From 197b32bd43c202a1e5e1a04adc7ac8dd7e6ac974 Mon Sep 17 00:00:00 2001
From: Kenzo-Hugo Hillion <kenzo-hugo.hillion1@pasteur.fr>
Date: Fri, 23 Aug 2019 16:21:54 +0200
Subject: [PATCH] start class to contact metagenedb api
---
backend/metagenedb/api/catalog/views/gene.py | 16 -------
.../metagenedb/common/utils/api/__init__.py | 1 +
.../metagenedb/common/utils/api/metagenedb.py | 45 +++++++++++++++++++
.../common/{api.py => utils/api/togows.py} | 0
4 files changed, 46 insertions(+), 16 deletions(-)
create mode 100644 backend/metagenedb/common/utils/api/__init__.py
create mode 100644 backend/metagenedb/common/utils/api/metagenedb.py
rename backend/metagenedb/common/{api.py => utils/api/togows.py} (100%)
diff --git a/backend/metagenedb/api/catalog/views/gene.py b/backend/metagenedb/api/catalog/views/gene.py
index db94f34..fe811b9 100644
--- a/backend/metagenedb/api/catalog/views/gene.py
+++ b/backend/metagenedb/api/catalog/views/gene.py
@@ -1,5 +1,4 @@
import pandas as pd
-from django.core.exceptions import ObjectDoesNotExist
from drf_yasg import openapi
from drf_yasg.utils import swagger_auto_schema
from rest_framework import status
@@ -51,21 +50,6 @@ class GeneViewSet(ModelViewSet):
def get_permissions(self):
return super(self.__class__, self).get_permissions()
- def create(self, request, *args, **kwargs):
- """
- Overload create to behave like an upsert method.
- """
- serializer = self.get_serializer(data=request.data)
- try:
- gene_obj = self.queryset.get(gene_id=request.data.get('gene_id'))
- serializer = self.get_serializer(gene_obj, data=request.data)
- except ObjectDoesNotExist:
- serializer = self.get_serializer(data=request.data)
- serializer.is_valid(raise_exception=True)
- self.perform_create(serializer)
- headers = self.get_success_headers(serializer.data)
- return Response(serializer.data, status=status.HTTP_201_CREATED, headers=headers)
-
def _count_windows(self, df, window_size=10000, window_col=GENE_LENGTH_COL):
"""
Count how many line of the df belong to each windows defined by the window_size for the window_col
diff --git a/backend/metagenedb/common/utils/api/__init__.py b/backend/metagenedb/common/utils/api/__init__.py
new file mode 100644
index 0000000..17aa35c
--- /dev/null
+++ b/backend/metagenedb/common/utils/api/__init__.py
@@ -0,0 +1 @@
+from .togows import TogoWSEntry # noqa
diff --git a/backend/metagenedb/common/utils/api/metagenedb.py b/backend/metagenedb/common/utils/api/metagenedb.py
new file mode 100644
index 0000000..5db3dd0
--- /dev/null
+++ b/backend/metagenedb/common/utils/api/metagenedb.py
@@ -0,0 +1,45 @@
+import logging
+import requests
+from abc import ABC
+from urllib.parse import urljoin
+
+logging.basicConfig(level=logging.INFO)
+_LOGGER = logging.getLogger(__name__)
+
+
+class MetageneDB(ABC):
+ BASE_URL = 'http://localhost/'
+ ROUTE = ''
+ HEADERS = {
+ 'Content-type': 'application/json',
+ 'Accept': '*/*'
+ }
+
+ def __init__(self, base_url=BASE_URL):
+ self.url = urljoin(base_url, self.ROUTE)
+
+
+class MetageneDBCatalogGene(MetageneDB):
+ ROUTE = 'api/catalog/v1/genes/'
+
+ def get_genes(self):
+ response = requests.get(self.url)
+ response.raise_for_status()
+ return response.json()
+
+ def get(self, gene_id):
+ full_url = urljoin(self.url, gene_id)
+ response = requests.get(full_url)
+ response.raise_for_status()
+ return response.json()
+
+ def post(self, data):
+ response = requests.post(f"{self.url}", json=data, headers=self.HEADERS)
+ response.raise_for_status()
+ return response.json()
+
+ def put(self, gene_id, data):
+ full_url = urljoin(self.url, gene_id)
+ response = requests.put(f"{full_url}/", json=data, headers=self.HEADERS)
+ response.raise_for_status()
+ return response.json()
diff --git a/backend/metagenedb/common/api.py b/backend/metagenedb/common/utils/api/togows.py
similarity index 100%
rename from backend/metagenedb/common/api.py
rename to backend/metagenedb/common/utils/api/togows.py
--
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