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Project Archiver

Simple and easy command line tool to archive files at the end of a (research) project (for example for compliance reasons).

It supports:

  • creating md5 hashes for archived files as well as the archives themselves
  • creating a listing of the archived files
  • compression using plzip (LZMA)
  • splitting large archives (several TBs) into smaller, more manageable parts
  • optional encryption using gpg
  • integrity checks of existing archives
  • a good level of parallelization to significantly speed up operations on large archives, in particular on a high performance cluster (HPC).

Installation

Requirements

  • python >= 3.8
  • plzip (available for some package management systems like apt or brew)
  • gnupg (optional, only required for encryption)
  • jdupes (optional, for preparation checks)

Install Python Package

From PyPI:

pip install project-archiver

From GitHub (for developers):

git clone https://github.com/ratschlab/tools-project-archives.git
cd tools-project-archives
pip install -e .

For nicer output on the console, you can optionally install the coloredlogs package

pip install coloredlogs

Usage

Quickstart

Archive Creation

Optionally, verify directory structure before archiving - see more details in Prepare Files for Archiving section

archiver preparation-checks SOURCE_DIR

Create archive

archiver archive --threads 4 SOURCE_DIR ARCHIVE_DIR

Create archives in parts with a part size of at most 500GB (before compression):

archiver archive --threads 4 --part-size 500G SOURCE_DIR ARCHIVE_DIR

For archiving large directories (>few TBs) archiver create allows running the archiving step by step - see section Optimally Creating Large Split Archives

Listing and Extraction

List archive content

archiver list ARCHIVE_DIR

Extract entire archive

archiver extract ARCHIVE_DIR DESTINATION_DIR

Extract single file from archive

archiver extract --subpath testdir/testfile ARCHIVE_DIR DESTINATION_DIR

Integrity Check

Quick integrity check on archive: checking hash of compressed archives match

archiver check ARCHIVE_DIR

Deep integrity check on archive: extracting files and verifying all file hashes match

archiver check --deep --threads 4 ARCHIVE_DIR

Creating an Archive

In the next few sections some more details and recommendations on how to create an archive

Prepare Files for Archiving

First, prepare files for archiving by moving relevant files to a directory. Relevant files may include raw data, intermediate data artifacts, figures, publications, code, container images (e.g. docker or singularity)

README.txt

It is recommended to add a README.txt file to the archive destination directory containing some information about the project.

Here an example template:

[project name]
[short project abstract]

Key People:
[list of collaborators and authors]

Duration:
[start and end year]

Publications:
[publication list]

Relevant Code:
[if not included in archive, reference to where code is located]

Directory Structure:
[overview over directory structure]
e.g. (adapted output of `tree -L 2 -d`)

├── conda      <- conda environments
├── data
│   ├── preprocessed
│   └── varia
├── models
└── reports
Check File Structure

Before attempting to create an archive, it is recommended to verify the file structure to avoid issues when creating the archive or later on using it:

archiver preparation-checks SOURCE_DIR

Among other points, the above command

  • checks you have read access to all files, fix if necessary. Otherwise, the archiving step will fail
  • checks if there are unnecessary files or duplicates
  • checks for broken symlinks
  • looks for absolute symlinks (e.g pointing to a file like /data/myproject/samples/myfile.txt) which should be replaced by relative symlinks (e.g. samples/myfile.txt)

If some check fails, look in the output for suggestions on how to fix it.

Creating the Archive

Not too large archives can directly be created using archiver archive:

archiver archive --threads 4 SOURCE_DIR ARCHIVE_DIR | tee archiving.log

where SOURCE_DIR is the directory tree to be archived and ARCHIVE_DIR is the destination directory for the archive files - see section Archive Package Structure for details on the files generated during archiving.

Larger archives (maybe >1TB) can be split into parts, that is, instead of creating one huge compressed tar file, several tar files are generated. Splitting the archive into parts can simplify file handling as moving large files between systems can be painful. There may also be file size limits on the target system. Furthermore, archive creation, integrity checks and partial extractions can be done faster with a split archive due to parallelization.

Splitting can be done by adding the --part-size argument. The part size is with respect to the uncompressed size. Note, that for already highly compressed data, it is possible that the final compressed files can be slightly larger (e.g + ~1%) than the size specified in --part-size due to the overhead of the compression format.

Refer to archiver archive --help for more details.

Optimally Creating Large Split Archives

For really large archives (perhaps several TBs upwards) it may be beneficial to execute the archive creation workflow step by step. This can help to use available processing resources optimally as the different steps have different resource usage characteristics (I/O and CPU). Also, if a steps fails for some reason, starting from scratch may not be necessary.

The creation workflow looks like this:

  1. archiver create filelist: collects the files to be archived and generates the hash for every file. Parallelization is at file level.
  2. archiver create tar: creates a tar archive and a listing for every part independently. The parallelization is hence over parts.
  3. archiver create compressed-tar: compresses the tar archive. This is very CPU bound and parallelization is over file chunks, where the different parts are processed sequentially. Use as many CPUs as you can spare.

Note, that the create tar and create compressed-tar commands can be invoked to work on a single part only using the --part argument. This can be useful to schedule the processing on different machines.

Here an execution example. Assume you like to archive 2.5TB of data before compression on a machine with 8 available cores using a part size of 500GB (resulting in 5 parts):

archiver create filelist --threads 5 --part-size 500G SOURCE_DIR ARCHIVE_DIR | tee archiving.log
archiver create tar --threads 5 SOURCE_DIR ARCHIVE_DIR | tee -a archiving.log
archiver create compressed-tar --threads 8 ARCHIVE_DIR | tee -a archiving.log

Archive Package Structure

A standard archive directory generated with this CLI-Tool consists of the following files in a new directory:

  • Base archive: project_name.tar.lz
  • Content listing: project_name.tar.lst
  • Content md5 hashes: project_name.md5
  • Archive md5 hash: project_name.tar.md5
  • Compressed archive hash: project_name.tar.lz.md5

Split archives have a similar structure for every part, but contain a 'partX.' as suffix, where X is the part number. So the archive of part 1 would be called project_name.part1.tar.lz. For split archive, there is also a file project_name.parts.txt containing the total number of parts.

Handling of Links

Symlinks

Symlinks are included as is by tar. However, the archiver tool will emit warnings in case of broken symlinks or absolute symlinks. Absolute symlinks are problematic, as in case the archive gets extracted on a different system, absoulte symlinks will likely be broken. It is therefore recommendable to replace absolute symlinks with relative symlinks where the target is expressed relative to the symlink location.

Hardlinks

For standard archives consisting of a single part, hardlinked files are considered separate files in the listings, but as single files by tar.

For split archives, it may be that two hardlinked files end up in different parts and hence appearing in two different tar files. For this reason, it is recommended to replace hardlinks with symlinks to avoid a possible duplication of data.

Compression

Currently, only lzip (LZMA) is supported. It was chosen for its design for long-term archiving providing additional integrity checks and recovery mechansims, see also lzip documentation

GPG encryption

All key-handling is done by the user using GPG. This tool assumes a private key to decrypt an archive exists in the GPG keychain.

Cluster Integration

Parallelism

In case the number of threads/workers is not specified on the command line, the function multiprocessing.cpu_count() is used to determine the number of workers used.

In some environments, this value is not determined correctly. For instance, on some HPC scheduler (e.g. LSF) the value does not represent the amount of CPUs reserved for a job but CPUs available on the whole machine. The correct value may be specified in an environment variable though (on LSF it is LSB_MAX_NUM_PROCESSOR). Setting the environment variable ARCHIVER_MAX_CPUS_ENV_VAR to e.g. LSB_MAX_NUM_PROCESSOR instructs the archiver tool to go look whether the LSB_MAX_NUM_PROCESSOR variable is set and take this number instead.

Development

Testing

# run in project root
python3 -m pytest tests/ -s

Version Bumping

Currently, the example config of bumpversion is used as is, see example commands in bumpversion documentation.