Species/Strain cleanup, split out species list
This commit is contained in:
Matthew Dillon
parent
630fe07554
commit
a8cfc8fe8b
2 changed files with 93 additions and 85 deletions
111
species.go
111
species.go
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@ -98,31 +98,7 @@ func (s SpeciesService) list(val *url.Values, claims Claims) (entity, *appError)
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return nil, newJSONError(err, http.StatusInternalServerError)
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}
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var vals []interface{}
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sql := `SELECT sp.*, g.genus_name, array_agg(st.id) AS strains,
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COUNT(st) AS total_strains,
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rank() OVER (ORDER BY sp.species_name ASC) AS sort_order
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FROM species sp
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INNER JOIN genera g ON g.id=sp.genus_id AND LOWER(g.genus_name)=$1
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LEFT OUTER JOIN strains st ON st.species_id=sp.id`
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vals = append(vals, opt.Genus)
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if len(opt.Ids) != 0 {
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var conds []string
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s := "sp.id IN ("
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for i, id := range opt.Ids {
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s = s + fmt.Sprintf("$%v,", i+2) // start param index at 2
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vals = append(vals, id)
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}
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s = s[:len(s)-1] + ")"
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conds = append(conds, s)
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sql += " WHERE (" + strings.Join(conds, ") AND (") + ")"
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}
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sql += " GROUP BY sp.id, g.genus_name;"
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species := make(ManySpecies, 0)
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err := DBH.Select(&species, sql, vals...)
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species, err := listSpecies(opt)
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if err != nil {
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return nil, newJSONError(err, http.StatusInternalServerError)
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}
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@ -139,12 +115,12 @@ func (s SpeciesService) list(val *url.Values, claims Claims) (entity, *appError)
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edit_list := make(map[int64]int64)
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for _, v := range species {
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for _, v := range *species {
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edit_list[v.Id] = v.CreatedBy
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}
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payload := ManySpeciesPayload{
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Species: &species,
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Species: species,
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Strains: strains,
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Meta: &SpeciesMeta{
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CanAdd: canAdd(claims),
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@ -155,30 +131,6 @@ func (s SpeciesService) list(val *url.Values, claims Claims) (entity, *appError)
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return &payload, nil
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}
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func strainOptsFromSpecies(opt ListOptions) (*ListOptions, error) {
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relatedStrainIds := make([]int64, 0)
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if opt.Ids == nil {
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q := `SELECT DISTINCT st.id
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FROM strains st
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INNER JOIN species sp ON sp.id=st.species_id
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INNER JOIN genera g ON g.id=sp.genus_id AND LOWER(g.genus_name)=LOWER($1);`
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if err := DBH.Select(&relatedStrainIds, q, opt.Genus); err != nil {
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return nil, err
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}
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} else {
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var vals []interface{}
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var count int64 = 1
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q := fmt.Sprintf("SELECT DISTINCT id FROM strains WHERE %s;", valsIn("species_id", opt.Ids, &vals, &count))
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if err := DBH.Select(&relatedStrainIds, q, vals...); err != nil {
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return nil, err
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}
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}
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return &ListOptions{Genus: opt.Genus, Ids: relatedStrainIds}, nil
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}
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func (s SpeciesService) get(id int64, genus string, claims Claims) (entity, *appError) {
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var species Species
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q := `SELECT sp.*, g.genus_name, array_agg(st.id) AS strains,
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@ -270,3 +222,60 @@ func genusIdFromName(genus_name string) (int64, error) {
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}
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return genus_id.Id, nil
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}
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func strainOptsFromSpecies(opt ListOptions) (*ListOptions, error) {
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relatedStrainIds := make([]int64, 0)
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if opt.Ids == nil {
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q := `SELECT DISTINCT st.id
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FROM strains st
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INNER JOIN species sp ON sp.id=st.species_id
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INNER JOIN genera g ON g.id=sp.genus_id AND LOWER(g.genus_name)=LOWER($1);`
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if err := DBH.Select(&relatedStrainIds, q, opt.Genus); err != nil {
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return nil, err
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}
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} else {
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var vals []interface{}
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var count int64 = 1
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q := fmt.Sprintf("SELECT DISTINCT id FROM strains WHERE %s;", valsIn("species_id", opt.Ids, &vals, &count))
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if err := DBH.Select(&relatedStrainIds, q, vals...); err != nil {
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return nil, err
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}
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}
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return &ListOptions{Genus: opt.Genus, Ids: relatedStrainIds}, nil
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}
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func listSpecies(opt ListOptions) (*ManySpecies, error) {
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var vals []interface{}
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q := `SELECT sp.*, g.genus_name, array_agg(st.id) AS strains,
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COUNT(st) AS total_strains,
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rank() OVER (ORDER BY sp.species_name ASC) AS sort_order
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FROM species sp
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INNER JOIN genera g ON g.id=sp.genus_id AND LOWER(g.genus_name)=$1
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LEFT OUTER JOIN strains st ON st.species_id=sp.id`
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vals = append(vals, opt.Genus)
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if len(opt.Ids) != 0 {
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var conds []string
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s := "sp.id IN ("
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for i, id := range opt.Ids {
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s = s + fmt.Sprintf("$%v,", i+2) // start param index at 2
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vals = append(vals, id)
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}
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s = s[:len(s)-1] + ")"
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conds = append(conds, s)
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q += " WHERE (" + strings.Join(conds, ") AND (") + ")"
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}
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q += " GROUP BY sp.id, g.genus_name;"
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species := make(ManySpecies, 0)
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err := DBH.Select(&species, q, vals...)
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if err != nil {
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return nil, err
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}
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return &species, nil
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}
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67
strains.go
67
strains.go
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@ -84,7 +84,6 @@ func (s StrainService) list(val *url.Values, claims Claims) (entity, *appError)
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}
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strains, err := listStrains(opt)
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if err != nil {
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return nil, newJSONError(err, http.StatusInternalServerError)
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}
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@ -92,39 +91,6 @@ func (s StrainService) list(val *url.Values, claims Claims) (entity, *appError)
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return strains, nil
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}
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func listStrains(opt ListOptions) (*Strains, error) {
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var vals []interface{}
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sql := `SELECT st.*, array_agg(m.id) AS measurements, COUNT(m) AS total_measurements,
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rank() OVER (ORDER BY sp.species_name ASC, st.type_strain ASC, st.strain_name ASC) AS sort_order
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FROM strains st
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INNER JOIN species sp ON sp.id=st.species_id
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INNER JOIN genera g ON g.id=sp.genus_id AND LOWER(g.genus_name)=$1
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LEFT OUTER JOIN measurements m ON m.strain_id=st.id`
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vals = append(vals, opt.Genus)
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if len(opt.Ids) != 0 {
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var conds []string
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s := "st.id IN ("
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for i, id := range opt.Ids {
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s = s + fmt.Sprintf("$%v,", i+2) // start param index at 2
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vals = append(vals, id)
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}
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s = s[:len(s)-1] + ")"
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conds = append(conds, s)
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sql += " WHERE (" + strings.Join(conds, ") AND (") + ")"
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}
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sql += " GROUP BY st.id, st.species_id, sp.species_name;"
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strains := make(Strains, 0)
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err := DBH.Select(&strains, sql, vals...)
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if err != nil {
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return nil, err
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}
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return &strains, nil
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}
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func (s StrainService) get(id int64, genus string, claims Claims) (entity, *appError) {
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var strain Strain
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q := `SELECT st.*, array_agg(m.id) AS measurements, COUNT(m) AS total_measurements,
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@ -173,3 +139,36 @@ func (s StrainService) create(e *entity, claims Claims) *appError {
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}
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return nil
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}
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func listStrains(opt ListOptions) (*Strains, error) {
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var vals []interface{}
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q := `SELECT st.*, array_agg(m.id) AS measurements, COUNT(m) AS total_measurements,
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rank() OVER (ORDER BY sp.species_name ASC, st.type_strain ASC, st.strain_name ASC) AS sort_order
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FROM strains st
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INNER JOIN species sp ON sp.id=st.species_id
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INNER JOIN genera g ON g.id=sp.genus_id AND LOWER(g.genus_name)=$1
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LEFT OUTER JOIN measurements m ON m.strain_id=st.id`
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vals = append(vals, opt.Genus)
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if len(opt.Ids) != 0 {
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var conds []string
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s := "st.id IN ("
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for i, id := range opt.Ids {
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s = s + fmt.Sprintf("$%v,", i+2) // start param index at 2
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vals = append(vals, id)
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}
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s = s[:len(s)-1] + ")"
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conds = append(conds, s)
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q += " WHERE (" + strings.Join(conds, ") AND (") + ")"
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}
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q += " GROUP BY st.id, st.species_id, sp.species_name;"
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strains := make(Strains, 0)
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err := DBH.Select(&strains, q, vals...)
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if err != nil {
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return nil, err
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}
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return &strains, nil
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}
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