Adding ability to pick up sample to barcoding map from a csv file in …

…the runtime directory

package.json

@@ -1,6 +1,6 @@
 {
   "name": "artic-rampart",
-  "version": "1.0.2-0",
+  "version": "1.0.3-0",
   "main": "src/electron.js",
   "author": "James Hadfield, Ainé O'Toole, ARTIC network, Nick Loman, Andrew Rambaut",
   "bin": {

recipes/conda/meta.yaml

@@ -1,13 +1,13 @@
-{% set version = "1.0.1" %}
+{% set version = "1.0.3" %}
 
 package:
   name: rampart
   version: {{ version }}
 
 source:
-  url: https://github.com/artic-network/rampart/archive/v1.0.1-1.tar.gz
+  url: https://github.com/artic-network/rampart/archive/v1.0.3.tar.gz
   folder: rampart
-  sha256: 424a9e60cc663234fcabe49b24c8e44a6900e86aa64b9e5d031e95644f3ef4a7
+  sha256: 3235c4296320bbfc06a80142d30ae9f36848bee7f563bc1677270883a77a9155
 
 requirements:
   build:

server/config.js

@@ -18,6 +18,7 @@
  * @type {module:fs}
  */
 const fs = require('fs');
+const dsv = require('d3-dsv');
 // const path = require('path')
 const { normalizePath, getAbsolutePath, verbose, log, warn, fatal } = require("./utils");
 const { getNthReferenceColour } = require("./colours");
@@ -28,6 +29,7 @@ const GENOME_CONFIG_FILENAME= "genome.json";
 const PRIMERS_CONFIG_FILENAME = "primers.json";
 const PIPELINES_CONFIG_FILENAME = "pipelines.json";
 const RUN_CONFIG_FILENAME = "run_configuration.json";
+const BARCODES_TO_SAMPLE_FILENAME = "barcodes.csv";
 
 const UNMAPPED_LABEL = "unmapped";
 const UNASSIGNED_LABEL = "unassigned";
@@ -171,7 +173,7 @@ function checkPipeline(config, pipeline, index = 0, giveWarning = false) {
 
 }
 
-const getInitialConfig = (args) => {
+function getInitialConfig(args) {
     const serverDir = __dirname;
     const rampartSourceDir = serverDir.substring(0, serverDir.length - 7); // no trailing slash
 
@@ -211,11 +213,35 @@ const getInitialConfig = (args) => {
         config.run.title = args.title;
     }
 
+    // attempt to open a csv file containing a mapping of barcodes to samples (this will override anything
+    // in the config files).
+    const barcodeFile = findConfigFile(pathCascade, BARCODES_TO_SAMPLE_FILENAME);
+    if (barcodeFile) {
+        try {
+            verbose("config", `Reading sample to barcode mapping from ${barcodeFile}`);
+            const samples = dsv.csvParse(fs.readFileSync(barcodeFile).toString());
+
+            const sampleMap = samples.reduce( (sampleMap, d) => {
+                sampleMap[d.sample] = (d.sample in sampleMap ? [...sampleMap[d.sample], d.barcode] : [d.barcode]);
+                return sampleMap;
+            }, {});
+            config.run.samples = Object.keys(sampleMap).map((d) => {
+                return {
+                    'name': d,
+                    'barcodes': sampleMap[d]
+                };
+            });
+        } catch (err) {
+            warn("Unable to read barcode to sample map file: " + barcodeFile)
+        }
+    }
+
     config.run.barcodeNames = {};
     if (config.run.samples) {
 
         // if barcode names have been specified then limit demuxing to only those barcodes...
         config.run.samples.forEach((sample, index) => {
+            verbose("config", `Sample: ${sample.name} -> ${sample.barcodes.join(",")}`);
             sample.barcodes.forEach((barcode) => {
                 // // find an integer in the barcode name
                 // const matches = barcode.match(/(\d\d?)/);
@@ -334,6 +360,7 @@ const getInitialConfig = (args) => {
         config.pipelines.annotation.configOptions = { ...config.pipelines.annotation.configOptions, ...config.run.annotationOptions };
     }
 
+
     if (Object.keys(config.run.barcodeNames).length > 0) {
         config.pipelines.annotation.configOptions["limit_barcodes_to"] = Object.keys(config.run.barcodeNames).join(',');
     }