package main import ( "database/sql" "encoding/json" "errors" "fmt" "net/http" "net/url" "github.com/thermokarst/bactdb/Godeps/_workspace/src/github.com/jmoiron/modl" ) var ( ErrCharacteristicNotFound = errors.New("Characteristic not found") ErrCharacteristicNotUpdated = errors.New("Characteristic not updated") ) func init() { DB.AddTableWithName(CharacteristicBase{}, "characteristics").SetKeys(true, "Id") } func (c *CharacteristicBase) PreInsert(e modl.SqlExecutor) error { ct := currentTime() c.CreatedAt = ct c.UpdatedAt = ct return nil } func (c *CharacteristicBase) PreUpdate(e modl.SqlExecutor) error { c.UpdatedAt = currentTime() return nil } type CharacteristicService struct{} type CharacteristicBase struct { Id int64 `json:"id,omitempty"` CharacteristicName string `db:"characteristic_name" json:"characteristicName"` CharacteristicTypeId int64 `db:"characteristic_type_id" json:"-"` SortOrder NullInt64 `db:"sort_order" json:"sortOrder"` CreatedAt NullTime `db:"created_at" json:"createdAt"` UpdatedAt NullTime `db:"updated_at" json:"updatedAt"` DeletedAt NullTime `db:"deleted_at" json:"deletedAt"` CreatedBy int64 `db:"created_by" json:"createdBy"` UpdatedBy int64 `db:"updated_by" json:"updatedBy"` DeletedBy NullInt64 `db:"deleted_by" json:"deletedBy"` } type Characteristic struct { *CharacteristicBase Measurements NullSliceInt64 `db:"measurements" json:"measurements"` Strains NullSliceInt64 `db:"strains" json:"strains"` CharacteristicType string `db:"characteristic_type_name" json:"characteristicTypeName"` CanEdit bool `db:"-" json:"canEdit"` } type Characteristics []*Characteristic type CharacteristicMeta struct { CanAdd bool `json:"canAdd"` } type CharacteristicPayload struct { Characteristic *Characteristic `json:"characteristic"` Measurements *Measurements `json:"measurements"` Strains *Strains `json:"strains"` Species *ManySpecies `json:"species"` Meta *CharacteristicMeta `json:"meta"` } type CharacteristicsPayload struct { Characteristics *Characteristics `json:"characteristics"` Measurements *Measurements `json:"measurements"` Strains *Strains `json:"strains"` Species *ManySpecies `json:"species"` Meta *CharacteristicMeta `json:"meta"` } func (c *CharacteristicPayload) marshal() ([]byte, error) { return json.Marshal(c) } func (c *CharacteristicsPayload) marshal() ([]byte, error) { return json.Marshal(c) } func (c CharacteristicService) unmarshal(b []byte) (entity, error) { var cj CharacteristicPayload err := json.Unmarshal(b, &cj) return &cj, err } func (c CharacteristicService) list(val *url.Values, claims *Claims) (entity, *appError) { if val == nil { return nil, ErrMustProvideOptionsJSON } var opt ListOptions if err := schemaDecoder.Decode(&opt, *val); err != nil { return nil, newJSONError(err, http.StatusInternalServerError) } characteristics, err := listCharacteristics(opt, claims) if err != nil { return nil, newJSONError(err, http.StatusInternalServerError) } strains_opt, err := strainOptsFromCharacteristics(opt) if err != nil { return nil, newJSONError(err, http.StatusInternalServerError) } strains, err := listStrains(*strains_opt, claims) if err != nil { return nil, newJSONError(err, http.StatusInternalServerError) } species_opt, err := speciesOptsFromStrains(*strains_opt) if err != nil { return nil, newJSONError(err, http.StatusInternalServerError) } species, err := listSpecies(*species_opt, claims) if err != nil { return nil, newJSONError(err, http.StatusInternalServerError) } measurements_opt, err := measurementOptsFromCharacteristics(opt) if err != nil { return nil, newJSONError(err, http.StatusInternalServerError) } measurements, err := listMeasurements(*measurements_opt, claims) if err != nil { return nil, newJSONError(err, http.StatusInternalServerError) } payload := CharacteristicsPayload{ Characteristics: characteristics, Measurements: measurements, Strains: strains, Species: species, Meta: &CharacteristicMeta{ CanAdd: canAdd(claims), }, } return &payload, nil } func (c CharacteristicService) get(id int64, genus string, claims *Claims) (entity, *appError) { characteristic, err := getCharacteristic(id, genus, claims) if err != nil { return nil, newJSONError(err, http.StatusInternalServerError) } strains, strain_opts, err := strainsFromCharacteristicId(id, genus, claims) if err != nil { return nil, newJSONError(err, http.StatusInternalServerError) } species_opt, err := speciesOptsFromStrains(*strain_opts) if err != nil { return nil, newJSONError(err, http.StatusInternalServerError) } species, err := listSpecies(*species_opt, claims) if err != nil { return nil, newJSONError(err, http.StatusInternalServerError) } measurements, _, err := measurementsFromCharacteristicId(id, genus, claims) if err != nil { return nil, newJSONError(err, http.StatusInternalServerError) } payload := CharacteristicPayload{ Characteristic: characteristic, Measurements: measurements, Strains: strains, Species: species, } return &payload, nil } func (c CharacteristicService) update(id int64, e *entity, genus string, claims *Claims) *appError { payload := (*e).(*CharacteristicPayload) payload.Characteristic.UpdatedBy = claims.Sub payload.Characteristic.Id = id // First, handle Characteristic Type id, err := insertOrGetCharacteristicType(payload.Characteristic.CharacteristicType, claims) if err != nil { return newJSONError(err, http.StatusInternalServerError) } payload.Characteristic.CanEdit = canEdit(claims, payload.Characteristic.CreatedBy) payload.Characteristic.CharacteristicTypeId = id count, err := DBH.Update(payload.Characteristic.CharacteristicBase) if err != nil { return newJSONError(err, http.StatusInternalServerError) } if count != 1 { return newJSONError(ErrCharacteristicNotUpdated, http.StatusBadRequest) } strains, strain_opts, err := strainsFromCharacteristicId(id, genus, claims) if err != nil { return newJSONError(err, http.StatusInternalServerError) } species_opt, err := speciesOptsFromStrains(*strain_opts) if err != nil { return newJSONError(err, http.StatusInternalServerError) } species, err := listSpecies(*species_opt, claims) if err != nil { return newJSONError(err, http.StatusInternalServerError) } payload.Strains = strains // TODO: tack on measurements payload.Measurements = nil payload.Species = species return nil } func (c CharacteristicService) create(e *entity, genus string, claims *Claims) *appError { payload := (*e).(*CharacteristicPayload) payload.Characteristic.CreatedBy = claims.Sub payload.Characteristic.UpdatedBy = claims.Sub id, err := insertOrGetCharacteristicType(payload.Characteristic.CharacteristicType, claims) if err != nil { return newJSONError(err, http.StatusInternalServerError) } payload.Characteristic.CharacteristicTypeId = id err = DBH.Insert(payload.Characteristic.CharacteristicBase) if err != nil { return newJSONError(err, http.StatusInternalServerError) } characteristic, err := getCharacteristic(payload.Characteristic.Id, genus, claims) if err != nil { return newJSONError(err, http.StatusInternalServerError) } payload.Characteristic = characteristic payload.Meta = &CharacteristicMeta{ CanAdd: canAdd(claims), } return nil } func listCharacteristics(opt ListOptions, claims *Claims) (*Characteristics, error) { var vals []interface{} q := `SELECT c.*, ct.characteristic_type_name, array_agg(DISTINCT st.id) AS strains, array_agg(DISTINCT m.id) AS measurements 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)=LOWER($1) INNER JOIN measurements m ON m.strain_id=st.id RIGHT OUTER JOIN characteristics c ON c.id=m.characteristic_id INNER JOIN characteristic_types ct ON ct.id=c.characteristic_type_id` vals = append(vals, opt.Genus) if len(opt.Ids) != 0 { var counter int64 = 2 w := valsIn("c.id", opt.Ids, &vals, &counter) q += fmt.Sprintf(" WHERE %s", w) } q += ` GROUP BY c.id, ct.characteristic_type_name ORDER BY ct.characteristic_type_name, c.sort_order ASC;` var characteristics Characteristics err := DBH.Select(&characteristics, q, vals...) if err != nil { return nil, err } for _, c := range characteristics { c.CanEdit = canEdit(claims, c.CreatedBy) } return &characteristics, nil } func strainOptsFromCharacteristics(opt ListOptions) (*ListOptions, error) { relatedStrainIds := make([]int64, 0) baseQ := `SELECT DISTINCT m.strain_id FROM measurements m INNER JOIN strains st ON st.id=m.strain_id 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)=LOWER($1)` if opt.Ids == nil { q := fmt.Sprintf("%s;", baseQ) if err := DBH.Select(&relatedStrainIds, q, opt.Genus); err != nil { return nil, err } } else { var vals []interface{} var count int64 = 2 vals = append(vals, opt.Genus) q := fmt.Sprintf("%s WHERE %s ", baseQ, valsIn("m.characteristic_id", opt.Ids, &vals, &count)) if err := DBH.Select(&relatedStrainIds, q, vals...); err != nil { return nil, err } } return &ListOptions{Genus: opt.Genus, Ids: relatedStrainIds}, nil } func measurementOptsFromCharacteristics(opt ListOptions) (*MeasurementListOptions, error) { relatedMeasurementIds := make([]int64, 0) baseQ := `SELECT m.id FROM measurements m INNER JOIN strains st ON st.id=m.strain_id 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)=LOWER($1)` if opt.Ids == nil { q := fmt.Sprintf("%s;", baseQ) if err := DBH.Select(&relatedMeasurementIds, q, opt.Genus); err != nil { return nil, err } } else { var vals []interface{} var count int64 = 2 vals = append(vals, opt.Genus) q := fmt.Sprintf("%s WHERE %s;", baseQ, valsIn("characteristic_id", opt.Ids, &vals, &count)) if err := DBH.Select(&relatedMeasurementIds, q, vals...); err != nil { return nil, err } } return &MeasurementListOptions{ListOptions: ListOptions{Genus: opt.Genus, Ids: relatedMeasurementIds}, Strains: nil, Characteristics: nil}, nil } func strainsFromCharacteristicId(id int64, genus string, claims *Claims) (*Strains, *ListOptions, error) { opt := ListOptions{ Genus: genus, Ids: []int64{id}, } strains_opt, err := strainOptsFromCharacteristics(opt) if err != nil { return nil, nil, err } strains, err := listStrains(*strains_opt, claims) if err != nil { return nil, nil, err } return strains, strains_opt, nil } func measurementsFromCharacteristicId(id int64, genus string, claims *Claims) (*Measurements, *MeasurementListOptions, error) { opt := ListOptions{ Genus: genus, Ids: []int64{id}, } measurement_opt, err := measurementOptsFromCharacteristics(opt) if err != nil { return nil, nil, err } measurements, err := listMeasurements(*measurement_opt, claims) if err != nil { return nil, nil, err } return measurements, measurement_opt, nil } func getCharacteristic(id int64, genus string, claims *Claims) (*Characteristic, error) { var characteristic Characteristic q := `SELECT c.*, ct.characteristic_type_name, array_agg(DISTINCT st.id) AS strains, array_agg(DISTINCT m.id) AS measurements 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)=LOWER($1) INNER JOIN measurements m ON m.strain_id=st.id RIGHT OUTER JOIN characteristics c ON c.id=m.characteristic_id INNER JOIN characteristic_types ct ON ct.id=c.characteristic_type_id WHERE c.id=$2 GROUP BY c.id, ct.characteristic_type_name;` if err := DBH.SelectOne(&characteristic, q, genus, id); err != nil { if err == sql.ErrNoRows { return nil, ErrCharacteristicNotFound } return nil, err } characteristic.CanEdit = canEdit(claims, characteristic.CreatedBy) return &characteristic, nil } func insertOrGetCharacteristicType(val string, claims *Claims) (int64, error) { var id int64 q := `SELECT id FROM characteristic_types WHERE characteristic_type_name=$1;` if err := DBH.SelectOne(&id, q, val); err != nil { if err == sql.ErrNoRows { i := `INSERT INTO characteristic_types (characteristic_type_name, created_at, updated_at, created_by, updated_by) VALUES ($1, $2, $3, $4, $5) RETURNING id;` ct := currentTime() var result sql.Result var insertErr error stmt, err := DB.Db.Prepare(i) if result, insertErr = stmt.Exec(val, ct, ct, claims.Sub, claims.Sub); insertErr != nil { return 0, insertErr } id, err = result.LastInsertId() if err != nil { return 0, err } } else { return 0, err } } return id, nil }