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

@@ -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
 }
 

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)
+}

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)
+	// }
+}

datastore/datastore.go

@@ -11,6 +11,7 @@ import (
 type Datastore struct {
 	Users   models.UsersService
 	Genera  models.GeneraService
+	Species models.SpeciesService
 	dbh     modl.SqlExecutor
 }
 
@@ -29,6 +30,7 @@ func NewDatastore(dbh modl.SqlExecutor) *Datastore {
 	d := &Datastore{dbh: dbh}
 	d.Users = &usersStore{d}
 	d.Genera = &generaStore{d}
+	d.Species = &speciesStore{d}
 	return d
 }
 
@@ -36,5 +38,6 @@ func NewMockDatastore() *Datastore {
 	return &Datastore{
 		Users:   &models.MockUsersService{},
 		Genera:  &models.MockGeneraService{},
+		Species: &models.MockSpeciesService{},
 	}
 }

datastore/migrations/00003_AddSpecies_down.sql

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

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)
+);

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
+}

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)
+	}
+}

models/client.go

@@ -18,6 +18,7 @@ import (
 type Client struct {
 	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
 }
 

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)
+}

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)
+	}
+}

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
 }

router/routes.go

@@ -10,4 +10,6 @@ const (
 	Genera      = "genera"
 	UpdateGenus = "genus:update"
 	DeleteGenus = "genus:delete"
+
+	Species = "species"
 )