galaxyproject / galaxyproject/galaxy

Require an "active" database/genome index selection on tool forms

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Python
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Description

Many tools have the genome select list propagated where the first in the list is automatically selected by default.

It would avoid a common usage error (user doesn't change the genome) to have the first "entry" in the list state "Select database" or something else similar. Then trap the required missing database selection at job submission (model after existing required field warnings).

Even if we just modified mapping tools, the majority of reported usage issues due to genome form-entry mistakes would be avoided. Examples: BWA/BWA-MEM, Bowtie2, HISAT2

_Update_: recent examples
- 2/13/18 https://biostar.usegalaxy.org/p/26707/
- 2/14/18 https://biostar.usegalaxy.org/p/26732

Contributor guide

Open the contributing guide

Research direction

Start by tracing the genome select list in the tool forms and the job submission validation, using the BWA/BWA-MEM, Bowtie2, and HISAT2 mapping tools as examples. Compare their behavior with existing required field warnings. Done means no genome is selected by default, the list prompts for a database selection, and submission reports the missing required selection.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
backend, frontend
Issue type
Feature
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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