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

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

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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.

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titleClick 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.

  1. Invoke the REST API using either Postman or HTTP client.

    Image Modified

    <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

  2. Form ID can be retrieved from DB using below SQL

    Code Block
    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.

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When CRF has many fields (100-200), the database doesn’t allow pulling all these fields in OS. Resulting OS throws the above error.

To resolve this error, you can either exclude the fields/CRFs you don’t want to sync in OS or include only those fields/CRFs you wish to pull from OC into OID mapping csv.

Refer to https://openspecimen.atlassian.net/wiki/spaces/CAT/pages/1919779095/OC+Study+Setup#Exclude-and-Include-CRFs for steps to import the mapping csvRefer to the wiki page for more details.

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

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

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When you are trying to collect any primary specimen or child specimen, and their visit or primary specimen is not collected respectively due to any reason, then this error occurs.

  • If you get the error for primary specimens, check if the visit is collected or not.

  • If this error is for child specimens, ensure that parent is collected or not.

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

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When you sync any specimen from OC and OS doesn’t have the same specimen with the label. Then this error occurs. To resolve this, you will need to add the specimen requirements that will match the label format.

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

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This error is reported when the auto-generated label conflicts with an existing label.

Eg: The subject '74580' has more than one 'Baseline' event in OC. Whereas in OS, there is only one 'Baseline' event configured. 

In this case, there are two ways to resolve this error.

  • Configure the multiple events with unique label formats in each.

  • Fix the data in OC and sync.

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

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When the OC field has any value that is not configured in the OS, this error occurs. E.g., In the ‘Clinical Diagnosis’ dropdown field has PV values like 10 weeks gestation, 13 weeks gestation, etc. These values are not available in OS for the mapped field, then the data for these subjects won’t sync.

To resolve this, add the same values in the OS dropdown as OC.

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.

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This error means the data that you are trying to insert/update cannot be stored in column DE_A_(n) because of its size limitation.

Steps to resolve:

  1. Login to DB and find the table where the column DE_A_(n) is stored. Run below SQL:

Code Block
languagesql
select cast (xml as char) from dyextn_containers where name = '<Form Name>'

  1. In the first few lines of the XML, you will find the table name in the <dbTable> tag, e.g., DE_E_11607.

  2. Now run the below command to increase the size of the column.

Syntax of the code: alter table <table_name> change <column_name where issue is found> mediumtext;

Check the below example code for the reference:

Code Block
languagesql
alter table DE_E_11607 change DE_A_37 mediumtext;

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

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The ‘502 Bad Gateway Error’ occurs when the source server is down or not reachable. Please contact client to get this resolved.

14. Specimen label already exists.

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When duplicate specimen labels are entered in OpenClinica. OpenSpecimen syncs the first specimen and throws error for second duplicate specimen that this Specimen label already exists in the system.

To resolve this issue user needs to update the OpenClinica data entry and remove the specimen label which is entered more than once.