OC FAQs and Errors

This page explains how to solve the errors faced during OC sync. You can download the error csv from the import log page, as shown in the below image.

Go to the OpenClinica Study Configuration page of the study → Click on Import Logs → Download the csv file.

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

The error states that there are specimen characters like +-/*(){}%, whitespaces (space, tab, newline, carriage return, etc.) in the CRF name. The OC 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.

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

The error is displayed when the DE form ‘PATHOLOGY’ for the event ‘BASELINE’ is not yet created; hence the data cannot be imported. It would help if you made sure that the form error is fixed and imported.

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

The error is displayed when the participant was created in Open Clinica with PPID ABC01, deleted, and recreated. It would help if you cleaned up the mapping tables to remove the mapping of the deleted participants.

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

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 OC in REST API Invoker.
The username used in the configuration should have access to OC.
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.

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

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.

6. com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Row size too large. The maximum row size for the used table type, not counting BLOBs, is 65535. This includes storage overhead. Check the manual. You have to change some columns to TEXT or BLOBs.

7. java.lang.RuntimeException: Error retrieving participants of the site: I-Spy2: 400: Error: {"message":"errorCode.studyNotExist","params":{"siteOid":null,"studyOid":"I-SPY2"}}

8. com.krishagni.catissueplus.core.common.errors.OpenSpecimenException: Parent specimen should be either in collected or missed state.

9. No anticipated specimens with labels: EP_017-00-02-07-1

10. com.mysql.jdbc.exceptions.jdbc4.MySQLIntegrityConstraintViolationException: Duplicate entry '4-EP_021-00-04-01-2' for key 'CAT_SPEC_CP_ID_LABEL_UQ'

11. com.krishagni.catissueplus.core.common.errors.OpenSpecimenException: Invalid form data. Reason: COVID_Specimen_Extension.Reason specimen not collected:INVALID_VALUE

12. SQL error: 'com.mysql.cj.jdbc.exceptions.MysqlDataTruncation: Data truncation: Data too long for column 'DE_A_(n)' at row 1', where n is any number.

13. 502 Bad Gateway Error. An error was encountered when invoking the OpenClinica API. The details are present in the error log file.

14. Specimen label already exists.

OC FAQs and Errors

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