package models import ( "database/sql" "fmt" "github.com/thermokarst/bactdb/Godeps/_workspace/src/github.com/jmoiron/modl" "github.com/thermokarst/bactdb/errors" "github.com/thermokarst/bactdb/helpers" "github.com/thermokarst/bactdb/types" ) func init() { DB.AddTableWithName(CharacteristicBase{}, "characteristics").SetKeys(true, "ID") } // PreInsert is a modl hook func (c *CharacteristicBase) PreInsert(e modl.SqlExecutor) error { ct := helpers.CurrentTime() c.CreatedAt = ct c.UpdatedAt = ct return nil } // PreUpdate is a modl hook func (c *CharacteristicBase) PreUpdate(e modl.SqlExecutor) error { c.UpdatedAt = helpers.CurrentTime() return nil } // CharacteristicBase is what the DB expects for write operations type CharacteristicBase struct { ID int64 `json:"id,omitempty"` CharacteristicName string `db:"characteristic_name" json:"characteristicName"` CharacteristicTypeID int64 `db:"characteristic_type_id" json:"-"` SortOrder types.NullInt64 `db:"sort_order" json:"sortOrder"` CreatedAt types.NullTime `db:"created_at" json:"createdAt"` UpdatedAt types.NullTime `db:"updated_at" json:"updatedAt"` DeletedAt types.NullTime `db:"deleted_at" json:"deletedAt"` CreatedBy int64 `db:"created_by" json:"createdBy"` UpdatedBy int64 `db:"updated_by" json:"updatedBy"` DeletedBy types.NullInt64 `db:"deleted_by" json:"deletedBy"` } // Characteristic is what the DB expects for read operations, and is what the API // expects to return to the requester. type Characteristic struct { *CharacteristicBase Measurements types.NullSliceInt64 `db:"measurements" json:"measurements"` Strains types.NullSliceInt64 `db:"strains" json:"strains"` CharacteristicType string `db:"characteristic_type_name" json:"characteristicTypeName"` CanEdit bool `db:"-" json:"canEdit"` } // Characteristics are multiple characteristic entities type Characteristics []*Characteristic // CharacteristicMeta stashes some metadata related to the entity type CharacteristicMeta struct { CanAdd bool `json:"canAdd"` } // ListCharacteristics returns all characteristics func ListCharacteristics(opt helpers.ListOptions, claims *types.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 := helpers.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 = helpers.CanEdit(claims, c.CreatedBy) } return &characteristics, nil } // StrainOptsFromCharacteristics returns the options for finding all related strains // for a set of characteristics. func StrainOptsFromCharacteristics(opt helpers.ListOptions) (*helpers.ListOptions, error) { var relatedStrainIDs []int64 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, helpers.ValsIn("m.characteristic_id", opt.IDs, &vals, &count)) if err := DBH.Select(&relatedStrainIDs, q, vals...); err != nil { return nil, err } } return &helpers.ListOptions{Genus: opt.Genus, IDs: relatedStrainIDs}, nil } // MeasurementOptsFromCharacteristics returns the options for finding all related // measurements for a set of characteristics. func MeasurementOptsFromCharacteristics(opt helpers.ListOptions) (*helpers.MeasurementListOptions, error) { var relatedMeasurementIDs []int64 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, helpers.ValsIn("characteristic_id", opt.IDs, &vals, &count)) if err := DBH.Select(&relatedMeasurementIDs, q, vals...); err != nil { return nil, err } } return &helpers.MeasurementListOptions{ListOptions: helpers.ListOptions{Genus: opt.Genus, IDs: relatedMeasurementIDs}, Strains: nil, Characteristics: nil}, nil } // StrainsFromCharacteristicID returns a set of strains (as well as the options for // finding those strains) for a particular characteristic. func StrainsFromCharacteristicID(id int64, genus string, claims *types.Claims) (*Strains, *helpers.ListOptions, error) { opt := helpers.ListOptions{ Genus: genus, IDs: []int64{id}, } strainsOpt, err := StrainOptsFromCharacteristics(opt) if err != nil { return nil, nil, err } strains, err := ListStrains(*strainsOpt, claims) if err != nil { return nil, nil, err } return strains, strainsOpt, nil } // MeasurementsFromCharacteristicID returns a set of measurements (as well as the // options for finding those measurements) for a particular characteristic. func MeasurementsFromCharacteristicID(id int64, genus string, claims *types.Claims) (*Measurements, *helpers.MeasurementListOptions, error) { opt := helpers.ListOptions{ Genus: genus, IDs: []int64{id}, } measurementOpt, err := MeasurementOptsFromCharacteristics(opt) if err != nil { return nil, nil, err } measurements, err := ListMeasurements(*measurementOpt, claims) if err != nil { return nil, nil, err } return measurements, measurementOpt, nil } // GetCharacteristic returns a particular characteristic. func GetCharacteristic(id int64, genus string, claims *types.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, errors.ErrCharacteristicNotFound } return nil, err } characteristic.CanEdit = helpers.CanEdit(claims, characteristic.CreatedBy) return &characteristic, nil } // InsertOrGetCharacteristicType performs an UPSERT operation on the database // for a characteristic type. func InsertOrGetCharacteristicType(val string, claims *types.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 := helpers.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 }