add get_gene_differential_expression_values, no processor

NAMESPACE

@@ -21,6 +21,7 @@ export(get_dataset_samples)
 export(get_datasets)
 export(get_datasets_by_ids)
 export(get_differential_expression_values)
+export(get_gene_differential_expression_values)
 export(get_gene_go_terms)
 export(get_gene_locations)
 export(get_gene_probes)

R/processors.R

@@ -1040,6 +1040,12 @@ processQuantitationTypeValueObject <- function(d){
     )
 }
 
+processDifferentialExpressionAnalysisResultByGeneValueObject <- function(data){
+    browser()
+    return(data)
+}
+
+
 # processSVD <- function(d){
 #     d$vMatrix$rawMatrix
 #     browser()

R/validators.R

@@ -322,3 +322,13 @@ addToFilter <- function(filter,property,terms){
     filter <- glue::glue("{filter}{property} in ({paste(terms,collapse = ',')})")
     return(filter)
 }
+
+validateNumber = function(name,...){
+    number = unlist(list(...))
+
+    if(length(number)>1 || typeof(number)!= 'double'){
+        stop(glue::glue("{name} must be a double of length one"))
+    }
+
+    return(number)
+}

inst/script/registry.R

@@ -311,7 +311,7 @@ NULL
 
 
 registerEndpoint('datasets/{datasets}/expressions/genes/{genes}?keepNonSpecific={keepNonSpecific}&consolidate={consolidate}',
-                 'get_dataset_expression_for_genes', open_api_name = 'get_dataset_expression_for_genes',
+                 'get_dataset_expression_for_genes', open_api_name = 'get_datasets_expression_levels_for_genes',
                  keyword = 'dataset',
                  defaults = list(
                      datasets = bquote(),
@@ -562,6 +562,36 @@ registerEndpoint("datasets/{datasets}?&offset={offset}&limit={limit}&sort={sort}
 # datasets/categories -----
 # currently unimplemented
 
+# /datasets/analyses/differential/results/genes/gene
+registerEndpoint("datasets/analyses/differential/results/genes/{gene}?&query={query}&filter={filter}&threshold={threshold}&offset={offset}&limit={limit}",
+                 "get_gene_differential_expression_values",
+                 open_api_name = "get_datasets_differential_expression_analysis_results_for_gene",
+                 keyword = 'gene',
+                 header = "text/tab-separated-values",
+                 defaults = list(
+                     gene = bquote(),
+                     query = NA_character_,
+                     filter = NA_character_,
+                     offset = 0L,
+                     limit = 20L,
+                     threshold = 1
+                 ),
+                 compressibles = c('filter'),
+                 validators = c(
+                     gene = validateSingleID,
+                     query = validateOptionalQuery,
+                     filter = validateFilter,
+                     offset = validatePositiveInteger,
+                     limit = validateLimit,
+                     threshold = validateNumber
+                 ),
+                 preprocessor = quote(processDifferentialExpressionAnalysisResultByGeneValueObject)
+)
+
+
+# /datasets/analyses/differential/results/taxa/{taxon}/genes/gene
+# unimplemented along with other taxon specific endpoints
+
 # datasets/taxa -----
 # currently unimplemented
 
@@ -959,7 +989,7 @@ doFinalize <- function(document = getOption("gemmaAPI.document", "R/allEndpoints
 
     styler::style_file("./R/allEndpoints.R", transformers = biocthis::bioc_style())
     devtools::document()
-    devtools::build(vignettes = FALSE)
+    # devtools::build(vignettes = FALSE)
 }
 
 doFinalize()