clinical-genomics / cgbeacon2 Goto Github PK

Both in the database, in the query and in the returned results

So that pymongo doesn't have to be frozen

From Ensembl, likely

Write Dockerfile for the app

https://github.com/ga4gh-beacon/specification/blob/master/beacon.md#response-1

Keep them minimal in order to avoid a lot of messy lines. Not high prio, but easy!

with tests

Check and fix it if this is the case

To send post requests. It's also a way to test POST requests.

Add "requests"

with tests

Implement a token-based authentication so that submitting users or softwares that are submitting variants via the API are authenticated. Same for when the variants are removed via the API.

(): -> whatevs

So it looks like that you can interact with the button:

• Button to switch from SNVs to SVs
• Button for range queries

without filtering by panel

Right now it just adds 0 variants

This is a bit complicated and I have to think about it. Patterns matching anyway.

https://github.com/ga4gh-beacon/specification-v2-default-schemas/blob/clauw87-patch-1/beacon_v2_default_schemas_v2.0.pdf

Now only datasets with list of samples are saved so only number of samples (sampleCount) is available.
Add:

• callCount
• variantCount

They're optional fields so this is not high priority for now

• bad signature token
• Empty claims
• Non valid claims
• Couldn't find public key

This is important and has to be in place before deploying the software

Because variants positions were 0 based when I wrote the readme and the variant in the test query is not found now

With query examples and data types description

To be used in #83

• public, registered and controlled.
• Beacon class will have a private method to return the list of all its datasets, by authentication level

Use the info key/value for the access type and key "variantCount" for the variant count

Be less strict about content from incoming requests. Accept any request even if content is not specified in headers. If it's not JSON then return error. As the things are now requests are not accepted if content is not specified in their headers

https://github.com/ga4gh-beacon/specification/blob/master/beacon.md#info-endpoint

And fix it. Same for the update date

An API that accepts requests (from Scout). These requests contain:

• Dataset ID (scout customers)
• Path to VCF file
• Genome build
• Sample(s) to include variants from (must be in the VCF file)
• List of gene symbols (or hgnc ids?) to convert to coordinates (to a create a panel to filter VCF with)

https://github.com/ga4gh-beacon/specification/blob/master/beacon.md#query-endpoint

Using the info provided by the token's payload

use the command:
pip installl -e . instead, to make sure that all resources are found.

To be fixed more elegantly later.

Documentation about breakends in VCF files: https://samtools.github.io/hts-specs/VCFv4.2.pdf

Reference: https://beacon-project.io/roadmap/handover.html

Important to return links to downloadable resources

For instance when request variant build is GRCh37 but users want a dataset in build 38. This error is documented here: https://github.com/ga4gh-beacon/specification/blob/master/beacon.md#query-endpoint

Introduced probably with the latest update of Click. The error occurs only when testing using python=3.7 not 3.8.

Error description:

cgbeacon2/cli/add.py:85: in <module>
    type=click.Choice(["public", "registered", "controlled"], case_sensitive=False),
E   TypeError: __init__() got an unexpected keyword argument 'case_sensitive'

Using a POST request. To trigger variants removal from the Scout interface.