Connects to #1466: Allow query via DOIs when adding a new Article

src/clincoded/static/components/add_external_resource.js

@@ -370,19 +370,19 @@ function pubmedTxt(field, extra) {
  }
  switch(field) {
  case 'modalTitle':
- txt = 'Add new PubMed Article';
+ txt = 'Add new Article';
  break;
  case 'inputLabel':
- txt = 'Enter a PMID';
+ txt = 'Enter a PMID or DOI';
  break;
  case 'editLabel':
- txt = 'Edit PMID';
+ txt = 'Edit PMID/DOI';
  break;
  case 'inputButton':
- txt = 'Retrieve PubMed Article';
+ txt = 'Retrieve Article';
  break;
  case 'resourceResponse':
- txt = "Select \"" + extra + "\" (below) if the following citation is correct; otherwise, edit the PMID (above) to retrieve a different article.";
+ txt = "Select \"" + extra + "\" (below) if the following citation is correct; otherwise, edit the PMID/DOI (above) to retrieve a different article.";
  break;
  }
  return txt;
@@ -421,16 +421,25 @@ function pubmedValidateForm() {
  this.setFormErrors('resourceId', 'Please re-enter PMID without any leading 0\'s');
  this.setState({submitBusy: false});
  }
- // valid if the input only has numbers
- if (valid && !formInput.match(/^[0-9]*$/)) {
+ // Check if form input is a DOI/PMID, then validate
+ if (valid && formInput.match(/^10.\d{4,9}\/[-._;()\/:A-Z0-9]+$/gi)) {
+ var doiPresent = true; 
+ } else if (valid && formInput.match(/^[0-9]*$/)) {
+ var pmidPresent = true;
+ } else if (valid && !doiPresent && !formInput.match(/^[0-9]*$/)) {
  valid = false;
  this.setFormErrors('resourceId', 'PMID should contain only numbers');
  this.setState({submitBusy: false});
- }
+ } else if (valid && !pmidPresent && !formInput.match(/^10.\d{4,9}\/[-._;()\/:A-Z0-9]+$/gi)) {
+ valid = false;
+ this.setFormErrors('resourceId', 'Invalid DOI');
+ this.setState({submitBusy: false});
+ } 
+
  // valid if parent object is GDM and input isn't already associated with it
  if (valid && this.props.parentObj && this.props.parentObj['@type'] && this.props.parentObj['@type'][0] == 'gdm') {
  for (var i = 0; i < this.props.parentObj.annotations.length; i++) {
- if (this.props.parentObj.annotations[i].article.pmid == formInput) {
+ if (this.props.parentObj.annotations[i].article.pmid == formInput || this.props.parentObj.annotations[i].article.doi == formInput) {
  valid = false;
  this.setFormErrors('resourceId', 'This article has already been associated with this Gene-Disease Record');
  this.setState({submitBusy: false});
@@ -439,50 +448,76 @@ function pubmedValidateForm() {
  }
  }
  // valid if parent object is evidence list (VCI) and input isn't already associated with it - final behavior TBD
- /*
  if (valid && this.props.parentObj && this.props.parentObj['@type'] && this.props.parentObj['@type'][0] == 'evidenceList') {
  for (var j = 0; j < this.props.parentObj.evidenceList.length; j++) {
- if (this.props.parentObj.evidenceList[j].articles[0].pmid == formInput) {
+ if (this.props.parentObj.evidenceList[j].articles[0].pmid == formInput || this.props.parentObj.evidenceList[j].articles[0].doi == formInput) {
  valid = false;
  this.setFormErrors('resourceId', 'This article has already been associated with this evidence group');
  this.setState({submitBusy: false});
  break;
  }
  }
- }*/
+ }
  return valid;
 }
+function getPubmedResponse(id) {
+ this.getRestData('/articles/' + id)
+ .then(article => {
+ // article already exists in db
+ this.setState({queryResourceBusy: false, tempResource: article, resourceFetched: true});
+ }, () => {
+ var url = external_url_map['PubMedSearch'];
+ // PubMed article not in our DB; go out to PubMed itself to retrieve it as XML
+ this.getRestDataXml(external_url_map['PubMedSearch'] + id).then(xml => {
+ var data = parsePubmed(xml);
+ if (data.pmid) {
+ // found the result we want
+ this.setState({queryResourceBusy: false, tempResource: data, resourceFetched: true});
+ } else {
+ // no result from ClinVar
+ this.setFormErrors('resourceId', 'PMID not found');
+ this.setState({queryResourceBusy: false, resourceFetched: false});
+ }
+ });
+ }).catch(e => {
+ // error handling for PubMed query
+ this.setFormErrors('resourceId', 'Error querying PubMed. Please check your input and try again.');
+ this.setState({queryResourceBusy: false, resourceFetched: false});
+ });
+}
 function pubmedQueryResource() {
  // for pinging and parsing data from PubMed
  this.saveFormValue('resourceId', this.state.inputValue);
+ // Give 'getPubmedResponse' correct scope for 'this'
+ const receivePubmed = getPubmedResponse.bind(this);
  if (pubmedValidateForm.call(this)) {
  var url = external_url_map['PubMedSearch'];
  var data;
 
  // Remove possible prefix like "PMID:" before sending queries
  var id = this.state.inputValue.replace(/^PMID\s*:\s*(\S*)$/i, '$1');
- this.getRestData('/articles/' + id).then(article => {
- // article already exists in db
- this.setState({queryResourceBusy: false, tempResource: article, resourceFetched: true});
- }, () => {
- var url = external_url_map['PubMedSearch'];
- // PubMed article not in our DB; go out to PubMed itself to retrieve it as XML
- this.getRestDataXml(external_url_map['PubMedSearch'] + id).then(xml => {
- var data = parsePubmed(xml);
- if (data.pmid) {
- // found the result we want
- this.setState({queryResourceBusy: false, tempResource: data, resourceFetched: true});
- } else {
- // no result from ClinVar
- this.setFormErrors('resourceId', 'PMID not found');
- this.setState({queryResourceBusy: false, resourceFetched: false});
- }
+ // Check whether input is a valid DOI
+ const doiRegex = /^10.\d{4,9}\/[-._;()\/:A-Z0-9]+$/gi;
+ const validDoi = id.match(doiRegex);
+ // Handle search via DOI
+ if (validDoi) {
+ const doiUrl = external_url_map['DoiToPubMed'] + validDoi[0];
+ const doiData = this.getRestDataXml(doiUrl).then(xml => {
+ let data = parsePubmed(xml);
+ return data;
+ })
+ Promise.resolve(doiData).then(res => {
+ id = res.pmid;
+ return id;
+ })
+ // Take the resolved PMID and then query PubMed
+ .then(id => {
+ receivePubmed(id);
  });
- }).catch(e => {
- // error handling for PubMed query
- this.setFormErrors('resourceId', 'Error querying PubMed. Please check your input and try again.');
- this.setState({queryResourceBusy: false, resourceFetched: false});
- });
+ // If not a DOI, query PubMed using PMID
+ } else {
+ receivePubmed(id);
+ }
  } else {
  this.setState({queryResourceBusy: false});
  }

src/clincoded/static/components/curation_central.js

@@ -269,7 +269,7 @@ var PmidSelectionList = createReactClass({
  <div className="pmid-selection-wrapper">
  <div className="pmid-selection-add">
  <AddResourceId resourceType="pubmed" wrapperClass="inline-button-wrapper-fullwidth" buttonWrapperClass="inline-button-wrapper-fullwidth" buttonClass="btn btn-primary pmid-selection-add-btn"
- protocol={this.props.protocol} parentObj={this.props.currGdm} buttonText="Add New PMID" modalButtonText="Add Article" updateParentForm={this.props.updateGdmArticles} buttonOnly={true} />
+ protocol={this.props.protocol} parentObj={this.props.currGdm} buttonText="Add New Article" modalButtonText="Add Article" updateParentForm={this.props.updateGdmArticles} buttonOnly={true} />
  </div>
  {annotations ?
  <div className="pmid-selection-list" id="user-pmid-list">
@@ -283,14 +283,15 @@ var PmidSelectionList = createReactClass({
  <PmidSummary article={annotation.article} />
  </div>
  <div className="pmid-selection-list-pmid"><a href={external_url_map['PubMed'] + annotation.article.pmid} target="_blank">PMID: {annotation.article.pmid}</a></div>
+ { annotation.article.doi ? <div className="pmid-selection-list-pmid"><a href={external_url_map['PubMed'] + annotation.article.pmid} target="_blank">DOI: {annotation.article.doi}</a></div> : null}
  </div>
  );
  })}
  </div>
  : null}
  {annotations.length === 0 ?
  <div className="pmid-selection-help">
- <i>Add papers to this Gene-Disease Record using the <strong>Add New PMID(s)</strong> button; click on any added paper to view its abstract and begin curating evidence from that paper.</i>
+ <i>Add papers to this Gene-Disease Record using the <strong>Add New Article(s)</strong> button; click on any added paper to view its abstract and begin curating evidence from that paper.</i>
  </div>
  :null }
  </div>

src/clincoded/static/components/globals.js

@@ -164,6 +164,7 @@ module.exports.dbxref_prefix_map = {
 
 module.exports.external_url_map = {
  'PubMedSearch': 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?api_key=986bd80f43a3ba6ec1bc7a50e7bda60c1b09&db=PubMed&retmode=xml&id=',
+ 'DoiToPubMed': 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=',
  'PubMed': 'https://www.ncbi.nlm.nih.gov/pubmed/',
  'OrphaNet': 'http://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=EN&Expert=',
  'OrphanetHome': 'http://www.orpha.net/',

src/clincoded/static/libs/parse-pubmed.js

@@ -13,15 +13,28 @@ function parsePubmed(xml){
  var article = {};
  var doc = new DOMParser().parseFromString(xml, 'text/xml');
 
+ // Get PMID from DOI XML
+ var $DOIResult = doc.getElementsByTagName('eSearchResult')[0];
+ if($DOIResult) {
+ var $PMID = $DOIResult.getElementsByTagName('Id')[0];
+ if($PMID) {
+ article.pmid = $PMID.textContent;
+ }
+ }
+
  var $PubmedArticle = doc.getElementsByTagName('PubmedArticle')[0];
  if($PubmedArticle){
  var publicationData = '';
 
- // Get the PMID
+ // Get the PMID and DOI
  var $PMID = $PubmedArticle.getElementsByTagName('PMID')[0];
+ var $DOI = $PubmedArticle.querySelector('[IdType="doi"]')
  if($PMID) {
  article.pmid = $PMID.textContent;
  }
+ if($DOI) {
+ article.doi = $DOI.textContent;
+ }
 
  // Get the journal name
  var $Journal = $PubmedArticle.getElementsByTagName('Journal')[0];

src/clincoded/static/scss/clincoded/modules/_curator.scss

@@ -2,9 +2,6 @@
  margin-top: 10px;
 }
 
-.curr-pmid-overview {
-}
-
 .pmid-doi-btns {
  margin: 10px 0;
 
@@ -255,6 +252,7 @@
  border: 1px solid darken(#dddddd, 10%);
  cursor: pointer;
  background-color: #ffffff;
+ overflow: hidden;
  @include border-radius(3px);
 
  div {
@@ -276,7 +274,7 @@
 }
 
 .pmid-selection-list-pmid {
- font-weight: bold;
+ font-weight: bold; 
 }
 
 .pmid-selection-help {

src/clincoded/tests/features/curation_central.feature

@@ -37,19 +37,19 @@ Feature: Curation Central
  Then I should see "Any user may explore the demo version of the ClinGen interfaces"
 
 
- Scenario: Test PMID modal in Curation-central
+ Scenario: Test Article modal in Curation-central
  When I visit "/logout"
  Then I should see "Demo Login"
  When I press "Demo Login"
  And I wait for 10 seconds
  Then I should see "Logout ClinGen Test Curator"
  When I go to "/curation-central/?gdm=9ffd7c1e-16d9-11e5-b283-60f81dc5b05a/"
- Then I should see "Add New PMID" within 5 seconds
- When I press "Add New PMID"
+ Then I should see "Add New Article" within 5 seconds
+ When I press "Add New Article"
  Then I should see an element with the css selector ".modal-dialog" within 5 seconds
- Then I should see "Enter a PMID"
+ Then I should see "Enter a PMID or DOI"
  When I fill in the css element field "input.form-control" with "123456"
- When I press the button "Retrieve PubMed Article"
+ When I press the button "Retrieve Article"
  Then I should see "Grados OB. " within 10 seconds
  When I press the button "Add Article"
  Then I should not see an element with the css selector ".modal-open"