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Merged
cybersiddhu merged 2 commits into from
Apr 20, 2026
Merged

Auto-generated Pull Request for fix/list-plasmids #610

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91f62a0
feat(plasmid): add support for plasmid type filtering in stock queries
cybersiddhu Apr 20, 2026
e09a124
fix(plasmid): update plasmid tag constants to match stock service exp…
cybersiddhu Apr 20, 2026
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20 changes: 3 additions & 17 deletions internal/graphql/resolver/stock_plasmid_fp.go
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Original file line number Diff line number Diff line change
Expand Up @@ -127,23 +127,9 @@ func computeListPlasmidParams(
}

func buildListPlasmidFilterQuery(ctx withListPlasmidParams) IOE.IOEither[error, string] {
return F.Pipe2(
ctx.filter,
func(filter *models.PlasmidListFilter) E.Either[error, string] {
if filter == nil {
return E.Right[error]("")
}
return F.Pipe5(
filter,
resolverutils.CheckIDField,
E.Chain(resolverutils.CheckInStockField),
E.Chain(resolverutils.CheckUnverifiedPlasmidType),
E.Chain(resolverutils.CheckValidPlasmidType),
E.Map[error](resolverutils.BuildPlasmidFieldQuery),
)
},
IOE.FromEither[error, string],
)
return IOE.TryCatchError(func() (string, error) {
return resolverutils.PlasmidFilterToQuery(ctx.filter)
})
}

func fetchListPlasmidCollection(
Expand Down
58 changes: 40 additions & 18 deletions internal/graphql/resolver/stock_test.go
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Original file line number Diff line number Diff line change
Expand Up @@ -629,42 +629,64 @@ func TestListPlasmidsUnsupportedIDFilter(t *testing.T) {
require.Empty(result.Plasmids)
}

func TestListPlasmidsUnverifiedRegularTypeFilter(t *testing.T) {
func TestListPlasmidsRegularTypeFilter(t *testing.T) {
t.Parallel()
require := require.New(t)

resolver := &QueryResolver{
Registry: &mocks.MockRegistry{},
Logger: mocks.TestLogger(),
mockedStockClient := new(clients.StockServiceClient)
mockedStockClient.On(
"ListPlasmids",
mock.MatchedBy(func(ctx context.Context) bool { return true }),
mock.MatchedBy(func(params *pb.StockParameters) bool {
return params.Cursor == 0 &&
params.Limit == 10 &&
params.Filter == "ontology==dicty_plasmid_keyword;tag==vector"
}),
).Return(mocks.MockPlasmidCollection(), nil)

reg := &stockClientRegistry{
MockRegistry: &mocks.MockRegistry{ConnMap: nil},
stockClient: mockedStockClient,
}
resolver := &QueryResolver{Registry: reg, Logger: mocks.TestLogger()}
cursor := 0
limit := 10

ctx := graphql.WithResponseContext(context.Background(), graphql.DefaultErrorPresenter, graphql.DefaultRecover)
result, err := resolver.ListPlasmids(ctx, &cursor, &limit, &models.PlasmidListFilter{
result, err := resolver.ListPlasmids(context.Background(), &cursor, &limit, &models.PlasmidListFilter{
PlasmidType: models.PlasmidTypeRegular,
})
require.Error(err)
require.Contains(err.Error(), "plasmid_type filter is not yet verified")
require.Empty(result.Plasmids)
require.NoError(err)
require.Len(result.Plasmids, 3)
mockedStockClient.AssertExpectations(t)
}

func TestListPlasmidsUnverifiedGoldenBraidTypeFilter(t *testing.T) {
func TestListPlasmidsGoldenBraidTypeFilter(t *testing.T) {
t.Parallel()
require := require.New(t)

resolver := &QueryResolver{
Registry: &mocks.MockRegistry{},
Logger: mocks.TestLogger(),
mockedStockClient := new(clients.StockServiceClient)
mockedStockClient.On(
"ListPlasmids",
mock.MatchedBy(func(ctx context.Context) bool { return true }),
mock.MatchedBy(func(params *pb.StockParameters) bool {
return params.Cursor == 0 &&
params.Limit == 10 &&
params.Filter == "ontology==dicty_plasmid_keyword;tag==GB vector"
}),
).Return(mocks.MockPlasmidCollection(), nil)

reg := &stockClientRegistry{
MockRegistry: &mocks.MockRegistry{ConnMap: nil},
stockClient: mockedStockClient,
}
resolver := &QueryResolver{Registry: reg, Logger: mocks.TestLogger()}
cursor := 0
limit := 10

ctx := graphql.WithResponseContext(context.Background(), graphql.DefaultErrorPresenter, graphql.DefaultRecover)
result, err := resolver.ListPlasmids(ctx, &cursor, &limit, &models.PlasmidListFilter{
result, err := resolver.ListPlasmids(context.Background(), &cursor, &limit, &models.PlasmidListFilter{
PlasmidType: models.PlasmidTypeGoldenBraid,
})
require.Error(err)
require.Contains(err.Error(), "plasmid_type filter is not yet verified")
require.Empty(result.Plasmids)
require.NoError(err)
require.Len(result.Plasmids, 3)
mockedStockClient.AssertExpectations(t)
}
95 changes: 46 additions & 49 deletions internal/graphql/resolverutils/plasmid_filter.go
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Original file line number Diff line number Diff line change
Expand Up @@ -5,21 +5,19 @@ package resolverutils

import (
"fmt"
"strings"

A "github.com/IBM/fp-go/v2/array"
E "github.com/IBM/fp-go/v2/either"
eq "github.com/IBM/fp-go/v2/eq"
F "github.com/IBM/fp-go/v2/function"
O "github.com/IBM/fp-go/v2/option"
P "github.com/IBM/fp-go/v2/predicate"
S "github.com/IBM/fp-go/v2/string"

"github.com/dictyBase/graphql-server/internal/graphql/models"
"github.com/dictyBase/graphql-server/internal/registry"
)

var (
plasmidTypeEq = eq.FromStrictEquals[models.PlasmidType]()

isNilID = F.Pipe1(
P.IsZero[*string](),
P.ContraMap(func(f *models.PlasmidListFilter) *string {
Expand Down Expand Up @@ -51,56 +49,55 @@ var (
)
},
)
)

isRegularPlasmidType = eq.Equals(plasmidTypeEq)(models.PlasmidTypeRegular)
isGoldenBraidPlasmidType = eq.Equals(plasmidTypeEq)(models.PlasmidTypeGoldenBraid)
isUnverifiedPlasmidType = F.Pipe2(
isRegularPlasmidType,
P.Or(isGoldenBraidPlasmidType),
P.ContraMap(func(f *models.PlasmidListFilter) models.PlasmidType {
return f.PlasmidType
}),
)
CheckUnverifiedPlasmidType = E.FromPredicate(
P.Not(isUnverifiedPlasmidType),
func(filter *models.PlasmidListFilter) error {
return fmt.Errorf(
"plasmid list filter %v: plasmid_type filter is not yet verified for stock query conversion",
filter,
)
},
)

isAllPlasmidType = F.Pipe1(
eq.Equals(plasmidTypeEq)(models.PlasmidTypeAll),
P.ContraMap(func(f *models.PlasmidListFilter) models.PlasmidType {
return f.PlasmidType
}),
)
CheckValidPlasmidType = E.FromPredicate(
isAllPlasmidType,
func(f *models.PlasmidListFilter) error {
return fmt.Errorf("invalid plasmid type %s", f.PlasmidType.String())
},
)
func PlasmidFilterToQuery(filter *models.PlasmidListFilter) (string, error) {
if filter == nil {
return "", nil
}

validateFilterPipeline = F.Flow5(
if _, err := E.UnwrapError(F.Pipe2(
filter,
CheckIDField,
E.Chain(CheckInStockField),
E.Chain(CheckUnverifiedPlasmidType),
E.Chain(CheckValidPlasmidType),
E.Map[error](BuildPlasmidFieldQuery),
)
)
)); err != nil {
return "", err
}

func PlasmidFilterToQuery(filter *models.PlasmidListFilter) (string, error) {
return E.UnwrapError(F.Pipe1(
O.FromNillable(filter),
O.Fold(
F.Constant(E.Right[error]("")),
validateFilterPipeline,
),
))
fieldQuery := BuildPlasmidFieldQuery(filter)
typeQuery, err := plasmidTypeQuery(filter)
if err != nil {
return fieldQuery, err
Comment on lines +68 to +70
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@coderabbitai coderabbitai Bot Apr 20, 2026

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⚠️ Potential issue | 🟡 Minor

Return an empty query when type validation fails.

Line 70 returns fieldQuery together with err; for a filter like {Summary: ..., PlasmidType: "INVALID"}, direct callers could accidentally use the partial summary query despite the failed full conversion. Return the zero query on error.

🐛 Proposed fix 
 	typeQuery, err := plasmidTypeQuery(filter)
 	if err != nil {
-		return fieldQuery, err
+		return "", err
 	}
📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
typeQuery, err := plasmidTypeQuery(filter)
if err != nil {
return fieldQuery, err
typeQuery, err := plasmidTypeQuery(filter)
if err != nil {
return "", err
}
🤖 Prompt for AI Agents 
Verify each finding against the current code and only fix it if needed.

In `@internal/graphql/resolverutils/plasmid_filter.go` around lines 68 - 70, When
plasmidTypeQuery(filter) returns an error, the current code returns the
partially built fieldQuery which may be misused; change the error path so you
return the zero-value/empty query instead of fieldQuery along with the error.
Locate the call to plasmidTypeQuery in plasmid_filter.go (the variables
typeQuery and fieldQuery) and replace the return of fieldQuery on error with an
empty query value (the zero-value for the query type) plus err so callers won't
get a partial query when type validation fails.

}
if fieldQuery == "" {
return typeQuery, nil
}
if typeQuery == "" {
return fieldQuery, nil
}

return strings.Join([]string{fieldQuery, typeQuery}, ";"), nil
}

func plasmidTypeQuery(filter *models.PlasmidListFilter) (string, error) {
switch filter.PlasmidType {
case models.PlasmidTypeAll:
return "", nil
case models.PlasmidTypeRegular:
return fmt.Sprintf(
"ontology==%s;tag==%s",
registry.DictyPlasmidPropOntology,
registry.RegularPlasmidTag,
), nil
case models.PlasmidTypeGoldenBraid:
return fmt.Sprintf(
"ontology==%s;tag==%s",
registry.DictyPlasmidPropOntology,
registry.GoldenBraidPlasmidTag,
), nil
default:
return "", fmt.Errorf("invalid plasmid type %s", filter.PlasmidType.String())
}
}

func BuildPlasmidFieldQuery(filter *models.PlasmidListFilter) string {
Expand Down
40 changes: 32 additions & 8 deletions internal/graphql/resolverutils/plasmid_filter_test.go
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@ import (
"testing"

"github.com/dictyBase/graphql-server/internal/graphql/models"
"github.com/dictyBase/graphql-server/internal/registry"
"github.com/stretchr/testify/require"
)

Expand Down Expand Up @@ -58,22 +59,45 @@ func TestPlasmidFilterToQueryPlasmidTypeAllOnly(t *testing.T) {
require.Equal(t, "", query)
}

func TestPlasmidFilterToQueryPlasmidTypeRegularUnverified(t *testing.T) {
func TestPlasmidFilterToQueryPlasmidTypeRegularOnly(t *testing.T) {
t.Parallel()
_, err := PlasmidFilterToQuery(&models.PlasmidListFilter{
query, err := PlasmidFilterToQuery(&models.PlasmidListFilter{
PlasmidType: models.PlasmidTypeRegular,
})
require.Error(t, err)
require.Contains(t, err.Error(), "plasmid_type filter is not yet verified")
require.NoError(t, err)
require.Equal(
t,
"ontology=="+registry.DictyPlasmidPropOntology+";tag=="+registry.RegularPlasmidTag,
query,
)
}

func TestPlasmidFilterToQueryPlasmidTypeGoldenBraidUnverified(t *testing.T) {
func TestPlasmidFilterToQueryPlasmidTypeGoldenBraidOnly(t *testing.T) {
t.Parallel()
_, err := PlasmidFilterToQuery(&models.PlasmidListFilter{
query, err := PlasmidFilterToQuery(&models.PlasmidListFilter{
PlasmidType: models.PlasmidTypeGoldenBraid,
})
require.Error(t, err)
require.Contains(t, err.Error(), "plasmid_type filter is not yet verified")
require.NoError(t, err)
require.Equal(
t,
"ontology=="+registry.DictyPlasmidPropOntology+";tag=="+registry.GoldenBraidPlasmidTag,
query,
)
}

func TestPlasmidFilterToQueryCombinedSummaryAndRegularType(t *testing.T) {
t.Parallel()
summary := "test"
query, err := PlasmidFilterToQuery(&models.PlasmidListFilter{
Summary: &summary,
PlasmidType: models.PlasmidTypeRegular,
})
require.NoError(t, err)
require.Equal(
t,
"summary=~test;ontology=="+registry.DictyPlasmidPropOntology+";tag=="+registry.RegularPlasmidTag,
query,
)
}

func TestPlasmidFilterToQueryInvalidPlasmidType(t *testing.T) {
Expand Down
4 changes: 2 additions & 2 deletions internal/registry/registry.go
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Original file line number Diff line number Diff line change
Expand Up @@ -39,8 +39,8 @@ const (
MutmethodTag = "mutagenesis method"
MuttypeTag = "mutant type"
GenoTag = "genotype"
GoldenBraidPlasmidTag = "golden braid"
RegularPlasmidTag = "regular plasmid"
GoldenBraidPlasmidTag = "GB vector"
RegularPlasmidTag = "vector"
SynTag = "synonym"
EmptyValue = "novalue"
S3Bucket = "s3bucket"
Expand Down
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