Fpbase graphql

DESCRIPTION

@@ -28,3 +28,4 @@ Imports:
     tidyr,
     tidyselect,
     utils
+    ghql

R/fpbase_api.R

@@ -0,0 +1,216 @@
+#' @import ghql
+#' @import jsonlite
+
+# global GraphQL client
+client <- ghql::GraphqlClient$new(url = "https://www.fpbase.org/graphql/")
+# global protein ID mapping cache
+protein_id_map_cache <- NULL
+
+#' Get detailed info for a specific protein at FPbase
+#'
+#' @param name_or_slug_or_id A string representing the case-insensitive name,
+#'   slug, or FPbase accession ID of the protein to retrieve.
+#' @return A nested list containing details of the protein.
+#'
+#' @examples
+#' \dontrun{
+#' get_protein_detail("mcherry")
+#' }
+#'
+#' @export
+get_protein_detail <- function(name_or_slug_or_id) {
+  # Get the protein ID from the mapping
+  protein_id <- protein_id_map()[[name_or_slug_or_id]]
+  if (is.null(protein_id)) {
+    stop("Not recognized as a protein name, slug, or id: ", name_or_slug_or_id)
+  }
+  return(get_protein_detail_by_id(protein_id))
+}
+
+#' Get detailed info for a specific dye at FPbase
+#'
+#' @param name_or_slug_or_id A string representing the case-insensitive name
+#'   of the dye to retrieve.
+#' @return A list containing details of the dye.
+#'
+#' @examples
+#' \dontrun{
+#' get_dye_detail("Alexa Fluor 488")
+#' }
+#'
+#' @export
+get_dye_detail <- function(name_or_slug) {
+  qry <- ghql::Query$new()
+  qry$query("dyeDetail", "query getDyeDetail($dyeName: String!)
+    {
+      dye(name:$dyeName) {
+        id
+        name
+        slug
+        exMax
+        emMax
+        extCoeff
+        qy
+        brightness
+        pka
+        lifetime
+        manufacturer
+        url
+        spectra {
+          subtype
+          data
+        }
+      }
+    }
+  ")
+  # Execute the GraphQL query
+  tryCatch(
+    {
+      response <- client$exec(
+        qry$queries$dyeDetail, list(dyeName = name_or_slug)
+      )
+    },
+    error = function(e) {
+      stop("Error in call to FPbase API: ", e$message)
+    }
+  )
+  # Parse the result as JSON
+  d <- jsonlite::fromJSON(response)
+  # if the data has a keys "errors", print the first error message
+  if ("errors" %in% names(d)) {
+    stop("Error in call to FPbase API: ", d$errors[[1]])
+  }
+  return(d$data$dye)
+}
+
+
+#' Get detailed info for a specific protein at FPbase
+#'
+#' @param protein_id A string representing the ID of the protein to retrieve.
+#' @return A list containing details of the protein.
+#'
+#' @examples
+#' \dontrun{
+#' get_protein_detail_by_id("ZERB6")
+#' }
+get_protein_detail_by_id <- function(protein_id) {
+  # Initialize the GraphQL client
+
+  # Define the GraphQL query
+  # Use https://www.fpbase.org/graphql/ to play with queries and paste
+  # your desired query below.  The query here shows the structure of the
+  # data that will be returned.
+  qry <- ghql::Query$new()
+  qry$query("proteinDetail", "query getProteinDetail($protId: String!)
+    {
+      protein(id: $protId) {
+        id
+        name
+        slug
+        aliases
+        seq
+        seqValidated
+        genbank
+        agg
+        switchType
+        primaryReference{
+          doi
+          journal
+          date
+          title
+        }
+        states {
+          slug
+          exMax
+          emMax
+          extCoeff
+          qy
+          brightness
+          pka
+          lifetime
+          maturation
+          spectra {
+            subtype
+            data
+          }
+        }
+      }
+    }
+  ")
+
+  # Execute the GraphQL query
+  tryCatch(
+    {
+      response <- client$exec(
+        qry$queries$proteinDetail, list(protId = protein_id)
+      )
+    },
+    error = function(e) {
+      stop("Error in call to FPbase API: ", e$message)
+    }
+  )
+
+  # Parse the result as JSON
+  d <- jsonlite::fromJSON(response)
+  # if the data has a keys "errors", print the first error message
+  if ("errors" %in% names(d)) {
+    stop("Error in call to FPbase API: ", d$errors[[1]])
+  }
+
+  return(d$data$protein)
+}
+
+#' Memoized function to fetch the protein ID mapping
+#'
+#' Facilitates easy lookup of protein IDs from protein names and slugs.
+#' Names and slugs are case-insensitive.
+#'
+#' @return A list containing the mapping from protein slug/name to ID.
+#'
+#' @export
+protein_id_map <- function() {
+  # If the cache is empty, fetch the protein ID mapping
+  if (is.null(protein_id_map_cache)) {
+    protein_id_map_cache <<- fetch_protein_id_map()
+  }
+  return(protein_id_map_cache)
+}
+
+#' Fetch Protein ID Mapping from FPbase
+#'
+#' Facilitates easy lookup of protein IDs from protein names and slugs. There is
+#' a memoization version of this function, `protein_id_map` which should be used
+#' most of the time.
+#'
+#' @return A list containing the mapping from protein slug/name to ID.
+#'
+#' @examples
+#' \dontrun{
+#' map <- fetch_protein_id_map()
+#' map[["mClover"]]
+#' }
+#'
+fetch_protein_id_map <- function() {
+  qry <- ghql::Query$new()
+  qry$query("proteinList", "{ proteins { id name slug } }")
+
+  # Execute the query and parse the JSON response
+  response <- client$exec(qry$queries$proteinList)
+  all_proteins <- jsonlite::fromJSON(response)$data$proteins
+
+  mapping <- list()
+
+  # Iterate over each row of the proteins data frame
+  for (i in seq_len(nrow(all_proteins))) {
+    # Map the protein name and slug to the protein ID
+    name <- all_proteins[i, "name"]
+    id <- all_proteins[i, "id"]
+    slug <- all_proteins[i, "slug"]
+    mapping[[slug]] <- id
+    mapping[[name]] <- id
+    # also map lower case names to the id
+    mapping[[tolower(name)]] <- id
+  }
+
+  return(mapping)
+}