Merge branch 'develop' into 470-notif-user-loop

.gitignore

@@ -164,7 +164,8 @@ fabric.properties
 elixir_daisy/settings_local.py
 static/css/*
 web/static/vendor/node_modules/*
-
+web/static/js/*.bundle.js
+web/static/js/*.bundle.js.LICENSE.txt
 
 
 /log/*.log

.pre-commit-config.yaml

@@ -4,3 +4,13 @@ repos:
     hooks:
       - id: black
         language_version: python3
+  - repo: https://github.com/pre-commit/mirrors-eslint
+    rev: v8.15.0
+    hooks:
+      - id: eslint
+        files: web/static/vendor/(components|tests)/.*\.[jt]sx?$
+        types: [file]
+        additional_dependencies:
+          - eslint@8.15.0
+          - eslint-plugin-react@7.29.4
+          - eslint-plugin-react-hooks@4.6.0

DEPLOYMENT.md

@@ -36,8 +36,11 @@ sudo /usr/local/bin/pip3.9 install gunicorn
 ## NPM and Node.js
 
 ```bash
-curl -sL https://rpm.nodesource.com/setup_16.x | sudo bash -
-sudo yum install nodejs
+apt-get update && apt-get install -y ca-certificates curl gnupg
+mkdir -p /etc/apt/keyrings
+curl -fsSL https://deb.nodesource.com/gpgkey/nodesource-repo.gpg.key | gpg --dearmor -o /etc/apt/keyrings/nodesource.gpg
+echo "deb [signed-by=/etc/apt/keyrings/nodesource.gpg] https://deb.nodesource.com/node_18.x nodistro main" | tee /etc/apt/sources.list.d/nodesource.list
+apt-get update && apt-get install -y nodejs
 ```
 
 Then you need to compile the static files.

README.md

@@ -53,6 +53,9 @@ You are encouraged to try Daisy for yourself using our [DEMO deployment](https:/
 1. Compile and deploy static files
 
     ```bash
+    cd web/static/vendor
+    npm run build
+    cd ../../../
     docker-compose exec web python manage.py collectstatic
     ```
 1. Create initial data in the database
@@ -224,7 +227,7 @@ cd web/static/vendor/
 npm ci
 ```
 
-### Compile daisy.scss
+### Compile daisy.scss and React
 ```bash
 cd web/static/vendor
 npm run-script build

conftest.py

@@ -141,6 +141,26 @@ def user_data_steward(django_user_model):
     return u
 
 
+@pytest.fixture
+def user_legal(django_user_model):
+    u = django_user_model.objects.create_user(
+        username="user.legal", password="password", email="legal@email.com"
+    )
+    g, _ = Group.objects.get_or_create(name=GroupConstants.LEGAL.value)
+    u.groups.add(g)
+    return u
+
+
+@pytest.fixture
+def user_auditor(django_user_model):
+    u = django_user_model.objects.create_user(
+        username="user.auditor", password="password", email="auditor@email.com"
+    )
+    g, _ = Group.objects.get_or_create(name=GroupConstants.AUDITOR.value)
+    u.groups.add(g)
+    return u
+
+
 @pytest.fixture
 def user_admin(django_user_model):
     u = django_user_model.objects.create_superuser(

core/forms/__init__.py

@@ -11,6 +11,7 @@
     DataDeclarationSubFormFromExisting,
 )
 from .document import DocumentForm
+from .project import ProjectForm
 from .partner import PartnerForm
 from .permission import UserPermFormSet
 from .legal_basis import LegalBasisForm
@@ -35,6 +36,7 @@
     "PartnerForm",
     "LegalBasisForm",
     "PartnerRoleForm",
+    "ProjectForm",
     "UserPermFormSet",
     "PublicationForm",
     "ShareForm",

core/forms/dataset.py

@@ -53,10 +53,13 @@ class Meta:
         heading_help = "Provide basic information for the new dataset."
 
     def __init__(self, *args, **kwargs):
-        dataset = None
-        if "dataset" in kwargs:
-            dataset = kwargs.pop("dataset")
+        kwargs.pop("dataset", None)
+        keep_metadata = kwargs.pop("keep_metadata_field", False)
+
         super().__init__(*args, **kwargs)
+        if not keep_metadata:
+            del self.fields["scientific_metadata"]
+
         self.fields["local_custodians"].queryset = User.objects.exclude(
             username="AnonymousUser"
         )

core/forms/importer.py

@@ -0,0 +1,5 @@
+from django import forms
+
+
+class ImportForm(forms.Form):
+    file = forms.FileField(required=True, label="Choose File")

core/forms/project.py

@@ -51,7 +51,10 @@ class Meta:
 
     def __init__(self, *args, **kwargs):
         kwargs["label_suffix"] = ""
+        keep_metadata_field = kwargs.pop("keep_metadata_field", False)
         super().__init__(*args, **kwargs)
+        if not keep_metadata_field:
+            del self.fields["scientific_metadata"]
         instance = kwargs.get("instance", None)
 
         if "data" not in kwargs:

core/models/contract.py

@@ -1,5 +1,6 @@
 from django.contrib.contenttypes.fields import GenericRelation
 from django.db import models
+from django.urls import reverse
 
 from core import constants
 from core.permissions.mapping import PERMISSION_MAPPING
@@ -118,6 +119,8 @@ class AppMeta:
     )
 
     # metadata = JSONField(null=True, blank=True, default=dict)
+    def get_absolute_url(self):
+        return reverse("contract", args=[str(self.pk)])
 
     def add_partner_with_role(self, partner, role, contact=None):
         partner_role = self.partners_roles.create(partner=partner)

core/models/data_declaration.py

@@ -1,6 +1,7 @@
 import uuid
 
 from django.db import models
+from django.urls import reverse
 from enumchoicefield import EnumChoiceField, ChoiceEnum
 
 from core import constants
@@ -217,6 +218,9 @@ class Meta:
         help_text="This is the unique identifier used by DAISY for this dataset. This field annot be edited.",
     )
 
+    def get_absolute_url(self):
+        return reverse("data_declaration", args=[str(self.pk)])
+
     def copy(
         self, source_data_declaration, excluded_fields=None, ignore_many_to_many=False
     ):

core/models/project.py

@@ -8,6 +8,7 @@
 from django.contrib.auth import get_user_model
 from django.db import models
 from django.db.models import Q
+from django.urls import reverse
 from django.utils.safestring import mark_safe
 from django.utils.module_loading import import_string
 from guardian.models import GroupObjectPermissionBase, UserObjectPermissionBase
@@ -219,6 +220,9 @@ class AppMeta:
     def __str__(self):
         return self.acronym or self.title or "undefined"
 
+    def get_absolute_url(self):
+        return reverse("project", args=[str(self.pk)])
+
     @property
     def is_published(self):
         return any(dataset.is_published for dataset in self.datasets.all())

core/models/user.py

@@ -160,6 +160,9 @@ def is_part_of(self, *args):
     def can_publish(self):
         return self.is_superuser or self.is_part_of(constants.Groups.DATA_STEWARD.value)
 
+    def can_edit_metadata(self):
+        return self.is_part_of(constants.Groups.DATA_STEWARD.value)
+
     # Permission management
     # ======================================================================
 

data/demo/elu-core.json

@@ -0,0 +1,84 @@
+{
+  "$id": "https://raw.githubusercontent.com/elixir-luxembourg/json-schemas/v0.0.5/schemas/elu-core.json",
+  "title": "ELIXIR Luxembourg Core json schema",
+  "description": "Schema containing core attributes for any json serialisable ELIXIR Luxembourg record.",
+  "$schema": "http://json-schema.org/draft-04/schema#",
+  "type": "object",
+  "required": [
+    "source",
+    "name"
+  ],
+  "properties": {
+    "source": {
+      "type": "string",
+      "format": "uri"
+    },
+    "acronym": {
+      "type": ["string", "null"]
+    },
+    "name": {
+      "type": "string"
+    },
+    "description": {
+      "type":  ["string", "null"]
+    },
+    "external_id": {
+      "type": ["string", "null"]
+    },
+    "elu_uuid": {
+      "type": ["string", "null"]
+    },
+    "other_external_id": {
+      "type": ["string", "null"]
+    },
+    "url": {
+      "type":  ["string", "null"]
+    },
+    "contacts": {
+      "type": "array",
+      "items": {
+        "type": "object",
+        "properties": {
+          "first_name": {
+            "type": "string"
+          },
+          "last_name": {
+            "type": "string"
+          },
+          "role": {
+            "type": "string",
+            "enum": [
+              "Principal_Investigator",
+              "Researcher",
+              "Data_Manager",
+              "Data_Protection_Officer",
+              "Legal_Representative",
+              "Other"
+            ]
+          },
+          "email": {
+            "type": "string",
+            "format": "email"
+          },
+          "affiliations": {
+            "description": "Names of the affiliated institutions.",
+            "type": "array",
+            "minItems": 1,
+            "uniqueItems": true,
+            "items": {
+              "type": ["string", "null"]
+            }
+          }
+        },
+        "required": [
+          "first_name",
+          "last_name",
+          "role",
+          "email",
+          "affiliations"
+        ]
+      }
+    }
+  }
+}
+

data/demo/partners.json

@@ -0,0 +1,26 @@
+{
+    "items": [
+        {
+            "name": "Centre Hospitalier de Togo",
+            "external_id": "ELU_I_19309",
+            "acronym": "CHT",
+            "is_clinical": true,
+            "geo_category": "National",
+            "sector_category": "PUBLIC",
+            "address": "Ave De La 6, Espoir Vie Togo, Lome",
+            "country_code": "TO",
+            "source": "example.com"
+        },
+        {
+            "name": "Hospitalier de Madagascar",
+            "external_id": "ELU_I_1939",
+            "acronym": "HMDGSK",
+            "is_clinical": true,
+            "geo_category": "National",
+            "sector_category": "PUBLIC",
+            "address": "Ave De La 6, Espoir Vie Togo, Antananarivo",
+            "country_code": "MG",
+            "source": "example.com"
+        }
+    ]
+}

docker-compose.yaml

@@ -20,7 +20,7 @@ services:
     # database
     db:
         image: postgres:10.1
-        restart: always
+        restart: on-failure
         environment:
             POSTGRES_PASSWORD: daisy
             POSTGRES_USER: daisy
@@ -32,7 +32,7 @@ services:
     # web werver frontend
     nginx:
         build: ./docker/nginx
-        restart: always
+        restart: on-failure
         volumes:
             - statics:/public/static:ro
         ports:
@@ -50,7 +50,7 @@ services:
      # rabbit mq
     mq:
         image: rabbitmq:3.9-management-alpine
-        restart: "always"
+        restart: on-failure
         ports:
             - "15672:15672"
             - "5672:5672"

elixir_daisy/settings.py

@@ -95,6 +95,7 @@
                 "django.contrib.messages.context_processors.messages",
                 "web.views.context_processors.daisy_version",
                 "web.views.context_processors.instance_branding",
+                "notification.views.context_processors.daisy_notifications_enabled",
             ],
         },
     },

elixir_daisy/settings_local.template.py

@@ -23,6 +23,7 @@
 COMPANY = "LCSB"  # Used for generating some models' verbose names
 
 HELPDESK_EMAIL = "lcsb-sysadmins@uni.lu"
+ADMIN_NOTIFICATIONS_EMAIL = ""  # used when there are notifications errors
 
 # Placeholders on login page
 # LOGIN_USERNAME_PLACEHOLDER = ''
@@ -79,6 +80,11 @@
 # KEYCLOAK_USER = 'your service user for daisy'
 # KEYCLOAK_PASS = 'the password for the service user'
 
+# Email related setting
+EMAIL_HOST = ""
+EMAIL_PORT = 25
+EMAIL_SENDER = ""
+
 # Celery beat setting to schedule tasks on docker creation
 CELERY_BEAT_SCHEDULE = {
     "clean-accesses-every-day": {
@@ -87,6 +93,10 @@
     },
     "create-notifications-every-day": {
         "task": "notification.tasks.create_notifications_for_entities",
-        "schedule": crontab(minute=15, hour=0),
+        "schedule": crontab(minute=15, hour=0)
+    },
+    "notifications-email-every-day": {
+        "task": "notification.tasks.send_notifications_for_user_upcoming_events",
+        "schedule": crontab(minute=0, hour=7),  # Execute task in the morning
     },
 }

elixir_daisy/urls.py

@@ -22,6 +22,7 @@
 
 from core.forms.user import UserAuthForm
 from web.urls import web_urls
+from notification.urls import notif_urls
 
 urlpatterns = [
     url(
@@ -31,6 +32,7 @@
     ),
     url(r"^logout/$", auth_views.LogoutView.as_view(), name="logout"),
     url(r"^admin/", admin.site.urls),
+    url(r"^notifications/", include(notif_urls)),
     url(r"", include(web_urls)),
 ]