@sjcrh/proteinpaint-server 2.96.0 → 2.96.2-0

package/src/serverconfig.js

@@ -115,8 +115,9 @@ if (!serverconfig.binpath) {
 	}
 }
 
-if (serverconfig.debugmode) {
-	// only apply optional routeSetters in debugmode
+if (serverconfig.debugmode && !serverconfig.binpath.includes('sjcrh/')) {
+	// only apply optional routeSetters in debugmode and when the binpath
+	// indicates the server code is not installed as a node_module
 	const routeSetters = []
 	const defaultDir = path.join(serverconfig.binpath, 'src/test/routes')
 	// will add testing routes as needed and if found, such as in dev environment
@@ -146,8 +147,9 @@ if (serverconfig.debugmode) {
 	// since the serverconfig.binpath prefix may
 	// have been applied to locate optional routeSetter files
 	serverconfig.routeSetters = routeSetters
-	// server-sent events dir
-	serverconfig.sseDir = path.join(serverconfig.binpath, '../.sse')
+	// server-sent events dir, can manually set sseDir to false
+	// to prevent the default SSE setup in dev
+	if (serverconfig.sseDir !== false) serverconfig.sseDir = path.join(serverconfig.binpath, '../.sse')
 }
 
 if (serverconfig.allow_env_overrides) {

package/utils/edge.R

@@ -1,158 +1,143 @@
-# Usage: echo <in_json> | Rscript edge.R > <out_json>
-
-#   in_json: [string] input data in JSON format. Streamed through stdin.
-#   out_json: [string] clustering results in JSON format. Streamed to stdout.
-
-
-# json='{"case":"SJMB066856,SJMB069601,SJMB030827,SJMB030838,SJMB031131,SJMB031227,SJMB077221,SJMB077223","control":"SJMB069596,SJMB069587,SJMB074736,SJMB030488,SJMB030825,SJMB031110,SJMB032998,SJMB033002","input_file":"/Users/rpaul1/pp_data/files/hg38/sjmb12/rnaseq/geneCounts.txt"}' && time echo $json | Rscript edge.R
-
-# json='{"case":"SJMB030827,SJMB030838,SJMB064540,SJMB064538,SJMB064520,SJMB064535,SJMB031131,SJMB031227","control":"SJMB030488,SJMB030825,SJMB064537,SJMB064510,SJMB064533,SJMB064534,SJMB031110","input_file":"/Users/rpaul1/pp_data/files/hg38/sjmb12/rnaseq/geneCounts.txt"}' && time echo $json | Rscript edge.R
-
-# Checking if all R packages are installed or not, if not installing each one of them
-
-#jsonlite_path <- system.file(package='jsonlite')
-#if (nchar(jsonlite_path) == 0) {
-#  install.packages("jsonlite", repos='https://cran.case.edu/')
-#}
-#
-#edgeR_path <- system.file(package='edgeR')
-#if (nchar(edgeR_path) == 0) {
-#  BiocManager::install("edgeR")
-#}
-#
-#readr_path <- system.file(package='readr')
-#if (nchar(readr_path) == 0) {
-#  install.packages("readr", repos='https://cran.case.edu/')
-#}
-
-
-library(jsonlite)
-library(rhdf5)
-library(stringr)
-library(readr)
+# Load required packages
 suppressWarnings({
+    library(jsonlite)
+    library(rhdf5)
+    library(stringr)
+    library(readr)
     suppressPackageStartupMessages(library(edgeR))
     suppressPackageStartupMessages(library(dplyr))
 })
 
-con <- file("stdin", "r")
-json <- readLines(con, warn=FALSE)
-close(con)
-input <- fromJSON(json)
-#print (input)
-#print (input$output_path)
+# Read JSON input from stdin
+read_json_time <- system.time({
+    con <- file("stdin", "r")
+    json <- readLines(con, warn=FALSE)
+    close(con)
+    input <- fromJSON(json)
+    
+    cases <- unlist(strsplit(input$case, ","))
+    controls <- unlist(strsplit(input$control, ","))
+    combined <- c("geneID", "geneSymbol", cases, controls)
+})
+cat("Time to read JSON: ", read_json_time[3], " seconds\n")
 
-cases <- unlist(strsplit(input$case, ","))
-controls <- unlist(strsplit(input$control, ","))
-combined <- c("geneID","geneSymbol",cases,controls)
-#data %>% select(all_of(combined))
-#read_file_time_start <- Sys.time()
-if (exists(input$storage_type)==FALSE) {
+# Read counts data
+read_counts_time <- system.time({
     if (input$storage_type == "HDF5") {
-        #print(h5ls(input$input_file))
         geneIDs <- h5read(input$input_file, "gene_names")
         geneSymbols <- h5read(input$input_file, "gene_symbols")
         samples <- h5read(input$input_file, "samples")
-
-        samples_indicies <- c()
-        for (sample in cases) {
-            sample_index <- which(samples == sample)
-            if (length(sample_index) == 1) {
-                samples_indicies <- c(samples_indicies,sample_index)
-            } else {
-                print (paste(sample,"not found"))
-                quit(status = 1)
-            }
+        
+        # Find indices of case and control samples in the HDF5 file
+        case_indices <- match(cases, samples)
+        control_indices <- match(controls, samples)
+        
+        # Check for missing samples
+        if (any(is.na(case_indices))) {
+            missing_cases <- cases[is.na(case_indices)]
+            stop(paste(missing_cases, "not found"))
         }
-
-        for (sample in controls) {
-            sample_index <- which(samples == sample)
-            if (length(sample_index) == 1) {
-                samples_indicies <- c(samples_indicies,sample_index)
-            } else {
-                print (paste(sample,"not found"))
-                quit(status = 1)
-            }
+        if (any(is.na(control_indices))) {
+            missing_controls <- controls[is.na(control_indices)]
+            stop(paste(missing_controls, "not found"))
         }
-        read_counts <- t(h5read(input$input_file,"counts",index=list(samples_indicies, 1:length(geneIDs))))
-
+        
+        samples_indices <- c(case_indices, control_indices)
+        read_counts <- t(h5read(input$input_file, "counts", index = list(samples_indices, 1:length(geneIDs))))
+        colnames(read_counts) <- c(cases, controls)
     } else if (input$storage_type == "text") {
         suppressWarnings({
-          suppressMessages({
-        read_counts <- read_tsv(input$input_file, col_names = TRUE, col_select = combined)
-          })
+            suppressMessages({
+                read_counts <- read_tsv(input$input_file, col_names = TRUE, col_select = combined)
+            })
         })
         geneIDs <- unlist(read_counts[1])
         geneSymbols <- unlist(read_counts[2])
         read_counts <- select(read_counts, -geneID)
         read_counts <- select(read_counts, -geneSymbol)
     } else {
-        print ("Unknown storage type")
+        stop("Unknown storage type")
     }
-} else { # If not defined, parse data from a text file
-    suppressWarnings({
-      suppressMessages({
-    read_counts <- read_tsv(input$input_file, col_names = TRUE, col_select = combined)
-      })
-    })
-    geneIDs <- unlist(read_counts[1])
-    geneSymbols <- unlist(read_counts[2])
-    read_counts <- select(read_counts, -geneID)
-    read_counts <- select(read_counts, -geneSymbol)
-}
+})
+cat("Time to read counts data: ", read_counts_time[3], " seconds\n")
 
-#read_file_time_stop <- Sys.time()
-#print (read_file_time_stop - read_file_time_start)
+# Create conditions vector
+conditions <- c(rep("Diseased", length(cases)), rep("Control", length(controls)))
+gene_id_symbols <- paste0(geneIDs, "\t", geneSymbols)
 
-diseased <- rep("Diseased", length(cases))
-control <- rep("Control", length(controls))
-conditions <- c(diseased, control)
-tabs <- rep("\t",length(geneIDs))
-gene_id_symbols <- paste0(geneIDs,tabs,geneSymbols)
-y <- DGEList(counts = as.matrix(read_counts), group = conditions, genes = gene_id_symbols)
-keep <- filterByExpr(y, min.count = input$min_count, min.total.count = input$min_total_count)
-y <- y[keep, keep.lib.sizes = FALSE]
-y <- calcNormFactors(y, method = "TMM")
-#print (y)
-calculate_dispersion_time_start <- Sys.time()
-suppressWarnings({
-  suppressMessages({
-      dge <- estimateDisp(y = y)
-  })
+# Create DGEList object
+dge_list_time <- system.time({
+    y <- DGEList(counts = read_counts, group = conditions, genes = gene_id_symbols)
 })
-calculate_dispersion_time_stop <- Sys.time()
-print("Dispersion Time")
-print (calculate_dispersion_time_stop - calculate_dispersion_time_start)
-calculate_exact_test_time_start <- Sys.time()
-et <- exactTest(object = dge)
-calculate_exact_test_time_stop <- Sys.time()
-print("Exact Time")
-print(calculate_exact_test_time_stop - calculate_exact_test_time_start)
-#print ("Time to calculate DE")
-#print (calculate_DE_time_stop - calculate_DE_time_start)
-#print (et)
-logfc <- et$table$logFC
-logcpm <- et$table$logCPM
-pvalues <- et$table$PValue
-genes_matrix <- str_split_fixed(unlist(et$genes),"\t",2)
-geneids <- unlist(genes_matrix[,1])
-genesymbols <- unlist(genes_matrix[,2])
-adjust_p_values <- p.adjust(pvalues, method = "fdr")
+cat("Time to generate DGEList: ", dge_list_time[3], " seconds\n")
 
-output <- data.frame(geneids,genesymbols,logfc,-log10(pvalues),-log10(adjust_p_values))
-names(output)[1] <- "gene_name"
-names(output)[2] <- "gene_symbol"
-names(output)[3] <- "fold_change"
-names(output)[4] <- "original_p_value"
-names(output)[5] <- "adjusted_p_value"
-#write_csv(output,"DE_output.txt")
-cat(paste0("adjusted_p_values:",toJSON(output)))
-#output_json <- toJSON(output)
-#print ("output_json")
-#output_file <- paste0(input$output_path,"/r_output.txt")
-#print (output_file)
-#cat(output_json, file = output_file)
+# Filter and normalize counts
+filter_time <- system.time({
+    keep <- filterByExpr(y, min.count = input$min_count, min.total.count = input$min_total_count)
+})
+cat("Time to filter by expression: ", filter_time[3], " seconds\n")
+
+normalization_time <- system.time({
+    y <- y[keep, keep.lib.sizes = FALSE]
+    y <- calcNormFactors(y, method = "TMM")
+})
+cat("Normalization time: ", normalization_time[3], " seconds\n")
+
+# Differential expression analysis
+if (length(input$conf1) == 0) { # No adjustment of confounding factors
+    dispersion_time <- system.time({
+        suppressWarnings({
+            suppressMessages({
+                y <- estimateDisp(y)
+            })
+        })
+    })
+    cat("Dispersion time: ", dispersion_time[3], " seconds\n")
+    
+    exact_test_time <- system.time({
+        et <- exactTest(y)
+    })
+    cat("Exact test time: ", exact_test_time[3], " seconds\n")
+} else { # Adjusting for confounding factors
+    y$samples <- data.frame(conditions = conditions, conf1 = input$conf1)
+    model_gen_time <- system.time({
+        design <- model.matrix(~ conf1 + conditions, data = y$samples)
+    })
+    cat("Time for making design matrix: ", model_gen_time[3], " seconds\n")
+    
+    dispersion_time <- system.time({
+        y <- estimateDisp(y, design)
+    })
+    cat("Dispersion time: ", dispersion_time[3], " seconds\n")
+    
+    fit_time <- system.time({
+        fit <- glmFit(y, design)
+    })
+    cat("Fit time: ", fit_time[3], " seconds\n")
+    
+    test_statistics_time <- system.time({
+        et <- glmLRT(fit, coef = 2)
+    })
+    cat("Test statistics time: ", test_statistics_time[3], " seconds\n")
+}
+
+# Multiple testing correction
+multiple_testing_correction_time <- system.time({
+    logfc <- et$table$logFC
+    logcpm <- et$table$logCPM
+    pvalues <- et$table$PValue
+    genes_matrix <- str_split_fixed(unlist(et$genes), "\t", 2)
+    geneids <- unlist(genes_matrix[, 1])
+    genesymbols <- unlist(genes_matrix[, 2])
+    adjust_p_values <- p.adjust(pvalues, method = "fdr")
+    output <- data.frame(geneids, genesymbols, logfc, -log10(pvalues), -log10(adjust_p_values))
+    names(output)[1] <- "gene_name"
+    names(output)[2] <- "gene_symbol"
+    names(output)[3] <- "fold_change"
+    names(output)[4] <- "original_p_value"
+    names(output)[5] <- "adjusted_p_value"
+})
+cat("Time for multiple testing correction: ", multiple_testing_correction_time[3], " seconds\n")
 
-#top_degs = topTags(object = et, n = "Inf")
-#print ("top_degs")
-#print (top_degs)
+# Output results
+cat(paste0("adjusted_p_values:", toJSON(output)))