Add group field to subject and minor frontend fixes (#284)

* Add group field to subject * Cosmetic changes * Add selected project id key to current tasks map * Change fill character for progress bar
MedVIC-Lab · Feb 28, 2023 · 6a5d82f · 6a5d82f
1 parent d84b76f
commit 6a5d82f
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Showing 10 changed files with 84 additions and 41 deletions.
diff --git a/shapeworks_cloud/core/migrations/0025_subject_group.py b/shapeworks_cloud/core/migrations/0025_subject_group.py
@@ -0,0 +1,17 @@
+# Generated by Django 3.2.17 on 2023-02-25 00:19
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ('core', '0024_world_local_nullable'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='subject',
+            name='group',
+            field=models.CharField(blank=True, max_length=100, null=True),
+        ),
+    ]
diff --git a/shapeworks_cloud/core/models.py b/shapeworks_cloud/core/models.py
@@ -70,6 +70,7 @@ def safe_get(model, **kwargs):
 
 class Subject(TimeStampedModel, models.Model):
     name = models.CharField(max_length=255)
+    group = models.CharField(max_length=100, null=True, blank=True)
     dataset = models.ForeignKey(Dataset, on_delete=models.CASCADE, related_name='subjects')
 
 

diff --git a/swcc/examples/ellipsoid/ellipsoid.swproj b/swcc/examples/ellipsoid/ellipsoid.swproj
@@ -2,6 +2,7 @@
     "data": [
         {
             "name": "ellipsoid_00_DT",
+            "group": "A",
             "shape_1": "./ellipsoid_00_DT.nrrd",
             "groomed_1": "./groomed/ellipsoid_00_DT.nrrd",
             "local_particles_1": "./particles/ellipsoid_00_DT_local.particles",
@@ -11,6 +12,7 @@
         },
         {
             "name": "ellipsoid_01_DT",
+            "group": "B",
             "shape_1": "./ellipsoid_01_DT.nrrd",
             "groomed_1": "./groomed/ellipsoid_01_DT.nrrd",
             "local_particles_1": "./particles/ellipsoid_01_DT_local.particles",
@@ -20,6 +22,7 @@
         },
         {
             "name": "ellipsoid_02_DT",
+            "group": "B",
             "shape_1": "./ellipsoid_02_DT.nrrd",
             "groomed_1": "./groomed/ellipsoid_02_DT.nrrd",
             "local_particles_1": "./particles/ellipsoid_02_DT_local.particles",

diff --git a/swcc/swcc/models/project.py b/swcc/swcc/models/project.py
@@ -87,7 +87,9 @@ def interpret_data(self, input_data):
             if len(subjects) > 0:
                 subject = subjects[0]
             else:
-                subject = Subject(name=entry.get('name'), dataset=self.project.dataset).create()
+                subject = Subject(
+                    name=entry.get('name'), group=entry.get('group'), dataset=self.project.dataset
+                ).create()
 
             entry_values: Dict = {p: [] for p in expected_key_prefixes}
             entry_values['anatomy_ids'] = []

diff --git a/swcc/swcc/models/subject.py b/swcc/swcc/models/subject.py
@@ -1,5 +1,5 @@
 from pathlib import Path
-from typing import Iterator, List
+from typing import Iterator, List, Optional
 
 from .api_model import ApiModel
 from .dataset import Dataset
@@ -12,6 +12,7 @@ class Subject(ApiModel):
 
     name: NonEmptyString
     dataset: Dataset
+    group: Optional[str]
 
     @property
     def segmentations(self) -> Iterator[Segmentation]:

diff --git a/swcc/swcc/models/utils.py b/swcc/swcc/models/utils.py
@@ -141,7 +141,7 @@ def print_progress_bar(
     suffix='Complete.',
     decimals=1,
     length=30,
-    fill='█',
+    fill='X',
 ):
     percent = ('{0:.' + str(decimals) + 'f}').format(100 * (iteration / float(total)))
     filled_length = int(length * iteration // total)

diff --git a/web/shapeworks/src/components/AnalysisTab.vue b/web/shapeworks/src/components/AnalysisTab.vue
@@ -3,6 +3,7 @@ import {
     analysis, analysisFileShown,
     currentAnalysisFileParticles, meanAnalysisFileParticles,
     currentTasks,
+    selectedProject,
 } from '@/store'
 import { defineComponent, ref, computed, watch } from '@vue/composition-api'
 import { lineChartOptions, lineChartProps } from '@/charts'
@@ -66,7 +67,7 @@ export default defineComponent({
                     {text: 'value', value: 'value', align: 'end'}
                 ],
                 items: [
-                    {key: 'Lambda', value: currPCA.value?.lambda_value},
+                    {key: 'Lambda', value: currPCA.value?.lambda_value || 0},
                     {key: 'Eigenvalue', value: currMode.value?.eigen_value},
                     {key: 'Explained Variance', value: currMode.value?.explained_variance, class: 'percentage'},
                     {key: 'Cumulative Explained Variance', value: currMode.value?.cumulative_explained_variance, class:'percentage'},
@@ -104,7 +105,10 @@ export default defineComponent({
         }
 
         const taskData = computed(
-            () => currentTasks.value['analyze_task']
+            () => {
+                if (!selectedProject.value) return undefined
+                return currentTasks.value[selectedProject.value.id]['analyze_task']
+            }
         )
 
         return {
@@ -169,12 +173,12 @@ export default defineComponent({
                         :max="stdDevRange[1]"
                         :step="stdDevRange[2]"
                         ticks="always"
-                        tick-size="8"
-                    >
-                        <template v-slot:prepend>
-                            Std. Devs. from Mean
-                        </template>
-                    </v-slider>
+                        tick-size="4"
+                        thumb-label
+                        track-color="#aaa"
+                        track-fill-color="#aaa"
+                        label="Std. Devs. from Mean"
+                    />
                     <br/>
                     <v-data-table
                         :headers="pcaInfo.headers"

diff --git a/web/shapeworks/src/components/DataList.vue b/web/shapeworks/src/components/DataList.vue
@@ -115,7 +115,9 @@ export default defineComponent({
                         v-model="selectedAnatomies"
                         :value="anatomy_type"
                     ></v-checkbox>
-                    <v-list-item-title v-text="anatomy_type"/>
+                    <v-list-item-title>
+                        {{ anatomy_type }}
+                    </v-list-item-title>
                 </v-list-item>
             </v-list-item-group>
             <v-subheader>SUBJECTS</v-subheader>
@@ -139,6 +141,9 @@ export default defineComponent({
                                     v-on="on"
                                 >
                                     Subject: {{ subject.name }}
+                                    <span v-if="subject.group" class="pl-3">
+                                        (Group {{ subject.group }})
+                                    </span>
                                 </v-list-item-title>
                             </template>
                             <span>

diff --git a/web/shapeworks/src/components/TabForm.vue b/web/shapeworks/src/components/TabForm.vue
@@ -7,7 +7,7 @@ import VJsf from '@koumoul/vjsf'
 import '@koumoul/vjsf/dist/main.css'
 import Ajv from 'ajv';
 import defaults from 'json-schema-defaults';
-import { spawnJob, jobAlreadyDone, allDataObjectsInDataset, currentTasks, spawnJobProgressPoll } from '../store';
+import { spawnJob, jobAlreadyDone, allDataObjectsInDataset, currentTasks, spawnJobProgressPoll, selectedProject } from '../store';
 import { DataObject } from '../types/index';
 
 Vue.use(Vuetify)
@@ -87,8 +87,9 @@ export default defineComponent({
         }
 
         async function submitForm(_: Event, confirmed=false){
-            if(currentTasks.value[`${props.form}_task`]) {
-                currentTasks.value[`${props.form}_task`] = undefined
+            if (!selectedProject.value) return
+            if (!currentTasks.value[selectedProject.value.id]) {
+                currentTasks.value[selectedProject.value.id] = {}
             }
             if(alreadyDone.value && !confirmed){
                 showSubmissionConfirmation.value = true
@@ -100,13 +101,17 @@ export default defineComponent({
                 setTimeout(() => messages.value = '', 10000)
             } else {
                 messages.value = `Successfully submitted ${props.form} job. Awaiting results...`
-                currentTasks.value = Object.assign(currentTasks.value, taskIds)
+                currentTasks.value[selectedProject.value.id] = taskIds
                 spawnJobProgressPoll()
             }
         }
 
         const taskData = computed(
-            () => currentTasks.value[`${props.form}_task`]
+            () => {
+                if(!selectedProject.value?.id ||
+                !currentTasks.value[selectedProject.value.id]) return undefined
+                return currentTasks.value[selectedProject.value.id][`${props.form}_task`]
+            }
         )
 
 

diff --git a/web/shapeworks/src/store.ts b/web/shapeworks/src/store.ts
@@ -103,11 +103,7 @@ export const vtkShapesByType = ref<Record<string, any[]>>({
     "Particles": []
 })
 
-export const currentTasks = ref<Record<string, Task| undefined>>({
-    groom_task: undefined,
-    optimize_task: undefined,
-    analyze_task: undefined
-})
+export const currentTasks = ref<Record<number, Record<string, Task| undefined>>>({})
 
 export const jobProgressPoll = ref();
 
@@ -198,25 +194,34 @@ export async function spawnJobProgressPoll() {
 }
 
 export async function pollJobProgress(){
-    const refreshedTasks = await Promise.all(Object.entries(currentTasks.value)
-    .map(async ([taskName, task]) => {
-        if (task?.task_id){
-            task = await getTaskProgress(task.task_id)
-            if (task?.task_id && task?.percent_complete === 100) {
-                await deleteTaskProgress(task?.task_id)
-                task.task_id = undefined
-                setTimeout(() => {
-                    currentTasks.value[taskName] = undefined
-                }, 1000)
-                fetchJobResults(taskName.replace('_task', ''))
-            }
+    if(selectedProject.value && currentTasks.value[selectedProject.value.id]){
+        const refreshedTasks = await Promise.all(
+            Object.entries(currentTasks.value[selectedProject.value.id])
+            .map(async ([taskName, task]) => {
+                if (task?.task_id){
+                    task = await getTaskProgress(task.task_id)
+                    if (task?.task_id && task?.percent_complete === 100) {
+                        await deleteTaskProgress(task?.task_id)
+                        task.task_id = undefined
+                        setTimeout(() => {
+                            if (selectedProject.value){
+                                currentTasks.value[selectedProject.value.id][taskName] = undefined
+                            }
+                        }, 1000)
+                        fetchJobResults(taskName.replace('_task', ''))
+                    }
+                }
+                return [taskName, task]
+            }))
+        currentTasks.value[selectedProject.value.id] = Object.fromEntries(refreshedTasks)
+        currentTasks.value = {...currentTasks.value}  // reassign for watch response
+        if (
+            Object.values(currentTasks.value[selectedProject.value.id])
+            .every(task => task?.task_id === undefined)
+        ) {
+            clearInterval(jobProgressPoll.value)
+            jobProgressPoll.value = undefined
         }
-        return [taskName, task]
-    }))
-    currentTasks.value = Object.fromEntries(refreshedTasks)
-    if (Object.values(currentTasks.value).every(task => task?.task_id === undefined)) {
-        clearInterval(jobProgressPoll.value)
-        jobProgressPoll.value = undefined
     }
 }
 
@@ -263,7 +268,7 @@ export async function switchTab(tabName: string){
     switch(tabName) {
         // add any other tab-switching updates here
         case 'analyze':
-            if (refreshedProject && !currentTasks.value['analyze_task']) {
+            if (refreshedProject && !currentTasks.value[selectedProject.value.id]['analyze_task']) {
                 analysis.value = refreshedProject.last_cached_analysis
             }
     }