Configuration and Maintenance

Configuration

The TIES node can be configured using the TIES Control Panel that is bundled with every TIES installation. The control panel is found in the <tiesinstallation>\configuration folder. There are two tabs in the control panel: The Configuration tab and the Utilities Tab. In the Configuration tab, you can see a list of TIES modules that are available for configuration on the current server. If you do not see a module, make sure it is in fact installed on this server and you are running the control panel from within the correct installation folder. The possible configuration modules are:

Maintenance

From the perspective of maintenance, TIES has two components: data processing and web services. The data processing component consists of the database and the processing pipelines. The web services component consists of the tomcat web servers.

Monitor Processing Status

You can monitor the status of the processing from the TIES Control Panel’s Database Configuration screen’s ‘Processing Status’ tab. Identified Documents Status These status types are set on the ties_private.ident_document table’s application_status column.

• NOPATIENT – No patient was found attached to this document
• DEIDENTIFYING – Pending de-identification by DeidPipeController
• PURGE – Manually set by user to indicate this document needs to be deleted. Run Database Cleanup Utility to do actual deletion of PURGE records.
• DELETING – Data Cleanup Utility is in the process of deleting this document.
• IDLING – All processing finished for this document.
• NOSECTIONS – No sections were found for this document.
• DEIDERR – De-identification Error
• SAVEERROR – Save Error. Occurs when any pipeline has a problem saving changes to database.
• SYNTHERROR – Synthesis error.
• SYNTHESIZING – Pending concatenation of document sections into document text by HL7PipeController or DelimitedFileImporter
• IMPORTERROR – Import Error
• OMITTING – Skipping this document from further processing due to missing required data fields like observation date or patient information.
• EMPTYREPORT – No text found or no usable sections for this documents

De-Identified Documents Status These status types are set on the ties_private.ident_document table’s application_status column.

• NOPATIENT – No patient was found attached to this document
• CODING -Pending coding by TIESPipeController
• PURGE – Manually set by user to indicate this document needs to be deleted. Run Database Cleanup Utility to do actual deletion of PURGE records.
• DELETING – Data Cleanup Utility is in the process of deleting this document.
• DEINDEXING – Data Cleanup Utility is in the process of de-indexing this document.
• INDEXING – Pending indexing by the IndexPipeController
• IDLING – All processing finished for this document.
• CODINGERR – Coding Error
• NOSECTIONS – No sections were found for this document.
• INDEXNGERR – Indexing Error
• SAVEERROR – Save Error. Occurs when any pipeline has a problem saving changes to database.
• EMPTYREPORT – No text found or no usable sections for this documents
• <DOCTYPE>_CODING_INPROGRESS – Is currently being coded by the TiesPipeController.
• <DOCTYPE>_INDEXING_INPROGRESS – Is currently being indexed by the IndexPipeController.

For installations using the JavaMessaging Service Queue and JMS processing pipelines:

• <DOCTYPE>_QUEUEING_ERR – Error when attempting to add this document to the queue.
• <DOCTYPE>_CODING_QUEUE – In the CODING queue awaiting processing.
• <DOCTYPE>_INDEXING_QUEUE – In the INDEXING queue awaiting processing.

Reprocessing Records

Documents are processed in several stages. each stage is run by a different processing pipeline as show below. The HL7ImportPipeController in the figure below, can be replaced by the DelimitedFileImporter, or your own custom import service.  See Loading You Data for more information. You can force the reprocessing of documents through any stage, by setting the appropriate value in the APPLICATION_STATUS column for either the ties_private.IDENT_DOCUMENT or ties_public.DOCUMENT tables. After re-processing is triggered at a particular stage, the record has to go through all downstream stages before any changes are reflected in the search results. Select a stage below for instructions:

Remove Tags

Tags information is stored in the document_attr_value table. The full_name is set to ties.model.tag and the short_value column contains the tag name. You can remove specific tags from TIES as follows:

1. Turn off the DeidPipeController.
2. Set the application status of the ident_document rows which will be updated to DEIDENTIFYING as follows:

   UPDATE ties_private.ident_document 
   SET application_status = 'DEIDENTIFYING' 
   WHERE id IN (
          SELECT * FROM ties_private.document_attr_value 
          WHERE full_name = 'ties.model.tag' AND short_value = ‘<tagnametodelete>’
   );

3. Delete the document_attr_value rows

   DELETE FROM ties_private.document_attr_value 
   WHERE full_name = 'ties.model.tag' AND short_value = ‘<tagnametodelete>’

Remove Individual Records

You can remove specific records from TIES as follows:

1. Identify the rows in the ties_private.ident_document table for the records to be removed.
2. Set the APPLICATION_STATUS to ‘PURGE’ for all the rows identified in (1).
3. Run the Data Cleanup Utility.

Remove All Data

If you need to clear out all data from the database as follows:

1. Connect to the database server and run the following SQL script. This will delete and re-create empty database schemas:

   DELETE ties_private;
   DELETE ties_public;
   CREATE SCHEMA ties_private;
   CREATE SCHEMA ties_public;
   

2. Run the Database Updater Utility. This will recreate empty TIES tables in the ties_private and ties_public schemas.
3. Delete all files in /indices/PRODINDEX. This will delete the search index.

Utilities