mirror of
https://github.com/OFFIS-ESC/constellation-analyzer
synced 2026-01-26 23:43:40 +00:00
feat: add PubMed and software citation format support
Extends bibliography smart import capabilities with additional citation.js plugins: - @citation-js/plugin-pubmed: Support for PubMed IDs (PMID/PMCID) - @citation-js/plugin-software-formats: Support for software citations (CFF, GitHub, npm, Zenodo) Updates smart-parser.ts to recognize and validate Zenodo DOI format (10.5281/zenodo.xxxxx). Improves input type detection for better user feedback. Includes code formatting improvements to bibliographyStore.ts for consistency. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
This commit is contained in:
Jan-Henrik Bruhn
parent
14ccb2da5b
commit
ef16b9d060
4 changed files with 169 additions and 86 deletions
106
package-lock.json
generated
106
package-lock.json
generated
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@ -12,7 +12,9 @@
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"@citation-js/plugin-bibtex": "^0.7.18",
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"@citation-js/plugin-csl": "^0.7.18",
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"@citation-js/plugin-doi": "^0.7.18",
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"@citation-js/plugin-pubmed": "^0.3.0",
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"@citation-js/plugin-ris": "^0.7.18",
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"@citation-js/plugin-software-formats": "^0.6.1",
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"@emotion/react": "^11.11.3",
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"@emotion/styled": "^11.11.0",
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"@mui/icons-material": "^5.15.10",
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@ -377,6 +379,18 @@
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"@citation-js/core": "^0.7.0"
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}
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},
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"node_modules/@citation-js/plugin-cff": {
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"version": "0.6.1",
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"resolved": "https://registry.npmjs.org/@citation-js/plugin-cff/-/plugin-cff-0.6.1.tgz",
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"integrity": "sha512-tLjTgsfzNOdQWGn5mNc2NAaydHnlRucSERoyAXLN7u0BQBfp7j5zwdxCmxcQD/N7hH3fpDKMG+qDzbqpJuKyNA==",
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"dependencies": {
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"@citation-js/date": "^0.5.0",
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"@citation-js/plugin-yaml": "^0.6.1"
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},
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"engines": {
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"node": ">=14.0.0"
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}
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},
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"node_modules/@citation-js/plugin-csl": {
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"version": "0.7.18",
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"resolved": "https://registry.npmjs.org/@citation-js/plugin-csl/-/plugin-csl-0.7.18.tgz",
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@ -406,6 +420,41 @@
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"@citation-js/core": "^0.7.0"
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}
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},
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"node_modules/@citation-js/plugin-github": {
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"version": "0.6.1",
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"resolved": "https://registry.npmjs.org/@citation-js/plugin-github/-/plugin-github-0.6.1.tgz",
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"integrity": "sha512-1ZeSgQ5AoYsa8n2acVooUeRk76oA8rLszYNBjzj5z6MPa11BZlQJ9O+Gy4tHjlImvsENLbLPx5f8/V1VHXaCfQ==",
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"dependencies": {
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"@citation-js/date": "^0.5.0",
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"@citation-js/name": "^0.4.2"
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},
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"engines": {
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"node": ">=14.0.0"
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}
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},
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"node_modules/@citation-js/plugin-npm": {
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"version": "0.6.1",
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"resolved": "https://registry.npmjs.org/@citation-js/plugin-npm/-/plugin-npm-0.6.1.tgz",
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"integrity": "sha512-rojJA+l/p2KBpDoY+8n0YfNyQO1Aw03fQR5BN+gXD1LNAP1V+8wqvdPsaHnzPsrhrd4ZXDR7ch/Nk0yynPkJ3Q==",
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"dependencies": {
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"@citation-js/date": "^0.5.0",
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"@citation-js/name": "^0.4.2"
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},
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"engines": {
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"node": ">=14.0.0"
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}
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},
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"node_modules/@citation-js/plugin-pubmed": {
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"version": "0.3.0",
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"resolved": "https://registry.npmjs.org/@citation-js/plugin-pubmed/-/plugin-pubmed-0.3.0.tgz",
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"integrity": "sha512-E3l83VP5UnTh6lLJaTaNBIkNgIx3U6IjDNf7j5l4geBOaOwDIhkl9X+Ss33/MMNEIMNDsBoodoMJTZ8Cq+C/ug==",
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"engines": {
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"node": ">=14"
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},
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"peerDependencies": {
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"@citation-js/core": ">=0.5.1 <=0.6"
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}
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},
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"node_modules/@citation-js/plugin-ris": {
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"version": "0.7.18",
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"resolved": "https://registry.npmjs.org/@citation-js/plugin-ris/-/plugin-ris-0.7.18.tgz",
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@ -421,6 +470,44 @@
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"@citation-js/core": "^0.7.0"
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}
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},
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"node_modules/@citation-js/plugin-software-formats": {
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"version": "0.6.1",
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"resolved": "https://registry.npmjs.org/@citation-js/plugin-software-formats/-/plugin-software-formats-0.6.1.tgz",
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"integrity": "sha512-BDF9rqi56K0hoTgYTVANCFVRSbWKC9V06Uap7oa8SjqCTgnHJAy8t/F3NxsyYPPG+zmRsLW9VNbcIsJOl0eu/w==",
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"dependencies": {
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"@citation-js/plugin-cff": "^0.6.1",
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"@citation-js/plugin-github": "^0.6.1",
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"@citation-js/plugin-npm": "^0.6.1",
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"@citation-js/plugin-yaml": "^0.6.1",
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"@citation-js/plugin-zenodo": "^0.6.1"
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},
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"engines": {
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"node": ">=14.0.0"
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}
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},
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"node_modules/@citation-js/plugin-yaml": {
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"version": "0.6.1",
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"resolved": "https://registry.npmjs.org/@citation-js/plugin-yaml/-/plugin-yaml-0.6.1.tgz",
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"integrity": "sha512-XEVVks1cJTqRbjy+nmthfw/puR6NwRB3fyJWi1tX13UYXlkhP/h45nsv4zjgLLGekdcMHQvhad9MAYunOftGKA==",
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"dependencies": {
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"js-yaml": "^4.0.0"
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},
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"engines": {
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"node": ">=14.0.0"
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}
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},
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"node_modules/@citation-js/plugin-zenodo": {
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"version": "0.6.1",
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"resolved": "https://registry.npmjs.org/@citation-js/plugin-zenodo/-/plugin-zenodo-0.6.1.tgz",
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"integrity": "sha512-bUybENHoZqJ6gheUqgkumjI+mu+fA2bg6VoniDmZTb7Qng9iEpi+IWEAR26/vBE0gK0EWrJjczyDW3HCwrhvVw==",
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"dependencies": {
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"@citation-js/date": "^0.5.0",
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"@citation-js/name": "^0.4.2"
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},
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"engines": {
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"node": ">=14.0.0"
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}
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},
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"node_modules/@emotion/babel-plugin": {
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"version": "11.13.5",
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"resolved": "https://registry.npmjs.org/@emotion/babel-plugin/-/babel-plugin-11.13.5.tgz",
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@ -2103,6 +2190,7 @@
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"version": "18.3.26",
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"resolved": "https://registry.npmjs.org/@types/react/-/react-18.3.26.tgz",
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"integrity": "sha512-RFA/bURkcKzx/X9oumPG9Vp3D3JUgus/d0b67KB0t5S/raciymilkOa66olh78MUI92QLbEJevO7rvqU/kjwKA==",
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"dev": true,
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"dependencies": {
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"@types/prop-types": "*",
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"csstype": "^3.0.2"
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@ -2436,8 +2524,7 @@
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"node_modules/argparse": {
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"version": "2.0.1",
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"resolved": "https://registry.npmjs.org/argparse/-/argparse-2.0.1.tgz",
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"integrity": "sha512-8+9WqebbFzpX9OR+Wa6O29asIogeRMzcGtAINdpMHHyAg10f05aSFVBbcEqGf/PXw1EjAZ+q2/bEBg3DvurK3Q==",
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"dev": true
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"integrity": "sha512-8+9WqebbFzpX9OR+Wa6O29asIogeRMzcGtAINdpMHHyAg10f05aSFVBbcEqGf/PXw1EjAZ+q2/bEBg3DvurK3Q=="
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},
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"node_modules/array-union": {
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"version": "2.1.0",
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@ -3784,7 +3871,6 @@
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"version": "4.1.0",
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"resolved": "https://registry.npmjs.org/js-yaml/-/js-yaml-4.1.0.tgz",
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"integrity": "sha512-wpxZs9NoxZaJESJGIZTyDEaYpl0FKSA+FB9aJiyemKhMwkxQg63h4T1KJgUGHpTqPDNRcmmYLugrRjJlBtWvRA==",
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"dev": true,
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"dependencies": {
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"argparse": "^2.0.1"
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},
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@ -5402,20 +5488,6 @@
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"integrity": "sha512-a4UGQaWPH59mOXUYnAG2ewncQS4i4F43Tv3JoAM+s2VDAmS9NsK8GpDMLrCHPksFT7h3K6TOoUNn2pb7RoXx4g==",
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"dev": true
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},
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"node_modules/yaml": {
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"version": "2.8.1",
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"resolved": "https://registry.npmjs.org/yaml/-/yaml-2.8.1.tgz",
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"integrity": "sha512-lcYcMxX2PO9XMGvAJkJ3OsNMw+/7FKes7/hgerGUYWIoWu5j/+YQqcZr5JnPZWzOsEBgMbSbiSTn/dv/69Mkpw==",
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"dev": true,
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"optional": true,
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"peer": true,
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"bin": {
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"yaml": "bin.mjs"
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},
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"engines": {
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"node": ">= 14.6"
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}
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},
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"node_modules/yocto-queue": {
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"version": "0.1.0",
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"resolved": "https://registry.npmjs.org/yocto-queue/-/yocto-queue-0.1.0.tgz",
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@ -14,7 +14,9 @@
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"@citation-js/plugin-bibtex": "^0.7.18",
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"@citation-js/plugin-csl": "^0.7.18",
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"@citation-js/plugin-doi": "^0.7.18",
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"@citation-js/plugin-pubmed": "^0.3.0",
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"@citation-js/plugin-ris": "^0.7.18",
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"@citation-js/plugin-software-formats": "^0.6.1",
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"@emotion/react": "^11.11.3",
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"@emotion/styled": "^11.11.0",
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"@mui/icons-material": "^5.15.10",
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@ -1,29 +1,31 @@
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import { create } from 'zustand';
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import { create } from "zustand";
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// @ts-expect-error - citation.js doesn't have TypeScript definitions
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import { Cite } from '@citation-js/core';
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import { Cite } from "@citation-js/core";
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// Load plugins
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import '@citation-js/plugin-csl';
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import '@citation-js/plugin-doi';
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import '@citation-js/plugin-bibtex';
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import '@citation-js/plugin-ris';
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import "@citation-js/plugin-csl";
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import "@citation-js/plugin-doi";
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import "@citation-js/plugin-bibtex";
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import "@citation-js/plugin-ris";
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import "@citation-js/plugin-pubmed";
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import "@citation-js/plugin-software-formats";
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import type {
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BibliographyReference,
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CSLReference,
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ReferenceAppMetadata,
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BibliographySettings
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} from '../types/bibliography';
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BibliographySettings,
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} from "../types/bibliography";
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interface BibliographyStore {
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// State
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citeInstance: Cite; // The citation.js instance
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appMetadata: Record<string, ReferenceAppMetadata>; // App-specific data
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citeInstance: Cite; // The citation.js instance
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appMetadata: Record<string, ReferenceAppMetadata>; // App-specific data
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settings: BibliographySettings;
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// Getters
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getReferences: () => BibliographyReference[]; // Merges CSL + app data
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getReferences: () => BibliographyReference[]; // Merges CSL + app data
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getReferenceById: (id: string) => BibliographyReference | undefined;
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getCSLData: () => CSLReference[]; // Raw CSL-JSON from Cite
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getCSLData: () => CSLReference[]; // Raw CSL-JSON from Cite
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// CRUD operations (use citation.js methods)
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addReference: (ref: Partial<CSLReference>) => string;
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setSettings: (settings: BibliographySettings) => void;
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// Citation.js powered operations
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formatReference: (id: string, style?: string, format?: 'html' | 'text') => string;
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formatBibliography: (style?: string, format?: 'html' | 'text') => string;
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formatReference: (
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id: string,
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style?: string,
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format?: "html" | "text",
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) => string;
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formatBibliography: (style?: string, format?: "html" | "text") => string;
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parseInput: (input: string) => Promise<CSLReference[]>;
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exportAs: (format: 'bibtex' | 'ris' | 'json') => string;
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exportAs: (format: "bibtex" | "ris" | "json") => string;
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}
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export const useBibliographyStore = create<BibliographyStore>((set, get) => ({
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citeInstance: new Cite([]),
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appMetadata: {},
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settings: {
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defaultStyle: 'apa',
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sortOrder: 'author',
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defaultStyle: "apa",
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sortOrder: "author",
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},
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getReferences: () => {
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const metadata = get().appMetadata;
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// Merge CSL data with app metadata
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return csl.map(ref => ({
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return csl.map((ref) => ({
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...ref,
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_app: metadata[ref.id],
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}));
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getReferenceById: (id) => {
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const refs = get().getReferences();
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return refs.find(ref => ref.id === id);
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return refs.find((ref) => ref.id === id);
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},
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getCSLData: () => {
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const { citeInstance } = get();
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// Generate ID if not provided
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const id = ref.id || `ref-${Date.now()}-${Math.random().toString(36).slice(2, 9)}`;
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const id =
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ref.id || `ref-${Date.now()}-${Math.random().toString(36).slice(2, 9)}`;
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const fullRef = { ...ref, id };
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// Use citation.js add() method
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@ -89,7 +96,7 @@ export const useBibliographyStore = create<BibliographyStore>((set, get) => ({
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// Add app metadata
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const now = new Date().toISOString();
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set(state => ({
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set((state) => ({
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appMetadata: {
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...state.appMetadata,
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[id]: {
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@ -109,15 +116,15 @@ export const useBibliographyStore = create<BibliographyStore>((set, get) => ({
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const data = citeInstance.data as CSLReference[];
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// Find and update the reference
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const updatedData = data.map(ref =>
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ref.id === id ? { ...ref, ...updates } : ref
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const updatedData = data.map((ref) =>
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ref.id === id ? { ...ref, ...updates } : ref,
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);
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// Use citation.js set() method to replace all data
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citeInstance.set(updatedData);
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// Update metadata timestamp
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set(state => ({
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set((state) => ({
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appMetadata: {
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...state.appMetadata,
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[id]: {
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@ -133,11 +140,11 @@ export const useBibliographyStore = create<BibliographyStore>((set, get) => ({
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const data = citeInstance.data as CSLReference[];
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// Remove from citation.js
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const filteredData = data.filter(ref => ref.id !== id);
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const filteredData = data.filter((ref) => ref.id !== id);
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citeInstance.set(filteredData);
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// Remove metadata
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set(state => {
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set((state) => {
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// eslint-disable-next-line @typescript-eslint/no-unused-vars
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const { [id]: _removed, ...rest } = state.appMetadata;
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return { appMetadata: rest };
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@ -146,7 +153,7 @@ export const useBibliographyStore = create<BibliographyStore>((set, get) => ({
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duplicateReference: (id) => {
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const original = get().getReferenceById(id);
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if (!original) return '';
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if (!original) return "";
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const newId = `ref-${Date.now()}-${Math.random().toString(36).slice(2, 9)}`;
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const duplicate = {
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@ -173,7 +180,7 @@ export const useBibliographyStore = create<BibliographyStore>((set, get) => ({
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const metadata: Record<string, ReferenceAppMetadata> = {};
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const now = new Date().toISOString();
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refs.forEach(ref => {
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refs.forEach((ref) => {
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metadata[ref.id] = {
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id: ref.id,
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tags: [],
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@ -193,9 +200,9 @@ export const useBibliographyStore = create<BibliographyStore>((set, get) => ({
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// Add metadata for new references
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const now = new Date().toISOString();
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set(state => {
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set((state) => {
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const newMetadata = { ...state.appMetadata };
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refs.forEach(ref => {
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refs.forEach((ref) => {
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if (!newMetadata[ref.id]) {
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newMetadata[ref.id] = {
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id: ref.id,
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@ -210,12 +217,12 @@ export const useBibliographyStore = create<BibliographyStore>((set, get) => ({
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},
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clearAll: () => {
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get().citeInstance.reset(); // citation.js method to clear all data
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get().citeInstance.reset(); // citation.js method to clear all data
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set({ appMetadata: {} });
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},
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updateMetadata: (id, updates) => {
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set(state => ({
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set((state) => ({
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appMetadata: {
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...state.appMetadata,
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[id]: {
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@ -229,34 +236,34 @@ export const useBibliographyStore = create<BibliographyStore>((set, get) => ({
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setSettings: (settings) => set({ settings }),
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formatReference: (id, style, format = 'html') => {
|
||||
formatReference: (id, style, format = "html") => {
|
||||
const { citeInstance, settings } = get();
|
||||
const styleToUse = style || settings.defaultStyle;
|
||||
|
||||
// Find the reference
|
||||
const ref = (citeInstance.data as CSLReference[]).find(r => r.id === id);
|
||||
if (!ref) return '';
|
||||
const ref = (citeInstance.data as CSLReference[]).find((r) => r.id === id);
|
||||
if (!ref) return "";
|
||||
|
||||
// Create temporary Cite instance for single reference
|
||||
const cite = new Cite(ref);
|
||||
|
||||
// Use citation.js format() method
|
||||
return cite.format('bibliography', {
|
||||
return cite.format("bibliography", {
|
||||
format: format,
|
||||
template: styleToUse,
|
||||
lang: 'en-US',
|
||||
lang: "en-US",
|
||||
});
|
||||
},
|
||||
|
||||
formatBibliography: (style, format = 'html') => {
|
||||
formatBibliography: (style, format = "html") => {
|
||||
const { citeInstance, settings } = get();
|
||||
const styleToUse = style || settings.defaultStyle;
|
||||
|
||||
// Use citation.js format() method on entire instance
|
||||
return citeInstance.format('bibliography', {
|
||||
return citeInstance.format("bibliography", {
|
||||
format: format,
|
||||
template: styleToUse,
|
||||
lang: 'en-US',
|
||||
lang: "en-US",
|
||||
});
|
||||
},
|
||||
|
||||
|
|
@ -267,8 +274,8 @@ export const useBibliographyStore = create<BibliographyStore>((set, get) => ({
|
|||
const cite = await Cite.async(input);
|
||||
return cite.data as CSLReference[];
|
||||
} catch (error) {
|
||||
console.error('Failed to parse input:', error);
|
||||
throw new Error('Could not parse citation data');
|
||||
console.error("Failed to parse input:", error);
|
||||
throw new Error("Could not parse citation data");
|
||||
}
|
||||
},
|
||||
|
||||
|
|
@ -277,14 +284,14 @@ export const useBibliographyStore = create<BibliographyStore>((set, get) => ({
|
|||
|
||||
// Use citation.js format() method
|
||||
switch (format) {
|
||||
case 'bibtex':
|
||||
return citeInstance.format('bibtex');
|
||||
case 'ris':
|
||||
return citeInstance.format('ris');
|
||||
case 'json':
|
||||
case "bibtex":
|
||||
return citeInstance.format("bibtex");
|
||||
case "ris":
|
||||
return citeInstance.format("ris");
|
||||
case "json":
|
||||
return JSON.stringify(citeInstance.data, null, 2);
|
||||
default:
|
||||
return '';
|
||||
return "";
|
||||
}
|
||||
},
|
||||
}));
|
||||
|
|
@ -295,8 +302,8 @@ export const clearBibliographyForDocumentSwitch = () => {
|
|||
citeInstance: new Cite([]),
|
||||
appMetadata: {},
|
||||
settings: {
|
||||
defaultStyle: 'apa',
|
||||
sortOrder: 'author',
|
||||
defaultStyle: "apa",
|
||||
sortOrder: "author",
|
||||
},
|
||||
});
|
||||
};
|
||||
|
|
|
|||
|
|
@ -1,17 +1,21 @@
|
|||
// @ts-expect-error - citation.js doesn't have TypeScript definitions
|
||||
import { Cite } from '@citation-js/core';
|
||||
import type { CSLReference } from '../../types/bibliography';
|
||||
import { Cite } from "@citation-js/core";
|
||||
import type { CSLReference } from "../../types/bibliography";
|
||||
|
||||
/**
|
||||
* Parse any citation input using citation.js
|
||||
* Handles: DOI, URL, BibTeX, RIS, ISBN, PubMed ID, etc.
|
||||
*/
|
||||
export const parseSmartInput = async (input: string): Promise<CSLReference[]> => {
|
||||
export const parseSmartInput = async (
|
||||
input: string,
|
||||
): Promise<CSLReference[]> => {
|
||||
try {
|
||||
const cite = await Cite.async(input);
|
||||
return cite.data as CSLReference[];
|
||||
} catch (error) {
|
||||
throw new Error(`Could not parse input: ${error instanceof Error ? error.message : 'Unknown error'}`);
|
||||
throw new Error(
|
||||
`Could not parse input: ${error instanceof Error ? error.message : "Unknown error"}`,
|
||||
);
|
||||
}
|
||||
};
|
||||
|
||||
|
|
@ -46,9 +50,8 @@ export const isValidCitationInput = (input: string): boolean => {
|
|||
// Wikidata ID (Q followed by numbers)
|
||||
if (/^(wikidata:)?Q\d+$/i.test(trimmed)) return true;
|
||||
|
||||
// Zenodo ID or URL
|
||||
if (/^zenodo\.\d+$/i.test(trimmed)) return true;
|
||||
if (/zenodo\.org\/record\/\d+/i.test(trimmed)) return true;
|
||||
// Zenodo DOI (10.5281/zenodo.xxxxx)
|
||||
if (/^10\.5281\/zenodo\.\d+/i.test(trimmed)) return true;
|
||||
|
||||
// CFF (Citation File Format) - YAML-based
|
||||
if (/^cff-version:/m.test(trimmed)) return true;
|
||||
|
|
@ -62,17 +65,16 @@ export const isValidCitationInput = (input: string): boolean => {
|
|||
export const getInputTypeHint = (input: string): string => {
|
||||
const trimmed = input.trim();
|
||||
|
||||
if (/^10\.\d{4,}\//.test(trimmed)) return 'DOI';
|
||||
if (/zenodo\.org\/record\/\d+/i.test(trimmed)) return 'Zenodo URL';
|
||||
if (/^zenodo\.\d+$/i.test(trimmed)) return 'Zenodo ID';
|
||||
if (/^https?:\/\//.test(trimmed)) return 'URL';
|
||||
if (/^@\w+\{/.test(trimmed)) return 'BibTeX';
|
||||
if (/^TY\s+-\s+/m.test(trimmed)) return 'RIS Format';
|
||||
if (/^PMID:/i.test(trimmed)) return 'PubMed ID (PMID)';
|
||||
if (/^PMC\d+/i.test(trimmed)) return 'PubMed Central ID (PMCID)';
|
||||
if (/^ISBN/i.test(trimmed)) return 'ISBN';
|
||||
if (/^(wikidata:)?Q\d+$/i.test(trimmed)) return 'Wikidata ID';
|
||||
if (/^cff-version:/m.test(trimmed)) return 'Citation File Format (CFF)';
|
||||
if (/^10\.5281\/zenodo\.\d+/i.test(trimmed)) return "Zenodo DOI";
|
||||
if (/^10\.\d{4,}\//.test(trimmed)) return "DOI";
|
||||
if (/^https?:\/\//.test(trimmed)) return "URL";
|
||||
if (/^@\w+\{/.test(trimmed)) return "BibTeX";
|
||||
if (/^TY\s+-\s+/m.test(trimmed)) return "RIS Format";
|
||||
if (/^PMID:/i.test(trimmed)) return "PubMed ID (PMID)";
|
||||
if (/^PMC\d+/i.test(trimmed)) return "PubMed Central ID (PMCID)";
|
||||
if (/^ISBN/i.test(trimmed)) return "ISBN";
|
||||
if (/^(wikidata:)?Q\d+$/i.test(trimmed)) return "Wikidata ID";
|
||||
if (/^cff-version:/m.test(trimmed)) return "Citation File Format (CFF)";
|
||||
|
||||
return 'Unknown';
|
||||
return "Unknown";
|
||||
};
|
||||
|
|
|
|||
Loading…
Reference in a new issue