jats-xml 0.0.7 → 0.0.9

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Files changed (26) hide show
  1. package/LICENSE +21 -0
  2. package/README.md +5 -1
  3. package/dist/cjs/cli/parse.js +4 -4
  4. package/dist/cjs/download.js +37 -40
  5. package/dist/cjs/resolvers.js +4 -3
  6. package/dist/cjs/version.js +1 -1
  7. package/dist/esm/cli/parse.js +4 -4
  8. package/dist/esm/download.js +37 -40
  9. package/dist/esm/resolvers.js +4 -3
  10. package/dist/esm/version.js +1 -1
  11. package/dist/jats.js +667 -772
  12. package/dist/types/cli/parse.d.ts.map +1 -1
  13. package/dist/types/download.d.ts +4 -5
  14. package/dist/types/download.d.ts.map +1 -1
  15. package/dist/types/jats.d.ts +1 -1
  16. package/dist/types/jats.d.ts.map +1 -1
  17. package/dist/types/resolvers.d.ts +2 -6
  18. package/dist/types/resolvers.d.ts.map +1 -1
  19. package/dist/types/types/elements.d.ts +23 -23
  20. package/dist/types/types/elements.d.ts.map +1 -1
  21. package/dist/types/types/session.d.ts +9 -1
  22. package/dist/types/types/session.d.ts.map +1 -1
  23. package/dist/types/utils.d.ts +1 -1
  24. package/dist/types/utils.d.ts.map +1 -1
  25. package/dist/types/version.d.ts +1 -1
  26. package/package.json +22 -13
package/LICENSE ADDED
@@ -0,0 +1,21 @@
1
+ The MIT License (MIT)
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+
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+ Copyright (c) 2023 Curvenote Inc.
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+
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+ Permission is hereby granted, free of charge, to any person obtaining a copy
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+ of this software and associated documentation files (the "Software"), to deal
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+ in the Software without restriction, including without limitation the rights
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+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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+ copies of the Software, and to permit persons to whom the Software is
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+ furnished to do so, subject to the following conditions:
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+
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+ The above copyright notice and this permission notice shall be included in all
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+ copies or substantial portions of the Software.
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+
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+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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+ SOFTWARE.
package/README.md CHANGED
@@ -1,5 +1,9 @@
1
1
  # jats-xml
2
2
 
3
+ [![jats-xml on npm](https://img.shields.io/npm/v/jats-xml.svg)](https://www.npmjs.com/package/jats-xml)
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+ [![MIT License](https://img.shields.io/badge/license-MIT-blue.svg)](https://github.com/curvenote/jats-xml/blob/main/LICENSE)
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+ [![CI](https://github.com/curvenote/jats-xml/workflows/CI/badge.svg)](https://github.com/curvenote/jats-xml/actions)
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+
3
7
  Types and utilities for working with JATS XML documents in Node and Typescript.
4
8
 
5
9
  Read and write JATS XML from node or see summries from the command line.
@@ -41,7 +45,7 @@ jats summary /local/article.jats
41
45
 
42
46
  This will provide a summary, including a list of what the JATS file contains.
43
47
 
44
- ![Output of `jats summary`](/packages/jats-xml/images/jats-output.png)
48
+ ![Output of `jats summary`](/images/jats-output.png)
45
49
 
46
50
  ## Working in Typescript
47
51
 
package/dist/cjs/cli/parse.js CHANGED
@@ -30,7 +30,7 @@ const utils_1 = require("../utils");
30
30
  function hasValidExtension(output) {
31
31
  return ['.xml', '.jats'].includes((0, path_1.extname)(output).toLowerCase());
32
32
  }
33
- function downloadAndSaveJats(session, urlOrDoi, output) {
33
+ function downloadAndSaveJats(session, urlOrDoi, output, opts = { resolvers: resolvers_1.DEFAULT_RESOLVERS }) {
34
34
  return __awaiter(this, void 0, void 0, function* () {
35
35
  if (fs_1.default.existsSync(urlOrDoi)) {
36
36
  throw new Error(`File "${urlOrDoi}" is local and cannot be downloaded!`);
@@ -41,12 +41,12 @@ function downloadAndSaveJats(session, urlOrDoi, output) {
41
41
  if (!hasValidExtension(output)) {
42
42
  session.log.warn(`The extension ${(0, path_1.extname)(output)} is not a valid extension for JATS, try using ".xml" or ".jats"`);
43
43
  }
44
- const { data } = yield (0, download_1.downloadJatsFromUrl)(session, urlOrDoi, resolvers_1.DEFAULT_RESOLVERS);
44
+ const { data } = yield (0, download_1.downloadJatsFromUrl)(session, urlOrDoi, opts);
45
45
  (0, myst_cli_utils_1.writeFileToFolder)(output, data);
46
46
  return data;
47
47
  });
48
48
  }
49
- function parseJats(session, file) {
49
+ function parseJats(session, file, opts = { resolvers: resolvers_1.DEFAULT_RESOLVERS }) {
50
50
  return __awaiter(this, void 0, void 0, function* () {
51
51
  const toc = (0, myst_cli_utils_1.tic)();
52
52
  if (fs_1.default.existsSync(file)) {
@@ -54,7 +54,7 @@ function parseJats(session, file) {
54
54
  const data = fs_1.default.readFileSync(file).toString();
55
55
  return new jats_1.Jats(data, { log: session.log });
56
56
  }
57
- const { source, data } = yield (0, download_1.downloadJatsFromUrl)(session, file, resolvers_1.DEFAULT_RESOLVERS);
57
+ const { source, data } = yield (0, download_1.downloadJatsFromUrl)(session, file, opts);
58
58
  const jats = new jats_1.Jats(data, { source, log: session.log });
59
59
  session.log.debug(toc(`Downloaded and parsed JATS file in %s`));
60
60
  return jats;
package/dist/cjs/download.js CHANGED
@@ -27,28 +27,17 @@ function logAboutJatsFailing(session, jatsUrls) {
27
27
  session.log.debug((0, fair_principles_1.formatPrinciples)('A*', { chalk: chalk_1.default }));
28
28
  session.log.info(`${chalk_1.default.blue('The link may work in a browser.')}\n`);
29
29
  }
30
- function dowloadFromUrl(session, jatsUrl) {
30
+ function dowloadFromUrl(session, jatsUrl, opts) {
31
+ var _a, _b;
31
32
  return __awaiter(this, void 0, void 0, function* () {
32
33
  const toc = (0, myst_cli_utils_1.tic)();
33
34
  session.log.debug(`Fetching JATS from ${jatsUrl}`);
34
- const resp = yield (0, node_fetch_1.default)(jatsUrl, {
35
- headers: [
36
- ['accept', 'application/xml'],
37
- [
38
- 'user-agent',
39
- // A bunch of publishers just show the login screen or quickly block you.
40
- // We don't want to DDOS these publishers, they are the _good ones_ for sharing the XML!!
41
- // But some block on the second request?!
42
- // So we can pretend to be a random browser, I guess. How silly. 🤷‍♂️
43
- `Mozilla/5.0 (Macintosh; Intel Mac OS X ${Math.floor(Math.random() * 100)})`,
44
- ],
45
- ],
46
- });
35
+ const resp = yield ((_a = opts === null || opts === void 0 ? void 0 : opts.fetcher) !== null && _a !== void 0 ? _a : defaultFetcher)(jatsUrl, 'xml');
47
36
  if (!resp.ok) {
48
37
  session.log.debug(`JATS failed to download from "${jatsUrl}"`);
49
38
  throw new Error(`STATUS ${resp.status}: ${resp.statusText}`);
50
39
  }
51
- const contentType = resp.headers.get('content-type');
40
+ const contentType = (_b = resp.headers) === null || _b === void 0 ? void 0 : _b.get('content-type');
52
41
  if (!((contentType === null || contentType === void 0 ? void 0 : contentType.includes('application/xml')) ||
53
42
  (contentType === null || contentType === void 0 ? void 0 : contentType.includes('text/xml')) ||
54
43
  (contentType === null || contentType === void 0 ? void 0 : contentType.includes('text/plain')))) {
@@ -59,6 +48,16 @@ function dowloadFromUrl(session, jatsUrl) {
59
48
  return data;
60
49
  });
61
50
  }
51
+ function defaultFetcher(url, kind) {
52
+ switch (kind) {
53
+ case 'json':
54
+ return (0, node_fetch_1.default)(url, { headers: [['Accept', 'application/json']] });
55
+ case 'xml':
56
+ return (0, node_fetch_1.default)(url, { headers: [['Accept', 'application/xml']] });
57
+ default:
58
+ return (0, node_fetch_1.default)(url);
59
+ }
60
+ }
62
61
  /**
63
62
  * There are 5.8M or so DOIs that have a full XML record:
64
63
  *
@@ -66,26 +65,26 @@ function dowloadFromUrl(session, jatsUrl) {
66
65
  *
67
66
  * This function tries to find the correct URL for the record.
68
67
  */
69
- function checkIfDoiHasJats(session, urlOrDoi) {
70
- var _a, _b, _c, _d;
68
+ function checkIfDoiHasJats(session, urlOrDoi, opts) {
69
+ var _a, _b, _c, _d, _e;
71
70
  return __awaiter(this, void 0, void 0, function* () {
72
71
  if (!doi_utils_1.default.validate(urlOrDoi))
73
72
  return;
74
73
  const toc = (0, myst_cli_utils_1.tic)();
75
74
  const doiUrl = doi_utils_1.default.buildUrl(urlOrDoi);
76
75
  session.log.debug(`Attempting to resolving full XML from DOI ${doiUrl}`);
77
- const resp = yield (0, node_fetch_1.default)(doiUrl, { headers: [['Accept', 'application/json']] });
76
+ const resp = yield ((_a = opts === null || opts === void 0 ? void 0 : opts.fetcher) !== null && _a !== void 0 ? _a : defaultFetcher)(doiUrl, 'json');
78
77
  if (!resp.ok) {
79
78
  // Silently return -- other functions can try!
80
79
  session.log.debug(`DOI failed to resolve: ${doiUrl}`);
81
80
  return;
82
81
  }
83
82
  const data = (yield resp.json());
84
- session.log.debug(toc(`DOI resolved in %s with ${(_b = (_a = data.link) === null || _a === void 0 ? void 0 : _a.length) !== null && _b !== void 0 ? _b : 0} links to content`));
83
+ session.log.debug(toc(`DOI resolved in %s with ${(_c = (_b = data.link) === null || _b === void 0 ? void 0 : _b.length) !== null && _c !== void 0 ? _c : 0} links to content`));
85
84
  if (data.link) {
86
85
  session.log.debug(['', ...data.link.map((link) => `content-type: ${link['content-type']}, ${link.URL}\n`)].join(' - '));
87
86
  }
88
- const fullXml = (_d = (_c = data.link) === null || _c === void 0 ? void 0 : _c.find((link) => { var _a; return ['text/xml', 'application/xml'].includes((_a = link['content-type']) !== null && _a !== void 0 ? _a : ''); })) === null || _d === void 0 ? void 0 : _d.URL;
87
+ const fullXml = (_e = (_d = data.link) === null || _d === void 0 ? void 0 : _d.find((link) => { var _a; return ['text/xml', 'application/xml'].includes((_a = link['content-type']) !== null && _a !== void 0 ? _a : ''); })) === null || _e === void 0 ? void 0 : _e.URL;
89
88
  if (fullXml)
90
89
  return fullXml;
91
90
  session.log.debug(`Could not find XML in DOI record ${doiUrl}`);
@@ -95,26 +94,24 @@ function checkIfDoiHasJats(session, urlOrDoi) {
95
94
  /**
96
95
  * https://www.ncbi.nlm.nih.gov/pmc/tools/id-converter-api/
97
96
  */
98
- function convertPMID2PMCID(session, PMID) {
99
- var _a, _b;
97
+ function convertPMID2PMCID(session, PMID, opts) {
98
+ var _a, _b, _c;
100
99
  return __awaiter(this, void 0, void 0, function* () {
101
100
  if (PMID.startsWith('https://')) {
102
101
  const idPart = new URL(PMID).pathname.slice(1);
103
102
  session.log.debug(`Extract ${PMID} to ${idPart}`);
104
- return convertPMID2PMCID(session, idPart);
103
+ return convertPMID2PMCID(session, idPart, opts);
105
104
  }
106
105
  const toc = (0, myst_cli_utils_1.tic)();
107
106
  const converter = 'https://www.ncbi.nlm.nih.gov/pmc/utils/idconv/v1.0/';
108
- const resp = yield (0, node_fetch_1.default)(`${converter}?tool=jats-xml&format=json&ids=${PMID}`, {
109
- headers: [['Accept', 'application/json']],
110
- });
107
+ const resp = yield ((_a = opts === null || opts === void 0 ? void 0 : opts.fetcher) !== null && _a !== void 0 ? _a : defaultFetcher)(`${converter}?tool=jats-xml&format=json&ids=${PMID}`, 'json');
111
108
  if (!resp.ok) {
112
109
  // Silently return -- other functions can try!
113
110
  session.log.debug(`Failed to convert PubMedID: ${PMID}`);
114
111
  return;
115
112
  }
116
113
  const data = yield resp.json();
117
- const PMCID = (_b = (_a = data === null || data === void 0 ? void 0 : data.records) === null || _a === void 0 ? void 0 : _a[0]) === null || _b === void 0 ? void 0 : _b.pmcid;
114
+ const PMCID = (_c = (_b = data === null || data === void 0 ? void 0 : data.records) === null || _b === void 0 ? void 0 : _b[0]) === null || _c === void 0 ? void 0 : _c.pmcid;
118
115
  session.log.debug(toc(`Used nih.gov to transform ${PMID} to ${PMCID} in %s.`));
119
116
  return PMCID;
120
117
  });
@@ -124,8 +121,8 @@ function pubMedCentralJats(PMCID) {
124
121
  const normalized = PMCID.replace(/^PMC:?/, '');
125
122
  return `https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&id=${normalized}`;
126
123
  }
127
- function checkIfPubMedCentralHasJats(session, urlOrDoi) {
128
- var _a, _b;
124
+ function checkIfPubMedCentralHasJats(session, urlOrDoi, opts) {
125
+ var _a, _b, _c;
129
126
  return __awaiter(this, void 0, void 0, function* () {
130
127
  if (urlOrDoi.match(/^PMC:?([0-9]+)$/))
131
128
  return pubMedCentralJats(urlOrDoi);
@@ -135,18 +132,18 @@ function checkIfPubMedCentralHasJats(session, urlOrDoi) {
135
132
  const doiUrl = doi_utils_1.default.buildUrl(urlOrDoi);
136
133
  session.log.debug(`Attempting to resolve PMCID using OpenAlex from ${doiUrl}`);
137
134
  const openAlexUrl = `https://api.openalex.org/works/${doiUrl}`;
138
- const resp = yield (0, node_fetch_1.default)(openAlexUrl, { headers: [['Accept', 'application/json']] });
135
+ const resp = yield ((_a = opts === null || opts === void 0 ? void 0 : opts.fetcher) !== null && _a !== void 0 ? _a : defaultFetcher)(openAlexUrl, 'json');
139
136
  if (!resp.ok) {
140
137
  // Silently return -- other functions can try!
141
138
  session.log.debug(`Failed to lookup on OpenAlex: ${openAlexUrl}`);
142
139
  return;
143
140
  }
144
141
  const data = (yield resp.json());
145
- const PMID = (_a = data === null || data === void 0 ? void 0 : data.ids) === null || _a === void 0 ? void 0 : _a.pmid;
146
- let PMCID = (_b = data === null || data === void 0 ? void 0 : data.ids) === null || _b === void 0 ? void 0 : _b.pmcid;
142
+ const PMID = (_b = data === null || data === void 0 ? void 0 : data.ids) === null || _b === void 0 ? void 0 : _b.pmid;
143
+ let PMCID = (_c = data === null || data === void 0 ? void 0 : data.ids) === null || _c === void 0 ? void 0 : _c.pmcid;
147
144
  if (!PMCID && !!PMID) {
148
145
  session.log.debug(toc(`OpenAlex resolved ${data === null || data === void 0 ? void 0 : data.ids.openalex} in %s. There is no PMCID, but there is a PMID`));
149
- PMCID = yield convertPMID2PMCID(session, PMID);
146
+ PMCID = yield convertPMID2PMCID(session, PMID, opts);
150
147
  if (!PMCID) {
151
148
  session.log.debug(toc(`PubMed does not have a record of ${PMID}`));
152
149
  return;
@@ -161,18 +158,18 @@ function checkIfPubMedCentralHasJats(session, urlOrDoi) {
161
158
  });
162
159
  }
163
160
  exports.checkIfPubMedCentralHasJats = checkIfPubMedCentralHasJats;
164
- function downloadJatsFromUrl(session, urlOrDoi, resolvers) {
161
+ function downloadJatsFromUrl(session, urlOrDoi, opts = {}) {
165
162
  return __awaiter(this, void 0, void 0, function* () {
166
163
  const expectedUrls = (yield Promise.all([
167
- checkIfPubMedCentralHasJats(session, urlOrDoi),
168
- checkIfDoiHasJats(session, urlOrDoi),
164
+ checkIfPubMedCentralHasJats(session, urlOrDoi, opts),
165
+ checkIfDoiHasJats(session, urlOrDoi, opts),
169
166
  ])).filter((u) => !!u);
170
167
  if (expectedUrls.length > 0) {
171
168
  session.log.debug(['Trying URLs:\n', ...expectedUrls.map((url) => ` ${url}\n`)].join(' - '));
172
169
  for (let index = 0; index < expectedUrls.length; index++) {
173
170
  const url = expectedUrls[index];
174
171
  try {
175
- const data = yield dowloadFromUrl(session, url);
172
+ const data = yield dowloadFromUrl(session, url, opts);
176
173
  if (data)
177
174
  return { source: url, data };
178
175
  }
@@ -184,13 +181,13 @@ function downloadJatsFromUrl(session, urlOrDoi, resolvers) {
184
181
  logAboutJatsFailing(session, expectedUrls);
185
182
  }
186
183
  if (doi_utils_1.default.validate(urlOrDoi)) {
187
- const jatsUrl = yield (0, resolvers_1.customResolveJatsUrlFromDoi)(session, urlOrDoi, resolvers);
188
- const data = yield dowloadFromUrl(session, jatsUrl);
184
+ const jatsUrl = yield (0, resolvers_1.customResolveJatsUrlFromDoi)(session, urlOrDoi, opts);
185
+ const data = yield dowloadFromUrl(session, jatsUrl, opts);
189
186
  return { source: jatsUrl, data };
190
187
  }
191
188
  if ((0, myst_cli_utils_1.isUrl)(urlOrDoi)) {
192
189
  session.log.debug("No resolver matched, and the URL doesn't look like a DOI. We will attempt to download it directly.");
193
- const data = yield dowloadFromUrl(session, urlOrDoi);
190
+ const data = yield dowloadFromUrl(session, urlOrDoi, opts);
194
191
  return { source: urlOrDoi, data };
195
192
  }
196
193
  throw new Error(`Could not find ${urlOrDoi} locally, and it doesn't look like a URL or DOI`);
package/dist/cjs/resolvers.js CHANGED
@@ -47,16 +47,17 @@ exports.DEFAULT_RESOLVERS = [exports.elife, exports.plos, exports.joss];
47
47
  /**
48
48
  * Use the known custom resolvers to pick where the JATS should be downloaded from.
49
49
  */
50
- function customResolveJatsUrlFromDoi(session, doiString, resolvers = exports.DEFAULT_RESOLVERS) {
50
+ function customResolveJatsUrlFromDoi(session, doiString, opts = { resolvers: exports.DEFAULT_RESOLVERS }) {
51
+ var _a, _b;
51
52
  return __awaiter(this, void 0, void 0, function* () {
52
53
  if (!doi_utils_1.default.validate(doiString))
53
54
  throw new Error(`The doi ${doiString} is not valid`);
54
55
  const doiUrl = doi_utils_1.default.buildUrl(doiString);
55
56
  session.log.debug(`Resolving DOI ${doiUrl}`);
56
- const resp = yield (0, node_fetch_1.default)(doiUrl);
57
+ const resp = yield ((_a = opts === null || opts === void 0 ? void 0 : opts.fetcher) !== null && _a !== void 0 ? _a : node_fetch_1.default)(doiUrl);
57
58
  const articleUrl = resp.url;
58
59
  session.log.debug(`Found resolved URL for DOI at ${articleUrl}`);
59
- const resolver = resolvers.find((r) => r.test(articleUrl));
60
+ const resolver = (_b = opts === null || opts === void 0 ? void 0 : opts.resolvers) === null || _b === void 0 ? void 0 : _b.find((r) => r.test(articleUrl));
60
61
  if (!resolver)
61
62
  throw new Error(`Could not resolve JATS for ${articleUrl}, no resolver matched`);
62
63
  const jatsUrl = resolver.jatsUrl(articleUrl);
package/dist/cjs/version.js CHANGED
@@ -1,4 +1,4 @@
1
1
  "use strict";
2
2
  Object.defineProperty(exports, "__esModule", { value: true });
3
- const version = '0.0.7';
3
+ const version = '0.0.9';
4
4
  exports.default = version;
package/dist/esm/cli/parse.js CHANGED
@@ -24,7 +24,7 @@ import { findArticleId, formatDate, toDate } from '../utils';
24
24
  function hasValidExtension(output) {
25
25
  return ['.xml', '.jats'].includes(extname(output).toLowerCase());
26
26
  }
27
- function downloadAndSaveJats(session, urlOrDoi, output) {
27
+ function downloadAndSaveJats(session, urlOrDoi, output, opts = { resolvers: DEFAULT_RESOLVERS }) {
28
28
  return __awaiter(this, void 0, void 0, function* () {
29
29
  if (fs.existsSync(urlOrDoi)) {
30
30
  throw new Error(`File "${urlOrDoi}" is local and cannot be downloaded!`);
@@ -35,12 +35,12 @@ function downloadAndSaveJats(session, urlOrDoi, output) {
35
35
  if (!hasValidExtension(output)) {
36
36
  session.log.warn(`The extension ${extname(output)} is not a valid extension for JATS, try using ".xml" or ".jats"`);
37
37
  }
38
- const { data } = yield downloadJatsFromUrl(session, urlOrDoi, DEFAULT_RESOLVERS);
38
+ const { data } = yield downloadJatsFromUrl(session, urlOrDoi, opts);
39
39
  writeFileToFolder(output, data);
40
40
  return data;
41
41
  });
42
42
  }
43
- function parseJats(session, file) {
43
+ function parseJats(session, file, opts = { resolvers: DEFAULT_RESOLVERS }) {
44
44
  return __awaiter(this, void 0, void 0, function* () {
45
45
  const toc = tic();
46
46
  if (fs.existsSync(file)) {
@@ -48,7 +48,7 @@ function parseJats(session, file) {
48
48
  const data = fs.readFileSync(file).toString();
49
49
  return new Jats(data, { log: session.log });
50
50
  }
51
- const { source, data } = yield downloadJatsFromUrl(session, file, DEFAULT_RESOLVERS);
51
+ const { source, data } = yield downloadJatsFromUrl(session, file, opts);
52
52
  const jats = new Jats(data, { source, log: session.log });
53
53
  session.log.debug(toc(`Downloaded and parsed JATS file in %s`));
54
54
  return jats;
package/dist/esm/download.js CHANGED
@@ -21,28 +21,17 @@ function logAboutJatsFailing(session, jatsUrls) {
21
21
  session.log.debug(formatPrinciples('A*', { chalk }));
22
22
  session.log.info(`${chalk.blue('The link may work in a browser.')}\n`);
23
23
  }
24
- function dowloadFromUrl(session, jatsUrl) {
24
+ function dowloadFromUrl(session, jatsUrl, opts) {
25
+ var _a, _b;
25
26
  return __awaiter(this, void 0, void 0, function* () {
26
27
  const toc = tic();
27
28
  session.log.debug(`Fetching JATS from ${jatsUrl}`);
28
- const resp = yield fetch(jatsUrl, {
29
- headers: [
30
- ['accept', 'application/xml'],
31
- [
32
- 'user-agent',
33
- // A bunch of publishers just show the login screen or quickly block you.
34
- // We don't want to DDOS these publishers, they are the _good ones_ for sharing the XML!!
35
- // But some block on the second request?!
36
- // So we can pretend to be a random browser, I guess. How silly. 🤷‍♂️
37
- `Mozilla/5.0 (Macintosh; Intel Mac OS X ${Math.floor(Math.random() * 100)})`,
38
- ],
39
- ],
40
- });
29
+ const resp = yield ((_a = opts === null || opts === void 0 ? void 0 : opts.fetcher) !== null && _a !== void 0 ? _a : defaultFetcher)(jatsUrl, 'xml');
41
30
  if (!resp.ok) {
42
31
  session.log.debug(`JATS failed to download from "${jatsUrl}"`);
43
32
  throw new Error(`STATUS ${resp.status}: ${resp.statusText}`);
44
33
  }
45
- const contentType = resp.headers.get('content-type');
34
+ const contentType = (_b = resp.headers) === null || _b === void 0 ? void 0 : _b.get('content-type');
46
35
  if (!((contentType === null || contentType === void 0 ? void 0 : contentType.includes('application/xml')) ||
47
36
  (contentType === null || contentType === void 0 ? void 0 : contentType.includes('text/xml')) ||
48
37
  (contentType === null || contentType === void 0 ? void 0 : contentType.includes('text/plain')))) {
@@ -53,6 +42,16 @@ function dowloadFromUrl(session, jatsUrl) {
53
42
  return data;
54
43
  });
55
44
  }
45
+ function defaultFetcher(url, kind) {
46
+ switch (kind) {
47
+ case 'json':
48
+ return fetch(url, { headers: [['Accept', 'application/json']] });
49
+ case 'xml':
50
+ return fetch(url, { headers: [['Accept', 'application/xml']] });
51
+ default:
52
+ return fetch(url);
53
+ }
54
+ }
56
55
  /**
57
56
  * There are 5.8M or so DOIs that have a full XML record:
58
57
  *
@@ -60,26 +59,26 @@ function dowloadFromUrl(session, jatsUrl) {
60
59
  *
61
60
  * This function tries to find the correct URL for the record.
62
61
  */
63
- function checkIfDoiHasJats(session, urlOrDoi) {
64
- var _a, _b, _c, _d;
62
+ function checkIfDoiHasJats(session, urlOrDoi, opts) {
63
+ var _a, _b, _c, _d, _e;
65
64
  return __awaiter(this, void 0, void 0, function* () {
66
65
  if (!doi.validate(urlOrDoi))
67
66
  return;
68
67
  const toc = tic();
69
68
  const doiUrl = doi.buildUrl(urlOrDoi);
70
69
  session.log.debug(`Attempting to resolving full XML from DOI ${doiUrl}`);
71
- const resp = yield fetch(doiUrl, { headers: [['Accept', 'application/json']] });
70
+ const resp = yield ((_a = opts === null || opts === void 0 ? void 0 : opts.fetcher) !== null && _a !== void 0 ? _a : defaultFetcher)(doiUrl, 'json');
72
71
  if (!resp.ok) {
73
72
  // Silently return -- other functions can try!
74
73
  session.log.debug(`DOI failed to resolve: ${doiUrl}`);
75
74
  return;
76
75
  }
77
76
  const data = (yield resp.json());
78
- session.log.debug(toc(`DOI resolved in %s with ${(_b = (_a = data.link) === null || _a === void 0 ? void 0 : _a.length) !== null && _b !== void 0 ? _b : 0} links to content`));
77
+ session.log.debug(toc(`DOI resolved in %s with ${(_c = (_b = data.link) === null || _b === void 0 ? void 0 : _b.length) !== null && _c !== void 0 ? _c : 0} links to content`));
79
78
  if (data.link) {
80
79
  session.log.debug(['', ...data.link.map((link) => `content-type: ${link['content-type']}, ${link.URL}\n`)].join(' - '));
81
80
  }
82
- const fullXml = (_d = (_c = data.link) === null || _c === void 0 ? void 0 : _c.find((link) => { var _a; return ['text/xml', 'application/xml'].includes((_a = link['content-type']) !== null && _a !== void 0 ? _a : ''); })) === null || _d === void 0 ? void 0 : _d.URL;
81
+ const fullXml = (_e = (_d = data.link) === null || _d === void 0 ? void 0 : _d.find((link) => { var _a; return ['text/xml', 'application/xml'].includes((_a = link['content-type']) !== null && _a !== void 0 ? _a : ''); })) === null || _e === void 0 ? void 0 : _e.URL;
83
82
  if (fullXml)
84
83
  return fullXml;
85
84
  session.log.debug(`Could not find XML in DOI record ${doiUrl}`);
@@ -89,26 +88,24 @@ function checkIfDoiHasJats(session, urlOrDoi) {
89
88
  /**
90
89
  * https://www.ncbi.nlm.nih.gov/pmc/tools/id-converter-api/
91
90
  */
92
- export function convertPMID2PMCID(session, PMID) {
93
- var _a, _b;
91
+ export function convertPMID2PMCID(session, PMID, opts) {
92
+ var _a, _b, _c;
94
93
  return __awaiter(this, void 0, void 0, function* () {
95
94
  if (PMID.startsWith('https://')) {
96
95
  const idPart = new URL(PMID).pathname.slice(1);
97
96
  session.log.debug(`Extract ${PMID} to ${idPart}`);
98
- return convertPMID2PMCID(session, idPart);
97
+ return convertPMID2PMCID(session, idPart, opts);
99
98
  }
100
99
  const toc = tic();
101
100
  const converter = 'https://www.ncbi.nlm.nih.gov/pmc/utils/idconv/v1.0/';
102
- const resp = yield fetch(`${converter}?tool=jats-xml&format=json&ids=${PMID}`, {
103
- headers: [['Accept', 'application/json']],
104
- });
101
+ const resp = yield ((_a = opts === null || opts === void 0 ? void 0 : opts.fetcher) !== null && _a !== void 0 ? _a : defaultFetcher)(`${converter}?tool=jats-xml&format=json&ids=${PMID}`, 'json');
105
102
  if (!resp.ok) {
106
103
  // Silently return -- other functions can try!
107
104
  session.log.debug(`Failed to convert PubMedID: ${PMID}`);
108
105
  return;
109
106
  }
110
107
  const data = yield resp.json();
111
- const PMCID = (_b = (_a = data === null || data === void 0 ? void 0 : data.records) === null || _a === void 0 ? void 0 : _a[0]) === null || _b === void 0 ? void 0 : _b.pmcid;
108
+ const PMCID = (_c = (_b = data === null || data === void 0 ? void 0 : data.records) === null || _b === void 0 ? void 0 : _b[0]) === null || _c === void 0 ? void 0 : _c.pmcid;
112
109
  session.log.debug(toc(`Used nih.gov to transform ${PMID} to ${PMCID} in %s.`));
113
110
  return PMCID;
114
111
  });
@@ -117,8 +114,8 @@ function pubMedCentralJats(PMCID) {
117
114
  const normalized = PMCID.replace(/^PMC:?/, '');
118
115
  return `https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&id=${normalized}`;
119
116
  }
120
- export function checkIfPubMedCentralHasJats(session, urlOrDoi) {
121
- var _a, _b;
117
+ export function checkIfPubMedCentralHasJats(session, urlOrDoi, opts) {
118
+ var _a, _b, _c;
122
119
  return __awaiter(this, void 0, void 0, function* () {
123
120
  if (urlOrDoi.match(/^PMC:?([0-9]+)$/))
124
121
  return pubMedCentralJats(urlOrDoi);
@@ -128,18 +125,18 @@ export function checkIfPubMedCentralHasJats(session, urlOrDoi) {
128
125
  const doiUrl = doi.buildUrl(urlOrDoi);
129
126
  session.log.debug(`Attempting to resolve PMCID using OpenAlex from ${doiUrl}`);
130
127
  const openAlexUrl = `https://api.openalex.org/works/${doiUrl}`;
131
- const resp = yield fetch(openAlexUrl, { headers: [['Accept', 'application/json']] });
128
+ const resp = yield ((_a = opts === null || opts === void 0 ? void 0 : opts.fetcher) !== null && _a !== void 0 ? _a : defaultFetcher)(openAlexUrl, 'json');
132
129
  if (!resp.ok) {
133
130
  // Silently return -- other functions can try!
134
131
  session.log.debug(`Failed to lookup on OpenAlex: ${openAlexUrl}`);
135
132
  return;
136
133
  }
137
134
  const data = (yield resp.json());
138
- const PMID = (_a = data === null || data === void 0 ? void 0 : data.ids) === null || _a === void 0 ? void 0 : _a.pmid;
139
- let PMCID = (_b = data === null || data === void 0 ? void 0 : data.ids) === null || _b === void 0 ? void 0 : _b.pmcid;
135
+ const PMID = (_b = data === null || data === void 0 ? void 0 : data.ids) === null || _b === void 0 ? void 0 : _b.pmid;
136
+ let PMCID = (_c = data === null || data === void 0 ? void 0 : data.ids) === null || _c === void 0 ? void 0 : _c.pmcid;
140
137
  if (!PMCID && !!PMID) {
141
138
  session.log.debug(toc(`OpenAlex resolved ${data === null || data === void 0 ? void 0 : data.ids.openalex} in %s. There is no PMCID, but there is a PMID`));
142
- PMCID = yield convertPMID2PMCID(session, PMID);
139
+ PMCID = yield convertPMID2PMCID(session, PMID, opts);
143
140
  if (!PMCID) {
144
141
  session.log.debug(toc(`PubMed does not have a record of ${PMID}`));
145
142
  return;
@@ -153,18 +150,18 @@ export function checkIfPubMedCentralHasJats(session, urlOrDoi) {
153
150
  return pubMedCentralJats(PMCID);
154
151
  });
155
152
  }
156
- export function downloadJatsFromUrl(session, urlOrDoi, resolvers) {
153
+ export function downloadJatsFromUrl(session, urlOrDoi, opts = {}) {
157
154
  return __awaiter(this, void 0, void 0, function* () {
158
155
  const expectedUrls = (yield Promise.all([
159
- checkIfPubMedCentralHasJats(session, urlOrDoi),
160
- checkIfDoiHasJats(session, urlOrDoi),
156
+ checkIfPubMedCentralHasJats(session, urlOrDoi, opts),
157
+ checkIfDoiHasJats(session, urlOrDoi, opts),
161
158
  ])).filter((u) => !!u);
162
159
  if (expectedUrls.length > 0) {
163
160
  session.log.debug(['Trying URLs:\n', ...expectedUrls.map((url) => ` ${url}\n`)].join(' - '));
164
161
  for (let index = 0; index < expectedUrls.length; index++) {
165
162
  const url = expectedUrls[index];
166
163
  try {
167
- const data = yield dowloadFromUrl(session, url);
164
+ const data = yield dowloadFromUrl(session, url, opts);
168
165
  if (data)
169
166
  return { source: url, data };
170
167
  }
@@ -176,13 +173,13 @@ export function downloadJatsFromUrl(session, urlOrDoi, resolvers) {
176
173
  logAboutJatsFailing(session, expectedUrls);
177
174
  }
178
175
  if (doi.validate(urlOrDoi)) {
179
- const jatsUrl = yield customResolveJatsUrlFromDoi(session, urlOrDoi, resolvers);
180
- const data = yield dowloadFromUrl(session, jatsUrl);
176
+ const jatsUrl = yield customResolveJatsUrlFromDoi(session, urlOrDoi, opts);
177
+ const data = yield dowloadFromUrl(session, jatsUrl, opts);
181
178
  return { source: jatsUrl, data };
182
179
  }
183
180
  if (isUrl(urlOrDoi)) {
184
181
  session.log.debug("No resolver matched, and the URL doesn't look like a DOI. We will attempt to download it directly.");
185
- const data = yield dowloadFromUrl(session, urlOrDoi);
182
+ const data = yield dowloadFromUrl(session, urlOrDoi, opts);
186
183
  return { source: urlOrDoi, data };
187
184
  }
188
185
  throw new Error(`Could not find ${urlOrDoi} locally, and it doesn't look like a URL or DOI`);
package/dist/esm/resolvers.js CHANGED
@@ -41,16 +41,17 @@ export const DEFAULT_RESOLVERS = [elife, plos, joss];
41
41
  /**
42
42
  * Use the known custom resolvers to pick where the JATS should be downloaded from.
43
43
  */
44
- export function customResolveJatsUrlFromDoi(session, doiString, resolvers = DEFAULT_RESOLVERS) {
44
+ export function customResolveJatsUrlFromDoi(session, doiString, opts = { resolvers: DEFAULT_RESOLVERS }) {
45
+ var _a, _b;
45
46
  return __awaiter(this, void 0, void 0, function* () {
46
47
  if (!doi.validate(doiString))
47
48
  throw new Error(`The doi ${doiString} is not valid`);
48
49
  const doiUrl = doi.buildUrl(doiString);
49
50
  session.log.debug(`Resolving DOI ${doiUrl}`);
50
- const resp = yield fetch(doiUrl);
51
+ const resp = yield ((_a = opts === null || opts === void 0 ? void 0 : opts.fetcher) !== null && _a !== void 0 ? _a : fetch)(doiUrl);
51
52
  const articleUrl = resp.url;
52
53
  session.log.debug(`Found resolved URL for DOI at ${articleUrl}`);
53
- const resolver = resolvers.find((r) => r.test(articleUrl));
54
+ const resolver = (_b = opts === null || opts === void 0 ? void 0 : opts.resolvers) === null || _b === void 0 ? void 0 : _b.find((r) => r.test(articleUrl));
54
55
  if (!resolver)
55
56
  throw new Error(`Could not resolve JATS for ${articleUrl}, no resolver matched`);
56
57
  const jatsUrl = resolver.jatsUrl(articleUrl);
package/dist/esm/version.js CHANGED
@@ -1,2 +1,2 @@
1
- const version = '0.0.7';
1
+ const version = '0.0.9';
2
2
  export default version;