dxda

dx-download-agent

CLI tool to manage the download of files from DNAnexus

Quick Start

To get started with dx-download-agent, download the the latest pre-compiled binary from the release page. The download agent takes a BZ2-compressed JSON manifest file that describes, at minimimum, the following information for a download, for example:

{
  "project-AAAA": [
    {
      "id": "file-XXXX",
      "name": "foo",
      "folder": "/path/to",
      "parts": {
        "1": { "size": 10, "md5": "49302323" },
        "2": { "size": 5,  "md5": "39239329" }
      }
    },
    {
      "id": "file-YYYY",
      "name": "foo",
      "folder": "/path/to",
      "checksumType": "CRC64NVME"
      "parts": {
        "1": { "size": 10, "checksum": "12xUBUlUwUM=" },
      }
    },
    "..."
  ],
  "project-BBBB": [ "..." ]
}

Before starting a download process, first generate a DNAnexus API token that is valid for a time period that you plan on downloading the files. Store it in the following environment variable:

export DX_API_TOKEN=<INSERT API TOKEN HERE>

If no API token is provided, the download agent will look to the ~/.dnanexus_config/environment.json also used by the dx-toolkit.

To start the download:

dx-download-agent download exome_bams_manifest.json.bz2
Obtained token using environment
Creating manifest database manifest.json.bz2.stats.db
Required disk space = 1.2TB, available = 3.6TB
Logging detailed output to: manifest.json.bz2.download.log
Preparing files for download
Downloading files using 8 threads
Downloaded 11904/1098469 MB     124/11465 Parts (104.0 MB written to disk in the last 60s)

A continuous report on download progress is written to the screen. Prior to starting the data transfer, a check is made to see that there is sufficient disk space for the entire list of files. If not, an error is reported, and nothing is downloaded. Download speed reflects not only network bandwidth, but also the IO capability of your machine.

A download log contains more detailed information about the download should an error occur. If an error does occur and you do not understand how to deal with it, please contact [email protected] with the log file attached and we will assist you.

Please note that rerunning dx-download-agent download command will NOT re-download any previously downloaded files that were subsequently moved, deleted or modified. Please run dx-download-agent inspect (described below) to detect any changes to previously downloaded files and mark them for re-download. See Moving downloaded files for more details.

You can query the progress of an existing download in a separate terminal

dx-download-agent progress exome_bams_manifest.json.bz2

and you will get a brief summary of the status the downloads:

21.6 MB/sec	1184/27078 MB	18/327 Parts Downloaded and written to disk

To check the integrity of the downloaded files, you can run

dx-download-agent inspect exome_bams_manifest.json.bz2

This command will perform an inspection of the files and ensure that their MD5sums match the manifest. If a file is missing or an MD5sum does not match, the download agent will report the affected files and you can then run dx-download-agent download again to re-download the affected files.

Execution options

• -num_threads (integer): maximum # of concurrent threads to use when downloading or inspecting files

For example, the commmand

dx-download-agent download -num_threads=20 exome_bams_manifest.json.bz2

will create a worker pool of 20 threads that will download parts of files in parallel. A maximum of 20 workers will perform downloads at any time. Rate-limiting of downloads can be controlled to an extent by varying this number.

Manifest stats database spec

Information about what parts have been downloaded is maintained in a sqlite3 database file that contains similar information as to what's in the JSON file format plus an additional bytes_fetched field.

Table name: manifest_stats

Fields (all fields are strings unless otherwise specified)

• file_id: file ID for file part
• project: project ID for file part
• name: name of file
• folder: folder containing file on DNAnexus
• part_id (integer): part ID for file
• md5: md5sum for part ID
• size (integer): size of the part
• block_size (integer): primary block size of file (assumed equal to size except for the last part)
• bytes_fetched (integer <= size): total number of bytes downloaded
• checksum_type (optional): type of checksum used (e.g. CRC64NVME, CRC32C, CRC32, SHA256, SHA1)
• checksum (optional): checksum value for the part ID if not using md5

It is up to the implementation to decide whether or not bytes_fetched is updated in a more coarse- vs. fine-grained fashion. For example, bytes_fetched can be updated only when the part download is complete. In this case, its values will only be 0 or the value of size.

The manifest includes four fields for each file: file_id, project, name, and parts. If all four are specified, the file is assumed to be live and closed, making it available for download. If the parts field is omitted, the file will be described on the platform. Bulk describes are used to do this efficiently for many files in batch. Files that are archived or not closed cannot be downloaded, and will trigger an error.

It is possible to download DNAx symbolic links, which do not have parts. The required fields for symbolic links are file_id, project, and name. Note that a symbolic link has a global MD5 checksum, which is checked at the end of the download.

Running using Docker

Aside the self-contained Go binary we provide also Dockerized version. It can be used in a very similar manner as a standalone executable with exception of neccessity to mount your local folder and to provide your DX API token.

Currently, we offer following image tags:

• latest - the most recent build of master branch
• 0.5.11, 0.5.12, ... - dedicated tags for each release (starting from 0.5.11)
• <commit_hash> - development builds for each commit on master branch

Example usage:

$ docker run -v $PWD:/workdir -w /workdir -e DX_API_TOKEN=$DX_API_TOKEN dnanexus/dxda:latest download -max_threads=20 manifest.json.bz2

where:

• $PWD is a path to directory on your computer to download files to
• DX_API_TOKEN is a token to access our platform (see Quick start)

Proxy and TLS settings

To direct dx-download-agent to a proxy, please set the HTTP_PROXY environment variable to something like export HTTP_PROXY=hostname:port. HTTPS_PROXY is also supported.

By default, dx-download-agent uses certificates installed on the system to create secure connections. If your system requires an additional TLS certificate and the dx-download-agent doesn't appear to be using a certificate installed on your system, there are two options in order of preference. First, set the DX_TLS_CERTIFICATE_FILE environment variable to the path of the PEM-encoded TLS certificate file required by your parent organization. As a last-resort, you can connect insecurely by avoiding certificate verification all together by setting DX_TLS_SKIP_VERIFY=true. Use this for testing purposes only.

Creating and filtering manifest files

For convenience, the create_manifest.py file in the scripts/ directory is the recommended way to create manifest files for the download agent. This script requires that the dx-toolkit is installed on your system and that you are logged in to the DNAnexus platform. An example of how it can be used:

python3 create_manifest.py "Project:/Folder" --recursive --output_file "myfiles.manifest.json.bz2"

Here, a manifest is created for recursively all files under the project name Project and in the folder Folder.

The manifest can be subsequently filtered using the filter_manifest.py script. For example, if you want to capture files in a particular folder (e.g. Folder) with testcall in them (e.g. /Folder/ALL.chr22._testcall_20190222.genotypes.vcf.gz), you can run the command:

$ python3 filter_manifest.py manifest.json.bz2 '^/Folder.*testcall.*'

where the second argument given to the script is a regular expression on the entire path (folder + filename).

Splitting manifest files

In some cases it may be desirable to split the download manifest into multiple manifest files for testing purposes or to manage multiple downloads of an entire data set across different environments. To split the file, we provide a simple Python utility that requires no additional packages in the scripts/ directory. For example, executing the command:

python3 scripts/split_manifest.py manifest.json.bz2 -n 100

will create manifest files containing each containing 100 files per project. For example if there are 300 total files in manifest.json.bz2, the output of this command will create three files named: manifest_001.json.bz2, manifest_002.json.bz2, and manifest_003.json.bz2. Each of these files can be used independently with the download agent.

Development environment

This repository can be used directly as a Go module as well. In the cmd/dx-download-agent directory, the dx-download-agent.go file is an example of how it can be used.

For developing and experimenting with the source inside isolated Docker environment, the Dockerfile in this repository may be a good start.

Moving downloaded files

After successfully downloading (and optionally inspecting post-download) it should be safe to move files to your desired location.

WARNING: In general we advise not to move files during the course of a download but moving them could be safe in certain special cases.The download agent works by maintaining a lightweight database of what parts of files have and havent been downloaded so that is what it primarily operates off of. This means that even if you move files the download agent won’t realize it until you run the inspect sub command that performs post-download checks for file integrity on disk. The inspect command will notice the files are missing, update the database, and when you re-issue a download command attempt to download them again. Therefore, if you move completed files and don’t run the inspect subcommand, the download agent should continue from where it left off. This being said, there is a danger in moving files is if a file download is not yet complete. In that case you will have moved an incomplete file.

Additional notes

• Only objects of class File in the closed state can be downloaded.

Support

For any support, bugs, or suggestions please contact [email protected]