Merge pull request #4 from thermokarst/genus

Genus / Genera, gtg.
This commit is contained in:
Matthew Dillon 2014-10-13 15:32:49 -08:00
commit 205a932e2a
15 changed files with 898 additions and 6 deletions

94
api/genera.go Normal file
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@ -0,0 +1,94 @@
package api
import (
"encoding/json"
"strconv"
"github.com/gorilla/mux"
"net/http"
"github.com/thermokarst/bactdb/models"
)
func serveGenus(w http.ResponseWriter, r *http.Request) error {
id, err := strconv.ParseInt(mux.Vars(r)["Id"], 10, 0)
if err != nil {
return err
}
genus, err := store.Genera.Get(id)
if err != nil {
return err
}
return writeJSON(w, genus)
}
func serveCreateGenus(w http.ResponseWriter, r *http.Request) error {
var genus models.Genus
err := json.NewDecoder(r.Body).Decode(&genus)
if err != nil {
return err
}
created, err := store.Genera.Create(&genus)
if err != nil {
return err
}
if created {
w.WriteHeader(http.StatusCreated)
}
return writeJSON(w, genus)
}
func serveGenera(w http.ResponseWriter, r *http.Request) error {
var opt models.GenusListOptions
if err := schemaDecoder.Decode(&opt, r.URL.Query()); err != nil {
return err
}
genera, err := store.Genera.List(&opt)
if err != nil {
return err
}
if genera == nil {
genera = []*models.Genus{}
}
return writeJSON(w, genera)
}
func serveUpdateGenus(w http.ResponseWriter, r *http.Request) error {
id, _ := strconv.ParseInt(mux.Vars(r)["Id"], 10, 0)
var genus models.Genus
err := json.NewDecoder(r.Body).Decode(&genus)
if err != nil {
return err
}
updated, err := store.Genera.Update(id, &genus)
if err != nil {
return err
}
if updated {
w.WriteHeader(http.StatusOK)
}
return writeJSON(w, genus)
}
func serveDeleteGenus(w http.ResponseWriter, r *http.Request) error {
id, _ := strconv.ParseInt(mux.Vars(r)["Id"], 10, 0)
deleted, err := store.Genera.Delete(id)
if err != nil {
return err
}
if deleted {
w.WriteHeader(http.StatusOK)
}
return writeJSON(w, &models.Genus{})
}

147
api/genera_test.go Normal file
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@ -0,0 +1,147 @@
package api
import (
"testing"
"github.com/thermokarst/bactdb/models"
)
func TestGenus_Get(t *testing.T) {
setup()
want := &models.Genus{Id: 1, GenusName: "Test Genus"}
calledGet := false
store.Genera.(*models.MockGeneraService).Get_ = func(id int64) (*models.Genus, error) {
if id != want.Id {
t.Errorf("wanted request for genus %d but got %d", want.Id, id)
}
calledGet = true
return want, nil
}
got, err := apiClient.Genera.Get(want.Id)
if err != nil {
t.Fatal(err)
}
if !calledGet {
t.Error("!calledGet")
}
if !normalizeDeepEqual(want, got) {
t.Errorf("got genus %+v but wanted genus %+v", got, want)
}
}
func TestGenus_Create(t *testing.T) {
setup()
want := &models.Genus{Id: 1, GenusName: "Test Genus"}
calledPost := false
store.Genera.(*models.MockGeneraService).Create_ = func(genus *models.Genus) (bool, error) {
if !normalizeDeepEqual(want, genus) {
t.Errorf("wanted request for genus %d but got %d", want, genus)
}
calledPost = true
return true, nil
}
success, err := apiClient.Genera.Create(want)
if err != nil {
t.Fatal(err)
}
if !calledPost {
t.Error("!calledPost")
}
if !success {
t.Error("!success")
}
}
func TestGenus_List(t *testing.T) {
setup()
want := []*models.Genus{{Id: 1, GenusName: "Test Genus"}}
wantOpt := &models.GenusListOptions{ListOptions: models.ListOptions{Page: 1, PerPage: 10}}
calledList := false
store.Genera.(*models.MockGeneraService).List_ = func(opt *models.GenusListOptions) ([]*models.Genus, error) {
if !normalizeDeepEqual(wantOpt, opt) {
t.Errorf("wanted options %d but got %d", wantOpt, opt)
}
calledList = true
return want, nil
}
genera, err := apiClient.Genera.List(wantOpt)
if err != nil {
t.Fatal(err)
}
if !calledList {
t.Error("!calledList")
}
if !normalizeDeepEqual(&want, &genera) {
t.Errorf("got genera %+v but wanted genera %+v", genera, want)
}
}
func TestGenus_Update(t *testing.T) {
setup()
want := &models.Genus{Id: 1, GenusName: "Test Genus"}
calledPut := false
store.Genera.(*models.MockGeneraService).Update_ = func(id int64, genus *models.Genus) (bool, error) {
if id != want.Id {
t.Errorf("wanted request for genus %d but got %d", want.Id, id)
}
if !normalizeDeepEqual(want, genus) {
t.Errorf("wanted request for genus %d but got %d", want, genus)
}
calledPut = true
return true, nil
}
success, err := apiClient.Genera.Update(1, want)
if err != nil {
t.Fatal(err)
}
if !calledPut {
t.Error("!calledPut")
}
if !success {
t.Error("!success")
}
}
func TestGenus_Delete(t *testing.T) {
setup()
want := &models.Genus{Id: 1, GenusName: "Test Genus"}
calledDelete := false
store.Genera.(*models.MockGeneraService).Delete_ = func(id int64) (bool, error) {
if id != want.Id {
t.Errorf("wanted request for genus %d but got %d", want.Id, id)
}
calledDelete = true
return true, nil
}
success, err := apiClient.Genera.Delete(1)
if err != nil {
t.Fatal(err)
}
if !calledDelete {
t.Error("!calledDelete")
}
if !success {
t.Error("!success")
}
}

View file

@ -18,9 +18,17 @@ var (
func Handler() *mux.Router {
m := router.API()
m.Get(router.User).Handler(handler(serveUser))
m.Get(router.CreateUser).Handler(handler(serveCreateUser))
m.Get(router.Users).Handler(handler(serveUsers))
m.Get(router.Genus).Handler(handler(serveGenus))
m.Get(router.CreateGenus).Handler(handler(serveCreateGenus))
m.Get(router.Genera).Handler(handler(serveGenera))
m.Get(router.UpdateGenus).Handler(handler(serveUpdateGenus))
m.Get(router.DeleteGenus).Handler(handler(serveDeleteGenus))
return m
}

View file

@ -1,16 +1,24 @@
package datastore
import (
"errors"
"github.com/jmoiron/modl"
"github.com/thermokarst/bactdb/models"
)
// A datastore access point (in PostgreSQL)
type Datastore struct {
Users models.UsersService
dbh modl.SqlExecutor
Users models.UsersService
Genera models.GeneraService
dbh modl.SqlExecutor
}
var (
ErrNoRowsUpdated = errors.New(`no rows updated`)
ErrNoRowsDeleted = errors.New(`no rows deleted`)
)
// NewDatastore creates a new client for accessing the datastore (in PostgreSQL).
// If dbh is nil, it uses the global DB handle.
func NewDatastore(dbh modl.SqlExecutor) *Datastore {
@ -20,11 +28,13 @@ func NewDatastore(dbh modl.SqlExecutor) *Datastore {
d := &Datastore{dbh: dbh}
d.Users = &usersStore{d}
d.Genera = &generaStore{d}
return d
}
func NewMockDatastore() *Datastore {
return &Datastore{
Users: &models.MockUsersService{},
Users: &models.MockUsersService{},
Genera: &models.MockGeneraService{},
}
}

View file

@ -26,7 +26,7 @@ var connectOnce sync.Once
func Connect() {
connectOnce.Do(func() {
var err error
DB.Dbx, err = sqlx.Open("postgres", "sslmode=disable")
DB.Dbx, err = sqlx.Open("postgres", "timezone=UTC sslmode=disable")
if err != nil {
log.Fatal("Error connecting to PostgreSQL database (using PG* environment variables): ", err)
}

85
datastore/genera.go Normal file
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@ -0,0 +1,85 @@
package datastore
import (
"strings"
"github.com/thermokarst/bactdb/models"
)
func init() {
DB.AddTableWithName(models.Genus{}, "genera").SetKeys(true, "Id")
}
type generaStore struct {
*Datastore
}
func (s *generaStore) Get(id int64) (*models.Genus, error) {
var genus []*models.Genus
if err := s.dbh.Select(&genus, `SELECT * FROM genera WHERE id=$1;`, id); err != nil {
return nil, err
}
if len(genus) == 0 {
return nil, models.ErrGenusNotFound
}
return genus[0], nil
}
func (s *generaStore) Create(genus *models.Genus) (bool, error) {
if err := s.dbh.Insert(genus); err != nil {
if strings.Contains(err.Error(), `violates unique constraint "genus_idx"`) {
return false, err
}
}
return true, nil
}
func (s *generaStore) List(opt *models.GenusListOptions) ([]*models.Genus, error) {
if opt == nil {
opt = &models.GenusListOptions{}
}
var genera []*models.Genus
err := s.dbh.Select(&genera, `SELECT * FROM genera LIMIT $1 OFFSET $2;`, opt.PerPageOrDefault(), opt.Offset())
if err != nil {
return nil, err
}
return genera, nil
}
func (s *generaStore) Update(id int64, genus *models.Genus) (bool, error) {
_, err := s.Get(id)
if err != nil {
return false, err
}
if id != genus.Id {
return false, models.ErrGenusNotFound
}
changed, err := s.dbh.Update(genus)
if err != nil {
return false, err
}
if changed == 0 {
return false, ErrNoRowsUpdated
}
return true, nil
}
func (s *generaStore) Delete(id int64) (bool, error) {
genus, err := s.Get(id)
if err != nil {
return false, err
}
deleted, err := s.dbh.Delete(genus)
if err != nil {
return false, err
}
if deleted == 0 {
return false, ErrNoRowsDeleted
}
return true, nil
}

140
datastore/genera_test.go Normal file
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@ -0,0 +1,140 @@
package datastore
import (
"reflect"
"testing"
"github.com/thermokarst/bactdb/models"
)
func TestGeneraStore_Get_db(t *testing.T) {
want := &models.Genus{Id: 1, GenusName: "Test Genus"}
tx, _ := DB.Begin()
defer tx.Rollback()
// Test on a clean database
tx.Exec(`DELETE FROM genera;`)
if err := tx.Insert(want); err != nil {
t.Fatal(err)
}
d := NewDatastore(tx)
genus, err := d.Genera.Get(1)
if err != nil {
t.Fatal(err)
}
normalizeTime(&want.CreatedAt, &want.UpdatedAt, &want.DeletedAt)
if !reflect.DeepEqual(genus, want) {
t.Errorf("got genus %+v, want %+v", genus, want)
}
}
func TestGeneraStore_Create_db(t *testing.T) {
genus := &models.Genus{Id: 1, GenusName: "Test Genus"}
tx, _ := DB.Begin()
defer tx.Rollback()
// Test on a clean database
tx.Exec(`DELETE FROM genera;`)
d := NewDatastore(tx)
created, err := d.Genera.Create(genus)
if err != nil {
t.Fatal(err)
}
if !created {
t.Error("!created")
}
if genus.Id == 0 {
t.Error("want nonzero genus.Id after submitting")
}
}
func TestGeneraStore_List_db(t *testing.T) {
want := []*models.Genus{{Id: 1, GenusName: "Test Genus"}}
tx, _ := DB.Begin()
defer tx.Rollback()
// Test on a clean database
tx.Exec(`DELETE FROM genera;`)
if err := tx.Insert(want[0]); err != nil {
t.Fatal(err)
}
d := NewDatastore(tx)
genera, err := d.Genera.List(&models.GenusListOptions{ListOptions: models.ListOptions{Page: 1, PerPage: 10}})
if err != nil {
t.Fatal(err)
}
for _, g := range want {
normalizeTime(&g.CreatedAt, &g.UpdatedAt, &g.DeletedAt)
}
if !reflect.DeepEqual(genera, want) {
t.Errorf("got genera %+v, want %+v", genera, want)
}
}
func TestGeneraStore_Update_db(t *testing.T) {
tx, _ := DB.Begin()
defer tx.Rollback()
// Test on a clean database
tx.Exec(`DELETE FROM genera;`)
d := NewDatastore(nil)
// Add a new record
genus := &models.Genus{GenusName: "Test Genus"}
created, err := d.Genera.Create(genus)
if err != nil {
t.Fatal(err)
}
if !created {
t.Error("!created")
}
// Tweak it
genus.GenusName = "Updated Genus"
updated, err := d.Genera.Update(genus.Id, genus)
if err != nil {
t.Fatal(err)
}
if !updated {
t.Error("!updated")
}
}
func TestGeneraStore_Delete_db(t *testing.T) {
tx, _ := DB.Begin()
defer tx.Rollback()
// Test on a clean database
tx.Exec(`DELETE FROM genera;`)
d := NewDatastore(tx)
// Add a new record
genus := &models.Genus{GenusName: "Test Genus"}
created, err := d.Genera.Create(genus)
if err != nil {
t.Fatal(err)
}
if !created {
t.Error("!created")
}
// Delete it
deleted, err := d.Genera.Delete(genus.Id)
if err != nil {
t.Fatal(err)
}
if !deleted {
t.Error("!delete")
}
}

View file

@ -0,0 +1,5 @@
-- bactdb
-- Matthew R Dillon
DROP TABLE genera;

View file

@ -0,0 +1,19 @@
-- bactdb
-- Matthew R Dillon
CREATE TABLE genera (
id BIGSERIAL NOT NULL,
genusname CHARACTER VARYING(100),
createdat TIMESTAMP WITH TIME ZONE,
updatedat TIMESTAMP WITH TIME ZONE,
deletedat TIMESTAMP WITH TIME ZONE,
CONSTRAINT genus_pkey PRIMARY KEY (id)
);
CREATE UNIQUE INDEX genusname_idx
ON genera
USING btree
(genusname COLLATE pg_catalog."default");

View file

@ -16,7 +16,8 @@ import (
// A Client communicates with bactdb's HTTP API.
type Client struct {
Users UsersService
Users UsersService
Genera GeneraService
// BaseURL for HTTP requests to bactdb's API.
BaseURL *url.URL
@ -45,6 +46,7 @@ func NewClient(httpClient *http.Client) *Client {
httpClient: httpClient,
}
c.Users = &usersService{c}
c.Genera = &generaService{c}
return c
}

200
models/genera.go Normal file
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@ -0,0 +1,200 @@
package models
import (
"errors"
"net/http"
"strconv"
"time"
"github.com/thermokarst/bactdb/router"
)
// A Genus is a high-level classifier in bactdb.
type Genus struct {
Id int64 `json:"id,omitempty"`
GenusName string `json:"genus_name"`
CreatedAt time.Time `json:"created_at"`
UpdatedAt time.Time `json:"updated_at"`
DeletedAt time.Time `json:"deleted_at"`
}
// GeneraService interacts with the genus-related endpoints in bactdb's API.
type GeneraService interface {
// Get a genus.
Get(id int64) (*Genus, error)
// List all genera.
List(opt *GenusListOptions) ([]*Genus, error)
// Create a new genus. The newly created genus's ID is written to genus.Id
Create(genus *Genus) (created bool, err error)
// Update an existing genus.
Update(id int64, genus *Genus) (updated bool, err error)
// Delete an existing genus.
Delete(id int64) (deleted bool, err error)
}
var (
ErrGenusNotFound = errors.New("genus not found")
)
type generaService struct {
client *Client
}
func (s *generaService) Get(id int64) (*Genus, error) {
// Pass in key value pairs as strings, so that the gorilla mux URL
// generation is happy.
strId := strconv.FormatInt(id, 10)
url, err := s.client.url(router.Genus, map[string]string{"Id": strId}, nil)
if err != nil {
return nil, err
}
req, err := s.client.NewRequest("GET", url.String(), nil)
if err != nil {
return nil, err
}
var genus *Genus
_, err = s.client.Do(req, &genus)
if err != nil {
return nil, err
}
return genus, nil
}
func (s *generaService) Create(genus *Genus) (bool, error) {
url, err := s.client.url(router.CreateGenus, nil, nil)
if err != nil {
return false, err
}
req, err := s.client.NewRequest("POST", url.String(), genus)
if err != nil {
return false, err
}
resp, err := s.client.Do(req, &genus)
if err != nil {
return false, err
}
return resp.StatusCode == http.StatusCreated, nil
}
type GenusListOptions struct {
ListOptions
}
func (s *generaService) List(opt *GenusListOptions) ([]*Genus, error) {
url, err := s.client.url(router.Genera, nil, opt)
if err != nil {
return nil, err
}
req, err := s.client.NewRequest("GET", url.String(), nil)
if err != nil {
return nil, err
}
var genera []*Genus
_, err = s.client.Do(req, &genera)
if err != nil {
return nil, err
}
return genera, nil
}
func (s *generaService) Update(id int64, genus *Genus) (bool, error) {
strId := strconv.FormatInt(id, 10)
url, err := s.client.url(router.UpdateGenus, map[string]string{"Id": strId}, nil)
if err != nil {
return false, err
}
req, err := s.client.NewRequest("PUT", url.String(), genus)
if err != nil {
return false, err
}
resp, err := s.client.Do(req, &genus)
if err != nil {
return false, err
}
return resp.StatusCode == http.StatusOK, nil
}
func (s *generaService) Delete(id int64) (bool, error) {
strId := strconv.FormatInt(id, 10)
url, err := s.client.url(router.DeleteGenus, map[string]string{"Id": strId}, nil)
if err != nil {
return false, err
}
req, err := s.client.NewRequest("DELETE", url.String(), nil)
if err != nil {
return false, err
}
var genus *Genus
resp, err := s.client.Do(req, &genus)
if err != nil {
return false, err
}
return resp.StatusCode == http.StatusOK, nil
}
type MockGeneraService struct {
Get_ func(id int64) (*Genus, error)
List_ func(opt *GenusListOptions) ([]*Genus, error)
Create_ func(genus *Genus) (bool, error)
Update_ func(id int64, genus *Genus) (bool, error)
Delete_ func(id int64) (bool, error)
}
var _ GeneraService = &MockGeneraService{}
func (s *MockGeneraService) Get(id int64) (*Genus, error) {
if s.Get_ == nil {
return nil, nil
}
return s.Get_(id)
}
func (s *MockGeneraService) Create(genus *Genus) (bool, error) {
if s.Create_ == nil {
return false, nil
}
return s.Create_(genus)
}
func (s *MockGeneraService) List(opt *GenusListOptions) ([]*Genus, error) {
if s.List_ == nil {
return nil, nil
}
return s.List_(opt)
}
func (s *MockGeneraService) Update(id int64, genus *Genus) (bool, error) {
if s.Update_ == nil {
return false, nil
}
return s.Update_(id, genus)
}
func (s *MockGeneraService) Delete(id int64) (bool, error) {
if s.Delete_ == nil {
return false, nil
}
return s.Delete_(id)
}

167
models/genera_test.go Normal file
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@ -0,0 +1,167 @@
package models
import (
"net/http"
"reflect"
"testing"
"github.com/thermokarst/bactdb/router"
)
func TestGeneraService_Get(t *testing.T) {
setup()
defer teardown()
want := &Genus{Id: 1, GenusName: "Test Genus"}
var called bool
mux.HandleFunc(urlPath(t, router.Genus, map[string]string{"Id": "1"}), func(w http.ResponseWriter, r *http.Request) {
called = true
testMethod(t, r, "GET")
writeJSON(w, want)
})
genus, err := client.Genera.Get(1)
if err != nil {
t.Errorf("Genera.Get returned error: %v", err)
}
if !called {
t.Fatal("!called")
}
normalizeTime(&want.CreatedAt, &want.UpdatedAt, &want.DeletedAt)
if !reflect.DeepEqual(genus, want) {
t.Errorf("Genera.Get returned %+v, want %+v", genus, want)
}
}
func TestGeneraService_Create(t *testing.T) {
setup()
defer teardown()
want := &Genus{Id: 1, GenusName: "Test Genus"}
var called bool
mux.HandleFunc(urlPath(t, router.CreateGenus, nil), func(w http.ResponseWriter, r *http.Request) {
called = true
testMethod(t, r, "POST")
testBody(t, r, `{"id":1,"genus_name":"Test Genus","created_at":"0001-01-01T00:00:00Z","updated_at":"0001-01-01T00:00:00Z","deleted_at":"0001-01-01T00:00:00Z"}`+"\n")
w.WriteHeader(http.StatusCreated)
writeJSON(w, want)
})
genus := &Genus{Id: 1, GenusName: "Test Genus"}
created, err := client.Genera.Create(genus)
if err != nil {
t.Errorf("Genera.Create returned error: %v", err)
}
if !created {
t.Error("!created")
}
if !called {
t.Fatal("!called")
}
normalizeTime(&want.CreatedAt, &want.UpdatedAt, &want.DeletedAt)
if !reflect.DeepEqual(genus, want) {
t.Errorf("Genera.Create returned %+v, want %+v", genus, want)
}
}
func TestGeneraService_List(t *testing.T) {
setup()
defer teardown()
want := []*Genus{{Id: 1, GenusName: "Test Genus"}}
var called bool
mux.HandleFunc(urlPath(t, router.Genera, nil), func(w http.ResponseWriter, r *http.Request) {
called = true
testMethod(t, r, "GET")
testFormValues(t, r, values{})
writeJSON(w, want)
})
genera, err := client.Genera.List(nil)
if err != nil {
t.Errorf("Genera.List returned error: %v", err)
}
if !called {
t.Fatal("!called")
}
for _, u := range want {
normalizeTime(&u.CreatedAt, &u.UpdatedAt, &u.DeletedAt)
}
if !reflect.DeepEqual(genera, want) {
t.Errorf("Genera.List return %+v, want %+v", genera, want)
}
}
func TestGeneraService_Update(t *testing.T) {
setup()
defer teardown()
want := &Genus{Id: 1, GenusName: "Test Genus"}
var called bool
mux.HandleFunc(urlPath(t, router.UpdateGenus, map[string]string{"Id": "1"}), func(w http.ResponseWriter, r *http.Request) {
called = true
testMethod(t, r, "PUT")
testBody(t, r, `{"id":1,"genus_name":"Test Genus Updated","created_at":"0001-01-01T00:00:00Z","updated_at":"0001-01-01T00:00:00Z","deleted_at":"0001-01-01T00:00:00Z"}`+"\n")
w.WriteHeader(http.StatusOK)
writeJSON(w, want)
})
genus := &Genus{Id: 1, GenusName: "Test Genus Updated"}
updated, err := client.Genera.Update(1, genus)
if err != nil {
t.Errorf("Genera.Update returned error: %v", err)
}
if !updated {
t.Error("!updated")
}
if !called {
t.Fatal("!called")
}
}
func TestGeneraService_Delete(t *testing.T) {
setup()
defer teardown()
want := &Genus{Id: 1, GenusName: "Test Genus"}
var called bool
mux.HandleFunc(urlPath(t, router.DeleteGenus, map[string]string{"Id": "1"}), func(w http.ResponseWriter, r *http.Request) {
called = true
testMethod(t, r, "DELETE")
w.WriteHeader(http.StatusOK)
writeJSON(w, want)
})
deleted, err := client.Genera.Delete(1)
if err != nil {
t.Errorf("Genera.Delete returned error: %v", err)
}
if !deleted {
t.Error("!deleted")
}
if !called {
t.Fatal("!called")
}
}

View file

@ -4,8 +4,17 @@ import "github.com/gorilla/mux"
func API() *mux.Router {
m := mux.NewRouter()
// Users
m.Path("/users").Methods("GET").Name(Users)
m.Path("/users").Methods("POST").Name(CreateUser)
m.Path("/users/{Id:.+}").Methods("GET").Name(User)
// Genera
m.Path("/genera").Methods("GET").Name(Genera)
m.Path("/genera").Methods("POST").Name(CreateGenus)
m.Path("/genera/{Id:.+}").Methods("GET").Name(Genus)
m.Path("/genera/{Id:.+}").Methods("PUT").Name(UpdateGenus)
m.Path("/genera/{Id:.+}").Methods("DELETE").Name(DeleteGenus)
return m
}

View file

@ -4,4 +4,10 @@ const (
User = "user"
CreateUser = "user:create"
Users = "users"
Genus = "genus"
CreateGenus = "genus:create"
Genera = "genera"
UpdateGenus = "genus:update"
DeleteGenus = "genus:delete"
)

View file

@ -1,4 +1,4 @@
#!/usr/bin/env bash
PGTZ=UTC PGSSLMODE=disable go test -v ./...
go test -v ./...