTTP.responseText)
'WScript.Echo "finished"
End if

'the following procedure is used to check the responses of the HTTP requests
'it opens a browser window and displays whatever is given as parameter myText
Sub Debug( myText )
'open a browser window if it is not already open
If Not IsObject( objIEDebugWindow ) Then
Set objIEDebugWindow = CreateObject( "InternetExplorer.Application" )
objIEDebugWindow.Navigate "about:blank"
objIEDebugWindow.Visible = True
objIEDebugWindow.ToolBar = False
objIEDebugWindow.Width = 200
objIEDebugWindow.Height = 300
objIEDebugWindow.Left = 10
objIEDebugWindow.Top = 10
Do While objIEDebugWindow.Busy
WScript.Sleep 100
Loop
objIEDebugWindow.Document.Title = "IE Debug Window"
objIEDebugWindow.Document.Body.InnerHTML = "" & Now & ""
End If
'add the text from the parameter to what's already there
objIEDebugWindow.Document.Body.InnerHTML = _
objIEDebugWindow.Document.Body.InnerHTML _
& myText & "
" & vbCrLf
End Sub

Kind regards,
Gerben Rienk

GerbenRienk

Re: Rounding up in calculations

Hi there,

In the WIDTH_DECIMAL cell for BMI, enter w(2) - this rounds it to 2 decimal
places. The w means "I don't care how wide the result is, and the (2)
means...but...round it to 2 decimal places. If you want to control the
width, replace the w with the total width, and be sure to count the decimal
as one of those spaces. For example, to allow for 999.99, WIDTH_DECIMAL
should be 6(2).

I hope this helps!

Best regards,

*Laura*

*Laura Keita *|* OpenClinica, LLC*
Director of Training and Compliance
Direct: *+1.781.547.8462*
[email protected] | www.openclinica.com

lkeita

Re: No sign case record book icon

Hi Richard
I assume that the sign icon isn't shown to your Investigator. If there
are repeating events, please check that all occurrences are marked
complete. The subject matrix shows a completed icon for the event if one
occurrence is completed and the status of a second one is "data entry
started". So this might be misleading your investigator. If that's not
the case, please provide some more informations about your set-up.
Regards,
Christian
------------------------------------------------------------------------
Dipl.-Inf. Christian Hänsel
IT / Software Developer
Tel.: +49-(0)89-5526189-16
Fax : +49-(0)89-5526189-55
E-Mail: [email protected]
ReliaTec GmbH
Schleissheimer Str. 37
85748 Garching Germany
HRB 150060 / AG München
Gf Thomas Herbig
http://www.reliatec.de
=========================================================================
Am 24.02.2014 23:52, schrieb Richard Brookes:
> > Hi,
> >
> >
> >
> > We have a study where the case record book icon is not visible to the
> > investigator role on two subjects.
> >
> >
> >
> > - All the events are marked as complete for all subjects in the
> > study.
> >
> > - There is only one site and all subjects are assigned to that
> > site. The investigator is also assigned to that site.
> >
> > - The investigator was able to sign the case record book for
> > all subjects other than these two subjects.
> >
> > - The investigator user can sign off each event individually
> > for these two subjects
> >
> >
> >
> >
> >
> >
> >
> > Can anyone think of why this may be happening, and how to resolve it?
> >
> >
> >
> >
> >
> > Thanks
> >
> >
> >
> > Richard
> >
> >
> >
> >
> >
> >

haensel

Investigator signatures - where is the right hand green stamp?

We have a pretty large study with some 30 sites running now for a year and some patients are being completed. Normally we would expect the green stamp in the right margin indicating that some visits are ready to be signed. The stamp is absent but it is possible to sign the visits by updating the study events. This is creating more work, though.....How can we get the green stamp back? We are running version 3.6

kristiak

Missing data in items when downloading a dataset

Dear community,
We are using OpenClinica 3.13 (Version: 3.13 - Changeset: 74f4df3481b6 2017-02-28 15:27 +0000), and we are facing a problem when extracting data.

We are working in a multicentre study (4 sites). We have longitudinal data on 340 subjects (expecting about 500), collected in 4 different events/CRFs. We realised we were not getting all the information from OpenClinica when downloading the dataset corresponding to one of the CRFs.

For this CRF, data has been collected using three versions of the same CRF, so we end up with a file that contains 851 variables. We download from OpenClinica all available CRFs (marked as complete and not marked as complete) in SPSS version. It takes a bit long to generate the file, but it seems to work. However, when we started working with the data, we realised there was some missing information. We could not identify the missingness pattern as it did not depend on the subject nor the CRF version. So we had some observations having empty “age” but with information on “sex” and others.

Alternatively we checked if there was any problem with the age variable, so we downloaded a dataset with this single variable and obtained all ages collected. So, we think that the problem is related to the amount of data we are trying to manage.

Has anyone encountered the same problem before? Any suggestions will be really appreciated.

smcresib