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Issue 1612 - clean up codes to share common codes. #1948

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Issue 1612 - clean up codes to share common codes. #1948

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59 changes: 8 additions & 51 deletions src/clincoded/static/components/gene_disease_summary/case_control.js
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Original file line number Diff line number Diff line change
Expand Up @@ -31,29 +31,13 @@ class GeneDiseaseEvidenceSummaryCaseControl extends Component {
}
}

/**
* Method to assemble the authors list for the given evidence
* @param {object} evidence - scored evidence and its associated case-control evidence
*/
getEvidenceAuthors(evidence) {
let authors;
if (evidence.authors && evidence.authors.length) {
if (evidence.authors.length > 1) {
authors = evidence.authors[0] + ', et al.';
} else {
authors = evidence.authors[0];
}
}
return authors;
}

/**
* Method to render individual table row of the logged-in user's scored evidence
* @param {object} evidence - scored evidence and its associated case-control evidence
* @param {number} key - unique key
*/
renderCaseControlEvidence(evidence, key) {
let authors = this.getEvidenceAuthors(evidence);
let authors = this.props.getEvidenceAuthors(evidence);

return (
<tr key={key} className="scored-case-control-evidence">
Expand Down Expand Up @@ -142,38 +126,9 @@ class GeneDiseaseEvidenceSummaryCaseControl extends Component {
return parseFloat(totalScore).toFixed(2);
}

/**
* Sort table rows given a list of evidence and column name
* @param {array} evidenceList - A list of evidence items
* @param {string} colName - sort by column name
*/
sortListbyColName(evidenceList, colName) {
let sortedList = [];
let dir = this.state.reversed ? -1 : 1;
if (evidenceList.length) {
switch (colName) {
case 'reference':
sortedList = evidenceList.sort((x,y) => {
let referenceX = this.getEvidenceAuthors(x) + x.pubYear + x.pmid;
let referenceY = this.getEvidenceAuthors(y) + y.pubYear + y.pmid;
return (referenceX.toLowerCase().localeCompare(referenceY.toLowerCase()) * dir);
});
break;
case 'studyType':
sortedList = evidenceList.sort((x, y) => x[colName].toLowerCase().localeCompare(y[colName].toLowerCase()) * dir);
break;
default:
sortedList = evidenceList;
break;
}
}
return sortedList;
}

render() {
const caseControlEvidenceList = this.props.caseControlEvidenceList;
let sortedEvidenceList = this.state.mounted ? this.sortListbyColName(caseControlEvidenceList, this.state.sortCol) : caseControlEvidenceList;
let self = this;
let sortedEvidenceList = this.state.mounted ? this.props.sortListByColName(caseControlEvidenceList, this.state.sortCol, this.state.reversed) : caseControlEvidenceList;
let sortIconClass = {reference: 'tcell-sort'};
sortIconClass[this.state.sortCol] = this.state.reversed ? 'tcell-desc' : 'tcell-asc';

Expand All @@ -188,7 +143,7 @@ class GeneDiseaseEvidenceSummaryCaseControl extends Component {
<thead>
<tr>
<th rowSpan="2">Label</th>
<th rowSpan="2" onClick={(e) => self.handleClickHeader(e, 'reference')}>Reference (PMID)<span className={sortIconClass.reference}></span></th>
<th rowSpan="2" onClick={(e) => this.handleClickHeader(e, 'reference')}>Reference (PMID)<span className={sortIconClass.reference}></span></th>
<th rowSpan="2">Disease (Case)</th>
<th rowSpan="2">Study type</th>
<th rowSpan="2">Detection method (Case)</th>
Expand All @@ -209,7 +164,7 @@ class GeneDiseaseEvidenceSummaryCaseControl extends Component {
</thead>
<tbody>
{sortedEvidenceList.map((item, i) => {
return (self.renderCaseControlEvidence(item, i));
return (this.renderCaseControlEvidence(item, i));
})}
<tr>
<td colSpan="13" className="total-score-label">Total points:</td>
Expand All @@ -230,7 +185,9 @@ class GeneDiseaseEvidenceSummaryCaseControl extends Component {

GeneDiseaseEvidenceSummaryCaseControl.propTypes = {
caseControlEvidenceList: PropTypes.array,
hpoTerms: PropTypes.object
hpoTerms: PropTypes.object,
getEvidenceAuthors: PropTypes.func,
sortListByColName: PropTypes.func
};

export default GeneDiseaseEvidenceSummaryCaseControl;
export default GeneDiseaseEvidenceSummaryCaseControl;
64 changes: 10 additions & 54 deletions src/clincoded/static/components/gene_disease_summary/case_level.js
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -32,29 +32,13 @@ class GeneDiseaseEvidenceSummaryCaseLevel extends Component {
}
}

/**
* Method to assemble the authors list for the given evidence
* @param {object} evidence - scored evidence and its associated case-control evidence
*/
getEvidenceAuthors(evidence) {
let authors;
if (evidence.authors && evidence.authors.length) {
if (evidence.authors.length > 1) {
authors = evidence.authors[0] + ', et al.';
} else {
authors = evidence.authors[0];
}
}
return authors;
}

/**
* Method to render individual table row of the logged-in user's scored evidence
* @param {object} evidence - scored evidence and its associated case-control evidence
* @param {number} key - unique key
*/
renderCaseLevelEvidence(evidence, key) {
let authors = this.getEvidenceAuthors(evidence);
let authors = this.props.getEvidenceAuthors(evidence);

return (
<tr key={key} className="scored-case-level-evidence">
Expand Down Expand Up @@ -166,39 +150,9 @@ class GeneDiseaseEvidenceSummaryCaseLevel extends Component {
return parseFloat(totalScore).toFixed(2);
}

/**
* Sort table rows given a list of evidence and column name
* @param {array} evidenceList - A list of evidence items
* @param {string} colName - sort by column name
*/
sortListbyColName(evidenceList, colName) {
let sortedList = [];
let dir = this.state.reversed ? -1 : 1;
if (evidenceList.length) {
switch (colName) {
case 'reference':
sortedList = evidenceList.sort((x,y) => {
let referenceX = this.getEvidenceAuthors(x) + x.pubYear + x.pmid;
let referenceY = this.getEvidenceAuthors(y) + y.pubYear + y.pmid;
return (referenceX.toLowerCase().localeCompare(referenceY.toLowerCase()) * dir);
});
break;
case 'variantType':
case 'scoreStatus':
sortedList = evidenceList.sort((x, y) => x[colName].toLowerCase().localeCompare(y[colName].toLowerCase()) * dir);
break;
default:
sortedList = evidenceList;
break;
}
}
return sortedList;
}

render() {
const caseLevelEvidenceList = this.props.caseLevelEvidenceList;
let sortedEvidenceList = this.state.mounted ? this.sortListbyColName(caseLevelEvidenceList, this.state.sortCol) : caseLevelEvidenceList;
let self = this;
let sortedEvidenceList = this.state.mounted ? this.props.sortListByColName(caseLevelEvidenceList, this.state.sortCol, this.state.reversed) : caseLevelEvidenceList;
let sortIconClass = {variantType: 'tcell-sort', reference: 'tcell-sort', scoreStatus: 'tcell-sort'};
sortIconClass[this.state.sortCol] = this.state.reversed ? 'tcell-desc' : 'tcell-asc';

Expand All @@ -213,17 +167,17 @@ class GeneDiseaseEvidenceSummaryCaseLevel extends Component {
<thead>
<tr>
<th rowSpan="2">Label</th>
<th rowSpan="2" onClick={(e) => self.handleClickHeader(e, 'variantType')}>Variant type<span className={sortIconClass.variantType}></span></th>
<th rowSpan="2" onClick={(e) => this.handleClickHeader(e, 'variantType')}>Variant type<span className={sortIconClass.variantType}></span></th>
<th rowSpan="2">Variant</th>
<th rowSpan="2" onClick={(e) => self.handleClickHeader(e, 'reference')}>Reference<span className={sortIconClass.reference}></span></th>
<th rowSpan="2" onClick={(e) => this.handleClickHeader(e, 'reference')}>Reference<span className={sortIconClass.reference}></span></th>
<th rowSpan="2">Proband sex</th>
<th rowSpan="2">Proband age</th>
<th rowSpan="2">Proband ethnicity</th>
<th rowSpan="2">Proband phenotypes</th>
<th colSpan="5">Segregations</th>
<th rowSpan="2">Proband previous testing</th>
<th rowSpan="2">Proband methods of detection</th>
<th rowSpan="2" onClick={(e) => self.handleClickHeader(e, 'scoreStatus')}>Score status<span className={sortIconClass.scoreStatus}></span></th>
<th rowSpan="2" onClick={(e) => this.handleClickHeader(e, 'scoreStatus')}>Score status<span className={sortIconClass.scoreStatus}></span></th>
<th rowSpan="2">Proband points (default points)</th>
<th rowSpan="2">Reason for changed score</th>
</tr>
Expand All @@ -237,7 +191,7 @@ class GeneDiseaseEvidenceSummaryCaseLevel extends Component {
</thead>
<tbody>
{sortedEvidenceList.map((item, i) => {
return (self.renderCaseLevelEvidence(item, i));
return (this.renderCaseLevelEvidence(item, i));
})}
<tr>
<td colSpan="16" className="total-score-label">Total points:</td>
Expand All @@ -258,7 +212,9 @@ class GeneDiseaseEvidenceSummaryCaseLevel extends Component {

GeneDiseaseEvidenceSummaryCaseLevel.propTypes = {
caseLevelEvidenceList: PropTypes.array,
hpoTerms: PropTypes.object
hpoTerms: PropTypes.object,
getEvidenceAuthors: PropTypes.func,
sortListByColName: PropTypes.func
};

export default GeneDiseaseEvidenceSummaryCaseLevel;
export default GeneDiseaseEvidenceSummaryCaseLevel;
61 changes: 8 additions & 53 deletions src/clincoded/static/components/gene_disease_summary/case_level_segregation.js
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -31,29 +31,13 @@ class GeneDiseaseEvidenceSummarySegregation extends Component {
}
}

/**
* Method to assemble the authors list for the given evidence
* @param {object} evidence - scored evidence and its associated case-control evidence
*/
getEvidenceAuthors(evidence) {
let authors;
if (evidence.authors && evidence.authors.length) {
if (evidence.authors.length > 1) {
authors = evidence.authors[0] + ', et al.';
} else {
authors = evidence.authors[0];
}
}
return authors;
}

/**
* Method to render individual table row of the logged-in user's segregation evidence
* @param {object} evidence - segregation evidence with LOD score but without proband
* @param {number} key - unique key
*/
renderSegregationEvidence(evidence, key) {
let authors = this.getEvidenceAuthors(evidence);
let authors = this.props.getEvidenceAuthors(evidence);

return (
<tr key={key} className="scored-segregation-evidence">
Expand Down Expand Up @@ -119,40 +103,9 @@ class GeneDiseaseEvidenceSummarySegregation extends Component {
return parseFloat(totalScore).toFixed(2);
}

/**
* Sort table rows given a list of evidence and column name
* @param {array} evidenceList - A list of evidence items
* @param {string} colName - sort by column name
*/
sortListbyColName(evidenceList, colName) {
let sortedList = [];
let dir = this.state.reversed ? -1 : 1;
if (evidenceList.length) {
switch (colName) {
case 'reference':
sortedList = evidenceList.sort((x,y) => {
let referenceX = this.getEvidenceAuthors(x) + x.pubYear + x.pmid;
let referenceY = this.getEvidenceAuthors(y) + y.pubYear + y.pmid;
return (referenceX.toLowerCase().localeCompare(referenceY.toLowerCase()) * dir);
});
break;
case 'lodScore':
sortedList = evidenceList.sort((x, y) =>
(x['segregationPublishedLodScore'] ? x['segregationPublishedLodScore'] : x['segregationEstimatedLodScore'] - y['segregationPublishedLodScore'] ? y['segregationPublishedLodScore'] : y['segregationEstimatedLodScore']) * dir
);
break;
default:
sortedList = evidenceList;
break;
}
}
return sortedList;
}

render() {
const segregationEvidenceList = this.props.segregationEvidenceList;
let sortedEvidenceList = this.state.mounted ? this.sortListbyColName(segregationEvidenceList, this.state.sortCol) : segregationEvidenceList;
let self = this;
let sortedEvidenceList = this.state.mounted ? this.props.sortListByColName(segregationEvidenceList, this.state.sortCol, this.state.reversed) : segregationEvidenceList;
let sortIconClass = {reference: 'tcell-sort'};
sortIconClass[this.state.sortCol] = this.state.reversed ? 'tcell-desc' : 'tcell-asc';

Expand All @@ -167,7 +120,7 @@ class GeneDiseaseEvidenceSummarySegregation extends Component {
<thead>
<tr>
<th>Label</th>
<th onClick={(e) => self.handleClickHeader(e, 'reference')}>Reference<span className={sortIconClass.reference}></span></th>
<th onClick={(e) => this.handleClickHeader(e, 'reference')}>Reference<span className={sortIconClass.reference}></span></th>
<th>Family ethnicity</th>
<th>Family phenotypes</th>
<th>Number of affected individuals</th>
Expand All @@ -179,7 +132,7 @@ class GeneDiseaseEvidenceSummarySegregation extends Component {
</thead>
<tbody>
{sortedEvidenceList.map((item, i) => {
return (self.renderSegregationEvidence(item, i));
return (this.renderSegregationEvidence(item, i));
})}
<tr>
<td colSpan="6" className="total-score-label">Total LOD score:</td>
Expand All @@ -200,7 +153,9 @@ class GeneDiseaseEvidenceSummarySegregation extends Component {

GeneDiseaseEvidenceSummarySegregation.propTypes = {
segregationEvidenceList: PropTypes.array,
hpoTerms: PropTypes.object
hpoTerms: PropTypes.object,
getEvidenceAuthors: PropTypes.func,
sortListByColName: PropTypes.func
};

export default GeneDiseaseEvidenceSummarySegregation;
export default GeneDiseaseEvidenceSummarySegregation;
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