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Metagenomics
metagenedb
Commits
5389788c
Commit
5389788c
authored
Jun 18, 2019
by
Kenzo-Hugo Hillion
♻
Browse files
flake8 and refacto
parent
94f0faad
Changes
14
Hide whitespace changes
Inline
Side-by-side
backend/metagenedb/apps/catalog/admin/__init__.py
View file @
5389788c
from
.gene
import
GeneAdmin
from
.function
import
FunctionAdmin
,
KeggOrthologyAdmin
__all__
=
[
'GeneAdmin'
,
'FunctionAdmin'
,
'KeggOrthologyAdmin'
]
backend/metagenedb/apps/catalog/admin/admin.py
View file @
5389788c
...
...
@@ -26,4 +26,3 @@ class FunctionAdmin(admin.ModelAdmin):
list_display
=
(
'function_id'
,
'name'
,
'source'
)
search_fields
=
(
'function_id'
,)
backend/metagenedb/apps/catalog/migrations/0001_initial.py
View file @
5389788c
...
...
@@ -18,13 +18,13 @@ class Migration(migrations.Migration):
(
'id'
,
models
.
AutoField
(
auto_created
=
True
,
primary_key
=
True
,
serialize
=
False
,
verbose_name
=
'ID'
)),
(
'function_id'
,
models
.
CharField
(
db_index
=
True
,
max_length
=
100
)),
(
'name'
,
models
.
CharField
(
max_length
=
100
)),
(
'source'
,
models
.
CharField
(
choices
=
[(
'undef'
,
'Undefined'
),
(
'kegg'
,
'KEGG'
),
(
'eggnog'
,
'EggNOG'
)],
default
=
'undef'
,
max_length
=
10
)),
(
'source'
,
models
.
CharField
(
choices
=
[(
'undef'
,
'Undefined'
),
(
'kegg'
,
'KEGG'
),
(
'eggnog'
,
'EggNOG'
)],
default
=
'undef'
,
max_length
=
10
)),
# noqa
],
),
migrations
.
CreateModel
(
name
=
'KeggOrthology'
,
fields
=
[
(
'function_ptr'
,
models
.
OneToOneField
(
auto_created
=
True
,
on_delete
=
django
.
db
.
models
.
deletion
.
CASCADE
,
parent_link
=
True
,
primary_key
=
True
,
serialize
=
False
,
to
=
'catalog.Function'
)),
(
'function_ptr'
,
models
.
OneToOneField
(
auto_created
=
True
,
on_delete
=
django
.
db
.
models
.
deletion
.
CASCADE
,
parent_link
=
True
,
primary_key
=
True
,
serialize
=
False
,
to
=
'catalog.Function'
)),
# noqa
(
'ec_number'
,
models
.
CharField
(
blank
=
True
,
default
=
''
,
max_length
=
200
)),
(
'long_name'
,
models
.
CharField
(
max_length
=
500
)),
],
...
...
backend/metagenedb/apps/catalog/models/__init__.py
View file @
5389788c
from
.function
import
Function
,
KeggOrthology
from
.gene
import
Gene
__all__
=
[
'Function'
,
'KeggOrthology'
,
'Gene'
]
backend/metagenedb/apps/catalog/models/gene.py
View file @
5389788c
...
...
@@ -10,4 +10,3 @@ class Gene(models.Model):
def
__str__
(
self
):
return
self
.
gene_id
backend/metagenedb/apps/catalog/serializers.py
View file @
5389788c
...
...
@@ -14,4 +14,3 @@ class GeneSerializer(serializers.ModelSerializer):
class
Meta
:
model
=
Gene
fields
=
(
'gene_id'
,
'gene_length'
,
'functions'
)
backend/metagenedb/apps/catalog/tests.py
deleted
100644 → 0
View file @
94f0faad
from
django.test
import
TestCase
# Create your tests here.
backend/metagenedb/apps/catalog/views.py
View file @
5389788c
...
...
@@ -11,6 +11,7 @@ from .serializers import GeneSerializer
def
index
(
request
):
return
HttpResponse
(
f
"Welcome to the catalog page."
)
@
api_view
([
'GET'
])
def
gene_list
(
request
):
"""
...
...
@@ -37,7 +38,7 @@ def gene_list(request):
return
Response
({
'data'
:
serializer
.
data
,
'count'
:
paginator
.
count
,
'numpages'
:
paginator
.
num_pages
,
'nextlink'
:
'/api/genes/?page='
+
str
(
nextPage
),
'prevlink'
:
'/api/genes/?page='
+
str
(
previousPage
)})
@
api_view
([
'GET'
])
def
gene_detail
(
request
,
gene_id
):
...
...
backend/metagenedb/tests/test_user.py
0 → 100644
View file @
5389788c
from
django.contrib.auth.models
import
User
from
django.test
import
TestCase
class
TestDatabase
(
TestCase
):
def
test_create_user
(
self
):
user
=
User
.
objects
.
create_user
(
username
=
'user'
,
email
=
'user@foo.com'
,
password
=
'pass'
)
user
.
save
()
user_count
=
User
.
objects
.
all
().
count
()
self
.
assertEqual
(
user_count
,
1
)
backend/metagenedb/urls.py
View file @
5389788c
...
...
@@ -16,7 +16,6 @@ Including another URLconf
from
django.contrib
import
admin
from
django.urls
import
include
,
path
from
rest_framework
import
routers
urlpatterns
=
[
path
(
'admin/'
,
admin
.
site
.
urls
),
...
...
backend/requirements_dev.txt
View file @
5389788c
...
...
@@ -49,3 +49,4 @@ traitlets==4.3.2
wcwidth==0.1.7
webencodings==0.5.1
widgetsnbextension==3.4.2
flake8
backend/scripts/import_igc_data.py
View file @
5389788c
...
...
@@ -12,7 +12,7 @@ from django.core.exceptions import ValidationError
os
.
environ
.
setdefault
(
"DJANGO_SETTINGS_MODULE"
,
"metagenedb.settings"
)
django
.
setup
()
from
metagenedb.apps.catalog.models
import
Gene
,
Function
from
metagenedb.apps.catalog.models
import
Gene
,
Function
# noqa
logging
.
basicConfig
(
level
=
logging
.
INFO
)
_LOGGER
=
logging
.
getLogger
(
__name__
)
...
...
backend/scripts/load_kegg_ko.py
View file @
5389788c
...
...
@@ -12,7 +12,7 @@ from django.core.exceptions import ValidationError
os
.
environ
.
setdefault
(
"DJANGO_SETTINGS_MODULE"
,
"metagenedb.settings"
)
django
.
setup
()
from
metagenedb.apps.catalog.models
import
KeggOrthology
from
metagenedb.apps.catalog.models
import
KeggOrthology
# noqa
logging
.
basicConfig
(
level
=
logging
.
INFO
)
_LOGGER
=
logging
.
getLogger
(
__name__
)
...
...
@@ -62,7 +62,7 @@ def create_kegg_ko(kegg_ko):
def
run
():
args
=
parse_arguments
()
args
=
parse_arguments
()
# noqa
all_ko
=
requests
.
get
(
"http://rest.kegg.jp/list/ko"
)
all_ko
.
raise_for_status
()
inserted_kegg
=
0
...
...
@@ -84,6 +84,5 @@ def run():
# Create unknown entry
if
__name__
==
"__main__"
:
run
()
backend/setup.py
View file @
5389788c
...
...
@@ -11,5 +11,4 @@ setup(name="metagenedb",
'djangorestframework'
],
packages
=
find_packages
(),
scripts
=
[
'scripts/manage.py'
],
)
scripts
=
[
'scripts/manage.py'
])
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