Commit ef6b8007 authored by Maxime Chaillet's avatar Maxime Chaillet

Merge branch 'issue76' into 'master'

Issue76

Closes #76

See merge request !91
parents 75806d13 52cd60be
Pipeline #13841 passed with stages
in 2 minutes and 12 seconds
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The 2.1-Å crystal structure of glycosylated human afamin reveals an almost exclusively hydrophobic binding cleft capable of harboring large hydrophobic moieties. Lipid analysis confirms the presence of lipids, and density in the primary binding pocket of afamin was modeled as palmitoleic acid, presenting the native O-acylation on serine 209 in human Wnt3a. The modeled complex between the experimental afamin structure and a Wnt3a homology model based on the XWnt8-Fz8-CRD fragment complex crystal structure is compelling, with favorable interactions comparable with the crystal structure complex. 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Several hundred crystals were analysed, and unusual variability in cell volume and difficulty solving the structure despite a ~34% sequence identity with non-glycosylated human serum albumin indicated that the molecule exhibits variable and context-sensitive packing, despite greatly simplified glycosylation in insect cell expressed recombinant afamin. Controlled dehydration of the crystals was able to stabilise the orthorhombic crystal form reducing the number of molecules in the asymmetric unit from the monoclinic form and changing the conformational states of the protein. An iterative strategy using fully automatic experiments available on MASSIF-1 was used to quickly determine the optimal protocol to achieve the phase transition that should be readily applicable to many types of sample. The study also highlights the drawback of using a single crystallographic structure model for computation modelling purposes given that conformational state of the binding sites and electron density in the binding site, likely resulting from PEGs, greatly varies between models. This also holds for the analysis of unspecific low-affinity ligands, where often a variety fragments with similar uncertainty can be modelled, inviting interpretative bias. As a promiscuous transporter, afamin can also bind Gadoteridol, a magnetic resonance imaging contrast compound in two sites, one near the human albumin Sudlow-site and a second hitherto unknown binding site.",descriptionType:"Abstract"}],geoLocations:[],fundingReferences:[],relatedIdentifiers:[],schemaVersion:"http://datacite.org/schema/kernel-3",providerId:"inist",clientId:"inist.esrf",state:"findable"};Event.prototype={attach:function(e){this._listeners.push(e)},notify:function(e){for(var t=0;t<this._listeners.length;t++)this._listeners[t](this._sender,e)}},ExperimentalReportController.prototype.normalizeProposalName=function(e){var t;try{return t=new RegExp(/^(.*)-(.*)/),{categoryCode:t.exec(e)[1],categoryCounter:t.exec(e)[2]}}catch(r){t=new RegExp(/\d+$/);try{return{categoryCode:e.substring(0,e.length-t.exec(e)[0].length),categoryCounter:t.exec(e)[0]}}catch(e){return console.log(e),null}}},ExperimentalReportController.prototype.requestFilenameList=function(e){var t=this;if(e){var r=this.normalizeProposalName(e);r?$.ajax({type:"GET",timeout:this.timeout,url:this.server,data:r,dataType:"json",success:function(e){t.onSuccess.notify(e)},error:function(e){t.onError.notify(e)}}):t.onError.notify("Proposal could not be normalized: "+e)}else t.onError.notify("Proposal is null")},ExperimentalReportController.prototype.openFileInNewTab=function(e){if(e)try{window.open("ftp://www.esrf.eu/pub/UserReports/"+e,"_blank")}catch(t){alert("The requested file "+e+" could not be downloaded.")}},JsonExtractor.prototype.getTitle=function(e){return e&&e.titles&&e.titles.length>0&&e.titles[0].title?e.titles[0].title:(console.log("[JSON EXTRACTOR ERROR] title extraction failed."),null)},JsonExtractor.prototype.getDOI=function(e){return e&&e.doi?e.doi.toUpperCase():(console.log("[JSON EXTRACTOR ERROR] doi extraction failed."),null)},JsonExtractor.prototype.getPublisher=function(e){return e&&e.publisher?e.publisher:(console.log("[JSON EXTRACTOR ERROR] publisher extraction failed."),null)},JsonExtractor.prototype.getCreators=function(e){return e&&e.creators?_.map(e.creators,function(e){return e.givenName&&e.familyName||e.name?e:(console.log("[JSON EXTRACTOR ERROR] one of the creator could not be properly extracted."),{})}):(console.log("[JSON EXTRACTOR ERROR] Extraction of the creators failed."),null)},JsonExtractor.prototype.getPubliclyAccessibleYear=function(e){return e&&e.publicationYear?e.publicationYear:(console.log("[JSON EXTRACTOR ERROR] Extraction of the publication year failed."),null)},JsonExtractor.prototype.getInvestigationId=function(e){var t=RegExp(/\/\w*-*[Ee][Ss][Rr][Ff]-[Ee][Ss]-(\d+)$/);return t.exec(e.doi)?t.exec(e.doi)[1]:(console.log("[JSON EXTRACTOR ERROR] investigationId extraction failed."),null)},JsonExtractor.prototype.getFieldFromSubject=function(e,t){if(e)for(var r=new RegExp("^"+t+"$","i"),n=0;n<e.length;n++)if(r.test(e[n].subjectScheme)&&e[n].subject)return _.split(e[n].subject,",");return null},JsonExtractor.prototype.getMintingYear=function(e){},JsonExtractor.prototype.getSessionDate=function(e){if(e&&e.dates&&e.dates instanceof Array){var t=_.find(e.dates,function(e){if(e.dateType)return"collected"===e.dateType.toLowerCase()});if(t&&t.date)return moment(t.date).format("YYYY-MM-DD")}return console.log("[JSON EXTRACTOR ERROR] Extraction of session date failed."),null},JsonExtractor.prototype.getResourceTypeGeneral=function(e){if(e&&e.types)for(var t in e.types)if("resourceTypeGeneral"===t)return e.types[t];return console.log("[JSON EXTRACTOR ERROR] Extraction of resource type general failed."),null},JsonExtractor.prototype.getResourceType=function(e){if(e&&e.types)for(var t in e.types)if("resourceType"===t){if("Experiment Session"===e.types[t])return CONSTANTS.ES_RESOURCE_TYPE;if("Datacollection"===e.types[t])return CONSTANTS.DC_RESOURCE_TYPE}return console.log("[JSON EXTRACTOR ERROR] Extraction of resource type failed."),null},JsonExtractor.prototype.getAbstract=function(e){if(e&&e.descriptions){var t=_.find(e.descriptions,function(e){return"abstract"===e.descriptionType.toLowerCase()});if(t)return t.description}return console.log("[JSON EXTRACTOR ERROR] Extraction of the abstract failed."),null},JsonExtractor.prototype.getMergedProposalAndBeamline=function(e,t,r){if(e&&t&&r&&e.length===t.length&&e.length===r.length){for(var n=[],i=0;i<e.length;i++)n.push({proposal:e[i],beamline:t[i],beamlineUrl:r[i]});return _.uniqBy(n,function(e){return JSON.stringify(e)})}return null},dust.helpers.proposalBeamlineTable=proposalBeamlineTable,dust.helpers.abstract=abstract;
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Please use the DOI search engine at <a href="https://www.doi.org"> doi.org</a>. </p>':'<h2> Not found ! </h2> <p> The DOI was not found at ESRF because its prefix is not ESRF specific. </br> Please use the DOI search engine at <a href="https://www.doi.org"> doi.org</a>. </p>':"Not Found"===t?"welcome-page"===r?"<h3> Not found ! </h3> <p> Sorry, the requested DOI was not found. </p>":"<h2> Not found ! </h2> <p> Sorry, the requested DOI was not found. </p>":"timeout"===t?"welcome-page"===r?"<h3> Not found ! </h3> <p> Sorry, the server took too long to reply. Try again later. </p>":"<h2> Not found ! </h2> <p> Sorry, the server took too long to reply. Try again later. </p>":""===t&&"The resource you are looking for doesn't exist."===e.responseText?"welcome-page"===r?"<h3> Not found ! </h3> <p>It may take up to 24 hours for a newly generated DOI to become available. 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Currently, they are only accessible to proposal team members.":void 0},DOIView.prototype.addDOIMetadataToHead=function(e){var t=document.createElement("script");t.type="application/ld+json",t.text=e,document.getElementById("test").appendChild(t)};var ESRF_DC_142893590={id:"https://doi.org/10.15151/esrf-dc-142893590",doi:"10.15151/ESRF-DC-142893590",url:"https://doi.esrf.fr/10.15151/ESRF-DC-142893590",types:{ris:"DATA",bibtex:"misc",citeproc:"dataset",schemaOrg:"Dataset",resourceType:"Datacollection",resourceTypeGeneral:"Dataset"},creators:[{name:"Naschberger, Andreas",nameType:"Personal",givenName:"Andreas",familyName:"Naschberger"},{name:"Bowler, Matthew W.",nameType:"Personal",givenName:"Matthew W.",familyName:"Bowler"},{name:"Rupp, Bernhard",nameType:"Personal",givenName:"Bernhard",familyName:"Rupp"}],titles:[{title:"Structural Evidence for a Role of the Multi-functional Human Glycoprotein Afamin in Wnt Transport"}],publisher:"European Synchrotron Radiation Facility",container:{},subjects:[{subject:"OPID-1",subjectScheme:"Proposal"},{subject:"ID30A1",subjectScheme:"Instrument"}],contributors:[],dates:[{date:"2018",dateType:"Issued"}],publicationYear:2018,language:"en",identifiers:[{identifier:"https://doi.org/10.15151/esrf-dc-142893590",identifierType:"DOI"}],sizes:[],formats:[],rightsList:[],descriptions:[{description:"Afamin, a human plasma glycoprotein and putative transporter of hydrophobic molecules, has been shown to act as extracellular chaperone for poorly soluble, acylated Wnt proteins, forming a stable, soluble complex with functioning Wnt proteins. The 2.1-Å crystal structure of glycosylated human afamin reveals an almost exclusively hydrophobic binding cleft capable of harboring large hydrophobic moieties. Lipid analysis confirms the presence of lipids, and density in the primary binding pocket of afamin was modeled as palmitoleic acid, presenting the native O-acylation on serine 209 in human Wnt3a. The modeled complex between the experimental afamin structure and a Wnt3a homology model based on the XWnt8-Fz8-CRD fragment complex crystal structure is compelling, with favorable interactions comparable with the crystal structure complex. Afamin readily accommodates the conserved palmitoylated serine 209 of Wnt3a, providing a structural basis how afamin solubilizes hydrophobic and poorly soluble Wnt proteins.",descriptionType:"Abstract"}],geoLocations:[],fundingReferences:[],relatedIdentifiers:[],schemaVersion:"http://datacite.org/schema/kernel-3",providerId:"inist",clientId:"inist.esrf",state:"findable"},ESRF_DC_142915526={id:"https://doi.org/10.15151/esrf-dc-142915526",doi:"10.15151/ESRF-DC-142915526",url:"https://doi.esrf.fr/10.15151/ESRF-DC-142915526",types:{ris:"DATA",bibtex:"misc",citeproc:"dataset",schemaOrg:"Dataset",resourceType:"Datacollection",resourceTypeGeneral:"Dataset"},creators:[{name:"Naschberger, Andreas",nameType:"Personal",givenName:"Andreas",familyName:"Naschberger"},{name:"Bowler, Matthew W.",nameType:"Personal",givenName:"Matthew W.",familyName:"Bowler"},{name:"Rupp, Bernhard",nameType:"Personal",givenName:"Bernhard",familyName:"Rupp"}],titles:[{title:"Controlled dehydration, structural flexibility, and Gadolinium MRI contrast compound binding in human plasma glycoprotein afamin"}],publisher:"European Synchrotron Radiation Facility",container:{},subjects:[{subject:"OPID-1",subjectScheme:"Proposal"},{subject:"ID30A1",subjectScheme:"Instrument"}],contributors:[],dates:[{date:"2018",dateType:"Issued"}],publicationYear:2018,language:"en",identifiers:[{identifier:"https://doi.org/10.15151/esrf-dc-142915526",identifierType:"DOI"}],sizes:[],formats:[],rightsList:[],descriptions:[{description:"Afamin, a human blood plasma glycoprotein, a putative multi-functional transporter of hydrophobic molecules and a marker for metabolic syndrome, poses multiple challenges for crystallographic structure determination, both practically and in analysis of the models. Several hundred crystals were analysed, and unusual variability in cell volume and difficulty solving the structure despite a ~34% sequence identity with non-glycosylated human serum albumin indicated that the molecule exhibits variable and context-sensitive packing, despite greatly simplified glycosylation in insect cell expressed recombinant afamin. Controlled dehydration of the crystals was able to stabilise the orthorhombic crystal form reducing the number of molecules in the asymmetric unit from the monoclinic form and changing the conformational states of the protein. An iterative strategy using fully automatic experiments available on MASSIF-1 was used to quickly determine the optimal protocol to achieve the phase transition that should be readily applicable to many types of sample. The study also highlights the drawback of using a single crystallographic structure model for computation modelling purposes given that conformational state of the binding sites and electron density in the binding site, likely resulting from PEGs, greatly varies between models. This also holds for the analysis of unspecific low-affinity ligands, where often a variety fragments with similar uncertainty can be modelled, inviting interpretative bias. As a promiscuous transporter, afamin can also bind Gadoteridol, a magnetic resonance imaging contrast compound in two sites, one near the human albumin Sudlow-site and a second hitherto unknown binding site.",descriptionType:"Abstract"}],geoLocations:[],fundingReferences:[],relatedIdentifiers:[],schemaVersion:"http://datacite.org/schema/kernel-3",providerId:"inist",clientId:"inist.esrf",state:"findable"};Event.prototype={attach:function(e){this._listeners.push(e)},notify:function(e){for(var t=0;t<this._listeners.length;t++)this._listeners[t](this._sender,e)}},ExperimentalReportController.prototype.normalizeProposalName=function(e){var t;try{return t=new RegExp(/^(.*)-(.*)/),{categoryCode:t.exec(e)[1],categoryCounter:t.exec(e)[2]}}catch(r){t=new RegExp(/\d+$/);try{return{categoryCode:e.substring(0,e.length-t.exec(e)[0].length),categoryCounter:t.exec(e)[0]}}catch(e){return console.log(e),null}}},ExperimentalReportController.prototype.requestFilenameList=function(e){var t=this;if(e){var r=this.normalizeProposalName(e);r?$.ajax({type:"GET",timeout:this.timeout,url:this.server,data:r,dataType:"json",success:function(e){t.onSuccess.notify(e)},error:function(e){t.onError.notify(e)}}):t.onError.notify("Proposal could not be normalized: "+e)}else t.onError.notify("Proposal is null")},ExperimentalReportController.prototype.openFileInNewTab=function(e){if(e)try{window.open("ftp://www.esrf.eu/pub/UserReports/"+e,"_blank")}catch(t){alert("The requested file "+e+" could not be downloaded.")}},JsonExtractor.prototype.getTitle=function(e){return e&&e.titles&&e.titles.length>0&&e.titles[0].title?e.titles[0].title:(console.log("[JSON EXTRACTOR ERROR] title extraction failed."),null)},JsonExtractor.prototype.getDOI=function(e){return e&&e.doi?e.doi.toUpperCase():(console.log("[JSON EXTRACTOR ERROR] doi extraction failed."),null)},JsonExtractor.prototype.getPublisher=function(e){return e&&e.publisher?e.publisher:(console.log("[JSON EXTRACTOR ERROR] publisher extraction failed."),null)},JsonExtractor.prototype.getCreators=function(e){return e&&e.creators?_.map(e.creators,function(e){return e.givenName&&e.familyName||e.name?e:(console.log("[JSON EXTRACTOR ERROR] one of the creator could not be properly extracted."),{})}):(console.log("[JSON EXTRACTOR ERROR] Extraction of the creators failed."),null)},JsonExtractor.prototype.getPubliclyAccessibleYear=function(e){return e&&e.publicationYear?e.publicationYear:(console.log("[JSON EXTRACTOR ERROR] Extraction of the publication year failed."),null)},JsonExtractor.prototype.getInvestigationId=function(e){var t=RegExp(/\/\w*-*[Ee][Ss][Rr][Ff]-[Ee][Ss]-(\d+)$/);return t.exec(e.doi)?t.exec(e.doi)[1]:(console.log("[JSON EXTRACTOR ERROR] investigationId extraction failed."),null)},JsonExtractor.prototype.getFieldFromSubject=function(e,t){if(e)for(var r=new RegExp("^"+t+"$","i"),n=0;n<e.length;n++)if(r.test(e[n].subjectScheme)&&e[n].subject)return _.split(e[n].subject,",");return null},JsonExtractor.prototype.getMintingYear=function(e){},JsonExtractor.prototype.getSessionDate=function(e){if(e&&e.dates&&e.dates instanceof Array){var t=_.find(e.dates,function(e){if(e.dateType)return"collected"===e.dateType.toLowerCase()});if(t&&t.date)return moment(t.date).format("YYYY-MM-DD")}return console.log("[JSON EXTRACTOR ERROR] Extraction of session date failed."),null},JsonExtractor.prototype.getResourceTypeGeneral=function(e){if(e&&e.types)for(var t in e.types)if("resourceTypeGeneral"===t)return e.types[t];return console.log("[JSON EXTRACTOR ERROR] Extraction of resource type general failed."),null},JsonExtractor.prototype.getResourceType=function(e){if(e&&e.types)for(var t in e.types)if("resourceType"===t){if("Experiment Session"===e.types[t])return CONSTANTS.ES_RESOURCE_TYPE;if("Datacollection"===e.types[t])return CONSTANTS.DC_RESOURCE_TYPE}return console.log("[JSON EXTRACTOR ERROR] Extraction of resource type failed."),null},JsonExtractor.prototype.getAbstract=function(e){if(e&&e.descriptions){var t=_.find(e.descriptions,function(e){return"abstract"===e.descriptionType.toLowerCase()});if(t)return t.description}return console.log("[JSON EXTRACTOR ERROR] Extraction of the abstract failed."),null},JsonExtractor.prototype.getMergedProposalAndBeamline=function(e,t,r){if(e&&t&&r){var n=[],i=0;if(e.length===t.length&&e.length===r.length){for(;i<e.length;i++)n.push({proposal:e[i],beamline:t[i],beamlineUrl:r[i]});return _.uniqBy(n,function(e){return JSON.stringify(e)})}if(e.length>=1&&1===t.length&&1===r.length){for(i=0;i<e.length;i++)n.push({proposal:e[i],beamline:t[0],beamlineUrl:r[0]});return _.uniqBy(n,function(e){return JSON.stringify(e)})}}return null},dust.helpers.proposalBeamlineTable=proposalBeamlineTable,dust.helpers.abstract=abstract;
\ No newline at end of file
......@@ -19,6 +19,7 @@
"grunt-contrib-jshint": "^1.1.0",
"grunt-include-source": "^1.1.0",
"grunt-plato": "^1.4.0",
"it-each": "^0.4.0",
"jasmine-core": "^3.2.1",
"karma": "^3.0.0",
"karma-browserify": "^5.3.0",
......
......@@ -134,7 +134,7 @@ JsonExtractor.prototype.getFieldFromSubject = function (subjects, field) {
* @return {string} The minting year. Null if it does not exist.
*/
JsonExtractor.prototype.getMintingYear = function (data) {
// if (data) {
// if (data.date_registered && data.date_registered != null) {
// return moment(data.date_registered).year();
......@@ -242,16 +242,30 @@ JsonExtractor.prototype.getAbstract = function (data) {
* @return {array} array of the form [ {proposal: 'proposal1', beamline: 'beamline1', beamlineUrl: 'beamlineUrl' ] , {}, ... ]. Null if input array length are not equal
*/
JsonExtractor.prototype.getMergedProposalAndBeamline = function (proposals, beamlines, beamlineUrls) {
if (proposals && beamlines && beamlineUrls && proposals.length === beamlines.length && proposals.length === beamlineUrls.length) {
if (proposals && beamlines && beamlineUrls) {
var result = [];
for (var index = 0; index < proposals.length; index++) {
result.push({
proposal: proposals[index],
beamline: beamlines[index],
beamlineUrl: beamlineUrls[index]
});
var index = 0;
if (proposals.length === beamlines.length && proposals.length === beamlineUrls.length) {
for (index; index < proposals.length; index++) {
result.push({
proposal: proposals[index],
beamline: beamlines[index],
beamlineUrl: beamlineUrls[index]
});
}
return _.uniqBy(result, function (value) { return JSON.stringify(value); });
}
if (proposals.length >= 1 && beamlines.length === 1 && beamlineUrls.length === 1) {
for (index = 0; index < proposals.length; index++) {
result.push({
proposal: proposals[index],
beamline: beamlines[0],
beamlineUrl: beamlineUrls[0]
});
}
return _.uniqBy(result, function (value) { return JSON.stringify(value); });
}
return _.uniqBy(result, function (value) { return JSON.stringify(value); });
}
return null;
};
......
describe("jsonExtractor", () => {
describe("getFieldFromSubject()", () => {
it("extract field composed of a string without coma", () => {
let actualSubject = [
{
"subjectScheme": "Proposal",
"subject": "IH-HC-3376"
}
];
let expectedField = ["IH-HC-3376"];
let myJsonExtractor = new JsonExtractor();
expect(myJsonExtractor.getFieldFromSubject(actualSubject, "Proposal")).toEqual(expectedField);
})
it("extract field composed of a string with coma", () => {
let actualSubject = [
{
"subjectScheme": "Proposal",
"subject": "MA-4196,MD-1207"
}
];
let expectedField = ["MA-4196", "MD-1207"];
let myJsonExtractor = new JsonExtractor();
expect(myJsonExtractor.getFieldFromSubject(actualSubject, "Proposal")).toEqual(expectedField);
})
it("is case insensitive on the field", () => {
let actualSubject = [
{
"subjectScheme": "instrument",
"subject": "id01"
}
];
let expectedField = ["id01"];
let myJsonExtractor = new JsonExtractor();
expect(myJsonExtractor.getFieldFromSubject(actualSubject, "Instrument")).toEqual(expectedField);
})
it("returns null when the field does not exist in the subject", () => {
let actualSubject = [
{
"subject_scheme": "Instrument",
"text": "id01"
}
];
let expectedField = null;
let myJsonExtractor = new JsonExtractor();
expect(myJsonExtractor.getFieldFromSubject(actualSubject, "Proposal")).toEqual(expectedField);
})
require('it-each')({ testPerIteration: true });
let resources = require('./resources/jsonExtractor.resource');
it("returns null when the field exists but has no text associated", () => {
let actualSubject = [
{
"subject_scheme": "Proposal",
}
];
let expectedField = null;
let myJsonExtractor = new JsonExtractor();
describe("jsonExtractor unit tests", () => {
describe("getFieldFromSubject()", () => {
it.each(resources.getFieldFromSubject, '[getFieldFromSubject: %s ]', ['aboutThisTest'],
function (element, next) {
let jsonExtractor = new JsonExtractor();
expect(myJsonExtractor.getFieldFromSubject(actualSubject, "Proposal")).toEqual(expectedField);
})
expect(jsonExtractor.getFieldFromSubject(element.subjects, element.field)).toEqual(element.expected);
next();
})
})
describe("getResourceType()", () => {
it("returns ES_RESOURCE_TYPE when the doi resource type is 'experiment session'", () => {
let actualDoiData = require('./resources/doi_ES.js')
let expectedResourceType = CONSTANTS.ES_RESOURCE_TYPE;
let myJsonExtractor = new JsonExtractor();
expect(myJsonExtractor.getResourceType(actualDoiData)).toEqual(expectedResourceType);
})
it("returns DC_RESOURCE_TYPE when the doi resource type is 'Datacollection'", () => {
let actualDoiData = require('./resources/doi_DC.js');
let expectedResourceType = CONSTANTS.DC_RESOURCE_TYPE;
let myJsonExtractor = new JsonExtractor();
expect(myJsonExtractor.getResourceType(actualDoiData)).toEqual(expectedResourceType);
})
it("returns null when the doi resource type is not present", () => {
let actualDoiData = {
"title": "just a title",
};
let expectedResourceType = null;
let myJsonExtractor = new JsonExtractor();
it.each(resources.getResourceType, '[getResourceType: %s ]', ['aboutThisTest'],
function (element, next) {
let jsonExtractor = new JsonExtractor();
expect(myJsonExtractor.getResourceType(actualDoiData)).toEqual(expectedResourceType);
})
expect(jsonExtractor.getResourceType(element.doi)).toEqual(element.expected);
next();
})
})
describe('getResourceTypeGeneral', () => {
it("returns the resource type general when the doi resource type is 'experiment session'", () => {
let actualDoiData = require('./resources/doi_ES.js')
let expectedResourceTypeGeneral = 'Dataset';
let myJsonExtractor = new JsonExtractor();
it.each(resources.getResourceTypeGeneral, '[getResourceTypeGeneral: %s ]', ['aboutThisTest'],
function (element, next) {
let jsonExtractor = new JsonExtractor();
expect(myJsonExtractor.getResourceTypeGeneral(actualDoiData)).toEqual(expectedResourceTypeGeneral);
})
it("returns null when the resource type general is not available", () => {
let actualDoiData = {
"title": "just a title",
}
let expectedResourceTypeGeneral = null;
let myJsonExtractor = new JsonExtractor();
expect(myJsonExtractor.getResourceTypeGeneral(actualDoiData)).toEqual(expectedResourceTypeGeneral);
})
expect(jsonExtractor.getResourceTypeGeneral(element.doi)).toEqual(element.expected);
next();
})
})
describe('getSessionDate', () => {
it("returns the session date when the doi resource type is 'experiment session'", () => {
let actualDoiData = require('./resources/doi_ES.js')
let expectedSessionDate = '2018-03-26';
let myJsonExtractor = new JsonExtractor();
expect(myJsonExtractor.getSessionDate(actualDoiData)).toEqual(expectedSessionDate);
})
it.each(resources.getSessionDate, '[getSessionDate: %s ]', ['aboutThisTest'],
function (element, next) {
let jsonExtractor = new JsonExtractor();
it("returns null when the doi resource type is 'datacollection'", () => {
let actualDoiData = require('./resources/doi_DC.js')
let expectedSessionDate = null;
let myJsonExtractor = new JsonExtractor();
expect(myJsonExtractor.getSessionDate(actualDoiData)).toEqual(expectedSessionDate);
})
expect(jsonExtractor.getSessionDate(element.doi)).toEqual(element.expected);
next();
})
})
describe("getMergedProposalAndBeamline", () => {
it('merge proposals and beamlines in a single table', () => {
let actualProposals = ['MA-4196', 'MD-1207'];
let actualBeamlines = ['ID11', 'ID21'];
let actualBeamlineUrls = ["http://www.esrf.fr/UsersAndScience/Experiments/StructMaterials/ID11", "http://www.esrf.eu/UsersAndScience/Experiments/XNP/ID21"];
let expectedMerge = [
{ proposal: 'MA-4196', beamline: 'ID11', beamlineUrl: "http://www.esrf.fr/UsersAndScience/Experiments/StructMaterials/ID11" },
{ proposal: 'MD-1207', beamline: 'ID21', beamlineUrl: "http://www.esrf.eu/UsersAndScience/Experiments/XNP/ID21" }
];
let myJsonExtractor = new JsonExtractor();
expect(myJsonExtractor.getMergedProposalAndBeamline(actualProposals, actualBeamlines, actualBeamlineUrls)).toEqual(expectedMerge);
})
it('merge proposals and beamlines in a single table and remove duplicates', () => {
let actualProposals = ['MA-4196', 'MD-1207', 'MA-4196'];
let actualBeamlines = ['ID11', 'ID21', 'ID11'];
let actualBeamlineUrls = ["http://www.esrf.fr/UsersAndScience/Experiments/StructMaterials/ID11", "http://www.esrf.eu/UsersAndScience/Experiments/XNP/ID21", "http://www.esrf.fr/UsersAndScience/Experiments/StructMaterials/ID11"];
it.each(resources.getMergedProposalAndBeamline, '[getMergedProposalAndBeamline: %s ]', ['aboutThisTest'],
function (element, next) {
let jsonExtractor = new JsonExtractor();
let expectedMerge = [
{ proposal: 'MA-4196', beamline: 'ID11', beamlineUrl: "http://www.esrf.fr/UsersAndScience/Experiments/StructMaterials/ID11" },
{ proposal: 'MD-1207', beamline: 'ID21', beamlineUrl: "http://www.esrf.eu/UsersAndScience/Experiments/XNP/ID21" },
];
let myJsonExtractor = new JsonExtractor();
expect(myJsonExtractor.getMergedProposalAndBeamline(actualProposals, actualBeamlines, actualBeamlineUrls)).toEqual(expectedMerge);
})
expect(jsonExtractor.getMergedProposalAndBeamline(element.proposals, element.beamlines, element.beamlineUrls)).toEqual(element.expected);
next();
})
})
describe("GetInvestigationId", () => {
it("returns investigationId for a experimental session doi", () => {
let actualDOIdata = require("./resources/doi_ES.js");;
let expectedInvestigationId = "92162610";
let myJsonExtractor = new JsonExtractor();
expect(myJsonExtractor.getInvestigationId(actualDOIdata)).toEqual(expectedInvestigationId);
})
describe("getInvestigationId()", () => {
it.each(resources.getInvestigationId, '[getInvestigationId: %s ]', ['aboutThisTest'],
function (element, next) {
let jsonExtractor = new JsonExtractor();
it("returns null for a data collection doi", () => {
let actualDOIdata = { doi: "10.15151/ESRF-DC-i130874985" };
let expectedInvestigationId = null;
let myJsonExtractor = new JsonExtractor();
expect(myJsonExtractor.getInvestigationId(actualDOIdata)).toEqual(expectedInvestigationId);
})
expect(jsonExtractor.getInvestigationId(element.doi)).toEqual(element.expected);
next();
})
})
describe("GetTitle", () => {
it('returns the title for an experimental session doi', () => {
let actualDOIdata = {
"titles": [
{
"title": "Kmapping of Ge microdisks"
}
],
};
let expectedDOITitle = "Kmapping of Ge microdisks";
let myJsonExtractor = new JsonExtractor();
expect(myJsonExtractor.getTitle(actualDOIdata)).toEqual(expectedDOITitle);
})
it('returns null when titles is empty', () => {
let actualDOIdata = {
"titles": [
],
};
let expectedDOITitle = null;
let myJsonExtractor = new JsonExtractor();
expect(myJsonExtractor.getTitle(actualDOIdata)).toBeNull();
})
it('returns null when title is empty', () => {
let actualDOIdata = {
"titles": [
{
"title": null
}
],
};
let expectedDOITitle = null;
let myJsonExtractor = new JsonExtractor();
expect(myJsonExtractor.getTitle(actualDOIdata)).toBeNull();
})
describe("getTitle()", () => {
it.each(resources.getTitle, '[getTitle: %s ]', ['aboutThisTest'],
function (element, next) {
let jsonExtractor = new JsonExtractor();
expect(jsonExtractor.getTitle(element.doi)).toEqual(element.expected);
next();
})
})
describe("GetDOI", () => {
it('returns the DOI for an experimental session doi', () => {
let actualDOIdata = {
"doi": "10.15151/esrf-es-90632078",
};
let expectedDOINumber = "10.15151/ESRF-ES-90632078";
let myJsonExtractor = new JsonExtractor();
expect(myJsonExtractor.getDOI(actualDOIdata)).toEqual(expectedDOINumber);
})
describe("getDOI()", () => {
it.each(resources.getDOI, '[getDOI: %s ]', ['aboutThisTest'],
function (element, next) {
let jsonExtractor = new JsonExtractor();
it('returns null when doi is empty', () => {
let actualDOIdata = {
"doi": null,
};
let expectedDOINumber = null;
let myJsonExtractor = new JsonExtractor();
expect(myJsonExtractor.getDOI(actualDOIdata)).toBeNull();
})
expect(jsonExtractor.getDOI(element.doi)).toEqual(element.expected);
next();
})
})
describe("GetPublisher", () => {
it('returns the publisher for an experimental session doi', () => {
let actualDOIdata = {
"publisher": "European Synchrotron Radiation Facility",
};
let expectedPublisher = "European Synchrotron Radiation Facility";
let myJsonExtractor = new JsonExtractor();
expect(myJsonExtractor.getPublisher(actualDOIdata)).toEqual(expectedPublisher);
})
describe("getPublisher()", () => {
it.each(resources.getPublisher, '[getPublisher: %s ]', ['aboutThisTest'],
function (element, next) {
let jsonExtractor = new JsonExtractor();
it('returns null when the publisher is not set', () => {
let actualDOIdata = {
"publisher": null,
};
let expectedPublisher = null;
let myJsonExtractor = new JsonExtractor();
expect(myJsonExtractor.getPublisher(actualDOIdata)).toEqual(expectedPublisher);
})
expect(jsonExtractor.getPublisher(element.doi)).toEqual(element.expected);
next();
})
})
describe("GetCreators", () => {
it('returns the creators for an experimental session doi', () => {
let actualDOIdata = {
"creators": [
{
"nameType": "Personal",
"name": "LEAKE, Steven",
"givenName": "Steven",
"familyName": "LEAKE"
},
{
"nameType": "Personal",
"name": "ZATTERIN, Edoardo",
"givenName": "Edoardo",
"familyName": "ZATTERIN"
}
]
};
let expectedCreators = [
{
"nameType": "Personal",
"name": "LEAKE, Steven",
"givenName": "Steven",
"familyName": "LEAKE"
},
{
"nameType": "Personal",
"name": "ZATTERIN, Edoardo",
"givenName": "Edoardo",
"familyName": "ZATTERIN"
}
];
let myJsonExtractor = new JsonExtractor();
expect(myJsonExtractor.getCreators(actualDOIdata)).toEqual(expectedCreators);
})
it('returns only the creators for which givenName && familyName is defined or name is defined', () => {
let actualDOIdata = {
"creators": [
{
"nameType": "Personal",
"name": "LEAKE, Steven",
},
{
"nameType": "Personal",
},
{
"nameType": "Personal",
"name": "ZATTERIN, Edoardo",
"givenName": "Edoardo",
"familyName": "ZATTERIN"
}
describe("getCreators()", () => {
it.each(resources.getCreators, '[getCreators: %s ]', ['aboutThisTest'],
function (element, next) {
let jsonExtractor = new JsonExtractor();
]
};
let expectedCreators = [
{
"nameType": "Personal",
"name": "LEAKE, Steven",
},
{},
{
"nameType": "Personal",
"name": "ZATTERIN, Edoardo",
"givenName": "Edoardo",
"familyName": "ZATTERIN"
}
];
let myJsonExtractor = new JsonExtractor();
expect(myJsonExtractor.getCreators(actualDOIdata)).toEqual(expectedCreators);
})
expect(jsonExtractor.getCreators(element.doi)).toEqual(element.expected);
next();
})
})
describe("GetPubliclyAccessibleYear", () => {
it('returns the year the data will be publicly accessible', () => {
let actualDOIdata = {
"publicationYear": 2021
};
let expectedCreators = 2021;
let myJsonExtractor = new JsonExtractor();
expect(myJsonExtractor.getPubliclyAccessibleYear(actualDOIdata)).toEqual(expectedCreators);
})
it('returns null when the year the data will be publicly accessible is not available', () => {
let actualDOIdata = {
"publicationYear": null
};
let expectedCreators = null;
let myJsonExtractor = new JsonExtractor();
expect(myJsonExtractor.getPubliclyAccessibleYear(actualDOIdata)).toEqual(expectedCreators);
})
describe("getPubliclyAccessibleYear", () => {
it.each(resources.getPubliclyAccessibleYear, '[getPubliclyAccessibleYear: %s ]', ['aboutThisTest'],
function (element, next) {
let jsonExtractor = new JsonExtractor();