Restructuring into packages.

models/characteristics.go

@@ -0,0 +1,236 @@
+package models
+
+import (
+	"database/sql"
+	"errors"
+	"fmt"
+
+	"github.com/thermokarst/bactdb/Godeps/_workspace/src/github.com/jmoiron/modl"
+	"github.com/thermokarst/bactdb/helpers"
+	"github.com/thermokarst/bactdb/types"
+)
+
+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 := helpers.CurrentTime()
+	c.CreatedAt = ct
+	c.UpdatedAt = ct
+	return nil
+}
+
+func (c *CharacteristicBase) PreUpdate(e modl.SqlExecutor) error {
+	c.UpdatedAt = helpers.CurrentTime()
+	return nil
+}
+
+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"`
+}
+
+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"`
+}
+
+type Characteristics []*Characteristic
+
+type CharacteristicMeta struct {
+	CanAdd bool `json:"canAdd"`
+}
+
+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
+}
+
+func StrainOptsFromCharacteristics(opt helpers.ListOptions) (*helpers.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, 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
+}
+
+func MeasurementOptsFromCharacteristics(opt helpers.ListOptions) (*helpers.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, 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
+}
+
+func StrainsFromCharacteristicId(id int64, genus string, claims *types.Claims) (*Strains, *helpers.ListOptions, error) {
+	opt := helpers.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 *types.Claims) (*Measurements, *helpers.MeasurementListOptions, error) {
+	opt := helpers.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 *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, ErrCharacteristicNotFound
+		}
+		return nil, err
+	}
+
+	characteristic.CanEdit = helpers.CanEdit(claims, characteristic.CreatedBy)
+
+	return &characteristic, nil
+}
+
+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
+}

models/database.go

@@ -0,0 +1,8 @@
+package models
+
+import "github.com/thermokarst/bactdb/Godeps/_workspace/src/github.com/jmoiron/modl"
+
+var (
+	DB                   = &modl.DbMap{Dialect: modl.PostgresDialect{}}
+	DBH modl.SqlExecutor = DB
+)

models/measurements.go

@@ -0,0 +1,234 @@
+package models
+
+import (
+	"database/sql"
+	"encoding/json"
+	"errors"
+	"fmt"
+	"net/http"
+
+	"github.com/thermokarst/bactdb/Godeps/_workspace/src/github.com/jmoiron/modl"
+	"github.com/thermokarst/bactdb/helpers"
+	"github.com/thermokarst/bactdb/types"
+)
+
+var (
+	ErrMeasurementNotFound     = errors.New("Measurement not found")
+	ErrMeasurementNotFoundJSON = types.NewJSONError(ErrMeasurementNotFound, http.StatusNotFound)
+)
+
+func init() {
+	DB.AddTableWithName(MeasurementBase{}, "measurements").SetKeys(true, "Id")
+}
+
+func (m *MeasurementBase) PreInsert(e modl.SqlExecutor) error {
+	ct := helpers.CurrentTime()
+	m.CreatedAt = ct
+	m.UpdatedAt = ct
+	return nil
+}
+
+func (m *MeasurementBase) PreUpdate(e modl.SqlExecutor) error {
+	m.UpdatedAt = helpers.CurrentTime()
+	return nil
+}
+
+// There are three types of supported measurements: fixed-text, free-text,
+// & numerical. The table has a constraint that will allow at most one
+// for a particular combination of strain & characteristic.
+// MeasurementBase is what the DB expects to see for inserts/updates
+type MeasurementBase struct {
+	Id                    int64             `json:"id,omitempty"`
+	StrainId              int64             `db:"strain_id" json:"strain"`
+	CharacteristicId      int64             `db:"characteristic_id" json:"characteristic"`
+	TextMeasurementTypeId types.NullInt64   `db:"text_measurement_type_id" json:"-"`
+	TxtValue              types.NullString  `db:"txt_value" json:"-"`
+	NumValue              types.NullFloat64 `db:"num_value" json:"-"`
+	ConfidenceInterval    types.NullFloat64 `db:"confidence_interval" json:"confidenceInterval"`
+	UnitTypeId            types.NullInt64   `db:"unit_type_id" json:"-"`
+	Notes                 types.NullString  `db:"notes" json:"notes"`
+	TestMethodId          types.NullInt64   `db:"test_method_id" json:"-"`
+	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"`
+}
+
+type Measurement struct {
+	*MeasurementBase
+	TextMeasurementType types.NullString `db:"text_measurement_type_name" json:"-"`
+	UnitType            types.NullString `db:"unit_type_name" json:"unitType"`
+	TestMethod          types.NullString `db:"test_method_name" json:"testMethod"`
+	CanEdit             bool             `db:"-" json:"canEdit"`
+}
+
+type FakeMeasurement Measurement
+
+func (m *Measurement) MarshalJSON() ([]byte, error) {
+	fm := FakeMeasurement(*m)
+	return json.Marshal(struct {
+		*FakeMeasurement
+		Value string `json:"value"`
+	}{
+		FakeMeasurement: &fm,
+		Value:           m.Value(),
+	})
+}
+
+func (m *Measurement) UnmarshalJSON(b []byte) error {
+	var measurement struct {
+		FakeMeasurement
+		Value interface{} `json:"value"`
+	}
+	if err := json.Unmarshal(b, &measurement); err != nil {
+		return err
+	}
+
+	switch v := measurement.Value.(type) {
+	case string:
+		// Test if actually a lookup
+		id, err := GetTextMeasurementTypeId(v)
+		if err != nil {
+			if err == sql.ErrNoRows {
+				measurement.TxtValue = types.NullString{sql.NullString{String: v, Valid: true}}
+			} else {
+				return err
+			}
+		} else {
+			measurement.TextMeasurementTypeId = types.NullInt64{sql.NullInt64{Int64: id, Valid: true}}
+		}
+	case int64:
+		measurement.NumValue = types.NullFloat64{sql.NullFloat64{Float64: float64(v), Valid: true}}
+	case float64:
+		measurement.NumValue = types.NullFloat64{sql.NullFloat64{Float64: v, Valid: true}}
+	}
+
+	*m = Measurement(measurement.FakeMeasurement)
+
+	return nil
+}
+
+func (m *Measurement) Value() string {
+	if m.TextMeasurementType.Valid {
+		return m.TextMeasurementType.String
+	}
+	if m.TxtValue.Valid {
+		return m.TxtValue.String
+	}
+	if m.NumValue.Valid {
+		return fmt.Sprintf("%f", m.NumValue.Float64)
+	}
+	return ""
+}
+
+type Measurements []*Measurement
+
+type MeasurementMeta struct {
+	CanAdd bool `json:"canAdd"`
+}
+
+func ListMeasurements(opt helpers.MeasurementListOptions, claims *types.Claims) (*Measurements, error) {
+	var vals []interface{}
+
+	q := `SELECT m.*, t.text_measurement_name AS text_measurement_type_name,
+		u.symbol AS unit_type_name, te.name AS test_method_name
+		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)=$1
+		LEFT OUTER JOIN characteristics c ON c.id=m.characteristic_id
+		LEFT OUTER JOIN text_measurement_types t ON t.id=m.text_measurement_type_id
+		LEFT OUTER JOIN unit_types u ON u.id=m.unit_type_id
+		LEFT OUTER JOIN test_methods te ON te.id=m.test_method_id`
+	vals = append(vals, opt.Genus)
+
+	strainIds := len(opt.Strains) != 0
+	charIds := len(opt.Characteristics) != 0
+	ids := len(opt.Ids) != 0
+
+	if strainIds || charIds || ids {
+		var paramsCounter int64 = 2
+		q += "\nWHERE ("
+
+		// Filter by strains
+		if strainIds {
+			q += helpers.ValsIn("st.id", opt.Strains, &vals, &paramsCounter)
+		}
+
+		if strainIds && (charIds || ids) {
+			q += " AND "
+		}
+
+		// Filter by characteristics
+		if charIds {
+			q += helpers.ValsIn("c.id", opt.Characteristics, &vals, &paramsCounter)
+		}
+
+		if charIds && ids {
+			q += " AND "
+		}
+
+		// Get specific records
+		if ids {
+			q += helpers.ValsIn("m.id", opt.Ids, &vals, &paramsCounter)
+		}
+		q += ")"
+	}
+	q += ";"
+
+	measurements := make(Measurements, 0)
+	err := DBH.Select(&measurements, q, vals...)
+	if err != nil {
+		return nil, err
+	}
+
+	for _, m := range measurements {
+		m.CanEdit = helpers.CanEdit(claims, m.CreatedBy)
+	}
+
+	return &measurements, nil
+}
+
+func GetMeasurement(id int64, genus string, claims *types.Claims) (*Measurement, error) {
+	var measurement Measurement
+
+	q := `SELECT m.*, t.text_measurement_name AS text_measurement_type_name,
+		u.symbol AS unit_type_name, te.name AS test_method_name
+		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)
+		LEFT OUTER JOIN characteristics c ON c.id=m.characteristic_id
+		LEFT OUTER JOIN text_measurement_types t ON t.id=m.text_measurement_type_id
+		LEFT OUTER JOIN unit_types u ON u.id=m.unit_type_id
+		LEFT OUTER JOIN test_methods te ON te.id=m.test_method_id
+		WHERE m.id=$2;`
+	if err := DBH.SelectOne(&measurement, q, genus, id); err != nil {
+		if err == sql.ErrNoRows {
+			return nil, ErrMeasurementNotFound
+		}
+		return nil, err
+	}
+
+	measurement.CanEdit = helpers.CanEdit(claims, measurement.CreatedBy)
+
+	return &measurement, nil
+}
+
+func CharacteristicOptsFromMeasurements(opt helpers.MeasurementListOptions) (*helpers.ListOptions, error) {
+	return &helpers.ListOptions{Genus: opt.Genus, Ids: opt.Characteristics}, nil
+}
+
+func StrainOptsFromMeasurements(opt helpers.MeasurementListOptions) (*helpers.ListOptions, error) {
+	return &helpers.ListOptions{Genus: opt.Genus, Ids: opt.Strains}, nil
+}
+
+func GetTextMeasurementTypeId(val string) (int64, error) {
+	var id int64
+	q := `SELECT id FROM text_measurement_types WHERE text_measurement_name=$1;`
+
+	if err := DBH.SelectOne(&id, q, val); err != nil {
+		return 0, err
+	}
+	return id, nil
+}

models/species.go

@@ -0,0 +1,174 @@
+package models
+
+import (
+	"database/sql"
+	"errors"
+	"fmt"
+	"strings"
+
+	"github.com/thermokarst/bactdb/Godeps/_workspace/src/github.com/jmoiron/modl"
+	"github.com/thermokarst/bactdb/helpers"
+	"github.com/thermokarst/bactdb/types"
+)
+
+var (
+	ErrSpeciesNotFound   = errors.New("Species not found")
+	ErrSpeciesNotUpdated = errors.New("Species not updated")
+)
+
+func init() {
+	DB.AddTableWithName(SpeciesBase{}, "species").SetKeys(true, "Id")
+}
+
+func (s *SpeciesBase) PreInsert(e modl.SqlExecutor) error {
+	ct := helpers.CurrentTime()
+	s.CreatedAt = ct
+	s.UpdatedAt = ct
+	return nil
+}
+
+func (s *SpeciesBase) PreUpdate(e modl.SqlExecutor) error {
+	s.UpdatedAt = helpers.CurrentTime()
+	return nil
+}
+
+type SpeciesBase struct {
+	Id                  int64            `db:"id" json:"id"`
+	GenusID             int64            `db:"genus_id" json:"-"`
+	SubspeciesSpeciesID types.NullInt64  `db:"subspecies_species_id" json:"-"`
+	SpeciesName         string           `db:"species_name" json:"speciesName"`
+	TypeSpecies         types.NullBool   `db:"type_species" json:"typeSpecies"`
+	Etymology           types.NullString `db:"etymology" json:"etymology"`
+	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"`
+}
+
+type Species struct {
+	*SpeciesBase
+	GenusName    string               `db:"genus_name" json:"genusName"`
+	Strains      types.NullSliceInt64 `db:"strains" json:"strains"`
+	TotalStrains int64                `db:"total_strains" json:"totalStrains"`
+	SortOrder    int64                `db:"sort_order" json:"sortOrder"`
+	CanEdit      bool                 `db:"-" json:"canEdit"`
+}
+
+type ManySpecies []*Species
+
+type SpeciesMeta struct {
+	CanAdd bool `json:"canAdd"`
+}
+
+func GenusIdFromName(genus_name string) (int64, error) {
+	var genus_id struct{ Id int64 }
+	q := `SELECT id FROM genera WHERE LOWER(genus_name) = LOWER($1);`
+	if err := DBH.SelectOne(&genus_id, q, genus_name); err != nil {
+		return 0, err
+	}
+	return genus_id.Id, nil
+}
+
+func StrainOptsFromSpecies(opt helpers.ListOptions) (*helpers.ListOptions, error) {
+	relatedStrainIds := make([]int64, 0)
+
+	if opt.Ids == nil {
+		q := `SELECT DISTINCT st.id
+			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);`
+		if err := DBH.Select(&relatedStrainIds, q, opt.Genus); err != nil {
+			return nil, err
+		}
+	} else {
+		var vals []interface{}
+		var count int64 = 1
+		q := fmt.Sprintf("SELECT DISTINCT id FROM strains WHERE %s;", helpers.ValsIn("species_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
+}
+
+func StrainsFromSpeciesId(id int64, genus string, claims *types.Claims) (*Strains, error) {
+	opt := helpers.ListOptions{
+		Genus: genus,
+		Ids:   []int64{id},
+	}
+
+	strains_opt, err := StrainOptsFromSpecies(opt)
+	if err != nil {
+		return nil, err
+	}
+
+	strains, err := ListStrains(*strains_opt, claims)
+	if err != nil {
+		return nil, err
+	}
+
+	return strains, nil
+}
+
+func ListSpecies(opt helpers.ListOptions, claims *types.Claims) (*ManySpecies, error) {
+	var vals []interface{}
+
+	q := `SELECT sp.*, g.genus_name, array_agg(st.id) AS strains,
+			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)=LOWER($1)
+			LEFT OUTER JOIN strains st ON st.species_id=sp.id`
+	vals = append(vals, opt.Genus)
+
+	if len(opt.Ids) != 0 {
+		var conds []string
+		s := "sp.id IN ("
+		for i, id := range opt.Ids {
+			s = s + fmt.Sprintf("$%v,", i+2) // start param index at 2
+			vals = append(vals, id)
+		}
+		s = s[:len(s)-1] + ")"
+		conds = append(conds, s)
+		q += " WHERE (" + strings.Join(conds, ") AND (") + ")"
+	}
+
+	q += " GROUP BY sp.id, g.genus_name;"
+
+	species := make(ManySpecies, 0)
+	err := DBH.Select(&species, q, vals...)
+	if err != nil {
+		return nil, err
+	}
+
+	for _, s := range species {
+		s.CanEdit = helpers.CanEdit(claims, s.CreatedBy)
+	}
+
+	return &species, nil
+}
+
+func GetSpecies(id int64, genus string, claims *types.Claims) (*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
+	}
+
+	species.CanEdit = helpers.CanEdit(claims, species.CreatedBy)
+
+	return &species, nil
+}

models/strains.go

@@ -0,0 +1,184 @@
+package models
+
+import (
+	"database/sql"
+	"errors"
+	"fmt"
+	"strings"
+
+	"github.com/thermokarst/bactdb/Godeps/_workspace/src/github.com/jmoiron/modl"
+	"github.com/thermokarst/bactdb/helpers"
+	"github.com/thermokarst/bactdb/types"
+)
+
+var (
+	ErrStrainNotFound   = errors.New("Strain not found")
+	ErrStrainNotUpdated = errors.New("Strain not updated")
+)
+
+func init() {
+	DB.AddTableWithName(StrainBase{}, "strains").SetKeys(true, "Id")
+}
+
+func (s *StrainBase) PreInsert(e modl.SqlExecutor) error {
+	ct := helpers.CurrentTime()
+	s.CreatedAt = ct
+	s.UpdatedAt = ct
+	return nil
+}
+
+func (s *StrainBase) PreUpdate(e modl.SqlExecutor) error {
+	s.UpdatedAt = helpers.CurrentTime()
+	return nil
+}
+
+type StrainBase struct {
+	Id                  int64            `db:"id" json:"id"`
+	SpeciesId           int64            `db:"species_id" json:"species"`
+	StrainName          string           `db:"strain_name" json:"strainName"`
+	TypeStrain          bool             `db:"type_strain" json:"typeStrain"`
+	AccessionNumbers    types.NullString `db:"accession_numbers" json:"accessionNumbers"`
+	Genbank             types.NullString `db:"genbank" json:"genbank"`
+	WholeGenomeSequence types.NullString `db:"whole_genome_sequence" json:"wholeGenomeSequence"`
+	IsolatedFrom        types.NullString `db:"isolated_from" json:"isolatedFrom"`
+	Notes               types.NullString `db:"notes" json:"notes"`
+	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"`
+}
+
+type Strain struct {
+	*StrainBase
+	Measurements      types.NullSliceInt64 `db:"measurements" json:"measurements"`
+	Characteristics   types.NullSliceInt64 `db:"characteristics" json:"characteristics"`
+	TotalMeasurements int64                `db:"total_measurements" json:"totalMeasurements"`
+	SortOrder         int64                `db:"sort_order" json:"sortOrder"`
+	CanEdit           bool                 `db:"-" json:"canEdit"`
+}
+
+type Strains []*Strain
+
+type StrainMeta struct {
+	CanAdd bool `json:"canAdd"`
+}
+
+func (s StrainBase) SpeciesName() string {
+	var species SpeciesBase
+	if err := DBH.Get(&species, s.SpeciesId); err != nil {
+		return ""
+	}
+	return species.SpeciesName
+}
+
+func ListStrains(opt helpers.ListOptions, claims *types.Claims) (*Strains, error) {
+	var vals []interface{}
+
+	q := `SELECT st.*, array_agg(m.id) AS measurements,
+		array_agg(DISTINCT m.characteristic_id) AS characteristics,
+		COUNT(m) AS total_measurements,
+		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)=LOWER($1)
+		LEFT OUTER JOIN measurements m ON m.strain_id=st.id`
+	vals = append(vals, opt.Genus)
+
+	if len(opt.Ids) != 0 {
+		var conds []string
+		s := "st.id IN ("
+		for i, id := range opt.Ids {
+			s = s + fmt.Sprintf("$%v,", i+2) // start param index at 2
+			vals = append(vals, id)
+		}
+		s = s[:len(s)-1] + ")"
+		conds = append(conds, s)
+		q += " WHERE (" + strings.Join(conds, ") AND (") + ")"
+	}
+
+	q += " GROUP BY st.id, st.species_id, sp.species_name;"
+
+	strains := make(Strains, 0)
+	err := DBH.Select(&strains, q, vals...)
+	if err != nil {
+		return nil, err
+	}
+
+	for _, s := range strains {
+		s.CanEdit = helpers.CanEdit(claims, s.CreatedBy)
+	}
+
+	return &strains, nil
+}
+
+func GetStrain(id int64, genus string, claims *types.Claims) (*Strain, error) {
+	var strain Strain
+	q := `SELECT st.*, array_agg(DISTINCT m.id) AS measurements,
+		array_agg(DISTINCT m.characteristic_id) AS characteristics,
+		COUNT(m) AS total_measurements, 0 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)=LOWER($1)
+		LEFT OUTER JOIN measurements m ON m.strain_id=st.id
+		WHERE st.id=$2
+		GROUP BY st.id;`
+	if err := DBH.SelectOne(&strain, q, genus, id); err != nil {
+		if err == sql.ErrNoRows {
+			return nil, ErrStrainNotFound
+		}
+		return nil, err
+	}
+
+	strain.CanEdit = helpers.CanEdit(claims, strain.CreatedBy)
+
+	return &strain, nil
+}
+
+func SpeciesOptsFromStrains(opt helpers.ListOptions) (*helpers.ListOptions, error) {
+	relatedSpeciesIds := make([]int64, 0)
+
+	if opt.Ids == nil || len(opt.Ids) == 0 {
+		q := `SELECT DISTINCT st.species_id
+			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);`
+		if err := DBH.Select(&relatedSpeciesIds, q, opt.Genus); err != nil {
+			return nil, err
+		}
+	} else {
+		var vals []interface{}
+		var count int64 = 1
+		q := fmt.Sprintf("SELECT DISTINCT species_id FROM strains WHERE %s;", helpers.ValsIn("id", opt.Ids, &vals, &count))
+		if err := DBH.Select(&relatedSpeciesIds, q, vals...); err != nil {
+			return nil, err
+		}
+	}
+
+	return &helpers.ListOptions{Genus: opt.Genus, Ids: relatedSpeciesIds}, nil
+}
+
+func CharacteristicsOptsFromStrains(opt helpers.ListOptions) (*helpers.ListOptions, error) {
+	relatedCharacteristicsIds := make([]int64, 0)
+
+	if opt.Ids == nil || len(opt.Ids) == 0 {
+		q := `SELECT DISTINCT m.characteristic_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 err := DBH.Select(&relatedCharacteristicsIds, q, opt.Genus); err != nil {
+			return nil, err
+		}
+	} else {
+		var vals []interface{}
+		var count int64 = 1
+		q := fmt.Sprintf("SELECT DISTINCT characteristic_id FROM measurements WHERE %s;", helpers.ValsIn("strain_id", opt.Ids, &vals, &count))
+		if err := DBH.Select(&relatedCharacteristicsIds, q, vals...); err != nil {
+			return nil, err
+		}
+	}
+
+	return &helpers.ListOptions{Genus: opt.Genus, Ids: relatedCharacteristicsIds}, nil
+}

models/users.go

@@ -0,0 +1,156 @@
+package models
+
+import (
+	"database/sql"
+	"encoding/json"
+	"errors"
+	"regexp"
+
+	"github.com/thermokarst/bactdb/Godeps/_workspace/src/golang.org/x/crypto/bcrypt"
+	"github.com/thermokarst/bactdb/helpers"
+	"github.com/thermokarst/bactdb/types"
+)
+
+var (
+	ErrUserNotFound           = errors.New("User not found")
+	ErrUserNotUpdated         = errors.New("User not updated")
+	ErrInvalidEmailOrPassword = errors.New("Invalid email or password")
+	ErrEmailAddressTaken      = errors.New("Email address already registered")
+)
+
+func init() {
+	DB.AddTableWithName(UserBase{}, "users").SetKeys(true, "Id")
+}
+
+type UserBase struct {
+	Id        int64          `json:"id,omitempty"`
+	Email     string         `db:"email" json:"email"`
+	Password  string         `db:"password" json:"password,omitempty"`
+	Name      string         `db:"name" json:"name"`
+	Role      string         `db:"role" json:"role"`
+	Verified  bool           `db:"verified" json:"-"`
+	CreatedAt types.NullTime `db:"created_at" json:"createdAt"`
+	UpdatedAt types.NullTime `db:"updated_at" json:"updatedAt"`
+	DeletedAt types.NullTime `db:"deleted_at" json:"deletedAt"`
+}
+
+type User struct {
+	*UserBase
+	CanEdit bool `db:"-" json:"canEdit"`
+}
+
+type UserValidation struct {
+	Email    []string `json:"email,omitempty"`
+	Password []string `json:"password,omitempty"`
+	Name     []string `json:"name,omitempty"`
+	Role     []string `json:"role,omitempty"`
+}
+
+func (uv UserValidation) Error() string {
+	errs, err := json.Marshal(struct {
+		UserValidation `json:"errors"`
+	}{uv})
+	if err != nil {
+		return err.Error()
+	}
+	return string(errs)
+}
+
+type Users []*User
+
+type UserJSON struct {
+	User *User `json:"user"`
+}
+
+type UsersJSON struct {
+	Users *Users `json:"users"`
+}
+
+type UserMeta struct {
+	CanAdd bool `json:"canAdd"`
+}
+
+func (u *Users) Marshal() ([]byte, error) {
+	return json.Marshal(&UsersJSON{Users: u})
+}
+
+func (u *User) Validate() error {
+	var uv UserValidation
+	validationError := false
+
+	if u.Name == "" {
+		uv.Name = append(uv.Name, helpers.MustProvideAValue)
+		validationError = true
+	}
+
+	if u.Email == "" {
+		uv.Email = append(uv.Email, helpers.MustProvideAValue)
+		validationError = true
+	}
+
+	regex, _ := regexp.Compile(`(\w[-._\w]*\w@\w[-._\w]*\w\.\w{2,3})`)
+	if u.Email != "" && !regex.MatchString(u.Email) {
+		uv.Email = append(uv.Email, "Must provide a valid email address")
+		validationError = true
+	}
+
+	if len(u.Password) < 8 {
+		uv.Password = append(uv.Password, "Password must be at least 8 characters")
+		validationError = true
+	}
+
+	if validationError {
+		return uv
+	}
+	return nil
+}
+
+// for thermokarst/jwt: authentication callback
+func DbAuthenticate(email string, password string) error {
+	var user User
+	q := `SELECT *
+		FROM users
+		WHERE lower(email)=lower($1)
+		AND verified IS TRUE
+		AND deleted_at IS NULL;`
+	if err := DBH.SelectOne(&user, q, email); err != nil {
+		return ErrInvalidEmailOrPassword
+	}
+	if err := bcrypt.CompareHashAndPassword([]byte(user.Password), []byte(password)); err != nil {
+		return ErrInvalidEmailOrPassword
+	}
+	return nil
+}
+
+func DbGetUserById(id int64) (*User, error) {
+	var user User
+	q := `SELECT *
+		FROM users
+		WHERE id=$1
+		AND verified IS TRUE
+		AND deleted_at IS NULL;`
+	if err := DBH.SelectOne(&user, q, id); err != nil {
+		if err == sql.ErrNoRows {
+			return nil, ErrUserNotFound
+		}
+		return nil, err
+	}
+	return &user, nil
+}
+
+// for thermokarst/jwt: setting user in claims bundle
+func DbGetUserByEmail(email string) (*User, error) {
+	var user User
+	q := `SELECT *
+		FROM users
+		WHERE lower(email)=lower($1)
+		AND verified IS TRUE
+		AND deleted_at IS NULL;`
+	if err := DBH.SelectOne(&user, q, email); err != nil {
+		if err == sql.ErrNoRows {
+			return nil, ErrUserNotFound
+		}
+		return nil, err
+	}
+	return &user, nil
+}