Merge pull request #5 from thermokarst/species

Implement Species

api/handler.go

@@ -29,6 +29,12 @@ 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))
+	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
 }
 

api/species.go

@@ -0,0 +1,92 @@
+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 {
+	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)
+}
+
+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)
+}
+
+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)
+}
+
+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)
+}
+
+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{})
+}

api/species_test.go

@@ -0,0 +1,147 @@
+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
+	}
+
+	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)
+	}
+}
+
+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")
+	}
+}
+
+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)
+	}
+}
+
+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")
+	}
+}
+
+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")
+	}
+}

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/00001_AddUsers_up.sql

@@ -5,9 +5,9 @@ CREATE TABLE users (
     id BIGSERIAL NOT NULL,
     username CHARACTER VARYING(100),
 
-    createdat TIMESTAMP WITH TIME ZONE,
+    created_at TIMESTAMP WITH TIME ZONE,
-    updatedat TIMESTAMP WITH TIME ZONE,
+    updated_at TIMESTAMP WITH TIME ZONE,
-    deletedat TIMESTAMP WITH TIME ZONE,
+    deleted_at TIMESTAMP WITH TIME ZONE,
 
     CONSTRAINT users_pkey PRIMARY KEY (id)
 );

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,
+    created_at TIMESTAMP WITH TIME ZONE,
-    updatedat TIMESTAMP WITH TIME ZONE,
+    updated_at TIMESTAMP WITH TIME ZONE,
-    deletedat 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");
 

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,
+    genus_id BIGINT NOT NULL,
+    species_name CHARACTER VARYING(100),
+
+    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 (genus_id) REFERENCES genera(id)
+);

datastore/migrations/00004_AddStrain_down.sql

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

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)
+);
+

datastore/migrations/00005_AddObservationTypes_down.sql

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

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)
+);
+

datastore/migrations/00006_AddObservations_down.sql

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

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)
+);
+

datastore/migrations/00007_AddStrainsObservations_down.sql

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

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)
+);
+

datastore/migrations/00008_AddText_Measurements_down.sql

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

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)
+);
+

datastore/migrations/00009_AddUnit_Types_down.sql

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

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)
+);
+

datastore/migrations/00010_AddNumerical_Measurements_down.sql

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

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)
+);
+

datastore/migrations/00011_AddStrainObsMeasurements_down.sql

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

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)
+);
+

datastore/species.go

@@ -0,0 +1,79 @@
+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
+}
+
+func (s *speciesStore) Create(species *models.Species) (bool, error) {
+	if err := s.dbh.Insert(species); err != nil {
+		return false, err
+	}
+	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
+}
+
+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
+}
+
+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
+}

datastore/species_test.go

@@ -0,0 +1,172 @@
+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;`)
+	tx.Exec(`DELETE FROM genera;`)
+
+	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)
+	}
+}
+
+func TestSpeciesStore_Create_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;`)
+
+	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")
+	}
+}
+
+func TestSpeciesStore_List_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;`)
+
+	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)
+	}
+}
+
+func TestSpeciesStore_Update_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(nil)
+	// 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")
+	}
+
+	// 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")
+	}
+}
+
+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")
+	}
+}

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/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"`
+	GenusName string    `db:"genus_name" json:"genus_name"`
-	CreatedAt time.Time `json:"created_at"`
+	CreatedAt time.Time `db:"created_at" json:"created_at"`
-	UpdatedAt time.Time `json:"updated_at"`
+	UpdatedAt time.Time `db:"updated_at" json:"updated_at"`
-	DeletedAt time.Time `json:"deleted_at"`
+	DeletedAt time.Time `db:"deleted_at" json:"deleted_at"`
 }
 
 // GeneraService interacts with the genus-related endpoints in bactdb's API.

models/species.go

@@ -0,0 +1,200 @@
+package models
+
+import (
+	"errors"
+	"net/http"
+	"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     `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.
+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)
+
+	// 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 (
+	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
+}
+
+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 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
+}
+
+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
+}
+
+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{}
+
+func (s *MockSpeciesService) Get(id int64) (*Species, error) {
+	if s.Get_ == nil {
+		return nil, nil
+	}
+	return s.Get_(id)
+}
+
+func (s *MockSpeciesService) Create(species *Species) (bool, error) {
+	if s.Create_ == nil {
+		return false, nil
+	}
+	return s.Create_(species)
+}
+
+func (s *MockSpeciesService) List(opt *SpeciesListOptions) ([]*Species, error) {
+	if s.List_ == nil {
+		return nil, nil
+	}
+	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)
+}
+
+func (s *MockSpeciesService) Delete(id int64) (bool, error) {
+	if s.Delete_ == nil {
+		return false, nil
+	}
+	return s.Delete_(id)
+}

models/species_test.go

@@ -0,0 +1,167 @@
+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)
+	}
+}
+
+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)
+	}
+}
+
+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)
+	}
+}
+
+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")
+	}
+}
+
+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")
+	}
+}

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"`
+	UserName  string    `json:"user_name"`
-	CreatedAt time.Time `json:"created_at"`
+	CreatedAt time.Time `db:"created_at" json:"created_at"`
-	UpdatedAt time.Time `json:"updated_at"`
+	UpdatedAt time.Time `db:"updated_at" json:"updated_at"`
-	DeletedAt time.Time `json:"deleted_at"`
+	DeletedAt time.Time `db:"deleted_at" json:"deleted_at"`
 }
 
 // UsersService interacts with the user-related endpoints in bactdb's API.

router/api.go

@@ -16,5 +16,13 @@ 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").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)
+	m.Path("/species/{Id:.+}").Methods("DELETE").Name(DeleteSpecies)
+
 	return m
 }

router/routes.go

@@ -10,4 +10,10 @@ const (
 	Genera      = "genera"
 	UpdateGenus = "genus:update"
 	DeleteGenus = "genus:delete"
+
+	Species       = "species"
+	CreateSpecies = "species:create"
+	SpeciesList   = "species:list"
+	UpdateSpecies = "species:update"
+	DeleteSpecies = "species:delete"
 )