update filters and use from frontend

backend/metagenedb/api/catalog/filters/gene.py

@@ -24,6 +24,9 @@ class GeneFilter(filters.FilterSet):
     tax_id = filters.CharFilter(
         method='filter_annotated_tax'
     )
+    source = filters.CharFilter(
+        field_name="source__slug"
+    )
     function = filters.ModelMultipleChoiceFilter(
         queryset=Function.objects.all(),
         field_name='functions__function_id',
@@ -37,4 +40,4 @@ class GeneFilter(filters.FilterSet):
 
     class Meta:
         model = Gene
-        fields = ['length', 'name', 'source']
+        fields = ['length', 'name']

backend/metagenedb/api/catalog/urls.py

@@ -61,6 +61,7 @@ api_router.register(r'kegg-orthologies', views.KeggOrthologyViewSet, basename='k
 api_router.register(r'eggnogs', views.EggNOGViewSet, basename='eggnogs')
 api_router.register(r'genes', views.GeneViewSet, basename='genes')
 api_router.register(r'taxonomy', views.TaxonomyViewSet, basename='taxonomy')
+api_router.register(r'sources', views.SourceViewSet, basename='sources')
 api_router.register(r'statistics', views.StatisticsViewSet, basename='statistics')
 
 

backend/metagenedb/api/catalog/views/__init__.py

 from .function import EggNOGViewSet, KeggOrthologyViewSet, FunctionViewSet  # noqa
 from .gene import GeneViewSet  # noqa
 from .statistics import StatisticsViewSet  # noqa
+from .source import SourceViewSet  # noqa
 from .taxonomy import TaxonomyViewSet  # noqa

backend/metagenedb/api/catalog/views/source.py

+from drf_yasg.utils import swagger_auto_schema
+
+from metagenedb.apps.catalog.models import Source
+from metagenedb.apps.catalog.serializers import SourceSerializer
+
+from .base import BulkViewSet
+
+
+class SourceViewSet(BulkViewSet):
+    queryset = Source.objects.all()
+    serializer_class = SourceSerializer
+    lookup_field = 'slug'
+
+    @swagger_auto_schema(
+        operation_description="List all gene sources",
+        operation_summary="API to list all gene sources of the catalog.",
+        tags=['Source'],
+    )
+    def list(self, *args, **kwargs):
+        return super().list(*args, **kwargs)
+
+    @swagger_auto_schema(
+        operation_description="Retrieve gene source from a name",
+        operation_summary="API to retrieve gene source.",
+        tags=['Source'],
+    )
+    def retrieve(self, *args, **kwargs):
+        return super().retrieve(*args, **kwargs)
+
+    @swagger_auto_schema(
+        tags=['Source'],
+    )
+    def create(self, *args, **kwargs):
+        return super().create(*args, **kwargs)
+
+    @swagger_auto_schema(
+        tags=['Source'],
+    )
+    def update(self, *args, **kwargs):
+        return super().update(*args, **kwargs)
+
+    @swagger_auto_schema(
+        tags=['Source'],
+    )
+    def partial_update(self, *args, **kwargs):
+        return super().partial_update(*args, **kwargs)

backend/metagenedb/apps/catalog/admin/source.py

@@ -5,5 +5,5 @@ from metagenedb.apps.catalog.models import Source
 
 @admin.register(Source)
 class SourceAdmin(admin.ModelAdmin):
-    list_display = ('name', 'url', 'doi')
+    list_display = ('name', 'slug', 'url', 'doi')
     search_fields = ('name',)

backend/metagenedb/apps/catalog/migrations/0030_source_slug.py

+# Generated by Django 3.1.7 on 2021-04-15 13:16
+
+from django.db import migrations, models
+from slugify import slugify
+
+
+def add_slug(apps, schema_editor):
+    Source = apps.get_model('catalog', 'Source')
+    for item in Source.objects.all():
+        item.slug = slugify(item.name)
+        item.save()
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('catalog', '0029_source'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='source',
+            name='slug',
+            field=models.CharField(db_index=True, max_length=100, unique=True, null=True),
+            preserve_default=False,
+        ),
+        migrations.RunPython(add_slug),
+        migrations.AlterField(
+            model_name='source',
+            name='slug',
+            field=models.CharField(db_index=True, max_length=100, unique=True),
+        ),
+    ]

backend/metagenedb/apps/catalog/models/source.py

 from django.db import models
+from slugify import slugify
 
 
 class Source(models.Model):
 
     name = models.CharField(max_length=100, unique=True, db_index=True)
+    slug = models.CharField(max_length=100, unique=True, db_index=True)
     url = models.CharField(max_length=100, blank=True)
     doi = models.CharField(max_length=100, blank=True)
     tools = models.JSONField(blank=True, null=True)
 
+    def save(self, *args, **kwargs):
+        self.slug=slugify(self.name)
+        super(Source, self).save(*args, **kwargs)
+
     def __str__(self):
         return f"{self.name}"

backend/metagenedb/apps/catalog/serializers/__init__.py

 from .function import EggNOGSerializer, FunctionSerializer, KeggOrthologySerializer  # noqa
 from .gene import GeneSerializer  # noqa
 from .statistics import StatisticsSerializer  # noqa
+from .source import SourceSerializer  # noqa
 from .taxonomy import TaxonomySerializer  # noqa

backend/metagenedb/apps/catalog/serializers/source.py

@@ -7,5 +7,5 @@ class SourceSerializer(serializers.ModelSerializer):
     class Meta:
         model = Source
         fields = (
-            'name', 'url', 'doi'
+            'name', 'slug', 'url', 'doi'
         )

frontend/src/views/genes/genes.html

@@ -66,7 +66,7 @@
                       <!-- Gene source -->
                       <v-flex xs12 sm6 md4 lg2>
                         <v-select
-                          :items="geneSources"
+                          :items="Object.keys(geneSources)"
                           v-model="geneSource"
                           label="Gene source"
                           @input="getTaxoPresenceOptional"

frontend/src/views/genes/genes.js

@@ -21,6 +21,8 @@ export default {
       searchGeneName: null,
       filterGeneLength: false,
       geneLengthFilterRange: [0, 2000],
+      // - Source
+      geneSources: {},
       // - Taxonomy
       taxLevel: null,
       taxItems: [],
@@ -63,12 +65,6 @@ export default {
       ];
       return this.formatList(texts);
     },
-    geneSources() {
-      const texts =  [
-        'IGC', 'Virgo',
-      ];
-      return this.formatList(texts);
-    },
     rowsPerPageItems() {
       return [this.page_size];
     },
@@ -78,7 +74,7 @@ export default {
         page: this.pageNumber
       };
       if (this.geneSource && this.geneSource != 'all') {
-        qParams.source = this.geneSource
+        qParams.source = this.geneSources[this.geneSource];
       }
       if (this.filterGeneLength) {
         qParams.length__gt = this.geneLengthFilterRange[0];
@@ -199,6 +195,7 @@ export default {
     }
   },
   mounted() {
+    this.getSources();
     this.getGenes();
   },
   methods: {
@@ -270,6 +267,23 @@ export default {
           this.requestDone = true;
         });
     },
+    getSources() {
+      axios.get('/api/catalog/v1/sources', {
+        params: this.qParams,
+        headers: {
+          Accept: 'application/json',
+        },
+      })
+        .then((response) => {
+          const sources = response.data.results;
+          sources.forEach((item, index) => {
+            this.geneSources[item.name] = item.slug;
+          });
+        })
+        .catch((error) => {
+          console.error(error);
+        });
+    },
     forceFileDownload(response, fileName){
       const url = window.URL.createObjectURL(new Blob([response.data]))
       const link = document.createElement('a')