Merge branch 'main' into feature/htsget

.github/integration/setup/setup.sh

@@ -16,9 +16,29 @@ if [ ! -f "dummy.ega.nbis.se.pem" ]; then
     chmod 644 keys/dummy.ega.nbis.se.pub dummy.ega.nbis.se.pem
 fi
 
+cp s3cmd-template.conf s3cmd.conf
 output=$(python sign_jwt.py)
 echo "access_token=$output" >> s3cmd.conf
 
+# Create crypt4gh keys for testing the download service
+cat << EOF > c4gh.pub.pem
+-----BEGIN CRYPT4GH PUBLIC KEY-----
+avFAerx0ZWuJE6fTI8S/0wv3yMo1n3SuNTV6zvKdxQc=
+-----END CRYPT4GH PUBLIC KEY-----
+EOF
+
+chmod 444 c4gh.pub.pem
+
+cat << EOF > c4gh.sec.pem
+-----BEGIN CRYPT4GH ENCRYPTED PRIVATE KEY-----
+YzRnaC12MQAGc2NyeXB0ABQAAAAAwAs5mVkXda50vqeYv6tbkQARY2hhY2hhMjBf
+cG9seTEzMDUAPAd46aTuoVWAe+fMGl3VocCKCCWmgFUsFIHejJoWxNwy62c1L/Vc
+R9haQsAPfJMLJSvUXStJ04cyZnDHSw==
+-----END CRYPT4GH ENCRYPTED PRIVATE KEY-----
+EOF
+
+chmod 444 c4gh.sec.pem
+
 # get latest image tag for s3inbox
 latest_tag=$(curl -s https://api.github.com/repos/neicnordic/sensitive-data-archive/tags | jq -r '.[0].name')
 
@@ -66,4 +86,77 @@ do echo "waiting for buckets to be created"
     sleep 10
 done
 
+# Populate database with for testing the download service
+# Insert entry in sda.files
+file_id=$(docker run --rm --name client --network testing_default \
+    neicnordic/pg-client:latest \
+    postgresql://postgres:rootpasswd@postgres:5432/sda \
+    -t -q -c "INSERT INTO sda.files (stable_id, submission_user, \
+        submission_file_path, submission_file_size, archive_file_path, \
+        archive_file_size, decrypted_file_size, backup_path, header, \
+        encryption_method) VALUES ('urn:neic:001-002', 'integration-test', '5baa61e4c9b93f3f0682250b6cf8331b7ee68fd8_elixir-europe.org/main/subfolder/dummy_data.c4gh', \
+        1048729, '4293c9a7-dc50-46db-b79a-27ddc0dad1c6', 1049081, 1048605, \
+        '', '637279707434676801000000010000006c000000000000006af1407abc74656b8913a7d323c4bfd30bf7c8ca359f74ae35357acef29dc5073799e207ec5d022b2601340585ff082565e55fbff5b6cdbbbe6b12a0d0a19ef325a219f8b62344325e22c8d26a8e82e45f053f4dcee10c0ec4bb9e466d5253f139dcd4be', 'CRYPT4GH') RETURNING id;" | xargs)
+
+if [ -z "$file_id" ]; then
+    echo "Failed to insert file entry into database"
+    exit 1
+fi
+
+# Insert entry in sda.file_event_log
+docker run --rm --name client --network testing_default \
+    neicnordic/pg-client:latest \
+    postgresql://postgres:rootpasswd@postgres:5432/sda \
+    -t -q -c "INSERT INTO sda.file_event_log (file_id, event) \
+        VALUES ('$file_id', 'ready');"
+
+# Insert entries in sda.checksums
+docker run --rm --name client --network testing_default \
+	neicnordic/pg-client:latest \
+    postgresql://postgres:rootpasswd@postgres:5432/sda \
+    -t -q -c "INSERT INTO sda.checksums (file_id, checksum, type, source) \
+        VALUES ('$file_id', '06bb0a514b26497b4b41b30c547ad51d059d57fb7523eb3763cfc82fdb4d8fb7', 'SHA256', 'UNENCRYPTED');"
+
+docker run --rm --name client --network testing_default \
+	neicnordic/pg-client:latest \
+    postgresql://postgres:rootpasswd@postgres:5432/sda \
+    -t -q -c "INSERT INTO sda.checksums (file_id, checksum, type, source) \
+        VALUES ('$file_id', '5e9c767958cc3f6e8d16512b8b8dcab855ad1e04e05798b86f50ef600e137578', 'SHA256', 'UPLOADED');"
+
+docker run --rm --name client --network testing_default \
+	neicnordic/pg-client:latest \
+    postgresql://postgres:rootpasswd@postgres:5432/sda \
+    -t -q -c "INSERT INTO sda.checksums (file_id, checksum, type, source) \
+        VALUES ('$file_id', '74820dbcf9d30f8ccd1ea59c17d5ec8a714aabc065ae04e46ad82fcf300a731e', 'SHA256', 'ARCHIVED');"
+
+# Insert dataset in sda.datasets
+dataset_id=$(docker run --rm --name client --network testing_default \
+    neicnordic/pg-client:latest \
+    postgresql://postgres:rootpasswd@postgres:5432/sda \
+    -t -q -c "INSERT INTO sda.datasets (stable_id) VALUES ('https://doi.example/ty009.sfrrss/600.45asasga') \
+        ON CONFLICT (stable_id) DO UPDATE \
+        SET stable_id=excluded.stable_id RETURNING id;")
+
+if [ -z "$dataset_id" ]; then
+    echo "Failed to insert dataset entry into database"
+    exit 1
+fi
+
+# Add file to dataset
+docker run --rm --name client --network testing_default \
+    neicnordic/pg-client:latest \
+    postgresql://postgres:rootpasswd@postgres:5432/sda \
+    -t -q -c "INSERT INTO sda.file_dataset (file_id, dataset_id) \
+        VALUES ('$file_id', $dataset_id);"
+
+# Add file to archive
+s3cmd -c directS3 put archive_data/4293c9a7-dc50-46db-b79a-27ddc0dad1c6 s3://archive/4293c9a7-dc50-46db-b79a-27ddc0dad1c6
+
+# Get the correct token form mockoidc
+token=$(curl "http://localhost:8002/tokens" | jq -r  '.[0]')
+
+# Create s3cmd-download.conf file for download
+cp s3cmd-template.conf s3cmd-download.conf
+echo "access_token=$token" >> s3cmd-download.conf
+
 docker ps

.github/integration/tests/tests.sh

@@ -321,4 +321,22 @@ fi
 
 rm -r downloads
 
+# Download file by using the sda download service
+./sda-cli sda-download -config testing/s3cmd-download.conf -dataset https://doi.example/ty009.sfrrss/600.45asasga -url http://localhost:8080 -outdir test-download main/subfolder/dummy_data.c4gh
+
+# check if file exists in the path
+if [ ! -f "test-download/main/subfolder/dummy_data" ]; then
+    echo "Downloaded file not found"
+    exit 1
+fi
+
+# check the first line of that file
+first_line=$(head -n 1 test-download/main/subfolder/dummy_data)
+if [[ $first_line != *"THIS FILE IS JUST DUMMY DATA"* ]]; then
+    echo "First line does not contain the expected string"
+    exit 1
+fi
+
+rm -r test-download
+
 echo "Integration test finished successfully"

.github/workflows/release.yml

@@ -28,7 +28,7 @@ jobs:
           fi
 
       - name: Run GoReleaser
-        uses: goreleaser/goreleaser-action@v5.1.0
+        uses: goreleaser/goreleaser-action@v6.0.0
         with:
           version: latest
           args: release --rm-dist

.github/workflows/test.yml

@@ -32,7 +32,7 @@ jobs:
         run: go test -v -coverprofile=coverage -covermode=atomic ./...
 
       - name: Codecov
-        uses: codecov/codecov-action@v4.4.1
+        uses: codecov/codecov-action@v4.5.0
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           file: ./coverage

README.md

@@ -174,9 +174,14 @@ If no config is given by the user, the tool will look for a previous login from
 
 ## Download
 
-The SDA/BP archive enables for downloading files and datasets in a secure manner. That can be achieved using the `sda-cli` tool and the process consists of the following two steps
+The SDA/BP archive enables for downloading files and datasets in a secure manner. That can be achieved using the `sda-cli` tool and and it can be done in two ways:
+- by downloading from a S3 bucket (`./sda-cli download`)
+- by using the download API (`./sda-cli sda-download`)
 
-### Create keys
+### Download from S3 bucket
+This process consists of the following two steps: create keys and downloading the file. These steps are explained in the following sections.
+
+#### Create keys
 
 In order to make sure that the files are downloaded from the archive in a secure manner, the user is supposed to create the key pair that the files will be encrypted with. The key pair can be created using the following command:
 ```bash
@@ -186,7 +191,7 @@ where `<keypair_name>` is the base name of the key files. This command will crea
 
 **NOTE:** Make sure to keep these keys safe. Losing the keys could lead to sensitive data leaks.
 
-### Download file
+#### Download file
 
 The `sda-cli` tool allows for downloading file(s)/datasets. The URLs of the respective dataset files that are available for downloading are stored in a file named `urls_list.txt`. `sda-cli` allows to download files only by using such a file or the URL where it is stored. There are three different ways to pass the location of the file to the tool, similar to the [dataset size section](#get-dataset-size):
 1. a direct URL to `urls_list.txt` or a file with a different name but containing the locations of the dataset files
@@ -204,6 +209,19 @@ The tool also allows for selecting a folder where the files will be downloaded,
 ```
 **Note**: If needed, the user can download a selection of files from an available dataset by providing a customized `urls_list.txt` file.
 
+### Download using the download API
+
+The download API allows for downloading files from the archive and it requires the user to have access to the dataset, therefore a [configuration file](#download-the-configuration-file) needs to be downloaded before starting the downloading of the files.
+For downloading files the user also needs to know the download service URL, the dataset ID and the path of the file. Given those four arguments files can be downloaded using the following command:
+```bash
+./sda-cli sda-download -config <configuration_file> -dataset <datasetID> -url <download-service-URL> <filepath_1_to_download> <filepath_2_to_download> ...
+```
+where `<configuration_file>` the file downloaded in the [previous step](#download-the-configuration-file), `<dataset_id>` the ID of the dataset and `<filepath>` the path of the file in the dataset.
+The tool also allows for downloading multiple files at once, by listing their filepaths separated with space and it also allows for selecting a folder where the files will be downloaded, using the `outdir` argument:
+```bash
+./sda-cli sda-download -config <configuration_file> -dataset <datasetID> -url <download-service-url> -outdir <outdir> <filepath_1_to_download> <filepath_2_to_download> ...
+```
+
 ## Decrypt file
 
 Given that the instructions in the [download section](#download) have been followed, the key pair and the data files should be stored in some location. The last step is to decrypt the files in order to access their content. That can be achieved using the following command:

go.mod

@@ -3,7 +3,7 @@ module github.com/NBISweden/sda-cli
 go 1.22.3
 
 require (
-	github.com/aws/aws-sdk-go v1.53.10
+	github.com/aws/aws-sdk-go v1.54.6
 	github.com/manifoldco/promptui v0.9.0
 	github.com/neicnordic/crypt4gh v1.12.0
 	github.com/sirupsen/logrus v1.9.3

go.sum

@@ -71,8 +71,6 @@ golang.org/x/sys v0.20.0/go.mod h1:/VUhepiaJMQUp4+oa/7Zr1D23ma6VTLIYjOOTFZPUcA=
 golang.org/x/term v0.20.0 h1:VnkxpohqXaOBYJtBmEppKUG6mXpi+4O6purfc2+sMhw=
 golang.org/x/term v0.20.0/go.mod h1:8UkIAJTvZgivsXaD6/pH6U9ecQzZ45awqEOzuCvwpFY=
 golang.org/x/text v0.3.0/go.mod h1:NqM8EUOU14njkJ3fqMW+pc6Ldnwhi/IjpwHt7yyuwOQ=
-golang.org/x/text v0.15.0 h1:h1V/4gjBv8v9cjcR6+AR5+/cIYK5N/WAgiv4xlsEtAk=
-golang.org/x/text v0.15.0/go.mod h1:18ZOQIKpY8NJVqYksKHtTdi31H5itFRjB5/qKTNYzSU=
 golang.org/x/tools v0.0.0-20190308174544-00c44ba9c14f/go.mod h1:25r3+/G6/xytQM8iWZKq3Hn0kr0rgFKPUNVEL/dr3z4=
 golang.org/x/tools v0.6.0 h1:BOw41kyTf3PuCW1pVQf8+Cyg8pMlkYB1oo9iJ6D/lKM=
 golang.org/x/tools v0.6.0/go.mod h1:Xwgl3UAJ/d3gWutnCtw505GrjyAbvKui8lOU390QaIU=

main.go

@@ -14,6 +14,7 @@ import (
 	"github.com/NBISweden/sda-cli/htsget"
 	"github.com/NBISweden/sda-cli/list"
 	"github.com/NBISweden/sda-cli/login"
+	sdaDownload "github.com/NBISweden/sda-cli/sda_download"
 	"github.com/NBISweden/sda-cli/upload"
 	"github.com/NBISweden/sda-cli/version"
 	log "github.com/sirupsen/logrus"
@@ -44,6 +45,7 @@ var Commands = map[string]commandInfo{
 	"list":        {list.Args, list.Usage, list.ArgHelp},
 	"htsget":      {htsget.Args, htsget.Usage, htsget.ArgHelp},
 	"login":       {login.Args, login.Usage, login.ArgHelp},
+  "sda-download": {sdaDownload.Args, sdaDownload.Usage, sdaDownload.ArgHelp},
 	"version":     {version.Args, version.Usage, version.ArgHelp},
 }
 
@@ -74,6 +76,8 @@ func main() {
 		err = htsget.Htsget(args)
 	case "login":
 		err = login.NewLogin(args)
+	case "sda-download":
+		err = sdaDownload.SdaDownload(args)
 	case "version":
 		err = version.Version(Version)
 	default: