280 lines
8.9 KiB
Go
280 lines
8.9 KiB
Go
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
|
|
}
|
|
|
|
// UpdateError satisfies base interface.
|
|
func (c *CharacteristicBase) UpdateError() error {
|
|
return errors.ErrCharacteristicNotUpdated
|
|
}
|
|
|
|
// DeleteError satisfies base interface.
|
|
func (c *CharacteristicBase) DeleteError() error {
|
|
return errors.ErrCharacteristicNotDeleted
|
|
}
|
|
|
|
func (c *CharacteristicBase) validate() types.ValidationError {
|
|
cv := make(types.ValidationError, 0)
|
|
|
|
if c.CharacteristicName == "" {
|
|
cv = append(cv, types.NewValidationError(
|
|
"characteristicName",
|
|
helpers.MustProvideAValue))
|
|
}
|
|
|
|
if c.CharacteristicTypeID == 0 {
|
|
cv = append(cv, types.NewValidationError(
|
|
"characteristicType",
|
|
helpers.MustProvideAValue))
|
|
}
|
|
|
|
if len(cv) > 0 {
|
|
return cv
|
|
}
|
|
|
|
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"`
|
|
CreatedBy int64 `db:"created_by" json:"createdBy"`
|
|
UpdatedBy int64 `db:"updated_by" json:"updatedBy"`
|
|
}
|
|
|
|
// 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
|
|
}
|