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Organism dropdown misc #869

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Merged
merged 4 commits into from
Oct 9, 2020
Merged

Organism dropdown misc #869

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6f18854
Allow for excluding entities in doc organism counts
maxkfranz Oct 9, 2020
b0431a2
Allow for entity comparison via `ele.same(otherEle)`
maxkfranz Oct 9, 2020
79c9ca3
Exclude popover entity from being included in organism count
maxkfranz Oct 9, 2020
4eee4b6
Use grounding IDs instead of indices for dropdowns
maxkfranz Oct 9, 2020
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31 changes: 14 additions & 17 deletions src/client/components/element-info/entity-info.js
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Original file line number Diff line number Diff line change
Expand Up @@ -192,7 +192,7 @@ class EntityInfo extends DataComponent {
name: name,
limit: s.limit,
offset: offset,
organismCounts: doc.organismCountsJson()
organismCounts: doc.organismCountsJson(el) // exclude el from org count (avoids mid typing biases)
};

if( s.updatePromise ){
Expand Down Expand Up @@ -467,7 +467,6 @@ class EntityInfo extends DataComponent {

orgMatches = _.sortBy(orgMatches, m => m.organismName);

const selectedIndex = _.findIndex(orgMatches, match => match.id === m.id && match.namespace === m.namespace);
const selectedOrg = assoc ? assoc.organism : null;

const getSelectDisplay = (om, includeName = false) => {
Expand All @@ -490,20 +489,20 @@ class EntityInfo extends DataComponent {
organism = h('div.entity-info-section.entity-info-organism-refinement', [
h('span.entity-info-title', 'Organism'),
h('select.entity-info-organism-dropdown', {
defaultValue: selectedIndex,
value: `${m.namespace}:${m.id}`,
onChange: e => {
const val = e.target.value;
const index = parseInt(val);
const om = orgMatches[index];
const [ns, id] = val.split(':');
const om = s.matches.find(match => match.namespace === ns && match.id === id);

if( om ){
this.associate(om);
} else {
this.enableManualMatchMode();
}
}
}, orgMatches.map((om, index) => {
const value = index;
}, orgMatches.map((om) => {
const value = `${om.namespace}:${om.id}`;
const orgMatches = orgToMatches.get(om.organism);
const multOrgMatches = orgMatches.length > 1;
const isFirstOrgMatch = orgMatches[0].id === om.id && orgMatches[0].namespace === om.namespace;
Expand All @@ -514,7 +513,7 @@ class EntityInfo extends DataComponent {

return h('option', { value }, getSelectDisplay(om));
}).concat([
selectedIndex < 0 ? h('option', { value: -1 }, getSelectDisplay(m, true)) : null,
// selectedIndex < 0 ? h('option', { value: -1 }, getSelectDisplay(m, true)) : null,
h('option', { value: -2 }, 'Other')
]))
]);
Expand All @@ -524,30 +523,28 @@ class EntityInfo extends DataComponent {
const needDisam = ambigGrs && ambigGrs.length > 1;

if( needDisam ){
const selectedAmIndex = _.findIndex(ambigGrs, match => match.id === m.id && match.namespace === m.namespace);

disambiguation = h('div.entity-info-section.entity-info-organism-refinement', [
h('span.entity-info-title', 'Which' + (s.name ? ` ${s.name}` : '') + ''),
h('select.entity-info-organism-dropdown', {
defaultValue: selectedAmIndex,
value: `${m.namespace}:${m.id}`,
onChange: e => {
const val = e.target.value;
const index = parseInt(val);
const om = ambigGrs[index];
const [ns, id] = val.split(':');
const om = s.matches.find(om => om.namespace === ns && om.id === id);

if( om ){
this.associate(om);
} else {
this.enableManualMatchMode();
}
}
}, ambigGrs.map((om, index) => {
const value = index;
}, ambigGrs.map((om) => {
const value = `${om.namespace}:${om.id}`;

return h('option', { value }, getDisamtDisplay(om));
}).concat([
selectedIndex < 0 ? h('option', { value: -1 }, getSelectDisplay(m, true)) : null,
h('option', { value: -2 }, 'Other')
// selectedIndex < 0 ? h('option', { value: -1 }, getSelectDisplay(m, true)) : null,
h('option', { value: 'other:other' }, 'Other')
]))
]);
}
Expand Down
8 changes: 5 additions & 3 deletions src/model/document/document.js
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Original file line number Diff line number Diff line change
Expand Up @@ -242,17 +242,19 @@ class Document {
}

// mention count for all organisms (toggle + ent mentions)
organismCounts(){
organismCounts(excludedEnt){
let cnt = new Map(); // org => mention count
let addToCount = org => cnt.set( org, !cnt.has(org) ? 1 : cnt.get(org) + 1 );
let entIsAssocd = ent => ent.associated();
let entIsNotExcluded = ent => excludedEnt == null || !ent.same(excludedEnt);
let getOrgIdForEnt = ent => _.get( ent.association(), ['organism'] );

this.toggledOrganisms().forEach( addToCount );

(
this.entities()
.filter( entIsAssocd )
.filter( entIsNotExcluded )
.map( getOrgIdForEnt )
.filter( isNonNil ) // may be an entity w/o org
.forEach( addToCount )
Expand All @@ -261,10 +263,10 @@ class Document {
return cnt;
}

organismCountsJson(){
organismCountsJson(excludedEnt){
let json = {};

for( let [org, count] of this.organismCounts() ){
for( let [org, count] of this.organismCounts(excludedEnt) ){
json[ org ] = count;
}

Expand Down
4 changes: 4 additions & 0 deletions src/model/element/element.js
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Original file line number Diff line number Diff line change
Expand Up @@ -94,6 +94,10 @@ class Element {
return this.syncher.get('id');
}

same(otherEle){
return this.id() === otherEle.id();
}

secret(){
return this.syncher.get('secret');
}
Expand Down