icarda-git/qbms

R package to query Breeding Management System (BMS) database

qbms's Issues

Submit to CRAN package repository

Make sure that the package follows CRAN policies and goes through the CRAN submission checklist.

Check compatibility with BMS v19

Check compatibility against changes in the API of version 19 of BMS.

Replace deprecated germplasm-search

DEPRECATED in BMS API v16: https://app.swaggerhub.com/apis/ibp_bms/BMSAPI/16.0#/germplasm-resource-brapi/searchGermplasmsUsingGET

This call used in the get_germplasm_data function

Minimise package dependencies

• plyr::rbind.fill (hint).
• data.table::rbindlist (hint).
• dplyr::left_join (hint).

Extract entry type (test or check)

See the POST call /crops/{cropName}/programs/{programUUID}/studies/{studyId}/entries
You’ll find the entry type as an ontology property (8255 - ENTRY_TYPE) with the defined value as an ontology term (10170 -Test Entry & 10180 - Check Entry).

Error in list_programs() function in QBMS

I get this error whenever I try to access the list of programs from BMS.

QBMS::list_programs() # data frame
Error in stop(http_error(resp)) : Forbidden (HTTP 403)

Error in brapi_get_call() -- namespace issue?

I'm using QBMS v0.9.1. Following the Breedbase vignette, I get the following error after list_crops():

Error: 'synchronise' is not an exported object from 'namespace:async'

This happens with other QBMS functions too, not just list_crops() -- async::synchronise() is called in the brapi_get_call() function in qbms.R (lines 444 and 450). From what I can tell, synchronise is not a function exported by the CRAN package async, which is why it's throwing an error.

This is my first time trying out QBMS, so entirely possible I'm missing something. Thanks in advance for your help!

QBMS `trial_snapshot()` function

Export/publish the current version of a given trial into Dataverse (zip file includes the CSV dataset + ontology and metadata) in collaboration with the MEL team: Project Harvesting Datasets (Use of API)

Error in list_crops()

I get this error in R whenever I try importing trials from BMS. The error is related to the async package. It appears the author of the async package made recent changes in the async function, triggering the error below.

crops <- QBMS::list_crops()

Error in async::async({ :
unused arguments (local = FALSE, split_pipes = TRUE, compileLevel = 0, debugR = FALSE, debugInternal = FALSE, trace = FALSE)

Migrate from BrAPI v1 to v2

Migrate internal calls from BrAPI v1 to v2 wherever supporting by BMS.

Error when listing programs

set_qbms_config("https://cassavabase.org/brapi/v2", no_auth = TRUE, engine = "breedbase")
list_crops()
[1] "Cassava"
set_crop("Cassava")
list_programs() ## The issue happens here
Error: lexical error: invalid char in json text.
<?xml version="1.0" encoding="U
(right here) ------^

Robust pagination mechanism

Check and test if we have a robust pagination mechanism, follow the best practices.

Upload BLUEs & Summary Stats back to BMS

QBMS function to upload BLUEs & Summary Stats back to BMS for the given Single-Site Analysis using BMS API /breeding-view/saveSsaResultSummaryUsingGET endpoint where:

• mainOutputFilePath: Path and filename of the SSA output file (e.g., BMSOutput.csv)
• SummaryOutputFilePath: Path and filename of the Summary output file (e.g., BMSSummary.csv)

We may need to upload a CSV file using googledrive
Deprecated: write.csv(iris, "iris.csv"); info <- gs_upload("iris.csv")

Get the germplasm pedigree tree in a single call

See the GET call /crops/{cropName}/germplasm/{gid}/tree