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elixir-cloud-aai/proTES
fix: Handle None Values Correctly in List Task Endpoint Query Filter

When building the query filter with potential None values for name_prefix and user_id, the filter should be adjusted accordingly to avoid incorrect queries. Expected Behavior: - If name_prefix is None, ...
  • Ayush5120
  • Opened 
    on Jun 12, 2024
  • #177

elixir-cloud-aai/proTES
fix: add ignore_error executor field

Describe the bug TES v1.1 defines an ignore_error field as a property of an executor (defined here). Currently, the TesExecutor model does not have this attribute. As a result, the following error occurs ...
  • athith-g
  • 2
  • Opened 
    on Jun 7, 2024
  • #176

elixir-cloud-aai/proTES
fix: Getting list of tasks not working without name prefix

Describe the bug Making a GET request to the /tasks endpoint proTES with an empty body always returns an empty list of tasks, even when a task has been created. This is because of this line in task_runs.py. ...
  • athith-g
  • Opened 
    on May 20, 2024
  • #175

elixir-cloud-aai/proTES
build: upgrade gunicorn

See security vulnerability here: https://github.com/advisories/GHSA-w3h3-4rj7-4ph4
  • uniqueg
  • Opened 
    on May 18, 2024
  • #174

elixir-cloud-aai/proTES
fix: infinite loop with jsonschema>3.2.0

Describe the bug Starting proTES fails with jsonschema versions 3.2.0. This is due to the tesNextTes schema in pro_tes/api/additional_logs.yaml referencing itself, causing an infinite loop during validation ...
  • athith-g
  • 1
  • Opened 
    on May 17, 2024
  • #173

elixir-cloud-aai/proTES
Update Mongo image version

Running docker compose up on a machine with an Apple Silicon chip produces the following error: no matching manifest for linux/arm64/v8 in the manifest list entries This is due to the version of the Mongo ...
  • athith-g
  • Opened 
    on May 10, 2024
  • #171

elixir-cloud-aai/proTES
Middleware for Crypt4GH Support

Problem Crypt4GH is a file format developed by GA4GH that allows sensitive genomic data to remain encrypted at rest and in transit. Currently, TES implementations do not support the use of crypt4GH files ...
  • athith-g
  • 1
  • Opened 
    on May 9, 2024
  • #170

elixir-cloud-aai/proTES
fix: unit tests

Describe the bug Unit test aren t working using pytest ./tests. Idk if I am missing something but there are someother issues as well. for example, in #160 in pro_tes/exceptions.py InputUriError and IPDistanceCalculationError ...
  • JaeAeich
  • 3
  • Opened 
    on Feb 7, 2024
  • #168

elixir-cloud-aai/proTES
build: exclude Connexion >3

Problem Recently, v3 of Connexion has been released: https://connexion.readthedocs.io/en/latest/quickstart.html Unfortunately, Connexion v3 breaks the deployment of proTES. Solution Until Connexion ...
  • uniqueg
  • Opened 
    on Nov 13, 2023
  • #166

elixir-cloud-aai/proTES
Next page cursor loop

Describe the bug The API response seems to give next page cursor even if the number of tasks have finished. Ideally it should stop giving next page cursors if there are no further task to be shown.
flag: good 1st issue
priority: high
type: bug
workload: minutes
  • JaeAeich
  • Opened 
    on Nov 3, 2023
  • #165
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