From 830a8805c9e06920da0f021a77a66bd25bae94d5 Mon Sep 17 00:00:00 2001
From: Matthew Dillon <mrdillon@alaska.edu>
Date: Wed, 15 Oct 2014 13:01:11 -0800
Subject: [PATCH 1/9] Species Read - Order of ops:
router/routes.go
router/api.go
models/species_test.go
models/species.go
models/client.go
datastore/migrations/addspecies.sql
datastore/migrations/dropspecies.sql
datastore/species_test.go
datastore/species.go
datastore/datastore.go
api/species_test.go
api/species.go
api/handler.go
---
api/handler.go | 2 +
api/species.go | 22 ++++++
api/species_test.go | 34 +++++++++
datastore/datastore.go | 13 ++--
.../migrations/00003_AddSpecies_down.sql | 5 ++
datastore/migrations/00003_AddSpecies_up.sql | 15 ++++
datastore/species.go | 22 ++++++
datastore/species_test.go | 37 ++++++++++
models/client.go | 6 +-
models/species.go | 69 +++++++++++++++++++
models/species_test.go | 39 +++++++++++
router/api.go | 4 ++
router/routes.go | 2 +
13 files changed, 263 insertions(+), 7 deletions(-)
create mode 100644 api/species.go
create mode 100644 api/species_test.go
create mode 100644 datastore/migrations/00003_AddSpecies_down.sql
create mode 100644 datastore/migrations/00003_AddSpecies_up.sql
create mode 100644 datastore/species.go
create mode 100644 datastore/species_test.go
create mode 100644 models/species.go
create mode 100644 models/species_test.go
diff --git a/api/handler.go b/api/handler.go
index a01506b..384740a 100644
--- a/api/handler.go
+++ b/api/handler.go
@@ -29,6 +29,8 @@ func Handler() *mux.Router {
m.Get(router.UpdateGenus).Handler(handler(serveUpdateGenus))
m.Get(router.DeleteGenus).Handler(handler(serveDeleteGenus))
+ m.Get(router.Species).Handler(handler(serveSpecies))
+
return m
}
diff --git a/api/species.go b/api/species.go
new file mode 100644
index 0000000..c8e127c
--- /dev/null
+++ b/api/species.go
@@ -0,0 +1,22 @@
+package api
+
+import (
+ "net/http"
+ "strconv"
+
+ "github.com/gorilla/mux"
+)
+
+func serveSpecies(w http.ResponseWriter, r *http.Request) error {
+ id, err := strconv.ParseInt(mux.Vars(r)["Id"], 10, 0)
+ if err != nil {
+ return err
+ }
+
+ species, err := store.Species.Get(id)
+ if err != nil {
+ return err
+ }
+
+ return writeJSON(w, species)
+}
diff --git a/api/species_test.go b/api/species_test.go
new file mode 100644
index 0000000..5d1bf87
--- /dev/null
+++ b/api/species_test.go
@@ -0,0 +1,34 @@
+package api
+
+import (
+ "testing"
+
+ "github.com/thermokarst/bactdb/models"
+)
+
+func TestSpecies_Get(t *testing.T) {
+ setup()
+
+ want := &models.Species{Id: 1, GenusId: 1, SpeciesName: "Test Species"}
+
+ calledGet := false
+ store.Species.(*models.MockSpeciesService).Get_ = func(id int64) (*models.Species, error) {
+ if id != want.Id {
+ t.Errorf("wanted request for species %d but got %d", want.Id, id)
+ }
+ calledGet = true
+ return want, nil
+ }
+
+ _, err := apiClient.Species.Get(want.Id)
+ if err != nil {
+ t.Fatal(err)
+ }
+
+ // if !calledGet {
+ // t.Error("!calledGet")
+ // }
+ // if !normalizeDeepEqual(want, got) {
+ // t.Errorf("got species %+v but wanted species %+v", got, want)
+ // }
+}
diff --git a/datastore/datastore.go b/datastore/datastore.go
index 43faafd..1919e3a 100644
--- a/datastore/datastore.go
+++ b/datastore/datastore.go
@@ -9,9 +9,10 @@ import (
// A datastore access point (in PostgreSQL)
type Datastore struct {
- Users models.UsersService
- Genera models.GeneraService
- dbh modl.SqlExecutor
+ Users models.UsersService
+ Genera models.GeneraService
+ Species models.SpeciesService
+ dbh modl.SqlExecutor
}
var (
@@ -29,12 +30,14 @@ func NewDatastore(dbh modl.SqlExecutor) *Datastore {
d := &Datastore{dbh: dbh}
d.Users = &usersStore{d}
d.Genera = &generaStore{d}
+ d.Species = &speciesStore{d}
return d
}
func NewMockDatastore() *Datastore {
return &Datastore{
- Users: &models.MockUsersService{},
- Genera: &models.MockGeneraService{},
+ Users: &models.MockUsersService{},
+ Genera: &models.MockGeneraService{},
+ Species: &models.MockSpeciesService{},
}
}
diff --git a/datastore/migrations/00003_AddSpecies_down.sql b/datastore/migrations/00003_AddSpecies_down.sql
new file mode 100644
index 0000000..3ce7db5
--- /dev/null
+++ b/datastore/migrations/00003_AddSpecies_down.sql
@@ -0,0 +1,5 @@
+-- bactdb
+-- Matthew R Dillon
+
+DROP TABLE species;
+
diff --git a/datastore/migrations/00003_AddSpecies_up.sql b/datastore/migrations/00003_AddSpecies_up.sql
new file mode 100644
index 0000000..d290de1
--- /dev/null
+++ b/datastore/migrations/00003_AddSpecies_up.sql
@@ -0,0 +1,15 @@
+-- bactdb
+-- Matthew Dillon
+
+CREATE TABLE species (
+ id BIGSERIAL NOT NULL,
+ genusid BIGINT,
+ speciesname CHARACTER VARYING(100),
+
+ createdat TIMESTAMP WITH TIME ZONE,
+ updatedat TIMESTAMP WITH TIME ZONE,
+ deletedat TIMESTAMP WITH TIME ZONE,
+
+ CONSTRAINT species_pkey PRIMARY KEY (id),
+ FOREIGN KEY (genusid) REFERENCES genera(id)
+);
diff --git a/datastore/species.go b/datastore/species.go
new file mode 100644
index 0000000..a7f3c17
--- /dev/null
+++ b/datastore/species.go
@@ -0,0 +1,22 @@
+package datastore
+
+import "github.com/thermokarst/bactdb/models"
+
+func init() {
+ DB.AddTableWithName(models.Species{}, "species").SetKeys(true, "Id")
+}
+
+type speciesStore struct {
+ *Datastore
+}
+
+func (s *speciesStore) Get(id int64) (*models.Species, error) {
+ var species []*models.Species
+ if err := s.dbh.Select(&species, `SELECT * FROM species WHERE id=$1;`, id); err != nil {
+ return nil, err
+ }
+ if len(species) == 0 {
+ return nil, models.ErrSpeciesNotFound
+ }
+ return species[0], nil
+}
diff --git a/datastore/species_test.go b/datastore/species_test.go
new file mode 100644
index 0000000..915d522
--- /dev/null
+++ b/datastore/species_test.go
@@ -0,0 +1,37 @@
+package datastore
+
+import (
+ "reflect"
+ "testing"
+
+ "github.com/thermokarst/bactdb/models"
+)
+
+func TestSpeciesStore_Get_db(t *testing.T) {
+ tx, _ := DB.Begin()
+ defer tx.Rollback()
+
+ // Test on a clean database
+ tx.Exec(`DELETE FROM species;`)
+
+ wantGenus := &models.Genus{GenusName: "Test Genus"}
+ if err := tx.Insert(wantGenus); err != nil {
+ t.Fatal(err)
+ }
+
+ want := &models.Species{Id: 1, GenusId: wantGenus.Id, SpeciesName: "Test Species"}
+ if err := tx.Insert(want); err != nil {
+ t.Fatal(err)
+ }
+
+ d := NewDatastore(tx)
+ species, err := d.Species.Get(1)
+ if err != nil {
+ t.Fatal(err)
+ }
+
+ normalizeTime(&want.CreatedAt, &want.UpdatedAt, &want.DeletedAt)
+ if !reflect.DeepEqual(species, want) {
+ t.Errorf("got species %+v, want %+v", species, want)
+ }
+}
diff --git a/models/client.go b/models/client.go
index bb321e7..b94f3f1 100644
--- a/models/client.go
+++ b/models/client.go
@@ -16,8 +16,9 @@ import (
// A Client communicates with bactdb's HTTP API.
type Client struct {
- Users UsersService
- Genera GeneraService
+ Users UsersService
+ Genera GeneraService
+ Species SpeciesService
// BaseURL for HTTP requests to bactdb's API.
BaseURL *url.URL
@@ -47,6 +48,7 @@ func NewClient(httpClient *http.Client) *Client {
}
c.Users = &usersService{c}
c.Genera = &generaService{c}
+ c.Species = &speciesService{c}
return c
}
diff --git a/models/species.go b/models/species.go
new file mode 100644
index 0000000..336c474
--- /dev/null
+++ b/models/species.go
@@ -0,0 +1,69 @@
+package models
+
+import (
+ "errors"
+ "strconv"
+ "time"
+
+ "github.com/thermokarst/bactdb/router"
+)
+
+// A Species is a high-level classifier in bactdb.
+type Species struct {
+ Id int64 `json:"id,omitempty"`
+ GenusId int64 `json:"genus_id"`
+ SpeciesName string `json:"species_name"`
+ CreatedAt time.Time `json:"created_at"`
+ UpdatedAt time.Time `json:"updated_at"`
+ DeletedAt time.Time `json:"deleted_at"`
+}
+
+// SpeciesService interacts with the species-related endpoints in bactdb's API.
+type SpeciesService interface {
+ // Get a species
+ Get(id int64) (*Species, error)
+}
+
+var (
+ ErrSpeciesNotFound = errors.New("species not found")
+)
+
+type speciesService struct {
+ client *Client
+}
+
+func (s *speciesService) Get(id int64) (*Species, error) {
+ // Pass in key value pairs as strings, sp that the gorilla mux URL generation is happy
+ strId := strconv.FormatInt(id, 10)
+
+ url, err := s.client.url(router.Species, 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 species *Species
+ _, err = s.client.Do(req, &species)
+ if err != nil {
+ return nil, err
+ }
+
+ return species, nil
+}
+
+type MockSpeciesService struct {
+ Get_ func(id int64) (*Species, error)
+}
+
+var _ SpeciesService = &MockSpeciesService{}
+
+func (s *MockSpeciesService) Get(id int64) (*Species, error) {
+ if s.Get_ == nil {
+ return nil, nil
+ }
+ return s.Get_(id)
+}
diff --git a/models/species_test.go b/models/species_test.go
new file mode 100644
index 0000000..e080179
--- /dev/null
+++ b/models/species_test.go
@@ -0,0 +1,39 @@
+package models
+
+import (
+ "net/http"
+ "reflect"
+ "testing"
+
+ "github.com/thermokarst/bactdb/router"
+)
+
+func TestSpeciesService_Get(t *testing.T) {
+ setup()
+ defer teardown()
+
+ want := &Species{Id: 1, GenusId: 1, SpeciesName: "Test Species"}
+
+ var called bool
+ mux.HandleFunc(urlPath(t, router.Species, map[string]string{"Id": "1"}), func(w http.ResponseWriter, r *http.Request) {
+ called = true
+ testMethod(t, r, "GET")
+
+ writeJSON(w, want)
+ })
+
+ species, err := client.Species.Get(1)
+ if err != nil {
+ t.Errorf("Species.Get returned error: %v", err)
+ }
+
+ if !called {
+ t.Fatal("!called")
+ }
+
+ normalizeTime(&want.CreatedAt, &want.UpdatedAt, &want.DeletedAt)
+
+ if !reflect.DeepEqual(species, want) {
+ t.Errorf("Species.Get returned %+v, want %+v", species, want)
+ }
+}
diff --git a/router/api.go b/router/api.go
index 1df34ee..229bddc 100644
--- a/router/api.go
+++ b/router/api.go
@@ -16,5 +16,9 @@ func API() *mux.Router {
m.Path("/genera/{Id:.+}").Methods("GET").Name(Genus)
m.Path("/genera/{Id:.+}").Methods("PUT").Name(UpdateGenus)
m.Path("/genera/{Id:.+}").Methods("DELETE").Name(DeleteGenus)
+
+ // Species
+ m.Path("/species/{Id:.+}").Methods("GET").Name(Species)
+
return m
}
diff --git a/router/routes.go b/router/routes.go
index e3bb7bb..9c4ed37 100644
--- a/router/routes.go
+++ b/router/routes.go
@@ -10,4 +10,6 @@ const (
Genera = "genera"
UpdateGenus = "genus:update"
DeleteGenus = "genus:delete"
+
+ Species = "species"
)
From ed2ba266544498e39cd0fb241b1e555cfaf8e8a2 Mon Sep 17 00:00:00 2001
From: Matthew Dillon <mrdillon@alaska.edu>
Date: Wed, 15 Oct 2014 14:11:17 -0800
Subject: [PATCH 2/9] Removed commented portion
---
api/species_test.go | 14 +++++++-------
1 file changed, 7 insertions(+), 7 deletions(-)
diff --git a/api/species_test.go b/api/species_test.go
index 5d1bf87..407a952 100644
--- a/api/species_test.go
+++ b/api/species_test.go
@@ -20,15 +20,15 @@ func TestSpecies_Get(t *testing.T) {
return want, nil
}
- _, err := apiClient.Species.Get(want.Id)
+ got, err := apiClient.Species.Get(want.Id)
if err != nil {
t.Fatal(err)
}
- // if !calledGet {
- // t.Error("!calledGet")
- // }
- // if !normalizeDeepEqual(want, got) {
- // t.Errorf("got species %+v but wanted species %+v", got, want)
- // }
+ if !calledGet {
+ t.Error("!calledGet")
+ }
+ if !normalizeDeepEqual(want, got) {
+ t.Errorf("got species %+v but wanted species %+v", got, want)
+ }
}
From 7fe5566edfd22068c1b0394c130f8e4622080cd2 Mon Sep 17 00:00:00 2001
From: Matthew Dillon <mrdillon@alaska.edu>
Date: Wed, 15 Oct 2014 16:43:09 -0800
Subject: [PATCH 3/9] Create species, cleanup schema. - create species -
species genus_id not null
---
api/handler.go | 1 +
api/species.go | 20 +++++++++++
api/species_test.go | 27 +++++++++++++++
datastore/migrations/00003_AddSpecies_up.sql | 2 +-
datastore/species.go | 7 ++++
datastore/species_test.go | 28 +++++++++++++++
models/species.go | 33 +++++++++++++++++-
models/species_test.go | 36 ++++++++++++++++++++
router/api.go | 1 +
router/routes.go | 3 +-
10 files changed, 155 insertions(+), 3 deletions(-)
diff --git a/api/handler.go b/api/handler.go
index 384740a..65bbc79 100644
--- a/api/handler.go
+++ b/api/handler.go
@@ -30,6 +30,7 @@ func Handler() *mux.Router {
m.Get(router.DeleteGenus).Handler(handler(serveDeleteGenus))
m.Get(router.Species).Handler(handler(serveSpecies))
+ m.Get(router.CreateSpecies).Handler(handler(serveCreateSpecies))
return m
}
diff --git a/api/species.go b/api/species.go
index c8e127c..b8bae18 100644
--- a/api/species.go
+++ b/api/species.go
@@ -1,10 +1,12 @@
package api
import (
+ "encoding/json"
"net/http"
"strconv"
"github.com/gorilla/mux"
+ "github.com/thermokarst/bactdb/models"
)
func serveSpecies(w http.ResponseWriter, r *http.Request) error {
@@ -20,3 +22,21 @@ func serveSpecies(w http.ResponseWriter, r *http.Request) error {
return writeJSON(w, species)
}
+
+func serveCreateSpecies(w http.ResponseWriter, r *http.Request) error {
+ var species models.Species
+ err := json.NewDecoder(r.Body).Decode(&species)
+ if err != nil {
+ return err
+ }
+
+ created, err := store.Species.Create(&species)
+ if err != nil {
+ return err
+ }
+ if created {
+ w.WriteHeader(http.StatusCreated)
+ }
+
+ return writeJSON(w, species)
+}
diff --git a/api/species_test.go b/api/species_test.go
index 407a952..24fd557 100644
--- a/api/species_test.go
+++ b/api/species_test.go
@@ -32,3 +32,30 @@ func TestSpecies_Get(t *testing.T) {
t.Errorf("got species %+v but wanted species %+v", got, want)
}
}
+
+func TestSpecies_Create(t *testing.T) {
+ setup()
+
+ want := &models.Species{Id: 1, GenusId: 1, SpeciesName: "Test Species"}
+
+ calledPost := false
+ store.Species.(*models.MockSpeciesService).Create_ = func(species *models.Species) (bool, error) {
+ if !normalizeDeepEqual(want, species) {
+ t.Errorf("wanted request for species %d but got %d", want, species)
+ }
+ calledPost = true
+ return true, nil
+ }
+
+ success, err := apiClient.Species.Create(want)
+ if err != nil {
+ t.Fatal(err)
+ }
+
+ if !calledPost {
+ t.Error("!calledPost")
+ }
+ if !success {
+ t.Error("!success")
+ }
+}
diff --git a/datastore/migrations/00003_AddSpecies_up.sql b/datastore/migrations/00003_AddSpecies_up.sql
index d290de1..aff073b 100644
--- a/datastore/migrations/00003_AddSpecies_up.sql
+++ b/datastore/migrations/00003_AddSpecies_up.sql
@@ -3,7 +3,7 @@
CREATE TABLE species (
id BIGSERIAL NOT NULL,
- genusid BIGINT,
+ genusid BIGINT NOT NULL,
speciesname CHARACTER VARYING(100),
createdat TIMESTAMP WITH TIME ZONE,
diff --git a/datastore/species.go b/datastore/species.go
index a7f3c17..f7e6dee 100644
--- a/datastore/species.go
+++ b/datastore/species.go
@@ -20,3 +20,10 @@ func (s *speciesStore) Get(id int64) (*models.Species, error) {
}
return species[0], nil
}
+
+func (s *speciesStore) Create(species *models.Species) (bool, error) {
+ if err := s.dbh.Insert(species); err != nil {
+ return false, err
+ }
+ return true, nil
+}
diff --git a/datastore/species_test.go b/datastore/species_test.go
index 915d522..db81db6 100644
--- a/datastore/species_test.go
+++ b/datastore/species_test.go
@@ -35,3 +35,31 @@ func TestSpeciesStore_Get_db(t *testing.T) {
t.Errorf("got species %+v, want %+v", species, want)
}
}
+
+func TestSpeciesStore_Create_db(t *testing.T) {
+ tx, _ := DB.Begin()
+ defer tx.Rollback()
+
+ // Test on a clean database
+ tx.Exec(`DELETE FROM species;`)
+
+ genus := &models.Genus{}
+ if err := tx.Insert(genus); err != nil {
+ t.Fatal(err)
+ }
+
+ species := &models.Species{Id: 1, GenusId: genus.Id, SpeciesName: "Test Species"}
+
+ d := NewDatastore(tx)
+ created, err := d.Species.Create(species)
+ if err != nil {
+ t.Fatal(err)
+ }
+
+ if !created {
+ t.Error("!created")
+ }
+ if species.Id == 0 {
+ t.Error("want nonzero species.Id after submitting")
+ }
+}
diff --git a/models/species.go b/models/species.go
index 336c474..3437d8e 100644
--- a/models/species.go
+++ b/models/species.go
@@ -2,6 +2,7 @@ package models
import (
"errors"
+ "net/http"
"strconv"
"time"
@@ -22,6 +23,9 @@ type Species struct {
type SpeciesService interface {
// Get a species
Get(id int64) (*Species, error)
+
+ // Create a species record
+ Create(species *Species) (bool, error)
}
var (
@@ -55,8 +59,28 @@ func (s *speciesService) Get(id int64) (*Species, error) {
return species, nil
}
+func (s *speciesService) Create(species *Species) (bool, error) {
+ url, err := s.client.url(router.CreateSpecies, nil, nil)
+ if err != nil {
+ return false, err
+ }
+
+ req, err := s.client.NewRequest("POST", url.String(), species)
+ if err != nil {
+ return false, err
+ }
+
+ resp, err := s.client.Do(req, &species)
+ if err != nil {
+ return false, err
+ }
+
+ return resp.StatusCode == http.StatusCreated, nil
+}
+
type MockSpeciesService struct {
- Get_ func(id int64) (*Species, error)
+ Get_ func(id int64) (*Species, error)
+ Create_ func(species *Species) (bool, error)
}
var _ SpeciesService = &MockSpeciesService{}
@@ -67,3 +91,10 @@ func (s *MockSpeciesService) Get(id int64) (*Species, error) {
}
return s.Get_(id)
}
+
+func (s *MockSpeciesService) Create(species *Species) (bool, error) {
+ if s.Create_ == nil {
+ return false, nil
+ }
+ return s.Create_(species)
+}
diff --git a/models/species_test.go b/models/species_test.go
index e080179..338d13b 100644
--- a/models/species_test.go
+++ b/models/species_test.go
@@ -37,3 +37,39 @@ func TestSpeciesService_Get(t *testing.T) {
t.Errorf("Species.Get returned %+v, want %+v", species, want)
}
}
+
+func TestSpeciesService_Create(t *testing.T) {
+ setup()
+ defer teardown()
+
+ want := &Species{Id: 1, GenusId: 1, SpeciesName: "Test Species"}
+
+ var called bool
+ mux.HandleFunc(urlPath(t, router.CreateSpecies, nil), func(w http.ResponseWriter, r *http.Request) {
+ called = true
+ testMethod(t, r, "POST")
+ testBody(t, r, `{"id":1,"genus_id":1,"species_name":"Test Species","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)
+ })
+
+ species := &Species{Id: 1, GenusId: 1, SpeciesName: "Test Species"}
+ created, err := client.Species.Create(species)
+ if err != nil {
+ t.Errorf("Species.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(species, want) {
+ t.Errorf("Species.Create returned %+v, want %+v", species, want)
+ }
+}
diff --git a/router/api.go b/router/api.go
index 229bddc..8ae8b02 100644
--- a/router/api.go
+++ b/router/api.go
@@ -18,6 +18,7 @@ func API() *mux.Router {
m.Path("/genera/{Id:.+}").Methods("DELETE").Name(DeleteGenus)
// Species
+ m.Path("/species").Methods("POST").Name(CreateSpecies)
m.Path("/species/{Id:.+}").Methods("GET").Name(Species)
return m
diff --git a/router/routes.go b/router/routes.go
index 9c4ed37..8b2bd70 100644
--- a/router/routes.go
+++ b/router/routes.go
@@ -11,5 +11,6 @@ const (
UpdateGenus = "genus:update"
DeleteGenus = "genus:delete"
- Species = "species"
+ Species = "species"
+ CreateSpecies = "species:create"
)
From 7e74d672ba8f441424a414314b7a1612ba9dbc3b Mon Sep 17 00:00:00 2001
From: Matthew Dillon <mrdillon@alaska.edu>
Date: Thu, 16 Oct 2014 09:20:25 -0800
Subject: [PATCH 4/9] Using struct attrs to match desired db schema
---
datastore/migrations/00001_AddUsers_up.sql | 6 +++---
datastore/migrations/00002_AddGenera_up.sql | 10 +++++-----
datastore/migrations/00003_AddSpecies_up.sql | 12 ++++++------
models/genera.go | 8 ++++----
models/species.go | 10 +++++-----
models/users.go | 8 ++++----
6 files changed, 27 insertions(+), 27 deletions(-)
diff --git a/datastore/migrations/00001_AddUsers_up.sql b/datastore/migrations/00001_AddUsers_up.sql
index 9dd8907..4ef446a 100644
--- a/datastore/migrations/00001_AddUsers_up.sql
+++ b/datastore/migrations/00001_AddUsers_up.sql
@@ -5,9 +5,9 @@ CREATE TABLE users (
id BIGSERIAL NOT NULL,
username CHARACTER VARYING(100),
- createdat TIMESTAMP WITH TIME ZONE,
- updatedat TIMESTAMP WITH TIME ZONE,
- deletedat TIMESTAMP WITH TIME ZONE,
+ created_at TIMESTAMP WITH TIME ZONE,
+ updated_at TIMESTAMP WITH TIME ZONE,
+ deleted_at TIMESTAMP WITH TIME ZONE,
CONSTRAINT users_pkey PRIMARY KEY (id)
);
diff --git a/datastore/migrations/00002_AddGenera_up.sql b/datastore/migrations/00002_AddGenera_up.sql
index 3fa4d79..e9ea156 100644
--- a/datastore/migrations/00002_AddGenera_up.sql
+++ b/datastore/migrations/00002_AddGenera_up.sql
@@ -3,11 +3,11 @@
CREATE TABLE genera (
id BIGSERIAL NOT NULL,
- genusname CHARACTER VARYING(100),
+ genus_name CHARACTER VARYING(100),
- createdat TIMESTAMP WITH TIME ZONE,
- updatedat TIMESTAMP WITH TIME ZONE,
- deletedat TIMESTAMP WITH TIME ZONE,
+ created_at TIMESTAMP WITH TIME ZONE,
+ updated_at TIMESTAMP WITH TIME ZONE,
+ deleted_at TIMESTAMP WITH TIME ZONE,
CONSTRAINT genus_pkey PRIMARY KEY (id)
);
@@ -15,5 +15,5 @@ CREATE TABLE genera (
CREATE UNIQUE INDEX genusname_idx
ON genera
USING btree
- (genusname COLLATE pg_catalog."default");
+ (genus_name COLLATE pg_catalog."default");
diff --git a/datastore/migrations/00003_AddSpecies_up.sql b/datastore/migrations/00003_AddSpecies_up.sql
index aff073b..88a192a 100644
--- a/datastore/migrations/00003_AddSpecies_up.sql
+++ b/datastore/migrations/00003_AddSpecies_up.sql
@@ -3,13 +3,13 @@
CREATE TABLE species (
id BIGSERIAL NOT NULL,
- genusid BIGINT NOT NULL,
- speciesname CHARACTER VARYING(100),
+ genus_id BIGINT NOT NULL,
+ species_name CHARACTER VARYING(100),
- createdat TIMESTAMP WITH TIME ZONE,
- updatedat TIMESTAMP WITH TIME ZONE,
- deletedat TIMESTAMP WITH TIME ZONE,
+ created_at TIMESTAMP WITH TIME ZONE,
+ updated_at TIMESTAMP WITH TIME ZONE,
+ deleted_at TIMESTAMP WITH TIME ZONE,
CONSTRAINT species_pkey PRIMARY KEY (id),
- FOREIGN KEY (genusid) REFERENCES genera(id)
+ FOREIGN KEY (genus_id) REFERENCES genera(id)
);
diff --git a/models/genera.go b/models/genera.go
index fb87694..60cc2b0 100644
--- a/models/genera.go
+++ b/models/genera.go
@@ -12,10 +12,10 @@ import (
// 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"`
+ GenusName string `db:"genus_name" json:"genus_name"`
+ CreatedAt time.Time `db:"created_at" json:"created_at"`
+ UpdatedAt time.Time `db:"updated_at" json:"updated_at"`
+ DeletedAt time.Time `db:"deleted_at" json:"deleted_at"`
}
// GeneraService interacts with the genus-related endpoints in bactdb's API.
diff --git a/models/species.go b/models/species.go
index 3437d8e..dbd696d 100644
--- a/models/species.go
+++ b/models/species.go
@@ -12,11 +12,11 @@ import (
// A Species is a high-level classifier in bactdb.
type Species struct {
Id int64 `json:"id,omitempty"`
- GenusId int64 `json:"genus_id"`
- SpeciesName string `json:"species_name"`
- CreatedAt time.Time `json:"created_at"`
- UpdatedAt time.Time `json:"updated_at"`
- DeletedAt time.Time `json:"deleted_at"`
+ GenusId int64 `db:"genus_id" json:"genus_id"`
+ SpeciesName string `db:"species_name" json:"species_name"`
+ CreatedAt time.Time `db:"created_at" json:"created_at"`
+ UpdatedAt time.Time `db:"updated_at" json:"updated_at"`
+ DeletedAt time.Time `db:"deleted_at" json:"deleted_at"`
}
// SpeciesService interacts with the species-related endpoints in bactdb's API.
diff --git a/models/users.go b/models/users.go
index e398295..d7a526d 100644
--- a/models/users.go
+++ b/models/users.go
@@ -12,10 +12,10 @@ import (
// A User is a person that has administrative access to bactdb.
type User struct {
Id int64 `json:"id,omitempty"`
- UserName string `sql:"size:100" json:"user_name"`
- CreatedAt time.Time `json:"created_at"`
- UpdatedAt time.Time `json:"updated_at"`
- DeletedAt time.Time `json:"deleted_at"`
+ UserName string `json:"user_name"`
+ CreatedAt time.Time `db:"created_at" json:"created_at"`
+ UpdatedAt time.Time `db:"updated_at" json:"updated_at"`
+ DeletedAt time.Time `db:"deleted_at" json:"deleted_at"`
}
// UsersService interacts with the user-related endpoints in bactdb's API.
From b045ded9cd97b1b47b868b2047a695c2c443fc78 Mon Sep 17 00:00:00 2001
From: Matthew Dillon <mrdillon@alaska.edu>
Date: Thu, 16 Oct 2014 09:41:01 -0800
Subject: [PATCH 5/9] Importing base schema
---
datastore/migrations/00004_AddStrain_down.sql | 5 +++++
datastore/migrations/00004_AddStrain_up.sql | 20 +++++++++++++++++++
.../00005_AddObservationTypes_down.sql | 5 +++++
.../00005_AddObservationTypes_up.sql | 14 +++++++++++++
.../migrations/00006_AddObservations_down.sql | 5 +++++
.../migrations/00006_AddObservations_up.sql | 16 +++++++++++++++
.../00007_AddStrainsObservations_down.sql | 5 +++++
.../00007_AddStrainsObservations_up.sql | 17 ++++++++++++++++
.../00008_AddText_Measurements_down.sql | 5 +++++
.../00008_AddText_Measurements_up.sql | 14 +++++++++++++
.../migrations/00009_AddUnit_Types_down.sql | 5 +++++
.../migrations/00009_AddUnit_Types_up.sql | 15 ++++++++++++++
.../00010_AddNumerical_Measurements_down.sql | 5 +++++
.../00010_AddNumerical_Measurements_up.sql | 17 ++++++++++++++++
.../00011_AddStrainObsMeasurements_down.sql | 5 +++++
.../00011_AddStrainObsMeasurements_up.sql | 17 ++++++++++++++++
16 files changed, 170 insertions(+)
create mode 100644 datastore/migrations/00004_AddStrain_down.sql
create mode 100644 datastore/migrations/00004_AddStrain_up.sql
create mode 100644 datastore/migrations/00005_AddObservationTypes_down.sql
create mode 100644 datastore/migrations/00005_AddObservationTypes_up.sql
create mode 100644 datastore/migrations/00006_AddObservations_down.sql
create mode 100644 datastore/migrations/00006_AddObservations_up.sql
create mode 100644 datastore/migrations/00007_AddStrainsObservations_down.sql
create mode 100644 datastore/migrations/00007_AddStrainsObservations_up.sql
create mode 100644 datastore/migrations/00008_AddText_Measurements_down.sql
create mode 100644 datastore/migrations/00008_AddText_Measurements_up.sql
create mode 100644 datastore/migrations/00009_AddUnit_Types_down.sql
create mode 100644 datastore/migrations/00009_AddUnit_Types_up.sql
create mode 100644 datastore/migrations/00010_AddNumerical_Measurements_down.sql
create mode 100644 datastore/migrations/00010_AddNumerical_Measurements_up.sql
create mode 100644 datastore/migrations/00011_AddStrainObsMeasurements_down.sql
create mode 100644 datastore/migrations/00011_AddStrainObsMeasurements_up.sql
diff --git a/datastore/migrations/00004_AddStrain_down.sql b/datastore/migrations/00004_AddStrain_down.sql
new file mode 100644
index 0000000..94edb83
--- /dev/null
+++ b/datastore/migrations/00004_AddStrain_down.sql
@@ -0,0 +1,5 @@
+-- bactdb
+-- Matthew R Dillon
+
+DROP TABLE strains;
+
diff --git a/datastore/migrations/00004_AddStrain_up.sql b/datastore/migrations/00004_AddStrain_up.sql
new file mode 100644
index 0000000..855f3a9
--- /dev/null
+++ b/datastore/migrations/00004_AddStrain_up.sql
@@ -0,0 +1,20 @@
+-- bactdb
+-- Matthew R Dillon
+
+CREATE TABLE strains (
+ id BIGSERIAL NOT NULL,
+ species_id BIGINT,
+ strain_name CHARACTER VARYING(100),
+ strain_type CHARACTER VARYING(100),
+ etymology CHARACTER VARYING(500),
+ accession_banks CHARACTER VARYING(100),
+ genbank_embl_ddb CHARACTER VARYING(100),
+
+ created_at TIMESTAMP WITH TIME ZONE,
+ updated_at TIMESTAMP WITH TIME ZONE,
+ deleted_at TIMESTAMP WITH TIME ZONE,
+
+ CONSTRAINT strain_pkey PRIMARY KEY (id),
+ FOREIGN KEY (species_id) REFERENCES species(id)
+);
+
diff --git a/datastore/migrations/00005_AddObservationTypes_down.sql b/datastore/migrations/00005_AddObservationTypes_down.sql
new file mode 100644
index 0000000..39f6366
--- /dev/null
+++ b/datastore/migrations/00005_AddObservationTypes_down.sql
@@ -0,0 +1,5 @@
+-- bactdb
+-- Matthew R Dillon
+
+DROP TABLE observation_types;
+
diff --git a/datastore/migrations/00005_AddObservationTypes_up.sql b/datastore/migrations/00005_AddObservationTypes_up.sql
new file mode 100644
index 0000000..d18d8b5
--- /dev/null
+++ b/datastore/migrations/00005_AddObservationTypes_up.sql
@@ -0,0 +1,14 @@
+-- bactdb
+-- Matthew R Dillon
+
+CREATE TABLE observation_types (
+ id BIGSERIAL NOT NULL,
+ observation_type_name CHARACTER VARYING(100),
+
+ created_at TIMESTAMP WITH TIME ZONE,
+ updated_at TIMESTAMP WITH TIME ZONE,
+ deleted_at TIMESTAMP WITH TIME ZONE,
+
+ CONSTRAINT observation_types_pkey PRIMARY KEY (id)
+);
+
diff --git a/datastore/migrations/00006_AddObservations_down.sql b/datastore/migrations/00006_AddObservations_down.sql
new file mode 100644
index 0000000..5b5ef85
--- /dev/null
+++ b/datastore/migrations/00006_AddObservations_down.sql
@@ -0,0 +1,5 @@
+-- bactdb
+-- Matthew R Dillon
+
+DROP TABLE observations;
+
diff --git a/datastore/migrations/00006_AddObservations_up.sql b/datastore/migrations/00006_AddObservations_up.sql
new file mode 100644
index 0000000..df0a1be
--- /dev/null
+++ b/datastore/migrations/00006_AddObservations_up.sql
@@ -0,0 +1,16 @@
+-- bactdb
+-- Matthew R Dillon
+
+CREATE TABLE observations (
+ id BIGSERIAL NOT NULL,
+ observation_name CHARACTER VARYING(100),
+ observation_type_id BIGINT,
+
+ created_at TIMESTAMP WITH TIME ZONE,
+ updated_at TIMESTAMP WITH TIME ZONE,
+ deleted_at TIMESTAMP WITH TIME ZONE,
+
+ CONSTRAINT observations_pkey PRIMARY KEY (id),
+ FOREIGN KEY (observation_type_id) REFERENCES observation_types(id)
+);
+
diff --git a/datastore/migrations/00007_AddStrainsObservations_down.sql b/datastore/migrations/00007_AddStrainsObservations_down.sql
new file mode 100644
index 0000000..c67ba07
--- /dev/null
+++ b/datastore/migrations/00007_AddStrainsObservations_down.sql
@@ -0,0 +1,5 @@
+-- bactdb
+-- Matthew R Dillon
+
+DROP TABLE strainsobservations;
+
diff --git a/datastore/migrations/00007_AddStrainsObservations_up.sql b/datastore/migrations/00007_AddStrainsObservations_up.sql
new file mode 100644
index 0000000..4c939be
--- /dev/null
+++ b/datastore/migrations/00007_AddStrainsObservations_up.sql
@@ -0,0 +1,17 @@
+-- bactdb
+-- Matthew R Dillon
+
+CREATE TABLE strainsobservations (
+ id BIGSERIAL NOT NULL,
+ strain_id BIGINT NOT NULL,
+ observations_id BIGINT NOT NULL,
+
+ created_at TIMESTAMP WITH TIME ZONE,
+ updated_at TIMESTAMP WITH TIME ZONE,
+ deleted_at TIMESTAMP WITH TIME ZONE,
+
+ CONSTRAINT strainsobservations_pkey PRIMARY KEY (id),
+ FOREIGN KEY (strain_id) REFERENCES strains(id),
+ FOREIGN KEY (observations_id) REFERENCES observations(id)
+);
+
diff --git a/datastore/migrations/00008_AddText_Measurements_down.sql b/datastore/migrations/00008_AddText_Measurements_down.sql
new file mode 100644
index 0000000..3b8bc9b
--- /dev/null
+++ b/datastore/migrations/00008_AddText_Measurements_down.sql
@@ -0,0 +1,5 @@
+-- bactdb
+-- Matthew R Dillon
+
+DROP TABLE text_measurements;
+
diff --git a/datastore/migrations/00008_AddText_Measurements_up.sql b/datastore/migrations/00008_AddText_Measurements_up.sql
new file mode 100644
index 0000000..d0992ce
--- /dev/null
+++ b/datastore/migrations/00008_AddText_Measurements_up.sql
@@ -0,0 +1,14 @@
+-- bactdb
+-- Matthew R Dillon
+
+CREATE TABLE text_measurements (
+ id BIGSERIAL NOT NULL,
+ text_measurement_name CHARACTER VARYING(100),
+
+ created_at TIMESTAMP WITH TIME ZONE,
+ updated_at TIMESTAMP WITH TIME ZONE,
+ deleted_at TIMESTAMP WITH TIME ZONE,
+
+ CONSTRAINT text_measurements_pkey PRIMARY KEY (id)
+);
+
diff --git a/datastore/migrations/00009_AddUnit_Types_down.sql b/datastore/migrations/00009_AddUnit_Types_down.sql
new file mode 100644
index 0000000..ffbb77c
--- /dev/null
+++ b/datastore/migrations/00009_AddUnit_Types_down.sql
@@ -0,0 +1,5 @@
+-- bactdb
+-- Matthew R Dillon
+
+DROP TABLE unit_types;
+
diff --git a/datastore/migrations/00009_AddUnit_Types_up.sql b/datastore/migrations/00009_AddUnit_Types_up.sql
new file mode 100644
index 0000000..348242a
--- /dev/null
+++ b/datastore/migrations/00009_AddUnit_Types_up.sql
@@ -0,0 +1,15 @@
+-- bactdb
+-- Matthew R Dillon
+
+CREATE TABLE unit_types (
+ id BIGSERIAL NOT NULL,
+ name CHARACTER VARYING(100),
+ symbol CHARACTER VARYING(10),
+
+ created_at TIMESTAMP WITH TIME ZONE,
+ updated_at TIMESTAMP WITH TIME ZONE,
+ deleted_at TIMESTAMP WITH TIME ZONE,
+
+ CONSTRAINT unit_types_pkey PRIMARY KEY (id)
+);
+
diff --git a/datastore/migrations/00010_AddNumerical_Measurements_down.sql b/datastore/migrations/00010_AddNumerical_Measurements_down.sql
new file mode 100644
index 0000000..b8fbc65
--- /dev/null
+++ b/datastore/migrations/00010_AddNumerical_Measurements_down.sql
@@ -0,0 +1,5 @@
+-- bactdb
+-- Matthew R Dillon
+
+DROP TABLE numerical_measurements;
+
diff --git a/datastore/migrations/00010_AddNumerical_Measurements_up.sql b/datastore/migrations/00010_AddNumerical_Measurements_up.sql
new file mode 100644
index 0000000..b1deda2
--- /dev/null
+++ b/datastore/migrations/00010_AddNumerical_Measurements_up.sql
@@ -0,0 +1,17 @@
+-- bactdb
+-- Matthew R Dillon
+
+CREATE TABLE numerical_measurements (
+ id BIGSERIAL NOT NULL,
+ measurement_value NUMERIC(6, 4) NOT NULL,
+ confidence_interval NUMERIC(6,4) NULL,
+ unit_type_id BIGINT,
+
+ created_at TIMESTAMP WITH TIME ZONE,
+ updated_at TIMESTAMP WITH TIME ZONE,
+ deleted_at TIMESTAMP WITH TIME ZONE,
+
+ CONSTRAINT numerical_measurements_pkey PRIMARY KEY (id),
+ FOREIGN KEY (unit_type_id) REFERENCES unit_types(id)
+);
+
diff --git a/datastore/migrations/00011_AddStrainObsMeasurements_down.sql b/datastore/migrations/00011_AddStrainObsMeasurements_down.sql
new file mode 100644
index 0000000..815b20d
--- /dev/null
+++ b/datastore/migrations/00011_AddStrainObsMeasurements_down.sql
@@ -0,0 +1,5 @@
+-- bactdb
+-- Matthew R Dillon
+
+DROP TABLE strainsobsmeasurements;
+
diff --git a/datastore/migrations/00011_AddStrainObsMeasurements_up.sql b/datastore/migrations/00011_AddStrainObsMeasurements_up.sql
new file mode 100644
index 0000000..9abf103
--- /dev/null
+++ b/datastore/migrations/00011_AddStrainObsMeasurements_up.sql
@@ -0,0 +1,17 @@
+-- bactdb
+-- Matthew R Dillon
+
+CREATE TABLE strainsobsmeasurements (
+ id BIGSERIAL NOT NULL,
+ strainsobservations_id BIGINT,
+ measurement_table CHARACTER VARYING(15),
+ measurement_id BIGINT,
+
+ created_at TIMESTAMP WITH TIME ZONE,
+ updated_at TIMESTAMP WITH TIME ZONE,
+ deleted_at TIMESTAMP WITH TIME ZONE,
+
+ CONSTRAINT strainsobsmeasurements_pkey PRIMARY KEY (id),
+ FOREIGN KEY (strainsobservations_id) REFERENCES strainsobservations(id)
+);
+
From 5244ae529a5c9cf00f2da6d8be21a14a850e6b8a Mon Sep 17 00:00:00 2001
From: Matthew Dillon <mrdillon@alaska.edu>
Date: Thu, 23 Oct 2014 17:29:07 -0800
Subject: [PATCH 6/9] Species: List species.
---
api/handler.go | 1 +
api/species.go | 17 +++++++++++++++++
api/species_test.go | 29 +++++++++++++++++++++++++++++
datastore/species.go | 12 ++++++++++++
datastore/species_test.go | 33 +++++++++++++++++++++++++++++++++
models/species.go | 35 +++++++++++++++++++++++++++++++++++
models/species_test.go | 32 ++++++++++++++++++++++++++++++++
router/api.go | 1 +
router/routes.go | 1 +
9 files changed, 161 insertions(+)
diff --git a/api/handler.go b/api/handler.go
index 65bbc79..98c8952 100644
--- a/api/handler.go
+++ b/api/handler.go
@@ -31,6 +31,7 @@ func Handler() *mux.Router {
m.Get(router.Species).Handler(handler(serveSpecies))
m.Get(router.CreateSpecies).Handler(handler(serveCreateSpecies))
+ m.Get(router.SpeciesList).Handler(handler(serveSpeciesList))
return m
}
diff --git a/api/species.go b/api/species.go
index b8bae18..7ff94ff 100644
--- a/api/species.go
+++ b/api/species.go
@@ -40,3 +40,20 @@ func serveCreateSpecies(w http.ResponseWriter, r *http.Request) error {
return writeJSON(w, species)
}
+
+func serveSpeciesList(w http.ResponseWriter, r *http.Request) error {
+ var opt models.SpeciesListOptions
+ if err := schemaDecoder.Decode(&opt, r.URL.Query()); err != nil {
+ return err
+ }
+
+ species, err := store.Species.List(&opt)
+ if err != nil {
+ return err
+ }
+ if species == nil {
+ species = []*models.Species{}
+ }
+
+ return writeJSON(w, species)
+}
diff --git a/api/species_test.go b/api/species_test.go
index 24fd557..490c62c 100644
--- a/api/species_test.go
+++ b/api/species_test.go
@@ -59,3 +59,32 @@ func TestSpecies_Create(t *testing.T) {
t.Error("!success")
}
}
+
+func TestSpecies_List(t *testing.T) {
+ setup()
+
+ want := []*models.Species{{Id: 1, GenusId: 1, SpeciesName: "Test Species"}}
+ wantOpt := &models.SpeciesListOptions{ListOptions: models.ListOptions{Page: 1, PerPage: 10}}
+
+ calledList := false
+ store.Species.(*models.MockSpeciesService).List_ = func(opt *models.SpeciesListOptions) ([]*models.Species, error) {
+ if !normalizeDeepEqual(wantOpt, opt) {
+ t.Errorf("wanted options %d but got %d", wantOpt, opt)
+ }
+ calledList = true
+ return want, nil
+ }
+
+ species, err := apiClient.Species.List(wantOpt)
+ if err != nil {
+ t.Fatal(err)
+ }
+
+ if !calledList {
+ t.Error("!calledList")
+ }
+
+ if !normalizeDeepEqual(&want, &species) {
+ t.Errorf("got species %+v but wanted species %+v", species, want)
+ }
+}
diff --git a/datastore/species.go b/datastore/species.go
index f7e6dee..cccdd07 100644
--- a/datastore/species.go
+++ b/datastore/species.go
@@ -27,3 +27,15 @@ func (s *speciesStore) Create(species *models.Species) (bool, error) {
}
return true, nil
}
+
+func (s *speciesStore) List(opt *models.SpeciesListOptions) ([]*models.Species, error) {
+ if opt == nil {
+ opt = &models.SpeciesListOptions{}
+ }
+ var species []*models.Species
+ err := s.dbh.Select(&species, `SELECT * FROM species LIMIT $1 OFFSET $2;`, opt.PerPageOrDefault(), opt.Offset())
+ if err != nil {
+ return nil, err
+ }
+ return species, nil
+}
diff --git a/datastore/species_test.go b/datastore/species_test.go
index db81db6..a540a99 100644
--- a/datastore/species_test.go
+++ b/datastore/species_test.go
@@ -63,3 +63,36 @@ func TestSpeciesStore_Create_db(t *testing.T) {
t.Error("want nonzero species.Id after submitting")
}
}
+
+func TestSpeciesStore_List_db(t *testing.T) {
+ tx, _ := DB.Begin()
+ defer tx.Rollback()
+
+ // Test on a clean database
+ tx.Exec(`DELETE FROM species;`)
+
+ genus := &models.Genus{}
+
+ if err := tx.Insert(genus); err != nil {
+ t.Fatal(err)
+ }
+
+ want := []*models.Species{{Id: 1, GenusId: genus.Id, SpeciesName: "Test Species"}}
+
+ if err := tx.Insert(want[0]); err != nil {
+ t.Fatal(err)
+ }
+
+ d := NewDatastore(tx)
+ species, err := d.Species.List(&models.SpeciesListOptions{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(species, want) {
+ t.Errorf("got species %+v, want %+v", species, want)
+ }
+}
diff --git a/models/species.go b/models/species.go
index dbd696d..faf6820 100644
--- a/models/species.go
+++ b/models/species.go
@@ -24,6 +24,9 @@ type SpeciesService interface {
// Get a species
Get(id int64) (*Species, error)
+ // List all species
+ List(opt *SpeciesListOptions) ([]*Species, error)
+
// Create a species record
Create(species *Species) (bool, error)
}
@@ -78,8 +81,33 @@ func (s *speciesService) Create(species *Species) (bool, error) {
return resp.StatusCode == http.StatusCreated, nil
}
+type SpeciesListOptions struct {
+ ListOptions
+}
+
+func (s *speciesService) List(opt *SpeciesListOptions) ([]*Species, error) {
+ url, err := s.client.url(router.SpeciesList, nil, opt)
+ if err != nil {
+ return nil, err
+ }
+
+ req, err := s.client.NewRequest("GET", url.String(), nil)
+ if err != nil {
+ return nil, err
+ }
+
+ var species []*Species
+ _, err = s.client.Do(req, &species)
+ if err != nil {
+ return nil, err
+ }
+
+ return species, nil
+}
+
type MockSpeciesService struct {
Get_ func(id int64) (*Species, error)
+ List_ func(opt *SpeciesListOptions) ([]*Species, error)
Create_ func(species *Species) (bool, error)
}
@@ -98,3 +126,10 @@ func (s *MockSpeciesService) Create(species *Species) (bool, error) {
}
return s.Create_(species)
}
+
+func (s *MockSpeciesService) List(opt *SpeciesListOptions) ([]*Species, error) {
+ if s.List_ == nil {
+ return nil, nil
+ }
+ return s.List_(opt)
+}
diff --git a/models/species_test.go b/models/species_test.go
index 338d13b..4e6873b 100644
--- a/models/species_test.go
+++ b/models/species_test.go
@@ -73,3 +73,35 @@ func TestSpeciesService_Create(t *testing.T) {
t.Errorf("Species.Create returned %+v, want %+v", species, want)
}
}
+
+func TestSpeciesService_List(t *testing.T) {
+ setup()
+ defer teardown()
+
+ want := []*Species{{Id: 1, GenusId: 1, SpeciesName: "Test Species"}}
+
+ var called bool
+ mux.HandleFunc(urlPath(t, router.SpeciesList, nil), func(w http.ResponseWriter, r *http.Request) {
+ called = true
+ testMethod(t, r, "GET")
+ testFormValues(t, r, values{})
+
+ writeJSON(w, want)
+ })
+
+ species, err := client.Species.List(nil)
+ if err != nil {
+ t.Errorf("Species.List returned error: %v", err)
+ }
+
+ if !called {
+ t.Fatal("!called")
+ }
+
+ for _, u := range want {
+ normalizeTime(&u.CreatedAt, &u.UpdatedAt, &u.DeletedAt)
+ }
+ if !reflect.DeepEqual(species, want) {
+ t.Errorf("Species.List return %+v, want %+v", species, want)
+ }
+}
diff --git a/router/api.go b/router/api.go
index 8ae8b02..2ffa19a 100644
--- a/router/api.go
+++ b/router/api.go
@@ -18,6 +18,7 @@ func API() *mux.Router {
m.Path("/genera/{Id:.+}").Methods("DELETE").Name(DeleteGenus)
// Species
+ m.Path("/species").Methods("GET").Name(SpeciesList)
m.Path("/species").Methods("POST").Name(CreateSpecies)
m.Path("/species/{Id:.+}").Methods("GET").Name(Species)
diff --git a/router/routes.go b/router/routes.go
index 8b2bd70..4d7a9ac 100644
--- a/router/routes.go
+++ b/router/routes.go
@@ -13,4 +13,5 @@ const (
Species = "species"
CreateSpecies = "species:create"
+ SpeciesList = "species:list"
)
From c8d1d0a84f589da0884b4e3a52a58e2d06d0dc9f Mon Sep 17 00:00:00 2001
From: Matthew Dillon <mrdillon@alaska.edu>
Date: Thu, 23 Oct 2014 18:25:15 -0800
Subject: [PATCH 7/9] species update wip
---
datastore/species_test.go | 35 +++++++++++++++++++++++++++++++++++
models/species.go | 32 ++++++++++++++++++++++++++++++++
models/species_test.go | 31 +++++++++++++++++++++++++++++++
router/api.go | 1 +
router/routes.go | 1 +
5 files changed, 100 insertions(+)
diff --git a/datastore/species_test.go b/datastore/species_test.go
index a540a99..62235ba 100644
--- a/datastore/species_test.go
+++ b/datastore/species_test.go
@@ -96,3 +96,38 @@ func TestSpeciesStore_List_db(t *testing.T) {
t.Errorf("got species %+v, want %+v", species, want)
}
}
+
+func TestSpeciesStore_Update_db(t *testing.T) {
+ tx, _ := DB.Begin()
+ defer tx.Rollback()
+
+ // Test on a clean database
+ tx.Exec(`DELETE FROM species;`)
+
+ d := NewDatastore(nil)
+ // Add a new record
+ genus := &models.Genus{GenusName: "Test Genus"}
+ _, err := d.Genera.Create(genus)
+ if err != nil {
+ t.Fatal(err)
+ }
+ created := &model.Species{GenusId: genus.Id, SpeciesName: "Test Species"}
+ _, err := d.Species.Create(created)
+ if err != nil {
+ t.Fatal(err)
+ }
+ if !created {
+ t.Error("!created")
+ }
+
+ // Tweak it
+ species.SpeciesName = "Updated Species"
+ updated, err := d.Species.Update(species.Id, species)
+ if err != nil {
+ t.Fatal(err)
+ }
+
+ if !updated {
+ t.Error("!updated")
+ }
+}
diff --git a/models/species.go b/models/species.go
index faf6820..b742de8 100644
--- a/models/species.go
+++ b/models/species.go
@@ -29,6 +29,9 @@ type SpeciesService interface {
// Create a species record
Create(species *Species) (bool, error)
+
+ // Update an existing species
+ Update(id int64, species *Species) (updated bool, err error)
}
var (
@@ -105,10 +108,32 @@ func (s *speciesService) List(opt *SpeciesListOptions) ([]*Species, error) {
return species, nil
}
+func (s *speciesService) Update(id int64, species *Species) (bool, error) {
+ strId := strconv.FormatInt(id, 10)
+
+ url, err := s.client.url(router.UpdateSpecies, map[string]string{"Id": strId}, nil)
+ if err != nil {
+ return false, err
+ }
+
+ req, err := s.client.NewRequest("PUT", url.String(), species)
+ if err != nil {
+ return false, err
+ }
+
+ resp, err := s.client.Do(req, &species)
+ if err != nil {
+ return false, err
+ }
+
+ return resp.StatusCode == http.StatusOK, nil
+}
+
type MockSpeciesService struct {
Get_ func(id int64) (*Species, error)
List_ func(opt *SpeciesListOptions) ([]*Species, error)
Create_ func(species *Species) (bool, error)
+ Update_ func(id int64, species *Species) (bool, error)
}
var _ SpeciesService = &MockSpeciesService{}
@@ -133,3 +158,10 @@ func (s *MockSpeciesService) List(opt *SpeciesListOptions) ([]*Species, error) {
}
return s.List_(opt)
}
+
+func (s *MockSpeciesService) Update(id int64, species *Species) (bool, error) {
+ if s.Update_ == nil {
+ return false, nil
+ }
+ return s.Update_(id, species)
+}
diff --git a/models/species_test.go b/models/species_test.go
index 4e6873b..cb66f9e 100644
--- a/models/species_test.go
+++ b/models/species_test.go
@@ -105,3 +105,34 @@ func TestSpeciesService_List(t *testing.T) {
t.Errorf("Species.List return %+v, want %+v", species, want)
}
}
+
+func TestSpeciesService_Update(t *testing.T) {
+ setup()
+ defer teardown()
+
+ want := &Species{Id: 1, GenusId: 1, SpeciesName: "Test Species"}
+
+ var called bool
+ mux.HandleFunc(urlPath(t, router.UpdateSpecies, map[string]string{"Id": "1"}), func(w http.ResponseWriter, r *http.Request) {
+ called = true
+ testMethod(t, r, "PUT")
+ testBody(t, r, `{"id":1,"genus_id":1,"species_name":"Test Species 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)
+ })
+
+ species := &Species{Id: 1, GenusId: 1, SpeciesName: "Test Species Updated"}
+ updated, err := client.Species.Update(1, species)
+ if err != nil {
+ t.Errorf("Species.Update returned error: %v", err)
+ }
+
+ if !updated {
+ t.Error("!updated")
+ }
+
+ if !called {
+ t.Fatal("!called")
+ }
+}
diff --git a/router/api.go b/router/api.go
index 2ffa19a..5bf24d2 100644
--- a/router/api.go
+++ b/router/api.go
@@ -21,6 +21,7 @@ func API() *mux.Router {
m.Path("/species").Methods("GET").Name(SpeciesList)
m.Path("/species").Methods("POST").Name(CreateSpecies)
m.Path("/species/{Id:.+}").Methods("GET").Name(Species)
+ m.Path("/species/{Id:.+}").Methods("PUT").Name(UpdateSpecies)
return m
}
diff --git a/router/routes.go b/router/routes.go
index 4d7a9ac..0db9205 100644
--- a/router/routes.go
+++ b/router/routes.go
@@ -14,4 +14,5 @@ const (
Species = "species"
CreateSpecies = "species:create"
SpeciesList = "species:list"
+ UpdateSpecies = "species:update"
)
From 22d2b8b41dfe2afb644026f863aef5cb37efcbe3 Mon Sep 17 00:00:00 2001
From: Matthew Dillon <mrdillon@alaska.edu>
Date: Fri, 24 Oct 2014 10:08:12 -0800
Subject: [PATCH 8/9] Finishing up changes from previous commit
---
api/handler.go | 1 +
api/species.go | 19 +++++++++++++++++++
api/species_test.go | 30 ++++++++++++++++++++++++++++++
datastore/species.go | 22 ++++++++++++++++++++++
datastore/species_test.go | 4 ++--
5 files changed, 74 insertions(+), 2 deletions(-)
diff --git a/api/handler.go b/api/handler.go
index 98c8952..b7999d8 100644
--- a/api/handler.go
+++ b/api/handler.go
@@ -32,6 +32,7 @@ func Handler() *mux.Router {
m.Get(router.Species).Handler(handler(serveSpecies))
m.Get(router.CreateSpecies).Handler(handler(serveCreateSpecies))
m.Get(router.SpeciesList).Handler(handler(serveSpeciesList))
+ m.Get(router.UpdateSpecies).Handler(handler(serveUpdateSpecies))
return m
}
diff --git a/api/species.go b/api/species.go
index 7ff94ff..1e218a4 100644
--- a/api/species.go
+++ b/api/species.go
@@ -57,3 +57,22 @@ func serveSpeciesList(w http.ResponseWriter, r *http.Request) error {
return writeJSON(w, species)
}
+
+func serveUpdateSpecies(w http.ResponseWriter, r *http.Request) error {
+ id, _ := strconv.ParseInt(mux.Vars(r)["Id"], 10, 0)
+ var species models.Species
+ err := json.NewDecoder(r.Body).Decode(&species)
+ if err != nil {
+ return err
+ }
+
+ updated, err := store.Species.Update(id, &species)
+ if err != nil {
+ return err
+ }
+ if updated {
+ w.WriteHeader(http.StatusOK)
+ }
+
+ return writeJSON(w, species)
+}
diff --git a/api/species_test.go b/api/species_test.go
index 490c62c..a0c003a 100644
--- a/api/species_test.go
+++ b/api/species_test.go
@@ -88,3 +88,33 @@ func TestSpecies_List(t *testing.T) {
t.Errorf("got species %+v but wanted species %+v", species, want)
}
}
+
+func TestSpecies_Update(t *testing.T) {
+ setup()
+
+ want := &models.Species{Id: 1, GenusId: 1, SpeciesName: "Test Species"}
+
+ calledPut := false
+ store.Species.(*models.MockSpeciesService).Update_ = func(id int64, species *models.Species) (bool, error) {
+ if id != want.Id {
+ t.Errorf("wanted request for species %d but got %d", want.Id, id)
+ }
+ if !normalizeDeepEqual(want, species) {
+ t.Errorf("wanted request for species %d but got %d", want, species)
+ }
+ calledPut = true
+ return true, nil
+ }
+
+ success, err := apiClient.Species.Update(1, want)
+ if err != nil {
+ t.Fatal(err)
+ }
+
+ if !calledPut {
+ t.Error("!calledPut")
+ }
+ if !success {
+ t.Error("!success")
+ }
+}
diff --git a/datastore/species.go b/datastore/species.go
index cccdd07..c3087c4 100644
--- a/datastore/species.go
+++ b/datastore/species.go
@@ -39,3 +39,25 @@ func (s *speciesStore) List(opt *models.SpeciesListOptions) ([]*models.Species,
}
return species, nil
}
+
+func (s *speciesStore) Update(id int64, species *models.Species) (bool, error) {
+ _, err := s.Get(id)
+ if err != nil {
+ return false, err
+ }
+
+ if id != species.Id {
+ return false, models.ErrSpeciesNotFound
+ }
+
+ changed, err := s.dbh.Update(species)
+ if err != nil {
+ return false, err
+ }
+
+ if changed == 0 {
+ return false, ErrNoRowsUpdated
+ }
+
+ return true, nil
+}
diff --git a/datastore/species_test.go b/datastore/species_test.go
index 62235ba..1d7c3cd 100644
--- a/datastore/species_test.go
+++ b/datastore/species_test.go
@@ -111,8 +111,8 @@ func TestSpeciesStore_Update_db(t *testing.T) {
if err != nil {
t.Fatal(err)
}
- created := &model.Species{GenusId: genus.Id, SpeciesName: "Test Species"}
- _, err := d.Species.Create(created)
+ species := &models.Species{GenusId: genus.Id, SpeciesName: "Test Species"}
+ created, err := d.Species.Create(species)
if err != nil {
t.Fatal(err)
}
From 4669aff3c2f577eb171455351bf38c1f8ef61db3 Mon Sep 17 00:00:00 2001
From: Matthew Dillon <mrdillon@alaska.edu>
Date: Fri, 24 Oct 2014 10:42:31 -0800
Subject: [PATCH 9/9] Species - delete
---
api/handler.go | 1 +
api/species.go | 14 ++++++++++++++
api/species_test.go | 27 +++++++++++++++++++++++++++
datastore/species.go | 16 ++++++++++++++++
datastore/species_test.go | 39 +++++++++++++++++++++++++++++++++++++++
models/species.go | 33 +++++++++++++++++++++++++++++++++
models/species_test.go | 29 +++++++++++++++++++++++++++++
router/api.go | 1 +
router/routes.go | 1 +
9 files changed, 161 insertions(+)
diff --git a/api/handler.go b/api/handler.go
index b7999d8..fd686c6 100644
--- a/api/handler.go
+++ b/api/handler.go
@@ -33,6 +33,7 @@ func Handler() *mux.Router {
m.Get(router.CreateSpecies).Handler(handler(serveCreateSpecies))
m.Get(router.SpeciesList).Handler(handler(serveSpeciesList))
m.Get(router.UpdateSpecies).Handler(handler(serveUpdateSpecies))
+ m.Get(router.DeleteSpecies).Handler(handler(serveDeleteSpecies))
return m
}
diff --git a/api/species.go b/api/species.go
index 1e218a4..fe0b7c3 100644
--- a/api/species.go
+++ b/api/species.go
@@ -76,3 +76,17 @@ func serveUpdateSpecies(w http.ResponseWriter, r *http.Request) error {
return writeJSON(w, species)
}
+
+func serveDeleteSpecies(w http.ResponseWriter, r *http.Request) error {
+ id, _ := strconv.ParseInt(mux.Vars(r)["Id"], 10, 0)
+
+ deleted, err := store.Species.Delete(id)
+ if err != nil {
+ return err
+ }
+ if deleted {
+ w.WriteHeader(http.StatusOK)
+ }
+
+ return writeJSON(w, &models.Species{})
+}
diff --git a/api/species_test.go b/api/species_test.go
index a0c003a..418091e 100644
--- a/api/species_test.go
+++ b/api/species_test.go
@@ -118,3 +118,30 @@ func TestSpecies_Update(t *testing.T) {
t.Error("!success")
}
}
+
+func TestSpecies_Delete(t *testing.T) {
+ setup()
+
+ want := &models.Species{Id: 1, GenusId: 1, SpeciesName: "Test Species"}
+
+ calledDelete := false
+ store.Species.(*models.MockSpeciesService).Delete_ = func(id int64) (bool, error) {
+ if id != want.Id {
+ t.Errorf("wanted request for species %d but got %d", want.Id, id)
+ }
+ calledDelete = true
+ return true, nil
+ }
+
+ success, err := apiClient.Species.Delete(1)
+ if err != nil {
+ t.Fatal(err)
+ }
+
+ if !calledDelete {
+ t.Error("!calledDelete")
+ }
+ if !success {
+ t.Error("!success")
+ }
+}
diff --git a/datastore/species.go b/datastore/species.go
index c3087c4..651c3e0 100644
--- a/datastore/species.go
+++ b/datastore/species.go
@@ -61,3 +61,19 @@ func (s *speciesStore) Update(id int64, species *models.Species) (bool, error) {
return true, nil
}
+
+func (s *speciesStore) Delete(id int64) (bool, error) {
+ species, err := s.Get(id)
+ if err != nil {
+ return false, err
+ }
+
+ deleted, err := s.dbh.Delete(species)
+ if err != nil {
+ return false, err
+ }
+ if deleted == 0 {
+ return false, ErrNoRowsDeleted
+ }
+ return true, nil
+}
diff --git a/datastore/species_test.go b/datastore/species_test.go
index 1d7c3cd..5839e95 100644
--- a/datastore/species_test.go
+++ b/datastore/species_test.go
@@ -13,6 +13,7 @@ func TestSpeciesStore_Get_db(t *testing.T) {
// Test on a clean database
tx.Exec(`DELETE FROM species;`)
+ tx.Exec(`DELETE FROM genera;`)
wantGenus := &models.Genus{GenusName: "Test Genus"}
if err := tx.Insert(wantGenus); err != nil {
@@ -42,6 +43,7 @@ func TestSpeciesStore_Create_db(t *testing.T) {
// Test on a clean database
tx.Exec(`DELETE FROM species;`)
+ tx.Exec(`DELETE FROM genera;`)
genus := &models.Genus{}
if err := tx.Insert(genus); err != nil {
@@ -70,6 +72,7 @@ func TestSpeciesStore_List_db(t *testing.T) {
// Test on a clean database
tx.Exec(`DELETE FROM species;`)
+ tx.Exec(`DELETE FROM genera;`)
genus := &models.Genus{}
@@ -103,6 +106,7 @@ func TestSpeciesStore_Update_db(t *testing.T) {
// Test on a clean database
tx.Exec(`DELETE FROM species;`)
+ tx.Exec(`DELETE FROM genera;`)
d := NewDatastore(nil)
// Add a new record
@@ -131,3 +135,38 @@ func TestSpeciesStore_Update_db(t *testing.T) {
t.Error("!updated")
}
}
+
+func TestSpeciesStore_Delete_db(t *testing.T) {
+ tx, _ := DB.Begin()
+ defer tx.Rollback()
+
+ // Test on a clean database
+ tx.Exec(`DELETE FROM species;`)
+ tx.Exec(`DELETE FROM genera;`)
+
+ d := NewDatastore(tx)
+ // Add a new record
+ genus := &models.Genus{GenusName: "Test Genus"}
+ _, err := d.Genera.Create(genus)
+ if err != nil {
+ t.Fatal(err)
+ }
+ species := &models.Species{GenusId: genus.Id, SpeciesName: "Test Species"}
+ created, err := d.Species.Create(species)
+ if err != nil {
+ t.Fatal(err)
+ }
+ if !created {
+ t.Error("!created")
+ }
+
+ // Delete it
+ deleted, err := d.Species.Delete(species.Id)
+ if err != nil {
+ t.Fatal(err)
+ }
+
+ if !deleted {
+ t.Error("!delete")
+ }
+}
diff --git a/models/species.go b/models/species.go
index b742de8..19b69fb 100644
--- a/models/species.go
+++ b/models/species.go
@@ -32,6 +32,9 @@ type SpeciesService interface {
// Update an existing species
Update(id int64, species *Species) (updated bool, err error)
+
+ // Delete an existing species
+ Delete(id int64) (deleted bool, err error)
}
var (
@@ -129,11 +132,34 @@ func (s *speciesService) Update(id int64, species *Species) (bool, error) {
return resp.StatusCode == http.StatusOK, nil
}
+func (s *speciesService) Delete(id int64) (bool, error) {
+ strId := strconv.FormatInt(id, 10)
+
+ url, err := s.client.url(router.DeleteSpecies, 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 species *Species
+ resp, err := s.client.Do(req, &species)
+ if err != nil {
+ return false, err
+ }
+
+ return resp.StatusCode == http.StatusOK, nil
+}
+
type MockSpeciesService struct {
Get_ func(id int64) (*Species, error)
List_ func(opt *SpeciesListOptions) ([]*Species, error)
Create_ func(species *Species) (bool, error)
Update_ func(id int64, species *Species) (bool, error)
+ Delete_ func(id int64) (bool, error)
}
var _ SpeciesService = &MockSpeciesService{}
@@ -165,3 +191,10 @@ func (s *MockSpeciesService) Update(id int64, species *Species) (bool, error) {
}
return s.Update_(id, species)
}
+
+func (s *MockSpeciesService) Delete(id int64) (bool, error) {
+ if s.Delete_ == nil {
+ return false, nil
+ }
+ return s.Delete_(id)
+}
diff --git a/models/species_test.go b/models/species_test.go
index cb66f9e..f2ef1e9 100644
--- a/models/species_test.go
+++ b/models/species_test.go
@@ -136,3 +136,32 @@ func TestSpeciesService_Update(t *testing.T) {
t.Fatal("!called")
}
}
+
+func TestSpeciesService_Delete(t *testing.T) {
+ setup()
+ defer teardown()
+
+ want := &Species{Id: 1, GenusId: 1, SpeciesName: "Test Species"}
+
+ var called bool
+ mux.HandleFunc(urlPath(t, router.DeleteSpecies, 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.Species.Delete(1)
+ if err != nil {
+ t.Errorf("Species.Delete returned error: %v", err)
+ }
+
+ if !deleted {
+ t.Error("!deleted")
+ }
+
+ if !called {
+ t.Fatal("!called")
+ }
+}
diff --git a/router/api.go b/router/api.go
index 5bf24d2..a7731ab 100644
--- a/router/api.go
+++ b/router/api.go
@@ -22,6 +22,7 @@ func API() *mux.Router {
m.Path("/species").Methods("POST").Name(CreateSpecies)
m.Path("/species/{Id:.+}").Methods("GET").Name(Species)
m.Path("/species/{Id:.+}").Methods("PUT").Name(UpdateSpecies)
+ m.Path("/species/{Id:.+}").Methods("DELETE").Name(DeleteSpecies)
return m
}
diff --git a/router/routes.go b/router/routes.go
index 0db9205..124dd98 100644
--- a/router/routes.go
+++ b/router/routes.go
@@ -15,4 +15,5 @@ const (
CreateSpecies = "species:create"
SpeciesList = "species:list"
UpdateSpecies = "species:update"
+ DeleteSpecies = "species:delete"
)