## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment  = "#>",
  message  = FALSE
)

## -----------------------------------------------------------------------------
library(dbparser)

## -----------------------------------------------------------------------------
drugbank <- parseDrugBank(
  system.file("extdata", "drugbank_record_biotech.xml", package = "dbparser"))

## -----------------------------------------------------------------------------
show_dvobject_metadata(drugbank)

## -----------------------------------------------------------------------------
metadata <- get_source_metadata(drugbank)
fields   <- c("source", "release", "release_date", "source_url",
              "licence_url", "parser")
data.frame(field = fields,
           value = vapply(fields, function(f) as.character(metadata[[f]]), ""),
           row.names = NULL)

## -----------------------------------------------------------------------------
cat(strwrap(metadata$attribution), sep = "\n")

## -----------------------------------------------------------------------------
metadata$files[[1]]

## -----------------------------------------------------------------------------
hgnc_dir <- system.file("extdata", "hgnc", package = "dbparser")
hgnc <- parseHGNC(file.path(hgnc_dir, "hgnc_complete_set.txt"),
                  withdrawn_path = file.path(hgnc_dir, "withdrawn.txt"),
                  release        = "2026-10",
                  retrieved_at   = "2026-10-16")

sapply(hgnc, dim)

## -----------------------------------------------------------------------------
pd1   <- hgnc$gene_name[hgnc$gene_name$name == "PD1", ]
genes <- hgnc$gene[, c("hgnc_id", "symbol", "name")]
names(genes)[3] <- "approved_name"
merge(pd1, genes, by = "hgnc_id")

## -----------------------------------------------------------------------------
hgnc$withdrawn[hgnc$withdrawn$withdrawn_symbol == "CBBM",
               c("hgnc_id", "withdrawn_symbol", "merged_into_symbol")]

## -----------------------------------------------------------------------------
hgnc_metadata <- get_source_metadata(hgnc)
fields        <- c("source", "release", "retrieved_at", "licence",
                   "licence_url")
data.frame(field = fields,
           value = vapply(fields,
                          function(f) as.character(hgnc_metadata[[f]]), ""),
           row.names = NULL)
cat(strwrap(hgnc_metadata$attribution), sep = "\n")
hgnc_metadata$files[[1]]