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katrinleinweber avatar katrinleinweber commented on June 21, 2024

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.

katrinleinweber avatar katrinleinweber commented on June 21, 2024

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.

from bacdiver.

katrinleinweber avatar katrinleinweber commented on June 21, 2024

Or dive_in...:

  • ...to_taxon(name = ...)
  • ...to_culture(collection_number = ...)
  • ...to_sequence(accession = ...)
  • ...to_dataset(id = ...)
    ?

from bacdiver.

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