import os
import uuid
from shutil import copyfile
from django.conf import settings
from django.contrib.auth.models import User
from django.contrib.postgres.fields import HStoreField
from django.db import models
from django.utils.translation import get_language
from django.utils.translation import ugettext_lazy as _
from private_storage.fields import PrivateFileField
from fsutils import md5sum
class ProfileManager(models.Manager):
def exclude_profile(self, profile):
return super().get_queryset().exclude(id=profile.id)
class Profile(models.Model):
"""example Documentation:
https://simpleisbetterthancomplex.com/tutorial/2016/07/22/how-to-extend-django-user-model.html#onetoone
"""
class Meta:
ordering = ['user__last_name', 'user__first_name']
accountname = models.CharField(max_length=150, null=True, blank=True)
user = models.OneToOneField(User, on_delete=models.CASCADE, related_name='profile')
labs = models.ManyToManyField('Lab', related_name='members')
unix_username = models.CharField(max_length=150, null=True, blank=True, verbose_name=_("Unix username"))
objects = ProfileManager()
def __str__(self):
return '{0}, {1} <{2}>'.format(self.user.last_name, self.user.first_name, self.user.email)
@property
def fullname(self):
return self.user.get_full_name()
class Institution(models.Model):
class Meta:
unique_together = (('abbr', 'name'))
ordering = ['name']
abbr = models.CharField(max_length=64, null=True, blank=True, unique=True, verbose_name=_('Abbreviation'))
name = models.CharField(max_length=256, unique=True, verbose_name=_('Name'))
def __str__(self):
return self.name
def get_identifier(self):
if self.abbr:
return self.abbr
else:
return self.name
class Lab(models.Model):
class Meta:
ordering = ['name']
name = models.CharField(max_length=64, verbose_name=_('Name'))
ldap = models.CharField(max_length=32, null=True, blank=True, verbose_name='LDAP')
pi = models.OneToOneField(
Profile,
on_delete=models.SET_NULL,
null=True,
blank=True,
limit_choices_to={'user__groups__name': settings.AUTH_LDAP_PI_GROUP},
related_name='pi_of')
data_managers = models.ManyToManyField(Profile, related_name='data_manager_of', verbose_name=_('Data managers'))
institution = models.ForeignKey(Institution, on_delete=models.PROTECT, related_name='labs')
def __str__(self):
return self.name
class DataFileManager(models.Manager):
def limit_to_profile(self, profile):
return super().get_queryset().filter(uploaded_by=profile)
# File Object ########
class DataFile(models.Model):
"""
DataFile is the basic file object to which a number of annotations can be attached.
File always belongs to 1 (and only 1) lab.
Access is granted to lab PI, Lab data managers and original Uploader.
To grant further access, files must be bundled in 'DataSets' for which independent access can be granted
File annotations are handled trough the use of PostgreSQL's hstore datatype
https://docs.djangoproject.com/en/2.2/ref/contrib/postgres/fields/#hstorefield
https://docs.djangoproject.com/en/2.2/ref/contrib/postgres/operations/#create-postgresql-extensions
Also of interest:
https://www.citusdata.com/blog/2016/07/14/choosing-nosql-hstore-json-jsonb/
"""
# Allow passing an NFS path at init?
# def __init__(self, src):
# self.upload_from_nfs(src)
# def get_hash()
file = PrivateFileField(max_length=256, null=True)
annotations = HStoreField(verbose_name=_('File Annotations'), null=True)
upload_ts = models.DateTimeField(verbose_name=_('Upload Timestamp'), auto_now_add=True)
uploaded_by = models.ForeignKey(Profile, on_delete=models.PROTECT, verbose_name=_('Uploaded by'), related_name='uploaded_files')
lab = models.ForeignKey(Lab, on_delete=models.PROTECT, related_name='files', verbose_name=_('Belongs to this lab'))
objects = DataFileManager()
def __str__(self):
return self.file.name
@property
def filext(self):
ext = os.path.splitext(self.file.name)[-1][1:].lower()
return ext
@property
def name(self):
return self.file.name
@property
def placeholder_icon(self):
default = 'fas fa-file-alt'
assoc = {
'pdf': 'fas fa-file-pdf',
'doc': 'fas fa-file-word',
'xls': 'fas fa-file-excel',
'ppt': 'fas fa-file-powerpoint',
'png': 'fas fa-file-image',
'jpg': 'fas fa-file-image',
'jpe': 'fas fa-file-image'
}
try:
return assoc[self.filext[:3]]
except KeyError:
return default
def upload_from_nfs(self, src):
"""
Copy to db storage partition from a local network path
Return new path after copy
"""
# TODO: Code in this function will be moved to the Queuing system
tmp_dst = settings.DATA_ROOT + "/" + str(uuid.uuid4())
copyfile(src, tmp_dst) # copy + hash at the same time?
md5 = md5sum(tmp_dst).hexdigest()
path = "{}/{}___{}".format(settings.DATA_ROOT, os.path.basename(src), md5)
os.rename(tmp_dst, path)
self.path = path
self.save()
class ManuallyCreatedDataSetManager(models.Manager):
def get_queryset(self):
return super().get_queryset().filter(name__isnull=False)
class UploadCreatedDataSetManager(models.Manager):
def get_queryset(self):
return super().get_queryset().filter(name__isnull=True)
class DataSet(models.Model):
"""
DataSets are collections of files for which specific access can be managed.
These are akin to folders.
Access can be granted to whole labs or distinctly to specific users or user groups.
New data imports will also automatically generate a DataSet wrapping the uploaded files.
This auto wrap will allow us to track dropzone uploaded files from incomplete uploads and mark them for deletion
"""
name = models.CharField(max_length=128, verbose_name=_('Name'), null=True)
creation_ts = models.DateTimeField(verbose_name=_('Creation Timestamp'), auto_now_add=True)
update_ts = models.DateTimeField(verbose_name=_('Last Update Timestamp'), auto_now=True)
created_by = models.ForeignKey(Profile, on_delete=models.PROTECT, related_name='datasets')
access_granted_to = models.ManyToManyField(Profile, blank=True, related_name='shared_datasets', verbose_name=_('Grant Access to'))
open_to_labs = models.ManyToManyField(Lab, related_name='shared_datasets', verbose_name=_('Open to these labs'))
files = models.ManyToManyField(DataFile, related_name='datasets', verbose_name=_('Files'))
objects = models.Manager()
uploads = UploadCreatedDataSetManager()
created = ManuallyCreatedDataSetManager()
class DataTypes(models.Model):
"""
DataTypes are a specialization of FSFile for which a set of annotation keys are pre-defined
Management of DataTypes should be restricted to specialized staff such as Scientific Platforms personnel
"""
name = models.CharField(max_length=128, verbose_name=_('Data Type'))
annotations = HStoreField(verbose_name=_('Suggested Annotations'))
class Alert(models.Model):
message_fr = models.TextField(null=True)
message_en = models.TextField(null=True)
start = models.DateTimeField()
end = models.DateTimeField()
@property
def localized(self):
if get_language() == 'en':
return self.message_en
else:
return self.message_fr
class AppSettings(models.Model):
home_institution = models.ForeignKey(Institution, null=True, blank=True, on_delete=models.SET_NULL)