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from django.db import models |
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from django.contrib.auth.models import User |
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from django.contrib.contenttypes.fields import GenericForeignKey |
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from django.contrib.contenttypes.models import ContentType |
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from django.contrib.postgres.fields import JSONField |
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from common.constants import STATUSES, WAITING, READY |
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from uid.models import Submission as UIDSubmission |
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# Create your models here. |
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class Account(models.Model): |
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user = models.OneToOneField( |
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User, |
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on_delete=models.CASCADE, |
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related_name='biosample_account') |
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name = models.SlugField() |
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team = models.ForeignKey( |
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'ManagedTeam', |
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on_delete=models.CASCADE, |
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help_text="Your AAP Team") |
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def __str__(self): |
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full_name = " ".join([self.user.first_name, self.user.last_name]) |
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return "%s (%s)" % (self.name, full_name) |
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class ManagedTeam(models.Model): |
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name = models.CharField(max_length=255, unique=True) |
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@classmethod |
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def get_teams(cls): |
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teams = cls.objects.all() |
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return [team.name for team in teams] |
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def __str__(self): |
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return self.name |
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class Meta: |
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verbose_name = "managed team" |
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verbose_name_plural = "managed teams" |
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class BaseSubmission(models.Model): |
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usi_submission_name = models.CharField( |
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max_length=255, |
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blank=True, |
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null=True, |
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db_index=True, |
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unique=True, |
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help_text='USI submission name') |
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created_at = models.DateTimeField(auto_now_add=True) |
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updated_at = models.DateTimeField(auto_now=True) |
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# a field to track errors in UID loading. Should be blank if no errors |
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# are found |
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message = models.TextField( |
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null=True, |
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blank=True) |
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# a column to track submission status |
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# HINT: should I limit by biosample status? |
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status = models.SmallIntegerField( |
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choices=[x.value for x in STATUSES], |
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help_text='example: Waiting', |
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default=WAITING) |
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samples_count = models.PositiveIntegerField(default=0) |
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samples_status = JSONField(default=dict) |
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class Meta: |
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# Abstract base classes are useful when you want to put some common |
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# information into a number of other models |
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abstract = True |
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class Submission(BaseSubmission): |
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uid_submission = models.ForeignKey( |
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UIDSubmission, |
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on_delete=models.CASCADE, |
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related_name='usi_submissions') |
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def __str__(self): |
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return "%s <%s> (%s): %s" % ( |
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self.id, |
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self.usi_submission_name, |
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self.uid_submission, |
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self.get_status_display()) |
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class SubmissionData(models.Model): |
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submission = models.ForeignKey( |
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Submission, |
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on_delete=models.CASCADE, |
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related_name='submission_data') |
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# limit choices for contenttypes |
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# https://axiacore.com/blog/how-use-genericforeignkey-django-531/ |
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name_limit = models.Q(app_label='uid', model='animal') | \ |
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models.Q(app_label='uid', model='sample') |
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# Below the mandatory fields for generic relation |
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# https://simpleisbetterthancomplex.com/tutorial/2016/10/13/how-to-use-generic-relations.html |
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content_type = models.ForeignKey( |
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ContentType, |
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on_delete=models.CASCADE, |
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limit_choices_to=name_limit) |
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object_id = models.PositiveIntegerField() |
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content_object = GenericForeignKey('content_type', 'object_id') |
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def __str__(self): |
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return "%s <%s>: %s" % ( |
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self.submission.id, |
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self.submission.usi_submission_name, |
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self.content_object.name) |
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class Meta: |
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verbose_name = "submission data" |
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verbose_name_plural = "submission data" |
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class OrphanSubmission(BaseSubmission): |
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def __str__(self): |
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return "%s <%s>: %s" % ( |
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self.id, |
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self.usi_submission_name, |
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self.get_status_display()) |
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class OrphanSample(models.Model): |
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submission = models.ForeignKey( |
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OrphanSubmission, |
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on_delete=models.PROTECT, |
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null=True, |
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default=None, |
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blank=True, |
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related_name='submission_data') |
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# This will be assigned after submission |
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biosample_id = models.CharField( |
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max_length=255, |
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unique=True) |
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found_at = models.DateTimeField(auto_now_add=True) |
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ignore = models.BooleanField( |
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default=False, |
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help_text='Should I ignore this record or not?') |
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name = models.CharField( |
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max_length=255) |
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team = models.ForeignKey( |
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'ManagedTeam', |
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on_delete=models.CASCADE, |
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help_text="Your AAP Team") |
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164
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# a column to track sample status |
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status = models.SmallIntegerField( |
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choices=[x.value for x in STATUSES], |
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help_text='example: Waiting', |
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default=READY) |
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removed = models.BooleanField( |
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default=False, |
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help_text='Is this sample still available?') |
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removed_at = models.DateTimeField( |
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null=True, |
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blank=True) |
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def __str__(self): |
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return "%s (%s)" % (self.biosample_id, self.found_at) |
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cnr-ibba /
IMAGE-InjectTool
