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Added a test for the NMDC database and fixed up study ID retrieval.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,137 @@ | ||
| package nmdc | ||
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| import ( | ||
| "encoding/json" | ||
| "os" | ||
| "testing" | ||
|
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| "github.com/stretchr/testify/assert" | ||
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| "github.com/kbase/dts/config" | ||
| "github.com/kbase/dts/databases" | ||
| "github.com/kbase/dts/dtstest" | ||
| "github.com/kbase/dts/endpoints" | ||
| "github.com/kbase/dts/endpoints/globus" | ||
| ) | ||
|
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| const nmdcConfig string = ` | ||
| databases: | ||
| nmdc: | ||
| name: National Microbiome Data Collaborative | ||
| organization: DOE | ||
| endpoints: | ||
| nersc: globus-nmdc-nersc | ||
| emsl: globus-nmdc-emsl | ||
| endpoints: | ||
| globus-nmdc-nersc: | ||
| name: NMDC (NERSC) | ||
| id: ${DTS_GLOBUS_TEST_ENDPOINT} | ||
| provider: globus | ||
| root: / | ||
| auth: | ||
| client_id: ${DTS_GLOBUS_CLIENT_ID} | ||
| client_secret: ${DTS_GLOBUS_CLIENT_SECRET} | ||
| globus-nmdc-emsl: | ||
| name: NMDC Bulk Data Cache | ||
| id: ${DTS_GLOBUS_TEST_ENDPOINT} | ||
| provider: globus | ||
| root: / | ||
| auth: | ||
| client_id: ${DTS_GLOBUS_CLIENT_ID} | ||
| client_secret: ${DTS_GLOBUS_CLIENT_SECRET} | ||
| globus-jdp: | ||
| name: Globus NERSC DTN | ||
| id: ${DTS_GLOBUS_TEST_ENDPOINT} | ||
| provider: globus | ||
| auth: | ||
| client_id: ${DTS_GLOBUS_CLIENT_ID} | ||
| client_secret: ${DTS_GLOBUS_CLIENT_SECRET} | ||
| ` | ||
|
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| // since NMDC doesn't support search queries at this time, we search for | ||
| // data objects related to a study | ||
| var nmdcSearchParams map[string]json.RawMessage | ||
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| // this function gets called at the begіnning of a test session | ||
| func setup() { | ||
| dtstest.EnableDebugLogging() | ||
| config.Init([]byte(nmdcConfig)) | ||
| databases.RegisterDatabase("nmdc", NewDatabase) | ||
| endpoints.RegisterEndpointProvider("globus", globus.NewEndpoint) | ||
|
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| // construct NMDC-specific search parameters for a study | ||
| nmdcSearchParams = make(map[string]json.RawMessage) | ||
| studyId, _ := json.Marshal("nmdc:sty-11-5tgfr349") | ||
| nmdcSearchParams["study_id"] = studyId | ||
| } | ||
|
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| // this function gets called after all tests have been run | ||
| func breakdown() { | ||
| } | ||
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| func TestNewDatabase(t *testing.T) { | ||
| assert := assert.New(t) | ||
| orcid := os.Getenv("DTS_KBASE_TEST_ORCID") | ||
| db, err := NewDatabase(orcid) | ||
| assert.NotNil(db, "NMDC database not created") | ||
| assert.Nil(err, "NMDC database creation encountered an error") | ||
| } | ||
|
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| func TestNewDatabaseWithoutOrcid(t *testing.T) { | ||
| assert := assert.New(t) | ||
| db, err := NewDatabase("") | ||
| assert.Nil(db, "Invalid NMDC database somehow created") | ||
| assert.NotNil(err, "NMDC database creation without ORCID encountered no error") | ||
| } | ||
|
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| func TestSearch(t *testing.T) { | ||
| assert := assert.New(t) | ||
| orcid := os.Getenv("DTS_KBASE_TEST_ORCID") | ||
| db, _ := NewDatabase(orcid) | ||
|
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| params := databases.SearchParameters{ | ||
| Query: "", | ||
| Specific: nmdcSearchParams, | ||
| } | ||
| results, err := db.Search(params) | ||
| assert.True(len(results.Resources) > 0, "NMDC search query returned no results") | ||
| assert.Nil(err, "NMDC search query encountered an error") | ||
| } | ||
|
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| func TestResources(t *testing.T) { | ||
| assert := assert.New(t) | ||
| orcid := os.Getenv("DTS_KBASE_TEST_ORCID") | ||
| db, _ := NewDatabase(orcid) | ||
| params := databases.SearchParameters{ | ||
| Query: "", | ||
| Specific: nmdcSearchParams, | ||
| } | ||
| results, _ := db.Search(params) | ||
| fileIds := make([]string, len(results.Resources)) | ||
| for i, res := range results.Resources { | ||
| fileIds[i] = res.Id | ||
| } | ||
| resources, err := db.Resources(fileIds[:10]) | ||
| assert.Nil(err, "NMDC resource query encountered an error") | ||
| assert.Equal(10, len(resources), | ||
| "NMDC resource query didn't return requested number of results") | ||
| for i, resource := range resources { | ||
| jdpSearchResult := results.Resources[i] | ||
| assert.Equal(jdpSearchResult.Id, resource.Id, "Resource ID mismatch") | ||
| assert.Equal(jdpSearchResult.Name, resource.Name, "Resource name mismatch") | ||
| assert.Equal(jdpSearchResult.Path, resource.Path, "Resource path mismatch") | ||
| assert.Equal(jdpSearchResult.Format, resource.Format, "Resource format mismatch") | ||
| assert.Equal(jdpSearchResult.Bytes, resource.Bytes, "Resource size mismatch") | ||
| assert.Equal(jdpSearchResult.MediaType, resource.MediaType, "Resource media type mismatch") | ||
| assert.Equal(jdpSearchResult.Credit.Identifier, resource.Credit.Identifier, "Resource credit ID mismatch") | ||
| assert.Equal(jdpSearchResult.Credit.ResourceType, resource.Credit.ResourceType, "Resource credit resource type mismatch") | ||
| } | ||
| } | ||
|
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||
| // this runs setup, runs all tests, and does breakdown | ||
| func TestMain(m *testing.M) { | ||
| setup() | ||
| status := m.Run() | ||
| breakdown() | ||
| os.Exit(status) | ||
| } |