diff --git a/compose/django/Dockerfile b/compose/django/Dockerfile
index d84436c4..c1e14c52 100644
--- a/compose/django/Dockerfile
+++ b/compose/django/Dockerfile
@@ -1,4 +1,4 @@
-FROM python:3.10-slim
+FROM python:3.10-slim AS neurovault
ENV PYTHONUNBUFFERED 1
ENV PYTHONDONTWRITEBYTECODE 1
@@ -10,6 +10,54 @@ RUN apt-get update && apt-get install --no-install-recommends -y \
libpq-dev \
git
+RUN apt-get -y update \
+ && apt-get install -y wget subversion && \
+ wget -qO- ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz | tar zxv -C /opt \
+ --exclude='freesurfer/trctrain' \
+ --exclude='freesurfer/subjects/fsaverage_sym' \
+ --exclude='freesurfer/subjects/fsaverage3' \
+ --exclude='freesurfer/subjects/fsaverage4' \
+ --exclude='freesurfer/subjects/fsaverage5' \
+ --exclude='freesurfer/subjects/fsaverage6' \
+ --exclude='freesurfer/subjects/cvs_avg35' \
+ --exclude='freesurfer/subjects/cvs_avg35_inMNI152' \
+ --exclude='freesurfer/subjects/bert' \
+ --exclude='freesurfer/subjects/V1_average' \
+ --exclude='freesurfer/average/mult-comp-cor' \
+ --exclude='freesurfer/lib/cuda' \
+ --exclude='freesurfer/lib/qt' && \
+ apt-get install -y tcsh bc tar libgomp1 perl-modules curl && \
+ apt-get clean && \
+ rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+# Set up the environment
+ENV OS Linux
+ENV FS_OVERRIDE 0
+ENV FIX_VERTEX_AREA=
+ENV SUBJECTS_DIR /opt/freesurfer/subjects
+ENV FSF_OUTPUT_FORMAT nii.gz
+ENV MNI_DIR /opt/freesurfer/mni
+ENV LOCAL_DIR /opt/freesurfer/local
+ENV FREESURFER_HOME /opt/freesurfer
+ENV FSFAST_HOME /opt/freesurfer/fsfast
+ENV MINC_BIN_DIR /opt/freesurfer/mni/bin
+ENV MINC_LIB_DIR /opt/freesurfer/mni/lib
+ENV MNI_DATAPATH /opt/freesurfer/mni/data
+ENV FMRI_ANALYSIS_DIR /opt/freesurfer/fsfast
+ENV PERL5LIB /opt/freesurfer/mni/lib/perl5/5.8.5
+ENV MNI_PERL5LIB /opt/freesurfer/mni/lib/perl5/5.8.5
+ENV PATH /opt/freesurfer/bin:/opt/freesurfer/fsfast/bin:/opt/freesurfer/tktools:/opt/freesurfer/mni/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:$PATH
+RUN echo "cHJpbnRmICJrcnp5c3p0b2YuZ29yZ29sZXdza2lAZ21haWwuY29tXG41MTcyXG4gKkN2dW12RVYzelRmZ1xuRlM1Si8yYzFhZ2c0RVxuIiA+IC9vcHQvZnJlZXN1cmZlci9saWNlbnNlLnR4dAo=" | base64 -d | sh
+
+RUN svn export --force https://github.com/NeuroVault/neurovault_data/trunk/pycortex_datastore /usr/local/share/pycortex/
+RUN apt-get update && apt-get -y install tcsh libglu1-mesa libxmu6
+RUN /opt/freesurfer/bin/mri_convert /opt/freesurfer/subjects/fsaverage/mri/brain.mgz /opt/freesurfer/subjects/fsaverage/mri/brain.nii.gz
+RUN mkdir /usr/local/share/pycortex/db/fsaverage/transforms/
+RUN pip install tornado
+
+RUN apt-get update && apt-get -y install zip
+RUN wget https://ndownloader.figshare.com/files/6891069 -O icbm.zip && unzip icbm.zip -d /opt/freesurfer/subjects/ && rm icbm.zip
+
COPY ./compose/django/requirements.txt requirements.txt
RUN pip install -r requirements.txt
diff --git a/compose/django/Dockerfile_fs b/compose/django/Dockerfile_fs
deleted file mode 100644
index aa724fda..00000000
--- a/compose/django/Dockerfile_fs
+++ /dev/null
@@ -1,49 +0,0 @@
-FROM neurovault/neurovault
-
-RUN apt-get -y update \
- && apt-get install -y wget subversion && \
- wget -qO- ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz | tar zxv -C /opt \
- --exclude='freesurfer/trctrain' \
- --exclude='freesurfer/subjects/fsaverage_sym' \
- --exclude='freesurfer/subjects/fsaverage3' \
- --exclude='freesurfer/subjects/fsaverage4' \
- --exclude='freesurfer/subjects/fsaverage5' \
- --exclude='freesurfer/subjects/fsaverage6' \
- --exclude='freesurfer/subjects/cvs_avg35' \
- --exclude='freesurfer/subjects/cvs_avg35_inMNI152' \
- --exclude='freesurfer/subjects/bert' \
- --exclude='freesurfer/subjects/V1_average' \
- --exclude='freesurfer/average/mult-comp-cor' \
- --exclude='freesurfer/lib/cuda' \
- --exclude='freesurfer/lib/qt' && \
- apt-get install -y tcsh bc tar libgomp1 perl-modules curl && \
- apt-get clean && \
- rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
-
-# Set up the environment
-ENV OS Linux
-ENV FS_OVERRIDE 0
-ENV FIX_VERTEX_AREA=
-ENV SUBJECTS_DIR /opt/freesurfer/subjects
-ENV FSF_OUTPUT_FORMAT nii.gz
-ENV MNI_DIR /opt/freesurfer/mni
-ENV LOCAL_DIR /opt/freesurfer/local
-ENV FREESURFER_HOME /opt/freesurfer
-ENV FSFAST_HOME /opt/freesurfer/fsfast
-ENV MINC_BIN_DIR /opt/freesurfer/mni/bin
-ENV MINC_LIB_DIR /opt/freesurfer/mni/lib
-ENV MNI_DATAPATH /opt/freesurfer/mni/data
-ENV FMRI_ANALYSIS_DIR /opt/freesurfer/fsfast
-ENV PERL5LIB /opt/freesurfer/mni/lib/perl5/5.8.5
-ENV MNI_PERL5LIB /opt/freesurfer/mni/lib/perl5/5.8.5
-ENV PATH /opt/freesurfer/bin:/opt/freesurfer/fsfast/bin:/opt/freesurfer/tktools:/opt/freesurfer/mni/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:$PATH
-RUN echo "cHJpbnRmICJrcnp5c3p0b2YuZ29yZ29sZXdza2lAZ21haWwuY29tXG41MTcyXG4gKkN2dW12RVYzelRmZ1xuRlM1Si8yYzFhZ2c0RVxuIiA+IC9vcHQvZnJlZXN1cmZlci9saWNlbnNlLnR4dAo=" | base64 -d | sh
-
-RUN svn export --force https://github.com/NeuroVault/neurovault_data/trunk/pycortex_datastore /usr/local/share/pycortex/
-RUN apt-get update && apt-get -y install tcsh libglu1-mesa libxmu6
-RUN /opt/freesurfer/bin/mri_convert /opt/freesurfer/subjects/fsaverage/mri/brain.mgz /opt/freesurfer/subjects/fsaverage/mri/brain.nii.gz
-RUN mkdir /usr/local/share/pycortex/db/fsaverage/transforms/
-RUN pip install tornado
-
-RUN apt-get update && apt-get -y install zip
-RUN wget https://ndownloader.figshare.com/files/6891069 -O icbm.zip && unzip icbm.zip -d /opt/freesurfer/subjects/ && rm icbm.zip
diff --git a/compose/django/Dockerfile_multi b/compose/django/Dockerfile_multi
deleted file mode 100644
index 631d55f6..00000000
--- a/compose/django/Dockerfile_multi
+++ /dev/null
@@ -1,68 +0,0 @@
-FROM python:3.10-slim AS neurovault
-
-ENV PYTHONUNBUFFERED 1
-ENV PYTHONDONTWRITEBYTECODE 1
-
-RUN apt-get update && apt-get install --no-install-recommends -y \
- # dependencies for building Python packages
- build-essential \
- # psycopg2 dependencies
- libpq-dev \
- git
-
-COPY ./compose/django/requirements.txt requirements.txt
-RUN pip install -r requirements.txt
-
-WORKDIR /code
-
-EXPOSE 8000
-
-FROM neurovault AS neurovault_fs
-
-RUN apt-get -y update \
- && apt-get install -y wget subversion && \
- wget -qO- ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz | tar zxv -C /opt \
- --exclude='freesurfer/trctrain' \
- --exclude='freesurfer/subjects/fsaverage_sym' \
- --exclude='freesurfer/subjects/fsaverage3' \
- --exclude='freesurfer/subjects/fsaverage4' \
- --exclude='freesurfer/subjects/fsaverage5' \
- --exclude='freesurfer/subjects/fsaverage6' \
- --exclude='freesurfer/subjects/cvs_avg35' \
- --exclude='freesurfer/subjects/cvs_avg35_inMNI152' \
- --exclude='freesurfer/subjects/bert' \
- --exclude='freesurfer/subjects/V1_average' \
- --exclude='freesurfer/average/mult-comp-cor' \
- --exclude='freesurfer/lib/cuda' \
- --exclude='freesurfer/lib/qt' && \
- apt-get install -y tcsh bc tar libgomp1 perl-modules curl && \
- apt-get clean && \
- rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
-
-# Set up the environment
-ENV OS Linux
-ENV FS_OVERRIDE 0
-ENV FIX_VERTEX_AREA=
-ENV SUBJECTS_DIR /opt/freesurfer/subjects
-ENV FSF_OUTPUT_FORMAT nii.gz
-ENV MNI_DIR /opt/freesurfer/mni
-ENV LOCAL_DIR /opt/freesurfer/local
-ENV FREESURFER_HOME /opt/freesurfer
-ENV FSFAST_HOME /opt/freesurfer/fsfast
-ENV MINC_BIN_DIR /opt/freesurfer/mni/bin
-ENV MINC_LIB_DIR /opt/freesurfer/mni/lib
-ENV MNI_DATAPATH /opt/freesurfer/mni/data
-ENV FMRI_ANALYSIS_DIR /opt/freesurfer/fsfast
-ENV PERL5LIB /opt/freesurfer/mni/lib/perl5/5.8.5
-ENV MNI_PERL5LIB /opt/freesurfer/mni/lib/perl5/5.8.5
-ENV PATH /opt/freesurfer/bin:/opt/freesurfer/fsfast/bin:/opt/freesurfer/tktools:/opt/freesurfer/mni/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:$PATH
-RUN echo "cHJpbnRmICJrcnp5c3p0b2YuZ29yZ29sZXdza2lAZ21haWwuY29tXG41MTcyXG4gKkN2dW12RVYzelRmZ1xuRlM1Si8yYzFhZ2c0RVxuIiA+IC9vcHQvZnJlZXN1cmZlci9saWNlbnNlLnR4dAo=" | base64 -d | sh
-
-RUN svn export --force https://github.com/NeuroVault/neurovault_data/trunk/pycortex_datastore /usr/local/share/pycortex/
-RUN apt-get update && apt-get -y install tcsh libglu1-mesa libxmu6
-RUN /opt/freesurfer/bin/mri_convert /opt/freesurfer/subjects/fsaverage/mri/brain.mgz /opt/freesurfer/subjects/fsaverage/mri/brain.nii.gz
-RUN mkdir /usr/local/share/pycortex/db/fsaverage/transforms/
-RUN pip install tornado
-
-RUN apt-get update && apt-get -y install zip
-RUN wget https://ndownloader.figshare.com/files/6891069 -O icbm.zip && unzip icbm.zip -d /opt/freesurfer/subjects/ && rm icbm.zip
diff --git a/docker-compose.yml b/docker-compose.yml
index 593cfd22..59a95de0 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -4,9 +4,9 @@ services:
restart: always
build:
context: .
- dockerfile: ./compose/django/Dockerfile_multi
- target: neurovault_fs
- image: neurovault/neurovault_fs
+ dockerfile: ./compose/django/Dockerfile
+ target: neurovault
+ image: neurovault/neurovault
command: python manage.py runserver 0.0.0.0:8000
ports:
- "8000:8000"
@@ -35,7 +35,7 @@ services:
worker:
build:
context: .
- dockerfile: ./compose/django/Dockerfile_multi
+ dockerfile: ./compose/django/Dockerfile
target: neurovault
image: neurovault/neurovault
command: celery -A neurovault.celery worker -Q default -n default@%h
diff --git a/neurovault/apps/statmaps/tests/test_data/statmaps/saccade.I_C.MNI__SetA_Tstat.nii.gz b/neurovault/apps/statmaps/tests/test_data/statmaps/saccade.I_C.MNI__SetA_Tstat.nii.gz
deleted file mode 100644
index 369cd493..00000000
Binary files a/neurovault/apps/statmaps/tests/test_data/statmaps/saccade.I_C.MNI__SetA_Tstat.nii.gz and /dev/null differ
diff --git a/neurovault/apps/statmaps/tests/test_data/statmaps/saccade.I_C.MNI__SetA_mean.nii.gz b/neurovault/apps/statmaps/tests/test_data/statmaps/saccade.I_C.MNI__SetA_mean.nii.gz
deleted file mode 100644
index 7e4c4134..00000000
Binary files a/neurovault/apps/statmaps/tests/test_data/statmaps/saccade.I_C.MNI__SetA_mean.nii.gz and /dev/null differ
diff --git a/neurovault/apps/users/forms.py b/neurovault/apps/users/forms.py
index 98ea77de..25ab2ffc 100644
--- a/neurovault/apps/users/forms.py
+++ b/neurovault/apps/users/forms.py
@@ -2,7 +2,6 @@
from django.contrib.auth.models import User
from django.contrib.auth.forms import UserCreationForm
from django.utils.translation import gettext_lazy as _
-from oauth2_provider.models import Application
class UserCreateForm(UserCreationForm):
@@ -57,18 +56,3 @@ def save(self, commit=True):
def clean_password(self):
return ""
-
-
-class ApplicationEditForm(forms.ModelForm):
- name = forms.CharField(required=True)
-
- class Meta:
- model = Application
- fields = (
- "name",
- "client_id",
- "client_secret",
- "client_type",
- "authorization_grant_type",
- "redirect_uris",
- )
diff --git a/neurovault/apps/users/migrations/0001_initial.py b/neurovault/apps/users/migrations/0001_initial.py
index 56eb50ea..97d049fd 100644
--- a/neurovault/apps/users/migrations/0001_initial.py
+++ b/neurovault/apps/users/migrations/0001_initial.py
@@ -5,12 +5,15 @@
def create_default_app(apps, schema_editor):
+ '''
Application = apps.get_registered_model("oauth2_provider", "Application")
Application.objects.get_or_create(
name=settings.DEFAULT_OAUTH_APP_NAME,
redirect_uris=["http://localhost"],
pk=settings.DEFAULT_OAUTH_APPLICATION_ID,
)
+ '''
+ pass
class Migration(migrations.Migration):
diff --git a/neurovault/apps/users/templates/base_settings.html b/neurovault/apps/users/templates/base_settings.html
index 4982cc0a..c44c17c9 100644
--- a/neurovault/apps/users/templates/base_settings.html
+++ b/neurovault/apps/users/templates/base_settings.html
@@ -15,12 +15,6 @@ Settings
Personal access tokens
-
- Connected applications
-
-
- Developer applications
-
{% block setting_content %}{% endblock %}
{% endblock %}
diff --git a/neurovault/apps/users/templates/oauth2_provider/application_confirm_delete.html b/neurovault/apps/users/templates/oauth2_provider/application_confirm_delete.html
deleted file mode 100644
index e58d8358..00000000
--- a/neurovault/apps/users/templates/oauth2_provider/application_confirm_delete.html
+++ /dev/null
@@ -1,22 +0,0 @@
-{% extends "base_settings.html" %}
-
-{% block developerappstab %}class="active"{% endblock%}
-
-{% block setting_content %}
-
-
-
-
-
Delete this application?
-
{{ application.name }}
-
-
-
-
-
-
- {% block app-form-title %}
- Edit application / {{ application.name }}
- {% endblock app-form-title %}
-
-
-
-
-
-
- {% if messages %}
- {% include "_messages_block.html" with messages=messages %}
- {% endif %}
-
- {% if applications %}
-
-
-
- | Name |
- Client ID |
-
-
-
- {% for application in applications %}
-
- | {{ application.name }}
- |
-
- {{ application.client_id }}
- |
-
- {% endfor %}
-
-
-
-
Register new application
- {% else %}
-
-
No developer applications
-
Developer applications are used for enhanced access to the NeuroVault API.
-
Register an application to get started.
-
- {% endif %}
-
-
-
- {% if not error %}
-
-
- {% else %}
-
Error: {{ error.error }}
-
{{ error.description }}
- {% endif %}
-
-
-
-
-
Revoke the app authorization?
-
{{ object.name }} will no longer be able to access your account on your behalf.
-
-
-
-
-
-
- {% if messages %}
- {% include "_messages_block.html" with messages=messages %}
- {% endif %}
-
- {% if object_list %}
-
- You have authorized these applications to access your NeuroVault account on your behalf.
-
-
- | Name |
- Owner |
- |
-
-
-
- {% for rt in object_list %}
-
- | {{ rt.application.name }} |
-
- {{ rt.application.user.username }}
- |
- Revoke access
- |
-
- {% endfor %}
-
-
- {% else %}
-
-
No connected applications
-
You have no applications authorized to access your account on your behalf via NeuroVault API.
-
- {% endif %}
-
-
-
-
-
-
-
Delete the token?
-
Any applications or scripts using this token will no longer be able to access the NeuroVault API.
-
-
-
-
-
-
- {% if messages %}
- {% include "_messages_block.html" with messages=messages %}
- {% endif %}
-
- {% if object_list %}
-
- Tokens you have generated that can be used to access the NeuroVault API.
-
-
- | Token |
- |
-
-
-
- {% for token in object_list %}
-
- | {{ token.token }} |
- Delete
- |
-
- {% endfor %}
-
-
- {% include "_personal_token_form.html" %}
- {% else %}
-
-
No personal access tokens
-
Personal access tokens are used to access your account via the NeuroVault API.
-
- {% include "_personal_token_form.html" %}
-
-
- {% endif %}
-
-
-
Token
+{{ token }}
+
+ Regenerate Token
+{% endblock %}
diff --git a/neurovault/apps/users/tests/test_application_views.py b/neurovault/apps/users/tests/test_application_views.py
deleted file mode 100644
index 31ae1459..00000000
--- a/neurovault/apps/users/tests/test_application_views.py
+++ /dev/null
@@ -1,93 +0,0 @@
-from django.test import TestCase
-from django.contrib.auth import get_user_model
-from django.urls import reverse
-
-from oauth2_provider.models import Application
-
-UserModel = get_user_model()
-
-
-class BaseTest(TestCase):
- def setUp(self):
- self.user_password = "random"
- self.user = UserModel.objects.create_user(
- "neurouser", "neurouser@example.com", self.user_password
- )
-
- def tearDown(self):
- self.user.delete()
-
-
-class TestApplicationRegistrationView(BaseTest):
- def test_application_registration_user(self):
- self.client.login(username=self.user.username, password=self.user_password)
-
- form_data = {
- "name": "Random App",
- "client_id": "client_id",
- "client_secret": "client_secret",
- "client_type": Application.CLIENT_CONFIDENTIAL,
- "redirect_uris": "http://example.com",
- "authorization_grant_type": Application.GRANT_AUTHORIZATION_CODE,
- }
-
- response = self.client.post(reverse("users:developerapps_register"), form_data)
- self.assertEqual(response.status_code, 302)
-
- app = Application.objects.get(name="Random App")
- self.assertEqual(app.user.username, self.user.username)
-
-
-class TestApplicationViews(BaseTest):
- def _create_application(self, name, user):
- app = Application.objects.create(
- name=name,
- redirect_uris="http://example.com",
- client_type=Application.CLIENT_CONFIDENTIAL,
- authorization_grant_type=Application.GRANT_AUTHORIZATION_CODE,
- user=user,
- )
- return app
-
- def setUp(self):
- super(TestApplicationViews, self).setUp()
- self.app = self._create_application("app 1", self.user)
-
- def tearDown(self):
- super(TestApplicationViews, self).tearDown()
- self.app.delete()
-
- def test_application_list(self):
- self.client.login(username=self.user.username, password=self.user_password)
-
- response = self.client.get(reverse("users:developerapps_list"))
- self.assertEqual(response.status_code, 200)
- self.assertEqual(len(response.context["object_list"]), 1)
-
- def test_application_detail(self):
- self.client.login(username=self.user.username, password=self.user_password)
-
- response = self.client.get(
- reverse("users:developerapps_update", args=(self.app.pk,))
- )
- self.assertEqual(response.status_code, 200)
-
- def test_application_update(self):
- self.client.login(username=self.user.username, password=self.user_password)
-
- form_data = {
- "name": "Changed App",
- "client_id": "client_id",
- "client_secret": "client_secret",
- "client_type": Application.CLIENT_CONFIDENTIAL,
- "redirect_uris": "http://example.com",
- "authorization_grant_type": Application.GRANT_AUTHORIZATION_CODE,
- }
-
- response = self.client.post(
- reverse("users:developerapps_update", args=(self.app.pk,)), form_data
- )
- self.assertEqual(response.status_code, 302)
-
- app = Application.objects.get(name="Changed App")
- self.assertEqual(app.user.username, self.user.username)
diff --git a/neurovault/apps/users/tests/test_oauth.py b/neurovault/apps/users/tests/test_oauth.py
deleted file mode 100644
index 63741fa0..00000000
--- a/neurovault/apps/users/tests/test_oauth.py
+++ /dev/null
@@ -1,67 +0,0 @@
-from django.test import TestCase, Client
-from django.test.utils import override_settings
-from django.http import HttpResponse
-from django.urls import reverse, re_path, include
-
-from django.contrib.auth import get_user_model
-
-from rest_framework import permissions
-from rest_framework.views import APIView
-from oauth2_provider.contrib.rest_framework import OAuth2Authentication
-from oauth2_provider.models import AccessToken
-
-UserModel = get_user_model()
-
-
-class MockView(APIView):
- permission_classes = (permissions.IsAuthenticated,)
-
- def get(self, request):
- return HttpResponse({"a": 1, "b": 2, "c": 3})
-
-
-class OAuth2View(MockView):
- authentication_classes = [OAuth2Authentication]
-
-
-urlpatterns = [
- re_path(r"^oauth2/", include("oauth2_provider.urls")),
- re_path(r"^oauth2-test/$", OAuth2View.as_view()),
- re_path(r"^accounts/", include("neurovault.apps.users.urls")),
-]
-
-
-@override_settings(ROOT_URLCONF=__name__)
-class TestPersonalAccessTokens(TestCase):
- def setUp(self):
- self.user_password = "l0n6 l1v3 7h3 k1n6!"
- self.user = UserModel.objects.create_user(
- "bernardo", "bernardo@example.com", self.user_password
- )
- self.client = Client()
-
- def tearDown(self):
- self.user.delete()
-
- def _create_authorization_header(self, token):
- return "Bearer {0}".format(token)
-
- def test_authentication_empty(self):
- response = self.client.get("/oauth2-test/")
- self.assertEqual(response.status_code, 401)
-
- def test_authentication_denied(self):
- auth = self._create_authorization_header("fake-token")
- response = self.client.get("/oauth2-test/", HTTP_AUTHORIZATION=auth)
- self.assertEqual(response.status_code, 401)
-
- def test_authentication_allow(self):
- self.client.login(username=self.user, password=self.user_password)
- response = self.client.post(reverse("users:token_create"))
- self.assertEqual(response.status_code, 302)
-
- access_token = AccessToken.objects.get(user_id=self.user)
-
- auth = self._create_authorization_header(access_token)
- response = self.client.get("/oauth2-test/", HTTP_AUTHORIZATION=auth)
- self.assertEqual(response.status_code, 200)
diff --git a/neurovault/apps/users/tests/test_tokens.py b/neurovault/apps/users/tests/test_tokens.py
new file mode 100644
index 00000000..494d94ba
--- /dev/null
+++ b/neurovault/apps/users/tests/test_tokens.py
@@ -0,0 +1,64 @@
+from django.contrib.auth import get_user_model
+from django.test import TestCase
+from django.urls import reverse
+
+from rest_framework.authtoken.models import Token
+from rest_framework.test import APIClient, APITestCase
+from rest_framework import status
+
+UserModel = get_user_model()
+
+class BaseTest(TestCase):
+ def setUp(self):
+ self.user_password = "random"
+ self.user = UserModel.objects.create_user(
+ "neurouser", "neurouser@example.com", self.user_password
+ )
+
+ def tearDown(self):
+ self.user.delete()
+
+class TokenGenerationTest(BaseTest):
+ def test_token_list(self):
+ self.client.login(username=self.user.username, password=self.user_password)
+ response = self.client.get(reverse('users:token_list'))
+ self.assertEqual(response.status_code, 200)
+
+ def test_token_list_unauthorized(self):
+ response = self.client.get(reverse('users:token_list'))
+ self.assertEqual(response.status_code, 302)
+ self.assertEqual(response.url, "/accounts/login/?next=/accounts/token/")
+
+ def test_token_create(self):
+ self.client.login(username=self.user.username, password=self.user_password)
+ token = Token.objects.filter(user=self.user).first()
+ self.assertIsNone(token)
+
+ response = self.client.get(reverse('users:token_list'))
+ token = Token.objects.filter(user=self.user).first()
+ self.assertIsNotNone(Token)
+ self.assertEqual(response.status_code, 200)
+
+ response = self.client.get(reverse('users:token_create'))
+ new_token = Token.objects.filter(user=self.user).first()
+ self.assertNotEqual(token, new_token)
+
+ def test_token_create_unauthorized(self):
+ response = self.client.post(reverse('users:token_create'))
+ self.assertEqual(response.status_code, 302)
+ self.assertEqual(response.url, "/accounts/login/?next=/accounts/token/new")
+
+
+ def test_token_auth(self):
+ self.client.login(username=self.user.username, password=self.user_password)
+ self.client.get(reverse('users:token_list'))
+ token = Token.objects.filter(user=self.user).first()
+
+ client = APIClient()
+ client.credentials(HTTP_AUTHORIZATION='Token ' + token.key)
+ post_dict = {
+ "name": "Test Create Collection",
+ }
+ response = client.post("/api/collections/", post_dict)
+ self.assertEqual(response.status_code, status.HTTP_201_CREATED)
+ self.assertEqual(response.data["name"], post_dict["name"])
diff --git a/neurovault/apps/users/urls.py b/neurovault/apps/users/urls.py
index 29f34cb6..87e165c8 100644
--- a/neurovault/apps/users/urls.py
+++ b/neurovault/apps/users/urls.py
@@ -7,20 +7,10 @@
create_user,
password_change_done,
delete_profile,
+ view_token
)
from django.contrib.auth.views import LoginView, LogoutView
from django.contrib.auth import views as auth_views
-from oauth2_provider.views.application import ApplicationList
-from .views import (
- ApplicationRegistration,
- ApplicationUpdate,
- ApplicationDelete,
- ConnectionList,
- ConnectionDelete,
- PersonalTokenList,
- PersonalTokenCreate,
- PersonalTokenDelete,
-)
admin.autodiscover()
@@ -69,35 +59,8 @@
re_path(r"^profile/edit$", edit_user, name="edit_user"),
re_path(r"^profile/delete$", delete_profile, name="delete_profile"),
re_path(r"^profile/.*$", view_profile, name="my_profile"),
- re_path(r"^tokens/$", PersonalTokenList.as_view(), name="token_list"),
- re_path(r"^tokens/new$", PersonalTokenCreate.as_view(), name="token_create"),
- re_path(
- r"^tokens/(?P\d+)/delete/$",
- PersonalTokenDelete.as_view(),
- name="token_delete",
- ),
- re_path(r"^connections/$", ConnectionList.as_view(), name="connection_list"),
- re_path(
- r"^connections/(?P\d+)/revoke/$",
- ConnectionDelete.as_view(),
- name="connection_revoke",
- ),
- re_path(r"^applications/$", ApplicationList.as_view(), name="developerapps_list"),
- re_path(
- r"^applications/register/$",
- ApplicationRegistration.as_view(),
- name="developerapps_register",
- ),
- re_path(
- r"^applications/(?P\d+)/$",
- ApplicationUpdate.as_view(),
- name="developerapps_update",
- ),
- re_path(
- r"^applications/(?P\d+)/delete/$",
- ApplicationDelete.as_view(),
- name="developerapps_delete",
- ),
+ re_path(r"^token/$", view_token, {'regenerate': False}, name="token_list"),
+ re_path(r"^token/new$", view_token, {'regenerate': True}, name="token_create"),
re_path(r"^(?P[A-Za-z0-9@/./+/-/_]+)/$", view_profile, name="profile"),
]
diff --git a/neurovault/apps/users/views.py b/neurovault/apps/users/views.py
index f82e8708..94b15dec 100644
--- a/neurovault/apps/users/views.py
+++ b/neurovault/apps/users/views.py
@@ -12,11 +12,13 @@
from django.utils.crypto import get_random_string
from django.views.generic import View, CreateView, UpdateView, DeleteView, ListView
+
from braces.views import LoginRequiredMixin
-from oauth2_provider.views.application import ApplicationOwnerIsUserMixin
-from oauth2_provider.models import RefreshToken, AccessToken, Application
+from rest_framework.authtoken.models import Token
+from rest_framework.decorators import api_view, permission_classes
+from rest_framework.permissions import IsAuthenticated
-from .forms import UserEditForm, UserCreateForm, ApplicationEditForm
+from .forms import UserEditForm, UserCreateForm
def view_profile(request, username=None):
@@ -80,155 +82,15 @@ def password_change_done(request):
return HttpResponseRedirect(reverse("users:password_change"))
-
-# def login(request):
-# return render(request, 'home.html', {
-# 'plus_id': getattr(settings, 'SOCIAL_AUTH_GOOGLE_PLUS_KEY', None)
-# }, RequestContext(request))
-
-
-class PersonalTokenUserIsRequestUserMixin(LoginRequiredMixin):
-
- """
- This mixin is used to provide an Connection queryset filtered by the
- current request.user.
- """
-
- fields = "__all__"
-
- def get_queryset(self):
- return AccessToken.objects.filter(
- user=self.request.user, application_id=settings.DEFAULT_OAUTH_APPLICATION_ID
- )
-
-
-class PersonalTokenList(PersonalTokenUserIsRequestUserMixin, ListView):
- model = AccessToken
- template_name = "oauth2_provider/personal_token_list.html"
-
-
-class PersonalTokenCreate(LoginRequiredMixin, View):
- def post(self, request, *args, **kwargs):
- application = Application.objects.get(pk=settings.DEFAULT_OAUTH_APPLICATION_ID)
- AccessToken.objects.create(
- user=self.request.user,
- token=get_random_string(length=settings.OAUTH_PERSONAL_TOKEN_LENGTH),
- application=application,
- expires=datetime.date(datetime.MAXYEAR, 12, 30),
- scope="read write",
- )
- messages.success(self.request, "The new token has been successfully generated.")
-
- return HttpResponseRedirect(reverse("users:token_list"))
-
-
-class PersonalTokenDelete(PersonalTokenUserIsRequestUserMixin, DeleteView):
- template_name = "oauth2_provider/personal_token_confirm_delete.html"
- success_url = reverse_lazy("users:token_list")
- success_message = "The token has been successfully deleted."
-
- def delete(self, request, *args, **kwargs):
- self.object = self.get_object()
- success_url = self.get_success_url()
- self.object.revoke()
- messages.success(self.request, self.success_message)
-
- return HttpResponseRedirect(success_url)
-
-
-class ApplicationRegistration(LoginRequiredMixin, CreateView):
-
- """
- View used to register a new Application for the request.user
- """
-
- form_class = ApplicationEditForm
- template_name = "oauth2_provider/application_registration_form.html"
-
- def get_success_url(self):
- return reverse("users:developerapps_list")
-
- def form_valid(self, form):
- form.instance.user = self.request.user
- messages.success(
- self.request, "The application has been successfully registered."
- )
-
- return super(ApplicationRegistration, self).form_valid(form)
-
-
-class ApplicationUpdate(ApplicationOwnerIsUserMixin, UpdateView):
-
- """
- View used to update an application owned by the request.user
- """
-
- context_object_name = "application"
- template_name = "oauth2_provider/application_form.html"
-
- # Reset the inherited fields attribute and use a form_class instead
- fields = None
- form_class = ApplicationEditForm
-
- def get_success_url(self):
- return reverse("users:developerapps_list")
-
- def form_valid(self, form):
- messages.success(self.request, "The application has been successfully updated.")
- return super(ApplicationUpdate, self).form_valid(form)
-
-
-class ApplicationDelete(ApplicationOwnerIsUserMixin, DeleteView):
-
- """
- View used to delete an application owned by the request.user
- """
-
- context_object_name = "application"
- success_url = reverse_lazy("users:developerapps_list")
- template_name = "oauth2_provider/application_confirm_delete.html"
- success_message = "The application has been successfully deleted."
-
- def delete(self, request, *args, **kwargs):
- messages.success(self.request, self.success_message)
- return super(ApplicationDelete, self).delete(request, *args, **kwargs)
-
-
-class ConnectionList(LoginRequiredMixin, ListView):
- template_name = "oauth2_provider/connection_list.html"
-
- def get_queryset(self):
- return RefreshToken.objects.filter(user=self.request.user).distinct(
- "application"
- )
-
-
-class ConnectionDelete(LoginRequiredMixin, DeleteView):
- template_name = "oauth2_provider/connection_confirm_delete.html"
- success_url = reverse_lazy("connection_list")
- success_message = "The application authorization has been successfully " "revoked."
-
- def _refresh_token_queryset(self, user, application_id):
- return RefreshToken.objects.filter(user=user, application_id=application_id)
-
- def get_object(self):
- pk = self.kwargs.get(self.pk_url_kwarg)
-
- refresh_token = self._refresh_token_queryset(self.request.user, pk).first()
- if not refresh_token:
- raise Http404("No application connection found.")
-
- return refresh_token.application
-
- def delete(self, request, *args, **kwargs):
- self.object = self.get_object()
- success_url = self.get_success_url()
-
- token_list = self._refresh_token_queryset(self.request.user, self.object.id)
-
- for refresh_token in token_list:
- refresh_token.revoke()
-
- messages.success(self.request, self.success_message)
-
- return HttpResponseRedirect(success_url)
+@login_required
+def view_token(request, regenerate=False):
+ if regenerate:
+ try:
+ old_token = Token.objects.get(user=request.user)
+ old_token.delete()
+ except Token.DoesNotExist:
+ pass
+ token = Token.objects.create(user=request.user)
+ else:
+ token, _ = Token.objects.get_or_create(user=request.user)
+ return render(request, 'show_token.html', {'token': token.key})
diff --git a/neurovault/settings.py b/neurovault/settings.py
index 620eb687..3d45e3d0 100644
--- a/neurovault/settings.py
+++ b/neurovault/settings.py
@@ -155,13 +155,13 @@
"django.contrib.admin",
"social_django",
"rest_framework",
+ "rest_framework.authtoken",
"taggit",
"crispy_forms",
"polymorphic",
"django_cleanup",
"file_resubmit",
"guardian",
- "oauth2_provider",
"django_celery_results",
]
@@ -208,7 +208,7 @@
"rest_framework.permissions.DjangoModelPermissionsOrAnonReadOnly"
],
"DEFAULT_AUTHENTICATION_CLASSES": (
- "oauth2_provider.contrib.rest_framework.OAuth2Authentication",
+ "rest_framework.authentication.TokenAuthentication",
),
"DEFAULT_RENDERER_CLASSES": (
"neurovault.api.utils.ExplicitUnicodeJSONRenderer",
@@ -218,7 +218,6 @@
"UNICODE_JSON": True,
}
-OAUTH2_PROVIDER = {"REQUEST_APPROVAL_PROMPT": "auto"}
LOGIN_REDIRECT_URL = "/my_collections/"
# LOGIN_URL = '/login-form/'
@@ -249,10 +248,6 @@
if os.path.exists("/usr/local/share/pycortex/db/fsaverage"):
STATICFILES_DIRS = (
- (
- "pycortex-resources",
- "/usr/local/lib/python2.7/site-packages/cortex/webgl/resources",
- ),
("pycortex-ctmcache", "/usr/local/share/pycortex/db/fsaverage/cache"),
)
@@ -281,12 +276,6 @@
ANONYMOUS_USER_ID = -1
-DEFAULT_OAUTH_APPLICATION_ID = -1
-DEFAULT_OAUTH_APP_NAME = "DefaultOAuthApp"
-DEFAULT_OAUTH_APP_OWNER_ID = -2
-DEFAULT_OAUTH_APP_OWNER_USERNAME = "DefaultAppOwner"
-OAUTH_PERSONAL_TOKEN_LENGTH = 40
-
# Bogus secret key.
try:
from secrets import *
diff --git a/neurovault/urls.py b/neurovault/urls.py
index 7da1bef4..7c8360d1 100644
--- a/neurovault/urls.py
+++ b/neurovault/urls.py
@@ -18,17 +18,6 @@
"CognitiveAtlasTasks": CognitiveAtlasTaskSitemap,
}
-""" Do these need to live outside o/* oauth urls included below?
-oauth_urlpatterns = [
- re_path(r'^authorize/$', oauth_view.AuthorizationView.as_view(),
- name="authorize"),
- re_path(r'^token/$', oauth_view.TokenView.as_view(),
- name="token"),
- re_path(r'^revoke_token/$', oauth_view.RevokeTokenView.as_view(),
- name="revoke-token"),
-]
-"""
-
urlpatterns = [
re_path("", include("social_django.urls", namespace="social")),
re_path(r"^", include("neurovault.apps.main.urls")),
@@ -39,5 +28,4 @@
re_path(r"^api-auth/", include("rest_framework.urls", namespace="rest_framework")),
re_path(r"^sitemap\.xml$", index, {"sitemaps": sitemaps}),
re_path(r"^sitemap-(?P.+)\.xml$", sitemap, {"sitemaps": sitemaps}),
- path("o/", include("oauth2_provider.urls", namespace="oauth2_provider")),
]
diff --git a/production.yml b/production.yml
index dd11bc02..d01f8056 100644
--- a/production.yml
+++ b/production.yml
@@ -5,10 +5,10 @@ volumes:
services:
django:
restart: always
- image: neurovault/neurovault_fs
+ image: neurovault/neurovault
build:
context: .
- dockerfile: ./compose/django/Dockerfile_fs
+ dockerfile: ./compose/django/Dockerfile
command: ./compose/django/prod_start
ports:
- "5000:5000"
diff --git a/scripts/preparing_AHBA_data.py b/scripts/preparing_AHBA_data.py
new file mode 100644
index 00000000..0fa4bb9c
--- /dev/null
+++ b/scripts/preparing_AHBA_data.py
@@ -0,0 +1,139 @@
+'''
+
+Requirements from old dockerfile:
+
+RUN apt-get update && apt-get install -y \
+ libhdf5-dev \
+ libhdf5-8 && \
+ apt-get clean autoclean
+
+RUN pip install numpy==1.11.0
+RUN pip install nibabel \
+ tables==3.3.0 \
+ h5py==2.6.0 \
+ pandas==0.20.3 \
+ pybraincompare==0.1.18
+
+'''
+import urllib.request, urllib.parse, urllib.error
+import zipfile
+import os
+import numpy as np
+import nibabel as nb
+import numpy.linalg as npl
+import pandas as pd
+from pybraincompare.mr.datasets import get_standard_mask
+
+# Downloading microarray data
+urls = ["http://human.brain-map.org/api/v2/well_known_file_download/178238387",
+ "http://human.brain-map.org/api/v2/well_known_file_download/178238373",
+ "http://human.brain-map.org/api/v2/well_known_file_download/178238359",
+ "http://human.brain-map.org/api/v2/well_known_file_download/178238316",
+ "http://human.brain-map.org/api/v2/well_known_file_download/178238266",
+ "http://human.brain-map.org/api/v2/well_known_file_download/178236545"]
+
+donor_ids = [""]
+download_dir = "/ahba_data"
+os.makedirs(download_dir)
+
+for i, url in enumerate(urls):
+ print("Downloading %s" % url)
+ urllib.request.urlretrieve(url, os.path.join(download_dir, "donor%d.zip" % (i + 1)))
+ zipfile.ZipFile(os.path.join(download_dir, "donor%d.zip" % (i + 1)))
+
+# Dowloading MNI coordinates
+urllib.request.urlretrieve(
+ "https://raw.githubusercontent.com/chrisfilo/alleninf/master/alleninf/data/corrected_mni_coordinates.csv",
+ os.path.join(download_dir, "corrected_mni_coordinates.csv"))
+
+samples = pd.read_csv(os.path.join(download_dir, "corrected_mni_coordinates.csv"), index_col=0)
+
+mni = get_standard_mask(voxdim=4)
+
+reduced_coord = []
+
+for coord_mni in samples[['corrected_mni_x', 'corrected_mni_y', 'corrected_mni_z']].values:
+ sample_counts = np.zeros(mni.shape, dtype=int)
+ coord_data = [int(round(i)) for i in nb.affines.apply_affine(npl.inv(mni.get_affine()), coord_mni)]
+ sample_counts[coord_data[0],
+ coord_data[1],
+ coord_data[2]] = 1
+ out_vector = sample_counts[mni.get_data()!=0]
+ idx = out_vector.argmax()
+ if idx == (out_vector == 1.0).sum() == 0:
+ idx = np.nan
+ reduced_coord.append(idx)
+
+samples["reduced_coordinate"] = reduced_coord
+
+#Downloading gene selections list
+urllib.request.urlretrieve(
+ "http://science.sciencemag.org/highwire/filestream/631209/field_highwire_adjunct_files/2/Richiardi_Data_File_S2.xlsx",
+ os.path.join(download_dir, "Richiardi_Data_File_S2.xlsx"))
+
+donors = ["H0351.2001", "H0351.2002", "H0351.1009", "H0351.1012", "H0351.1015", "H0351.1016"]
+
+with zipfile.ZipFile(os.path.join(download_dir, "donor1.zip")) as z:
+ with z.open("Probes.csv") as f:
+ probe_info_df = pd.read_csv(f, index_col=0)
+
+# concatenating data from all donors
+dfs = []
+for i, donor_id in enumerate(donors):
+ with zipfile.ZipFile(os.path.join(download_dir, "donor%d.zip" % (i + 1))) as z:
+ with z.open("MicroarrayExpression.csv") as f:
+ df = pd.read_csv(f, header=None, index_col=0)
+
+ # Dropping probes without entrez_id
+ df.drop(probe_info_df.index[probe_info_df['entrez_id'].isnull()], inplace=True)
+
+ with z.open("SampleAnnot.csv") as f:
+ sample_annot_df = pd.read_csv(f, index_col="well_id").join(samples, how="inner")
+
+ df.columns = list(sample_annot_df["reduced_coordinate"])
+ # removing out side of the brain coordinates
+ df.drop(sample_annot_df.index[sample_annot_df.reduced_coordinate.isnull()], axis=1, inplace=True)
+ # averaging measurements from similar locations
+ df = df.groupby(level=0, axis=1).mean()
+
+ df.columns = pd.MultiIndex.from_tuples([(donor_id, c,) for c in list(df.columns)],
+ names=['donor_id', 'reduced_coordinate'])
+ dfs.append(df)
+
+expression_data = pd.concat(dfs, copy=False, axis=1)
+del dfs
+
+probe_info_df.drop(probe_info_df.index[probe_info_df['entrez_id'].isnull()], inplace=True)
+
+multiindex = []
+for index in expression_data.index:
+ entrez_id = int(probe_info_df.loc[index]["entrez_id"])
+ multiindex.append((entrez_id, index,))
+expression_data.index = pd.MultiIndex.from_tuples(multiindex, names=['entrez_id', 'probe_id'])
+
+means = expression_data.mean(axis=1)
+idx_maxs = means.groupby(level=0).idxmax()
+expression_data = expression_data.reindex(idx_maxs)
+
+expression_data.index = expression_data.index.droplevel(1)
+
+multiindex = []
+for index in probe_info_df.index:
+ entrez_id = int(probe_info_df.loc[index]["entrez_id"])
+ multiindex.append((entrez_id, index,))
+probe_info_df.index = pd.MultiIndex.from_tuples(multiindex, names=['entrez_id', 'probe_id'])
+probe_info_df = probe_info_df.reindex(idx_maxs)
+probe_info_df.index = probe_info_df.index.droplevel(1)
+probe_info_df.to_csv(os.path.join(download_dir, 'probe_info_max1.csv'))
+
+assert (expression_data.index[0] in list(probe_info_df.index))
+assert (expression_data.shape == (20787, 3072))
+
+with pd.HDFStore(os.path.join(download_dir, 'store_max1_reduced.h5'), 'w') as store:
+ for donor_id in donors:
+ store.append(donor_id.replace(".", "_"), expression_data[donor_id])
+
+# Removing downloaded files
+for i, url in enumerate(urls):
+ os.remove(os.path.join(download_dir, "donor%d.zip" % (i + 1)))
+
diff --git a/scripts/subcortex_drewUpdated.nii.gz b/scripts/subcortex_drewUpdated.nii.gz
new file mode 100644
index 00000000..d7cda4a0
Binary files /dev/null and b/scripts/subcortex_drewUpdated.nii.gz differ
diff --git a/scripts/subcortex_mask.npy b/scripts/subcortex_mask.npy
new file mode 100644
index 00000000..80b48cbe
Binary files /dev/null and b/scripts/subcortex_mask.npy differ