Skip to content

Commit

Permalink
Merge pull request #105 from zitrosolrac/fixTableFormattingIssue
Browse files Browse the repository at this point in the history 
Fix general regression issues and implement other requested changes
  • Loading branch information
@guzman-raphael
guzman-raphael authored Nov 17, 2021
2 parents c4d48b8 + e64ae9d commit 29cd8b9
Show file tree
Hide file tree
Showing 7 changed files with 199 additions and 124 deletions.
6 changes: 5 additions & 1 deletion backend/iblapi.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -250,6 +250,10 @@ def handle_q(subpath, args, proj, fetch_args=None, **kwargs):
training_status='training_status', good_enough_for_brainwide_map='good_enough_for_brainwide_map',
keep_all_rows=True
)
subj = subject.Subject().aggr(
subject.Death().proj('death_date') * dj.U('death_date'),
death_date='IFNULL(death_date, NULL)',
keep_all_rows=True)
regions = kwargs.get('brain_regions', None)
# expected format of brain_regions = ["AB", "ABCa", "CS of TCV"]
if regions is not None and len(regions) > 0:
Expand All @@ -268,7 +272,7 @@ def handle_q(subpath, args, proj, fetch_args=None, **kwargs):
# subject.SubjectLab() * subject.SubjectUser() *
# analyses_behavior.SessionTrainingStatus()) & args & brain_restriction)

q = ((acquisition.Session() * sess_proj * psych_curve * ephys_data * subject.Subject() *
q = ((acquisition.Session() * sess_proj * psych_curve * ephys_data * subj *
subject.SubjectLab() * subject.SubjectUser() * trainingStatus) & args & brain_restriction)
q = q.proj(*proj) if proj else q
dj.conn().query("SET SESSION max_join_size={}".format('18446744073709551615'))
Expand Down
100 changes: 52 additions & 48 deletions ibl-frontend/frontend-content/src/app/mouse-list/mouse/mouse.component.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -7,56 +7,60 @@ <h5>Mouse <{{ mouse?.subject_nickname }}> Info</h5>
</div>
<div class="row mouse-info-table">
<table class="table col-lg-4 col-sm-6 col-xs-12 table-striped table-bordered table-sm">
<tr>
<th>Mouse Nickname</th>
<td>{{ mouse?.subject_nickname }}</td>
</tr>
<tr>
<th>Mouse UUID</th>
<td>{{ mouse?.subject_uuid }}</td>
</tr>
<tr>
<th>Mouse DOB</th>
<td>{{ mouse?.subject_birth_date }}</td>
</tr>
<tr>
<th>Lab</th>
<td>{{ mouse?.lab_name }}</td>
</tr>
<tr>
<th>Sex</th>
<td>{{ mouse?.sex }}</td>
</tr>
<tr>
<th>Project</th>
<td>{{ mouse?.projects }}</td>
</tr>
<tr>
<th>User</th>
<td>{{ mouse?.responsible_user }}</td>
</tr>
<tbody>
<tr>
<th>Mouse Nickname</th>
<td>{{ mouse?.subject_nickname }}</td>
</tr>
<tr>
<th>Mouse UUID</th>
<td>{{ mouse?.subject_uuid }}</td>
</tr>
<tr>
<th>Mouse DOB</th>
<td>{{ mouse?.subject_birth_date }}</td>
</tr>
<tr>
<th>Lab</th>
<td>{{ mouse?.lab_name }}</td>
</tr>
<tr>
<th>Sex</th>
<td>{{ mouse?.sex }}</td>
</tr>
<tr>
<th>Project</th>
<td>{{ mouse?.projects }}</td>
</tr>
<tr>
<th>User</th>
<td>{{ mouse?.responsible_user }}</td>
</tr>
</tbody>
</table>
<table class="table col-lg-3 col-sm-6 col-xs-12 table-striped table-bordered table-sm">
<tr>
<th>Ear Mark</th>
<td>{{ mouse?.ear_mark }}</td>
</tr>
<tr>
<th>Mouse Line</th>
<td>{{ mouse?.subject_line }}</td>
</tr>
<tr>
<th>Source</th>
<td>{{ mouse?.subject_source }}</td>
</tr>
<tr>
<th>Protocol Number</th>
<td>{{ mouse?.protocol_number }}</td>
</tr>
<tr>
<th>Description</th>
<td>{{ mouse?.subject_description }}</td>
</tr>
<tbody>
<tr>
<th>Ear Mark</th>
<td>{{ mouse?.ear_mark }}</td>
</tr>
<tr>
<th>Mouse Line</th>
<td>{{ mouse?.subject_line }}</td>
</tr>
<tr>
<th>Source</th>
<td>{{ mouse?.subject_source }}</td>
</tr>
<tr>
<th>Protocol Number</th>
<td>{{ mouse?.protocol_number }}</td>
</tr>
<tr>
<th>Description</th>
<td>{{ mouse?.subject_description }}</td>
</tr>
</tbody>
</table>
<div class="spinning-brain-container col-xs-12 col-sm-6 col-lg-4" *ngIf="mouse">
<app-spinning-brain [mouseInfo]="mouse"></app-spinning-brain>
Expand Down
8 changes: 8 additions & 0 deletions ibl-frontend/frontend-content/src/app/session-list/session-list.component.css
View file
Original file line number Diff line number Diff line change
Expand Up @@ -139,6 +139,14 @@ label {
position: relative;
overflow-x: auto;
}

.flipped, .flipped .col-12
{
transform:rotateX(180deg);
-ms-transform:rotateX(180deg); /* IE 9 */
-webkit-transform:rotateX(180deg); /* Safari and Chrome */
}

td.mat-cell,
td.mat-footer-cell,
th.mat-header-cell {
Expand Down
25 changes: 21 additions & 4 deletions ibl-frontend/frontend-content/src/app/session-list/session-list.component.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -155,11 +155,23 @@ <h4>
</mat-autocomplete>
</mat-form-field>

<div class="date-range-toggler">
<label for="isAlive">Mouse Vital Status</label>
<div>
Deceased&nbsp;<mat-slide-toggle name="isAlive" [checked]="isAlive" (change)="isAlive=!isAlive">Alive
</mat-slide-toggle>
</div>
</div>

<!-- // Brain Tree Selection Area -->
<div class="brain-tree-zone">
<mat-form-field>
<label>Brain Regions</label>
<input matInput (input)="filterChanged($event.target.value.toLowerCase())">
<input matInput type="text" name="brain_regions" formControlName="brain_regions">
<mat-autocomplete #autoCompRU="matAutocomplete">
<mat-option *ngFor="let responsible_user of dropDownMenuOptions.filteredResponsibleUserOptions | async"[value]="brain_regions"
(click)="updateMenu()">{{ brain_regions }}</mat-option>
</mat-autocomplete>
</mat-form-field>
<!-- <div>Selected Brain Region:
<div class="chip-list">
Expand Down Expand Up @@ -219,7 +231,7 @@ <h4>
<button mat-raised-button class="btn btn-refresh" (click)="refreshData()">Refresh Data</button>
</div>
</div>
<!-- <div class="checkbox-filters">
<div class="checkbox-filters">
<div class="chbox-filter">
<mat-checkbox class="nplot_status_chbox" [checked]="hideMissingPlots" (change)="toggleNplotStatus()">
Only show sessions with behavior plots
Expand All @@ -235,15 +247,15 @@ <h4>
Only show sessions with ephys data
</mat-checkbox>
</div>
</div> -->
</div>
</div>
</form>

<div [class]="isLoading && initialLoad ? 'loading-icon loading initial': isLoading ? 'loading-icon loading': 'loading-icon'">
<img src="assets/images/loading_icon.gif">
<p [class]="initialLoad ? 'session-list-loading-message show' : 'session-list-loading-message'"></p>
</div>
<div class="table-container">
<div class="table-container flipped">
<div class="session-list-loading-shade"
*ngIf="isLoadingTable">
<mat-spinner *ngIf="isLoadingTable"></mat-spinner>
Expand Down Expand Up @@ -304,6 +316,11 @@ <h4>
<td mat-cell *matCellDef="let session"class="to-center"> {{session.sex}} </td>
</ng-container>

<ng-container matColumnDef="death_date">
<th mat-header-cell *matHeaderCellDef mat-sort-header> Mouse Vital Status </th>
<td mat-cell *matCellDef="let session"class="to-center"> {{session.death_date}} </td>
</ng-container>

<ng-container matColumnDef="nplot">
<th mat-header-cell *matHeaderCellDef> Plot Availability </th>
<td mat-cell *matCellDef="let session" class="to-center"> {{session.nplot.toString() | i18nSelect: nplotMap}} </td>
Expand Down
89 changes: 64 additions & 25 deletions ibl-frontend/frontend-content/src/app/session-list/session-list.component.ts
View file
Original file line number Diff line number Diff line change
Expand Up @@ -51,7 +51,9 @@ export class SessionListComponent implements OnInit, OnDestroy {
sex: new FormArray([new FormControl(), new FormControl(), new FormControl()]),
subject_birth_date: new FormControl(),
subject_line: new FormControl(),
responsible_user: new FormControl()
responsible_user: new FormControl(),
brain_regions: new FormControl(),
death_date: new FormControl()
});
isLoading;
isLoadingTable = true;
Expand All @@ -65,6 +67,7 @@ export class SessionListComponent implements OnInit, OnDestroy {
sessionMinDate: Date;
sessionMaxDate: Date;
isSessionDateUsingRange: boolean;
isAlive: boolean
dropDownMenuOptions: any = {};
// filteredTaskProtocolOptions: Observable<string[]>;
// filteredSessionUuidOptions: Observable<string[]>;
Expand All @@ -83,7 +86,7 @@ export class SessionListComponent implements OnInit, OnDestroy {
// setup for the table columns
displayedColumns: string[] = ['session_lab', 'subject_nickname', 'subject_birth_date', 'session_start_time',
'task_protocol', 'subject_line', 'responsible_user',
'session_uuid', 'sex', 'subject_uuid', 'nplot', 'nprobe', 'session_project', 'good4bmap'];
'session_uuid', 'sex', 'death_date', 'subject_uuid', 'nplot', 'nprobe', 'session_project', 'good4bmap'];
nplotMap: any = { '0': '', '1': '\u2714' };
// setup for the paginator
dataSource;
Expand Down Expand Up @@ -338,52 +341,82 @@ export class SessionListComponent implements OnInit, OnDestroy {
.pipe(
startWith({}),
switchMap(() => {
let dj_restriction_conditions = [];

this.isLoadingTable = true;
if(this.sort.direction == ''){
this.sort.active = 'session_start_time';
this.sort.active = 'nprobe';
this.sort.direction = 'desc'
}
let filter = Object.assign({}, this.session_filter_form.getRawValue());
let newFilter = JSON.stringify(filter)

if(this.hideMissingPlots){
filter["nplot"] = 1;
}

if(this.hideNG4BrainMap){
filter["good_enough_for_brainwide_map"] = 1;
}

if(this.hideNotReady4Delay){
filter["training_status"] = "ready4delay";
}

if(this.hideMissingEphys){
dj_restriction_conditions.push("nprobe>0");
}

for (const [key, value] of Object.entries(filter)) {
if(key == 'sex'){
if(value[0] == true){
newObject[key] = 'F'
newObject[key] = 'F';
//female
continue
continue;
}
else if (value[1] == true){
newObject[key] = 'M'
newObject[key] = 'M';
//male
continue
continue;
}
else if (value[2] == true){
newObject[key] = 'U'
newObject[key] = 'U';
//undefined
continue
continue;
}
else{
continue
continue;
}
}
if(key == 'session_range_filter'){
for( const [key2, val] of Object.entries(value)){
if(val !== null){
newObject[key2] = val
newObject[key2] = val;
}
continue
continue;
}
}
if(key == 'brain_regions' && value !== null && value !== ""){
newObject["__json_kwargs"] = `{"brain_regions": ["${value}"]}`;
continue;
}
if(this.isAlive){
dj_restriction_conditions.push("death_date is null");
continue;
}
if(!this.isAlive){
dj_restriction_conditions.push("death_date is not null");
continue;
}
if(value !== null){
newObject[key] = value
newObject[key] = value;
}
}
this.isLoadingResults = true;

newObject["__page"] = this.paginator.pageIndex + 1;
newObject["__limit"] = this.paginator.pageSize;
newObject["__order"] = this.sort.active + ' ' + this.sort.direction
newObject["__order"] = this.sort.active + ' ' + this.sort.direction;
newObject["__json"] = JSON.stringify(dj_restriction_conditions);
return this.sessionService!.getSessions(
newObject)
.pipe(catchError(() => observableOf(null)));
Expand Down Expand Up @@ -474,7 +507,7 @@ export class SessionListComponent implements OnInit, OnDestroy {
private createMenu(restrictedSessions: Array<any>) {
const keys = ['task_protocol', 'session_start_time',
'session_uuid', 'session_lab', 'subject_birth_date', 'subject_line',
'subject_uuid', 'sex', 'subject_nickname', 'responsible_user', 'session_project'];
'subject_uuid', 'sex', 'subject_nickname', 'responsible_user', 'session_project', 'brain_regions', 'death_date'];

keys.forEach(key => {
this.uniqueValuesForEachAttribute[key] = new Set();
Expand Down Expand Up @@ -545,6 +578,8 @@ export class SessionListComponent implements OnInit, OnDestroy {
this.setDropDownFormOptions('filteredTaskProtocolOptions', this.session_filter_form.controls.task_protocol, 'task_protocol');
this.setDropDownFormOptions('filteredSubjectLineOptions', this.session_filter_form.controls.subject_line, 'subject_line');
this.setDropDownFormOptions('filteredResponsibleUserOptions', this.session_filter_form.controls.responsible_user, 'responsible_user');
this.setDropDownFormOptions('filteredBrainRegionsOptions', this.session_filter_form.controls.brain_regions, 'brain_regions');
this.setDropDownFormOptions('filteredDeathDateOptions', this.session_filter_form.controls.death_date, 'death_date');
}

/**
Expand Down Expand Up @@ -574,7 +609,7 @@ export class SessionListComponent implements OnInit, OnDestroy {
// The unique value does include the user restrction string, thus we need to add it to the validUniqueValues array
validUniqueValues.push(uniqueValue);
}

if (validUniqueValues.length > MAX_NUMBER_OF_SUGGESTIONS) {
return;
}
Expand Down Expand Up @@ -1157,27 +1192,31 @@ export class SessionListComponent implements OnInit, OnDestroy {
}
​
toggleNplotStatus() {
// hide or show sessions that have missing session plots
this.hideMissingPlots = !this.hideMissingPlots;
this.updateSelection();
this.isLoading = false;
this.paginator.pageIndex = 0;
this.ngAfterViewInit();
}
​
toggleNprobeStatus() {
// hide or show sessions that have missing ephys data (based on existence of probe insertion)
this.hideMissingEphys = !this.hideMissingEphys;
this.updateSelection();
this.isLoading = false;
this.paginator.pageIndex = 0;
this.ngAfterViewInit();
}

toggleG4BMviewStatus() {
// hide or show sessions that are not good enough for brain map
this.hideNG4BrainMap = !this.hideNG4BrainMap;
this.updateSelection();
this.isLoading = false;
this.paginator.pageIndex = 0;
this.ngAfterViewInit();
}

toggleR4DviewStatus() {
// hide or show session that are not ready for delay
this.hideNotReady4Delay = !this.hideNotReady4Delay;
this.updateSelection();
this.isLoading = false;
this.paginator.pageIndex = 0;
this.ngAfterViewInit();
}

//==**==**==**==**+=**+== [START] brain tree functions **==**==**==**==**==**==**==**==**==**+=//
Expand Down
Loading

0 comments on commit 29cd8b9

Please sign in to comment.