## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
    collapse = TRUE,
    cache = TRUE
)

## ----install, eval = FALSE----------------------------------------------------
# if (!require("BiocManager", quietly = TRUE))
#     install.packages("BiocManager")
# BiocManager::install("Bioconductor/BiocAzul")

## ----load-packages, message=FALSE, eval=TRUE, cache=FALSE---------------------
library(BiocAzul)

## ----azul-hca-init------------------------------------------------------------
hca <- Azul()
hca

## ----azul-anvil---------------------------------------------------------------
anvil <- Azul(provider = "anvil")
anvil

## ----list-catalogs------------------------------------------------------------
catalogs <- listCatalogs(hca)
catalogs
latest <- head(catalogs, n = 1)
latest

## ----project-table------------------------------------------------------------
projects <- projectTable(hca, catalog = latest)
head(projects)

## ----available-facets---------------------------------------------------------
facets <- availableFacets(hca, catalog = latest)
head(facets)

## ----facet-table--------------------------------------------------------------
facetTable(hca, facet = "genusSpecies", catalog = latest)

## ----make-filter--------------------------------------------------------------
filter <- makeFilter(
    ~  specimenOrgan == "brain" &
        genusSpecies == "Mus musculus" &
        fileFormat == "h5"
)
filter

## ----filter_sidebar, echo=FALSE, out.width="100%"-----------------------------
img_path <-
    if (knitr::opts_knit$get("child")) "man/figures/" else "../man/figures/"
knitr::include_graphics(paste0(img_path, "filter_sidebar.png"))

## ----import-to-terra, eval=FALSE----------------------------------------------
# importToTerra(
#     hca,
#     namespace = "your-terra-namespace",
#     name = "your-terra-workspace",
#     catalog = "dcp58",
#     filters = filter
# )

## ----terra_import, echo=FALSE, out.width="100%"-------------------------------
knitr::include_graphics(paste0(img_path, "request_link.png"))

## ----create_workspace, echo=FALSE, out.width="100%"---------------------------
knitr::include_graphics(paste0(img_path, "create_workspace.png"))

## ----session-info-------------------------------------------------------------
sessionInfo()