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Return species payload on PUT and POST

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This commit is contained in:
Matthew Dillon 2015-07-07 14:15:56 -08:00
parent a8cfc8fe8b
commit b5b6643dcc
2 changed files with 91 additions and 49 deletions
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136
species.go
View file

@ -39,7 +39,6 @@ type SpeciesBase struct {
DeletedBy NullInt64 `db:"deleted_by" json:"deletedBy"`
}
// Species & SpeciesJSON(s) are what ember expects to see
type Species struct {
*SpeciesBase
GenusName string `db:"genus_name" json:"genusName"`
@ -67,14 +66,6 @@ type ManySpeciesPayload struct {
Meta *SpeciesMeta `json:"meta"`
}
type SpeciesJSON struct {
Species *Species `json:"species"`
}
func (s *Species) marshal() ([]byte, error) {
return json.Marshal(&SpeciesJSON{Species: s})
}
func (s *SpeciesPayload) marshal() ([]byte, error) {
return json.Marshal(s)
}
@ -84,9 +75,9 @@ func (s *ManySpeciesPayload) marshal() ([]byte, error) {
}
func (s SpeciesService) unmarshal(b []byte) (entity, error) {
var sj SpeciesJSON
var sj SpeciesPayload
err := json.Unmarshal(b, &sj)
return sj.Species, err
return &sj, err
}
func (s SpeciesService) list(val *url.Values, claims Claims) (entity, *appError) {
@ -132,35 +123,18 @@ func (s SpeciesService) list(val *url.Values, claims Claims) (entity, *appError)
}
func (s SpeciesService) get(id int64, genus string, claims Claims) (entity, *appError) {
var species Species
q := `SELECT sp.*, g.genus_name, array_agg(st.id) AS strains,
COUNT(st) AS total_strains, 0 AS sort_order
FROM species sp
INNER JOIN genera g ON g.id=sp.genus_id AND LOWER(g.genus_name)=$1
LEFT OUTER JOIN strains st ON st.species_id=sp.id
WHERE sp.id=$2
GROUP BY sp.id, g.genus_name;`
if err := DBH.SelectOne(&species, q, genus, id); err != nil {
if err == sql.ErrNoRows {
return nil, ErrSpeciesNotFoundJSON
}
return nil, newJSONError(err, http.StatusInternalServerError)
}
opt := ListOptions{Genus: genus, Ids: []int64{id}}
strains_opt, err := strainOptsFromSpecies(opt)
species, err := getSpecies(id, genus)
if err != nil {
return nil, newJSONError(err, http.StatusInternalServerError)
}
strains, err := listStrains(*strains_opt)
strains, err := strainsFromSpeciesId(id, genus)
if err != nil {
return nil, newJSONError(err, http.StatusInternalServerError)
}
payload := SpeciesPayload{
Species: &species,
Species: species,
Strains: strains,
Meta: &SpeciesMeta{
CanAdd: canAdd(claims),
@ -172,45 +146,76 @@ func (s SpeciesService) get(id int64, genus string, claims Claims) (entity, *app
}
func (s SpeciesService) update(id int64, e *entity, claims Claims) *appError {
species := (*e).(*Species)
species.UpdatedBy = claims.Sub
species.UpdatedAt = currentTime()
species.Id = id
payload := (*e).(*SpeciesPayload)
payload.Species.UpdatedBy = claims.Sub
payload.Species.UpdatedAt = currentTime()
payload.Species.Id = id
genus_id, err := genusIdFromName(species.GenusName)
genus_id, err := genusIdFromName(payload.Species.GenusName)
if err != nil {
return newJSONError(err, http.StatusInternalServerError)
}
species.SpeciesBase.GenusID = genus_id
payload.Species.SpeciesBase.GenusID = genus_id
count, err := DBH.Update(species.SpeciesBase)
count, err := DBH.Update(payload.Species.SpeciesBase)
if err != nil {
return newJSONError(err, http.StatusInternalServerError)
}
if count != 1 {
return ErrSpeciesNotUpdatedJSON
}
species, err := getSpecies(id, payload.Species.GenusName)
if err != nil {
return newJSONError(err, http.StatusInternalServerError)
}
strains, err := strainsFromSpeciesId(id, payload.Species.GenusName)
if err != nil {
return newJSONError(err, http.StatusInternalServerError)
}
payload.Species = species
payload.Strains = strains
payload.Meta = &SpeciesMeta{
CanAdd: canAdd(claims),
CanEdit: canEdit(claims, map[int64]int64{payload.Species.Id: payload.Species.CreatedBy}),
}
return nil
}
func (s SpeciesService) create(e *entity, claims Claims) *appError {
species := (*e).(*Species)
payload := (*e).(*SpeciesPayload)
ct := currentTime()
species.CreatedBy = claims.Sub
species.CreatedAt = ct
species.UpdatedBy = claims.Sub
species.UpdatedAt = ct
payload.Species.CreatedBy = claims.Sub
payload.Species.CreatedAt = ct
payload.Species.UpdatedBy = claims.Sub
payload.Species.UpdatedAt = ct
genus_id, err := genusIdFromName(species.GenusName)
genus_id, err := genusIdFromName(payload.Species.GenusName)
if err != nil {
return newJSONError(err, http.StatusInternalServerError)
}
species.SpeciesBase.GenusID = genus_id
payload.Species.SpeciesBase.GenusID = genus_id
err = DBH.Insert(species.SpeciesBase)
err = DBH.Insert(payload.Species.SpeciesBase)
if err != nil {
return newJSONError(err, http.StatusInternalServerError)
}
species, err := getSpecies(payload.Species.Id, payload.Species.GenusName)
if err != nil {
return newJSONError(err, http.StatusInternalServerError)
}
// Note, no strains when new species
payload.Species = species
payload.Meta = &SpeciesMeta{
CanAdd: canAdd(claims),
CanEdit: canEdit(claims, map[int64]int64{payload.Species.Id: payload.Species.CreatedBy}),
}
return nil
}
@ -247,6 +252,25 @@ func strainOptsFromSpecies(opt ListOptions) (*ListOptions, error) {
return &ListOptions{Genus: opt.Genus, Ids: relatedStrainIds}, nil
}
func strainsFromSpeciesId(id int64, genus string) (*Strains, error) {
opt := ListOptions{
Genus: genus,
Ids: []int64{id},
}
strains_opt, err := strainOptsFromSpecies(opt)
if err != nil {
return nil, err
}
strains, err := listStrains(*strains_opt)
if err != nil {
return nil, err
}
return strains, nil
}
func listSpecies(opt ListOptions) (*ManySpecies, error) {
var vals []interface{}
@ -254,7 +278,7 @@ func listSpecies(opt ListOptions) (*ManySpecies, error) {
COUNT(st) AS total_strains,
rank() OVER (ORDER BY sp.species_name ASC) AS sort_order
FROM species sp
INNER JOIN genera g ON g.id=sp.genus_id AND LOWER(g.genus_name)=$1
INNER JOIN genera g ON g.id=sp.genus_id AND LOWER(g.genus_name)=LOWER($1)
LEFT OUTER JOIN strains st ON st.species_id=sp.id`
vals = append(vals, opt.Genus)
@ -279,3 +303,21 @@ func listSpecies(opt ListOptions) (*ManySpecies, error) {
}
return &species, nil
}
func getSpecies(id int64, genus string) (*Species, error) {
var species Species
q := `SELECT sp.*, g.genus_name, array_agg(st.id) AS strains,
COUNT(st) AS total_strains, 0 AS sort_order
FROM species sp
INNER JOIN genera g ON g.id=sp.genus_id AND LOWER(g.genus_name)=LOWER($1)
LEFT OUTER JOIN strains st ON st.species_id=sp.id
WHERE sp.id=$2
GROUP BY sp.id, g.genus_name;`
if err := DBH.SelectOne(&species, q, genus, id); err != nil {
if err == sql.ErrNoRows {
return nil, ErrSpeciesNotFound
}
return nil, err
}
return &species, nil
}

4
strains.go
View file

@ -26,7 +26,7 @@ type StrainService struct{}
// StrainBase is what the DB expects to see for inserts/updates
type StrainBase struct {
Id int64 `db:"id" json:"id"`
SpeciesId int64 `db:"species_id" json:"species,string"` // quirk in ember select
SpeciesId int64 `db:"species_id" json:"species"`
StrainName string `db:"strain_name" json:"strainName"`
TypeStrain bool `db:"type_strain" json:"typeStrain"`
AccessionNumbers string `db:"accession_numbers" json:"accessionNumbers"`
@ -147,7 +147,7 @@ func listStrains(opt ListOptions) (*Strains, error) {
rank() OVER (ORDER BY sp.species_name ASC, st.type_strain ASC, st.strain_name ASC) AS sort_order
FROM strains st
INNER JOIN species sp ON sp.id=st.species_id
INNER JOIN genera g ON g.id=sp.genus_id AND LOWER(g.genus_name)=$1
INNER JOIN genera g ON g.id=sp.genus_id AND LOWER(g.genus_name)=LOWER($1)
LEFT OUTER JOIN measurements m ON m.strain_id=st.id`
vals = append(vals, opt.Genus)