diff --git a/backend/metagenedb/apps/catalog/factory/function.py b/backend/metagenedb/apps/catalog/factory/function.py
index a8b077ebc828c9b5bd0894b8fa3b3bff182cdf07..4d0a275f9576bb2e094fba0e33772503b9516038 100644
--- a/backend/metagenedb/apps/catalog/factory/function.py
+++ b/backend/metagenedb/apps/catalog/factory/function.py
@@ -1,36 +1,33 @@
-from factory import DjangoModelFactory, fuzzy
-from faker import Factory
+from factory import DjangoModelFactory, Faker, fuzzy
from metagenedb.apps.catalog import models
-from .fuzzy_base import FuzzyLowerText
-
-faker = Factory.create()
SELECTED_SOURCE = [i[0] for i in models.Function.SOURCE_CHOICES]
EGGNOG_VERSIONS = [i[0] for i in models.EggNOG.VERSION_CHOICES]
-class BaseFunctionFactory(DjangoModelFactory):
- function_id = FuzzyLowerText(prefix='function-', length=15)
-
-
-class FunctionFactory(BaseFunctionFactory):
+class FunctionFactory(DjangoModelFactory):
class Meta:
model = models.Function
+ function_id = Faker('bothify', text='function-####')
source = fuzzy.FuzzyChoice(SELECTED_SOURCE)
- function_id = FuzzyLowerText(prefix='function-', length=15)
-class EggNOGFactory(BaseFunctionFactory):
+class EggNOGFactory(DjangoModelFactory):
+ function_id = Faker('bothify', text='COG####')
+ name = Faker('bothify', text='COG-????????')
+
class Meta:
model = models.EggNOG
version = fuzzy.FuzzyChoice(EGGNOG_VERSIONS)
-class KeggOrthologyFactory(BaseFunctionFactory):
+class KeggOrthologyFactory(DjangoModelFactory):
+ function_id = Faker('bothify', text='K0####')
+
class Meta:
model = models.KeggOrthology
diff --git a/backend/metagenedb/apps/catalog/factory/gene.py b/backend/metagenedb/apps/catalog/factory/gene.py
index 304d3edc8a12a90ee906b804da47c1933cc2151b..3637655ab605e2c8b6e0a3d59d61379869bba9ea 100644
--- a/backend/metagenedb/apps/catalog/factory/gene.py
+++ b/backend/metagenedb/apps/catalog/factory/gene.py
@@ -1,16 +1,12 @@
from factory import (
- DjangoModelFactory, RelatedFactory, SubFactory, fuzzy
+ DjangoModelFactory, Faker, RelatedFactory, SubFactory, fuzzy
)
-from faker import Factory
from metagenedb.apps.catalog import models
-from .fuzzy_base import FuzzyLowerText
-from .function import FunctionFactory
+from .function import FunctionFactory, KeggOrthologyFactory, EggNOGFactory
from .taxonomy import TaxonomyFactory
-faker = Factory.create()
-
GENE_SOURCES = [i[0] for i in models.Gene.SOURCE_CHOICES]
@@ -18,9 +14,9 @@ class GeneFactory(DjangoModelFactory):
class Meta:
model = models.Gene
- gene_id = FuzzyLowerText(prefix='gene-', length=15)
- name = fuzzy.FuzzyText(prefix='name-', length=15)
- length = fuzzy.FuzzyInteger(200, 10000)
+ gene_id = Faker('bothify', text='gene-?#?#??-#??#?#')
+ name = Faker('bothify', text='Gene_name-##-????')
+ length = Faker('pyint', min_value=200, max_value=4200)
source = fuzzy.FuzzyChoice(GENE_SOURCES)
@@ -36,9 +32,17 @@ class GeneFunctionFactory(DjangoModelFactory):
function = SubFactory(FunctionFactory)
+class GeneKeggFactory(GeneFunctionFactory):
+ function = SubFactory(KeggOrthologyFactory)
+
+
+class GeneEggNOGFactory(GeneFunctionFactory):
+ function = SubFactory(EggNOGFactory)
+
+
class GeneWithKeggFactory(GeneFactory):
- kegg = RelatedFactory(GeneFunctionFactory, 'gene', function__source='kegg')
+ kegg = RelatedFactory(GeneKeggFactory, 'gene')
class GeneWithEggNOGFactory(GeneFactory):
- eggnog = RelatedFactory(GeneFunctionFactory, 'gene', function__source='eggnog')
+ eggnog = RelatedFactory(GeneEggNOGFactory, 'gene')
diff --git a/backend/metagenedb/apps/catalog/factory/taxonomy.py b/backend/metagenedb/apps/catalog/factory/taxonomy.py
index 1cca70d4f2735b86cfdf6f8f6dcb8afaeffb021f..0f770047d2c1fd6524b172d5a29b145fee9c8ed3 100644
--- a/backend/metagenedb/apps/catalog/factory/taxonomy.py
+++ b/backend/metagenedb/apps/catalog/factory/taxonomy.py
@@ -30,6 +30,7 @@ class DbGenerator:
"""
Tree need to be an OrderedDict from higher to lower level
"""
+ self.last_tax = None
for rank, desc in tree.items():
if desc['tax_id'] not in self.created_ids:
self.last_tax = TaxonomyFactory.create(
diff --git a/backend/metagenedb/apps/catalog/management/commands/create_light_db.py b/backend/metagenedb/apps/catalog/management/commands/create_light_db.py
index 0945397ff10d331a1123a206536ce6951d32b74d..16bf6fa96ac8cd41645f469fd6813ba44c0f64b7 100644
--- a/backend/metagenedb/apps/catalog/management/commands/create_light_db.py
+++ b/backend/metagenedb/apps/catalog/management/commands/create_light_db.py
@@ -1,34 +1,25 @@
import logging
+from random import randint
from django.core.management.base import BaseCommand
+from metagenedb.apps.catalog.factory import GeneFactory, GeneWithEggNOGFactory, GeneWithKeggFactory
from metagenedb.apps.catalog.factory.taxonomy import generate_simple_db as gen_tax_db
from metagenedb.apps.catalog.models import (
- Gene, KeggOrthology, Taxonomy
+ Gene, Function, Taxonomy
+)
+from metagenedb.apps.catalog.management.commands.compute_stats import (
+ ComputeStatistics, ComputeCounts, ComputeGeneLength, ComputeTaxonomyRepartition, ComputeTaxonomyPresence
)
logging.basicConfig(format='[%(asctime)s] %(levelname)s:%(name)s:%(message)s')
-logger = logging.getLogger(__name__)
-
-
-def create_functions_db():
- KeggOrthology.objects.all().delete()
- keggs_to_create = {
- "K03556": {
- 'name': 'malT',
- 'long_name': "LuxR family transcriptional regulator, maltose regulon positive regulatory protein"
- },
- "K02229": {
- 'name': "cobG",
- 'long_name': 'precorrin-3B synthase [EC:1.14.13.83]'
- }
- }
- for kegg_id, values in keggs_to_create.items():
- KeggOrthology(
- function_id=kegg_id,
- name=values.get('name'),
- long_name=values.get('long_name')
- ).save()
+logger = logging.getLogger()
+
+
+def empty_db():
+ Gene.objects.all().delete()
+ Taxonomy.objects.all().delete()
+ Function.objects.all().delete()
def create_taxonomy_db():
@@ -37,13 +28,30 @@ def create_taxonomy_db():
def create_genes_db():
- pass
+ Gene.objects.all().delete()
+ GeneFactory.create_batch(50)
+ GeneWithEggNOGFactory.create_batch(15)
+ GeneWithKeggFactory.create_batch(12)
+ for tax in Taxonomy.objects.all():
+ GeneFactory.create_batch(randint(1, 10), taxonomy=tax)
+ GeneWithEggNOGFactory.create(taxonomy=tax)
+ GeneWithKeggFactory.create(taxonomy=tax)
+
+
+def compute_stats():
+ ComputeStatistics('all').clean_db()
+ for gene_source in ['all', 'virgo', 'igc']:
+ ComputeCounts(gene_source).all()
+ ComputeGeneLength(gene_source).all()
+ ComputeTaxonomyRepartition(gene_source).all()
+ ComputeTaxonomyPresence(gene_source).all()
def create_small_db():
- create_functions_db()
+ empty_db()
create_taxonomy_db()
create_genes_db()
+ compute_stats()
class Command(BaseCommand):
diff --git a/backend/metagenedb/apps/catalog/models/taxonomy.py b/backend/metagenedb/apps/catalog/models/taxonomy.py
index bd2bfe48466c6438ab1f20229e91dbaf2292f003..ffb2a12fd9c11b8b9d1cf7238be73fde4893484b 100644
--- a/backend/metagenedb/apps/catalog/models/taxonomy.py
+++ b/backend/metagenedb/apps/catalog/models/taxonomy.py
@@ -62,12 +62,13 @@ class Taxonomy(models.Model):
Build and save parental hierarchy for an entry
"""
hierarchy = {}
- if self.name != 'root' and self.parent is not None:
+ if self.name != 'root':
hierarchy[self.rank] = {
'tax_id': self.tax_id,
'name': self.name
}
- hierarchy = {**hierarchy, **getattr(self.parent, 'hierarchy', self.parent.build_hierarchy())}
+ if self.parent is not None:
+ hierarchy = {**hierarchy, **getattr(self.parent, 'hierarchy', self.parent.build_hierarchy())}
self.hierarchy = hierarchy
self.save()
return hierarchy
diff --git a/backend/scripts/populate_db/test_import_igc_data.py b/backend/scripts/populate_db/test_import_igc_data.py
index d43344693b235cc1430cc14de64fd806221ece72..1eeb0ef92c9b78f8ba72c7fd2b4f9b0ec7a55254 100644
--- a/backend/scripts/populate_db/test_import_igc_data.py
+++ b/backend/scripts/populate_db/test_import_igc_data.py
@@ -297,12 +297,12 @@ class TestBuildTaxoMapping(APITestCase):
self.assertDictEqual(self.import_igc_genes.phylum_mapping, expected_phylum_dict)
-class TestBuildBuildFunctionCatalog(APITestCase):
+class TestBuildFunctionCatalog(APITestCase):
@classmethod
def setUpTestData(cls):
- cls.keggs = KeggOrthologyFactory.create_batch(100)
- cls.eggnogs = EggNOGFactory.create_batch(100)
+ cls.keggs = KeggOrthologyFactory.create_batch(10)
+ cls.eggnogs = EggNOGFactory.create_batch(10)
def setUp(self):
self.import_igc_genes = ImportIGCGenes('test', 'test_url', 'test_token')