Feature/sof 5462 - get name from file content

.github/workflows/cicd.yml

@@ -18,6 +18,8 @@ jobs:
     steps:
       - name: Checkout this repository
         uses: actions/checkout@v2
+        with:
+            lfs: true
 
       - name: Checkout actions repository
         uses: actions/checkout@v2
@@ -40,7 +42,8 @@ jobs:
     steps:
       - name: Checkout this repository
         uses: actions/checkout@v2
-
+        with:
+          lfs: true
       - name: Checkout actions repository
         uses: actions/checkout@v2
         with:

src/parsers/poscar.js

@@ -63,8 +63,24 @@ export function atomsCount(poscarFileContent) {
     return atomsLine.map((x) => parseInt(x, 10)).reduce((a, b) => a + b);
 }
 
+/**
+ * Function returns the string on the first line of POSCAR file content. Generally the first line contains text
+ * containing the name of the structure.
+ * @param {String} name
+ * @param {String} fileContent
+ * @returns {String}
+ */
+export function materialNameFromFileContents(name, fileContent) {
+    const materialNameFromFile = fileContent.split(/\r?\n/)[0];
+    if (name === materialNameFromFile || !materialNameFromFile) {
+        return name;
+    }
+    return materialNameFromFile;
+}
+
 export default {
     toPoscar,
     atomicConstraintsCharFromBool,
     atomsCount,
+    materialNameFromFileContents,
 };

src/parsers/xyz.js

@@ -140,10 +140,26 @@ function fromMaterial(materialOrConfig, fractional = false) {
     return fromBasis(basis, "%11.6f");
 }
 
+/**
+ * Function returns the string on the second line of XYZ file content. Generally the second line contains text
+ * containing the name of the structure.
+ * @param {String} name
+ * @param {String} fileContent
+ * @returns {String}
+ */
+export function materialNameFromFileContents(name, fileContent) {
+    const materialNameFromFile = fileContent.split(/\r?\n/)[1];
+    if (name === materialNameFromFile || !materialNameFromFile) {
+        return name;
+    }
+    return materialNameFromFile;
+}
+
 export default {
     validate,
     fromMaterial,
     toBasisConfig,
     fromBasis,
     CombinatorialBasis,
+    materialNameFromFileContents,
 };

tests/enums.js

@@ -31,3 +31,5 @@ export const SiPWSCFInput = readFile(path.join(FIXTURES_DIR, "Si-pwscf.in"));
 export const Zr1H23Zr1H1 = readJSONFile(path.join(FIXTURES_DIR, "Zr1H23Zr1H1.json"));
 export const Zr1H23Zr1H1Poscar = readFile(path.join(FIXTURES_DIR, "Zr1H23Zr1H1.poscar"));
 export const H2O = readFile(path.join(FIXTURES_DIR, "H2O.poscar"));
+export const GenericPoscar = readFile(path.join(FIXTURES_DIR, "POSCAR.poscar"));
+export const GenericXYZ = readFile(path.join(FIXTURES_DIR, "Structure.xyz"));

tests/parsers/poscar.js

@@ -1,8 +1,8 @@
 import { expect } from "chai";
 
 import { Material } from "../../src/material";
-import { atomsCount } from "../../src/parsers/poscar";
-import { H2O, Na4Cl4, Na4Cl4Poscar, Zr1H23Zr1H1, Zr1H23Zr1H1Poscar } from "../enums";
+import { atomsCount, materialNameFromFileContents } from "../../src/parsers/poscar";
+import { GenericPoscar, H2O, Na4Cl4, Na4Cl4Poscar, Zr1H23Zr1H1, Zr1H23Zr1H1Poscar } from "../enums";
 
 describe("Parsers.POSCAR", () => {
     it("should return a valid poscar", () => {
@@ -18,4 +18,9 @@ describe("Parsers.POSCAR", () => {
     it("should return the number of atoms for a molecule in a poscar file", () => {
         expect(atomsCount(H2O)).to.be.equal(3);
     });
+    it("should return the material name based on the poscar file contents", () => {
+        const name = "POSCAR.poscar";
+        const fileContents = GenericPoscar;
+        expect(materialNameFromFileContents(name, fileContents)).to.be.equal("H2S");
+    });
 });

tests/parsers/xyz.js

@@ -1,5 +1,8 @@
+import { expect } from "chai";
+
 import parsers from "../../src/parsers/parsers";
-import { Si } from "../enums";
+import { materialNameFromFileContents } from "../../src/parsers/xyz";
+import { GenericXYZ, Si } from "../enums";
 import { assertDeepAlmostEqual } from "../utils";
 
 describe("Parsers:XYZ", () => {
@@ -11,4 +14,9 @@ describe("Parsers:XYZ", () => {
             "units",
         ]);
     });
+    it("should return the material name based on the xyz file contents", () => {
+        const name = "test.xyz";
+        const fileContents = GenericXYZ;
+        expect(materialNameFromFileContents(name, fileContents)).to.be.equal("Methane");
+    });
 });