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Chemical reference #71

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merged 3 commits into from
Jan 23, 2025
Merged

Chemical reference #71

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9f4a24b
Added the visited activities to know the stopping point
tmushayahama Jan 22, 2025
184cb40
added option to filter CC out
tmushayahama Jan 22, 2025
cf39ec0
bug with complex number and,
tmushayahama Jan 23, 2025
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2 changes: 1 addition & 1 deletion src/components/gocam-viz/gocam-viz.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -405,7 +405,7 @@ export class GoCamViz {
});

const truncatedGps = gps.slice(0, 3)
let geneString = gps.join(', ')
let geneString = truncatedGps.join(', ')

if (gps.length > truncatedGps.length) {
geneString += ' and ' + (gps.length - truncatedGps.length).toString() + ' more'
Expand Down
298 changes: 1 addition & 297 deletions src/globals/@noctua.form/models/activity/cam.ts
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Original file line number Diff line number Diff line change
@@ -1,14 +1,11 @@
import { noctuaFormConfig } from './../../noctua-form-config';
import { Activity, ActivitySortField, ActivityType } from './activity'
import { ActivityNode, ActivityNodeType } from './activity-node';
import { Group } from '../group';
import { Contributor } from '../contributor';
import { Evidence } from './evidence';
import { Triple } from './triple';
import { Entity } from './entity';
import { each, find, orderBy, groupBy } from 'lodash';
import { each, find, groupBy } from 'lodash';
import { NoctuaFormUtils } from './../../utils/noctua-form-utils';
import { PendingChange } from './pending-change';

export enum ReloadType {
RESET = 'reset',
Expand Down Expand Up @@ -135,7 +132,6 @@ export class Cam {
manualLayout = false;
layoutChanged = false;

private _filteredActivities: Activity[] = [];
activities: Activity[] = [];
storedActivities: Activity[] = [];
private _id: string;
Expand All @@ -153,15 +149,6 @@ export class Cam {
this.displayId = NoctuaFormUtils.cleanID(id);
}

updateSortBy(field: ActivitySortField, label: string) {
this.sortBy.field = field
this.sortBy.label = label
}

toggleExpand() {
this.expanded = !this.expanded;
}

groupActivitiesByProcess() {
const groupedActivities = groupBy(this.activities, (activity: Activity) => {
if (activity.activityType === ActivityType.molecule) {
Expand All @@ -174,57 +161,6 @@ export class Cam {
return groupedActivities;
}


expandAllActivities(expand: boolean) {
const self = this;

each(self.activities, (activity: Activity) => {
activity.expanded = expand;
});
}

getCausalRelation(subjectId: string, objectId: string): Triple<Activity> {
const self = this;

return self.causalRelations.find((triple: Triple<Activity>) => {
if (triple.predicate?.isReverseLink) {
return triple.object?.id === subjectId && triple.object?.id === subjectId;
}
return triple.subject?.id === subjectId && triple.object?.id === objectId;
})
}

clearHighlight() {
const self = this;

each(self.activities, (activity: Activity) => {
each(activity.nodes, (node: ActivityNode) => {
node.term.highlight = false;
each(node.predicate.evidence, (evidence: Evidence) => {
evidence.evidence.highlight = false;
evidence.referenceEntity.highlight = false;
evidence.withEntity.highlight = false;
});
});
});
}

findNodeById(uuid, activities: Activity[]): ActivityNode {
const self = this;
let found
each(activities, (activity) => {
found = find(activity.nodes, (node: ActivityNode) => {
return node.uuid === uuid;
});

if (found) {
return false;
}
})

return found;
}

findActivityById(id) {
const self = this;

Expand All @@ -233,220 +169,6 @@ export class Cam {
});
}

findActivityByNodeUuid(nodeId): Activity[] {
const self = this;

const result: Activity[] = [];

each(self.activities, (activity: Activity) => {
each(activity.nodes, (node: ActivityNode) => {
if (node.uuid === nodeId) {
result.push(activity)
}
each(node.predicate.evidence, (evidence: Evidence) => {
if (evidence.uuid === nodeId) {
result.push(activity)
}
});
});
});
return result;
}


applyFilter() {
const self = this;

self.clearHighlight();

if (self.queryMatch && self.queryMatch.terms.length > 0) {
self._filteredActivities = [];
self.matchedCount = 0;

each(self.activities, (activity: Activity) => {
let match = false;
each(activity.nodes, (node: ActivityNode) => {
each(self.queryMatch.terms, (term) => {

if (node.term.uuid === term.uuid) {
node.term.highlight = true;
node.term.activityDisplayId = term.activityDisplayId = activity.displayId;

self.matchedCount += 1;
match = true;
}
});

each(node.predicate.evidence, (evidence: Evidence) => {
each(self.queryMatch.terms, (term) => {

if (evidence.uuid === term.uuid) {
evidence.referenceEntity.highlight = true;
evidence.referenceEntity.activityDisplayId = term.activityDisplayId = activity.displayId;

self.matchedCount += 1;
match = true;
}
});
});
});

if (match) {
self._filteredActivities.push(activity);
}
});
}
}

applyWeights(weight = 0) {
const self = this;

if (self.queryMatch && self.queryMatch.terms.length > 0) {

each(self.activities, (activity: Activity) => {
each(activity.nodes, (node: ActivityNode) => {
const matchNode = find(self.queryMatch.terms, { uuid: node.term.uuid }) as Entity;

if (matchNode) {
matchNode.weight = node.term.weight = weight;
weight++;
}

each(node.predicate.evidence, (evidence: Evidence) => {
const matchNode = find(self.queryMatch.terms, { uuid: evidence.referenceEntity.uuid }) as Entity;

if (matchNode) {
matchNode.weight = evidence.referenceEntity.weight = weight;
weight++;
}
});
});

});
}
}

addPendingChanges(findEntities: Entity[], replaceWith: string, category) {
const self = this;

each(self.activities, (activity: Activity) => {
each(activity.nodes, (node: ActivityNode) => {
each(findEntities, (entity: Entity) => {
if (category.name === noctuaFormConfig.findReplaceCategory.options.reference.name) {
each(node.predicate.evidence, (evidence: Evidence, key) => {
if (evidence.uuid === entity.uuid) {
const oldReference = new Entity(evidence.reference, evidence.reference);
const newReference = new Entity(replaceWith, replaceWith);

evidence.pendingReferenceChanges = new PendingChange(evidence.uuid, oldReference, newReference);
evidence.pendingReferenceChanges.uuid = evidence.uuid;
}
});
} else {
if (node.term.uuid === entity.uuid) {
const newValue = new Entity(replaceWith, replaceWith);
node.pendingEntityChanges = new PendingChange(node.uuid, node.term, newValue);
}
}
});
});
});
}

getNodesByType(type: ActivityNodeType): any[] {
const self = this;
const result = [];

each(self.activities, (activity: Activity) => {
result.push({
activity,
title: activity.title,
activityNodes: activity.getNodesByType(type)
});
});

return result;
}

getNodesByTypeFlat(type: ActivityNodeType): ActivityNode[] {
const self = this;
const result = [];

each(self.activities, (activity: Activity) => {
result.push(...activity.getNodesByType(type));
});

return result;
}

getTerms(formActivity: Activity) {
const self = this;
const result = [];

if (formActivity && formActivity.nodes) {
each(formActivity.nodes, (node: ActivityNode) => {
result.push(node);
});
}

each(self.activities, (activity: Activity) => {
each(activity.nodes, (node: ActivityNode) => {
result.push(node);
});
});

return result;
}

getEvidences(formActivity?: Activity) {
const self = this;
const result = [];

if (formActivity && formActivity.nodes) {
each(formActivity.nodes, (node: ActivityNode) => {
each(node.predicate.evidence, (evidence: Evidence) => {
if (evidence.hasValue()) {
result.push(evidence);
}
});
});
}

each(self.activities, (activity: Activity) => {
each(activity.edges, (triple: Triple<ActivityNode>) => {
each(triple.predicate.evidence, (evidence: Evidence) => {
if (evidence.hasValue()) {
result.push(evidence);
}
});
});
});

return result;
}

tableCanDisplayEnabledBy(node: ActivityNode) {
return node.predicate.edge && node.predicate.edge.id === noctuaFormConfig.edge.enabledBy.id;
}

tableDisplayExtension(node: ActivityNode) {
if (node.id === 'mf') {
return '';
} else if (node.isComplement) {
return 'NOT ' + node.predicate.edge.label;
} else {
return node.predicate.edge.label;
}
}

updateActivityDisplayNumber() {
const self = this;

each(self.activities, (activity: Activity, key) => {
activity.displayNumber = self.displayNumber + '.' + (key + 1).toString();
});
}

updateProperties() {
const self = this;

Expand All @@ -457,23 +179,5 @@ export class Cam {
this.sortBy.label = noctuaFormConfig.activitySortField.options[this.sortBy.field]?.label
}

private _getGPText(a: Activity): string {
return a.presentation.gpText.toLowerCase()
}

private _getMFText(a: Activity): string {
if (!a.mfNode) return ''
return a.mfNode.term.label;
}
private _getBPText(a: Activity): string {
if (!a.bpNode) return ''
return a.bpNode.term.label;
}
private _getCCText(a: Activity): string {
if (!a.ccNode) return ''
return a.ccNode.term.label;
}


}

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