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Metagenomics
metagenedb
Commits
8924454a
Commit
8924454a
authored
Sep 09, 2019
by
Kenzo-Hugo Hillion
♻
Browse files
Clean code
parent
0b93bd25
Changes
8
Hide whitespace changes
Inline
Side-by-side
backend/metagenedb/api/catalog/views/bulk_viewset.py
View file @
8924454a
...
...
@@ -8,7 +8,6 @@ class BulkViewSet(ModelViewSet):
def
get_objects
(
self
,
instance_ids
):
return
self
.
queryset
.
in_bulk
(
instance_ids
,
field_name
=
self
.
lookup_field
)
def
_created_payload
(
self
,
serializer
,
request
):
if
isinstance
(
request
.
data
,
list
):
return
{
...
...
@@ -38,12 +37,10 @@ class BulkViewSet(ModelViewSet):
# perform the classic update
return
super
().
update
(
request
,
*
args
,
**
kwargs
)
instance_ids
=
set
([
element
[
self
.
lookup_field
]
for
element
in
request
.
data
])
instances_set
=
self
.
get_objects
(
instance_ids
)
instances
=
[
instance
for
instance
in
instances_set
.
values
()]
serializer
=
self
.
get_serializer
(
instances
,
data
=
request
.
data
,
many
=
True
)
instances
=
self
.
get_objects
(
instance_ids
)
serializer
=
self
.
get_serializer
(
instances
.
values
(),
data
=
request
.
data
,
many
=
True
)
serializer
.
is_valid
(
raise_exception
=
True
)
# instance = self.get_object()
# serializer = self.get_serializer(instance, data=request.data, partial=partial)
# serializer.is_valid(raise_exception=True)
...
...
backend/metagenedb/apps/catalog/serializers/gene.py
View file @
8924454a
...
...
@@ -6,7 +6,6 @@ from rest_framework.utils import model_meta
from
metagenedb.apps.catalog.models
import
Function
,
Gene
,
Taxonomy
from
metagenedb.apps.catalog.serializers
import
FunctionSerializer
logging
.
basicConfig
(
level
=
logging
.
INFO
)
_LOGGER
=
logging
.
getLogger
(
__name__
)
...
...
backend/metagenedb/common/utils/parsers/igc.py
View file @
8924454a
import
logging
logging
.
basicConfig
(
level
=
logging
.
INFO
)
_LOGGER
=
logging
.
getLogger
(
__name__
)
...
...
backend/metagenedb/common/utils/parsers/kegg.py
View file @
8924454a
import
logging
logging
.
basicConfig
(
level
=
logging
.
INFO
)
_LOGGER
=
logging
.
getLogger
(
__name__
)
...
...
backend/metagenedb/common/utils/parsers/ncbi_taxonomy.py
View file @
8924454a
import
logging
logging
.
basicConfig
(
level
=
logging
.
INFO
)
_LOGGER
=
logging
.
getLogger
(
__name__
)
...
...
backend/scripts/populate_db/import_igc_data.py
View file @
8924454a
...
...
@@ -10,7 +10,6 @@ from slugify import slugify
from
metagenedb.common.utils.parsers
import
IGCLineParser
logging
.
basicConfig
(
level
=
logging
.
INFO
)
_LOGGER
=
logging
.
getLogger
(
__name__
)
...
...
backend/scripts/populate_db/import_ncbi_taxonomy.py
View file @
8924454a
...
...
@@ -15,7 +15,6 @@ django.setup()
from
metagenedb.apps.catalog.models
import
Taxonomy
# noqa
from
metagenedb.apps.catalog.serializers
import
TaxonomySerializer
# noqa
logging
.
basicConfig
(
level
=
logging
.
INFO
)
_LOGGER
=
logging
.
getLogger
(
__name__
)
SELECT_RELATED_PARENT
=
"parent{}"
.
format
(
"__parent"
*
40
)
...
...
backend/scripts/populate_db/load_kegg_ko.py
View file @
8924454a
...
...
@@ -18,7 +18,6 @@ django.setup()
from
metagenedb.apps.catalog.models
import
KeggOrthology
# noqa
logging
.
basicConfig
(
level
=
logging
.
INFO
)
_LOGGER
=
logging
.
getLogger
(
__name__
)
KEGG_KO_LIST_API
=
"http://rest.kegg.jp/list/ko"
...
...
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