Subroutes: strains

api/handler.go

@@ -71,6 +71,7 @@ func Handler() *mux.Router {
 	m.Get(router.DeleteMeasurement).Handler(handler(serveDeleteMeasurement))
 
 	m.Get(router.SubrouterListSpecies).Handler(authHandler(serveSubrouterSpeciesList))
+	m.Get(router.SubrouterListStrains).Handler(authHandler(serveSubrouterStrainsList))
 
 	return m
 }

api/strains.go

@@ -90,3 +90,22 @@ func serveDeleteStrain(w http.ResponseWriter, r *http.Request) error {
 
 	return writeJSON(w, &models.Strain{})
 }
+
+func serveSubrouterStrainsList(w http.ResponseWriter, r *http.Request) error {
+	var opt models.StrainListOptions
+	if err := schemaDecoder.Decode(&opt, r.URL.Query()); err != nil {
+		return err
+	}
+
+	opt.Genus = mux.Vars(r)["genus"]
+
+	strains, err := store.Strains.List(&opt)
+	if err != nil {
+		return err
+	}
+	if strains == nil {
+		strains = []*models.Strain{}
+	}
+
+	return writeJSON(w, strains)
+}

datastore/strains.go

@@ -1,6 +1,8 @@
 package datastore
 
 import (
+	"fmt"
+	"strings"
 	"time"
 
 	"github.com/thermokarst/bactdb/models"
@@ -39,8 +41,27 @@ func (s *strainsStore) List(opt *models.StrainListOptions) ([]*models.Strain, er
 	if opt == nil {
 		opt = &models.StrainListOptions{}
 	}
+
+	sql := `SELECT * FROM strains`
+
+	var conds []string
+	var vals []interface{}
+
+	if opt.Genus != "" {
+		conds = append(conds, `species_id IN (SELECT s.id FROM species s
+		INNER JOIN genera g ON g.id = s.genus_id WHERE lower(g.genus_name) = $1)`)
+		vals = append(vals, opt.Genus)
+	}
+
+	if len(conds) > 0 {
+		sql += " WHERE (" + strings.Join(conds, ") AND (") + ")"
+	}
+
+	sql += fmt.Sprintf(" LIMIT $%v OFFSET $%v;", len(conds)+1, len(conds)+2)
+	vals = append(vals, opt.PerPageOrDefault(), opt.Offset())
+
 	var strains []*models.Strain
-	err := s.dbh.Select(&strains, `SELECT * FROM strains LIMIT $1 OFFSET $2;`, opt.PerPageOrDefault(), opt.Offset())
+	err := s.dbh.Select(&strains, sql, vals...)
 	if err != nil {
 		return nil, err
 	}

datastore/strains_test.go

@@ -1,6 +1,7 @@
 package datastore
 
 import (
+	"database/sql"
 	"reflect"
 	"testing"
 
@@ -21,9 +22,24 @@ func insertStrain(t *testing.T, tx *modl.Transaction) *models.Strain {
 func newStrain(t *testing.T, tx *modl.Transaction) *models.Strain {
 	// we want to create and insert a species (and genus) record too
 	species := insertSpecies(t, tx)
-	return &models.Strain{SpeciesId: species.Id, StrainName: "Test Strain",
+	return &models.Strain{
-		StrainType: "Test Type", Etymology: "Test Etymology",
+		SpeciesId:  species.Id,
-		AccessionBanks: "Test Bank", GenbankEmblDdb: "Test Genbank"}
+		StrainName: "Test Strain",
+		StrainType: "Test Type",
+		Etymology: models.NullString{
+			sql.NullString{
+				String: "Test Etymology",
+				Valid:  true,
+			},
+		},
+		AccessionBanks: "Test Bank",
+		GenbankEmblDdb: models.NullString{
+			sql.NullString{
+				String: "Test Genbank",
+				Valid:  true,
+			},
+		},
+	}
 }
 
 func TestStrainsStore_Get_db(t *testing.T) {

models/strains.go

@@ -1,7 +1,9 @@
 package models
 
 import (
+	"database/sql"
 	"errors"
+	"fmt"
 	"net/http"
 	"strconv"
 	"time"
@@ -15,22 +17,43 @@ type Strain struct {
 	SpeciesId      int64      `db:"species_id" json:"speciesId"`
 	StrainName     string     `db:"strain_name" json:"strainName"`
 	StrainType     string     `db:"strain_type" json:"strainType"`
-	Etymology      string     `db:"etymology" json:"etymology"`
+	Etymology      NullString `db:"etymology" json:"etymology"`
 	AccessionBanks string     `db:"accession_banks" json:"accessionBanks"`
-	GenbankEmblDdb string     `db:"genbank_embl_ddb" json:"genbankEmblDdb"`
+	GenbankEmblDdb NullString `db:"genbank_embl_ddb" json:"genbankEmblDdb"`
 	IsolatedFrom   NullString `db:"isolated_from" json:"isolatedFrom"`
 	CreatedAt      time.Time  `db:"created_at" json:"createdAt"`
 	UpdatedAt      time.Time  `db:"updated_at" json:"updatedAt"`
 	DeletedAt      NullTime   `db:"deleted_at" json:"deletedAt"`
 }
 
+func (s *Strain) String() string {
+	return fmt.Sprintf("%v", *s)
+}
+
 func NewStrain() *Strain {
 	return &Strain{
 		StrainName: "Test Strain",
 		StrainType: "Test Type",
-		Etymology:      "Test Etymology",
+		Etymology: NullString{
+			sql.NullString{
+				String: "Test Etymology",
+				Valid:  true,
+			},
+		},
 		AccessionBanks: "Test Accession",
-		GenbankEmblDdb: "Test Genbank"}
+		GenbankEmblDdb: NullString{
+			sql.NullString{
+				String: "Test Genbank",
+				Valid:  true,
+			},
+		},
+		IsolatedFrom: NullString{
+			sql.NullString{
+				String: "",
+				Valid:  false,
+			},
+		},
+	}
 }
 
 // StrainService interacts with the strain-related endpoints in bactdb's API
@@ -102,6 +125,7 @@ func (s *strainsService) Create(strain *Strain) (bool, error) {
 
 type StrainListOptions struct {
 	ListOptions
+	Genus string
 }
 
 func (s *strainsService) List(opt *StrainListOptions) ([]*Strain, error) {

models/strains_test.go

@@ -124,7 +124,7 @@ func TestStrainService_Update(t *testing.T) {
 	mux.HandleFunc(urlPath(t, router.UpdateStrain, map[string]string{"Id": "1"}), func(w http.ResponseWriter, r *http.Request) {
 		called = true
 		testMethod(t, r, "PUT")
-		testBody(t, r, `{"id":1,"speciesId":1,"strainName":"Test Strain Updated","strainType":"Test Type Updated","etymology":"Test Etymology Updated","accessionBanks":"Test Accession Updated","genbankEmblDdb":"Test Genbank Updated","isolatedFrom":null,"createdAt":"0001-01-01T00:00:00Z","updatedAt":"0001-01-01T00:00:00Z","deletedAt":null}`+"\n")
+		testBody(t, r, `{"id":1,"speciesId":1,"strainName":"Test Strain Updated","strainType":"Test Type Updated","etymology":"Test Etymology","accessionBanks":"Test Accession Updated","genbankEmblDdb":"Test Genbank Updated","isolatedFrom":null,"createdAt":"0001-01-01T00:00:00Z","updatedAt":"0001-01-01T00:00:00Z","deletedAt":null}`+"\n")
 		w.WriteHeader(http.StatusOK)
 		writeJSON(w, want)
 	})
@@ -132,9 +132,8 @@ func TestStrainService_Update(t *testing.T) {
 	strain := newStrain()
 	strain.StrainName = "Test Strain Updated"
 	strain.StrainType = "Test Type Updated"
-	strain.Etymology = "Test Etymology Updated"
 	strain.AccessionBanks = "Test Accession Updated"
-	strain.GenbankEmblDdb = "Test Genbank Updated"
+	strain.GenbankEmblDdb.String = "Test Genbank Updated"
 	updated, err := client.Strains.Update(strain.Id, strain)
 	if err != nil {
 		t.Errorf("Strains.Update returned error: %v", err)

router/api.go

@@ -70,6 +70,7 @@ func API() *mux.Router {
 	// Subrouter for auth/security
 	s := m.PathPrefix("/{genus}").Subrouter()
 	s.Path("/species").Methods("GET").Name(SubrouterListSpecies)
+	s.Path("/strains").Methods("GET").Name(SubrouterListStrains)
 
 	return m
 }

router/routes.go

@@ -55,4 +55,5 @@ const (
 	DeleteMeasurement = "measurements:delete"
 
 	SubrouterListSpecies = "subrouter_species:list"
+	SubrouterListStrains = "subrouter_strains:list"
 )