Elementary report template management.

WIP

File uploads not handled properly yet.

config/settings/base.py

@@ -111,6 +111,7 @@
     "maintenance.apps.MaintenanceConfig",
     "regmaps.apps.RegmapsConfig",
     "beaconsite.apps.BeaconsiteConfig",
+    "reports.apps.ReportsConfig",
 ]
 
 # See: https://docs.djangoproject.com/en/dev/ref/settings/#installed-apps
@@ -690,6 +691,7 @@ def set_logging(debug):
 # Default: None
 DJANGO_SU_CUSTOM_LOGIN_ACTION = None
 
+CRISPY_FAIL_SILENTLY = False
 
 # STORAGE CONFIGURATION
 # ------------------------------------------------------------------------------

config/urls.py

@@ -56,6 +56,7 @@ def handler500(request, *args, **argv):
     url(r"^su/", include("django_su.urls")),
     url(r"^cohorts/", include("cohorts.urls")),
     url(r"^clinvar-export/", include("clinvar_export.urls")),
+    url(r"^reports/", include("reports.urls")),
 ] + static(settings.MEDIA_URL, document_root=settings.MEDIA_ROOT)
 
 # Augment with URLs for Beacon site.

reports/admin.py

@@ -0,0 +1,6 @@
+from django.contrib import admin
+
+# from .models import HgmdPublicLocus
+
+# Register your models here.
+# admin.site.register(HgmdPublicLocus)

reports/apps.py

@@ -0,0 +1,5 @@
+from django.apps import AppConfig
+
+
+class ReportsConfig(AppConfig):
+    name = "reports"

reports/forms.py

@@ -0,0 +1,80 @@
+import hashlib
+
+from django import forms
+from django.core.exceptions import ValidationError
+from django.core.validators import RegexValidator
+
+from .models import ReportTemplate
+
+
+class ReportTemplateForm(forms.ModelForm):
+    class Meta:
+        model = ReportTemplate
+        fields = ("title", "filename")
+
+    title = forms.CharField(
+        label="Template Title", help_text="Leave empty to use file name", required=False
+    )
+
+    payload = forms.FileField(
+        label="Template File", help_text="Upload a .docx file to use for the template."
+    )
+
+    filename = forms.CharField(
+        required=False,
+        help_text="Specify the file name to override the file name of the uploaded file",
+        validators=[
+            RegexValidator(r"(^$)|(\.docx$)", message="File name must be blank or end in .docx"),
+            RegexValidator(
+                r"^[a-zA-Z0-9\._-]*$",
+                message="File name must only consist of alphanumeric characters, spaces, dots, hyphens, and underscores",
+            ),
+        ],
+    )
+
+    def __init__(self, project, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        self.project = project
+        if self.instance.pk:
+            self.fields["payload"].required = False
+
+    def clean(self):
+        cleaned_data = self.cleaned_data
+        if "payload" in cleaned_data and cleaned_data["payload"]:
+            import pdb
+
+            pdb.set_trace()
+            cleaned_data["title"] = cleaned_data["title"] or cleaned_data["payload"].name
+            cleaned_data["filename"] = cleaned_data["filename"] or cleaned_data["payload"].name
+            ctx = hashlib.sha256()
+            if cleaned_data["payload"].multiple_chunks():
+                for data in cleaned_data["payload"].chunks():
+                    ctx.update(data)
+            else:
+                ctx.update(cleaned_data["payload"].read())
+            cleaned_data["filehash"] = "sha256:%s" % ctx.hexdigest()
+            cleaned_data["filesize"] = cleaned_data["payload"].size
+
+        if not cleaned_data["filename"].endswith(".docx"):
+            raise ValidationError("The file name must end in .docx")
+
+        qs = ReportTemplate.objects.filter(project=self.project, filename=cleaned_data["filename"])
+        if self.instance.pk:
+            qs = qs.exclude(pk=self.instance.pk)
+        if qs:
+            raise ValidationError(
+                "There already exists a report template with file name %s in this project!"
+                % cleaned_data["filename"]
+            )
+
+        return cleaned_data
+
+    def save(self, commit=True):
+        super().save(commit=False)
+        if "filehash" in self.cleaned_data:
+            self.instance.filehash = self.cleaned_data["filehash"]
+        if "filesize" in self.cleaned_data:
+            self.instance.filesize = self.cleaned_data["filesize"]
+        self.instance.project = self.project
+        self.instance.save()
+        return self.instance

reports/migrations/0001_initial.py

@@ -0,0 +1,58 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.11.29 on 2021-04-07 15:27
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+import django.db.models.deletion
+import uuid
+
+
+class Migration(migrations.Migration):
+
+    initial = True
+
+    dependencies = [
+        ("projectroles", "0017_project_full_title"),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name="ReportTemplate",
+            fields=[
+                (
+                    "id",
+                    models.AutoField(
+                        auto_created=True, primary_key=True, serialize=False, verbose_name="ID"
+                    ),
+                ),
+                (
+                    "date_created",
+                    models.DateTimeField(auto_now_add=True, help_text="DateTime of creation"),
+                ),
+                (
+                    "date_modified",
+                    models.DateTimeField(auto_now=True, help_text="DateTime of last modification"),
+                ),
+                ("title", models.CharField(max_length=512)),
+                ("filename", models.CharField(max_length=512)),
+                ("filesize", models.IntegerField(default=0)),
+                ("filehash", models.CharField(max_length=128)),
+                (
+                    "sodar_uuid",
+                    models.UUIDField(default=uuid.uuid4, help_text="Case SODAR UUID", unique=True),
+                ),
+                (
+                    "project",
+                    models.ForeignKey(
+                        help_text="Project in which this objects belongs",
+                        on_delete=django.db.models.deletion.CASCADE,
+                        to="projectroles.Project",
+                    ),
+                ),
+            ],
+            options={"ordering": ("title",),},
+        ),
+        migrations.AlterUniqueTogether(
+            name="reporttemplate", unique_together=set([("project", "filename")]),
+        ),
+    ]

reports/models.py

@@ -0,0 +1,46 @@
+import uuid as uuid_object
+
+from django.db import models
+from django.conf import settings
+from django.urls import reverse
+from projectroles.models import Project
+
+#: Django user model.
+AUTH_USER_MODEL = getattr(settings, "AUTH_USER_MODEL", "auth.User")
+
+
+class ReportTemplate(models.Model):
+    """A report template."""
+
+    #: DateTime of creation
+    date_created = models.DateTimeField(auto_now_add=True, help_text="DateTime of creation")
+    #: DateTime of last modification
+    date_modified = models.DateTimeField(auto_now=True, help_text="DateTime of last modification")
+
+    #: UUID used for identification throughout SODAR.
+    sodar_uuid = models.UUIDField(
+        default=uuid_object.uuid4, unique=True, help_text="Case SODAR UUID"
+    )
+
+    #: The project containing this case.
+    project = models.ForeignKey(Project, help_text="Project in which this objects belongs")
+
+    #: Title of the report.
+    title = models.CharField(max_length=512)
+    #: File name of the report.
+    filename = models.CharField(max_length=512)
+
+    #: File size in bytes.
+    filesize = models.IntegerField(default=0)
+    #: File hash.
+    filehash = models.CharField(max_length=128)
+
+    class Meta:
+        unique_together = (("project", "filename"),)
+        ordering = ("title",)
+
+    def get_absolute_url(self):
+        return reverse(
+            "reports:template-view",
+            kwargs={"project": self.project.sodar_uuid, "template": self.sodar_uuid},
+        )

reports/plugins.py

@@ -0,0 +1,40 @@
+from projectroles.plugins import ProjectAppPluginPoint
+
+from .urls import urlpatterns
+
+
+class ProjectAppPlugin(ProjectAppPluginPoint):
+    """Plugin for registering app with Projectroles"""
+
+    name = "reports"
+    title = "Reports"
+    urls = urlpatterns
+    # ...
+
+    icon = "file-text-o"
+
+    entry_point_url_id = "reports:template-list"
+
+    description = "Generate reports on word processing templates"
+
+    #: Required permission for accessing the app
+    app_permission = "reports.view_data"
+
+    #: Enable or disable general search from project title bar
+    search_enable = False
+
+    #: List of search object types for the app
+    search_types = []
+
+    #: No settings for this app.
+    app_settings = {}
+
+    def get_object_link(self, model_str, uuid):
+        """
+        Return URL for referring to a object used by the app, along with a
+        label to be shown to the user for linking.
+        :param model_str: Object class (string)
+        :param uuid: sodar_uuid of the referred object
+        :return: Dict or None if not found
+        """
+        return None

reports/rules.py

@@ -0,0 +1,34 @@
+import rules
+from projectroles import rules as pr_rules
+
+
+rules.add_perm(
+    "reports.view_data",
+    rules.is_superuser
+    | pr_rules.is_project_owner
+    | pr_rules.is_project_delegate
+    | pr_rules.is_project_contributor
+    | pr_rules.is_project_guest,
+)
+
+rules.add_perm(
+    "reports.add_data",
+    rules.is_superuser
+    | pr_rules.is_project_owner
+    | pr_rules.is_project_delegate
+    | pr_rules.is_project_contributor,
+)
+rules.add_perm(
+    "reports.delete_data",
+    rules.is_superuser
+    | pr_rules.is_project_owner
+    | pr_rules.is_project_delegate
+    | pr_rules.is_project_contributor,
+)
+rules.add_perm(
+    "reports.update_data",
+    rules.is_superuser
+    | pr_rules.is_project_owner
+    | pr_rules.is_project_delegate
+    | pr_rules.is_project_contributor,
+)

reports/templates/reports/_report_template_buttons.html

@@ -0,0 +1,29 @@
+{% load rules %}
+
+{% has_perm 'reports.update_data' request.user as can_update_data %}
+{% has_perm 'reports.delete_data' request.user as can_delete_data %}
+
+<div class="btn-group sodar-list-btn-group pull-right">
+  <button class="btn btn-secondary dropdown-toggle sodar-list-dropdown"
+      type="button" data-toggle="dropdown" aria-expanded="false">
+    <i class="fa fa-cog"></i>
+  </button>
+  <div class="dropdown-menu dropdown-menu-right">
+    <a class="dropdown-item" href="{% url 'reports:template-view' project=project.sodar_uuid template=object.sodar_uuid %}">
+      <i class="fa fa-fw fa-eye"></i>
+      View
+    </a>
+    {% if can_update_data %}
+      <a class="dropdown-item" href="{% url 'reports:template-update' project=project.sodar_uuid template=object.sodar_uuid %}">
+        <i class="fa fa-fw fa-pencil"></i>
+        Edit
+      </a>
+    {% endif %}
+    {% if can_delete_data %}
+      <a class="dropdown-item" href="{% url 'reports:template-delete' project=project.sodar_uuid template=object.sodar_uuid %}">
+        <i class="fa fa-fw fa-eraser"></i>
+        Delete
+      </a>
+    {% endif %}
+  </div>
+</div>

reports/templates/reports/reporttemplate_confirm_delete.html

@@ -0,0 +1,35 @@
+{% extends 'projectroles/base.html' %}
+
+{% load rules %}
+{% load crispy_forms_filters %}
+{% load projectroles_common_tags %}
+
+{% block title %}Confirm Removal of Report Template{% endblock %}
+
+{% block projectroles %}
+
+<div class="row sodar-subtitle-container">
+  <h2>Confirm Removal of Report Template</h2>
+</div>
+
+<div class="container-fluid sodar-page-container">
+  <div class="alert alert-warning" role="alert">
+    Do you really want to remove the report template "<strong>{{ object.title }}</strong>" file file name "<strong>{{ object.filename }}</strong>"?
+    <strong>This action cannot be reverted!</strong>
+  </div>
+
+  <form method="post">
+    {% csrf_token %}
+    <div class="btn-group pull-right">
+      <a role="button" class="btn btn-secondary"
+         href="{% url 'reports:template-view' project=project.sodar_uuid template=object.sodar_uuid %}"
+        <i class="fa fa-arrow-circle-left"></i> Cancel
+      </a>
+      <button type="submit" class="btn btn-danger">
+        <i class="fa fa-times"></i> Remove
+      </button>
+    </div>
+  </form>
+</div>
+
+{% endblock projectroles %}