AlexsLemonade / AlexsLemonade/refinebio

GEO meta DB availability

Open
#3,247 0 comments 0 reactions 0 assignees View on GitHub
Dominant language
Python
Stars
135
Forks
21
PR merge metrics
No merged PRs in 30d

Description

### Context

In order to process all platform datasets properly we need a GEO meta db source available. As we found out recently one is available at https://gbnci.cancer.gov/geo/GEOmetadb.sqlite.gz

### Problem or idea
Add DB file into Docker container for immediate access to GEO meta data.

Future improvements: come up with a long term solution that'll work in a more sophisticated way by obtaining the DB file in a run-time instead of storing it in the Docker image.

### Solution or next step

- implement quick and dirty solution for now
- determine what the permanent file location would be
- migrate to dynamically downloaded GEO meta DB file

Contributor guide

No contributing guide indexed for this repository

Research direction

No files, tests, or entry points are named. Start by inspecting the repository's Docker build configuration and how platform datasets locate GEO metadata, using the linked GEOmetadb.sqlite.gz source; done means the database is immediately available in the image and the permanent runtime-download path is identified.

Written by the indexing model from the issue text.

Assessment

Tech stack
docker, sqlite
Domain
databases, devops
Issue type
Feature
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
30/100

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