Obtaining access to the production CIP-API¶
Before TPIs are issued production credentials, they need to complete the "Integrator Assurance" process.
The first step is to raise a "TPI Integration Request" via the Genomics England Service Desk here
Info
The whole "Integrator Assurance" process is co-ordinated by the NHSE "Integrator Assurance Board" (IAB), full details can be found on NHS Futures here
Described in this section is just the "technical" steps of the full assurance process.
Delays to onboarding
The full TPI assurance and onboarding process can take considerable time, it is reccommened that you reach out to Genomics England service desk and/or the NHSE Genomics Unit well ahead of your planned go live date
TPI Technical Assurance¶
"Technical" assurance of a TPI is split into two stages, 1) "witness testing" and working through various "edge case" scenarios.
The purpose of the technical assurance is to ensure TPIs are not making requests that may degrade the wider NGIS service and highlight various edge cases a TPI may encounter when querying the API endpoints.
Warning
It is not possible to cover all possible "edge case" scenarios and it is not the purpose of the technical assurance process to determine whether a TPI is functionally working as expected
Below are examples of the types of questions and scenarios you will be asked as part of the technical assurance
Info
Questions and edge cases may vary depending on the integration request.
1. Witness testing
For witness testing we run through the following questions:
- Ask the Integrator to briefly describe an overview of their application and how it integrates with the CIP-API?
- Ask the integrator to tell you the CIP-API URLs for Prod, UAT and SIT environment, and explain the difference in the data they contain?
- Ask the integrator to demonstrate how their application gets a JWT from AD and use that token to make a request to the CIP-API, confirm the AD tenant that is being used"
- Ask the integrator to demonstrate how their application, if relevant, accesses 100K cases?
- Ask the integrator to demonstrate how their application, if relevant, accesses GMS cases?
- Ask the integrator to demonstrate the endpoint they query to get a list of cases in their application? And any additional parameters they use. Ensure they are using pagination
- Ask the integrator to demonstrate which endpoint their application uses to query specific case details? and any additional parameters they use
- Ask the integrator to explain what an Interpreted Genome is?
- Ask the integrator to explain, if relevant, how their application integrates with PID?
- Ask the integrator to where they go for CIP-API documentation?
- Ask the integrator to explain what data is in a referral?
- Ask the integrator to explain how they get referral information?
- Ask the integrator if they use GeLReportModels in their application?
- Ask the integrator to explain how their application uses the CIP-API case status and / or workflow status?
- Ask the integrator how often their application queries the CIP-API?
- Ask the integrator if their application queries any additional endpoints in the CIP-API not covered above?
- Ask the integrator how they control user access to their application?
- Ask the integrator if their application records audit logs?
- Ask the integrator what measures are in place to ensure the client secret is kept secret?
- Ask the integrator whether they are aware of the health check endpoint in CIP-API
2. Edge cases
All TPIs need to go through some specific "edge case" scenarios
A meeting will be arranged with the TPI developers to review these scenarios and ensure where appropriate the integrating application is handling them appropriately.
| Scenario Id | Scenario Summary |
|---|---|
| STD_INT_TC-01 | Rare Disease for a Singleton |
| STD_INT_TC-02 | Rare Disease for a Duo (Proband and a family member) |
| STD_INT_TC-03 | Rare Disease for a Trio (Proband and 2 family members) |
| STD_INT_TC-04 | Rare Disease for a Quad (Proband and 3 family members) |
| STD_INT_TC-05 | Patient has no NHS number |
| STD_INT_TC-06 | Case has failed the SMS check |
| STD_INT_TC-07 | Family member agrees to WGS but family member changes their mind after the test request is submitted, and before the results reach the CIP-API and interpretation portal |
| STD_INT_TC-08 | Family member agrees to WGS but family member changes their mind after the test request is submitted, but after reaching interpretation portal |
| STD_INT_TC-09 | Where a RD proband and/or relative goes on to have a cancer WGS test (add additional test and new samples) |
| STD_INT_TC-10 | Where a RD proband forms part of a trio for a different clinical indication |
| STD_INT_TC-11 | A repeat test request is put on NGIS for the same Clinical Indication as has already be done (i.e. not picked-up immediately) |
| STD_INT_TC-12 | Patient Merge Test for RD Trio Primary patient record - record that is to remain. Secondary patient record - record to be removed. Merge process to be completed as per GEL SOP Primary patient record proband in referral 1 Secondary patient record proband in referral 2 Merge to happen after both referrals have been submitted, test orders have been sent but before either referral is in the IP Primary patient record proband in referral 1 Secondary patient record family member in referral 2 Merge to happen after both referrals have been submitted, test orders have been sent but before either referral is in the IP Primary patient record family member in referral 1 Secondary patient record proband in referral 2 Merge to happen after both referrals have been submitted, test orders have been sent but before either referral is in the IP Primary patient record family member in referral 1 Secondary patient record family member in referral 2 Merge to happen after both referrals have been submitted, test orders have been sent but before either referral is in the IP |
| STD_INT_TC-13 | Test is cancelled |
| STD_INT_TC-14 | Cases with Short Tandem Repeats for STR tiering |
| STD_INT_TC-15 | Cases with Small Variants (SNVs/Indels) for small variant tiering testing |
| STD_INT_TC-16 | Cases with Copy Number Variants for testing of CNV tiering |
| STD_INT_TC-17 | Cases with Small Variants (SNVs/Indels) for small variant tiering testing |
| STD_INT_TC-18 | Cases with Copy Number Variants for testing of CNV tiering |
| STD_INT_TC-19 | Cases with Short Tandem Repeats for STR tiering |
| STD_INT_TC-20 | Cases with Copy Number Variants for testing of CNV tiering |
| STD_INT_TC-21 | Cases with Copy Number Variants for testing of CNV tiering |
| STD_INT_TC-22 | Cases with Copy Number Variants for testing of CNV tiering |
| STD_INT_TC-23 | Cases with Small Variants (SNVs/Indels) for small variant tiering testing |
| STD_INT_TC-24 | Cases with Small Variants (SNVs/Indels) for small variant tiering testing |
| STD_INT_TC-25 | Cases with Copy Number Variants for testing of CNV tiering |
| STD_INT_TC-26 | Cases with Small Variants (SNVs/Indels) for small variant tiering testing |
| STD_INT_TC-27 | IBD sharing estimation and Mendelian inconsistencies. Family (Proband & Father) with unusual chromosomal phenomena (uniparental disomy of chromosome 4) |
| STD_INT_TC-28 | Coverage-based sex checks. RD referral to be created with Proband Reported KaryotypicSex (Clinical Questions) set as "UNKNOWN" and Genomic sex reported as "FEMALE" |
| STD_INT_TC-29 | Family Selection. RD referral to be created with Proband Fullsibling reported sex as "FEMALE" and Genomic sex reported as "MALE" |
| STD_INT_TC-30 | Sample data quality testing cases (Test data with poor quality CNV calls) |
| STD_INT_TC-31 | Adult with Solid Tumour |
| STD_INT_TC-32 | Adult with Haematological cancer |
| STD_INT_TC-33 | Child (pedi) with Solid Tumour |
| STD_INT_TC-34 | Child (pedi) with Haematological cancer |
Vanilla Test Cases¶
As well as the "edge cases" described above the UAT environment contains a number of "vanilla" test cases that can be loaded into TPI applications for their testing purposes.
Other APIs in NGIS¶
The CIP-API represents one of the applications within National Genomics Informatics Service (NGIS) that Genomic Laboratory Hubs (GLHs) within the Genomic Medicine Service (GMS) may wish to integrate with.
Other NGIS APIs include:
Warning
OpenCGA and CVA APIs do not yet have assurance processes in place therefore access will be limited on a case by case basis
Please contact Genomics England Service Desk for further info