Paperless approval

CHANGELOG.md

@@ -1,9 +1,3 @@
-<!--
-- **Updated our core dependency**, Django, to version 4.2 (LTS). The previous LTS release 3.2 reached end of extended support in April. We thank the Django core team that kept releasing security fixes even after.
-- New dependency added, navigate to `<URL>/schema-viewer` to enjoy it (installed on dev settings only). Remember: use `models` rule if you'd like to have these in static print-friendly PDF docs.
--->
-
-
 ??.??.??
 ========
 
@@ -17,7 +11,9 @@ Breaking changes:
 
 Non-breaking changes:
 
+- **Updated our core dependency**, Django, to version 4.2 (LTS). The previous LTS release 3.2 reached end of extended support in April. We thank the Django core team that kept releasing security fixes even after.
 - New dependency added, navigate to `<URL>/openapi/schema/redoc` or `<URL>/openapi/schema/swagger-ui` to enjoy either ReDoc or Swagger UI over the automagically generated OpenAPI 3.0 schema.
+- New dependency added, navigate to `<URL>/schema-viewer` to enjoy it (installed on dev settings only). Remember: use `models` rule if you'd like to have these in static print-friendly PDF docs.
 - Added a new Django management command: list_templates
 - Added `filepaths` JSONField to Request model. We'd like to track the location of, for example, delivered FASTQ files and QC reports.
 - Deprecated and removed bpython. shell_plus now uses ipython. This was to avoid runtime errors while compiling the requirements.txt files, given that greenlet dependecy would be pinned under contradicted version numbers (testing.txt has playwright that asks for greenlet v2, meanwhile bpython in dev.txt asked for v3..)
@@ -27,6 +23,8 @@ Non-breaking changes:
 - Renamed rules `import-migras` to `put-old-migras`, `export-migras` to `tar-old-migras`, and `restore-migras` to `put-new-migras`. This is to avoid confusion with `import-pgdb`, where importing means bringing file from prod VM.
 - Rule `import-pgdb` now brings migration files (to reproduce database schema) by default (if available).
 - The `<URL>/api/samples/<id>` doesn't fail anymore if no `pk` was given.
+- Added an EmailField to PrincipalInvestigator. This field is used in the 'paperless approval' feature (see next point.)
+- Added a 'Solicite approval via e-mail' context menu option for sequencing requests that belong users with both their own and their pi's email address at `settings.EMAIL_HOST` (that means, we can rely on the email spoofing as in the 'compose email' menu that staff users already had).
 
 23.09.20
 ========

parkour_app/common/models.py

@@ -105,6 +105,23 @@ def facility(self):
             membership = None
         return membership
 
+    @property
+    def can_solicite_paperless_approval(self):
+        result_user = False
+        result_pi = False
+        if self.pi is not None and self.pi.email != "Unset":
+            if (
+                not '"' in self.pi.email
+                and self.pi.email.split("@")[1] == settings.EMAIL_HOST
+            ):
+                result_pi = True
+            if (
+                not '"' in self.email
+                and self.email.split("@")[1] == settings.EMAIL_HOST
+            ):
+                result_user = True
+        return result_user and result_pi
+
     def __str__(self):
         this_user_email = self.email
         if not '"' in this_user_email:

parkour_app/common/views.py

@@ -36,6 +36,7 @@ def index(request):
                     "id": user.pk,
                     "name": user.full_name,
                     "is_staff": user.is_staff,
+                    "can_solicite_paperless_approval": user.can_solicite_paperless_approval,
                 }
             ),
         },

parkour_app/request/migrations/0005_request_token.py

@@ -0,0 +1,19 @@
+# Generated by Django 4.2.6 on 2023-10-19 14:53
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("request", "0004_request_filepaths"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="request",
+            name="token",
+            field=models.CharField(
+                blank=True, max_length=50, null=True, unique=True, verbose_name="Token"
+            ),
+        ),
+    ]

parkour_app/request/migrations/max_migration.txt

@@ -1 +1 @@
-0004_request_filepaths
+0005_request_token

parkour_app/request/models.py

@@ -27,6 +27,7 @@ def __str__(self):
 class Request(DateTimeMixin):
     name = models.CharField("Name", max_length=100, blank=True)
     description = models.TextField()
+    token = models.CharField("Token", max_length=50, blank=True, null=True, unique=True)
 
     user = models.ForeignKey(
         settings.AUTH_USER_MODEL,

parkour_app/request/templates/approval.html

@@ -0,0 +1,32 @@
+{% load i18n %}{% autoescape off %}
+<p>Dear {{ pi_name }},</p>
+<p>{{ full_name }} requested your approval on this experiment. They wrote:</p>
+<p>{{ message }}</p>
+<hr/>
+<p>That was the end of their message. <b>Please treat the link within this email message as a one-time password, scoped for the authorization of this sequencing request.</b> To approve it, just forward, or Reply "OK", to this email. Then {{ full_name }}, who'd be authenticated within Parkour LIMS, can click <a href={{ token_url }}>this special link</a>. Afterward, processing will be started right away at the facility.<br/></p>
+{% if records %}
+<hr/>
+<table style="width:100%;">
+    <thead>
+        <tr style="font-weight:bold;">
+            <td>Name</td>
+            <td>Barcode</td>
+            <td>Nucleic Acid Type</td>
+            <td>Protocol</td>
+        </tr>
+    </thead>
+    <tbody>
+        {% for record in records %}
+            <tr>
+                <td>{{ record.name }}</td>
+                <td>{{ record.barcode }}</td>
+                <td>{{ record.nucleic_acid_type.name }}</td>
+                <td>{{ record.library_protocol.name }}</td>
+            </tr>
+        {% endfor %}
+    </tbody>
+</table>
+<hr/>
+{% endif %}
+<p>--<br/><i>This e-mail was sent via Parkour2.</i><br/></p>
+{% endautoescape %}

parkour_app/request/views.py

@@ -3,17 +3,21 @@
 import logging
 import os
 from unicodedata import normalize
+from urllib.parse import urlencode
 
 from common.serializers import UserSerializer
 from common.utils import retrieve_group_items
 from common.views import CsrfExemptSessionAuthentication, StandardResultsSetPagination
 from django.apps import apps
 from django.conf import settings
 from django.contrib.auth import get_user_model
+from django.contrib.sites.shortcuts import get_current_site
 from django.core.mail import send_mail
 from django.db.models import Prefetch
-from django.http import Http404, HttpResponse, JsonResponse
+from django.http import Http404, HttpRequest, HttpResponse, JsonResponse
 from django.template.loader import render_to_string
+from django.urls import reverse
+from django.utils.crypto import get_random_string
 from docx import Document
 from docx.enum.text import WD_BREAK
 from docx.shared import Cm, Pt
@@ -600,6 +604,84 @@ def upload_deep_sequencing_request(self, request, pk=None):
 
         return JsonResponse({"success": True, "name": file_name, "path": file_path})
 
+    @action(methods=["post"], detail=True)
+    def solicite_approval(self, request, pk=None):  # pragma: no cover
+        """Send an email to the PI."""
+        error = ""
+        instance = self.get_object()
+        subject = f"[ Parkour2 | sequencing experiment is pending approval ] "
+        subject += request.data.get("subject", "")
+        message = request.data.get("message", "")
+        include_records = json.loads(request.POST.get("include_records", "true"))
+        records = []
+        try:
+            if instance.user.pi.archived:
+                raise ValueError(
+                    "PI: "
+                    + instance.user.pi
+                    + ", is no longer enrolled. Please ask: "
+                    + settings.ADMIN_EMAIL
+                    + " to un-archive the entry at the database."
+                )
+            elif instance.user.pi.email == "Unset":
+                raise ValueError(
+                    "PI: "
+                    + instance.user.pi
+                    + ", has no e-mail address assigned. Please contact: "
+                    + settings.ADMIN_EMAIL
+                )
+            records = list(instance.libraries.all()) + list(instance.samples.all())
+            for r in records:
+                if r.status != 0:
+                    raise ValueError("Not all records have status of zero.")
+            records = sorted(records, key=lambda x: x.barcode[3:])
+            if not include_records:
+                records = []
+            instance.token = get_random_string(30)
+            instance.save(update_fields=["token"])
+            url_scheme = request.is_secure() and "https" or "http"
+            url_domain = get_current_site(request).domain
+            url_query = urlencode({"token": instance.token})
+            send_mail(
+                subject=subject,
+                message="",
+                html_message=render_to_string(
+                    "approval.html",
+                    {
+                        "full_name": instance.user.full_name,
+                        "pi_name": instance.user.pi.name,
+                        "message": message,
+                        "token_url": f"{url_scheme}://{url_domain}/api/requests/{instance.id}/approve?{url_query}",
+                        "records": records,
+                    },
+                ),
+                from_email=instance.user.email,
+                recipient_list=[instance.user.pi.email],
+            )
+        except Exception as e:
+            error = str(e)
+            logger.exception(e)
+        return JsonResponse({"success": not error, "error": error})
+
+    @action(methods=["get"], detail=True)
+    def approve(self, request, *args, **kwargs):  # pragma: no cover
+        """Process token sent to PI."""
+        error = ""
+        instance = self.get_object()
+        try:
+            token = request.query_params.get("token")
+            if token == instance.token:
+                instance.libraries.all().update(status=1)
+                instance.samples.all().update(status=1)
+                instance.token = None
+                instance.save(update_fields=["token"])
+            else:
+                raise ValueError(f"Token mismatch.")
+        except Exception as e:
+            error = str(e)
+            logger.exception(e)
+        return JsonResponse({"success": not error, "error": error})
+
     @action(methods=["post"], detail=True, permission_classes=[IsAdminUser])
     def send_email(self, request, pk=None):  # pragma: no cover
         """Send an email to the user."""

parkour_app/requirements/base.in

@@ -1,4 +1,4 @@
-Django~=3.2
+Django~=4.2
 backports-zoneinfo ; python_version < "3.9"  # hardcoded conditional to avoid issues on latest Py
 django-authtools @ git+https://github.com/adRn-s/django-authtools@dev_adRn
 djangorestframework

parkour_app/requirements/base.txt

@@ -1,4 +1,4 @@
-# SHA1:06da873d282014bf43e73cbd9e89d494d2a01eb1
+# SHA1:abfe81091e270a773df33afe444dc6048d44fa7b
 #
 # This file is autogenerated by pip-compile-multi
 # To update, run:
@@ -19,12 +19,14 @@ attrs==23.1.0
     #   jsonschema
     #   referencing
 backports-zoneinfo==0.2.1 ; python_version < "3.9"
-    # via -r parkour_app/requirements/base.in
+    # via
+    #   -r parkour_app/requirements/base.in
+    #   django
 bioblend==1.2.0
     # via -r parkour_app/requirements/base.in
 certifi==2023.7.22
     # via requests
-charset-normalizer==3.3.1
+charset-normalizer==3.3.0
     # via
     #   aiohttp
     #   requests
@@ -36,7 +38,7 @@ diff-match-patch==20230430
     # via django-import-export
 dj-database-url==2.1.0
     # via -r parkour_app/requirements/base.in
-django==3.2.22
+django==4.2.6
     # via
     #   -r parkour_app/requirements/base.in
     #   dj-database-url
@@ -126,7 +128,6 @@ python-docx==1.0.1
     # via -r parkour_app/requirements/base.in
 pytz==2023.3.post1
     # via
-    #   django
     #   djangorestframework
     #   pandas
 pyyaml==6.0.1
@@ -156,7 +157,7 @@ sqlparse==0.4.4
     # via django
 tablib[html,ods,xls,xlsx,yaml]==3.5.0
     # via django-import-export
-tblib==3.0.0
+tblib==2.0.0
     # via -r parkour_app/requirements/base.in
 tinydb==4.8.0
     # via tuspy

parkour_app/requirements/dev.in

@@ -7,3 +7,4 @@ pywatchman
 Werkzeug
 rich
 django-migration-linter
+django-schema-viewer

parkour_app/requirements/dev.txt

@@ -1,4 +1,4 @@
-# SHA1:6876d98b78c887d5012dc7fa9466ef74f298e29e
+# SHA1:eb2ec713607c161f8a31504883b8ae96a1520bf3
 #
 # This file is autogenerated by pip-compile-multi
 # To update, run:
@@ -20,6 +20,8 @@ django-debug-toolbar==4.2.0
     # via -r parkour_app/requirements/dev.in
 django-migration-linter==5.0.0
     # via -r parkour_app/requirements/dev.in
+django-schema-viewer==0.1.0
+    # via -r parkour_app/requirements/dev.in
 executing==2.0.0
     # via stack-data
 ipdb==0.13.13