registry and documentation fixes

PavlidisLab · Jul 3, 2024 · 87ec765 · 87ec765
1 parent f6d0277
commit 87ec765
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Showing 2 changed files with 19 additions and 3 deletions.
diff --git a/inst/script/registry.R b/inst/script/registry.R
@@ -46,7 +46,7 @@ names(overrides) = overrides %>% sapply(function(x){
 })
 
 
-res = httr::GET('https://gemma.msl.ubc.ca/rest/v2/openapi.json')
+res = httr::GET(paste0(gemmaPath(),'openapi.json'))
 writeBin(res$content,con = 'inst/script/openapi.json')
 api_file = jsonlite::fromJSON(readLines('inst/script/openapi.json'),simplifyVector = FALSE)
 
@@ -131,6 +131,7 @@ registerEndpoint(
 #' query across multiple datasets and being able to use the filter argument
 #' to search based on result set properties.
 #' 
+#' @param datasets A vector of dataset IDs or short names
 #'
 #' @inherit processDifferentialExpressionAnalysisResultSetValueObject return
 #'
@@ -294,6 +295,9 @@ registerEndpoint('datasets/{dataset}/analyses/differential',
 # /datasets/{datasets}/expressions/genes/{genes}, get_dataset_expression_for_genes ------
 
 #' get_dataset_expression_for_genes
+#' 
+#' @param datasets A vector of dataset IDs or short names
+#' @param genes A vector of NCBI IDs, Ensembl IDs or gene symbols.
 #' @param consolidate An option for gene expression level consolidation. If empty,
 #' will return every probe for the genes. "pickmax" to
 #' pick the probe with the highest expression, "pickvar" to pick the prove with
@@ -636,6 +640,9 @@ registerEndpoint("genes/{gene}/probes?offset={offset}&limit={limit}",
 
 #' get_genes
 #'
+#'
+#' @param genes A vector of NCBI IDs, Ensembl IDs or gene symbols.
+#'
 #' @inherit processGenes return
 #'
 #' @examples

diff --git a/inst/script/registry_helpers.R b/inst/script/registry_helpers.R
@@ -41,7 +41,9 @@ parse_open_api_params <- function(prm){
         out = prm$schema$oneOf %>% purrr::map_chr('description') %>%  
             gsub('.','',.,fixed=  TRUE) %>% paste(collapse = ' or ') %>% 
             snakecase::to_sentence_case()
-    } else{
+    } else if(!is.null(prm$schema$type)) {
+        out = prm$schema$type
+    }else{
         browser()
         stop('help me!')
     }
@@ -85,7 +87,7 @@ registerEndpoint <- function(endpoint,
         return(NULL)
     }
 
-    logEndpoint(fname, logname)
+    logEndpoint(fname, open_api_name)
 
     # Make sure arguments are URL encoded
     endpoint <- gsub("\\{([^\\}]+)\\}", "\\{encode\\(\\1\\)\\}", endpoint)
@@ -224,6 +226,13 @@ logEndpoint <- function(fname, logname) {
     options(gemmaAPI.logged = c(getOption("gemmaAPI.logged"), setNames(fname, logname)))
 }
 
+clearLog <- function(){
+    options(gemmaAPI.logged = c())
+}
+
+getLog <- function(){
+    getOption('gemmaAPI.logged')
+}
 
 #' Comment a function
 #'