diff --git a/backend/metagenedb/api/catalog/admin_urls.py b/backend/metagenedb/api/catalog/admin_urls.py
index 59b4f8a8e705fa51682c85be9f3eef602349f868..5291f5983abeec9f4981f188a647616a1b9f3f12 100644
--- a/backend/metagenedb/api/catalog/admin_urls.py
+++ b/backend/metagenedb/api/catalog/admin_urls.py
@@ -7,4 +7,5 @@ urlpatterns = [
path('compute-counts/', admin_commands.ComputeCountsAPI.as_view()),
path('compute-gene-length/', admin_commands.ComputeGeneLengthAPI.as_view()),
path('compute-taxo-repartition/', admin_commands.ComputeTaxonomyRepartitionAPI.as_view()),
+ path('compute-taxo-presence/', admin_commands.ComputeTaxonomyPresenceAPI.as_view()),
]
diff --git a/backend/metagenedb/api/catalog/views/admin_commands.py b/backend/metagenedb/api/catalog/views/admin_commands.py
index 2898ceb8022b01caf3ebc0adccc572df92d9c72a..717ab196147822de87713a1c88aa2f1566e8318f 100644
--- a/backend/metagenedb/api/catalog/views/admin_commands.py
+++ b/backend/metagenedb/api/catalog/views/admin_commands.py
@@ -1,18 +1,19 @@
import logging
from drf_yasg.utils import swagger_auto_schema
-from drf_yasg.openapi import Response
+# from drf_yasg.openapi import Response
from rest_framework import permissions
-# from rest_framework.response import Response
+from rest_framework.response import Response
from rest_framework.status import HTTP_500_INTERNAL_SERVER_ERROR
from rest_framework.views import APIView
from rest_framework_jwt.authentication import JSONWebTokenAuthentication
from metagenedb.apps.catalog.management.commands.compute_stats import (
- ComputeCounts, ComputeGeneLength, ComputeTaxonomyRepartition
+ compute_gene_counts, compute_gene_length, compute_taxonomy_presence, compute_taxonomy_repartition
)
logger = logging.getLogger(__name__)
+SOURCE_CHOICES = ['all', 'virgo', 'igc']
class AdminCommandsAPI(APIView):
@@ -21,13 +22,13 @@ class AdminCommandsAPI(APIView):
class ComputeStatisticsAPI(AdminCommandsAPI):
- compute_class = None
+ compute_function = None
error_message = "Could not compute stats due to server error"
- success_message = "Stats successfully computed"
+ success_message = "Stats successfully computing on worker...."
def get(self, request, format=None):
try:
- self.compute_class().all()
+ self.compute_function.delay(SOURCE_CHOICES)
except Exception as exception:
logger.warning(exception)
return Response({"message": self.error_message},
@@ -36,8 +37,8 @@ class ComputeStatisticsAPI(AdminCommandsAPI):
class ComputeCountsAPI(ComputeStatisticsAPI):
- compute_class = ComputeCounts
- success_message = "Counts on gene annotation successfully computed"
+ compute_function = compute_gene_counts
+ success_message = "Gene counts successfully computing on worker...."
@swagger_auto_schema(
operation_description="Compute counts for the different annotations of the genes",
@@ -48,9 +49,22 @@ class ComputeCountsAPI(ComputeStatisticsAPI):
return super().get(*args, **kwargs)
+class ComputeGeneLengthAPI(ComputeStatisticsAPI):
+ compute_function = compute_gene_length
+ success_message = "Gene length successfully computing on worker...."
+
+ @swagger_auto_schema(
+ operation_description="Compute gene length distribution",
+ operation_summary="API to compute gene length distribution.",
+ tags=['admin-commands'],
+ )
+ def get(self, *args, **kwargs):
+ return super().get(*args, **kwargs)
+
+
class ComputeTaxonomyRepartitionAPI(ComputeStatisticsAPI):
- compute_class = ComputeTaxonomyRepartition
- success_message = "Different taxonomy repartition successfully computed"
+ compute_function = compute_taxonomy_repartition
+ success_message = "Taxonomy repartition successfully computing on worker...."
@swagger_auto_schema(
operation_description="Compute repartition of taxonomy among genes",
@@ -61,13 +75,13 @@ class ComputeTaxonomyRepartitionAPI(ComputeStatisticsAPI):
return super().get(*args, **kwargs)
-class ComputeGeneLengthAPI(ComputeStatisticsAPI):
- compute_class = ComputeGeneLength
- success_message = "Gene length for different windows size successfully computed"
+class ComputeTaxonomyPresenceAPI(ComputeStatisticsAPI):
+ compute_function = compute_taxonomy_presence
+ success_message = "Taxonomy presence successfully computing on worker...."
@swagger_auto_schema(
- operation_description="Compute gene length distribution",
- operation_summary="API to compute gene length distribution.",
+ operation_description="Compute presence of taxonomy among genes",
+ operation_summary="API to compute presence of taxonomy.",
tags=['admin-commands'],
)
def get(self, *args, **kwargs):
diff --git a/backend/metagenedb/api/catalog/views/celery_test.py b/backend/metagenedb/api/catalog/views/celery_test.py
index 23ce7289268a9666efba399e18bdc1584bd42fc3..43e2d0cfc75acf4cbdd67d79af42b7221cd6f9af 100644
--- a/backend/metagenedb/api/catalog/views/celery_test.py
+++ b/backend/metagenedb/api/catalog/views/celery_test.py
@@ -13,13 +13,7 @@ def test_task(msg):
return msg
-@task(name="poete")
-def mul(x, y):
- return x * y
-
-
@api_view()
def test_task_view(request):
- msg = test_task.delay("pirooooouettee")
- muli = mul.delay(2, 4)
- return Response({"message": f"Tested celery task: {msg.get(timeout=1)} {muli.get(timeout=1)}"})
+ msg = test_task.delay("I am alive")
+ return Response({"message": f"Tested celery task: {msg.get(timeout=60)}"})
diff --git a/backend/metagenedb/apps/catalog/management/commands/compute_stats.py b/backend/metagenedb/apps/catalog/management/commands/compute_stats.py
index 66aa0600c0d41af06c84fa28fcf2ab6a4db9e37a..424b5186a8cd500ce0ba414f9871641958b0bd95 100644
--- a/backend/metagenedb/apps/catalog/management/commands/compute_stats.py
+++ b/backend/metagenedb/apps/catalog/management/commands/compute_stats.py
@@ -1,5 +1,7 @@
import logging
+from typing import List
+from celery.decorators import task
from django.core.exceptions import ValidationError
from django.core.management.base import BaseCommand
from slugify import slugify
@@ -30,10 +32,6 @@ class ComputeStatistics:
raise(validation_error)
statistics.save()
- def clean_db(self):
- logger.info("Deleting all statistics entries...")
- Statistics.objects.all().delete()
-
class ComputeCounts(ComputeStatistics):
METHODS = [
@@ -163,6 +161,35 @@ class ComputeTaxonomyPresence(ComputeStatistics):
self._save_to_db(payload)
+def clean_db():
+ logger.info("Deleting all statistics entries...")
+ Statistics.objects.all().delete()
+
+
+@task(name="compute_stats.compute_gene_counts")
+def compute_gene_counts(gene_sources: List[str]):
+ for gene_source in gene_sources:
+ ComputeCounts(gene_source).all()
+
+
+@task(name="compute_stats.compute_gene_length")
+def compute_gene_length(gene_sources: List[str]):
+ for gene_source in gene_sources:
+ ComputeGeneLength(gene_source).all()
+
+
+@task(name="compute_stats.compute_taxonomy_repartition")
+def compute_taxonomy_repartition(gene_sources: List[str]):
+ for gene_source in gene_sources:
+ ComputeTaxonomyRepartition(gene_source).all()
+
+
+@task(name="compute_stats.compute_taxonomy_presence")
+def compute_taxonomy_presence(gene_sources: List[str]):
+ for gene_source in gene_sources:
+ ComputeTaxonomyPresence(gene_source).all()
+
+
class Command(BaseCommand):
help = "Compute gene catalog statistics."
STEP_CHOICES = ['clean', 'counts', 'gene-length', 'taxonomy_repartition', 'taxonomy_presence']
@@ -202,14 +229,13 @@ class Command(BaseCommand):
self.set_logger_level(int(options['verbosity']))
only_step = self._get_and_validate_only_step(options['only'])
gene_sources = self._get_and_validate_source(options['source'])
- for gene_source in gene_sources:
- if only_step == "clean":
- ComputeStatistics(gene_source).clean_db()
- if only_step is None or only_step == "counts":
- ComputeCounts(gene_source).all()
- if only_step is None or only_step == "gene-length":
- ComputeGeneLength(gene_source).all()
- if only_step is None or only_step == "taxonomy_repartition":
- ComputeTaxonomyRepartition(gene_source).all()
- if only_step is None or only_step == "taxonomy_presence":
- ComputeTaxonomyPresence(gene_source).all()
+ if only_step == "clean":
+ clean_db()
+ if only_step is None or only_step == "counts":
+ compute_gene_counts.delay(gene_sources)
+ if only_step is None or only_step == "gene-length":
+ compute_gene_length.delay(gene_sources)
+ if only_step is None or only_step == "taxonomy_repartition":
+ compute_taxonomy_repartition.delay(gene_sources)
+ if only_step is None or only_step == "taxonomy_presence":
+ compute_taxonomy_presence.delay(gene_sources)