Auto-generated Pull Request for feat/baserow-upload

.golangci.yml

@@ -2,6 +2,8 @@ run:
   allow-parallel-runners: true
   timeout: 5m
 linters-settings: 
+    unused:
+      local-variables-are-used: true
     gosec: 
       excludes: 
         - G402

cmd/baserow/main.go

@@ -52,10 +52,10 @@ func main() {
 				Action: baserow.CreateAccessToken,
 			},
 			{
-				Name:   "create-table",
-				Usage:  "Create a baserow database table",
-				Flags:  baserow.CreateTableFlag(),
-				Action: baserow.CreateTable,
+				Name:   "create-ontology-table",
+				Usage:  "Create a baserow table with ontology fields preset",
+				Flags:  baserow.CreateOntologyTableFlag(),
+				Action: baserow.CreateOntologyTableHandler,
 			},
 			{
 				Name:   "load-ontology",

internal/baserow/cli/action.go

@@ -0,0 +1,160 @@
+package cli
+
+import (
+	"context"
+	"fmt"
+
+	"slices"
+
+	"github.com/dictyBase/modware-import/internal/baserow/client"
+	"github.com/dictyBase/modware-import/internal/baserow/database"
+	"github.com/dictyBase/modware-import/internal/baserow/ontology"
+	"github.com/dictyBase/modware-import/internal/collection"
+	"github.com/dictyBase/modware-import/internal/registry"
+	"github.com/urfave/cli/v2"
+)
+
+func CreateDatabaseToken(cltx *cli.Context) error {
+	atoken, err := database.AccessToken(&database.AccessTokenProperties{
+		Email:    cltx.String("email"),
+		Password: cltx.String("password"),
+		Server:   cltx.String("server"),
+	})
+	if err != nil {
+		return cli.Exit(fmt.Errorf("error in creating access token %s", err), 2)
+	}
+	bclient := database.BaserowClient(cltx.String("server"))
+	authCtx := context.WithValue(
+		context.Background(),
+		client.ContextAccessToken,
+		atoken,
+	)
+	wlist, r, err := bclient.WorkspacesApi.ListWorkspaces(authCtx).
+		Execute()
+	defer r.Body.Close()
+	if err != nil {
+		return cli.Exit(
+			fmt.Errorf("error in executing list workspaces API call %s", err),
+			2,
+		)
+	}
+	wnames := collection.Map(
+		wlist,
+		func(w client.WorkspaceUserWorkspace) string { return w.GetName() },
+	)
+	idx := slices.Index(wnames, cltx.String("workspace"))
+	if idx == -1 {
+		return cli.Exit(
+			fmt.Errorf(
+				"workspace %s cannot be found",
+				cltx.String("workspace"),
+			),
+			2,
+		)
+	}
+	tok, r, err := bclient.DatabaseTokensApi.CreateDatabaseToken(authCtx).
+		TokenCreate(client.TokenCreate{
+			Name:      cltx.String("name"),
+			Workspace: wlist[idx].GetId(),
+		}).
+		Execute()
+	defer r.Body.Close()
+	if err != nil {
+		return cli.Exit(
+			fmt.Errorf("error in creating token %s", err),
+			2,
+		)
+	}
+	fmt.Printf("database token %s\n", tok.GetKey())
+	return nil
+}
+
+func CreateAccessToken(cltx *cli.Context) error {
+	token, err := database.AccessToken(&database.AccessTokenProperties{
+		Email:    cltx.String("email"),
+		Password: cltx.String("password"),
+		Server:   cltx.String("server"),
+	})
+	if err != nil {
+		return cli.Exit(err, 2)
+	}
+	fmt.Println(token)
+	return nil
+}
+
+func LoadOntologyToTable(cltx *cli.Context) error {
+	logger := registry.GetLogger()
+	bclient := database.BaserowClient(cltx.String("server"))
+	authCtx := context.WithValue(
+		context.Background(),
+		client.ContextDatabaseToken,
+		cltx.String("token"),
+	)
+	ontTbl := &database.OntologyTableManager{
+		TableManager: &database.TableManager{
+			Client:     bclient,
+			Logger:     logger,
+			Ctx:        authCtx,
+			Token:      cltx.String("token"),
+			DatabaseId: int32(cltx.Int("database-id")),
+		},
+	}
+	ok, err := ontTbl.CheckAllTableFields(
+		&client.Table{Id: int32(cltx.Int("table-id"))},
+	)
+	if err != nil {
+		return cli.Exit(err.Error(), 2)
+	}
+	if !ok {
+		return cli.Exit("table does not have the required fields", 2)
+	}
+	props := &ontology.LoadProperties{
+		File:    cltx.String("input"),
+		TableId: cltx.Int("table-id"),
+		Token:   cltx.String("token"),
+		Client:  bclient,
+		Logger:  logger,
+	}
+	if err := ontology.LoadNewOrUpdate(props); err != nil {
+		return cli.Exit(err.Error(), 2)
+	}
+
+	return nil
+}
+
+func CreateOntologyTableHandler(cltx *cli.Context) error {
+	logger := registry.GetLogger()
+	bclient := database.BaserowClient(cltx.String("server"))
+	authCtx := context.WithValue(
+		context.Background(),
+		client.ContextAccessToken,
+		cltx.String("token"),
+	)
+	ontTbl := &database.OntologyTableManager{
+		TableManager: &database.TableManager{
+			Client:     bclient,
+			Logger:     logger,
+			Ctx:        authCtx,
+			Token:      cltx.String("token"),
+			DatabaseId: int32(cltx.Int("database-id")),
+		},
+	}
+	tbl, err := ontTbl.CreateTable(cltx.String("table"), ontTbl.FieldNames())
+	if err != nil {
+		return cli.Exit(fmt.Sprintf("error in creating table %s", err), 2)
+	}
+	logger.Infof("created table with fields %s", tbl.GetName())
+	msg, err := ontTbl.UpdateField(
+		tbl,
+		"is_obsolete",
+		map[string]interface{}{"name": "is_obsolete", "type": "boolean"},
+	)
+	if err != nil {
+		return cli.Exit(
+			fmt.Sprintf("error in updating is_obsolete field %s", err),
+			2,
+		)
+	}
+	logger.Info(msg)
+	return nil
+}