Merge pull request #48 from bhklab/development

Development

.gitignore

@@ -18,3 +18,4 @@ Treatment-Annotation*.Rmd
 
 ./*.csv
 CCLE_treatmentMetadata.csv
+AnnotationGx.code-workspace

AnnotationGx.code-workspace

@@ -2,6 +2,9 @@
     "folders": [
         {
             "path": "."
+        },
+        {
+            "path": "../CoreGx"
         }
     ],
     "settings": {

R/cellosaurus.R

@@ -107,9 +107,9 @@ mapCell2Accession <- function(
 
   if (query_only) return(lapply(requests, function(req) req$url))
 
-  # perform the requests
+  # Submit requests using parallel httr2 since cellosaurus doesnt throttle
   .info(funContext, "Performing Cellosaurus queries")
-  responses <- .perform_request_parallel(requests)
+  responses <- .perform_request_parallel(requests, progress = "Querying Cellosaurus...")
   names(responses) <- as.character(ids) # in case its an numeric ID  like cosmic ids
   if (raw) return(responses)
 

R/cellosaurus_annotations.R

@@ -4,7 +4,9 @@
 #'
 #' @param accessions The Cellosaurus accession to annotate.
 #' @param to A character vector specifying the types of annotations to retrieve. Possible values include "id", "ac", "hi", "sy", "ca", "sx", "ag", "di", "derived-from-site", "misspelling", and "dt".
-#'
+#' @param query_only A logical value indicating whether to only return the query string.
+#' @param raw A logical value indicating whether to return the raw response.
+#' 
 #' @return A data frame containing the annotations for the cell line.
 #'
 #' @examples
@@ -14,10 +16,13 @@
 #' @export
 annotateCellAccession <- function(
     accessions,
-    to = c("id", "ac", "hi", "sy", "ca", "sx", "ag", "di", "derived-from-site", "misspelling", "dt")
+    to = c("id", "ac", "hi", "sy", "ca", "sx", "ag", "di", "derived-from-site", "misspelling", "dt"),
+    query_only = FALSE, raw = FALSE
     )
 {
+    funContext <- .funContext("annotateCellAccession")
 
+    .info(funContext, "Building Cellosaurus requests...")
     requests <- parallel::mclapply(accessions, function(accession) {
         .build_cellosaurus_request(
             query = accession,
@@ -29,19 +34,26 @@ annotateCellAccession <- function(
             query_only = FALSE
         )
     })
-
-    responses <- .perform_request_parallel(requests)
+
+    .info(funContext, "Performing Requests...")
+    responses <- .perform_request_parallel(requests, progress = "Querying Cellosaurus...")
     names(responses) <- accessions
-    responses_dt <- parallel::mclapply(accessions,function(name) {
+    if(raw) return(responses)
+
+    .info(funContext, "Parsing Responses...")
+    responses_dt <- parallel::mclapply(accessions, function(name) {
         resp <- responses[[name]]
         .parse_cellosaurus_lines(resp) |> 
             unlist(recursive = FALSE) |> 
             .processEntry() |>
             .formatSynonyms()
-    }
-    ) |> data.table::rbindlist(fill = TRUE)
-
-    responses_dt
+        }
+    )
+    names(responses_dt) <- accessions
 
+
+    responses_dt <- data.table::rbindlist(responses_dt, fill = TRUE)
+
+    return(responses_dt)
 }
 

R/pubchem_rest.R

@@ -21,10 +21,10 @@
 #' @export
 getPubchemCompound <- function(
     ids, from = "cid", to = "property", properties = c("Title", "InChIKey"),
-    raw = FALSE, query_only = FALSE, output = "JSON", ...) {
-  funContext <- .funContext("getPubchemCompound")
-
+    raw = FALSE, query_only = FALSE, output = "JSON", ...
+) {
 
+  funContext <- .funContext("getPubchemCompound")
   to_ <- if (to == "property") {
     checkmate::assert_atomic(properties, all.missing = FALSE)
     checkmate::assert_character(properties)
@@ -33,33 +33,37 @@ getPubchemCompound <- function(
     to
   }
 
+  .info(funContext, "Building PubChem REST queries...")
   requests <- lapply(ids, function(x) {
     .build_pubchem_rest_query(
       id = x, domain = "compound", namespace = from, operation = to_, output = output,
       raw = raw, query_only = query_only, ...
     )
   })
-  if (query_only) {
-    return(requests)
-  }
+  if (query_only) return(requests)
 
   tryCatch({
-    resps_raw <- httr2::req_perform_sequential(requests, on_error = "continue")
+    .info(funContext, "Retrieving compound information...")
+    resps_raw <- httr2::req_perform_sequential(
+      requests, 
+      on_error = "continue", 
+      progress = "Querying PubCHEM REST API...."
+    )
+    names(resps_raw) <- ids
   }, error = function(e) {
     .err(funContext, " An error occurred while retrieving the compound information:\n", e)
   })
 
   .debug(funContext, " Number of responses: ", length(resps_raw))
-  names(resps_raw) <- ids
-  if (raw) {
-    return(resps_raw)
-  }
-
+  if (raw) return(resps_raw)
 
   # Parse the responses
+  .info(funContext, "Parsing PubChem REST responses...")
   resps <- .parse_pubchem_rest_responses(resps_raw)
-  failed <- sapply(resps_raw, httr2::resp_is_error, USE.NAMES = T)
 
+  # filter failed 
+  # if any query failed, return the failed queries as attributes
+  failed <- sapply(resps_raw, httr2::resp_is_error, USE.NAMES = T)
   if (any(failed)) {
     .warn(funContext, " Some queries failed. See the 'failed' object for details.")
     failures <- lapply(resps_raw[failed], function(resp) {
@@ -69,7 +73,9 @@ getPubchemCompound <- function(
     failures <- NULL
   }
 
-  if (from != "name") {
+  # Combine the responses
+  # might be able to just do the else part...
+  if (from != "name") { 
     responses <- data.table::rbindlist(resps, fill = TRUE)
   } else {
     responses <- data.table::rbindlist(resps, idcol = from, fill = TRUE)
@@ -78,7 +84,7 @@ getPubchemCompound <- function(
 
   attributes(responses)$failed <- failures
 
-  responses
+  return(responses)
 }
 
 

R/pubchem_view_helpers.R

@@ -49,13 +49,14 @@
 ) {
   funContext <- .funContext(".build_pubchem_view_query")
 
-
+  # Check the inputs
   checkmate::assert_choice(
     annotation,
     c("data", "index", "annotations", "categories", "neighbors", "literature", "structure", "image", "qr", "linkout")
   )
   checkmate::assert_choice(record, c("compound", "substance", "assay", "cell", "gene", "protein"))
 
+  # Configure the options for the query
   opts_ <- list()
   if (!is.null(heading)) {
     if (record == "substance") {
@@ -95,7 +96,11 @@
 
   url |>
     httr2::url_build() |>
-    .build_request()
+    httr2::request()
+
+  # url |>
+    # httr2::url_build() |>
+    # .build_request()
 }
 
 #' Generic function to parse one of the annotation helpers

_pkgdown.yml

@@ -106,14 +106,14 @@ articles:
   navbar: Annotating Samples
   contents:
   - Cellosaurus
+  - OncoTree
 
 - title: Compounds
   navbar: Annotating Compounds
   contents:
   - PubChemAPI
   - Unichem
   - ChEMBL
-  - OncoTree
 
 - title: Pipelines
   navbar: Pipeline Tutorials