waldronlab / waldronlab/bedbaser

bedbase object representation

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Dominant language
R
Stars
3
Forks
2
PR merge metrics
No merged PRs in 30d

Description

I think the representation you get when you print the bedbase client to screen is confusing:

api <- BEDbase()
api
service: bedbase
tags(); use bedbase$<tab completion>:
# A tibble: 32 x 3
   tag   operation                                                       summary
   <chr> <chr>                                                           <chr>  
 1 base  get_bedbase_db_stats_v1_stats_get                               Get su~
 2 base  service_info_v1_service_info_get                                GA4GH ~
 3 bed   bed_to_bed_search_v1_bed_search_bed_post                        Search~
 4 bed   get_bed_classification_v1_bed__bed_id__metadata_classification~ Get cl~
 5 bed   get_bed_embedding_v1_bed__bed_id__embedding_get                 Get em~
 6 bed   get_bed_files_v1_bed__bed_id__metadata_files_get                Get me~
 7 bed   get_bed_metadata_v1_bed__bed_id__metadata_get                   Get me~
 8 bed   get_bed_pephub_v1_bed__bed_id__metadata_raw_get                 Get ra~
 9 bed   get_bed_plots_v1_bed__bed_id__metadata_plots_get                Get pl~
10 bed   get_bed_stats_v1_bed__bed_id__metadata_stats_get                Get st~
# i 22 more rows
# i Use `print(n = ...)` to see more rows
tag values:
  base, bed, bedset, home, objects, search, NA
schemas():
  AccessMethod, AccessURL, BedClassification, BedEmbeddingResult,
  BedFiles
  # ... with 34 more elements

First, it says "use bedbase$ [tab completion]" -- but this doesn't work. It would be great if we could use tab completion (related to #10)

Then, I don't understand what is meant by "service" and "tags()"

The summaries of the operations in the table not actually visible.

Basically, I would suggest we think about the string representation and make it something more friendly to the user. Something like:

  • what API are we connected to?
  • how many BED files are available?
  • where can I find more information?
  • what functions can I use? (maybe?)

Contributor guide

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by reproducing the printed bedbase client in R and reviewing the current output, including the broken “bedbase$” tab-completion guidance, service and tags() text, and truncated operation summaries. Done should mean the representation clearly explains the connected API, available information, further help, and usable functions.

Written by the indexing model from the issue text.

Assessment

Tech stack
r
Domain
api, developer-experience
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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