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Commit d243d56c authored by Maxime Chaillet's avatar Maxime Chaillet
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Merge branch 'issue61' into 'master' 

Issue61

Closes #61

See merge request icat/doi-landing-page!68
parents bb200e4d cf0bc77c
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www/karma.conf.js
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......@@ -4,6 +4,7 @@
module.exports = function (config) {
config.set({
// base path that will be used to resolve all patterns (eg. files, exclude)
basePath: '',
......@@ -54,8 +55,7 @@ module.exports = function (config) {
// enable / disable colors in the output (reporters and logs)
colors: true,
// level of logging
// possible values: config.LOG_DISABLE || config.LOG_ERROR || config.LOG_WARN || config.LOG_INFO || config.LOG_DEBUG
logLevel: config.LOG_INFO,
......
www/min/components.min.js
View file @ d243d56c
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www/min/doi.min.js
View file @ d243d56c
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Citation(e){this.isBuildable=!!(e&&e.creator&&0!==e.creator.length&&e.date_registered&&e.title&&e.publisher&&e.doi)}Citation.prototype.getAuthorsForCitation=function(e){if(this.isBuildable){var t=_.transform(e,function(e,t,r,a){a instanceof Array||(t=a);var n=null;if(t.givenName?((n=new Author).setFamilyName(t.familyName),n.setFirstName(t.givenName),e.push(n.getTitleCaseFamilyName()+" "+n.getFirstNameInitials())):((n=new Author).setSingleName(t.name),n.getRawFamilyName()&&n.getRawFirstName()?e.push(n.getTitleCaseFamilyName()+" "+n.getFirstNameInitials()):e.push(t.name)),!(a instanceof Array))return!1},[]);return _.join(t,", ")}return console.log("the author list for the citation could not be generated."),""};var CONSTANTS={ES_RESOURCE_TYPE:"experimental session resource type",DC_RESOURCE_TYPE:"dataset collection resource type"};function DOIController(e){var r=this;this.doiServer="https://data.datacite.org/",this.acceptedPrefix=["10.5072","10.15151"],this.view=e,this.experimentalReportController=new ExperimentalReportController,this.experimentalReportController.onSuccess.attach(function(e,t){r.view.renderExperimentalReportData(t)}),this.experimentalReportController.onError.attach(function(e,t){console.log("Error when retrieving fileList from SMIS."),r.view.renderErrorForExperimentalReport()})}function DoiData(e,t,r,a,n,i){this.title=e,this.doi=t,this.dataciteLink=r,this.publisher=a,this.creator=n,this.publiclyAccessibleYear=i}function DOIView(){this.mainPanelId="main",this.reportPanelId="expReport",this.badgePanelId="badges",this.metadataDivId="metadata",this.reportExperimentFileNames=null,this.failedRecievingExpReport=!1,this.isDOIAlreadyRendered=!1,this.onDOIRendered=new Event(this)}DOIController.prototype.isValidDOIData=function(e){return 3<_.keysIn(e).length&&0<_.find(_.keysIn(e),function(e){return"title"===e}).length},DOIController.prototype.render=function(e,t){var r=this;if(r.isValidDOIData(t)){var a=new DoiData(t.title,t.doi.toUpperCase(),r.doiServer+e,t.publisher,t.creator,t.publication_year),n=new JsonExtractor;a.abstract=n.getAbstract(t),a.investigationId=n.getInvestigationId(t),a.mintingYear=n.getMintingYear(t),a.proposalType=n.getFieldFromSubject(t.subject,"Proposal Type Description"),a.resourceType=n.getResourceType(t),a.resourceTypeGeneral=n.getResourceTypeGeneral(t),a.sessionDate=n.getSessionDate(t);var 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t==e})},DOIController.prototype.displayMainContent=function(e){"welcome-page"===this.origin&&dust.render("welcome_tpl",{},function(e,t){$("#main").html(t)}),"index"===this.origin&&this.getData(e)},DOIController.prototype.setOrigin=function(e){this.origin=e},DOIController.prototype.getBeamlineUrl=function(e,i,o){var s=[];return e.forEach(function(e){if(i){o===CONSTANTS.ES_RESOURCE_TYPE&&(i=moment(i)),o===CONSTANTS.DC_RESOURCE_TYPE&&(i=moment(i,"YYYY"));for(var t="",r=0;r<BEAMLINEURL.length;r++){var a=moment(BEAMLINEURL[r].startDate),n=moment(BEAMLINEURL[r].endDate);if(BEAMLINEURL[r].name.toLowerCase()===e.toLowerCase()&&a<=i&&i<=n){t=BEAMLINEURL[r].url;break}}""===t?s.push("noLink"):s.push(t)}else s.push("noLink")}),s},DOIController.prototype.createCitation=function(e){var t=new Citation(e);return t.isBuildable?t.getAuthorsForCitation(e.creator)+" ("+moment(e.date_registered).year()+"). 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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. Please try again later.</p>":"<h2> Not found ! </h2> <p>It may take up to 24 hours for a newly generated DOI to become available. Please try again later.</p>":"welcome-page"===r?"<h3> Not found ! </h3> <p> Connexion problem to the datacite server. Please try again later.</p>":"<h2> Not found ! </h2> <p> Connexion problem to the datacite server. Please try again later.</p>",dust.render(a,{message:n},function(e,t){$("#error").html(t)})},DOIView.prototype.renderErrorForExperimentalReport=function(){this.failedRecievingExpReport=!0;$("#"+this.reportPanelId).html('<div class="card-header text-center"> <label>Experimental report </label> </div> <div class="card-body padding10"> <p> The filename list is not available. </p> </div>')},DOIView.prototype.renderBadges=function(e){if(e){var r=this;dust.render("badges_tpl",{data:e,constants:CONSTANTS},function(e,t){$("#"+r.badgePanelId).html(t)})}},DOIView.prototype.renderMetadata=function(e){if(e){var r=this;dust.render("metadata_tpl",{data:e,constants:CONSTANTS},function(e,t){$("#"+r.metadataDivId).html(t)})}},DOIView.prototype.setDataAccessMessage=function(e){return"Open access"===e.accessibility?"The data can be accessed by clicking on the link below":"Restricted access"===e.accessibility?"The data are under embargo until <b>"+e.publiclyAccessibleYear+"</b> but could be released earlier. Currently, they are only accessible to proposal team members.":void 0};var ESRF_DC_142893590={id:"https://doi.org/10.15151/ESRF-DC-142893590",doi:"10.15151/ESRF-DC-142893590",creator:[{type:"Person",name:"Naschberger, Andreas",givenName:"Andreas",familyName:"Naschberger"},{type:"Person",name:"Bowler, Matthew W.",givenName:"Matthew W.",familyName:"Bowler"},{type:"Person",name:"Rupp, Bernhard",givenName:"Bernhard",familyName:"Rupp"}],title:"Structural Evidence for a Role of the Multi-functional Human Glycoprotein Afamin in Wnt Transport",publisher:"European Synchrotron Radiation Facility",resource_type_general:"Dataset",resource_type:"Datacollection",subject:[[{subject_scheme:"Proposal",text:"OPID-30A1"},{subject_scheme:"instrument",text:"ID30A1"}]],description:{type:"Abstract",text:"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."},date_collected:"2018-03-07",date_published:"2018",date_registered:"2018-03-07T14:37:09Z",date_updated:"2018-03-08T16:30:22Z",publication_year:2018,language:"eng",schemaVersion:"http://datacite.org/schema/kernel-3",provider_id:"INIST",client_id:"INIST.ESRF"},ESRF_DC_142915526={id:"https://doi.org/10.15151/esrf-dc-142915526",doi:"10.15151/ESRF-DC-142915526",creator:[{type:"Person",name:"Naschberger, Andreas",givenName:"Andreas",familyName:"Naschberger"},{type:"Person",name:"Bowler, Matthew W.",givenName:"Matthew W.",familyName:"Bowler"},{type:"Person",name:"Rupp, Bernhard",givenName:"Bernhard",familyName:"Rupp"}],title:"Controlled dehydration, structural flexibility, and Gadolinium MRI contrast compound binding in human plasma glycoprotein afamin",publisher:"European Synchrotron Radiation Facility",resource_type_general:"Dataset",resource_type:"Datacollection",subject:[[{subject_scheme:"Proposal",text:"OPID-30A1"},{subject_scheme:"instrument",text:"ID30A1"}]],description:{type:"Abstract",text:"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."},date_collected:"2018-03-07",date_published:"2018",date_registered:"2018-03-07T14:37:09Z",date_updated:"2018-03-08T16:30:22Z",publication_year:2018,language:"eng",schemaVersion:"http://datacite.org/schema/kernel-3",provider_id:"INIST",client_id:"INIST.ESRF"};function Event(e){this._sender=e,this._listeners=[]}function ExperimentalReportController(){this.server="https://wwws.esrf.fr/misapps/SMISServer/rest/reports/fileNames",this.timeout=5e3,this.onSuccess=new Event(this),this.onError=new Event(this)}function JsonExtractor(e){}function proposalBeamlineTable(e,t,r,a){var n=a.mergedProposalBeamlines;if(e.write('<table class="table table-striped">'),e.write("<thead>"),e.write("<tr>"),e.write('<th scope="col">Proposals</th>'),e.write('<th scope="col">Beamlines</th>'),e.write("</tr>"),e.write("</thead>"),e.write("<tbody>"),n){for(var i=0;i<n.length;i++)if(n[i]){var o=n[i].proposal||"unknown",s=n[i].beamline||"unknown",l=n[i].beamlineUrl;e.write("<tr>"),e.write("<td>"+o+"</td>"),"noLink"===l?e.write("<td>"+s+"</td>"):e.write('<td> <a href="'+l+'" target="_blank">'+s+" </a> </td>"),e.write("</tr>")}else e.write("<tr>"),chunck.write("<td> unknown </td>"),chunck.write("<td> unknown </td>"),e.write("</tr>");return e.write("</tbody>"),e.write("</table>"),e.render(r.block,t)}}function abstract(e,t,r,a){var n=a.abstract;return e.write('<div class="myBorder-left">'),e.write("<label> Abstract </label>"),e.write('<div class="padding-left-15">'),n?e.write(n):e.write("There is no abstract for this session."),e.write("</div >"),e.write("</div >"),e.render(r.block,t)}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.requestFilenameList=function(e){var t=this;if(e){var r=new RegExp(/^(.*)-(.*)/),a=r.exec(e)[1],n=r.exec(e)[2];a&&n&&$.ajax({type:"GET",timeout:this.timeout,url:this.server,data:{categoryCode:a,categoryCounter:n},dataType:"json",success:function(e){t.onSuccess.notify(e)},error:function(e){t.onError.notify(e)}})}else t.onError.notify("Proposal is null")},ExperimentalReportController.prototype.openFileInNewTab=function(t){if(t)try{window.open("ftp://www.esrf.eu/pub/UserReports/"+t,"_blank")}catch(e){alert("The requested file "+t+" could not be downloaded.")}},JsonExtractor.prototype.getInvestigationId=function(e){var t=RegExp(/\/\w*-*[Ee][Ss][Rr][Ff]-[Ee][Ss]-(\d+)$/);return t.exec(e.doi)?t.exec(e.doi)[1]:null},JsonExtractor.prototype.getFieldFromSubject=function(e,t){if(e&&e[0])for(var r=new RegExp("^"+t+"$","i"),a=0;a<e[0].length;a++)if(r.test(e[0][a].subject_scheme)&&e[0][a].text)return _.split(e[0][a].text,",");return null},JsonExtractor.prototype.getMintingYear=function(e){return e&&e.date_registered&&null!=e.date_registered?moment(e.date_registered).year():null},JsonExtractor.prototype.getSessionDate=function(e){return e&&e.date_collected&&null!=e.date_collected?moment(e.date_collected).format("YYYY-M-D"):null},JsonExtractor.prototype.getResourceTypeGeneral=function(e){return e&&e.resource_type_general?e.resource_type_general:null},JsonExtractor.prototype.getResourceType=function(e){if(e&&e.resource_type){if("Experiment Session"===e.resource_type)return CONSTANTS.ES_RESOURCE_TYPE;if("Datacollection"===e.resource_type)return CONSTANTS.DC_RESOURCE_TYPE}return null},JsonExtractor.prototype.getAbstract=function(e){if(e&&e.description){var t=e.description;if(t.type&&"Abstract"===t.type)return t.text}return null},JsonExtractor.prototype.getMergedProposalAndBeamline=function(e,t,r){if(e&&t&&r&&e.length===t.length&&e.length===r.length){for(var a=[],n=0;n<e.length;n++)a.push({proposal:e[n],beamline:t[n],beamlineUrl:r[n]});return _.uniqBy(a,function(e){return JSON.stringify(e)})}return null},dust.helpers.proposalBeamlineTable=proposalBeamlineTable,dust.helpers.abstract=abstract;
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e=new RegExp(/(\S+)/g),t=this.singleName.match(e);if(2===t.length)return this.familyName=t[1],this.familyName;var r=new RegExp(/\s([^a-z]+$)/).exec(this.singleName);return r&&(this.familyName=r[1]),this.familyName}},Author.prototype.getRawFirstName=function(){if(this.firstName)return this.firstName;if(this.singleName){var e=new RegExp(/(\S+)/g),t=this.singleName.match(e);if(2===t.length)return this.firstName=t[0],this.firstName;var r=new RegExp(/^(.[^A-Z]+)+\b/).exec(this.singleName);return r&&(this.firstName=r[0]),r}},Author.prototype.getTitleCaseFamilyName=function(){if(this.familyName){allLowerCase=this.familyName.toLowerCase();var e=new RegExp(/^./);return allLowerCase.replace(e,function(e){return e.toUpperCase()})}return console.log("family name is undefined"),null},Author.prototype.getFirstNameInitials=function(){var e=new RegExp(/(\S+)/g);return this.firstName?this.firstName.replace(e,function(e){return e.charAt(0)+"."}):(console.log("first name is undefined"),null)};var 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t=_.transform(e,function(e,t,r,i){i instanceof Array||(t=i);var n=null;if(t.givenName?((n=new Author).setFamilyName(t.familyName),n.setFirstName(t.givenName),e.push(n.getTitleCaseFamilyName()+" "+n.getFirstNameInitials())):((n=new Author).setSingleName(t.name),n.getRawFamilyName()&&n.getRawFirstName()?e.push(n.getTitleCaseFamilyName()+" "+n.getFirstNameInitials()):e.push(t.name)),!(i instanceof Array))return!1},[]);return _.join(t,", ")}return console.log("[CITATION GENERATION] Author list for the citation could not be generated."),""},Citation.prototype.getDOIRegistrationYear=function(e){return e.resourceType===CONSTANTS.ES_RESOURCE_TYPE?moment(e.sessionDate).year():e.resourceType===CONSTANTS.DC_RESOURCE_TYPE?e.publiclyAccessibleYear:(console.log("[CITATION GENERATION] Could not get the year to generate the citation."),"")};var CONSTANTS={ES_RESOURCE_TYPE:"experimental session resource type",DC_RESOURCE_TYPE:"dataset collection resource 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n=i.getFieldFromSubject(t.subjects,"Proposal"),a=i.getFieldFromSubject(t.subjects,"Instrument");this.experimentalReportController.requestFilenameList(n[0]),r.accessibility=r.getAccessibilityStatus(r.resourceType,r.sessionDate,r.publiclyAccessibleYear),r.accessMessage=this.view.setDataAccessMessage(r),r.citation=this.createCitation(r),r.resourceType===CONSTANTS.ES_RESOURCE_TYPE&&(r.beamlineUrls=this.getBeamlineUrl(a,r.sessionDate,r.resourceType),r.mintingYear=moment(r.sessionDate).year()),r.resourceType===CONSTANTS.DC_RESOURCE_TYPE&&(r.beamlineUrls=this.getBeamlineUrl(a,r.publiclyAccessibleYear,r.resourceType),r.mintingYear=r.publiclyAccessibleYear),r.mergedProposalBeamlines=i.getMergedProposalAndBeamline(n,a,r.beamlineUrls),this.view.renderDOIData(r)}else this.view.renderError("Not Found",this.origin)},DOIController.prototype.getData=function(e){var t=this;this.view.setDOIInTopBanner(e),"10.15151/ESRF-DC-142893590"!=e.toUpperCase()?"10.15151/ESRF-DC-142915526"!=e.toUpperCase()?this.hasAcceptedPrefix(e)?$.ajax({headers:{Accept:"application/vnd.datacite.datacite+json"},type:"GET",timeout:15e3,url:this.doiServer+e,beforeSend:function(){t.view.setLoading("Retrieving data from Server")},complete:function(){t.view.setLoading(!1)}}).done(function(r){r&&t.render(e,r)}).fail(function(e,r,i){t.view.renderError(e,i,t.origin),t.view.setLoading(!1)}):t.view.renderError("Bad Prefix",t.origin):this.render(e,ESRF_DC_142915526):this.render(e,ESRF_DC_142893590)},DOIController.prototype.hasAcceptedPrefix=function(e){var t=e.split("/")[0];return-1!=_.findIndex(this.acceptedPrefix,function(e){return t==e})},DOIController.prototype.displayMainContent=function(e){"welcome-page"===this.origin&&dust.render("welcome_tpl",{},function(e,t){$("#main").html(t)}),"index"===this.origin&&this.getData(e)},DOIController.prototype.setOrigin=function(e){this.origin=e},DOIController.prototype.getBeamlineUrl=function(e,t,r){var i=[];return e.forEach(function(e){if(t){r===CONSTANTS.ES_RESOURCE_TYPE&&(t=moment(t)),r===CONSTANTS.DC_RESOURCE_TYPE&&(t=moment(t,"YYYY"));for(var n="",a=0;a<BEAMLINEURL.length;a++){var o=moment(BEAMLINEURL[a].startDate),s=moment(BEAMLINEURL[a].endDate);if(BEAMLINEURL[a].name.toLowerCase()===e.toLowerCase()&&t>=o&&t<=s){n=BEAMLINEURL[a].url;break}}""===n?i.push("noLink"):i.push(n)}else i.push("noLink")}),i},DOIController.prototype.createCitation=function(e){var t=new Citation(e);if(t.isBuildable){return t.getAuthorsForCitation(e.creators)+" ("+t.getDOIRegistrationYear(e)+"). 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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. Please try again later.</p>":"<h2> Not found ! </h2> <p>It may take up to 24 hours for a newly generated DOI to become available. Please try again later.</p>":"welcome-page"===r?"<h3> Not found ! </h3> <p> Connexion problem to the datacite server. Please try again later.</p>":"<h2> Not found ! </h2> <p> Connexion problem to the datacite server. Please try again later.</p>",dust.render(i,{message:n},function(e,t){$("#error").html(t)})},DOIView.prototype.renderErrorForExperimentalReport=function(){this.failedRecievingExpReport=!0;$("#"+this.reportPanelId).html('<div class="card-header text-center"> <label>Experimental report </label> </div> <div class="card-body padding10"> <p> The filename list is not available. </p> </div>')},DOIView.prototype.renderBadges=function(e){if(e){var t=this;dust.render("badges_tpl",{data:e,constants:CONSTANTS},function(e,r){$("#"+t.badgePanelId).html(r)})}},DOIView.prototype.renderMetadata=function(e){if(e){var t=this;dust.render("metadata_tpl",{data:e,constants:CONSTANTS},function(e,r){$("#"+t.metadataDivId).html(r)})}},DOIView.prototype.setDataAccessMessage=function(e){return"Open access"===e.accessibility?"The data can be accessed by clicking on the link below":"Restricted access"===e.accessibility?"The data are under embargo until <b>"+e.publiclyAccessibleYear+"</b> but could be released earlier. Currently, they are only accessible to proposal team members.":void 0};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.requestFilenameList=function(e){var t=this;if(e){var r=new RegExp(/^(.*)-(.*)/),i=r.exec(e)[1],n=r.exec(e)[2];i&&n&&$.ajax({type:"GET",timeout:this.timeout,url:this.server,data:{categoryCode:i,categoryCounter:n},dataType:"json",success:function(e){t.onSuccess.notify(e)},error:function(e){t.onError.notify(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"),i=0;i<e.length;i++)if(r.test(e[i].subjectScheme)&&e[i].subject)return _.split(e[i].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-M-D")}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 i=[],n=0;n<e.length;n++)i.push({proposal:e[n],beamline:t[n],beamlineUrl:r[n]});return _.uniqBy(i,function(e){return JSON.stringify(e)})}return null},dust.helpers.proposalBeamlineTable=proposalBeamlineTable,dust.helpers.abstract=abstract;
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www/min/precompiled.templates.min.js
View file @ d243d56c
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www/src/ESRF-DC-142893590.js
View file @ d243d56c
var ESRF_DC_142893590 = {
"id": "https://doi.org/10.15151/ESRF-DC-142893590",
"id": "https://doi.org/10.15151/esrf-dc-142893590",
"doi": "10.15151/ESRF-DC-142893590",
"creator": [
{
"type": "Person",
"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"
},
{
"type": "Person",
"name": "Bowler, Matthew W.",
"nameType": "Personal",
"givenName": "Matthew W.",
"familyName": "Bowler"
},
{
"type": "Person",
{
"name": "Rupp, Bernhard",
"nameType": "Personal",
"givenName": "Bernhard",
"familyName": "Rupp"
}
],
"title": "Structural Evidence for a Role of the Multi-functional Human Glycoprotein Afamin in Wnt Transport",
"titles": [
{
"title": "Structural Evidence for a Role of the Multi-functional Human Glycoprotein Afamin in Wnt Transport"
}
],
"publisher": "European Synchrotron Radiation Facility",
"resource_type_general": "Dataset",
"resource_type": "Datacollection",
"subject": [
[
{
"subject_scheme": "Proposal",
"text": "OPID-30A1"
},
{
"subject_scheme": "instrument",
"text": "ID30A1"
}
]
"container": {},
"subjects": [
{
"subject": "OPID-1",
"subjectScheme": "Proposal"
},
{
"subject": "ID30A1",
"subjectScheme": "Instrument"
}
],
"description": {
"type": "Abstract",
"text": "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."
},
"date_collected": "2018-03-07",
"date_published": "2018",
"date_registered": "2018-03-07T14:37:09Z",
"date_updated": "2018-03-08T16:30:22Z",
"publication_year": 2018,
"language": "eng",
"contributors": [],
"dates": [
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