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#!/usr/bin/env python3 |
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# -*- coding: utf-8 -*- |
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""" |
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Created on Fri Jun 28 14:46:39 2019 |
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@author: Paolo Cozzi <[email protected]> |
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Define mixins classes for uid.models |
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""" |
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import logging |
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from django.db import connections |
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from django.utils import timezone |
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from common.constants import STATUSES |
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from common.helpers import format_attribute |
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# Get an instance of a logger |
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logger = logging.getLogger(__name__) |
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# Adding a classmethod to Category if you want to enable truncate |
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# https://books.agiliq.com/projects/django-orm-cookbook/en/latest/truncate.html |
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class BaseMixin(object): |
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"""Base class for UID tables. It implement common stuff for all UID |
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tables:: |
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from uid.models import BaseMixin |
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class Submission(BaseMixin): |
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pass |
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""" |
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@classmethod |
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def truncate(cls): |
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""" |
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Truncate table data and restart indexes from 0:: |
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from uid.models import Submission |
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Submission.truncate() |
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""" |
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# Django.db.connections is a dictionary-like object that allows you |
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# to retrieve a specific connection using its alias |
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with connections["default"].cursor() as cursor: |
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statement = "TRUNCATE TABLE {0} RESTART IDENTITY CASCADE".format( |
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cls._meta.db_table) |
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logger.debug(statement) |
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cursor.execute(statement) |
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class BioSampleMixin(BaseMixin): |
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""" |
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Common methods for animal and samples useful in biosample generation |
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Need to called with data into biosample or animals:: |
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from uid.models import Animal |
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animal = Animal.objects.get(pk=1) |
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biosample_data = animal.to_biosample() |
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""" |
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def __str__(self): |
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return str(self.name) |
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@property |
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def person(self): |
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"""Retrieve :py:class:`Person` information from owner relationship""" |
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return self.owner.person |
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@property |
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def organization(self): |
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"""Return :py:class:`Organization` relationship from related |
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:py:class:`Submission` object""" |
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return self.submission.organization |
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@property |
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def gene_bank_country(self): |
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"""Return :py:class:`DictCountry` relationship from related |
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:py:class:`Submission` object""" |
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return self.submission.gene_bank_country |
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@property |
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def gene_bank_name(self): |
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"""Return gene bank name from related :py:class:`Submission` object""" |
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return self.submission.gene_bank_name |
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@property |
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def data_source_id(self): |
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"""Get Data source id (original animal/sample name)""" |
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return self.name |
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@property |
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def specie(self): |
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raise NotImplementedError( |
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"You need to define this method in your class") |
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def get_attributes(self): |
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"""Common attribute definition required from Animal and samples. Need |
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to be called inside Animal/sample get_atribute method. Keys |
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is the name in metadata rules |
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Returns: |
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dict: a dictionary object |
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""" |
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attributes = {} |
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attributes['Data source ID'] = format_attribute( |
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value=self.data_source_id) |
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attributes['Alternative id'] = format_attribute( |
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value=self.alternative_id) |
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# HINT: this is a mandatory biosample field: could be removed from |
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# attributes? |
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attributes['Description'] = format_attribute( |
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value=self.description) |
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attributes["Project"] = format_attribute( |
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value="IMAGE") |
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# to retrieve where this sample belongs |
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attributes["IMAGE submission id"] = format_attribute( |
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value=self.submission.id) |
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attributes['Submission title'] = format_attribute( |
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value=self.submission.title) |
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attributes['Submission description'] = format_attribute( |
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value=self.submission.description) |
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attributes['Person last name'] = format_attribute( |
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value=self.owner.last_name) |
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attributes['Person initial'] = format_attribute( |
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value=self.person.initials) |
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attributes['Person first name'] = format_attribute( |
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value=self.owner.first_name) |
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attributes['Person email'] = format_attribute( |
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value="mailto:%s" % (self.owner.email)) |
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attributes['Person affiliation'] = format_attribute( |
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value=self.person.affiliation.name) |
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attributes['Person role'] = self.person.role.format_attribute() |
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attributes['Organization name'] = format_attribute( |
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value=self.organization.name) |
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attributes['Organization address'] = format_attribute( |
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value=self.organization.address) |
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attributes['Organization uri'] = format_attribute( |
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value=self.organization.URI) |
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attributes['Organization country'] = \ |
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self.organization.country.format_attribute() |
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attributes[ |
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'Organization role'] = self.organization.role.format_attribute() |
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# this could be present or not |
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if self.publication: |
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attributes['Publication DOI'] = format_attribute( |
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value=self.publication.doi) |
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attributes['Gene bank name'] = format_attribute( |
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value=self.gene_bank_name) |
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attributes[ |
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'Gene bank country'] = self.gene_bank_country.format_attribute() |
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attributes['Data source type'] = format_attribute( |
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value=self.submission.get_datasource_type_display()) |
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attributes['Data source version'] = format_attribute( |
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value=self.submission.datasource_version) |
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attributes['Species'] = self.specie.format_attribute() |
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return attributes |
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def to_biosample(self, release_date=None): |
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""" |
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Common stuff to generate a biosample object. Need to be called |
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inside Animal/Sample to_biosample method |
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Args: |
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release_date (str): data will no be published before this day |
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(YYYY-MM-DD) |
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Returns: |
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dict: a dictionary object |
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""" |
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result = {} |
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# define mandatory fields |
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result['alias'] = self.biosample_alias |
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result['title'] = self.name |
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# in case of update, I need to provide the old accession in payload |
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if self.biosample_id and self.biosample_id != '': |
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result['accession'] = self.biosample_id |
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if release_date: |
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result['releaseDate'] = release_date |
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else: |
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now = timezone.now() |
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result['releaseDate'] = str(now.date()) |
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result['taxonId'] = self.specie.taxon_id |
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result['taxon'] = self.specie.label |
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# define optinal fields |
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if self.description: |
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result['description'] = self.description |
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# define attributes that will be customized in Animal and sample |
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result['attributes'] = self.get_attributes() |
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return result |
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def __can_I(self, statuses): |
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""" |
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Return True id self.status in statuses |
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Args: |
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statuses (list): a list of :py:class:`common.constants.STATUSES` |
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Returns: |
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bool |
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""" |
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statuses = [x.value[0] for x in STATUSES if x.name in statuses] |
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if self.submission.status not in statuses: |
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return True |
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else: |
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return False |
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def can_edit(self): |
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"""Returns True if I can edit a sample/animal according to submission |
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status |
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Returns: |
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bool |
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""" |
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statuses = ['waiting', 'submitted'] |
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return self.__can_I(statuses) |
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def can_delete(self): |
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"""Returns True if I can delete a sample/animal according to submission |
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status |
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Returns: |
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bool |
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""" |
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statuses = ['waiting', 'submitted'] |
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return self.__can_I(statuses) |
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cnr-ibba /
IMAGE-InjectTool
