sda-admin cli

.github/workflows/code-linter.yaml

@@ -52,4 +52,27 @@ jobs:
         uses: golangci/[email protected]
         with:
           args: -E bodyclose,gocritic,gofmt,gosec,govet,nestif,nlreturn,rowserrcheck -e G401,G501,G107,G115 --timeout 5m
-          working-directory: sda
+          working-directory: sda
+
+  lint_sda_admin:
+    name: Lint sda-admin code
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        go-version: ['1.22']
+    steps:
+      - name: Set up Go ${{ matrix.go-version }}
+        uses: actions/setup-go@v5
+        with:
+          go-version: ${{ matrix.go-version }}
+        id: go
+
+      - name: Check out code into the Go module directory
+        uses: actions/checkout@v4
+
+      - name: Run golangci-lint
+        uses: golangci/[email protected]
+        with:
+          args: -E bodyclose,gocritic,gofmt,gosec,govet,nestif,nlreturn,rowserrcheck -e G401,G501,G107,G115 --timeout 5m
+          working-directory: sda-admin

.github/workflows/test.yml

@@ -86,7 +86,7 @@ jobs:
 
       - name: Get dependencies
         run: |
-          cd sda-download
+          cd sda
           go get -v -t -d ./...
           if [ -f Gopkg.toml ]; then
               curl https://raw.githubusercontent.com/golang/dep/master/install.sh | sh
@@ -104,3 +104,41 @@ jobs:
           file: ./sda/coverage.txt
           flags: unittests
           fail_ci_if_error: false
+
+  test_sda_admin:
+    name: Test SDA Admin
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        go-version: ['1.22']
+    steps:
+
+      - name: Set up Go ${{ matrix.go-version }}
+        uses: actions/setup-go@v5
+        with:
+          go-version: ${{ matrix.go-version }}
+        id: go
+
+      - name: Check out code into the Go module directory
+        uses: actions/checkout@v4
+
+      - name: Get dependencies
+        run: |
+          cd sda-admin
+          go get -v -t -d ./...
+          if [ -f Gopkg.toml ]; then
+              curl https://raw.githubusercontent.com/golang/dep/master/install.sh | sh
+              dep ensure
+          fi
+      - name: Test
+        run: |
+          cd sda-admin
+          go test -v -coverprofile=coverage.txt -covermode=atomic ./...
+
+      - name: Codecov
+        uses: codecov/[email protected]
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          file: ./sda-admin/coverage.txt
+          flags: unittests
+          fail_ci_if_error: false

Makefile

@@ -23,7 +23,7 @@ bootstrap: go-version-check docker-version-check
 		GO111MODULE=off go get golang.org/x/tools/cmd/goimports
 
 # build containers
-build-all: build-postgresql build-rabbitmq build-sda build-sda-download build-sda-sftp-inbox
+build-all: build-postgresql build-rabbitmq build-sda build-sda-download build-sda-sftp-inbox build-sda-admin
 build-postgresql:
 	@cd postgresql && docker build -t ghcr.io/neicnordic/sensitive-data-archive:PR$$(date +%F)-postgres .
 build-rabbitmq:
@@ -34,6 +34,8 @@ build-sda-download:
 	@cd sda-download && docker build -t ghcr.io/neicnordic/sensitive-data-archive:PR$$(date +%F)-download .
 build-sda-sftp-inbox:
 	@cd sda-sftp-inbox && docker build -t ghcr.io/neicnordic/sensitive-data-archive:PR$$(date +%F)-sftp-inbox .
+build-sda-admin:
+	@cd sda-admin && go build
 
 
 go-version-check: SHELL:=/bin/bash
@@ -81,13 +83,16 @@ integrationtest-sda: build-all
 	@PR_NUMBER=$$(date +%F) docker compose -f .github/integration/sda-posix-integration.yml down -v --remove-orphans
 
 # lint go code
-lint-all: lint-sda lint-sda-download
+lint-all: lint-sda lint-sda-download lint-sda-admin
 lint-sda:
 	@echo 'Running golangci-lint in the `sda` folder'
 	@cd sda && golangci-lint run $(LINT_INCLUDE) $(LINT_EXCLUDE)
 lint-sda-download:
 	@echo 'Running golangci-lint in the `sda-download` folder'
 	@cd sda-download && golangci-lint run $(LINT_INCLUDE) $(LINT_EXCLUDE)
+lint-sda-admin:
+	@echo 'Running golangci-lint in the `sda-admin` folder'
+	@cd sda-admin && golangci-lint run $(LINT_INCLUDE) $(LINT_EXCLUDE)
 
 # run static code tests
 test-all: test-sda test-sda-download test-sda-sftp-inbox
@@ -97,3 +102,5 @@ test-sda-download:
 	@cd sda-download && go test ./... -count=1
 test-sda-sftp-inbox:
 	@docker run --rm -v ./sda-sftp-inbox:/inbox maven:3.9.4-eclipse-temurin-21-alpine sh -c "cd /inbox && mvn test -B"
+test-sda-admin:
+	@cd sda-admin && go test ./... -count=1

sda-admin/README.md

@@ -0,0 +1,97 @@
+# sda-admin
+
+`sda-admin` is a command-line tool for managing sensitive data archives. It provides functionalities to list users and files, ingest and set accession IDs for files, and create or release datasets.
+
+## General Usage
+
+```sh
+sda-admin [-uri URI] [-token TOKEN] <command> [options]
+```
+
+## Global Options
+- `-uri URI`
+Set the URI for the API server (optional if the environmental variable `API_HOST` is set).
+- `-token TOKEN`
+Set the authentication token (optional if the environmental variable `ACCESS_TOKEN` is set).
+
+## List all users
+
+Use the following command to return all users with active uploads
+```sh
+sda-admin user list 
+```
+
+## List all files for a specified user
+
+Use the following command to return all files belonging to the specified user `[email protected]`
+```sh
+sda-admin file list -user [email protected]
+```
+
+## Ingest a file
+
+Use the following command to trigger the ingesting of a given file `/path/to/file.c4gh` that belongs to the user `[email protected]`
+
+```sh
+sda-admin file ingest -filepath /path/to/file.c4gh -user [email protected]
+```
+
+## Assign an accession ID to a file
+
+Use the following command to assign an accession ID `my-accession-id-1` to a given file `/path/to/file.c4gh` that belongs to the user `[email protected]`
+
+```sh
+sda-admin file set-accession -filepath /path/to/file.c4gh -user [email protected] -accession-id my-accession-id-1
+```
+
+## 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`
+
+```sh
+sda-admin dataset create -dataset-id dataset001 my-accession-id-1 my-accession-id-2 
+```
+
+
+## Release a dataset for downloading
+
+Use the following command to release the dataset `dataset001` for downloading
+
+```sh
+sda-admin dataset release -dataset-id dataset001
+```
+
+## Show version information
+
+Use the following command to show the version information for sda-admin.
+
+```sh
+sda-admin version
+```
+
+## Help
+
+For detailed usage information about specific commands or options, use:
+
+```sh
+sda-admin help <command>
+```
+
+### Examples 
+
+To get help on the `file` command:
+```sh
+sda-admin help file
+```
+
+To get help on the `file ingest` command:
+
+```sh
+sda-admin help file ingest
+```
+
+To get help on the `dataset create` command:
+
+```sh
+sda-admin help dataset create
+```

sda-admin/dataset/dataset.go

@@ -0,0 +1,57 @@
+package dataset
+
+import (
+	"encoding/json"
+	"fmt"
+	"net/url"
+	"path"
+
+	"github.com/neicnordic/sensitive-data-archive/sda-admin/helpers"
+)
+
+type RequestBodyDataset struct {
+	AccessionIDs []string `json:"accession_ids"`
+	DatasetID    string   `json:"dataset_id"`
+}
+
+// Create creates a dataset from a list of accession IDs and a dataset ID.
+func Create(apiURI, token, datasetID string, accessionIDs []string) error {
+	parsedURL, err := url.Parse(apiURI)
+	if err != nil {
+		return err
+	}
+	parsedURL.Path = path.Join(parsedURL.Path, "dataset/create")
+
+	requestBody := RequestBodyDataset{
+		AccessionIDs: accessionIDs,
+		DatasetID:    datasetID,
+	}
+
+	jsonBody, err := json.Marshal(requestBody)
+	if err != nil {
+		return fmt.Errorf("failed to marshal JSON, reason: %v", err)
+	}
+
+	_, err = helpers.PostRequest(parsedURL.String(), token, jsonBody)
+	if err != nil {
+		return err
+	}
+
+	return nil
+}
+
+// Release releases a dataset for downloading
+func Release(apiURI, token, datasetID string) error {
+	parsedURL, err := url.Parse(apiURI)
+	if err != nil {
+		return err
+	}
+	parsedURL.Path = path.Join(parsedURL.Path, "dataset/release") + "/" + datasetID
+
+	_, err = helpers.PostRequest(parsedURL.String(), token, nil)
+	if err != nil {
+		return err
+	}
+
+	return nil
+}

sda-admin/dataset/dataset_test.go

@@ -0,0 +1,93 @@
+package dataset
+
+import (
+	"errors"
+	"testing"
+
+	"github.com/neicnordic/sensitive-data-archive/sda-admin/helpers"
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/mock"
+)
+
+// MockHelpers is a mock implementation of the helpers package functions
+type MockHelpers struct {
+	mock.Mock
+}
+
+func (m *MockHelpers) PostRequest(url, token string, jsonBody []byte) ([]byte, error) {
+	args := m.Called(url, token, jsonBody)
+
+	return args.Get(0).([]byte), args.Error(1)
+}
+
+func TestCreate_Success(t *testing.T) {
+	mockHelpers := new(MockHelpers)
+	originalFunc := helpers.PostRequest
+	helpers.PostRequest = mockHelpers.PostRequest
+	defer func() { helpers.PostRequest = originalFunc }() // Restore original after test
+
+	expectedURL := "http://example.com/dataset/create"
+	token := "test-token"
+	datasetID := "dataset-123"
+	accessionIDs := []string{"accession-1", "accession-2"}
+	jsonBody := []byte(`{"accession_ids":["accession-1","accession-2"],"dataset_id":"dataset-123"}`)
+
+	mockHelpers.On("PostRequest", expectedURL, token, jsonBody).Return([]byte(`{}`), nil)
+
+	err := Create("http://example.com", token, datasetID, accessionIDs)
+	assert.NoError(t, err)
+	mockHelpers.AssertExpectations(t)
+}
+
+func TestCreate_PostRequestFailure(t *testing.T) {
+	mockHelpers := new(MockHelpers)
+	originalFunc := helpers.PostRequest
+	helpers.PostRequest = mockHelpers.PostRequest
+	defer func() { helpers.PostRequest = originalFunc }() // Restore original after test
+
+	expectedURL := "http://example.com/dataset/create"
+	token := "test-token"
+	datasetID := "dataset-123"
+	accessionIDs := []string{"accession-1", "accession-2"}
+	jsonBody := []byte(`{"accession_ids":["accession-1","accession-2"],"dataset_id":"dataset-123"}`)
+
+	mockHelpers.On("PostRequest", expectedURL, token, jsonBody).Return([]byte(nil), errors.New("failed to send request"))
+
+	err := Create("http://example.com", token, datasetID, accessionIDs)
+	assert.Error(t, err)
+	assert.EqualError(t, err, "failed to send request")
+	mockHelpers.AssertExpectations(t)
+}
+
+func TestRelease_Success(t *testing.T) {
+	mockHelpers := new(MockHelpers)
+	originalFunc := helpers.PostRequest
+	helpers.PostRequest = mockHelpers.PostRequest
+	defer func() { helpers.PostRequest = originalFunc }() // Restore original after test
+
+	expectedURL := "http://example.com/dataset/release/dataset-123"
+	token := "test-token"
+
+	mockHelpers.On("PostRequest", expectedURL, token, []byte(nil)).Return([]byte(`{}`), nil)
+
+	err := Release("http://example.com", token, "dataset-123")
+	assert.NoError(t, err)
+	mockHelpers.AssertExpectations(t)
+}
+
+func TestRelease_PostRequestFailure(t *testing.T) {
+	mockHelpers := new(MockHelpers)
+	originalFunc := helpers.PostRequest
+	helpers.PostRequest = mockHelpers.PostRequest
+	defer func() { helpers.PostRequest = originalFunc }() // Restore original after test
+
+	expectedURL := "http://example.com/dataset/release/dataset-123"
+	token := "test-token"
+
+	mockHelpers.On("PostRequest", expectedURL, token, []byte(nil)).Return([]byte(nil), errors.New("failed to send request"))
+
+	err := Release("http://example.com", token, "dataset-123")
+	assert.Error(t, err)
+	assert.EqualError(t, err, "failed to send request")
+	mockHelpers.AssertExpectations(t)
+}