Add assay extractor

index.js

@@ -1,12 +1,16 @@
 const extractor = require("./src/extractor");
 
-// The source extractor
-const options = {
+// *** The source extractor
+const sourceOptions = {
   ENAChecklist: "./input/Source/ENA.xml",
   ISAConfiguration: "./input/Source/ISA.xml",
-  outputPath: "./output/result.txt",
+  outputPath: "./output/sourceMerged.txt",
 };
-extractor.sourceExtractor.getData(options);
+extractor.sourceExtractor.getData(sourceOptions);
 
-// // The assay extractor
-// extractor.assayExtractor.getData();
+// *** The assay extractor
+const assayOptions = {
+  ISAConfiguration: "./input/Assay/genome_seq.xml",
+  outputPath: "./output/assayMerged.txt",
+};
+extractor.assayExtractor.getData(assayOptions);

src/extractor/assayExtractor.js

@@ -0,0 +1,58 @@
+const xml2js = require("xml2js"); //.parseString;
+const parser = new xml2js.Parser({ explicitChildren: true, preserveChildrenOrder: true }).parseString;
+const fs = require("fs");
+const fsPromises = fs.promises;
+
+const getData = async (options) => {
+  const { ISAConfiguration, outputPath } = options;
+  const ISA_XML = await fsPromises.readFile(ISAConfiguration);
+  const ISAParsed = await dataParse(ISA_XML);
+  const ISAData = ISAExtract(ISAParsed);
+  writeOutput(ISAData, outputPath);
+};
+
+const dataParse = async (data) => {
+  return new Promise((r) => {
+    parser(data, (e, result) => {
+      r(result);
+    });
+  });
+};
+
+const ISAExtract = (data) => {
+  const temp = data["isatab-config-file"]["isatab-configuration"][0]["$$"];
+  let result = { meta: {}, data: {} };
+  let lastProtocol = "";
+  temp.forEach((x) => {
+    if (x["#name"] == "protocol-field") {
+      result.data[x["$"]["protocol-type"]] = [];
+      lastProtocol = x["$"]["protocol-type"];
+    } else if (x["#name"] == "field") {
+      if (lastProtocol != "") {
+        result.data[lastProtocol].push({
+          name: x["$"]["header"],
+          description: x["description"][0].trim(),
+          dataType: x["$"]["data-type"],
+          required: x["$"]["is-required"],
+        });
+      }
+    } else if (x["#name"] == "measurement") {
+      result.meta["measurement"] = x["$"]["term-label"];
+    } else if (x["#name"] == "technology") {
+      result.meta["technology"] = x["$"]["term-label"];
+    }
+  });
+  // console.log(result);
+  return result;
+};
+
+const writeOutput = async (data, outputPath) => {
+  try {
+    await fsPromises.writeFile(outputPath, JSON.stringify(data));
+    console.log("Data was extracted successfully!");
+  } catch (e) {
+    console.log(`Error writing to file: ${e}`);
+  }
+};
+
+module.exports = { getData };