Create drug_df.R

drug_df.R

@@ -0,0 +1,41 @@
+drug_df <- function(rec) {
+  tibble(
+    primary_key = xmlValue(rec["drugbank-id"][[1]]),
+    other_keys = ifelse(length(rec["drugbank-id"]) > 1,
+                        paste(map_chr(c(2:length(rec["drugbank-id"])),
+                                      ~ xmlValue(rec["drugbank-id"][[.]]))
+                              , collapse = ","), NA),
+    type = xmlGetAttr(node = rec, name = "type"),
+    created = as.Date(xmlGetAttr(node = rec, name = "created")),
+    updated = as.Date(xmlGetAttr(node = rec, name = "updated")),
+    name = xmlValue(rec[["name"]]),
+    description = xmlValue(rec[["description"]]),
+    cas_number = xmlValue(rec[["cas-number"]]),
+    unii = xmlValue(rec[["unii"]]),
+    average_mass = xmlValue(rec[["average-mass"]]),
+    monoisotopic_mass = xmlValue(rec[["monoisotopic-mass"]]),
+    state = xmlValue(rec[["state"]]),
+    groups_count = xmlSize(rec[["groups"]]),
+    articles_count = xmlSize(rec[["general-references"]][["articles"]]),
+    books_count = xmlSize(rec[["general-references"]][["textbooks"]]),
+    links_count = xmlSize(rec[["general-references"]][["links"]]),
+    synthesis_reference = xmlValue(rec[["synthesis-reference"]]),
+    indication = xmlValue(rec[["indication"]]),
+    pharmacodynamics = xmlValue(rec[["pharmacodynamics"]]),
+    mechanism_of_action = xmlValue(rec[["mechanism-of-action"]]),
+    metabolism = xmlValue(rec[["metabolism"]]),
+    absorption = xmlValue(rec[["absorption"]]),
+    half_life = xmlValue(rec[["half-life"]]),
+    protein_binding = xmlValue(rec[["protein-binding"]]),
+    route_of_elimination = xmlValue(rec[["route-of-elimination"]]),
+    volume_of_distribution = xmlValue(rec[["volume-of-distribution"]]),
+    clearance = xmlValue(rec[["clearance"]]),
+    international_brands = xmlValue(rec[["international-brands"]]),
+    pdb_entries = xmlSize(rec[["pdb-entries"]]),
+    fda_label = xmlValue(rec[["fda-label"]]),
+    msds = xmlValue(rec[["msds"]]),
+    food_interactions = xmlSize(rec[["food-interactions"]]),
+    drug_interactions_count = xmlSize(rec[["drug-interactions"]]),
+    toxicity = xmlValue(rec[["toxicity"]])
+  )
+}