Merge branch 'tdd-upsert-doi' into main

lib/index.js

@@ -16,14 +16,17 @@ exports.main = void 0;
 const core_1 = require("@actions/core");
 const exec_1 = require("@actions/exec");
 const zenodraft_1 = __importDefault(require("zenodraft"));
+const upserting_1 = require("./upserting");
 const main = () => __awaiter(void 0, void 0, void 0, function* () {
     try {
         const collection_id = core_1.getInput('collection');
         const compression = core_1.getInput('compression');
         const filenames = core_1.getInput('filenames');
         const metadata = core_1.getInput('metadata');
-        const publish = core_1.getInput('publish');
+        const publish = core_1.getInput('publish') === 'true' ? true : false;
         const sandbox = core_1.getInput('sandbox') === 'false' ? false : true;
+        const upsert_doi = core_1.getInput('upsert-doi') === 'true' ? true : false;
+        const upsert_location = core_1.getInput('upsert-location');
         const verbose = false;
         // create the deposition as a new version in a new collection or
         // as a new version in an existing collection:
@@ -34,6 +37,10 @@ const main = () => __awaiter(void 0, void 0, void 0, function* () {
         else {
             latest_id = yield zenodraft_1.default.deposition_create_in_existing_collection(sandbox, collection_id, verbose);
         }
+        if (upsert_doi === true) {
+            const prereserved_doi = yield zenodraft_1.default.deposition_show_prereserved(sandbox, latest_id, verbose);
+            upserting_1.upsert_prereserved_doi(upsert_location, prereserved_doi);
+        }
         // upload only the files specified in the filenames argument, or
         // upload a snapshot of the complete repository
         if (filenames === '') {
@@ -59,7 +66,7 @@ const main = () => __awaiter(void 0, void 0, void 0, function* () {
         if (metadata !== '') {
             yield zenodraft_1.default.metadata_update(sandbox, latest_id, metadata, verbose);
         }
-        if (publish === 'true') {
+        if (publish === true) {
             yield zenodraft_1.default.deposition_publish(sandbox, latest_id, verbose);
         }
     }

lib/upserting.js

@@ -26,13 +26,35 @@ exports.upsert_prereserved_doi = void 0;
 const yaml = __importStar(require("js-yaml"));
 const fs = __importStar(require("fs"));
 const assert_1 = __importDefault(require("assert"));
+const assert_2 = require("assert");
 const has_cff_version_key = (cff) => {
     return Object.keys(cff).includes('cff-version');
 };
 const load_cff_file = () => {
-    const cffstr = fs.readFileSync('CITATION.cff', 'utf8');
-    const doc = yaml.load(cffstr);
+    let cffstr;
+    try {
+        cffstr = fs.readFileSync('CITATION.cff', 'utf8');
+    }
+    catch (err) {
+        if (err.code === 'ENOENT') {
+            // tell user file doesnt exist
+            throw new assert_2.AssertionError({ message: 'File CITATION.cff doesn\'t exist.' });
+        }
+        throw err;
+    }
+    let doc;
+    try {
+        doc = yaml.load(cffstr);
+    }
+    catch (err) {
+        if (err instanceof yaml.YAMLException) {
+            // tell user problem was yaml parsing
+            throw new assert_2.AssertionError({ message: 'Could not parse the contents of CITATION.cff as YAML. Try https://yamllint.com to fix the problem.' });
+        }
+        throw err;
+    }
     assert_1.default(typeof (doc) === 'object', 'Could not parse the contents of CITATION.cff into an object.');
+    assert_1.default(has_cff_version_key(doc), 'CITATION.cff is missing required key \'cff-version\'.');
     return doc;
 };
 const supports_identifiers_description_key = (cff) => {
@@ -45,47 +67,35 @@ const supports_identifiers_key = (cff) => {
     const versions = ['1.1.0', '1.2.0'];
     return versions.includes(cff_version);
 };
-const upsert_prereserved_doi = (upsert_doi, upsert_location, prereserved_doi) => {
-    if (upsert_doi === false) {
-        return;
-    }
-    let cff;
-    try {
-        cff = load_cff_file();
-    }
-    catch (err) {
-        if (err.code === 'ENOENT') {
-            // tell user file doesnt exist
-            throw new Error('File CITATION.cff doesn\'t exist.');
-        }
-        if (err instanceof yaml.YAMLException) {
-            // tell user problem was yaml parsing
-            throw new Error('Could not parse the contents of CITATION.cff as YAML. Try https://yamllint.com to fix the problem.');
-        }
-        // other error
-        throw err;
-    }
-    assert_1.default(has_cff_version_key(cff), 'CITATION.cff is missing required key \'cff-version\'.');
+const upsert_prereserved_doi = (upsert_location, prereserved_doi) => {
+    const cff = load_cff_file();
     if (upsert_location === 'identifiers') {
         upsert_location = 'identifiers[0]';
     }
-    const identifiers_regex = new RegExp('^identifiers\\[\\d\\]$');
+    const identifiers_regex = new RegExp('^identifiers\\[\\d+\\]$');
     if (upsert_location === 'doi') {
         cff.doi = prereserved_doi;
     }
     else if (identifiers_regex.test(upsert_location)) {
         assert_1.default(supports_identifiers_key(cff), `Your CITATION.cff file does not support key \'identifiers\'. Consider updating its \'cff-version\' value.`);
-        const index = parseInt(upsert_location.split(new RegExp('[\\[\\]]'))[1]);
-        let obj = {
-            type: 'doi',
-            value: prereserved_doi,
-        };
+        let obj;
         if (supports_identifiers_description_key(cff)) {
-            // include 'description' in the object if the cff version supports its use
-            obj = Object.assign(Object.assign({}, obj), { description: 'Version doi for this work.' });
+            obj = {
+                description: 'Version doi for this work.',
+                value: prereserved_doi,
+                type: 'doi'
+            };
+        }
+        else {
+            obj = {
+                value: prereserved_doi,
+                type: 'doi'
+            };
         }
-        if (Object.keys(cff).includes('identifiers') && cff.identifiers instanceof Array) {
-            assert_1.default(0 <= index && index <= cff.identifiers.length);
+        const index = parseInt(upsert_location.split(new RegExp('[\\[\\]]'))[1]);
+        if (Object.keys(cff).includes('identifiers')) {
+            assert_1.default(cff.identifiers instanceof Array, 'Expected \'identifiers\' to be of type Array.');
+            assert_1.default(0 <= index && index <= cff.identifiers.length, 'Invalid upsert location index.');
             if (index < cff.identifiers.length) {
                 // partially overwrite existing object
                 cff.identifiers[index].value = prereserved_doi;
@@ -96,12 +106,12 @@ const upsert_prereserved_doi = (upsert_doi, upsert_location, prereserved_doi) =>
             }
         }
         else {
-            assert_1.default(index === 0);
+            assert_1.default(index === 0, 'Invalid upsert location index.');
             cff.identifiers = [obj];
         }
     }
     else {
-        throw new Error('Invalid value for variable \'upsert-location\'.');
+        throw new assert_2.AssertionError({ message: 'Invalid value for variable \'upsert-location\'.' });
     }
     write_cff_file(cff);
     // use octokit to do the equivalent of
@@ -115,6 +125,7 @@ const upsert_prereserved_doi = (upsert_doi, upsert_location, prereserved_doi) =>
 };
 exports.upsert_prereserved_doi = upsert_prereserved_doi;
 const write_cff_file = (cff) => {
-    yaml.dump(cff, { sortKeys: false });
+    const cffstr = yaml.dump(cff, { sortKeys: false });
+    fs.writeFileSync('CITATION.cff', cffstr, 'utf8');
     return;
 };

tests/upserting/1.0.3/doi/append/upserting.test.js

@@ -0,0 +1,49 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    Object.defineProperty(o, k2, { enumerable: true, get: function() { return m[k]; } });
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || function (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __setModuleDefault(result, mod);
+    return result;
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const upserting_1 = require("../../../../../src/upserting");
+const fs = __importStar(require("fs"));
+const path = __importStar(require("path"));
+const os = __importStar(require("os"));
+let temporary_directory;
+beforeEach(() => {
+    const src = (f) => {
+        return path.join(__dirname, f);
+    };
+    const dest = (f) => {
+        return path.join(temporary_directory, f);
+    };
+    temporary_directory = fs.mkdtempSync(`${os.tmpdir()}${path.sep}zenodraft-action-testing.`);
+    fs.copyFileSync(src('CITATION.cff'), dest('CITATION.cff'));
+    fs.copyFileSync(src('expected.yml'), dest('expected.yml'));
+    process.chdir(temporary_directory);
+});
+test('upserting a doi', () => {
+    const upsert_location = 'doi';
+    const prereserved_doi = '10.5281/upserted.1234567';
+    upserting_1.upsert_prereserved_doi(upsert_location, prereserved_doi);
+    const actual = fs.readFileSync('CITATION.cff', 'utf8');
+    const expected = fs.readFileSync('expected.yml', 'utf8');
+    expect(actual).toEqual(expected);
+});
+afterEach(() => {
+    fs.rmdirSync(temporary_directory, { recursive: true });
+});

tests/upserting/1.0.3/doi/overwrite/upserting.test.js

@@ -0,0 +1,49 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    Object.defineProperty(o, k2, { enumerable: true, get: function() { return m[k]; } });
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || function (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __setModuleDefault(result, mod);
+    return result;
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const upserting_1 = require("../../../../../src/upserting");
+const fs = __importStar(require("fs"));
+const path = __importStar(require("path"));
+const os = __importStar(require("os"));
+let temporary_directory;
+beforeEach(() => {
+    const src = (f) => {
+        return path.join(__dirname, f);
+    };
+    const dest = (f) => {
+        return path.join(temporary_directory, f);
+    };
+    temporary_directory = fs.mkdtempSync(`${os.tmpdir()}${path.sep}zenodraft-action-testing.`);
+    fs.copyFileSync(src('CITATION.cff'), dest('CITATION.cff'));
+    fs.copyFileSync(src('expected.yml'), dest('expected.yml'));
+    process.chdir(temporary_directory);
+});
+test('upserting a doi', () => {
+    const upsert_location = 'doi';
+    const prereserved_doi = '10.5281/upserted.1234567';
+    upserting_1.upsert_prereserved_doi(upsert_location, prereserved_doi);
+    const actual = fs.readFileSync('CITATION.cff', 'utf8');
+    const expected = fs.readFileSync('expected.yml', 'utf8');
+    expect(actual).toEqual(expected);
+});
+afterEach(() => {
+    fs.rmdirSync(temporary_directory, { recursive: true });
+});

tests/upserting/1.0.3/errors/upserting.test.js

@@ -0,0 +1,55 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    Object.defineProperty(o, k2, { enumerable: true, get: function() { return m[k]; } });
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || function (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __setModuleDefault(result, mod);
+    return result;
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const upserting_1 = require("../../../../src/upserting");
+const fs = __importStar(require("fs"));
+const path = __importStar(require("path"));
+const os = __importStar(require("os"));
+const assert_1 = require("assert");
+let temporary_directory;
+beforeEach(() => {
+    const src = (f) => {
+        return path.join(__dirname, f);
+    };
+    const dest = (f) => {
+        return path.join(temporary_directory, f);
+    };
+    temporary_directory = fs.mkdtempSync(`${os.tmpdir()}${path.sep}zenodraft-action-testing.`);
+    fs.copyFileSync(src('CITATION.cff'), dest('CITATION.cff'));
+    process.chdir(temporary_directory);
+});
+test('upserting a doi', () => {
+    const upsert_location = 'identifiers[0]';
+    const prereserved_doi = '10.5281/upserted.1234567';
+    const throwfun = () => {
+        upserting_1.upsert_prereserved_doi(upsert_location, prereserved_doi);
+    };
+    expect(throwfun).toThrow(assert_1.AssertionError);
+    try {
+        throwfun();
+    }
+    catch (err) {
+        expect(err.message).toBe('Your CITATION.cff file does not support key \'identifiers\'. Consider updating its \'cff-version\' value.');
+    }
+});
+afterEach(() => {
+    fs.rmdirSync(temporary_directory, { recursive: true });
+});

tests/upserting/1.1.0/doi/append/upserting.test.js

@@ -0,0 +1,49 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    Object.defineProperty(o, k2, { enumerable: true, get: function() { return m[k]; } });
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || function (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __setModuleDefault(result, mod);
+    return result;
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const upserting_1 = require("../../../../../src/upserting");
+const fs = __importStar(require("fs"));
+const path = __importStar(require("path"));
+const os = __importStar(require("os"));
+let temporary_directory;
+beforeEach(() => {
+    const src = (f) => {
+        return path.join(__dirname, f);
+    };
+    const dest = (f) => {
+        return path.join(temporary_directory, f);
+    };
+    temporary_directory = fs.mkdtempSync(`${os.tmpdir()}${path.sep}zenodraft-action-testing.`);
+    fs.copyFileSync(src('CITATION.cff'), dest('CITATION.cff'));
+    fs.copyFileSync(src('expected.yml'), dest('expected.yml'));
+    process.chdir(temporary_directory);
+});
+test('upserting a doi', () => {
+    const upsert_location = 'doi';
+    const prereserved_doi = '10.5281/upserted.1234567';
+    upserting_1.upsert_prereserved_doi(upsert_location, prereserved_doi);
+    const actual = fs.readFileSync('CITATION.cff', 'utf8');
+    const expected = fs.readFileSync('expected.yml', 'utf8');
+    expect(actual).toEqual(expected);
+});
+afterEach(() => {
+    fs.rmdirSync(temporary_directory, { recursive: true });
+});