Restructuring into packages.

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
+}