@mantra-ai/core 0.1.0

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Files changed (385) hide show
  1. package/dist/ai/google/client.d.ts +67 -0
  2. package/dist/ai/google/client.d.ts.map +1 -0
  3. package/dist/ai/google/client.js +169 -0
  4. package/dist/ai/google/client.js.map +1 -0
  5. package/dist/ai/google/generate.d.ts +10 -0
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  7. package/dist/ai/google/generate.js +137 -0
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  9. package/dist/ai/google/index.d.ts +4 -0
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  11. package/dist/ai/google/index.js +4 -0
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  13. package/dist/ai/google/types.d.ts +88 -0
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  15. package/dist/ai/google/types.js +55 -0
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  17. package/dist/ai/index.d.ts +3 -0
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  19. package/dist/ai/index.js +3 -0
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  21. package/dist/ai/openai/client.d.ts +22 -0
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  23. package/dist/ai/openai/client.js +49 -0
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  25. package/dist/ai/openai/generate.d.ts +14 -0
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  27. package/dist/ai/openai/generate.js +178 -0
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  29. package/dist/ai/openai/index.d.ts +4 -0
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  37. package/dist/ai/prompts/index.d.ts +1 -0
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  53. package/dist/index.d.ts +21 -0
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  57. package/dist/normalization/jats/index.d.ts +4 -0
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  61. package/dist/normalization/jats/normalize.d.ts +7 -0
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  65. package/dist/normalization/jats/utils/build/finalize.d.ts +3 -0
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  73. package/dist/normalization/jats/utils/build/meta.d.ts +10 -0
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  77. package/dist/normalization/jats/utils/build/version.d.ts +3 -0
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  81. package/dist/normalization/jats/utils/category.d.ts +11 -0
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  105. package/dist/normalization/jats/utils/collectors/sections.d.ts +7 -0
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  109. package/dist/normalization/jats/utils/licenses.d.ts +5 -0
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  113. package/dist/normalization/jats/utils/po/nodes.d.ts +6 -0
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  117. package/dist/normalization/jats/utils/po/query.d.ts +7 -0
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  119. package/dist/normalization/jats/utils/po/query.js +67 -0
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  121. package/dist/normalization/jats/utils/po/serialize.d.ts +4 -0
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  123. package/dist/normalization/jats/utils/po/serialize.js +329 -0
  124. package/dist/normalization/jats/utils/po/serialize.js.map +1 -0
  125. package/dist/normalization/jats/utils/po/text.d.ts +7 -0
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  129. package/dist/normalization/jats/utils/references.d.ts +26 -0
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  133. package/dist/normalization/jats/utils/strings.d.ts +8 -0
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  137. package/dist/normalization/jats/utils/types.d.ts +233 -0
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  141. package/dist/normalization/jats/utils/xml.d.ts +5 -0
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  143. package/dist/normalization/jats/utils/xml.js +69 -0
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  145. package/dist/normalization/normalized-doc-schema.d.ts +1094 -0
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  149. package/dist/normalization/pdf/index.d.ts +4 -0
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  153. package/dist/normalization/pdf/normalize.d.ts +31 -0
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  161. package/dist/sources/arxiv/client.d.ts +4 -0
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  165. package/dist/sources/biorxiv/client.d.ts +21 -0
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package/dist/normalization/jats/utils/collectors/contributors.d.ts ADDED
@@ -0,0 +1,4 @@
1
+ import type { NormalizedJats } from "../types";
2
+ export declare function collectContributors(articleMeta: any, back?: any): NonNullable<NormalizedJats["contributors"]>;
3
+ export declare function collectAffiliations(articleMeta: any): NonNullable<NormalizedJats["affiliations"]>;
4
+ //# sourceMappingURL=contributors.d.ts.map
package/dist/normalization/jats/utils/collectors/contributors.d.ts.map ADDED
@@ -0,0 +1 @@
1
+ {"version":3,"file":"contributors.d.ts","sourceRoot":"","sources":["../../../../../src/normalization/jats/utils/collectors/contributors.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,UAAU,CAAC;AAK/C,wBAAgB,mBAAmB,CACjC,WAAW,EAAE,GAAG,EAChB,IAAI,CAAC,EAAE,GAAG,GACT,WAAW,CAAC,cAAc,CAAC,cAAc,CAAC,CAAC,CAmE7C;AAED,wBAAgB,mBAAmB,CACjC,WAAW,EAAE,GAAG,GACf,WAAW,CAAC,cAAc,CAAC,cAAc,CAAC,CAAC,CAQ7C"}
package/dist/normalization/jats/utils/collectors/contributors.js ADDED
@@ -0,0 +1,77 @@
1
+ import { normalizeArray, asString } from "../strings";
2
+ import { getText } from "../xml";
3
+ import { extractEmail } from "../strings";
4
+ export function collectContributors(articleMeta, back) {
5
+ const group = articleMeta?.["contrib-group"] || {};
6
+ const contribs = normalizeArray(group?.contrib);
7
+ const correspondences = new Map();
8
+ // author-notes -> corresp mapping for emails
9
+ const notes = articleMeta?.["author-notes"] || {};
10
+ for (const c of normalizeArray(notes?.corresp)) {
11
+ const id = c?.["@_id"] || undefined;
12
+ const email = asString(c?.email) || extractEmail(getText(c));
13
+ if (id)
14
+ correspondences.set(id, { email });
15
+ }
16
+ // back.fn-group -> fn[fn-type=corresp]
17
+ const fng = back?.["fn-group"];
18
+ for (const fn of normalizeArray(fng?.fn)) {
19
+ const fnType = asString(fn?.["@_fn-type"]) ||
20
+ asString(fn?.["@_fn_type"]) ||
21
+ asString(fn?.["@_type"]);
22
+ if ((fnType || "").toLowerCase() === "corresp") {
23
+ const id = asString(fn?.["@_id"]) || undefined;
24
+ const email = asString(fn?.email) || extractEmail(getText(fn));
25
+ if (id)
26
+ correspondences.set(id, { email });
27
+ }
28
+ }
29
+ const out = [];
30
+ for (const c of contribs) {
31
+ const role = asString(c?.["@_contrib-type"]) || undefined;
32
+ const name = c?.name || {};
33
+ const given = asString(name?.["given-names"]) || undefined;
34
+ const surname = asString(name?.surname) || undefined;
35
+ const full = !given && !surname ? getText(name) || getText(c) : undefined;
36
+ const xrefs = normalizeArray(c?.xref);
37
+ const splitRids = (rid) => rid ? rid.split(/\s+/).filter(Boolean) : [];
38
+ const xref_aff = xrefs
39
+ .filter((x) => (x?.["@_ref-type"] || "") === "aff")
40
+ .flatMap((x) => splitRids(asString(x?.["@_rid"]) || asString(x)));
41
+ const correspRids = xrefs
42
+ .filter((x) => (x?.["@_ref-type"] || "") === "corresp")
43
+ .flatMap((x) => splitRids(asString(x?.["@_rid"]) || asString(x)));
44
+ let email;
45
+ let corresp_id;
46
+ if (correspRids.length) {
47
+ corresp_id = correspRids[0];
48
+ email = correspondences.get(corresp_id)?.email || undefined;
49
+ }
50
+ if (!email) {
51
+ // direct email under contrib
52
+ email =
53
+ asString(c?.email) || extractEmail(getText(c?.email));
54
+ }
55
+ out.push({
56
+ role,
57
+ given,
58
+ surname,
59
+ full,
60
+ xref_aff: xref_aff.length ? xref_aff : undefined,
61
+ corresp: !!corresp_id,
62
+ corresp_id,
63
+ email,
64
+ });
65
+ }
66
+ return out;
67
+ }
68
+ export function collectAffiliations(articleMeta) {
69
+ const affs = normalizeArray(articleMeta?.aff);
70
+ return affs.map((a) => ({
71
+ id: asString(a?.["@_id"]) || asString(a?.id) || undefined,
72
+ label: getText(a?.label) || undefined,
73
+ text: getText(a) || undefined,
74
+ country: asString(a?.country) || undefined,
75
+ }));
76
+ }
77
+ //# sourceMappingURL=contributors.js.map
package/dist/normalization/jats/utils/collectors/contributors.js.map ADDED
@@ -0,0 +1 @@
1
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package/dist/normalization/jats/utils/collectors/keywords.d.ts ADDED
@@ -0,0 +1,2 @@
1
+ export declare function collectKeywords(articleMeta: any): string[];
2
+ //# sourceMappingURL=keywords.d.ts.map
package/dist/normalization/jats/utils/collectors/keywords.d.ts.map ADDED
@@ -0,0 +1 @@
1
+ {"version":3,"file":"keywords.d.ts","sourceRoot":"","sources":["../../../../../src/normalization/jats/utils/collectors/keywords.ts"],"names":[],"mappings":"AAGA,wBAAgB,eAAe,CAAC,WAAW,EAAE,GAAG,GAAG,MAAM,EAAE,CAU1D"}
package/dist/normalization/jats/utils/collectors/keywords.js ADDED
@@ -0,0 +1,14 @@
1
+ import { getText } from "../xml";
2
+ import { normalizeArray } from "../strings";
3
+ export function collectKeywords(articleMeta) {
4
+ const groups = normalizeArray(articleMeta?.["kwd-group"]);
5
+ const out = [];
6
+ for (const g of groups) {
7
+ const items = normalizeArray(g?.kwd)
8
+ .map((k) => getText(k))
9
+ .filter(Boolean);
10
+ out.push(...items);
11
+ }
12
+ return out;
13
+ }
14
+ //# sourceMappingURL=keywords.js.map
package/dist/normalization/jats/utils/collectors/keywords.js.map ADDED
@@ -0,0 +1 @@
1
+ {"version":3,"file":"keywords.js","sourceRoot":"","sources":["../../../../../src/normalization/jats/utils/collectors/keywords.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,MAAM,QAAQ,CAAC;AACjC,OAAO,EAAE,cAAc,EAAE,MAAM,YAAY,CAAC;AAE5C,MAAM,UAAU,eAAe,CAAC,WAAgB;IAC9C,MAAM,MAAM,GAAG,cAAc,CAAC,WAAW,EAAE,CAAC,WAAW,CAAC,CAAC,CAAC;IAC1D,MAAM,GAAG,GAAa,EAAE,CAAC;IACzB,KAAK,MAAM,CAAC,IAAI,MAAM,EAAE,CAAC;QACvB,MAAM,KAAK,GAAG,cAAc,CAAC,CAAC,EAAE,GAAG,CAAC;aACjC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC;aACtB,MAAM,CAAC,OAAO,CAAa,CAAC;QAC/B,GAAG,CAAC,IAAI,CAAC,GAAG,KAAK,CAAC,CAAC;IACrB,CAAC;IACD,OAAO,GAAG,CAAC;AACb,CAAC"}
package/dist/normalization/jats/utils/collectors/meta.d.ts ADDED
@@ -0,0 +1,6 @@
1
+ import type { NormalizedJats } from "../types";
2
+ export declare function collectIds(articleMeta: any): NormalizedJats["meta"]["ids"];
3
+ export declare function collectJournal(journalMeta: any): NormalizedJats["meta"]["journal"];
4
+ export declare function collectPubDates(articleMeta: any): NonNullable<NormalizedJats["meta"]["pub_dates"]>;
5
+ export declare function collectLicense(articleMeta: any, xml: string, domPO: any): NormalizedJats["meta"]["license"] | undefined;
6
+ //# sourceMappingURL=meta.d.ts.map
package/dist/normalization/jats/utils/collectors/meta.d.ts.map ADDED
@@ -0,0 +1 @@
1
+ {"version":3,"file":"meta.d.ts","sourceRoot":"","sources":["../../../../../src/normalization/jats/utils/collectors/meta.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,UAAU,CAAC;AAQ/C,wBAAgB,UAAU,CAAC,WAAW,EAAE,GAAG,GAAG,cAAc,CAAC,MAAM,CAAC,CAAC,KAAK,CAAC,CAgB1E;AAED,wBAAgB,cAAc,CAC5B,WAAW,EAAE,GAAG,GACf,cAAc,CAAC,MAAM,CAAC,CAAC,SAAS,CAAC,CA6BnC;AAED,wBAAgB,eAAe,CAC7B,WAAW,EAAE,GAAG,GACf,WAAW,CAAC,cAAc,CAAC,MAAM,CAAC,CAAC,WAAW,CAAC,CAAC,CA6BlD;AAED,wBAAgB,cAAc,CAC5B,WAAW,EAAE,GAAG,EAChB,GAAG,EAAE,MAAM,EACX,KAAK,EAAE,GAAG,GACT,cAAc,CAAC,MAAM,CAAC,CAAC,SAAS,CAAC,GAAG,SAAS,CAsB/C"}
package/dist/normalization/jats/utils/collectors/meta.js ADDED
@@ -0,0 +1,103 @@
1
+ import { normalizeArray, asString } from "../strings";
2
+ import { getText } from "../xml";
3
+ import { extractLicensesFromPreserveOrder, extractLicenseTextFromXml, } from "../licenses";
4
+ // ---------- collectors ----------
5
+ export function collectIds(articleMeta) {
6
+ const ids = normalizeArray(articleMeta?.["article-id"]).map((x) => ({
7
+ type: x?.["@_pub-id-type"],
8
+ value: asString(x?.["#text"]) ?? asString(x),
9
+ }));
10
+ const out = {};
11
+ for (const id of ids) {
12
+ const t = String(id?.type || "").toLowerCase();
13
+ const v = id?.value ? String(id.value) : undefined;
14
+ if (!v)
15
+ continue;
16
+ if (t === "pmcid")
17
+ out.pmcid = v;
18
+ else if (t === "doi")
19
+ out.doi = v;
20
+ else if (t === "publisher-id")
21
+ out.publisher_id = v;
22
+ else if (t === "art-access-id")
23
+ out.art_access_id = v;
24
+ }
25
+ return out;
26
+ }
27
+ export function collectJournal(journalMeta) {
28
+ const title = getText(journalMeta?.["journal-title-group"]?.["journal-title"]) ||
29
+ getText(journalMeta?.["journal-title"]) ||
30
+ undefined;
31
+ const journalIds = normalizeArray(journalMeta?.["journal-id"]).flatMap((x) => {
32
+ const value = asString(x?.["#text"]) ?? asString(x);
33
+ if (!value)
34
+ return [];
35
+ const type = x?.["@_journal-id-type"];
36
+ return [{ type, value }];
37
+ });
38
+ const issn = normalizeArray(journalMeta?.issn).flatMap((x) => {
39
+ const value = asString(x?.["#text"]) ?? asString(x);
40
+ if (!value)
41
+ return [];
42
+ const pub_type = x?.["@_pub-type"];
43
+ return [{ pub_type, value }];
44
+ });
45
+ const publisher = journalMeta?.publisher
46
+ ? {
47
+ name: asString(journalMeta?.publisher?.["publisher-name"]) ??
48
+ getText(journalMeta?.publisher),
49
+ location: asString(journalMeta?.publisher?.["publisher-loc"]) || undefined,
50
+ }
51
+ : undefined;
52
+ return { title: title || undefined, ids: journalIds, issn, publisher };
53
+ }
54
+ export function collectPubDates(articleMeta) {
55
+ const dates = [];
56
+ // Traditional publication dates
57
+ for (const d of normalizeArray(articleMeta?.["pub-date"])) {
58
+ dates.push({
59
+ pub_type: d?.["@_pub-type"],
60
+ day: asString(d?.day),
61
+ month: asString(d?.month),
62
+ season: asString(d?.season),
63
+ year: asString(d?.year),
64
+ });
65
+ }
66
+ // History dates (received/accepted/etc.)
67
+ const history = articleMeta?.history;
68
+ for (const d of normalizeArray(history?.date)) {
69
+ dates.push({
70
+ pub_type: asString(d?.["@_date-type"]) ||
71
+ asString(d?.["@_pub-type"]) ||
72
+ undefined,
73
+ day: asString(d?.day),
74
+ month: asString(d?.month),
75
+ season: asString(d?.season),
76
+ year: asString(d?.year),
77
+ });
78
+ }
79
+ return dates.filter((d) => d.day || d.month || d.season || d.year || d.pub_type);
80
+ }
81
+ export function collectLicense(articleMeta, xml, domPO) {
82
+ // Gather all license blocks with href/type and pick the most open; combine license-p text
83
+ const candidates = extractLicensesFromPreserveOrder(domPO);
84
+ if (!candidates.length) {
85
+ // Fallback to object-mode single license
86
+ const lic = articleMeta?.permissions?.license;
87
+ if (!lic)
88
+ return undefined;
89
+ const type = lic?.["@_license-type"] || undefined;
90
+ const href = lic?.["@_xlink:href"] || lic?.["@_href"] || undefined;
91
+ const textFromXml = extractLicenseTextFromXml(xml) || undefined;
92
+ const text = textFromXml || getText(lic?.["license-p"]) || getText(lic) || undefined;
93
+ return { type, href, text };
94
+ }
95
+ const best = candidates.sort((a, b) => b.score - a.score)[0];
96
+ const allText = candidates
97
+ .map((c) => c.text)
98
+ .filter(Boolean)
99
+ .join(" ")
100
+ .trim() || undefined;
101
+ return { type: best.type, href: best.href, text: allText ?? best.text };
102
+ }
103
+ //# sourceMappingURL=meta.js.map
package/dist/normalization/jats/utils/collectors/meta.js.map ADDED
@@ -0,0 +1 @@
1
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package/dist/normalization/jats/utils/collectors/sections.d.ts ADDED
@@ -0,0 +1,7 @@
1
+ import type { Section, SectionCategory } from "../types";
2
+ export declare function collectSections(article: any, body: any, domPO: any): Section[];
3
+ export declare function collectSectionNode(s: any, level: number, parentCategory: SectionCategory | undefined, domPO?: any, searchRootPO?: any, siblingIndex?: number): Section;
4
+ export declare function collectLooseBodyParagraphs(body: any): string[];
5
+ export declare function collectLooseBodyParagraphsFromPO(domPO: any): string[];
6
+ export declare function collectLooseBodyParagraphsFromPORoot(body: any): string[];
7
+ //# sourceMappingURL=sections.d.ts.map
package/dist/normalization/jats/utils/collectors/sections.d.ts.map ADDED
@@ -0,0 +1 @@
1
+ {"version":3,"file":"sections.d.ts","sourceRoot":"","sources":["../../../../../src/normalization/jats/utils/collectors/sections.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EACV,OAAO,EAKP,eAAe,EAChB,MAAM,UAAU,CAAC;AAsBlB,wBAAgB,eAAe,CAC7B,OAAO,EAAE,GAAG,EACZ,IAAI,EAAE,GAAG,EACT,KAAK,EAAE,GAAG,GACT,OAAO,EAAE,CAwDX;AAED,wBAAgB,kBAAkB,CAChC,CAAC,EAAE,GAAG,EACN,KAAK,EAAE,MAAM,EACb,cAAc,EAAE,eAAe,GAAG,SAAS,EAC3C,KAAK,CAAC,EAAE,GAAG,EACX,YAAY,CAAC,EAAE,GAAG,EAClB,YAAY,CAAC,EAAE,MAAM,GACpB,OAAO,CAwVT;AAED,wBAAgB,0BAA0B,CAAC,IAAI,EAAE,GAAG,GAAG,MAAM,EAAE,CAsC9D;AAED,wBAAgB,gCAAgC,CAAC,KAAK,EAAE,GAAG,GAAG,MAAM,EAAE,CAIrE;AAED,wBAAgB,oCAAoC,CAAC,IAAI,EAAE,GAAG,GAAG,MAAM,EAAE,CA8CxE"}