From 40a2ecaa7e1af283e769e0798f41675b08d16a8a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20=20MENAGER?= <herve.menager@pasteur.fr>
Date: Mon, 12 Jun 2017 16:08:27 +0200
Subject: [PATCH] refactor model data ws retrieval in AutoFillableModel
Former-commit-id: 6ce2b8f1ac3abdb736089b328505f7ed0992fa61
---
.../management/commands/import_v1_data.py | 6 +--
ippisite/ippidb/models.py | 47 ++++++++++++-------
2 files changed, 33 insertions(+), 20 deletions(-)
diff --git a/ippisite/ippidb/management/commands/import_v1_data.py b/ippisite/ippidb/management/commands/import_v1_data.py
index 30a3cab0..41c0a5b7 100644
--- a/ippisite/ippidb/management/commands/import_v1_data.py
+++ b/ippisite/ippidb/management/commands/import_v1_data.py
@@ -107,7 +107,7 @@ class Command(BaseCommand):
else:
b.source = 'PT'
b.id_source = row[2]
- b.save()
+ b.save(autofill=True)
except Exception as e:
self.stdout.write(self.style.ERROR('Failed inserting {}'.format(row[2])))
else:
@@ -125,7 +125,7 @@ class Command(BaseCommand):
try:
p = Protein()
p.uniprot_id = row[1]
- p.save()
+ p.save(autofill=True)
except Exception as e:
if options['stoponfail']:
import traceback
@@ -145,7 +145,7 @@ class Command(BaseCommand):
p = Domain()
p.pfam_acc = row[2]
p.domain_family = row[4]
- p.save()
+ p.save(autofill=True)
except Exception as e:
if options['stoponfail']:
import traceback
diff --git a/ippisite/ippidb/models.py b/ippisite/ippidb/models.py
index 43496e76..5cc9d3f7 100644
--- a/ippisite/ippidb/models.py
+++ b/ippisite/ippidb/models.py
@@ -4,7 +4,24 @@ from django.db import models
from .ws import get_pubmed_info, get_epo_info, get_uniprot_info, get_taxonomy_info, get_go_info, get_pfam_info
-class Bibliography(models.Model):
+class AutoFillableModel(models.Model):
+ """
+ AutoFillableModel makes it possible to automatically fill model fields from
+ external sources in the autofill() method
+ The save method allows to either include autofill or not. in autofill kwarg is
+ set to True, save() will first call autofill(), otherwise it won't
+ """
+
+ class Meta:
+ abstract = True
+
+ def save(self, *args, **kwargs):
+ if kwargs.get('autofill') is True:
+ self.autofill()
+ super(AutoFillableModel, self).save(*args, **kwargs)
+
+
+class Bibliography(AutoFillableModel):
"""
Bibliography data table
"""
@@ -26,7 +43,7 @@ class Bibliography(models.Model):
pharmacokinetic = models.BooleanField('pharmacokinetic study performed', default=False)
xray = models.BooleanField('contains xray data', default=False)
- def save(self, *args, **kwargs):
+ def autofill(self):
if self.source == 'PM':
info = get_pubmed_info(self.id_source)
else:
@@ -35,7 +52,6 @@ class Bibliography(models.Model):
self.journal_name = info['journal_name']
self.authors_list = info['authors_list']
self.biblio_year = info['biblio_year']
- super(Bibliography, self).save(*args, **kwargs)
class Meta:
verbose_name_plural = "bibliographies"
@@ -44,14 +60,13 @@ class Bibliography(models.Model):
return '{}, {}'.format(self.source, self.id_source)
-class Taxonomy(models.Model):
+class Taxonomy(AutoFillableModel):
taxonomy_id = models.DecimalField('NCBI TaxID', unique=True, max_digits=9, decimal_places=0)
name = models.CharField('Organism name', max_length=200)
- def save(self, *args, **kwargs):
+ def autofill(self):
info = get_taxonomy_info(self.taxonomy_id)
self.name = info['scientific_name']
- super(Taxonomy, self).save(*args, **kwargs)
def __str__(self):
return self.name
@@ -59,19 +74,18 @@ class Taxonomy(models.Model):
class Meta:
verbose_name_plural = "taxonomies"
-class MolecularFunction(models.Model):
+class MolecularFunction(AutoFillableModel):
go_id = models.CharField('Gene Ontology ID', unique=True, max_length=10) # GO term id format: 'GO:0000000'
description = models.CharField('description', max_length=500)
- def save(self, *args, **kwargs):
+ def autofill(self):
info = get_go_info(self.go_id)
self.description = info['label']
- super(MolecularFunction, self).save(*args, **kwargs)
def __str__(self):
return self.description
-class Protein(models.Model):
+class Protein(AutoFillableModel):
uniprot_id = models.CharField('Uniprot ID', unique=True, max_length=10)
recommended_name_long = models.CharField('Uniprot Recommended Name (long)', max_length=75)
short_name = models.CharField('Short name', max_length=50)
@@ -80,7 +94,7 @@ class Protein(models.Model):
organism = models.ForeignKey('Taxonomy')
molecular_functions = models.ManyToManyField(MolecularFunction)
- def save(self, *args, **kwargs):
+ def autofill(self):
info = get_uniprot_info(self.uniprot_id)
self.recommended_name_long = info['recommended_name']
self.gene_name = info['gene']
@@ -90,32 +104,31 @@ class Protein(models.Model):
except Taxonomy.DoesNotExist:
taxonomy = Taxonomy()
taxonomy.taxonomy_id = info['organism']
- taxonomy.save()
+ taxonomy.save(autofill=True)
self.organism = taxonomy
- super(Protein, self).save(*args, **kwargs)
+ #super(Protein, self).save(*args, **kwargs)
for go_id in info['molecular_functions']:
try:
mol_function = MolecularFunction.objects.get(go_id=go_id)
except MolecularFunction.DoesNotExist:
mol_function = MolecularFunction()
mol_function.go_id = go_id
- mol_function.save()
+ mol_function.save(autofill=True)
self.molecular_functions.add(mol_function)
def __str__(self):
return '{} ({})'.format(self.uniprot_id, self.recommended_name_long)
-class Domain(models.Model):
+class Domain(AutoFillableModel):
pfam_acc = models.CharField('Pfam Accession', max_length=10, unique=True)
pfam_id = models.CharField('Pfam Family Identifier', max_length=20)
pfam_description = models.CharField('Pfam Description', max_length=100)
domain_family = models.CharField('Domain family', max_length=25) #TODO: what is this field? check database contents
- def save(self, *args, **kwargs):
+ def autofill(self):
info = get_pfam_info(self.pfam_acc)
self.pfam_id = info['id']
self.pfam_description = info['description']
- super(Domain, self).save(*args, **kwargs)
def __str__(self):
return '{} ({}-{})'.format(self.pfam_acc, self.pfam_id, self.pfam_description)
--
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