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Connects to #1906: Disabled UI for criteria #1939

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Connects to #1906: Disabled UI for criteria #1939

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8bcddfb
#1906: Adds disabled UI for criteria
Jun 3, 2019
bf44160
Merge branch 'dev' of https://github.com/ClinGen/clincoded into 1906_…
Jun 5, 2019
1b4fa54
Merge branch 'dev' into 1906_ht_not_used_criterion
h-tong Jun 5, 2019
2966c9b
Adds variable check, fixes variable mistakes
Jun 11, 2019
488269e
Merge branch '1906_ht_not_used_criterion' of https://github.com/ClinG…
Jun 11, 2019
92d8c4c
Merge branch '1906_ht_not_used_criterion' of https://github.com/ClinG…
Jun 11, 2019
c9ff0ba
Merge branch 'dev' of https://github.com/ClinGen/clincoded into 1906_…
Aug 15, 2019
fbac126
Adds fix to comment for function
Aug 19, 2019
0262498
Merge branch '1906_ht_not_used_criterion' of https://github.com/ClinG…
Aug 19, 2019
640cb74
Merge branch 'dev' of https://github.com/ClinGen/clincoded into 1906_…
Aug 22, 2019
c7df492
Changes white bg to transparent for criteria
Aug 22, 2019
8b0d55d
Merge branch 'dev' into 1906_ht_not_used_criterion
h-tong Aug 26, 2019
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7 changes: 5 additions & 2 deletions src/clincoded/static/components/variant_central/index.js
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Original file line number Diff line number Diff line change
Expand Up @@ -31,6 +31,7 @@ var VariantCurationHub = createReactClass({
},

getInitialState: function() {
const unusedCriteria = ['BP6', 'PP5'];
return {
variantUuid: queryKeyValue('variant', this.props.href),
interpretationUuid: queryKeyValue('interpretation', this.props.href),
Expand Down Expand Up @@ -75,7 +76,8 @@ var VariantCurationHub = createReactClass({
classificationStatus: 'In progress',
classificationSnapshots: [],
publishProvisionalReady: false,
publishSnapshotListReady: false
publishSnapshotListReady: false,
unusedCriteria: unusedCriteria
};
},

Expand Down Expand Up @@ -582,14 +584,15 @@ var VariantCurationHub = createReactClass({
{!this.state.summaryVisible ?
<div>
<CurationInterpretationCriteria interpretation={interpretation} selectedTab={selectedTab}
updateSelectedCriteria={this.updateSelectedCriteria} />
updateSelectedCriteria={this.updateSelectedCriteria} unusedCriteria={this.state.unusedCriteria} />
<VariantCurationActions variantData={variantData} interpretation={interpretation} editKey={editKey} session={session}
href_url={this.props.href} updateInterpretationObj={this.updateInterpretationObj}
calculatedAssertion={calculated_pathogenicity} provisionalPathogenicity={this.state.provisionalPathogenicity}
affiliation={affiliation} />
<VariantCurationInterpretation variantData={variantData} interpretation={interpretation} editKey={editKey} session={session}
href_url={this.props.href_url} updateInterpretationObj={this.updateInterpretationObj} getSelectedTab={this.getSelectedTab}
getSelectedSubTab={this.getSelectedSubTab}
unusedCriteria={this.state.unusedCriteria}
ext_myGeneInfo={my_gene_info}
ext_pageData={this.state.ext_pageData}
ext_myVariantInfo={this.state.ext_myVariantInfo}
Expand Down
10 changes: 6 additions & 4 deletions src/clincoded/static/components/variant_central/interpretation.js
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Original file line number Diff line number Diff line change
Expand Up @@ -58,7 +58,8 @@ var VariantCurationInterpretation = module.exports.VariantCurationInterpretation
selectedTab: PropTypes.string,
selectedSubtab: PropTypes.string,
selectedCriteria: PropTypes.string,
affiliation: PropTypes.object
affiliation: PropTypes.object,
unusedCriteria: PropTypes.array
},

getInitialState: function() {
Expand Down Expand Up @@ -221,7 +222,7 @@ var VariantCurationInterpretation = module.exports.VariantCurationInterpretation
loading_myVariantInfo={this.state.loading_myVariantInfo}
loading_ensemblVariation={this.state.loading_ensemblVariation}
affiliation={this.props.affiliation}
selectedCriteria={this.state.selectedCriteria} />
selectedCriteria={this.state.selectedCriteria} unusedCriteria={this.props.unusedCriteria} />
</div>
: null}
{this.state.selectedTab == 'variant-type' ?
Expand All @@ -237,21 +238,22 @@ var VariantCurationInterpretation = module.exports.VariantCurationInterpretation
affiliation={this.props.affiliation}
selectedSubtab={this.state.selectedSubtab}
selectedCriteria={this.state.selectedCriteria}
unusedCriteria={this.props.unusedCriteria}
getSelectedSubTab={this.props.getSelectedSubTab} />
</div>
: null}
{this.state.selectedTab == 'experimental' ?
<div role="tabpanel" className="tab-panel">
<CurationInterpretationFunctional data={variant} data={variant} href_url={this.props.href_url} session={this.props.session}
interpretation={interpretation} updateInterpretationObj={this.props.updateInterpretationObj} affiliation={this.props.affiliation}
selectedCriteria={this.state.selectedCriteria} />
selectedCriteria={this.state.selectedCriteria} unusedCriteria={this.props.unusedCriteria} />
</div>
: null}
{this.state.selectedTab == 'segregation-case' ?
<div role="tabpanel" className="tab-panel">
<CurationInterpretationSegregation data={variant} data={variant} href_url={this.props.href_url} session={this.props.session}
interpretation={interpretation} updateInterpretationObj={this.props.updateInterpretationObj} affiliation={this.props.affiliation}
selectedCriteria={this.state.selectedCriteria} />
selectedCriteria={this.state.selectedCriteria} unusedCriteria={this.props.unusedCriteria} />
</div>
: null}
{this.state.selectedTab == 'gene-centric' ?
Expand Down
38 changes: 20 additions & 18 deletions src/clincoded/static/components/variant_central/interpretation/computational.js
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Original file line number Diff line number Diff line change
Expand Up @@ -127,7 +127,8 @@ var CurationInterpretationComputational = module.exports.CurationInterpretationC
affiliation: PropTypes.object,
selectedSubtab: PropTypes.string,
selectedCriteria: PropTypes.string,
getSelectedSubTab: PropTypes.func
getSelectedSubTab: PropTypes.func,
unusedCriteria: PropTypes.array
},

getInitialState: function() {
Expand Down Expand Up @@ -567,7 +568,8 @@ var CurationInterpretationComputational = module.exports.CurationInterpretationC
formDataUpdater={criteriaMissense1Update} variantUuid={variant['@id']}
criteria={['BP1', 'PP2', 'PP3', 'BP4']} criteriaCrossCheck={[['BP1', 'PP2'], ['PP3', 'BP4']]}
interpretation={this.state.interpretation} updateInterpretationObj={this.props.updateInterpretationObj}
affiliation={affiliation} session={session} criteriaEvalNote={this.renderCriteriaEvalNote} />
affiliation={affiliation} session={session} criteriaEvalNote={this.renderCriteriaEvalNote}
unusedCriteria={this.props.unusedCriteria} />
</div>
</div>
: null}
Expand Down Expand Up @@ -823,7 +825,7 @@ var CurationInterpretationComputational = module.exports.CurationInterpretationC
evidenceData={null} evidenceDataUpdated={true}
formDataUpdater={criteriaMissense2Update} variantUuid={variant['@id']}
interpretation={this.state.interpretation} updateInterpretationObj={this.props.updateInterpretationObj}
affiliation={affiliation} session={session} />
unusedCriteria={this.props.unusedCriteria} affiliation={affiliation} session={session} />
</div>
</div>
: null}
Expand Down Expand Up @@ -854,7 +856,7 @@ var CurationInterpretationComputational = module.exports.CurationInterpretationC
evidenceData={null} evidenceDataUpdated={true}
formDataUpdater={criteriaLof1Update} variantUuid={this.state.data['@id']}
interpretation={this.state.interpretation} updateInterpretationObj={this.props.updateInterpretationObj}
affiliation={affiliation} session={session} criteriaEvalNote={this.renderCriteriaEvalLink} />
unusedCriteria={this.props.unusedCriteria} affiliation={affiliation} session={session} criteriaEvalNote={this.renderCriteriaEvalLink} />
</div>
</div>
: null}
Expand Down Expand Up @@ -894,7 +896,7 @@ var CurationInterpretationComputational = module.exports.CurationInterpretationC
evidenceData={null} evidenceDataUpdated={true}
formDataUpdater={criteriaSilentIntron1Update} variantUuid={this.state.data['@id']}
interpretation={this.state.interpretation} updateInterpretationObj={this.props.updateInterpretationObj}
affiliation={affiliation} session={session} />
unusedCriteria={this.props.unusedCriteria} affiliation={affiliation} session={session} />
</div>
</div>
: null}
Expand Down Expand Up @@ -924,7 +926,7 @@ var CurationInterpretationComputational = module.exports.CurationInterpretationC
evidenceData={null} evidenceDataUpdated={true} criteriaCrossCheck={[['BP3', 'PM4']]}
formDataUpdater={criteriaIndel1Update} variantUuid={this.state.data['@id']}
interpretation={this.state.interpretation} updateInterpretationObj={this.props.updateInterpretationObj}
affiliation={affiliation} session={session} />
unusedCriteria={this.props.unusedCriteria} affiliation={affiliation} session={session} />
</div>
</div>
: null}
Expand Down Expand Up @@ -987,14 +989,14 @@ var CurationInterpretationComputational = module.exports.CurationInterpretationC
/**
* Code for rendering of this group of interpretation forms
*/
function criteriaMissense1() {
function criteriaMissense1(unusedCriteria) {
let criteriaList1 = ['BP1', 'PP2'], // array of criteria code handled subgroup of this section
criteriaList2 = ['PP3', 'BP4']; // array of criteria code handled subgroup of this section
return (
<div>
{vciFormHelper.renderEvalFormSection.call(this, criteriaList1, false)}
{vciFormHelper.renderEvalFormSection.call(this, criteriaList1, unusedCriteria)}
<div className="clear criteria-evaluation-divider"></div>
{vciFormHelper.renderEvalFormSection.call(this, criteriaList2, false)}
{vciFormHelper.renderEvalFormSection.call(this, criteriaList2, unusedCriteria)}
</div>
);
}
Expand All @@ -1011,14 +1013,14 @@ function criteriaMissense1Update(nextProps) {
/**
* Code for rendering of this group of interpretation forms
*/
function criteriaMissense2() {
function criteriaMissense2(unusedCriteria) {
let criteriaList1 = ['PM5'], // array of criteria code handled subgroup of this section
criteriaList2 = ['PS1']; // array of criteria code handled subgroup of this section
return (
<div>
{vciFormHelper.renderEvalFormSection.call(this, criteriaList1, false)}
{vciFormHelper.renderEvalFormSection.call(this, criteriaList1, unusedCriteria)}
<div className="clear criteria-evaluation-divider"></div>
{vciFormHelper.renderEvalFormSection.call(this, criteriaList2, false)}
{vciFormHelper.renderEvalFormSection.call(this, criteriaList2, unusedCriteria)}
</div>
);
}
Expand All @@ -1035,11 +1037,11 @@ function criteriaMissense2Update(nextProps) {
/**
* Code for rendering of this group of interpretation forms
*/
function criteriaLof1() {
function criteriaLof1(unusedCriteria) {
let criteriaList1 = ['PVS1']; // array of criteria code handled subgroup of this section
return (
<div>
{vciFormHelper.renderEvalFormSection.call(this, criteriaList1, false)}
{vciFormHelper.renderEvalFormSection.call(this, criteriaList1, unusedCriteria)}
</div>
);
}
Expand All @@ -1056,11 +1058,11 @@ function criteriaLof1Update(nextProps) {
/**
* Code for rendering of this group of interpretation forms
*/
function criteriaSilentIntron1() {
function criteriaSilentIntron1(unusedCriteria) {
let criteriaList1 = ['BP7']; // array of criteria code handled subgroup of this section
return (
<div>
{vciFormHelper.renderEvalFormSection.call(this, criteriaList1, false)}
{vciFormHelper.renderEvalFormSection.call(this, criteriaList1, unusedCriteria)}
</div>
);
}
Expand All @@ -1077,11 +1079,11 @@ function criteriaSilentIntron1Update(nextProps) {
/**
* Code for rendering of this group of interpretation forms
*/
function criteriaIndel1() {
function criteriaIndel1(unusedCriteria) {
let criteriaList1 = ['BP3', 'PM4']; // array of criteria code handled subgroup of this section
return (
<div>
{vciFormHelper.renderEvalFormSection.call(this, criteriaList1, false)}
{vciFormHelper.renderEvalFormSection.call(this, criteriaList1, unusedCriteria)}
</div>
);
}
Expand Down
12 changes: 10 additions & 2 deletions src/clincoded/static/components/variant_central/interpretation/criteria.js
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Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,8 @@ var CurationInterpretationCriteria = module.exports.CurationInterpretationCriter
propTypes: {
interpretation: PropTypes.object,
selectedTab: PropTypes.string,
updateSelectedCriteria: PropTypes.func
updateSelectedCriteria: PropTypes.func,
unusedCriteria: PropTypes.array
},

getInitialState() {
Expand Down Expand Up @@ -101,13 +102,20 @@ var CurationInterpretationCriteria = module.exports.CurationInterpretationCriter
});
}
}
const unused = Array.isArray(this.props.unusedCriteria) && (this.props.unusedCriteria.indexOf(key) > -1);
return (
<button className={'btn btn-default ' + evidence[key].class + ' ' + evidence[key].category + this.getCurrentTab(evidence[key].category)}
type="button" key={key} data-status={status}
data-toggle="tooltip" data-placement="top"
data-tooltip={evidence[key].definition}
onClick={this.handleClick.bind(this, key, evidence[key].category)}>
<span>{key}</span>
{unused &&
<div className="criteria-cross">
<div className="criteria-neg-slope-line" />
<div className="criteria-pos-slope-line" />
</div>
}
<span className="criteria-key">{key}</span>
</button>
);
},
Expand Down
15 changes: 8 additions & 7 deletions src/clincoded/static/components/variant_central/interpretation/functional.js
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Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,8 @@ var CurationInterpretationFunctional = module.exports.CurationInterpretationFunc
href_url: PropTypes.object,
affiliation: PropTypes.object,
session: PropTypes.object,
selectedCriteria: PropTypes.string
selectedCriteria: PropTypes.string,
unusedCriteria: PropTypes.array
},

getInitialState() {
Expand Down Expand Up @@ -69,7 +70,7 @@ var CurationInterpretationFunctional = module.exports.CurationInterpretationFunc
evidenceData={null} evidenceDataUpdated={true}
formDataUpdater={criteriaGroup1Update} variantUuid={this.state.data['@id']}
interpretation={this.state.interpretation} updateInterpretationObj={this.props.updateInterpretationObj}
affiliation={affiliation} session={session} />
unusedCriteria={this.props.unusedCriteria} affiliation={affiliation} session={session} />
</div>
</div>
: null}
Expand All @@ -87,7 +88,7 @@ var CurationInterpretationFunctional = module.exports.CurationInterpretationFunc
evidenceData={null} evidenceDataUpdated={true} criteriaCrossCheck={[['BS3', 'PS3']]}
formDataUpdater={criteriaGroup2Update} variantUuid={this.state.data['@id']}
interpretation={this.state.interpretation} updateInterpretationObj={this.props.updateInterpretationObj}
affiliation={affiliation} session={session} />
unusedCriteria={this.props.unusedCriteria} affiliation={affiliation} session={session} />
</div>
</div>
: null}
Expand All @@ -107,11 +108,11 @@ var CurationInterpretationFunctional = module.exports.CurationInterpretationFunc


// code for rendering of this group of interpretation forms
var criteriaGroup1 = function() {
var criteriaGroup1 = function(unusedCriteria) {
let criteriaList1 = ['PM1']; // array of criteria code handled subgroup of this section
return (
<div>
{vciFormHelper.renderEvalFormSection.call(this, criteriaList1, false)}
{vciFormHelper.renderEvalFormSection.call(this, criteriaList1, unusedCriteria)}
</div>
);
};
Expand All @@ -123,11 +124,11 @@ var criteriaGroup1Update = function(nextProps) {


// code for rendering of this group of interpretation forms
var criteriaGroup2 = function() {
var criteriaGroup2 = function(unusedCriteria) {
let criteriaList1 = ['BS3', 'PS3']; // array of criteria code handled subgroup of this section
return (
<div>
{vciFormHelper.renderEvalFormSection.call(this, criteriaList1, false)}
{vciFormHelper.renderEvalFormSection.call(this, criteriaList1, unusedCriteria)}
</div>
);
};
Expand Down
10 changes: 5 additions & 5 deletions src/clincoded/static/components/variant_central/interpretation/population.js
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Original file line number Diff line number Diff line change
Expand Up @@ -70,8 +70,8 @@ var CurationInterpretationPopulation = module.exports.CurationInterpretationPopu
href_url: PropTypes.object,
affiliation: PropTypes.object,
session: PropTypes.object,
selectedCriteria: PropTypes.string

selectedCriteria: PropTypes.string,
unusedCriteria: PropTypes.array
},

getInitialState: function() {
Expand Down Expand Up @@ -1158,7 +1158,7 @@ var CurationInterpretationPopulation = module.exports.CurationInterpretationPopu
formDataUpdater={criteriaGroup1Update} variantUuid={this.state.data['@id']}
criteria={['BA1', 'PM2', 'BS1']} criteriaCrossCheck={[['BA1', 'PM2', 'BS1']]}
interpretation={this.state.interpretation} updateInterpretationObj={this.props.updateInterpretationObj}
affiliation={affiliation} session={session} />
unusedCriteria={this.props.unusedCriteria} affiliation={affiliation} session={session} />
</div>
</div>
: null}
Expand Down Expand Up @@ -1437,7 +1437,7 @@ var CurationInterpretationPopulation = module.exports.CurationInterpretationPopu


// code for rendering of this group of interpretation forms
var criteriaGroup1 = function() {
var criteriaGroup1 = function(unusedCriteria) {
let criteriaList1 = ['BA1', 'BS1', 'PM2']; // array of criteria code handled subgroup of this section
let mafCutoffInput = (
<span>
Expand All @@ -1451,7 +1451,7 @@ var criteriaGroup1 = function() {
);
return (
<div>
{vciFormHelper.renderEvalFormSection.call(this, criteriaList1, false)}
{vciFormHelper.renderEvalFormSection.call(this, criteriaList1, unusedCriteria)}
{mafCutoffInput}
</div>
);
Expand Down
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