waldronlab / waldronlab/bedbaser
bedbase object representation
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- Dominant language
- R
- Stars
- 3
- Forks
- 2
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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
No contributing guide indexed for this repository
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- 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