Case statuses
As a referral completes processing through the bioinformatics pipeline, is registered in the CIP-API, sent to the DSS and interpreted by the GLH, the CIP-API referral "status" is updated.
As well as the overall status (shown in blue in the image here there is an independent "workflow status" (shown in orange) which tracks the status of the referral within the DSS.
CIP-API and Workflow statuses¶
CIP-API Statuses¶
See the following table to get a brief description of each different CIP-API status.
| GMS CIP-API Status | Description |
|---|---|
| waiting_payload | Interpretation Pipeline has completed |
| interpretation_generated | Interpretation Request has been created, ready to send to DSS |
| snp_check_pending | (Rare Disease) The referral test's samples do not have a complete set of all sample matching service results |
| snp_check_pass | (Rare Disease) The referral test's samples have a complete set of all samples passing the sample matching service comparison |
| snp_check_fail | (Rare Disease) At least one sample from a referral test has failed the sample matching service comparison |
| dispatched | Interpretation Request has been sent to DSS |
| sent_to_gmcs | The referral has been been successfully processed by the DSS and it's available for the GLHs to review in their system |
| report_generated | A report/summary of findings has been generated for this referral by the GLH (more than one report can be generated) |
| report_sent | The latest report/summary of findings' outcomes exit questionnaire has been submitted by the user |
| blocked | Interpretation of the referral has been blocked |
A look into the 100k CIP-API statuses
| 100k CIP-API Status | Description |
|---|---|
| waiting_payload | Interpretation Pipeline has completed |
| interpretation_generated | Interpretation Request has been created, ready to send to DSS |
| files_copied | VCF and tiering files have been sent to the DSS |
| dispatched | Interpretation Request has been sent to DSS |
| transfer_ready | DSS has completed their analysis of the case |
| transfer_complete | DSS has transferred their interpreted genome to the API |
| gel_qc_failed | The case has failed GeL QC checks and will be sent back to the DSS |
| rejected_wrong_format | Interpreted Genome has failed API validation |
| gel_qc_passed | The case has passed GeL QC checks |
| sent_to_gmcs | The case has been sent to the GMCs for them to generate the report in the DSS portal in Inuvika/web interface |
| report_generated | A report/summary of findings has been generated for this case by the GMC. More than one report can be generated |
| report_sent | The latest report/summary of findings' outcomes exit questionnaire has been submitted by the user |
| blocked | interpretation of the case has been blocked |
Workflow Statuses¶
As referrals in our system also get dispatched and analysed in the Decision Support Systems (DSS), there is a "workflow status" that defines each step in 'the DSS workflow'.
These statuses also get processed and are visible in the Intepretation Portal.
Please look at the following table for more information on these.
| DSS Workflow Status | Description | Corresponding status in Congenica |
|---|---|---|
| Pending Review | Processing complete of the referral, data can be viewed in the DSS | Ready for review |
| In Progress | Review of the referral in the DSS is underway: interpretation and classification of candidate variants | Primary review |
| Awaiting Approval | The sample is awaiting secondary approval and final review in the DSS | Secondary review and final review pending |
| Submitted | Analysis authorised by the GLH (VILs have been generated) | Review complete and Report available |
| Error | An issue on the processing of the referral has been raised by the DSS | Error |