EMPIAR depositor

Command line tool for depositing data into Electron Microscopy Public Image Archive.

How to use

Please follow these steps:

1. Create a JSON file according to the structure provided in the example.

2. Download and install ascp tool.

3. Set the environmental variable for Aspera password to the one that EMPIAR team has provided you with. Please note that this is not the API token from 1) and is a separate password from the one that you create when registering EMPIAR user.

   • On Linux and Mac OS X execute

     export ASPERA_SCP_PASS=<empiar_aspera_password>

   • On Windows execute

     set ASPERA_SCP_PASS=<empiar_aspera_password>

4. Run the script as:

   empiar-depositor [-h] [-e ENTRY_THUMBNAIL] [-r RESUME RESUME] [-i] [-v] EMPIAR_TOKEN JSON_INPUT ASCP_PATH DATA_PATH

Positional arguments:

EMPIAR_TOKEN

EMPIAR API token. Contact EMPIAR team to obtain it.

JSON_INPUT

The location of the JSON with EMPIAR deposition information.

ASCP

The location of the ascp executable. By default it is installed in ~/.aspera/connect/bin directory on Linux machines, in ~/Applications/AsperaConnect.app/Contents/Resources directory on Macs and in C:Users<username>AppDataLocalProgramsAsperaAspera Connectbin on Windows.

DATA

The location of the data that you would like to upload to EMPIAR. It should contain directories that correspond to the image set directories specified in the JSON file.

Optional arguments:

-h, --help

Show help message and exit

-e ENTRY_THUMBNAIL, --entry-thumbnail ENTRY_THUMBNAIL

Thumbnail image that will represent your deposition on EMPIAR pages. Minimum size is 400 x 400, preferred format is png. If none is provided, then the image from the related EMDB entry will be used.

-r ENTRY_ID ENTRY_DIR, --resume ENTRY_ID ENTRY_DIR

Resume Aspera upload or re-deposit an entry. The entry has to be successfully created as specifying EMPIAR entry ID and entry directory is required. All entry metadata will be replaced with the one provided in the JSON file. Aspera transfer will continue from where it stopped.

-i, --ignore-certificate

Activate this flag to skip the verification of SSL certificate.

-v, --version

Show program's version number and exit

Examples:

empiar-depositor 0123456789 ~/Documents/empiar_deposition_1.json ~/Applications/Aspera\ Connect.app/Contents/\ Resources/ascp ~/Downloads/micrographs

empiar-depositor -r 10 ABC123 -e ~/Downloads/dep_thumb.png 0123456789 ~/Documents/empiar_deposition_1.json ~/\ Applications/Aspera\ Connect.app/Contents/Resources/ascp ~/Downloads/micrographs