gene apis enhanced to support sorting

dataportal_api/dataportal/api.py

@@ -156,11 +156,20 @@ async def gene_autocomplete_suggestions(
 # API Endpoint to search genes by query string
 @gene_router.get("/search", response=GenePaginationSchema)
 async def search_genes_by_string(
-    request, query: str, page: int = 1, per_page: int = 10
+    request,
+    query: str,
+    page: int = 1,
+    per_page: int = 10,
+    sort_field: Optional[str] = None,
+    sort_order: Optional[str] = "asc",
 ):
     try:
         paginated_results = await gene_service.search_genes(
-            query=query, page=page, per_page=per_page
+            query=query,
+            page=page,
+            per_page=per_page,
+            sort_field=sort_field,
+            sort_order=sort_order,
         )
         return paginated_results
     except Exception as e:
@@ -176,17 +185,30 @@ async def get_gene_by_id(request, gene_id: int):
 
 # API Endpoint to retrieve all genes
 @gene_router.get("/", response=GenePaginationSchema)
-async def get_all_genes(request, page: int = 1, per_page: int = 10):
-    return await gene_service.get_all_genes(page, per_page)
+async def get_all_genes(
+    request,
+    page: int = 1,
+    per_page: int = 10,
+    sort_field: Optional[str] = None,
+    sort_order: Optional[str] = "asc",
+):
+    return await gene_service.get_all_genes(page, per_page, sort_field, sort_order)
 
 
 # API Endpoint to retrieve genes filtered by a single genome ID
 @genome_router.get("/{genome_id}/genes", response=GenePaginationSchema)
 async def get_genes_by_genome(
-    request, genome_id: int, page: int = 1, per_page: int = 10
+    request,
+    genome_id: int,
+    page: int = 1,
+    per_page: int = 10,
+    sort_field: Optional[str] = None,
+    sort_order: Optional[str] = "asc",
 ):
     try:
-        return await gene_service.get_genes_by_genome(genome_id, page, per_page)
+        return await gene_service.get_genes_by_genome(
+            genome_id, page, per_page, sort_field, sort_order
+        )
     except Exception as e:
         logger.error(f"Error in get_genes_by_genome: {e}")
         raise HttpError(500, f"Internal Server Error: {str(e)}")
@@ -195,10 +217,18 @@ async def get_genes_by_genome(
 # API Endpoint to search genes by genome ID and gene string
 @genome_router.get("/{genome_id}/genes/search", response=GenePaginationSchema)
 async def search_genes_by_genome_and_string(
-    request, genome_id: int, query: str, page: int = 1, per_page: int = 10
+    request,
+    genome_id: int,
+    query: str,
+    page: int = 1,
+    per_page: int = 10,
+    sort_field: Optional[str] = None,
+    sort_order: Optional[str] = "asc",
 ):
     try:
-        return await gene_service.search_genes(query, genome_id, page, per_page)
+        return await gene_service.search_genes(
+            query, genome_id, page, per_page, sort_field, sort_order
+        )
     except Exception as e:
         logger.error(f"Error in search_genes_by_genome_and_string: {e}")
         raise HttpError(500, f"Internal Server Error: {str(e)}")
@@ -213,10 +243,12 @@ async def search_genes_by_multiple_genomes_and_species_and_string(
     query: str = "",
     page: int = 1,
     per_page: int = 10,
+    sort_field: Optional[str] = None,
+    sort_order: Optional[str] = "asc",
 ):
     try:
         return await gene_service.get_genes_by_multiple_genomes_and_string(
-            genome_ids, species_id, query, page, per_page
+            genome_ids, species_id, query, page, per_page, sort_field, sort_order
         )
     except HttpError as e:
         raise e

dataportal_api/dataportal/services/gene_service.py

@@ -61,21 +61,19 @@ async def get_gene_by_id(self, gene_id: int) -> GeneResponseSchema:
             raise HttpError(500, "Internal Server Error")
 
     async def get_all_genes(
-        self, page: int = 1, per_page: int = 10
+        self,
+        page: int = 1,
+        per_page: int = 10,
+        sort_field: Optional[str] = None,
+        sort_order: Optional[str] = "asc",
     ) -> GenePaginationSchema:
         try:
             genes, total_results = await self._fetch_paginated_genes(
-                Q(), page, per_page
+                Q(), page, per_page, sort_field, sort_order
             )
             serialized_genes = [self._serialize_gene(gene) for gene in genes]
-
-            return GenePaginationSchema(
-                results=serialized_genes,
-                page_number=page,
-                num_pages=(total_results + per_page - 1) // per_page,
-                has_previous=page > 1,
-                has_next=(page * per_page) < total_results,
-                total_results=total_results,
+            return self._create_pagination_schema(
+                serialized_genes, page, per_page, total_results
             )
         except Exception as e:
             logger.error(f"Error fetching all genes: {e}")
@@ -87,7 +85,9 @@ async def search_genes(
         genome_id: Optional[int] = None,
         page: int = 1,
         per_page: int = 10,
-    ):
+        sort_field: Optional[str] = None,
+        sort_order: Optional[str] = "asc",
+    ) -> GenePaginationSchema:
         try:
             filters = Q()
             if query:
@@ -98,38 +98,31 @@ async def search_genes(
                 filters &= Q(strain_id=genome_id)
 
             genes, total_results = await self._fetch_paginated_genes(
-                filters, page, per_page
+                filters, page, per_page, sort_field, sort_order
             )
             serialized_genes = [self._serialize_gene(gene) for gene in genes]
-
-            return GenePaginationSchema(
-                results=serialized_genes,
-                page_number=page,
-                num_pages=(total_results + per_page - 1) // per_page,
-                has_previous=page > 1,
-                has_next=(page * per_page) < total_results,
-                total_results=total_results,
+            return self._create_pagination_schema(
+                serialized_genes, page, per_page, total_results
             )
         except Exception as e:
             logger.error(f"Error searching genes: {e}")
             raise HttpError(500, "Internal Server Error")
 
     async def get_genes_by_genome(
-        self, genome_id: int, page: int = 1, per_page: int = 10
-    ):
+        self,
+        genome_id: int,
+        page: int = 1,
+        per_page: int = 10,
+        sort_field: Optional[str] = None,
+        sort_order: Optional[str] = "asc",
+    ) -> GenePaginationSchema:
         try:
             genes, total_results = await self._fetch_paginated_genes(
-                Q(strain_id=genome_id), page, per_page
+                Q(strain_id=genome_id), page, per_page, sort_field, sort_order
             )
             serialized_genes = [self._serialize_gene(gene) for gene in genes]
-
-            return GenePaginationSchema(
-                results=serialized_genes,
-                page_number=page,
-                num_pages=(total_results + per_page - 1) // per_page,
-                has_previous=page > 1,
-                has_next=(page * per_page) < total_results,
-                total_results=total_results,
+            return self._create_pagination_schema(
+                serialized_genes, page, per_page, total_results
             )
         except Exception as e:
             logger.error(f"Error fetching genes for genome ID {genome_id}: {e}")
@@ -158,6 +151,8 @@ async def get_genes_by_multiple_genomes_and_string(
         query: str = None,
         page: int = 1,
         per_page: int = 10,
+        sort_field: Optional[str] = None,
+        sort_order: Optional[str] = "asc",
     ) -> GenePaginationSchema:
         try:
             genome_id_list = (
@@ -175,17 +170,11 @@ async def get_genes_by_multiple_genomes_and_string(
                 filters &= Q(gene_name__icontains=query.strip())
 
             genes, total_results = await self._fetch_paginated_genes(
-                filters, page, per_page
+                filters, page, per_page, sort_field, sort_order
             )
             serialized_genes = [self._serialize_gene(gene) for gene in genes]
-
-            return GenePaginationSchema(
-                results=serialized_genes,
-                page_number=page,
-                num_pages=(total_results + per_page - 1) // per_page,
-                has_previous=page > 1,
-                has_next=(page * per_page) < total_results,
-                total_results=total_results,
+            return self._create_pagination_schema(
+                serialized_genes, page, per_page, total_results
             )
         except ValueError:
             logger.error("Invalid genome ID provided")
@@ -278,14 +267,22 @@ def _create_pagination_schema(
         )
 
     async def _fetch_paginated_genes(
-        self, filter_criteria: Q, page: int, per_page: int
+        self,
+        filter_criteria: Q,
+        page: int,
+        per_page: int,
+        sort_field: Optional[str] = None,
+        sort_order: Optional[str] = "asc",
     ) -> Tuple[List[Gene], int]:
         start = (page - 1) * per_page
+        order_prefix = "-" if sort_order == "desc" else ""
+        sort_by = f"{order_prefix}{sort_field}" if sort_field else "gene_name"
+
         genes = await sync_to_async(
             lambda: list(
                 Gene.objects.select_related("strain")
                 .filter(filter_criteria)
-                .order_by("gene_name")[start : start + per_page]
+                .order_by(sort_by)[start : start + per_page]
             )
         )()
         total_results = await sync_to_async(

k8s-hl/dev/mett-dataportal-api-deployment.yaml

@@ -19,7 +19,7 @@ spec:
         runAsUser: 7123
         runAsGroup: 1347
       containers:
-        - image: quay.io/microbiome-informatics/mett-dataportal-api:v0.0.27
+        - image: quay.io/microbiome-informatics/mett-dataportal-api:v0.0.29
           imagePullPolicy: Always
           name: mett-dataportal-api-dev
           env:

k8s-hl/dev/mett-dataportal-app-deployment.yaml

@@ -16,7 +16,7 @@ spec:
         app: mett-dataportal-react-app-dev
     spec:
       containers:
-        - image: quay.io/microbiome-informatics/mett-dataportal-react-app:v0.0.27
+        - image: quay.io/microbiome-informatics/mett-dataportal-react-app:v0.0.29
           imagePullPolicy: Always
           name: mett-dataportal-react-app-dev
           env: