Merge pull request #319 from dictyBase/feat/geneid-test

Auto-generated Pull Request for feat/geneid-test

.github/workflows/ci.yml

@@ -19,7 +19,7 @@ jobs:
       - name: set up golang
         uses: actions/setup-go@v5
         with:
-          go-version: '~1.22'
+          go-version: 1.22
       - run: go version
       - name: unit test
         run: go test -covermode=atomic -coverprofile=profile.cov -v ./...

.github/workflows/lint.yml

@@ -4,16 +4,8 @@ on:
     branches-ignore:
       - master
 jobs:
-  lint:
-    runs-on: ubuntu-latest
-    steps:
-      - name: check out code
-        uses: actions/checkout@v4
-      - uses: actions/setup-go@v5
-        with:
-          go-version: 1.20.6
-          cache: false
-      - name: run linter
-        uses: golangci/golangci-lint-action@v6
-        with:
-          version: v1.52.2
+  call-lint:
+    uses: dictyBase/workflows/.github/workflows/golang-lint.yaml@develop
+    with:
+      repository: ${{ github.repository }}
+      ref: ${{ github.event.pull_request.head.sha }}

.github/workflows/testcov.yml

@@ -5,7 +5,7 @@ jobs:
     runs-on: ubuntu-latest
     services:
       arangodb:
-        image: arangodb:3.10.9
+        image: arangodb:3.11
         env:
           ARANGO_ROOT_PASSWORD: rootpass
         ports:
@@ -14,7 +14,7 @@ jobs:
       - name: set up golang
         uses: actions/setup-go@v5
         with:
-          go-version: '~1.20.6'
+          go-version: 1.22
       - name: check out code
         uses: actions/checkout@v4
       - name: unit test

.gitignore

@@ -1 +1,3 @@
-cover.out
+cover.out
+.aider*
+.env

.golangci.yml

@@ -21,10 +21,8 @@ linters:
     - bodyclose
     - bidichk
     - cyclop 
-    - depguard
     - decorder
     - dogsled
-    # - dupl
     - errcheck
     - funlen
     - goconst

CONVENTIONS.md

@@ -0,0 +1,2 @@
+- use at least three letters variable names
+- use fmt.Sprintf for string concatenation

dagger.json

@@ -0,0 +1,10 @@
+{
+  "name": "modware-import",
+  "dependencies": [
+    {
+      "name": "golang",
+      "source": "github.com/dictybase-docker/dagger-of-dcr/golang@aa46f8610edad8ecfb0776e4c9fe85a486da87eb"
+    }
+  ],
+  "engineVersion": "v0.11.9"
+}

go.mod

@@ -52,6 +52,6 @@ require (
 	gopkg.in/yaml.v3 v3.0.1 // indirect
 )
 
-go 1.21
+go 1.22
 
 toolchain go1.22.5

internal/app/service/strain.go

@@ -112,15 +112,15 @@ func (s *StockService) UpdateStrain(
 }
 
 // ListStrainsByIds gets a list of strains from a list of strain identifiers
-func (s *StockService) ListStrainsByIds(
+func (s *StockService) ListStrainsByIDs(
 	ctx context.Context,
 	r *stock.StockIdList,
 ) (*stock.StrainList, error) {
 	sl := &stock.StrainList{}
 	if err := r.Validate(); err != nil {
 		return sl, aphgrpc.HandleInvalidParamError(ctx, err)
 	}
-	mc, err := s.repo.ListStrainsByIds(r)
+	mc, err := s.repo.ListStrainsByIDs(r)
 	if err != nil {
 		return sl, aphgrpc.HandleGetError(ctx, err)
 	}

internal/repository/arangodb/plasmid_test.go

@@ -108,6 +108,7 @@ func TestListPlasmidsWithFilter(t *testing.T) {
 		)
 		_, err := repo.AddPlasmid(np)
 		assert.NoErrorf(err, "expect no error, received %s", err)
+		time.Sleep(100 * time.Millisecond)
 	}
 	sf, err := repo.ListPlasmids(
 		&stock.StockParameters{Limit: 10, Filter: georgeFilter},
@@ -176,6 +177,7 @@ func TestListPlasmids(t *testing.T) {
 		)
 		_, err := repo.AddPlasmid(np)
 		assert.NoErrorf(err, "expect no error adding plasmid, received %s", err)
+		time.Sleep(100 * time.Millisecond)
 	}
 	ls, err := repo.ListPlasmids(&stock.StockParameters{Limit: 4})
 	assert.NoErrorf(

internal/repository/arangodb/statement/read.go

@@ -60,7 +60,7 @@ const (
 		FOR stock_prop,e IN 1..1 INBOUND @strain_key GRAPH @parent_graph
 			RETURN e._key
 	`
-	StrainListFromIds = `
+	StrainListFromIDs = `
 		FOR id IN @ids
 			FOR stock_prop, e IN 1..1 OUTBOUND CONCAT(@stock_collection,"/",id) GRAPH @stock_prop_graph
 				LET parent = (

internal/repository/arangodb/strain_read.go

@@ -61,12 +61,12 @@ func (ar *arangorepository) ListStrains(
 	return omd, nil
 }
 
-func (ar *arangorepository) ListStrainsByIds(
+func (ar *arangorepository) ListStrainsByIDs(
 	p *stock.StockIdList,
 ) ([]*model.StockDoc, error) {
 	ms := make([]*model.StockDoc, 0)
 	rs, err := ar.database.SearchRows(
-		statement.StrainListFromIds,
+		statement.StrainListFromIDs,
 		map[string]interface{}{
 			"ids":                p.Id,
 			"limit":              len(p.Id),

internal/repository/arangodb/strain_test.go

@@ -16,6 +16,9 @@ import (
 )
 
 const (
+	filterGene     = `FILTER 'DDB_G0287317' IN s.genes`
+	filterGeneMore = `FILTER 'DDB_G098058933' IN s.genes`
+
 	filterOne = `FILTER s.depositor == '[email protected]'`
 	filterTwo = `FILTER s.depositor == '[email protected]' 
 		      AND s.depositor == '[email protected]'
@@ -92,6 +95,7 @@ func createTestStrainsWithIDs(
 		if err != nil {
 			return ids, err
 		}
+		time.Sleep(100 * time.Millisecond)
 		ids = append(ids, nps.StockID)
 		start++
 	}
@@ -116,6 +120,7 @@ func createTestStrains(
 		if err != nil {
 			return err
 		}
+		time.Sleep(100 * time.Millisecond)
 		start++
 	}
 	return nil
@@ -512,15 +517,15 @@ func TestListStrains(t *testing.T) {
 	testModelListSort(ls3, t)
 }
 
-func TestListStrainsByIds(t *testing.T) {
+func TestListStrainsByIDs(t *testing.T) {
 	t.Parallel()
 	assert, repo := setUp(t)
 	defer tearDown(repo)
 	// add 10 new test strains
 	ids, err := createTestStrainsWithIDs(30, General, repo)
 	assert.NoError(err, "expect no error from creating strains")
 	// get first five results
-	ls, err := repo.ListStrainsByIds(&stock.StockIdList{Id: ids})
+	ls, err := repo.ListStrainsByIDs(&stock.StockIdList{Id: ids})
 	assert.NoError(err, "expect no error in getting strains")
 	assert.Len(ls, 30, "should match the provided limit number")
 	for _, stock := range ls {
@@ -554,7 +559,7 @@ func TestListStrainsByIds(t *testing.T) {
 	)
 	pids, err := createTestStrainsWithParent(30, General, repo, pm.StockID)
 	assert.NoError(err, "expect no error from creating strains")
-	pls, err := repo.ListStrainsByIds(&stock.StockIdList{Id: pids})
+	pls, err := repo.ListStrainsByIDs(&stock.StockIdList{Id: pids})
 	assert.NoError(err, "expect no error in getting 30 stocks with parents")
 	assert.Len(pls, 30, "should match the provided limit number")
 	for _, stock := range pls {
@@ -581,7 +586,7 @@ func TestListStrainsByIds(t *testing.T) {
 		)
 	}
 	// Non-existing ids
-	els, err := repo.ListStrainsByIds(
+	els, err := repo.ListStrainsByIDs(
 		&stock.StockIdList{Id: []string{"DBN589343", "DBN48473232"}},
 	)
 	assert.NoErrorf(
@@ -909,6 +914,49 @@ func TestEditStrain(t *testing.T) {
 	)
 }
 
+func TestListStrainsWithGeneFilter(t *testing.T) {
+	t.Parallel()
+	assert, repo := setUp(t)
+	defer tearDown(repo)
+	// Create test strain with specific gene
+	ns := newTestStrain("[email protected]", General)
+	ns.Data.Attributes.Genes = []string{"DDB_G0287317", "DDB_G0287318"}
+	_, err := repo.AddStrain(ns)
+	assert.NoError(err, "expect no error from creating strain with genes")
+
+	// Create additional strains without the specific gene
+	err = createTestStrains(5, General, repo)
+	assert.NoError(err, "expect no error from creating additional strains")
+
+	// Test filtering by gene
+	ls, err := repo.ListStrains(&stock.StockParameters{
+		Limit:  10,
+		Filter: filterGene,
+	})
+	assert.NoError(err, "expect no error in getting strains filtered by gene")
+	assert.Len(ls, 1, "should find exactly one strain with the specific gene")
+	assert.Contains(
+		ls[0].Genes,
+		"DDB_G0287317",
+		"returned strain should contain the filtered gene",
+	)
+	ls2, err := repo.ListStrains(&stock.StockParameters{
+		Limit:  10,
+		Filter: filterGeneMore,
+	})
+	assert.NoError(err, "expect no error in getting strains filtered by gene")
+	assert.Len(
+		ls2,
+		5,
+		"should find exactly five strains with the specific gene",
+	)
+	assert.Contains(
+		ls2[1].Genes,
+		"DDB_G098058933",
+		"returned strain should contain the filtered gene",
+	)
+}
+
 func TestEditStrainWithParent(t *testing.T) {
 	t.Parallel()
 	assert, repo := setUp(t)

internal/repository/repository.go

@@ -18,7 +18,7 @@ type StockRepository interface {
 	EditStrain(us *stock.StrainUpdate) (*model.StockDoc, error)
 	EditPlasmid(us *stock.PlasmidUpdate) (*model.StockDoc, error)
 	ListStrains(s *stock.StockParameters) ([]*model.StockDoc, error)
-	ListStrainsByIds(s *stock.StockIdList) ([]*model.StockDoc, error)
+	ListStrainsByIDs(s *stock.StockIdList) ([]*model.StockDoc, error)
 	ListPlasmids(s *stock.StockParameters) ([]*model.StockDoc, error)
 	LoadStrain(id string, es *stock.ExistingStrain) (*model.StockDoc, error)
 	LoadPlasmid(id string, ep *stock.ExistingPlasmid) (*model.StockDoc, error)