merge: branch '109-add-commands-to-init-single-instance' into 'dev'

gunicorn@.service

@@ -8,15 +8,15 @@ User = www-data
 Group = www-data
 WorkingDirectory = /srv/www/%i
 EnvironmentFile = /srv/www/%i/.env
-TimeoutSec = 600
+TimeoutSec = 1200
 
-ExecStartPre = /srv/www/%i/.venv/bin/manage.py migrate --noinput
-ExecStartPre = /srv/www/%i/.venv/bin/manage.py collectstatic --noinput
-ExecStartPre = /srv/www/%i/.venv/bin/manage.py init_institutions
-ExecStartPre = /srv/www/%i/.venv/bin/manage.py init_users
-ExecStartPre = /srv/www/%i/.venv/bin/manage.py init_datasets
-ExecStartPre = /srv/www/%i/.venv/bin/manage.py init_riskmodels
-ExecStart = /srv/www/%i/.venv/bin/python -m gunicorn -c /srv/www/%i/gunicorn.conf.py
+ExecStartPre = .venv/bin/manage.py migrate --noinput
+ExecStartPre = .venv/bin/manage.py collectstatic --noinput
+ExecStartPre = .venv/bin/manage.py add_institutions --from-file initial/add_institutions
+ExecStartPre = .venv/bin/manage.py add_users --from-file initial/add_users
+ExecStartPre = .venv/bin/manage.py add_datasets --from-file initial/add_datasets
+ExecStartPre = .venv/bin/manage.py add_riskmodels --from-file initial/add_riskmodels
+ExecStart = .venv/bin/python -m gunicorn -c gunicorn.conf.py
 
 ExecReload = kill -s HUP $MAINPID
 ExecStop = kill -s TERM $MAINPID

initial/datasets.json

@@ -0,0 +1,32 @@
+[
+    {
+        "git_repo_url": "https://github.com/rmnldwg/lydata",
+        "revision": "main",
+        "data_path": "2021-usz-oropharynx/data.csv"
+    },
+    {
+        "git_repo_url": "https://github.com/rmnldwg/lydata",
+        "revision": "main",
+        "data_path": "2021-clb-oropharynx/data.csv"
+    },
+    {
+        "git_repo_url": "https://github.com/rmnldwg/lydata",
+        "revision": "main",
+        "data_path": "2023-isb-multisite/data.csv"
+    },
+    {
+        "git_repo_url": "https://github.com/rmnldwg/lydata",
+        "revision": "main",
+        "data_path": "2023-clb-multisite/data.csv"
+    },
+    {
+        "git_repo_url": "https://github.com/rmnldwg/lydata.private",
+        "revision": "2023-usz-hypopharynx-larynx",
+        "data_path": "2023-usz-hypopharynx-larynx/data.csv"
+    },
+    {
+        "git_repo_url": "https://github.com/rmnldwg/lydata.private",
+        "revision": "2023-hvh-oropharynx",
+        "data_path": "2023-hvh-oropharynx/data.csv"
+    }
+]

initial/institutions.json

@@ -0,0 +1,38 @@
+[
+    {
+        "name": "University Hospital Zurich",
+        "shortname": "USZ",
+        "street": "Rämistrasse 100",
+        "city": "Zürich",
+        "country": "CH",
+        "phone": "+41442553566",
+        "logo": "logos/usz.png"
+    },
+    {
+        "name": "Centre Léon Bérard",
+        "shortname": "CLB",
+        "street": "28 Rue Laennec",
+        "city": "Lyon",
+        "country": "FR",
+        "phone": "+33478782828",
+        "logo": "logos/clb.png"
+    },
+    {
+        "name": "Inselspital Bern",
+        "shortname": "ISB",
+        "street": "Freiburgstrasse 15",
+        "city": "Bern",
+        "country": "CH",
+        "phone": "+41316322111",
+        "logo": "logos/isb.png"
+    },
+    {
+        "name": "Vall d'Hebron Barcelona Hospital",
+        "shortname": "HVH",
+        "street": "Passeig de la Vall d'Hebron, 119-129",
+        "city": "Barcelona",
+        "country": "ES",
+        "phone": "+34934893000",
+        "logo": "logos/hvh.png"
+    }
+]

initial/riskmodels.json

@@ -0,0 +1,23 @@
+[
+    {
+        "git_repo_owner": "rmnldwg",
+        "git_repo_name": "lynference",
+        "revision": "win-graph-v1",
+        "params_path": "params.yaml",
+        "num_samples": 100
+    },
+    {
+        "git_repo_owner": "rmnldwg",
+        "git_repo_name": "lynference",
+        "revision": "complete-part1-v1",
+        "params_path": "params.yaml",
+        "num_samples": 100
+    },
+    {
+        "git_repo_owner": "rmnldwg",
+        "git_repo_name": "lynference",
+        "revision": "add-I-to-II-and-IV-to-V",
+        "params_path": "params.yaml",
+        "num_samples": 100
+    }
+]

initial/users.json

@@ -0,0 +1,83 @@
+[
+    {
+        "email": "roman.ludwig@usz.ch",
+        "first_name": "Roman",
+        "last_name": "Ludwig",
+        "institution": "USZ",
+        "is_active": true,
+        "is_staff": true,
+        "is_superuser": true
+    },
+    {
+        "email": "jan.unkelbach@usz.ch",
+        "first_name": "Jan",
+        "last_name": "Unkelbach",
+        "institution": "USZ",
+        "is_active": true,
+        "is_staff": false,
+        "is_superuser": false
+    },
+    {
+        "email": "vincent.gregoire@lyon.unicancer.fr",
+        "first_name": "Vincent",
+        "last_name": "Grégoire",
+        "institution": "CLB",
+        "is_active": true,
+        "is_staff": false,
+        "is_superuser": false
+    },
+    {
+        "email": "roland.giger@insel.ch",
+        "first_name": "Roland",
+        "last_name": "Giger",
+        "institution": "ISB",
+        "is_active": true,
+        "is_staff": false,
+        "is_superuser": false
+    },
+    {
+        "email": "lars.widmer@usz.ch",
+        "first_name": "Lars",
+        "last_name": "Widmer",
+        "institution": "USZ",
+        "is_active": true,
+        "is_staff": false,
+        "is_superuser": false
+    },
+    {
+        "email": "esmee.looman@usz.ch",
+        "first_name": "Esmee",
+        "last_name": "Looman",
+        "institution": "USZ",
+        "is_active": true,
+        "is_staff": false,
+        "is_superuser": false
+    },
+    {
+        "email": "yoel.perezhaas@usz.ch",
+        "first_name": "Yoel",
+        "last_name": "Perez Haas",
+        "institution": "USZ",
+        "is_active": true,
+        "is_staff": false,
+        "is_superuser": false
+    },
+    {
+        "email": "julian.broennimann@uzh.ch",
+        "first_name": "Julian",
+        "last_name": "Brönnimann",
+        "institution": "USZ",
+        "is_active": true,
+        "is_staff": false,
+        "is_superuser": false
+    },
+    {
+        "email": "sergi.benavente@vallhebron.cat",
+        "first_name": "Sergio",
+        "last_name": "Benavente Norza",
+        "institution": "HVH",
+        "is_active": true,
+        "is_staff": false,
+        "is_superuser": false
+    }
+]

lyprox/accounts/management/commands/add_institutions.py

@@ -0,0 +1,87 @@
+"""
+Management command to add institutions from a file or the command line.
+"""
+import json
+from pathlib import Path
+from django.core.management import base
+from django.core.management.base import CommandParser
+from django.db.utils import IntegrityError
+
+from lyprox.accounts.models import Institution
+
+
+class Command(base.BaseCommand):
+    """Command to add institutions from a file or the command line."""
+    help = __doc__
+
+    def add_arguments(self, parser: CommandParser) -> None:
+        """Add arguments to command."""
+        group = parser.add_mutually_exclusive_group(required=True)
+        group.add_argument(
+            "--from-file",
+            type=Path,
+            help="Path to JSON file with list of institutions.",
+        )
+        group.add_argument(
+            "--from-stdin",
+            action="store_true",
+            help="Use command line arguments to create a single institution.",
+        )
+        parser.add_argument(
+            "--name", type=str, help="Name of institution.",
+        )
+        parser.add_argument(
+            "--shortname", type=str, help="Abbreviation of institution.",
+        )
+        parser.add_argument(
+            "--street", type=str, help="Street and house number of institution.",
+        )
+        parser.add_argument(
+            "--city", type=str, help="City of institution.",
+        )
+        parser.add_argument(
+            "--country", type=str, help="Country of institution.",
+        )
+        parser.add_argument(
+            "--phone", type=str, help="Phone number of institution.",
+        )
+        parser.add_argument(
+            "--logo", type=str, help="Path of insitution's logo within media.",
+        )
+
+    def handle(self, *args, **options):
+        """Execute command."""
+        if not options["from_stdin"]:
+            with open(options["from_file"], "r", encoding="utf-8") as json_file:
+                institution_configurations = json.load(json_file)
+        else:
+            institution_configurations = [{
+                "name": options["name"],
+                "shortname": options["shortname"],
+                "street": options["street"],
+                "city": options["city"],
+                "country": options["country"],
+                "phone": options["phone"],
+                "logo": options["logo"],
+            }]
+
+        for config in institution_configurations:
+            try:
+                Institution.objects.create(**config)
+                self.stdout.write(
+                    self.style.SUCCESS(
+                        f"Institution '{config['name']}' created."
+                    )
+                )
+            except IntegrityError:
+                self.stdout.write(
+                    self.style.WARNING(
+                        f"Institution '{config['name']}' already exists. Skipping."
+                    )
+                )
+            except Exception as exc:
+                self.stdout.write(
+                    self.style.ERROR(
+                        f"Could not create institution '{config['name']}': {exc}"
+                    )
+                )