Merge pull request #1114 from neicnordic/feature/sda-admin-dataset-user

[sda-admin] Add user to create dataset command

sda-admin/README.md

@@ -46,10 +46,10 @@ sda-admin file set-accession -filepath /path/to/file.c4gh -user test-user@exampl
 
 ## Create a dataset from a list of accession IDs and a dataset ID
 
-Use the following command to create a dataset `dataset001` from accession IDs `my-accession-id-1` and `my-accession-id-2`
+Use the following command to create a dataset `dataset001` from accession IDs `my-accession-id-1` and `my-accession-id-2` for files that belongs to the user `[email protected]`
 
 ```sh
-sda-admin dataset create -dataset-id dataset001 my-accession-id-1 my-accession-id-2 
+sda-admin dataset create  -user [email protected] -dataset-id dataset001 my-accession-id-1 my-accession-id-2 
 ```
 
 ## Release a dataset for downloading

sda-admin/dataset/dataset.go

@@ -12,10 +12,11 @@ import (
 type RequestBodyDataset struct {
 	AccessionIDs []string `json:"accession_ids"`
 	DatasetID    string   `json:"dataset_id"`
+	User         string   `json:"user"`
 }
 
 // Create creates a dataset from a list of accession IDs and a dataset ID.
-func Create(apiURI, token, datasetID string, accessionIDs []string) error {
+func Create(apiURI, token, datasetID, username string, accessionIDs []string) error {
 	parsedURL, err := url.Parse(apiURI)
 	if err != nil {
 		return err
@@ -25,6 +26,7 @@ func Create(apiURI, token, datasetID string, accessionIDs []string) error {
 	requestBody := RequestBodyDataset{
 		AccessionIDs: accessionIDs,
 		DatasetID:    datasetID,
+		User:         username,
 	}
 
 	jsonBody, err := json.Marshal(requestBody)

sda-admin/dataset/dataset_test.go

@@ -28,13 +28,14 @@ func TestCreate_Success(t *testing.T) {
 
 	expectedURL := "http://example.com/dataset/create"
 	token := "test-token"
+	user := "[email protected]"
 	datasetID := "dataset-123"
 	accessionIDs := []string{"accession-1", "accession-2"}
-	jsonBody := []byte(`{"accession_ids":["accession-1","accession-2"],"dataset_id":"dataset-123"}`)
+	jsonBody := []byte(`{"accession_ids":["accession-1","accession-2"],"dataset_id":"dataset-123","user":"[email protected]"}`)
 
 	mockHelpers.On("PostRequest", expectedURL, token, jsonBody).Return([]byte(`{}`), nil)
 
-	err := Create("http://example.com", token, datasetID, accessionIDs)
+	err := Create("http://example.com", token, datasetID, user, accessionIDs)
 	assert.NoError(t, err)
 	mockHelpers.AssertExpectations(t)
 }
@@ -47,13 +48,14 @@ func TestCreate_PostRequestFailure(t *testing.T) {
 
 	expectedURL := "http://example.com/dataset/create"
 	token := "test-token"
+	user := "[email protected]"
 	datasetID := "dataset-123"
 	accessionIDs := []string{"accession-1", "accession-2"}
-	jsonBody := []byte(`{"accession_ids":["accession-1","accession-2"],"dataset_id":"dataset-123"}`)
+	jsonBody := []byte(`{"accession_ids":["accession-1","accession-2"],"dataset_id":"dataset-123","user":"[email protected]"}`)
 
 	mockHelpers.On("PostRequest", expectedURL, token, jsonBody).Return([]byte(nil), errors.New("failed to send request"))
 
-	err := Create("http://example.com", token, datasetID, accessionIDs)
+	err := Create("http://example.com", token, datasetID, user, accessionIDs)
 	assert.Error(t, err)
 	assert.EqualError(t, err, "failed to send request")
 	mockHelpers.AssertExpectations(t)

sda-admin/main.go

@@ -30,7 +30,7 @@ Commands:
                                 Trigger ingestion of a given file.
   file set-accession -filepath FILEPATH -user USERNAME -accession-id accessionID
                                 Assign accession ID to a file.
-  dataset create -dataset-id DATASET_ID accessionID [accessionID ...]
+  dataset create -user SUBMISSION_USER -dataset-id DATASET_ID accessionID [accessionID ...]
                                 Create a dataset from a list of accession IDs and a dataset ID.
   dataset release -dataset-id DATASET_ID
                                 Release a dataset for downloading.
@@ -92,7 +92,7 @@ Options:
   -accession-id ID     Specify the accession ID to assign to the file.`
 
 var datasetUsage = `Create a dataset:
-  Usage: sda-admin dataset create -dataset-id DATASET_ID [ACCESSION_ID ...]
+  Usage: sda-admin dataset create -user SUBMISSION_USER -dataset-id DATASET_ID [ACCESSION_ID ...]
     Create a dataset from a list of accession IDs and a dataset ID.
     
 Release a dataset:
@@ -105,8 +105,8 @@ Options:
 
 Use 'sda-admin help dataset <command>' for information on a specific command.`
 
-var datasetCreateUsage = `Usage: sda-admin dataset create -dataset-id DATASET_ID [ACCESSION_ID ...]
-  Create a dataset from a list of accession IDs and a dataset ID.
+var datasetCreateUsage = `Usage: sda-admin dataset create -user SUBMISSION_USER -dataset-id DATASET_ID [ACCESSION_ID ...]
+  Create a dataset from a list of accession IDs and a dataset ID belonging to a given user.
 
 Options:
   -dataset-id DATASET_ID    Specify the unique identifier for the dataset.
@@ -410,8 +410,9 @@ func handleDatasetCommand() error {
 
 func handleDatasetCreateCommand() error {
 	datasetCreateCmd := flag.NewFlagSet("create", flag.ExitOnError)
-	var datasetID string
+	var datasetID, username string
 	datasetCreateCmd.StringVar(&datasetID, "dataset-id", "", "ID of the dataset to create")
+	datasetCreateCmd.StringVar(&username, "user", "", "Username to associate with the file")
 
 	if err := datasetCreateCmd.Parse(flag.Args()[2:]); err != nil {
 		return fmt.Errorf("error: failed to parse command line arguments, reason: %v", err)
@@ -423,7 +424,11 @@ func handleDatasetCreateCommand() error {
 		return fmt.Errorf("error: -dataset-id and at least one accession ID are required.\n%s", datasetCreateUsage)
 	}
 
-	err := dataset.Create(apiURI, token, datasetID, accessionIDs)
+	if username == "" {
+		return fmt.Errorf("error: -user is required.\n%s", datasetCreateUsage)
+	}
+
+	err := dataset.Create(apiURI, token, datasetID, username, accessionIDs)
 	if err != nil {
 		return fmt.Errorf("error: failed to create dataset, reason: %v", err)
 	}