Add researcher and study import

VRE/apps/researcher/admin.py

@@ -1,14 +1,17 @@
 from django.contrib import admin
 
 from .models import Researcher
+from lib.models.admin import JSONImportMixin
 
 
 @admin.register(Researcher)
-class ResearcherAdmin(admin.ModelAdmin):
+class ResearcherAdmin(JSONImportMixin, admin.ModelAdmin):
     list_display = ('user', 'last_name', 'faculty')
     ordering = ('user', )
     search_fields = ('user__username', 'user__first_name', 'user__last_name')
     readonly_fields = ('created_at', 'updated_at', 'last_name')
+    change_list_template = 'admin/import_change_list.html'
+    import_type = 'researcher'
 
     def last_name(self, obj):
         return obj.user.last_name

VRE/apps/researcher/management/commands/import_researchers.py

@@ -0,0 +1,74 @@
+from django.core.management.base import BaseCommand, CommandError, no_translations
+from django.contrib.auth.models import User
+
+import json
+from pathlib import Path
+
+
+class Command(BaseCommand):
+    help = '''Import researchers from external data source
+
+    Valid JSON schema is:
+
+    {
+        'email_address' :'',
+        'first_name': '',
+        'last_name' : '',
+        'mobile': '',
+        'pmunber' :''
+    }
+    '''
+
+    def add_arguments(self, parser):
+        parser.add_argument('import_file', help='JSON Import file with researchers')
+
+    @no_translations
+    def handle(self, *args, **options):
+        if options.get('import_file'):
+
+            import_file = Path(options.get("import_file"))
+            if not import_file.exists():
+                raise CommandError('Import file "%s" does not exists' % (import_file,))
+
+            try:
+                researchers_list = json.loads(import_file.read_text())
+            except json.JSONDecodeError:
+                raise CommandError('Could not read file "%s" data is not a valid JSON file' % (import_file,))
+
+            self.stdout.write(f'Start importing file: {import_file}')
+
+            import_counter = 0
+            for researcher_data in researchers_list:
+                if 'email_address' not in researcher_data or 'first_name' not in researcher_data or 'last_name' not in researcher_data:
+                    self.stdout.write(self.style.ERROR('Skip import line due to wrong data...'))
+                    continue
+
+                user, created = User.objects.get_or_create(email=researcher_data['email_address'],
+                                                           defaults={
+                    'username': researcher_data['email_address'],
+                    'first_name': researcher_data['first_name'],
+                    'last_name': researcher_data['last_name'],
+                    'is_active': True}
+                )
+
+                if created:
+                    user.set_unusable_password()
+                    user.save()
+
+                update_researcher = False
+                if '' == user.researcher.mobilephone and 'mobile' in researcher_data and '' != researcher_data['mobile']:
+                    user.researcher.mobilephone = researcher_data['mobile']
+                    update_researcher = True
+
+                if '' == user.researcher.idnumber and 'pnumber' in researcher_data and '' != researcher_data['pnumber']:
+                    user.researcher.idnumber = researcher_data['pnumber']
+                    update_researcher = True
+
+                if update_researcher:
+                    user.researcher.save()
+
+                import_counter += 1
+
+                self.stdout.write(self.style.SUCCESS(f'Researcher {user.researcher.display_name} {"is created" if created else "does already exists"}'))
+
+            self.stdout.write(f'Done importing file: {import_file}, {import_counter} entries ok!')

VRE/apps/study/admin.py

@@ -2,6 +2,8 @@ from django.contrib import admin
 from django.template.defaultfilters import filesizeformat
 
 from .models import Study, StudyRole
+from lib.models.admin import JSONImportMixin
+
 
 # Register your models here.
 admin.site.register(StudyRole)
@@ -13,7 +15,7 @@ class role_inline(admin.TabularInline):
 
 
 @admin.register(Study)
-class StudyAdmin(admin.ModelAdmin):
+class StudyAdmin(JSONImportMixin, admin.ModelAdmin):
     inlines = (role_inline,)
 
     list_display = ('name', 'total_files', 'total_file_size', 'total_invitations', 'created_at')
@@ -21,5 +23,8 @@ class StudyAdmin(admin.ModelAdmin):
     search_fields = ('name', )
     readonly_fields = ('upload_uuid', 'api_upload_url', 'total_files', 'total_file_size', 'total_invitations', 'created_at', 'updated_at')
 
+    change_list_template = 'admin/import_change_list.html'
+    import_type = 'study'
+
     def total_file_size(self, obj):
         return filesizeformat(obj.total_file_size)

VRE/apps/study/management/commands/import_studies.py

@@ -0,0 +1,86 @@
+from django.core.management.base import BaseCommand, CommandError, no_translations
+from django.contrib.auth.models import User
+from apps.researcher.models import Researcher
+
+from apps.study.models import Study, StudyRole
+
+import json
+from pathlib import Path
+
+
+class Command(BaseCommand):
+    help = '''Import studies from external data source
+
+    Valid JSON schema is:
+
+    {
+        'email_address' :'',
+        'first_name': '',
+        'last_name' : '',
+        'mobile': '',
+        'pmunber' :''
+    }
+    '''
+
+    def add_arguments(self, parser):
+        parser.add_argument('import_file', help='JSON Import file with researchers')
+
+    @no_translations
+    def handle(self, *args, **options):
+        if options.get('import_file'):
+            import_file = Path(options.get("import_file"))
+            if not import_file.exists():
+                raise CommandError('Import file "%s" does not exists' % (import_file,))
+
+            self.stdout.write(f'Start importing file: {import_file}')
+            try:
+                studies_list = json.loads(import_file.read_text())
+            except json.JSONDecodeError:
+                raise CommandError('Could not read file "%s" data is not a valid JSON file' % (import_file,))
+
+            import_counter = 0
+            for study_data in studies_list:
+                if 'name' not in study_data or 'description' not in study_data or 'code' not in study_data or 'contributors' not in study_data:
+                    self.stdout.write(self.style.ERROR('Skip import line due to wrong data...'))
+                    continue
+
+                # Determen the owner.... For now, the first admin role will do
+                Owner = None
+                for role in study_data['contributors']:
+                    if 'Administrator' == role['role']:
+                        Owner = User.objects.get(email=role['uid']).researcher
+
+                if Owner is None:
+                    self.stdout.write(self.style.ERROR(f'Study {study.name} cannot be created as there is no owner defined (Administrator)'))
+                    continue
+
+                # TODO: Or do we match on study code field??? Not sure if that data is available and correct in the LDAP
+                study, created = Study.objects.get_or_create(name=study_data['name'],
+                                                             defaults={
+                    'description': study_data['description'],
+                    'code': study_data['code'],
+                    'human_subject': False,
+                    'field_id': 1,
+                    'owner_id': Owner.pk}
+                )
+
+                # Add the contributors to the study
+                for role in study_data['contributors']:
+                    try:
+                        researcher = Researcher.objects.get(user__email=role['uid'])
+                    except Researcher.DoesNotExist:
+                        # The researcher is not imported first, so we have to ignore the role here
+                        continue
+
+                    role, created = StudyRole.objects.get_or_create(study=study, researcher=researcher,
+                                                                    defaults={
+                                                                        'role': role['role'].upper(),
+                                                                        'active': True
+                                                                    })
+
+                    # Create the workspace also here (vre_app)
+
+                import_counter += 1
+                self.stdout.write(self.style.SUCCESS(f'Study {study.name} {"is created" if created else "does already exists"}'))
+
+            self.stdout.write(f'Done importing file: {import_file}, {import_counter} entries')

VRE/lib/models/admin.py

@@ -1,6 +1,13 @@
 from django import forms
 from django.contrib.contenttypes.models import ContentType
+from django.core.management import call_command
+from django.shortcuts import redirect, render
 from django.utils.safestring import mark_safe
+from django.urls import path
+from django.utils.translation import gettext_lazy as _
+
+
+from pathlib import Path
 
 
 class VMRelatedSelectWidget(forms.Select):
@@ -58,3 +65,42 @@ class VMRelatedSelectWidget(forms.Select):
 
         html = super().render(name, value, attrs, renderer) + '<script>' + javascript_data + '</script>'
         return mark_safe(html)
+
+
+class JSONImportForm(forms.Form):
+    json_file = forms.FileField( label='JSON Import file', allow_empty_file=False, required=True, help_text=_('Select a valid JSON file for uploading'))
+
+
+class JSONImportMixin():
+    def get_urls(self):
+        urls = super().get_urls()
+        my_urls = [
+            path('import-json/', self.import_json, name=f'{self.import_type}_import_json'),
+        ]
+        return my_urls + urls
+
+    def import_json(self, request):
+        if request.method == "POST":
+
+            import_file = '/tmp/' + 'study' if 'study' == self.import_type else 'researcher' + '.upload.json'
+            import_file = Path(import_file)
+            if import_file.exists():
+                import_file.unlink()
+
+            with request.FILES["json_file"].open('r') as source:
+                with open(import_file, mode='ab') as destination:
+                    for line in source:
+                        destination.write(line)
+
+            import_cmd = 'import_studies' if 'study' == self.import_type else 'import_researchers'
+            call_command(import_cmd, import_file)
+            import_file.unlink()
+
+            self.message_user(request, 'Your JSON file has been imported. Check if the results are ok below.')
+            return redirect("..")
+
+        form = JSONImportForm()
+        payload = {"form": form}
+        return render(
+            request, "admin/json_form.html", payload
+        )

VRE/templates/admin/import_change_list.html

@@ -0,0 +1,39 @@
+{% extends 'admin/change_list.html' %}
+{% load i18n %}
+
+{% block object-tools %}
+{{ block.super }}
+
+<style>
+    div#admin_json_import_popup {
+        position: absolute;
+        top: 150px;
+        right: 50px;
+        border: solid 1px black;
+        width: 600px;
+        background-color: white;
+    }
+</style>
+<script>
+    function showForm(url) {
+        window.django.jQuery.get(url.target.href, function (data, ok) {
+            let popup_div = window.django.jQuery('div#admin_json_import_popup');
+            if (popup_div.length == 0) {
+                popup_div = window.django.jQuery('<div>').attr('id', 'admin_json_import_popup').css('display', 'none');
+                window.django.jQuery('div#content').append(popup_div);
+            }
+            data = data.replace('<div id="container">', '<div id="container" style="display: inline">')
+            popup_div.html(data).show();
+            return false;
+        });
+        return false;
+    }
+
+    window.django.jQuery(function () {
+        let import_link = window.django.jQuery('<a>').attr('href', 'import-json/').addClass('addlink').text('{% translate "Import JSON" %}').on('click', showForm);
+        window.django.jQuery('#content-main ul.object-tools').append(
+            window.django.jQuery('<li>').append(import_link)
+        );
+    });
+</script>
+{% endblock %}

VRE/templates/admin/json_form.html

@@ -0,0 +1,21 @@
+{% extends "admin/base_site.html" %}
+{% load i18n admin_urls static admin_modify %}
+
+{% block content %}
+<h2>JSON Import</h2>
+<form action="import-json/" method="POST" enctype="multipart/form-data">
+    {% csrf_token %}
+    <div>
+        <fieldset class="module aligned ">
+            <div class="form-row">
+                {{ form.json_file.label_tag }}
+                {{ form.json_file }}
+                <div class="help">{{ form.json_file.help_text }}</div>
+            </div>
+        </fieldset>
+        <div class="submit-row">
+            <input type="submit" value="Upload JSON File" class="default" name="_save">
+        </div>
+    </div>
+</form>
+{% endblock %}