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Metagenomics
metagenedb
Commits
07f20010
Commit
07f20010
authored
Apr 01, 2021
by
Kenzo-Hugo Hillion
♻
Browse files
add logs and dependencies to build UML
parent
9c7e3bb2
Pipeline
#52538
failed with stages
in 2 minutes and 11 seconds
Changes
4
Pipelines
1
Hide whitespace changes
Inline
Side-by-side
backend/Pipfile
View file @
07f20010
...
...
@@ -30,6 +30,7 @@ pytest-factoryboy = "*"
pylint
=
"*"
mock
=
"*"
snakeviz
=
"*"
pydotplus
=
"*"
[packages]
certifi
=
"*"
...
...
@@ -67,6 +68,7 @@ django-health-check = "==3.0.0"
django-redis
=
"*"
kombu
=
"*"
dabeplech
=
"*"
pydotplus
=
"*"
[requires]
python_version
=
"3.7"
backend/metagenedb/apps/catalog/management/commands/create_update_eggnog.py
View file @
07f20010
...
...
@@ -40,6 +40,7 @@ class ImportEggNOG(object):
def
load_all
(
self
,
test
=
False
,
version
=
None
):
self
.
_build_functional_category_dict
()
self
.
total_eggnog_nb
=
file_len
(
self
.
annotation_file
)
logger
.
info
(
"Preparing to load %s items..."
,
self
.
total_eggnog_nb
)
with
open
(
self
.
annotation_file
,
"r"
)
as
file
:
for
line
in
file
:
eggnog_dict
=
self
.
eggnog_parser
.
get_dict
(
line
)
...
...
backend/metagenedb/apps/catalog/management/commands/create_update_kegg_ko.py
View file @
07f20010
...
...
@@ -28,6 +28,7 @@ class ImportKEGGKO(object):
all_ko_response
.
raise_for_status
()
all_ko
=
all_ko_response
.
text
.
splitlines
()
self
.
total_nb
=
len
(
all_ko
)
logger
.
info
(
"%s KEGG KO retrieved from KEGG API..."
,
self
.
total_nb
)
for
chunk
in
list_chunks
(
all_ko
,
chunk_size
):
ko_chunk
=
[
KEGGLineParser
.
ko_list
(
i
)
for
i
in
chunk
]
for
i
in
ko_chunk
:
...
...
backend/pyproject.toml
0 → 100644
View file @
07f20010
[build-system]
requires
=
[
"setuptools"
,
"wheel"
]
build-backend
=
"setuptools.build_meta:__legacy__"
\ No newline at end of file
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