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

@@ -4,6 +4,7 @@ import { ConstrainedBasis } from "../basis/constrained_basis";
 import { ATOMIC_COORD_UNITS } from "../constants";
 import { Lattice } from "../lattice/lattice";
 import math from "../math";
+import { getLineFromContent } from "./utils";
 
 const _print = (x, printFormat = "%14.9f") => s.sprintf(printFormat, math.precise(x));
 const _latticeVectorsToString = (vectors) =>
@@ -63,8 +64,22 @@ 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} fileContent
+ * @param {String} failoverName
+ * @returns {String}
+ */
+export function getNameFromContents(fileContent, failoverName = "material") {
+    const nameFromContent = getLineFromContent(fileContent, 0);
+    if (nameFromContent) return nameFromContent;
+    return failoverName;
+}
+
 export default {
     toPoscar,
     atomicConstraintsCharFromBool,
     atomsCount,
+    getNameFromContents,
 };

src/parsers/utils.js

@@ -0,0 +1,7 @@
+export function getLineFromContent(fileContent, lineNumber) {
+    return fileContent.split(/\r?\n/)[lineNumber];
+}
+
+export default {
+    getLineFromContent,
+};

src/parsers/xyz.js

@@ -6,6 +6,7 @@ import { ConstrainedBasis } from "../basis/constrained_basis";
 import { Lattice } from "../lattice/lattice";
 import math from "../math";
 import { InvalidLineError } from "./errors";
+import { getLineFromContent } from "./utils";
 import { CombinatorialBasis } from "./xyz_combinatorial_basis";
 
 // Regular expression for an XYZ line with atomic constraints, eg. Si    0.000000    0.500000    0.446678 1 1 1`
@@ -140,10 +141,24 @@ 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} fileContent
+ * @param {String} failoverName
+ * @returns {String}
+ */
+export function getNameFromContents(fileContent, failoverName = "material") {
+    const nameFromContent = getLineFromContent(fileContent, 1);
+    if (nameFromContent) return nameFromContent;
+    return failoverName;
+}
+
 export default {
     validate,
     fromMaterial,
     toBasisConfig,
     fromBasis,
     CombinatorialBasis,
+    getNameFromContents,
 };

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, getNameFromContents } from "../../src/parsers/poscar";
+import { GenericPoscar, H2O, Na4Cl4, Na4Cl4Poscar, Zr1H23Zr1H1, Zr1H23Zr1H1Poscar } from "../enums";
 
 describe("Parsers.POSCAR", () => {
     it("should return a valid poscar", () => {
@@ -18,4 +18,8 @@ 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 fileContents = GenericPoscar;
+        expect(getNameFromContents(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 { getNameFromContents } from "../../src/parsers/xyz";
+import { GenericXYZ, Si } from "../enums";
 import { assertDeepAlmostEqual } from "../utils";
 
 describe("Parsers:XYZ", () => {
@@ -11,4 +14,8 @@ describe("Parsers:XYZ", () => {
             "units",
         ]);
     });
+    it("should return the material name based on the xyz file contents", () => {
+        const fileContents = GenericXYZ;
+        expect(getNameFromContents(fileContents)).to.be.equal("Methane");
+    });
 });