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Merge pull request #195 from HFragnaud/master
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fix for #192,#176, #138,#154
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@HFragnaud
HFragnaud authored May 16, 2018
2 parents a6430ea + 62bb3ea commit f599255
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Showing 5 changed files with 206 additions and 131 deletions.
70 changes: 47 additions & 23 deletions model_validation_api/views.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@
import math
import json
import logging
import time
from urlparse import urlparse, parse_qs
from datetime import date
from django.shortcuts import render
Expand All @@ -25,9 +26,10 @@
HttpResponseNotAllowed, # 405
HttpResponseNotModified, # 304
HttpResponseRedirect) # 302
from django.db.models import Max, Count
from django.db.models import Max, Count, CASCADE
from django.conf import settings
from django.template import loader
from django.db import connection
import requests
from hbp_app_python_auth.auth import get_access_token, get_auth_header

Expand Down Expand Up @@ -190,29 +192,29 @@ def get(self, request, format=None, **kwargs):

serializer_context = {'request': request,}

data_modalities = Param_DataModalities.objects.all()
data_modalities = Param_DataModalities.objects.all().order_by('authorized_value')
data_modalities_serializer = Param_DataModalitiesSerializer(data_modalities, context=serializer_context, many=True)

test_type = Param_TestType.objects.all()
test_type = Param_TestType.objects.all().order_by('authorized_value')
test_type_serializer = Param_TestTypeSerializer(test_type, context=serializer_context, many=True)

species = Param_Species.objects.all()
species = Param_Species.objects.all().order_by('authorized_value')
species_serializer = Param_SpeciesSerializer(species, context=serializer_context, many=True)

brain_region = Param_BrainRegion.objects.all()
brain_region = Param_BrainRegion.objects.all().order_by('authorized_value')
brain_region_serializer = Param_BrainRegionSerializer(brain_region, context=serializer_context, many=True)

cell_type = Param_CellType.objects.all()
cell_type = Param_CellType.objects.all().order_by('authorized_value')
cell_type_serializer = Param_CellTypeSerializer(cell_type, context=serializer_context, many=True)

model_type = Param_ModelType.objects.all()
model_type_serializer = Param_ModelTypeSerializer(model_type, context=serializer_context, many=True)
model_type = Param_ModelType.objects.all().order_by('authorized_value')
model_type_serializer = Param_ModelTypeSerializer(model_type, context=serializer_context, many=True)

score_type = Param_ScoreType.objects.all()
score_type = Param_ScoreType.objects.all().order_by('authorized_value')
score_type_serializer = Param_ScoreTypeSerializer(score_type, context=serializer_context, many=True)

organization = Param_organizations.objects.all()
organization_serializer = Param_OrganizationsSerializer(organization, context=serializer_context, many=True)
organization = Param_organizations.objects.all().order_by('authorized_value')
organization_serializer = Param_OrganizationsSerializer(organization, context=serializer_context, many=True)

##for python client #'python_client=True' 'parameters= list()'
if python_client == 'true':
Expand Down Expand Up @@ -245,7 +247,7 @@ def get(self, request, format=None, **kwargs):
if (param == 'test_type'):
res['test_type'] = test_type.values_list('authorized_value', flat=True)
if (param == 'brain_region'):
res['brain_region'] = brain_region.values_list('authorized_value', flat=True)
res['brain_region'] = brain_region.values_list('authorized_value', flat=True)
if (param == 'cell_type'):
res['cell_type'] = cell_type.values_list('authorized_value', flat=True)
if (param == 'model_type'):
Expand Down Expand Up @@ -901,34 +903,47 @@ def get(self, request, format=None, **kwargs):
serializer_context = {
'request': request,
}

id = request.GET.getlist('id')
# time_spent=time.time()
# id = request.GET.getlist('id')
if check_list_uuid_validity(id) is False :
return Response("Badly formed uuid in : id", status=status.HTTP_400_BAD_REQUEST)


#if model id not specifiedorresponding to this alias.
if(len(id) == 0):


# print("after going in first loop :", time.time()-time_spent)
# time_spent=time.time()
web_app = request.GET.getlist('web_app')


#if the request comes from the webapp : uses collab_parameters
if len(web_app) > 0 and web_app[0] == 'True' :


# print("after going in first if :", time.time()-time_spent)
# time_spent=time.time()
app_id = request.GET.getlist('app_id')[0]
# print("after getting app_id:", time.time()-time_spent)
# time_spent=time.time()
collab_id = get_collab_id_from_app_id(app_id)

# print("after getting collab_id :", time.time()-time_spent)
# time_spent=time.time()
collab_params = CollabParameters.objects.get(id = app_id )

collab_ids = list(CollabParameters.objects.all().values_list('collab_id', flat=True).distinct())
# print("after getting collab_ids_list :", time.time()-time_spent)
# collab_ids = ["2180"] #######don't forget to erase it!!!!
# time_spent=time.time()
collab_ids_new = []
for collab in collab_ids:
if is_authorised(request, collab):
collab_ids_new.append(collab)

# print("after checking permissions :", time.time()-time_spent)
# time_spent=time.time()
all_ctx_from_collab = CollabParameters.objects.filter(collab_id__in=collab_ids_new).distinct()


# print("after getting all ctx :", time.time()-time_spent)
# time_spent=time.time()
#if one of the collab_param is empty, don't filter on it.
species_filter = collab_params.species.split(",")
if species_filter==[u'']:
Expand Down Expand Up @@ -958,8 +973,9 @@ def get(self, request, format=None, **kwargs):
if organization_filter==[u'']:
organization_filter = list(Param_organizations.objects.all().values_list('authorized_value', flat=True)) #+[u'']




# print("after filtering with config :", time.time()-time_spent)
# time_spent=time.time()
rq1 = ScientificModel.objects.filter(
private=1,
app__in=all_ctx_from_collab.values("id"),
Expand All @@ -981,8 +997,13 @@ def get(self, request, format=None, **kwargs):
models = (rq1 | rq2).distinct().order_by('-creation_date')
else:
models = rq2.distinct().order_by('-creation_date')

model_serializer = ScientificModelReadOnlyForHomeSerializer(models, context=serializer_context, many=True )

# print("after getting queries :", time.time()-time_spent)
# print("get models requests:")
# for query in connection.queries:
# print(query)
return Response({
'models': model_serializer.data,
})
Expand Down Expand Up @@ -1104,6 +1125,7 @@ def post(self, request, format=None):

collab_id = get_collab_id_from_app_id(app_id)
if not is_authorised(request, collab_id):
return HttpResponse('Unauthorized', status=401)
return HttpResponseForbidden()

serializer_context = {'request': request,}
Expand Down Expand Up @@ -1198,9 +1220,11 @@ def put(self, request, format=None):
app_id = model.app_id
collab_id = get_collab_id_from_app_id(app_id)
if not is_authorised(request, collab_id):
return HttpResponse('Unauthorized', status=401)
return HttpResponseForbidden()

app_id = value['app_id']

collab_id = get_collab_id_from_app_id(app_id)
if not is_authorised(request, collab_id):
return HttpResponseForbidden()
Expand All @@ -1221,7 +1245,7 @@ def put(self, request, format=None):
if model_serializer.is_valid() :
check_param = check_param_of_model_json(value)
if check_param is True :
model = model_serializer.save()
model = model_serializer.save(app_id=app_id)
else :
return Response(check_param, status=status.HTTP_400_BAD_REQUEST)

Expand Down
17 changes: 17 additions & 0 deletions validation_service/app/css/Model_catalog.css
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Original file line number Diff line number Diff line change
Expand Up @@ -262,7 +262,24 @@
overflow: auto;
}

.permissions-panel {
/*height:10px;
width: 320px;*/
padding: 5px;
border: 2px solid #dfe7ef;
float: right;
margin-right: 7%;
margin-left: 2%;
margin-bottom: 1%;
margin-top: 1%;
overflow: auto;
}

.text-justify {
text-align: justify;
text-justify: inter-word;
}

.text-centered {
text-align: center;
}
10 changes: 9 additions & 1 deletion validation_service/app/js/service.js
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Original file line number Diff line number Diff line change
Expand Up @@ -551,9 +551,11 @@ ParametersConfigurationServices.service('CollabParameters', ['$rootScope', 'Coll
var param = getParametersByType(type);

if (param.length > 0) {
param = _move_element_at_the_end_of_array("Other", param)
return param;
} else {
return default_parameters[type];
param = _move_element_at_the_end_of_array("Other", default_parameters[type])
return param;
}
};

Expand Down Expand Up @@ -662,6 +664,12 @@ ParametersConfigurationServices.service('CollabParameters', ['$rootScope', 'Coll
parameters.param[0]['organization'] = string_tab[6];
};

var _move_element_at_the_end_of_array = function(elem, array) {
array.splice(array.indexOf(elem), 1)
array.push(elem)
return array;
}

var setService = function(ctx_param) {
return new Promise(function(resolve, reject) {

Expand Down
24 changes: 24 additions & 0 deletions validation_service/app/templates/model_catalog/model-catalog-detail.tpl.html
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Original file line number Diff line number Diff line change
Expand Up @@ -8,24 +8,48 @@
<body>
<br>
<nav class="navbar ">

<panel id="panel-permissions" class=permissions-panel>
<table class="table-create text-centered">
<thead>
<th>
<div align=center> Permissions </div>
</th>
</thead>
<tbody>
<tr>
<td>
<div ng-if="is_collab_member == true"> Read and Write</div>
<div ng-if="is_collab_member == false"> Read only</div>
</td>
</tr>
</tbody>
</table>
</panel>

<h1 align=center> {{ model.models[0].name}}
</h1>
<h3 ng-if="model.models[0].owner && model.models[0].owner!=''" align=center> Owner: {{ model.models[0].owner }} </h3>
<h3 align=center> Author(s): {{ model.models[0].author }} </h3>

</nav>
<nav>

<button class="button-MC" ng-click="Context.modelCatalog_goToHomeView();">Home</button>&ensp;

<a ng-href="#/model-catalog/edit/{{model.models[0].id}}" ng-if="is_collab_member == true" class="button-MC">Edit</a>&ensp;
<a ng-href="#/model-catalog/version/{{model.models[0].id}}" class="button-MC">New version</a>&ensp;

</nav>
<br>
<br>

<br>
<h4 style="margin-left:33%"> <b>Model Description</b> </h4>
<br>



<panel class=caracteristics-panel>
<h4 align=center> <b> Model information </b></h4>
<br>
Expand Down
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