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Merge pull request #21 from ldsec/dev
MedCo v0.3.0
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,18 @@ | ||
| # MedCo Connector | ||
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| ## Source code organization | ||
| - *client*: client logic | ||
| - *cmd*: runnable applications | ||
| - *cmd/medco-cli-client*: client application | ||
| - *cmd/medco-connector-server*: server application | ||
| - *deployment*: docker image definition and docker-compose deployment | ||
| - *restapi*: go-swagger generated code for REST API | ||
| - *restapi/client*: client-related generated code | ||
| - *restapi/models*: generated models | ||
| - *restapi/server*: server-related generated code | ||
| - *server*: server logic | ||
| - *server/handlers*: server REST API endpoints handlers | ||
| - *swagger*: swagger REST API definitions | ||
| - *util*: utility code (configuration, security, etc.) | ||
| - *util*: | ||
| - *wrappers*: client library wrappers for external service (i2b2, unlynx, etc.) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,150 @@ | ||
| package medcoclient | ||
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| import ( | ||
| "crypto/tls" | ||
| httptransport "github.com/go-openapi/runtime/client" | ||
| "github.com/ldsec/medco-connector/restapi/client" | ||
| "github.com/ldsec/medco-connector/restapi/client/genomic_annotations" | ||
| utilclient "github.com/ldsec/medco-connector/util/client" | ||
| "github.com/sirupsen/logrus" | ||
| "net/http" | ||
| "net/url" | ||
| "strings" | ||
| "time" | ||
| ) | ||
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| // GenomicAnnotationsGetValues is a MedCo client genomic-annotations get-values request | ||
| type GenomicAnnotationsGetValues struct { | ||
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| // httpMedCoClient is the HTTP client for the MedCo connector | ||
| httpMedCoClient *client.MedcoCli | ||
| // authToken is the OIDC authentication JWT | ||
| authToken string | ||
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| annotation string | ||
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| value string | ||
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| limit *int64 | ||
| } | ||
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| // GenomicAnnotationsGetVariants is a MedCo client genomic-annotations get-variants request | ||
| type GenomicAnnotationsGetVariants struct { | ||
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| // httpMedCoClient is the HTTP client for the MedCo connector | ||
| httpMedCoClient *client.MedcoCli | ||
| // authToken is the OIDC authentication JWT | ||
| authToken string | ||
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| annotation string | ||
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| value string | ||
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| zygosity []string | ||
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| encrypted *bool | ||
| } | ||
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| // NewGenomicAnnotationsGetValues creates a new MedCo client genomic-annotations get-values request | ||
| func NewGenomicAnnotationsGetValues(authToken, annotation, value string, limit *int64, disableTLSCheck bool) (q *GenomicAnnotationsGetValues, err error) { | ||
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| q = &GenomicAnnotationsGetValues{ | ||
| authToken: authToken, | ||
| annotation: annotation, | ||
| value: value, | ||
| limit: limit, | ||
| } | ||
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| parsedURL, err := url.Parse(utilclient.MedCoConnectorURL) | ||
| if err != nil { | ||
| logrus.Error("cannot parse MedCo connector URL: ", err) | ||
| return | ||
| } | ||
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| transport := httptransport.New(parsedURL.Host, parsedURL.Path, []string{parsedURL.Scheme}) | ||
| transport.Transport.(*http.Transport).TLSClientConfig = &tls.Config{InsecureSkipVerify: disableTLSCheck} | ||
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| q.httpMedCoClient = client.New(transport, nil) | ||
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| return | ||
| } | ||
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| // NewGenomicAnnotationsGetVariants creates a new MedCo client genomic-annotations get-variants request | ||
| func NewGenomicAnnotationsGetVariants(authToken, annotation, value string, zygosity string, encrypted *bool, disableTLSCheck bool) (q *GenomicAnnotationsGetVariants, err error) { | ||
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| q = &GenomicAnnotationsGetVariants{ | ||
| authToken: authToken, | ||
| annotation: annotation, | ||
| value: value, | ||
| zygosity: strings.Split(zygosity, "|"), | ||
| encrypted: encrypted, | ||
| } | ||
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| parsedURL, err := url.Parse(utilclient.MedCoConnectorURL) | ||
| if err != nil { | ||
| logrus.Error("cannot parse MedCo connector URL: ", err) | ||
| return | ||
| } | ||
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| transport := httptransport.New(parsedURL.Host, parsedURL.Path, []string{parsedURL.Scheme}) | ||
| transport.Transport.(*http.Transport).TLSClientConfig = &tls.Config{InsecureSkipVerify: disableTLSCheck} | ||
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| q.httpMedCoClient = client.New(transport, nil) | ||
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| return | ||
| } | ||
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| // Execute executes the MedCo client get-values query | ||
| func (clientGenomicAnnotationsGetValues *GenomicAnnotationsGetValues) Execute() (result []string, err error) { | ||
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| result, err = clientGenomicAnnotationsGetValues.submitToNode() | ||
| return | ||
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| } | ||
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| // Execute executes the MedCo client get-variants query | ||
| func (clientGenomicAnnotationsGetVariants *GenomicAnnotationsGetVariants) Execute() (result []string, err error) { | ||
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| result, err = clientGenomicAnnotationsGetVariants.submitToNode() | ||
| return | ||
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| } | ||
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| func (clientGenomicAnnotationsGetValues *GenomicAnnotationsGetValues) submitToNode() (result []string, err error) { | ||
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| params := genomic_annotations.NewGetValuesParamsWithTimeout(time.Duration(utilclient.GenomicAnnotationsQueryTimeoutSeconds) * time.Second) | ||
| params.Annotation = clientGenomicAnnotationsGetValues.annotation | ||
| params.Value = clientGenomicAnnotationsGetValues.value | ||
| if *clientGenomicAnnotationsGetValues.limit != 0 { | ||
| params.Limit = clientGenomicAnnotationsGetValues.limit | ||
| } | ||
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| response, err := clientGenomicAnnotationsGetValues.httpMedCoClient.GenomicAnnotations.GetValues(params, httptransport.BearerToken(clientGenomicAnnotationsGetValues.authToken)) | ||
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| if err != nil { | ||
| logrus.Error("Genomic annotations get values error: ", err) | ||
| return nil, err | ||
| } | ||
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| return response.Payload, nil | ||
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| } | ||
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| func (clientGenomicAnnotationsGetVariants *GenomicAnnotationsGetVariants) submitToNode() (result []string, err error) { | ||
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| params := genomic_annotations.NewGetVariantsParamsWithTimeout(time.Duration(utilclient.GenomicAnnotationsQueryTimeoutSeconds) * time.Second) | ||
| params.Annotation = clientGenomicAnnotationsGetVariants.annotation | ||
| params.Value = clientGenomicAnnotationsGetVariants.value | ||
| params.Zygosity = clientGenomicAnnotationsGetVariants.zygosity | ||
| params.Encrypted = clientGenomicAnnotationsGetVariants.encrypted | ||
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| response, err := clientGenomicAnnotationsGetVariants.httpMedCoClient.GenomicAnnotations.GetVariants(params, httptransport.BearerToken(clientGenomicAnnotationsGetVariants.authToken)) | ||
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| if err != nil { | ||
| logrus.Error("Genomic annotations get variants error: ", err) | ||
| return nil, err | ||
| } | ||
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| return response.Payload, nil | ||
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| } |
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