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feat: Zenodo remote provider for transparent storage on and retrieval from Zenodo #1455

merged 2 commits into from Mar 4, 2022


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Follow-up on #125

tpall and others added 2 commits March 3, 2022 15:49
… from Zenodo (#125)

* added zenodo remote provider

* added test

* updated formatting

* added sandbox, access_token is required, create new deposition when deposition id is not provided

* updated test Snakefile

* added initial zenodo remote documentation

* added zenodo branches for ci

* fixed code formatting

* added zenodo sandbox pat to workflow

* added zenodo remote test

* fixed formatting

* deleted comment

* skip tibanna test for now

* deleted branch

* added zenodo file exception when hits api limit

* moves file size assertion to remoteobject

* updated test

* added test file

* run also too large upload test

* updated docs

* Delete superfluous file.

* removed error handling around requests and re as unnecessary

* updated error message

* moved download code to remoteobject

* use download url

* fixed formatting

* upload large files

* fixed formatting

* removed makedir

* updated test, download to subdir

* moved exception handling to request wrapper

* removed zen branch from ci

* fixed deposition id handling

* fixed stats is not defined

* fix download

* fixed test download path, updated docs

* Only run test if token is available.

* fmt

* envvars

* fix skip criterion

* fix error handling

* windows secret

Co-authored-by: Johannes Köster <>
Co-authored-by: Johannes Köster <>
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sonarcloud bot commented Mar 4, 2022

Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 0 Code Smells

No Coverage information No Coverage information
0.0% 0.0% Duplication

@johanneskoester johanneskoester merged commit 4586ef7 into main Mar 4, 2022
@johanneskoester johanneskoester deleted the zenodo branch March 4, 2022 09:03
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2 participants