fix: replace db with api

Author: zeidlitz

internal/accession/accession.go

@@ -15,7 +15,6 @@ import (
 	"github.com/NBISweden/sda-bpctl/helpers"
 	"github.com/NBISweden/sda-bpctl/internal/client"
 	"github.com/NBISweden/sda-bpctl/internal/config"
-	"github.com/NBISweden/sda-bpctl/internal/database"
 	"github.com/NBISweden/sda-bpctl/internal/models"
 	"github.com/spf13/cobra"
 )
@@ -87,9 +86,9 @@ func init() {
 	accessionCmd.Flags().StringVar(&dataDirectory, "data-directory", "data", "Path to directory to write / read intermediate files for stableIDs and fileIDs")
 }
 
-func Run(api client.APIClient, db database.PostgresDb, datasetFolder string, userID string) ([]string, error) {
+func Run(api client.APIClient, datasetFolder string, userID string) ([]string, error) {
 	slog.Info("starting accession")
-	files, err := db.GetUserFiles(userID, datasetFolder, true)
+	files, err := api.GetUsersFiles()
 	if err != nil {
 		return nil, err
 	}

internal/ingest/ingest.go

@@ -9,7 +9,6 @@ import (
 	"github.com/NBISweden/sda-bpctl/cmd"
 	"github.com/NBISweden/sda-bpctl/internal/client"
 	"github.com/NBISweden/sda-bpctl/internal/config"
-	"github.com/NBISweden/sda-bpctl/internal/database"
 	"github.com/NBISweden/sda-bpctl/internal/models"
 	"github.com/spf13/cobra"
 )
@@ -52,8 +51,8 @@ func init() {
 	ingestCmd.Flags().StringVar(&configPath, "config", "config.yaml", "Path to configuration file")
 }
 
-func Run(api client.APIClient, db database.PostgresDb, datasetFolder string, userID string, expectedFiles int) (int, error) {
-	files, err := db.GetUserFiles(userID, datasetFolder, true)
+func Run(api client.APIClient, datasetFolder string, userID string, expectedFiles int) (int, error) {
+	files, err := api.GetUsersFiles()
 	if err != nil {
 		return 0, err
 	}

internal/job/job.go

@@ -10,7 +10,6 @@ import (
 	"github.com/NBISweden/sda-bpctl/internal/accession"
 	"github.com/NBISweden/sda-bpctl/internal/client"
 	"github.com/NBISweden/sda-bpctl/internal/config"
-	"github.com/NBISweden/sda-bpctl/internal/database"
 	"github.com/NBISweden/sda-bpctl/internal/dataset"
 	"github.com/NBISweden/sda-bpctl/internal/ingest"
 	"github.com/spf13/cobra"
@@ -74,13 +73,7 @@ func runJob(expectedFiles int) error {
 		return err
 	}
 
-	db, err := database.New(cfg)
-	if err != nil {
-		return err
-	}
-	defer db.Close()
-
-	filesCount, err := ingest.Run(api, *db, datasetFolder, userID, expectedFiles)
+	filesCount, err := ingest.Run(api, datasetFolder, userID, expectedFiles)
 	if err != nil {
 		return err
 	}
@@ -94,7 +87,7 @@ func runJob(expectedFiles int) error {
 		return err
 	}
 
-	accessionIDs, err := accession.Run(api, *db, datasetFolder, userID)
+	accessionIDs, err := accession.Run(api, datasetFolder, userID)
 	if err != nil {
 		return err
 	}

main.go

@@ -13,7 +13,7 @@ import (
 	_ "github.com/NBISweden/sda-bpctl/internal/mail"
 )
 
-var version = "v1.1.1"
+var version = "v1.1.2"
 
 func main() {
 	slog.Info("running", "version", version)