From bf4feb29b03aa05257b613e120cf0152dab78b6c Mon Sep 17 00:00:00 2001
From: Kenzo-Hugo Hillion <kenzo-hugo.hillion1@pasteur.fr>
Date: Mon, 10 Aug 2020 16:39:19 +0200
Subject: [PATCH] use KEGGAPI instead of TOGOWS from dabeplech to retrieve KEGG
details
---
.../common/utils/external_api/test_togows.py | 6 +-
.../common/utils/external_api/togows.py | 8 +-
frontend/src/components/keggcard/keggcard.js | 89 ++++++++++---------
3 files changed, 55 insertions(+), 48 deletions(-)
diff --git a/backend/metagenedb/common/utils/external_api/test_togows.py b/backend/metagenedb/common/utils/external_api/test_togows.py
index 1752ead..88ad41c 100644
--- a/backend/metagenedb/common/utils/external_api/test_togows.py
+++ b/backend/metagenedb/common/utils/external_api/test_togows.py
@@ -14,11 +14,11 @@ class TestGetFunctionExternalInfo(TestCase):
external_info_retriever.get_details()
def test_get_details_kegg(self):
- with mock.patch('metagenedb.common.utils.external_api.togows.TogoWSEntryAPI') as MockTogoWSEntryAPI:
- MockTogoWSEntryAPI.return_value.get.return_value = [{"info": "some_info"}]
+ with mock.patch('metagenedb.common.utils.external_api.togows.KEGGAPI') as MockKEGGAPI:
+ MockKEGGAPI.return_value.get.return_value.dict.return_value = {"info": "some_info"}
test_url = "http://test.com/"
test_id = "test_kegg_id"
- MockTogoWSEntryAPI.return_value.url = test_url
+ MockKEGGAPI.return_value.url = test_url
expected_dict = {
'info': 'some_info',
settings.API_KEY_ADDITIONAL_INFO: {
diff --git a/backend/metagenedb/common/utils/external_api/togows.py b/backend/metagenedb/common/utils/external_api/togows.py
index 560b55c..14ff0a7 100644
--- a/backend/metagenedb/common/utils/external_api/togows.py
+++ b/backend/metagenedb/common/utils/external_api/togows.py
@@ -2,7 +2,7 @@ import logging
from django.conf import settings
-from dabeplech.togows import TogoWSEntryAPI
+from dabeplech import KEGGAPI
logger = logging.getLogger(__name__)
@@ -21,8 +21,9 @@ class GetFunctionExternalInfo:
"""
Get detailed information from KEGG orthology through Togows.
"""
- kegg_api = TogoWSEntryAPI("kegg-orthology")
- response = kegg_api.get(self.function_id)[0]
+ logger.info("Retrieving information from KEGG API")
+ kegg_api = KEGGAPI()
+ response = kegg_api.get(self.function_id).dict()
response[settings.API_KEY_ADDITIONAL_INFO] = {
'comment': f"Information retrieved from external source: {kegg_api.url}",
'url': f"{kegg_api.url}{self.function_id}"
@@ -30,5 +31,4 @@ class GetFunctionExternalInfo:
return response
def get_details(self):
- logger.info("Retrieving information from KEGG through togows")
return getattr(self, f"_get_{self.source}", self._get_unknown_source)()
diff --git a/frontend/src/components/keggcard/keggcard.js b/frontend/src/components/keggcard/keggcard.js
index 5e783a1..fd92c8a 100644
--- a/frontend/src/components/keggcard/keggcard.js
+++ b/frontend/src/components/keggcard/keggcard.js
@@ -69,7 +69,6 @@ export default {
this.buildPathways(response),
this.buildDiseases(response),
this.buildModules(response),
- this.buildReferences(response),
];
},
buildPathways(response) {
@@ -78,17 +77,19 @@ export default {
icon: 'fas fa-bezier-curve',
content: [],
};
- Object.entries(response.data.pathways).forEach(([key, value]) => {
- pathways.content.push(
- {
- id: key,
- name: value,
- url: `https://www.genome.jp/kegg-bin/show_pathway?${key}+${this.keggId}`,
- url_label: "Open in KEGG",
- fetch: true,
- },
- );
- });
+ if(response.data.pathways) {
+ Object.entries(response.data.pathways).forEach(([key, value]) => {
+ pathways.content.push(
+ {
+ id: key,
+ name: value,
+ url: `https://www.genome.jp/kegg-bin/show_pathway?${key}+${this.keggId}`,
+ url_label: "Open in KEGG",
+ fetch: true,
+ },
+ );
+ });
+ }
return pathways;
},
buildModules(response) {
@@ -97,16 +98,18 @@ export default {
icon: 'fas fa-bezier-curve',
content: [],
};
- Object.entries(response.data.modules).forEach(([key, value]) => {
- modules.content.push(
- {
- id: key,
- name: value,
- url: `https://www.genome.jp/kegg-bin/show_module?${key}+${this.keggId}`,
- url_label: "Open in KEGG"
- },
- );
- });
+ if(response.data.modules) {
+ Object.entries(response.data.modules).forEach(([key, value]) => {
+ modules.content.push(
+ {
+ id: key,
+ name: value,
+ url: `https://www.genome.jp/kegg-bin/show_module?${key}+${this.keggId}`,
+ url_label: "Open in KEGG"
+ },
+ );
+ });
+ }
return modules;
},
buildDiseases(response) {
@@ -115,15 +118,17 @@ export default {
icon: 'fas fa-laptop-medical',
content: [],
};
- Object.entries(response.data.diseases).forEach(([key, value]) => {
- diseases.content.push(
- {
- id: key,
- name: value,
- url: `https://www.genome.jp/dbget-bin/www_bget?ds:${key}`,
- },
- );
- });
+ if(response.data.diseases) {
+ Object.entries(response.data.diseases).forEach(([key, value]) => {
+ diseases.content.push(
+ {
+ id: key,
+ name: value,
+ url: `https://www.genome.jp/dbget-bin/www_bget?ds:${key}`,
+ },
+ );
+ });
+ }
return diseases;
},
buildReferences(response) {
@@ -132,16 +137,18 @@ export default {
icon: 'fas fa-book-open',
content: [],
};
- for (let i = 0; i < response.data.references.length; i++) {
- references.content.push(
- {
- id: response.data.references[i].title,
- name: `${response.data.references[i].authors[0]} et al. ${response.data.references[i].journal}`,
- url: `https://www.ncbi.nlm.nih.gov/pubmed/${response.data.references[i].pubmed}`,
- url_label: "Open in Pubmed"
- },
- );
- };
+ if (response.data.references) {
+ for (let i = 0; i < response.data.references.length; i++) {
+ references.content.push(
+ {
+ id: response.data.references[i].title,
+ name: `${response.data.references[i].authors[0]} et al. ${response.data.references[i].journal}`,
+ url: `https://www.ncbi.nlm.nih.gov/pubmed/${response.data.references[i].pubmed}`,
+ url_label: "Open in Pubmed"
+ },
+ );
+ };
+ }
return references;
},
},
--
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