OpenClinica FAQs

How to fix the errors?

Error importing CRF: PATHOLOGY","java.lang.RuntimeException: Following special characters in form names not allowed: [+-/*(){}%. ]

Click here to view the solution

The error states that there are specimen characters like +-/*(){}%, whitespaces (space, tab, newline, carriage return, etc) in the CRF name. The OpenClinica connector uses the OID as the form name. These special characters are not allowed in the DE form names, hence the error.

Also when importing the OID mapping CSV file, make sure that the column ‘OS_FORM_NAME’ does not contain any special characters.

For example, a form name can be added as ‘PATHOLOGY_DATA’ and not 'PATHOLOGY DATA'

Fix: Clean up the CRFs to ensure they don't contain special characters mentioned in the log file in the CRF.

Error importing CRF data. Subject: ABC01, Event: BASELINE. Error: DE form for PATHOLOGY (Path_Data) doesn't seem to be created"

Click here to view the solution

The error is displayed when the DE form ‘PATHOLOGY’ for the event ‘BASELINE’ is not yet created hence the data cannot be imported. You need to make sure that the form error is fixed and imported.

Error importing CRF data. Subject: ABC01, Event: SE_WEEK1FU.","com.krishagni.catissueplus.core.common.errors.OpenSpecimenException: Participant 48540 does not exist.

Click here to view the solution

The error is displayed when the participant was created in Open Clinica with PPID ABC01, deleted, and recreated. You need to clean up the mapping tables to remove the mapping of the deleted participants.

Failed to authenticate with the OpenClinica server. Check the following: a) auth credentials b) auth server URL c) server accessibility

Click here to view the solution

This error occurs when the configured server URL, Username, or Password is wrong. To fix this check the below details and update if needed in the server configuration

Configured URL of OpenClinica in REST API Invoker.
The username used in the configuration should have access to OpenClinica.
Password used in configuration should be in a working state.

To fix these details go to REST API Invoker >> use the ‘PUT' HTTP request >> ‘Resource URL’ as 'ServerURL/rest/ng/or-server-configs/{configured server ID}’

Once you update the necessary host, username and password click on 'Send'. You should get 200 status as a successful result.

How to cleanup mapping tables?

You can clean up the Open Clinica mapping tables using the below SQLs

Find the study ID from the table 'os_oc_studies'

//SQL to cleanup the visits mapping table, where 'N' is the study ID

SQL>delete from os_oc_visits where subject_id in (select identifier from os_oc_subjects where study_id = N);

//SQL to cleanup the participant mapping table, where 'N' is the study ID

SQL>delete from os_oc_subjects where study_id = N;

Error: Unknown column '<table name>' in 'field list'
Error: Column 'FORM_CTXT_ID' cannot be null

Click here to view the solution

When forms get corrupted due to any possible reason, this error occurs. In this case, you need to delete the existing form and resync the data for that form. Run below API to delete the form in OpenSpecimen.

Invoke the REST API using either Postman or HTTP client.
<app_url> : Server URL where the forms are available.
{FormId}: Form identifier for which you are getting an error. Get this from the #2 step.
<username>: OpenSpecimen Username
<password>: OpenSpecimen Password

Form ID can be retrieved from DB using below SQL

select identifier, name from dyextn_containers where name = '<form_OID>';

form_OID: You will get the form OID from XML of CRF from OC.