Comments (3)
I need to simplify that scheme to a flowchart with only high-level function calls & server responses:
graph TD
FC(function calls)
SR[server response]
cul(BD_retrieve_culture<br>collectionno='chr') --> JU
seq(BD_retrieve_sequence<br>accession='chr') --> JU
JU[.json url] -- JSON2list --> rb_URL
tax(BD_retrieve_by_taxon<br>name='chr')--> JR
JR[.json results] --> rb_URL
rb_adv(BD_retrieve_by_search<br>query_URL='chr') --> CSV
CSV[.csv] -- lines2list --> rb_ID
rb_ID(BD_retrieve_by_id<br>ID='chr')--> rb_URL
rb_URL(BD_retrieve_by_URL<br>URL='chr') --> DSL
DSL[list with 1 or more dataset*s]
classDef public fill:white
class cul,seq,tax,rb_adv public
classDef WS stroke:#A30000
class cul,seq,tax,I WS
classDef AdvSearch stroke:#5290b2
class rb_adv AdvSearch
classDef semi_public fill:lightgrey
class rb_ID,rb_URL semi_public
from bacdiver.
An alternative, simpler idea might be to provide the above-mentioned "front" functions in parallel to (or on top of) the current retrieve_data(searchTerm = "…" , searchType = "…")
:
graph TD
cul(bd_culture<br>collectionno='chr') --Type='culturecollectionno'--> rd
seq(bd_sequence<br>accession='chr') --Type='sequence'--> rd
tax(bd_taxon<br>name='chr')--Type='taxon'--> rd
bd_id --Type='bacdive_id'--> rd
rd(retrieve_data<br>Term='chr', Type='chr') --> DSL
DSL[list with 1 or more dataset*s]
rb_adv(bd_download_adv<br>searchURL='chr')--unchanged, just renamed-->DSL
This might lend itself to later converting this into object-oriented code.
- consider deprecation warning, see http://r-pkgs.had.co.nz/release.html#compatibility & https://github.com/search?q=org%3Atidyverse+deprecated & https://ropensci.org/technotes/2017/01/05/package-evolution/#functions-changing-function-names
- use
@rdname
to mass-document a function family (seepurrr::map
ordplyr::lead-lag
) - [-]
write ADRNo, already explained in the changelog
from bacdiver.
Or dive_in...
:
...to_taxon(name = ...)
...to_culture(collection_number = ...)
...to_sequence(accession = ...)
...to_dataset(id = ...)
?
from bacdiver.
Related Issues (20)
- Converting retrieve_data() results to a data frame (tibble) HOT 7
- Deploy docu with Travis
- Find smaller examples for docu & test them
- clarify development model: GitHub Flow
- Blank search results and not error when password changed but not in Renviron file HOT 3
- bd_retrieve_by_search output HOT 2
- How to download the full database HOT 3
- R devtools installation hangs on testing for >1 hour HOT 4
- Illegal character error for valid taxa HOT 1
- Failed to install the package HOT 2
- get a null result HOT 1
- installation HOT 1
- Error: lexical error: invalid character inside string HOT 7
- retrieve_data: argument is of length zero HOT 1
- Stop or warn if a dataset doesn't exist?
- Convenience functions for downloading entire domain, phylum, class, order & family
- Replace httr with crul?
- Reduce dependencies
- Simplify prepare_Renviron() with usethis::edit_r_environ()
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