Add metadata to -writeconfig

The -writeconfig option writes out an empty metadata block (or blocks if barcoded) and relevant comments to the config file.
richardmleggett · Nov 29, 2023 · 49fe7b9 · 49fe7b9
1 parent 30ec4cb
commit 49fe7b9
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diff --git a/bin/MARTiEngine.jar b/bin/MARTiEngine.jar
diff --git a/engine/src/main/java/uk/ac/earlham/marti/core/MARTiConfigFile.java b/engine/src/main/java/uk/ac/earlham/marti/core/MARTiConfigFile.java
@@ -181,6 +181,49 @@ public void writeConfigFile(String filename) {
             pw.println("LCAMinQueryCoverage:" + options.getLCAMinQueryCoverage());
             pw.println("LCAMinCombinedScore:" + options.getLCAMinCombinedScore());
             pw.println("LCAMinLength:" + options.getLCAMinLength());
+
+            pw.println("");
+            pw.println("# Metadata blocks can be used to describe the sample being analysed.");
+            pw.println("# Each field is optional and can be removed if not required.");
+            pw.println("# The 'keywords' field is used for searching in the GUI.");
+            if (options.isBarcoded()) {
+                BarcodesList bl = options.getBarcodesList();
+                String barcodes[] = bl.getCommaSeparatedList().split(",");
+                String barcodeString2 = "";
+                for(int i = 1; i < barcodes.length; i ++) {
+                    barcodeString2 += barcodes[i] + ",";
+                }
+                pw.println("# Each block can be assigned to one or more barcodes.");
+                pw.println("# If no barcode is specified the block is assumed to describe all barcodes.");
+                pw.println("");
+                pw.println("Metadata");
+                pw.println("    Location:");
+                pw.println("    Date:");
+                pw.println("    Time:");
+                pw.println("    Temperature:");
+                pw.println("    Humidity:");
+                pw.println("    Keywords:");
+                pw.println("    Barcodes:" + barcodes[0]);
+                pw.println("");
+                pw.println("Metadata");
+                pw.println("    Location:");
+                pw.println("    Date:");
+                pw.println("    Time:");
+                pw.println("    Temperature:");
+                pw.println("    Humidity:");
+                pw.println("    Keywords:");
+                pw.println("    Barcodes:" + barcodeString2.substring(0, barcodeString2.length() - 1));
+            } else {
+                pw.println("");
+                pw.println("Metadata");
+                pw.println("    Location:");
+                pw.println("    Date:");
+                pw.println("    Time:");
+                pw.println("    Temperature:");
+                pw.println("    Humidity:");
+                pw.println("    Keywords:");
+            }
+
             pw.close();
 
             System.out.println("Config file writen to "+filename);