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Ember data: convey species/strain relationships.

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This commit is contained in:
Matthew Dillon 2015-01-26 09:49:39 -09:00
parent 61c24fc843
commit 4be150f897
6 changed files with 32 additions and 23 deletions
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20
datastore/species.go
View file

@ -8,7 +8,7 @@ import (
)
func init() {
DB.AddTableWithName(models.Species{}, "species").SetKeys(true, "Id")
DB.AddTableWithName(models.SpeciesBase{}, "species").SetKeys(true, "Id")
}
type speciesStore struct {
@ -17,7 +17,8 @@ type speciesStore struct {
func (s *speciesStore) Get(id int64) (*models.Species, error) {
var species models.Species
if err := s.dbh.SelectOne(&species, `SELECT * FROM species WHERE id=$1;`, id); err != nil {
err := s.dbh.SelectOne(&species, `SELECT sp.*, array_agg(st.id) AS strains FROM species sp LEFT OUTER JOIN strains st ON st.species_id=sp.id WHERE sp.id=$1 GROUP BY sp.id;`, id)
if err != nil {
return nil, err
}
if &species == nil {
@ -30,9 +31,11 @@ func (s *speciesStore) Create(species *models.Species) (bool, error) {
currentTime := time.Now()
species.CreatedAt = currentTime
species.UpdatedAt = currentTime
if err := s.dbh.Insert(species); err != nil {
base := species.SpeciesBase
if err := s.dbh.Insert(base); err != nil {
return false, err
}
species.Id = base.Id
return true, nil
}
@ -41,13 +44,13 @@ func (s *speciesStore) List(opt *models.SpeciesListOptions) ([]*models.Species,
opt = &models.SpeciesListOptions{}
}
sql := `SELECT * FROM species`
sql := `SELECT sp.*, array_agg(st.id) AS strains FROM species sp LEFT OUTER JOIN strains st ON st.species_id=sp.id`
var conds []string
var vals []interface{}
if opt.Genus != "" {
conds = append(conds, "genus_id = (SELECT id FROM genera WHERE lower(genus_name) = $1)")
conds = append(conds, "sp.genus_id = (SELECT id FROM genera WHERE lower(genus_name) = $1)")
vals = append(vals, opt.Genus)
}
@ -55,7 +58,7 @@ func (s *speciesStore) List(opt *models.SpeciesListOptions) ([]*models.Species,
sql += " WHERE (" + strings.Join(conds, ") AND (") + ")"
}
sql += ";"
sql += " GROUP BY sp.id;"
var species []*models.Species
err := s.dbh.Select(&species, sql, vals...)
@ -76,7 +79,8 @@ func (s *speciesStore) Update(id int64, species *models.Species) (bool, error) {
}
species.UpdatedAt = time.Now()
changed, err := s.dbh.Update(species)
changed, err := s.dbh.Update(species.SpeciesBase)
if err != nil {
return false, err
}
@ -94,7 +98,7 @@ func (s *speciesStore) Delete(id int64) (bool, error) {
return false, err
}
deleted, err := s.dbh.Delete(species)
deleted, err := s.dbh.Delete(species.SpeciesBase)
if err != nil {
return false, err
}

16
datastore/species_test.go
View file

@ -11,17 +11,17 @@ import (
func insertSpecies(t *testing.T, tx *modl.Transaction) *models.Species {
// clean up our target table
tx.Exec(`DELETE FROM species;`)
species := newSpecies(t, tx)
if err := tx.Insert(species); err != nil {
s := newSpecies(t, tx)
if err := tx.Insert(s); err != nil {
t.Fatal(err)
}
return species
return &models.Species{s, []int64(nil)}
}
func newSpecies(t *testing.T, tx *modl.Transaction) *models.Species {
func newSpecies(t *testing.T, tx *modl.Transaction) *models.SpeciesBase {
// we want to create and insert a genus record, too
genus := insertGenus(t, tx)
return &models.Species{GenusId: genus.Id, SpeciesName: "Test Species"}
return &models.SpeciesBase{GenusId: genus.Id, SpeciesName: "Test Species"}
}
func TestSpeciesStore_Get_db(t *testing.T) {
@ -48,11 +48,11 @@ func TestSpeciesStore_Create_db(t *testing.T) {
tx, _ := DB.Begin()
defer tx.Rollback()
species := newSpecies(t, tx)
base_species := newSpecies(t, tx)
species := models.Species{base_species, []int64(nil)}
d := NewDatastore(tx)
created, err := d.Species.Create(species)
created, err := d.Species.Create(&species)
if err != nil {
t.Fatal(err)
}

9
models/species.go
View file

@ -11,7 +11,7 @@ import (
)
// A Species is a high-level classifier in bactdb.
type Species struct {
type SpeciesBase struct {
Id int64 `json:"id,omitempty"`
GenusId int64 `db:"genus_id" json:"genus"`
SpeciesName string `db:"species_name" json:"speciesName"`
@ -20,6 +20,11 @@ type Species struct {
DeletedAt NullTime `db:"deleted_at" json:"deletedAt"`
}
type Species struct {
*SpeciesBase
Strain NullSliceInt64 `db:"strains" json:"strains"`
}
type SpeciesJSON struct {
Species *Species `json:"species"`
}
@ -33,7 +38,7 @@ func (m *Species) String() string {
}
func NewSpecies() *Species {
return &Species{SpeciesName: "Test Species"}
return &Species{&SpeciesBase{SpeciesName: "Test Species"}, make([]int64, 0)}
}
// SpeciesService interacts with the species-related endpoints in bactdb's API.

4
models/species_test.go
View file

@ -55,7 +55,7 @@ func TestSpeciesService_Create(t *testing.T) {
mux.HandleFunc(urlPath(t, router.CreateSpecies, nil), func(w http.ResponseWriter, r *http.Request) {
called = true
testMethod(t, r, "POST")
testBody(t, r, `{"species":{"id":1,"genus":1,"speciesName":"Test Species","createdAt":"0001-01-01T00:00:00Z","updatedAt":"0001-01-01T00:00:00Z","deletedAt":null}}`+"\n")
testBody(t, r, `{"species":{"id":1,"genus":1,"speciesName":"Test Species","createdAt":"0001-01-01T00:00:00Z","updatedAt":"0001-01-01T00:00:00Z","deletedAt":null,"strains":[]}}`+"\n")
w.WriteHeader(http.StatusCreated)
writeJSON(w, want)
@ -124,7 +124,7 @@ func TestSpeciesService_Update(t *testing.T) {
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, `{"species":{"id":1,"genus":1,"speciesName":"Test Species Updated","createdAt":"0001-01-01T00:00:00Z","updatedAt":"0001-01-01T00:00:00Z","deletedAt":null}}`+"\n")
testBody(t, r, `{"species":{"id":1,"genus":1,"speciesName":"Test Species Updated","createdAt":"0001-01-01T00:00:00Z","updatedAt":"0001-01-01T00:00:00Z","deletedAt":null,"strains":[]}}`+"\n")
w.WriteHeader(http.StatusOK)
writeJSON(w, want)

2
models/strains.go
View file

@ -14,7 +14,7 @@ import (
// A Strain is a subclass of species
type Strain struct {
Id int64 `json:"id,omitempty"`
SpeciesId int64 `db:"species_id" json:"speciesId"`
SpeciesId int64 `db:"species_id" json:"species"`
StrainName string `db:"strain_name" json:"strainName"`
StrainType string `db:"strain_type" json:"strainType"`
Etymology NullString `db:"etymology" json:"etymology"`

4
models/strains_test.go
View file

@ -55,7 +55,7 @@ func TestStrainService_Create(t *testing.T) {
mux.HandleFunc(urlPath(t, router.CreateStrain, nil), func(w http.ResponseWriter, r *http.Request) {
called = true
testMethod(t, r, "POST")
testBody(t, r, `{"strain":{"id":1,"speciesId":1,"strainName":"Test Strain","strainType":"Test Type","etymology":"Test Etymology","accessionBanks":"Test Accession","genbankEmblDdb":"Test Genbank","isolatedFrom":null,"createdAt":"0001-01-01T00:00:00Z","updatedAt":"0001-01-01T00:00:00Z","deletedAt":null}}`+"\n")
testBody(t, r, `{"strain":{"id":1,"species":1,"strainName":"Test Strain","strainType":"Test Type","etymology":"Test Etymology","accessionBanks":"Test Accession","genbankEmblDdb":"Test Genbank","isolatedFrom":null,"createdAt":"0001-01-01T00:00:00Z","updatedAt":"0001-01-01T00:00:00Z","deletedAt":null}}`+"\n")
w.WriteHeader(http.StatusCreated)
writeJSON(w, want)
@ -124,7 +124,7 @@ func TestStrainService_Update(t *testing.T) {
mux.HandleFunc(urlPath(t, router.UpdateStrain, map[string]string{"Id": "1"}), func(w http.ResponseWriter, r *http.Request) {
called = true
testMethod(t, r, "PUT")
testBody(t, r, `{"strain":{"id":1,"speciesId":1,"strainName":"Test Strain Updated","strainType":"Test Type Updated","etymology":"Test Etymology","accessionBanks":"Test Accession Updated","genbankEmblDdb":"Test Genbank Updated","isolatedFrom":null,"createdAt":"0001-01-01T00:00:00Z","updatedAt":"0001-01-01T00:00:00Z","deletedAt":null}}`+"\n")
testBody(t, r, `{"strain":{"id":1,"species":1,"strainName":"Test Strain Updated","strainType":"Test Type Updated","etymology":"Test Etymology","accessionBanks":"Test Accession Updated","genbankEmblDdb":"Test Genbank Updated","isolatedFrom":null,"createdAt":"0001-01-01T00:00:00Z","updatedAt":"0001-01-01T00:00:00Z","deletedAt":null}}`+"\n")
w.WriteHeader(http.StatusOK)
writeJSON(w, want)
})