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Use saved crossref data for publications

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This commit is contained in:
Mickaël Véril 2020-11-01 16:18:00 +01:00
parent ad81e2bcbf
commit ed21b74fc8
14 changed files with 1286 additions and 83 deletions
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17
content/dataset.html
View File

@ -16,7 +16,7 @@ draft: false
<script src="/js/processingIndicator.js"></script>
<script src="/js/noNan.js"></script>
<script src="/js/websiteFile.js"></script>
<script src="/js/DOICache.js"></script>
<script src="/js/PubliData.js"></script>
<script src="/js/nestedCheckbox.js"></script>
<script src="/js/selectSelectAll.js"></script>
<script src="/js/numberRangeChange.js"></script>
@ -97,7 +97,7 @@ draft: false
delete (cbextl)
delete (extl)
delete (vertkindtl)
window.doiCache = new DOICache()
window.publiCache = new Map()
await loadFiles()
}
async function loadFiles() {
@ -460,7 +460,7 @@ draft: false
allowUnknow:$("#cb_nHUnknow").is(':checked')
}
}
window.doiCache.clear()
window.publiCache.clear()
processingIndicator.isActive = true
window.filtData = window.dats
//Filter with select
@ -494,7 +494,10 @@ draft: false
var exSets = new uniq(window.filtData.map((d) => d.set))
var mols = new Set(window.filtData.map((d) => d.molecule))
for (const exSet of exSets) {
await doiCache.tryAdd(await exSet.getDOIAsync())
const DOI= await exSet.getDOIAsync()
if (DOI!=null) {
publiCache.set(DOI,await PubliData.loadAsync(DOI))
}
const setName = exSet.name
window.T1ref.set(setName, new Map())
for (const mol of mols) {
@ -570,9 +573,9 @@ draft: false
$("<h1/>").text(CurrentsetName).appendTo(div)
}
var doi= await exSet.getDOIAsync()
if (doiCache.has(doi)) {
const doiDat = doiCache.get(doi).format('data', { format: 'object' })[0]
$("<h2/>").append($("<a>",{href:doiDat.URL,target:"_blank"}).text(doiDat.title)).appendTo(div)
if (publiCache.has(doi)) {
const publiDat = publiCache.get(doi)
$("<h2/>").append($("<a>",{href:publiDat.URL,target:"_blank"}).text(publiDat.title)).appendTo(div)
}
var table = $("<table/>").addClass("datatable").appendTo(div)
var head = $("<tr/>")

7
content/publications.html
View File

@ -14,6 +14,7 @@ draft: false
<script src="/js/websiteFile.js"></script>
<script src="/js/numberUtils.js"></script>
<script src="/js/DebugMode.js"></script>
<script src="/js/PubliData.js"></script>
<script src="/js/createPubliUI.js"></script>
<script src="/js/processingIndicator.js"></script>
<script src="/js/indexDB.js"></script>
@ -26,8 +27,7 @@ draft: false
var myDB = await indexDB.loadAsync()
const sets = myDB.sets
for (const [setName,publis] of sets) {
const publiscite = await Cite.async(publis)
const uopublis = publiscite.format('data', { format: 'object' })
const uopublis = await PubliData.loadManyAsync(publis)
if (uopublis.length !== 0) {
const mySetSec = $('<section>').addClass('publiSet').attr("data-setName", setName).attr("id",setName).appendTo(setsSec)
$("<h1>").text(setName).appendTo(mySetSec)
@ -39,8 +39,7 @@ draft: false
}
}
const odois = myDB.others
const opubliscite = await Cite.async(odois)
const uoopublis = opubliscite.format('data', { format: 'object' })
const uoopublis = await PubliData.loadManyAsync(odois)
const opublis = uoopublis.sort((puba, pubb) => pubUtils.getIssuedDate(puba) - pubUtils.getIssuedDate(pubb))
for (const publi of opublis) {
art = await createPubliUI(publi, true, true)

1
layouts/partials/head_custom.html
View File

@ -18,7 +18,6 @@ MathJax.Hub.Config({
<script type="text/javascript" async
src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.7/MathJax.js?config=TeX-MML-AM_CHTML" onload="MathJaxPolyfillInit()">
</script>
<script src="https://cdn.rawgit.com/larsgw/citation.js/archive/citation.js/citation-0.4.0-9.js" type="text/javascript"></script>
<script src="/js/pubUtils.js"></script>
<script src="https://unpkg.com/simple-statistics@7.0.2/dist/simple-statistics.min.js"></script>
<script src="https://cdn.jsdelivr.net/npm/bowser@2.5.3/es5.min.js"></script>

213
static/data/publis/10/1021/acs/jctc/0c00227/metadata.json Normal file
View File

@ -0,0 +1,213 @@
{
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2020,
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],
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"timestamp": 1597232840029
},
"reference-count": 179,
"publisher": "American Chemical Society (ACS)",
"issue": "6",
"funder": [
{
"DOI": "10.13039/501100001665",
"name": "Agence Nationale de la Recherche",
"doi-asserted-by": "publisher",
"award": [
"ANR-11-EQPX-0004"
]
},
{
"DOI": "10.13039/501100004794",
"name": "Centre National de la Recherche Scientifique",
"doi-asserted-by": "publisher",
"award": []
},
{
"name": "Centre de Calcul Intensif des Pays de la Loire",
"award": []
},
{
"name": "GENCI-TGCC",
"award": [
"2019-A0060801738"
]
},
{
"name": "CALMIP",
"award": []
}
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"domain": [],
"crossmark-restriction": false
},
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"J. Chem. Theory Comput."
],
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]
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"timestamp": 1588878560000
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"sequence": "first",
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{
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}
]
},
{
"given": "Anthony",
"family": "Scemama",
"sequence": "additional",
"affiliation": [
{
"name": "Laboratoire de Chimie et Physique Quantiques, CNRS, UPS, Universit\u00e9 de Toulouse, 31000 Toulouse, France"
}
]
},
{
"ORCID": "http://orcid.org/0000-0001-6684-5223",
"authenticated-orcid": true,
"given": "Martial",
"family": "Boggio-Pasqua",
"sequence": "additional",
"affiliation": [
{
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"ORCID": "http://orcid.org/0000-0002-4217-0708",
"authenticated-orcid": true,
"given": "Denis",
"family": "Jacquemin",
"sequence": "additional",
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{
"name": "CEISAM UMR 6230, CNRS, Universit\u00e9 de Nantes, F-44000 Nantes, France"
}
]
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"member": "316",
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"1549-9618",
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"type": "electronic"
}
],
"subject": [
"Physical and Theoretical Chemistry",
"Computer Science Applications"
]
}

216
static/data/publis/10/1021/acs/jctc/8b00406/metadata.json Normal file
View File

@ -0,0 +1,216 @@
{
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"date-time": "2020-10-16T15:03:35Z",
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},
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"publisher": "American Chemical Society (ACS)",
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"J. Chem. Theory Comput."
],
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},
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[
2018,
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2
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],
"date-time": "2018-07-02T22:35:43Z",
"timestamp": 1530570943000
},
"page": "4360-4379",
"source": "Crossref",
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"A Mountaineering Strategy to Excited States: Highly Accurate Reference Energies and Benchmarks"
],
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"sequence": "first",
"affiliation": [
{
"name": "Laboratoire de Chimie et Physique Quantiques, Universit\u00e9 de Toulouse, CNRS, UPS, 31013 Toulouse Cedex 6, France"
}
]
},
{
"given": "Anthony",
"family": "Scemama",
"sequence": "additional",
"affiliation": [
{
"name": "Laboratoire de Chimie et Physique Quantiques, Universit\u00e9 de Toulouse, CNRS, UPS, 31013 Toulouse Cedex 6, France"
}
]
},
{
"given": "Aymeric",
"family": "Blondel",
"sequence": "additional",
"affiliation": [
{
"name": "Laboratoire CEISAM - UMR CNRS 6230, Universit\u00e9 de Nantes, 2 Rue de la Houssini\u00e8re, BP 92208, 44322 Nantes Cedex 3, France"
}
]
},
{
"given": "Yann",
"family": "Garniron",
"sequence": "additional",
"affiliation": [
{
"name": "Laboratoire de Chimie et Physique Quantiques, Universit\u00e9 de Toulouse, CNRS, UPS, 31013 Toulouse Cedex 6, France"
}
]
},
{
"given": "Michel",
"family": "Caffarel",
"sequence": "additional",
"affiliation": [
{
"name": "Laboratoire de Chimie et Physique Quantiques, Universit\u00e9 de Toulouse, CNRS, UPS, 31013 Toulouse Cedex 6, France"
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]
},
{
"ORCID": "http://orcid.org/0000-0002-4217-0708",
"authenticated-orcid": true,
"given": "Denis",
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{
"name": "Laboratoire CEISAM - UMR CNRS 6230, Universit\u00e9 de Nantes, 2 Rue de la Houssini\u00e8re, BP 92208, 44322 Nantes Cedex 3, France"
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2018,
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208
static/data/publis/10/1021/acs/jctc/8b01205/metadata.json Normal file
View File

@ -0,0 +1,208 @@
{
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},
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}
]
},
{
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{
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}
]
},
{
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215
static/data/publis/10/1021/acs/jctc/9b01216/metadata.json Normal file
View File

@ -0,0 +1,215 @@
{
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},
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{
"name": "Laboratoire de Chimie et Physique Quantiques, CNRS et Universit\u00e9 Toulouse III - Paul Sabatier, 118 route de Narbonne, 31062 Toulouse, France"
}
]
},
{
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"authenticated-orcid": true,
"given": "Filippo",
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{
"name": "Dipartimento di Chimica e Chimica Industriale, University of Pisa, Via Moruzzi 3, 56124 Pisa, Italy"
}
]
},
{
"ORCID": "http://orcid.org/0000-0001-6684-5223",
"authenticated-orcid": true,
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{
"name": "Laboratoire de Chimie et Physique Quantiques, CNRS et Universit\u00e9 Toulouse III - Paul Sabatier, 118 route de Narbonne, 31062 Toulouse, France"
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]
},
{
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{
"name": "Laboratoire de Chimie et Physique Quantiques, CNRS et Universit\u00e9 Toulouse III - Paul Sabatier, 118 route de Narbonne, 31062 Toulouse, France"
}
]
},
{
"ORCID": "http://orcid.org/0000-0002-4217-0708",
"authenticated-orcid": true,
"given": "Denis",
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{
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],
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}
],
"deposited": {
"date-parts": [
[
2020,
4,
6
]
],
"date-time": "2020-04-06T22:40:19Z",
"timestamp": 1586212819000
},
"score": 1.0,
"subtitle": [],
"short-title": [],
"issued": {
"date-parts": [
[
2020,
1,
27
]
]
},
"references-count": 254,
"journal-issue": {
"published-print": {
"date-parts": [
[
2020,
3,
10
]
]
},
"issue": "3"
},
"alternative-id": [
"10.1021/acs.jctc.9b01216"
],
"URL": "http://dx.doi.org/10.1021/acs.jctc.9b01216",
"relation": {},
"ISSN": [
"1549-9618",
"1549-9626"
],
"issn-type": [
{
"value": "1549-9618",
"type": "print"
},
{
"value": "1549-9626",
"type": "electronic"
}
],
"subject": [
"Physical and Theoretical Chemistry",
"Computer Science Applications"
]
}

182
static/data/publis/10/1021/acs/jpclett/0c00014/metadata.json Normal file
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@ -0,0 +1,182 @@
{
"indexed": {
"date-parts": [
[
2020,
10,
16
]
],
"date-time": "2020-10-16T15:03:35Z",
"timestamp": 1602860615926
},
"reference-count": 114,
"publisher": "American Chemical Society (ACS)",
"issue": "6",
"funder": [
{
"DOI": "10.13039/501100004794",
"name": "Centre National de la Recherche Scientifique",
"doi-asserted-by": "publisher",
"award": []
},
{
"name": "R?gion des Pays de la Loire",
"award": []
}
],
"content-domain": {
"domain": [],
"crossmark-restriction": false
},
"short-container-title": [
"J. Phys. Chem. Lett."
],
"published-print": {
"date-parts": [
[
2020,
3,
19
]
]
},
"DOI": "10.1021/acs.jpclett.0c00014",
"type": "journal-article",
"created": {
"date-parts": [
[
2020,
3,
3
]
],
"date-time": "2020-03-03T19:29:26Z",
"timestamp": 1583263766000
},
"page": "2374-2383",
"source": "Crossref",
"is-referenced-by-count": 10,
"title": [
"The Quest for Highly Accurate Excitation Energies: A Computational Perspective"
],
"prefix": "10.1021",
"volume": "11",
"author": [
{
"ORCID": "http://orcid.org/0000-0003-0598-7425",
"authenticated-orcid": true,
"given": "Pierre-Fran\u00e7ois",
"family": "Loos",
"sequence": "first",
"affiliation": [
{
"name": "Laboratoire de Chimie et Physique Quantiques, Universit\u00e9 de Toulouse, CNRS, UPS, 31062 Toulouse, France"
}
]
},
{
"given": "Anthony",
"family": "Scemama",
"sequence": "additional",
"affiliation": [
{
"name": "Laboratoire de Chimie et Physique Quantiques, Universit\u00e9 de Toulouse, CNRS, UPS, 31062 Toulouse, France"
}
]
},
{
"ORCID": "http://orcid.org/0000-0002-4217-0708",
"authenticated-orcid": true,
"given": "Denis",
"family": "Jacquemin",
"sequence": "additional",
"affiliation": [
{
"name": "Universit\u00e9 de Nantes, CNRS, CEISAM UMR 6230, F-44000 Nantes, France"
}
]
}
],
"member": "316",
"published-online": {
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2020,
3,
3
]
]
},
"container-title": [
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],
"original-title": [],
"language": "en",
"link": [
{
"URL": "https://pubs.acs.org/doi/pdf/10.1021/acs.jpclett.0c00014",
"content-type": "unspecified",
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}
],
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[
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],
"date-time": "2020-04-06T18:58:24Z",
"timestamp": 1586199504000
},
"score": 1.0,
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},
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},
"issue": "6"
},
"alternative-id": [
"10.1021/acs.jpclett.0c00014"
],
"URL": "http://dx.doi.org/10.1021/acs.jpclett.0c00014",
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"ISSN": [
"1948-7185",
"1948-7185"
],
"issn-type": [
{
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"type": "print"
},
{
"value": "1948-7185",
"type": "electronic"
}
],
"subject": [
"General Materials Science"
]
}

177
static/data/publis/10/1021/acs/jpclett/9b03652/metadata.json Normal file
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@ -0,0 +1,177 @@
{
"indexed": {
"date-parts": [
[
2020,
5,
20
]
],
"date-time": "2020-05-20T11:06:57Z",
"timestamp": 1589972817879
},
"reference-count": 54,
"publisher": "American Chemical Society (ACS)",
"issue": "3",
"funder": [
{
"DOI": "10.13039/501100004794",
"name": "Centre National de la Recherche Scientifique",
"doi-asserted-by": "publisher",
"award": []
}
],
"content-domain": {
"domain": [],
"crossmark-restriction": false
},
"short-container-title": [
"J. Phys. Chem. Lett."
],
"published-print": {
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[
2020,
2,
6
]
]
},
"DOI": "10.1021/acs.jpclett.9b03652",
"type": "journal-article",
"created": {
"date-parts": [
[
2020,
1,
8
]
],
"date-time": "2020-01-08T20:22:46Z",
"timestamp": 1578514966000
},
"page": "974-980",
"source": "Crossref",
"is-referenced-by-count": 2,
"title": [
"Is ADC(3) as Accurate as CC3 for Valence and Rydberg Transition Energies?"
],
"prefix": "10.1021",
"volume": "11",
"author": [
{
"ORCID": "http://orcid.org/0000-0003-0598-7425",
"authenticated-orcid": true,
"given": "Pierre-Fran\u00e7ois",
"family": "Loos",
"sequence": "first",
"affiliation": [
{
"name": "Laboratoire de Chimie et Physique Quantiques (UMR 5626), CNRS, Universit\u00e9 de Toulouse, 31077 Toulouse, France"
}
]
},
{
"ORCID": "http://orcid.org/0000-0002-4217-0708",
"authenticated-orcid": true,
"given": "Denis",
"family": "Jacquemin",
"sequence": "additional",
"affiliation": [
{
"name": "Laboratoire CEISAM UMR UN-CNRS 6230, Universit\u00e9 de Nantes, F-44000 Nantes, France"
}
]
}
],
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{
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},
"issue": "3"
},
"alternative-id": [
"10.1021/acs.jpclett.9b03652"
],
"URL": "http://dx.doi.org/10.1021/acs.jpclett.9b03652",
"relation": {},
"ISSN": [
"1948-7185",
"1948-7185"
],
"issn-type": [
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"type": "print"
},
{
"value": "1948-7185",
"type": "electronic"
}
],
"subject": [
"General Materials Science"
]
}

52
static/js/DOICache.js
View File

@ -1,52 +0,0 @@
class DOICache{
constructor(){
this._doimap=new Map()
this._Cite=require("citation-js")
}
clear(){
this._doimap.clear()
}
delete(article){
return this._doimap.delete(doi)
}
forEach(callbackfn, thisArg=None){
return this._doimap.forEach(callbackfn,thisArg)
}
get(doi){
return this._doimap.get(doi)
}
has(doi){
return this._doimap.has(doi)
}
async add(doi){
if(!this.has(doi)){
const publi=await this._Cite.async(doi)
this._doimap.set(doi,publi)
}
}
async tryAdd(doi){
const publi = await this._Cite.async(doi)
if (publi.data.length === 0) {
return false
}
this._doimap.set(doi,publi)
return true
}
async addRange(dois){
const set=new Set(dois)
for(const doi of set){
await this.add(doi)
}
}
async tryAddRange(dois){
const set = new Set(dois)
return Promise.all(Array.from(set).map(doi=>this.tryAdd(doi)))
}
get size(){
return this._doimap.size()
}
keys() { return this._doimap.keys()}
values() { return this._doimap.values()}
entries() { return this._doimap.entries()}
[Symbol.iterator]() { return this.values()}
}

44
static/js/PubliData.js Normal file
View File

@ -0,0 +1,44 @@
class PubliData{
static async loadAsync(DOI){
const path = PubliData.GetPathForDOI(DOI)
var me = JSON.parse(await getTextFromFileUrlAsync(`${path}/metadata.json`))
Reflect.setPrototypeOf(me,PubliData.prototype)
return me
}
static async loadManyAsync(DOIs){
var data = []
for (const DOI of DOIs) {
if (DOI!=null) {
data.push(await PubliData.loadAsync(DOI))
}
}
return data
}
get Path(){
return PubliData.GetPathForDOI(this.DOI)
}
get PictureURL(){
return PubliData.GetPictureURLForDOI(this.DOI)
}
get AbstractURL(){
return PubliData.GetAbstractURLForDOI(this.DOI)
}
async getAbstractTextAsync(){
return await PubliData.getAbstractTexForDOIAsync(this.DOI)
}
static GetPathForDOI(DOI){
return `/data/publis/${DOI.replaceAll(".","/")}`
}
static GetAbstractURLForDOI(DOI){
return `${PubliData.GetPathForDOI(DOI)}/abstract.html`
}
static GetPictureURLForDOI(DOI){
return `${PubliData.GetPathForDOI(DOI)}/picture.jpeg`
}
static async getAbstractTexForDOIAsync(DOI){
return await getTextFromFileUrlAsync(PubliData.GetAbstractURLForDOI(DOI))
}
}

19
static/js/createPubliUI.js
View File

@ -1,14 +1,10 @@
function getPubliSubDir(DOI) {
return DOI.split(".").join("/")
}
async function createPubliUI(publi,toolTips=false,abstract=false) {
const art = $("<article/>").addClass("publi")
art.className = "publi"
$("<a/>", {
href: publi.URL,
target: "_blank"
}).html($("<h1/>").text(publi.title)).appendTo(art)
}).html($("<h1/>").text(publi.title[0])).appendTo(art)
const authors = publi.author
const ulauthors = $("<ul/>").addClass("authors-list").appendTo(art)
for (const author of authors) {
@ -35,18 +31,18 @@ async function createPubliUI(publi,toolTips=false,abstract=false) {
ulauthors.append(liauth)
}
journaldiv = $("<div/>").appendTo(art)
if ("container-title-short" in publi) {
var title_short = $("<span/>").text(publi["container-title-short"])
if ("container-title-short" in publi && publi["container-title-short"].length>0) {
var title_short = $("<span/>").text(publi["container-title-short"][0])
journaldiv.append(title_short)
if (toolTips) {
tippy(title_short[0], {
content: publi["container-title"],
content: publi["container-title"][0],
theme: 'light',
});
}
}
else {
$("<span/>").text(publi["container-title"]).appendTo(journaldiv)
$("<span/>").text(publi["container-title"][0]).appendTo(journaldiv)
}
var date = pubUtils.getIssuedDate(publi)
journaldiv.append(" ")
@ -70,12 +66,11 @@ async function createPubliUI(publi,toolTips=false,abstract=false) {
year: "numeric"
}))).appendTo(art)
if (abstract) {
const dir = "/data/publis/"+getPubliSubDir(publi.DOI)
var ab = $("<section>",{id: "abstract",}).addClass("well").addClass("abstract")
var abfig =$("<figure>").addClass("picture")
abfig.appendTo(ab)
$("<img>",{src:dir+"/picture.jpeg"}).appendTo(abfig)
var htmltxt =await getTextFromFileUrlAsync(dir+"/abstract.html")
$("<img>",{src:publi.PictureURL}).appendTo(abfig)
var htmltxt = await publi.getAbstractTextAsync()
abtxt=$("<p>").html(htmltxt)
abtxt.appendTo(ab)
art.append(ab)

2
static/js/indexDB.js
View File

@ -4,7 +4,7 @@ class indexDB {
const text = await getTextFromFileUrlAsync("/data/index.yaml")
const myYaml = jsyaml.load(text);
db.sets = ((myYaml.sets === null) ? new Map() : new Map(Object.entries(myYaml.sets)));
db.others = ((myYaml.others === null) ? new Map() : new Map(Object.entries(myYaml.others)));
db.others = ((myYaml.others === null) ? [] : Array.from(myYaml.others));
return db
}
}

16
tools/pubimport.py → tools/pubImport.py Normal file → Executable file
View File

@ -8,9 +8,9 @@ from pathlib import Path
from shutil import copyfile
import crossref_commons.retrieval
parser = argparse.ArgumentParser()
parser.add_argument("--DOI",type=str)
parser.add_argument('--abstract', type=Path,help="The html abstract text")
parser.add_argument('--picture', type=Path,help="The picture for the graphical abstact")
parser.add_argument("--DOI",type=str,required=True)
parser.add_argument('--abstract', type=Path,help="The html abstract text file",required=False)
parser.add_argument('--picture', type=Path,help="The jpeg picture for the graphical abstact",required=False)
args=parser.parse_args()
scriptpath=Path(sys.argv[0]).resolve()
publipath=scriptpath.parents[1]/"static"/"data"/"publis"
@ -22,6 +22,10 @@ picture=mydir/"picture.jpeg"
if not mydir.exists():
os.makedirs(str(mydir))
with open(str(metadata),"w") as f:
json.dump(result,f)
copyfile(args.abstract,abstract)
copyfile(args.picture,picture")
json.dump(result,f, indent=2)
if args.abstract!=None:
abstract=mydir/"abstract.html"
copyfile(args.abstract,abstract)
if args.picture!=None:
picture=mydir/"picture.html"
copyfile(args.picture,picture)