diff --git a/MirMachineWebapp/settings.py b/MirMachineWebapp/settings.py
index 7348b119..b0c14e31 100644
--- a/MirMachineWebapp/settings.py
+++ b/MirMachineWebapp/settings.py
@@ -39,7 +39,6 @@
'django.contrib.messages',
'django.contrib.staticfiles',
'lookupService.apps.LookupserviceConfig',
- 'corsheaders',
'manifest_loader',
'rest_framework',
]
@@ -47,7 +46,6 @@
MIDDLEWARE = [
'django.middleware.security.SecurityMiddleware',
'django.contrib.sessions.middleware.SessionMiddleware',
- 'corsheaders.middleware.CorsMiddleware',
'django.middleware.common.CommonMiddleware',
'django.middleware.csrf.CsrfViewMiddleware',
'django.contrib.auth.middleware.AuthenticationMiddleware',
@@ -133,5 +131,3 @@
# https://docs.djangoproject.com/en/3.2/ref/settings/#default-auto-field
DEFAULT_AUTO_FIELD = 'django.db.models.BigAutoField'
-
-CORS_ALLOWED_ORIGINS = ['https://localhost:3000']
diff --git a/lookupService/frontend/package.json b/lookupService/frontend/package.json
index 0120a4f4..980baace 100644
--- a/lookupService/frontend/package.json
+++ b/lookupService/frontend/package.json
@@ -4,7 +4,11 @@
"private": true,
"dependencies": {
"@babel/runtime": "^7.15.3",
+ "@sb1/ffe-core": "^19.1.0",
+ "@sb1/ffe-core-react": "^4.2.5",
"@sb1/ffe-icons-react": "^7.2.18",
+ "@sb1/ffe-spinner": "^4.0.0",
+ "@sb1/ffe-spinner-react": "^5.0.3",
"@testing-library/jest-dom": "^5.14.1",
"@testing-library/react": "^11.2.7",
"@testing-library/user-event": "^12.8.3",
diff --git a/lookupService/frontend/src/App.less b/lookupService/frontend/src/App.less
index bfeb899b..f749ee5c 100644
--- a/lookupService/frontend/src/App.less
+++ b/lookupService/frontend/src/App.less
@@ -257,4 +257,9 @@
padding: 10px;
width: 100%;
justify-content: center;
+}
+
+.spinner::before{
+ border-color: @main-green !important;
+ border-top-color: transparent !important;
}
\ No newline at end of file
diff --git a/lookupService/frontend/src/components/Form.js b/lookupService/frontend/src/components/Form.js
index e21f559f..eb511751 100644
--- a/lookupService/frontend/src/components/Form.js
+++ b/lookupService/frontend/src/components/Form.js
@@ -1,6 +1,7 @@
import { useState, useEffect } from "react";
import { ChevronIkon, ForstorrelsesglassIkon } from '@sb1/ffe-icons-react'
-import { fetchTree, submitJob, getFamilies, getFamiliesIncludedInSearch } from '../utils/Repository'
+import Spinner from '@sb1/ffe-spinner-react'
+import { fetchTree, submitJob, getFamilies, getFamiliesIncludedInSearch, validData } from '../utils/Repository'
import { Redirect } from 'react-router-dom'
import Tree from './Tree'
import SearchableDropdown from './SearchableDropdown'
@@ -12,6 +13,7 @@ export const SearchForm = () => {
const [optionalActive, setOptionalActive] = useState(false)
const [modal, setModal] = useState(false)
const [showIncluded, setShowIncluded] = useState(false)
+ const [submitting, setSubmitting] = useState(false)
// Form data
const [inputMode, setInputMode] = useState("text")
@@ -49,6 +51,13 @@ export const SearchForm = () => {
},[])
const handleSubmit = async () => {
+ setSubmitting(true)
+ let mode = document.getElementById('mode').value
+ let file
+ if(mode == 'file'){
+ file = document.getElementById('sequence').files[0]
+ document.getElementById('sequence').value = ''
+ }
const data = {
data: document.getElementById('sequence').value,
mode: document.getElementById('mode').value,
@@ -60,8 +69,21 @@ export const SearchForm = () => {
family: singleFam ? selectedFamily : '',
mail_address: document.getElementById('email').value
}
- const response = await submitJob(data)
- setRedirect(response.id)
+
+ if(validData(data, file)) {
+ try {
+ const response = await submitJob(data, file)
+ setRedirect(response.id)
+ } catch (e) {
+ if (e.name == 'JobPostError') {
+ alert(e.message)
+ }
+ setSubmitting(false)
+ }
+ } else {
+ alert('Required fields are missing')
+ setSubmitting(false)
+ }
}
const handleIncludedFamilyFetching = async (refresh) => {
@@ -93,6 +115,9 @@ export const SearchForm = () => {
)
diff --git a/lookupService/frontend/src/styles.less b/lookupService/frontend/src/styles.less
index 6a22bade..f6be6413 100644
--- a/lookupService/frontend/src/styles.less
+++ b/lookupService/frontend/src/styles.less
@@ -1,4 +1,6 @@
+@import '~@sb1/ffe-core/less/ffe';
+@import '~@sb1/ffe-spinner/less/spinner';
@import 'App';
@import 'index';
@import './components/Job';
-@import './components/Tree';
\ No newline at end of file
+@import './components/Tree';
diff --git a/lookupService/frontend/src/utils/Repository.js b/lookupService/frontend/src/utils/Repository.js
index 0ae04801..a3841343 100644
--- a/lookupService/frontend/src/utils/Repository.js
+++ b/lookupService/frontend/src/utils/Repository.js
@@ -1,9 +1,17 @@
const baseURL = 'http://localhost:8000/api/'
-export const submitJob = async (data) => {
+export const submitJob = async (data, file) => {
const csrftoken = getCookie('csrftoken')
+
+ let formData = new FormData()
const jsonString = JSON.stringify(data,null, ' ')
- console.log(jsonString)
+ formData.append('data', jsonString)
+
+ if(data.mode == 'file'){
+ if(!file) throw new JobPostError('Please select a file to upload')
+ formData.append('file', file)
+ }
+
const response = await fetch(baseURL + 'jobs/',{
method: 'POST',
@@ -11,13 +19,15 @@ export const submitJob = async (data) => {
cache: 'no-cache',
credentials: 'same-origin',
headers: {
- 'Content-Type': 'application/json',
'Accept': '*/*',
'X-CSRFToken': csrftoken,
'Accept-Encoding': 'gzip, deflate, br'
},
- body: jsonString
+ body: formData
});
+ if(response.status === 400){
+ throw new JobPostError('Invalid data, make sure you filled out the necessary fields')
+ }
return response.json()
}
@@ -127,3 +137,17 @@ export class JobFetchError extends Error {
this.name = "JobFetchError"
}
}
+
+export class JobPostError extends Error {
+ constructor(message) {
+ super(message)
+ this.name = "JobPostError"
+ }
+}
+
+export const validData = (data, file) => {
+ if(data.data === '' && !file) return false
+ else if(data.single_fam_mode && data.family === '') return false
+ else if(!data.single_fam_mode && data.node === '') return false
+ return true
+}
\ No newline at end of file
diff --git a/lookupService/job_pre_processor.py b/lookupService/job_pre_processor.py
new file mode 100644
index 00000000..4e668181
--- /dev/null
+++ b/lookupService/job_pre_processor.py
@@ -0,0 +1,27 @@
+import hashlib
+import json
+from lookupService.serializers import JobSerializer
+
+
+def process_form_data(request):
+ serializer = JobSerializer(data=json.loads(request.POST.get('data')))
+ if serializer.initial_data['mode'] == 'file':
+ file = request.FILES.get('file')
+ fasta = file.name.endswith(('.fa', '.fasta'))
+ parsed_header = False
+ _list = []
+ for chunk in file.chunks():
+ decoded = chunk.decode('utf-8')
+ if fasta and not parsed_header:
+ if serializer.initial_data['species'] == '':
+ lines = decoded.splitlines()
+ serializer.initial_data['species'] = lines[0][1:]
+ _list.append(''.join(lines[1:]))
+ parsed_header = True
+ continue
+ _list.append(decoded)
+ serializer.initial_data['data'] = ''.join(_list)
+ serializer.initial_data['hash'] = hashlib.md5(serializer.initial_data['data'].encode()).hexdigest()
+ return serializer
+
+
diff --git a/lookupService/migrations/0015_auto_20210923_1219.py b/lookupService/migrations/0015_auto_20210923_1219.py
new file mode 100644
index 00000000..f0dd2888
--- /dev/null
+++ b/lookupService/migrations/0015_auto_20210923_1219.py
@@ -0,0 +1,28 @@
+# Generated by Django 3.2.6 on 2021-09-23 12:19
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('lookupService', '0014_auto_20210915_1132'),
+ ]
+
+ operations = [
+ migrations.AlterField(
+ model_name='job',
+ name='data',
+ field=models.CharField(max_length=1000000),
+ ),
+ migrations.AlterField(
+ model_name='job',
+ name='mail_address',
+ field=models.EmailField(blank=True, max_length=254),
+ ),
+ migrations.AlterField(
+ model_name='job',
+ name='node',
+ field=models.CharField(blank=True, max_length=100),
+ ),
+ ]
diff --git a/lookupService/migrations/0016_alter_job_data.py b/lookupService/migrations/0016_alter_job_data.py
new file mode 100644
index 00000000..465c01b4
--- /dev/null
+++ b/lookupService/migrations/0016_alter_job_data.py
@@ -0,0 +1,18 @@
+# Generated by Django 3.2.6 on 2021-09-23 12:21
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('lookupService', '0015_auto_20210923_1219'),
+ ]
+
+ operations = [
+ migrations.AlterField(
+ model_name='job',
+ name='data',
+ field=models.CharField(max_length=500000),
+ ),
+ ]
diff --git a/lookupService/migrations/0017_alter_job_data.py b/lookupService/migrations/0017_alter_job_data.py
new file mode 100644
index 00000000..9ad8a982
--- /dev/null
+++ b/lookupService/migrations/0017_alter_job_data.py
@@ -0,0 +1,18 @@
+# Generated by Django 3.2.6 on 2021-09-23 12:24
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('lookupService', '0016_alter_job_data'),
+ ]
+
+ operations = [
+ migrations.AlterField(
+ model_name='job',
+ name='data',
+ field=models.TextField(),
+ ),
+ ]
diff --git a/lookupService/models.py b/lookupService/models.py
index d430336a..7de7f062 100644
--- a/lookupService/models.py
+++ b/lookupService/models.py
@@ -1,5 +1,6 @@
from django.db import models
from django.utils import timezone
+from django.template.defaultfilters import truncatechars
import uuid
# Create your models here.
@@ -39,15 +40,15 @@ class Job(models.Model):
status = models.CharField(choices=STATUSES, max_length=15, default=status_default)
hash = models.CharField(max_length=168, blank=True)
initiated = models.DateTimeField(auto_now_add=True)
- data = models.CharField(max_length=10000)
+ data = models.TextField()
mode = models.CharField(choices=MODE_OPTIONS, max_length=10)
species = models.CharField(blank=True, max_length=60, default=species_default)
- node = models.CharField(max_length=100)
+ node = models.CharField(max_length=100, blank=True)
model_type = models.CharField(choices=MODEL_TYPES, max_length=15)
single_node = models.BooleanField(default=boolean_default)
single_fam_mode = models.BooleanField(default=boolean_default)
family = models.CharField(blank=True, max_length=18)
- mail_address = models.CharField(blank=True, max_length=100)
+ mail_address = models.EmailField(max_length=254, blank=True)
class Node(models.Model):
diff --git a/lookupService/serializers.py b/lookupService/serializers.py
index 842a513d..2fc39b6f 100644
--- a/lookupService/serializers.py
+++ b/lookupService/serializers.py
@@ -2,14 +2,16 @@
from .models import Job, Node, Edge, Family, NodeFamilyRelation
+class StrippedJobSerializer(serializers.ModelSerializer):
+ class Meta:
+ model = Job
+ exclude = ['data']
+
+
class JobSerializer(serializers.HyperlinkedModelSerializer):
class Meta:
model = Job
- fields = ['id', 'initiated', 'status',
- 'data', 'hash', 'mode',
- 'species', 'node',
- 'model_type', 'single_node', 'family',
- 'single_fam_mode', 'mail_address']
+ fields = '__all__'
class NodeSerializer(serializers.HyperlinkedModelSerializer):
diff --git a/lookupService/urls.py b/lookupService/urls.py
index 11164aa9..43c53308 100644
--- a/lookupService/urls.py
+++ b/lookupService/urls.py
@@ -4,7 +4,7 @@
urlpatterns = [
path('jobs/', post_job),
- path('job/', get_job),
+ path('job/', get_job),
path('tree/', get_tree),
path('families/', get_families),
path('relations/', get_included_families)
diff --git a/lookupService/views.py b/lookupService/views.py
index 28755fb3..5be29642 100644
--- a/lookupService/views.py
+++ b/lookupService/views.py
@@ -1,8 +1,9 @@
-from pathlib import Path
-
from django.core.exceptions import ValidationError
from django.shortcuts import render
-from .serializers import JobSerializer, NodeSerializer, EdgeSerializer, FamilySerializer, NodeFamilyRelationSerializer
+
+from .job_pre_processor import process_form_data
+from .serializers import JobSerializer, NodeSerializer, \
+ EdgeSerializer, FamilySerializer, NodeFamilyRelationSerializer, StrippedJobSerializer
from .models import Job, Node, Edge, Family, NodeFamilyRelation
from django.http import JsonResponse
from django.views.decorators.csrf import ensure_csrf_cookie
@@ -11,22 +12,20 @@
from .tree_helper import parse_newick_tree
from .family_importer import import_all_families, import_node_to_family_db
from engine.scripts.MirMachine import show_node_families_args
-import hashlib
import json
-# Create your views here.
@ensure_csrf_cookie
def index_view(request, *args, **kwargs):
return render(request, 'frontend/index.html', context={}, status=200)
@api_view(['GET'])
-def get_job(request, id):
+def get_job(request, _id):
if request.method == 'GET':
try:
- job = Job.objects.get(id=id)
- serializer = JobSerializer(job)
+ job = Job.objects.get(id=_id)
+ serializer = StrippedJobSerializer(job)
return JsonResponse(serializer.data)
except ValidationError:
response = {"message": "Not a valid UUID"}
@@ -38,15 +37,14 @@ def get_job(request, id):
status=status.HTTP_404_NOT_FOUND)
-# remember to remove exemptions
-@api_view(['POST','GET'])
+@api_view(['POST', 'GET'])
def post_job(request):
if request.method == 'POST':
- serializer = JobSerializer(data=request.data)
- serializer.initial_data['hash'] = hashlib.md5(serializer.initial_data['data'].encode()).hexdigest()
+ serializer = process_form_data(request)
if serializer.is_valid():
- serializer.save()
- return JsonResponse(serializer.data, status=status.HTTP_201_CREATED)
+ instance = serializer.save()
+ stripped = StrippedJobSerializer(instance)
+ return JsonResponse(stripped.data, status=status.HTTP_201_CREATED)
return JsonResponse(serializer.errors, status=status.HTTP_400_BAD_REQUEST)
elif request.method == 'GET':
jobs = Job.objects.all()