From b1d5b335ac8262f6de63aa751b6265f35d2a740a Mon Sep 17 00:00:00 2001
From: Kenzo-Hugo Hillion <hillion.kenzo@posteo.net>
Date: Tue, 13 Apr 2021 16:48:34 +0200
Subject: [PATCH] update serializer and fix list on frontend
---
.../metagenedb/apps/catalog/migrations/0029_source.py | 2 +-
backend/metagenedb/apps/catalog/serializers/gene.py | 9 ++++++++-
backend/metagenedb/apps/catalog/serializers/source.py | 11 +++++++++++
frontend/src/views/genes/genes.html | 9 ++++++++-
frontend/src/views/genes/genes.js | 4 ++++
5 files changed, 32 insertions(+), 3 deletions(-)
create mode 100644 backend/metagenedb/apps/catalog/serializers/source.py
diff --git a/backend/metagenedb/apps/catalog/migrations/0029_source.py b/backend/metagenedb/apps/catalog/migrations/0029_source.py
index 57129c3..58f7b0d 100644
--- a/backend/metagenedb/apps/catalog/migrations/0029_source.py
+++ b/backend/metagenedb/apps/catalog/migrations/0029_source.py
@@ -15,7 +15,7 @@ def create_sources(apps, schema_editor):
{
'name': 'IGC-9.9M',
'url': 'https://db.cngb.org/microbiome/genecatalog/genecatalog_human/',
- 'doi': '10.1038/s41467-020-14677-3'
+ 'doi': '10.1038/nbt.2942'
},
]
for item in items_to_create:
diff --git a/backend/metagenedb/apps/catalog/serializers/gene.py b/backend/metagenedb/apps/catalog/serializers/gene.py
index 2f034bd..87368ea 100644
--- a/backend/metagenedb/apps/catalog/serializers/gene.py
+++ b/backend/metagenedb/apps/catalog/serializers/gene.py
@@ -3,11 +3,12 @@ import traceback
from rest_framework import serializers
from rest_framework.utils import model_meta
-from metagenedb.apps.catalog.models import Function, Gene, GeneFunction, Taxonomy
+from metagenedb.apps.catalog.models import Function, Gene, GeneFunction, Source, Taxonomy
from .asymetricslugrelatedfield import AsymetricSlugRelatedField
from .bulk_list import BulkListSerializer
from .function import FunctionSerializer
+from .source import SourceSerializer
from .taxonomy import SimpleTaxonomySerializer
@@ -65,6 +66,12 @@ class GeneSerializer(serializers.ModelSerializer):
slug_field='tax_id',
required=False,
)
+ source = AsymetricSlugRelatedField.from_serializer(
+ SourceSerializer,
+ queryset=Source.objects.all(),
+ slug_field='name',
+ required=False,
+ )
class Meta:
model = Gene
diff --git a/backend/metagenedb/apps/catalog/serializers/source.py b/backend/metagenedb/apps/catalog/serializers/source.py
new file mode 100644
index 0000000..97930a9
--- /dev/null
+++ b/backend/metagenedb/apps/catalog/serializers/source.py
@@ -0,0 +1,11 @@
+from rest_framework import serializers
+from metagenedb.apps.catalog.models import Source
+
+
+class SourceSerializer(serializers.ModelSerializer):
+
+ class Meta:
+ model = Source
+ fields = (
+ 'name', 'url', 'doi'
+ )
diff --git a/frontend/src/views/genes/genes.html b/frontend/src/views/genes/genes.html
index fccf073..a0d41bf 100644
--- a/frontend/src/views/genes/genes.html
+++ b/frontend/src/views/genes/genes.html
@@ -337,7 +337,14 @@
</v-btn>
</template>
</td>
- <td class="text-xs">{{ props.item.source }}</td>
+ <td class="text-xs">
+ {{ props.item.source }}
+ <v-btn :href="props.item.source_url" icon flat small target="_blank" class="secondary--text mt-1 ml-0" v-if="props.item.source">
+ <v-icon small>
+ open_in_new
+ </v-icon>
+ </v-btn>
+ </td>
</template>
</v-data-table>
</v-list>
diff --git a/frontend/src/views/genes/genes.js b/frontend/src/views/genes/genes.js
index 7e7c820..ba4c8ca 100644
--- a/frontend/src/views/genes/genes.js
+++ b/frontend/src/views/genes/genes.js
@@ -233,6 +233,10 @@ export default {
item.tax_url = ncbiTaxUrl + item.taxonomy.tax_id;
item.taxonomy = `${item.taxonomy.name} (${item.taxonomy.rank})`;
}
+ if (item.source) {
+ item.source_url = item.source.url;
+ item.source = item.source.name;
+ }
if (item.functions) {
const { functions } = item;
item.keggs = [];
--
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