Commit 2663d5b4 authored by Kenzo-Hugo Hillion's avatar Kenzo-Hugo Hillion
Browse files

Merge branch '162-standardize-import-data' into 'dev'

add logs and dependencies to build UML

See merge request !71
parents 9c7e3bb2 f25b2e66
Pipeline #52544 passed with stages
in 4 minutes and 30 seconds
...@@ -30,6 +30,7 @@ pytest-factoryboy = "*" ...@@ -30,6 +30,7 @@ pytest-factoryboy = "*"
pylint = "*" pylint = "*"
mock = "*" mock = "*"
snakeviz = "*" snakeviz = "*"
pydotplus = "*"
[packages] [packages]
certifi = "*" certifi = "*"
...@@ -67,6 +68,7 @@ django-health-check = "==3.0.0" ...@@ -67,6 +68,7 @@ django-health-check = "==3.0.0"
django-redis = "*" django-redis = "*"
kombu = "*" kombu = "*"
dabeplech = "*" dabeplech = "*"
pydotplus = "*"
[requires] [requires]
python_version = "3.7" python_version = "3.7"
This diff is collapsed.
...@@ -40,6 +40,7 @@ class ImportEggNOG(object): ...@@ -40,6 +40,7 @@ class ImportEggNOG(object):
def load_all(self, test=False, version=None): def load_all(self, test=False, version=None):
self._build_functional_category_dict() self._build_functional_category_dict()
self.total_eggnog_nb = file_len(self.annotation_file) 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: with open(self.annotation_file, "r") as file:
for line in file: for line in file:
eggnog_dict = self.eggnog_parser.get_dict(line) eggnog_dict = self.eggnog_parser.get_dict(line)
......
...@@ -28,6 +28,7 @@ class ImportKEGGKO(object): ...@@ -28,6 +28,7 @@ class ImportKEGGKO(object):
all_ko_response.raise_for_status() all_ko_response.raise_for_status()
all_ko = all_ko_response.text.splitlines() all_ko = all_ko_response.text.splitlines()
self.total_nb = len(all_ko) 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): for chunk in list_chunks(all_ko, chunk_size):
ko_chunk = [KEGGLineParser.ko_list(i) for i in chunk] ko_chunk = [KEGGLineParser.ko_list(i) for i in chunk]
for i in ko_chunk: for i in ko_chunk:
......
[build-system]
requires = ["setuptools", "wheel"]
build-backend = "setuptools.build_meta:__legacy__"
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