Package: empiar-depositor
Command line tool for depositing data intoElectron Microscopy Public Image Archive.How to usePlease follow these steps:1. Create a JSON file according to theschema. Anexampleof such a file.2. Download and installascp tooland/or install globus-cli (supported
version 1.7.0) withpipinstallglobus-cli==1.7.0Globus can be used as a separate upload option or as a fallback if Aspera fails.3. Set the environmental variable for EMPIAR transfer 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 executeexportEMPIAR_TRANSFER_PASS=<empiar_transfer_password>On Windows executesetEMPIAR_TRANSFER_PASS=<empiar_transfer_password>Run the script as:empiar-depositor[-h][-aASCP][-gGLOBUS][-f][-eENTRY_THUMBNAIL][-rENTRY_IDENTRY_DIR][-i][-v]EMPIAR_TOKENJSON_INPUTDATAPositional arguments:EMPIAR_TOKENEMPIAR API token. You can generate it athttps://empiar.org/deposition/api_token. Alternatively, instead of the
token you can use your EMPIAR username and provide your password with-poptional argument (see below for more
information).JSON_INPUTThe location of the JSON with EMPIAR deposition information.DATAThe 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,--helpShow help message and exit-pPASSWORD,--passwordPASSWORDUse basic authentication (username + password) instead of token authentication. If no password is provided for this
argument, then the user is prompted for a password.-aASCP,--ascpASCPThe location of the ascp executable. By default it is installed in ~/.aspera/connect/bin directory on Linux machines,
in ~/Applications/Aspera\ Connect.app/Contents/Resources directory on Macs and in
C:\Users\<username>\AppData\Local\Programs\Aspera\Aspera Connect\bin on Windows.-gGLOBUS,--globusGLOBUSUse Globus if Aspera is not specified or Aspera transfer fails. Requirement: globus-cli installed and an endpoint
created. Specify your unique user identifier (UUID) as the input parameter.-f,--globus-force-loginForce login to Globus. Login even if the globus-cli already has valid login credentials. Any existing credentials will
be removed from local storage and globally revoked.-eENTRY_THUMBNAIL,--entry-thumbnailENTRY_THUMBNAILThumbnail 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.-rENTRY_ID ENTRY_DIR,--resumeENTRY_ID ENTRY_DIRResume 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.-guUSERNAME_RIGHTS,--grant-rights-usernamesUSERNAME_RIGHTS-geEMAIL_RIGHTS,--grant-rights-emailsEMAIL_RIGHTS-guORCID_RIGHTS,--grant-rights-usernamesORCID_RIGHTSGrant rights based on usernames, emails or ORCiDs.USERNAME_RIGHTS,EMAIL_RIGHTSandORCID_RIGHTSare
comma separated lists of usernames, emails, ORCiDs and rights in formatusername:rights,email:rightsandorcid:rights. Rights can be 1 - Owner, 2 - View only, 3 - View and Edit, 4 - View, Edit and Submit. There can be
only one deposition owner.-i,--ignore-certificateActivate this flag to skip the verification of SSL certificate.-v,--versionShow program’s version number and exitExamples:empiar-depositor-a~/Applications/Aspera\Connect.app/Contents/Resources/ascp0123456789~/Documents/empiar_deposition_1.json~/Downloads/micrographsempiar-depositor-a~/Applications/Aspera\Connect.app/Contents/Resources/ascp0123456789~/Documents/empiar_deposition_1.json~/Downloads/micrographs-gujohndoe:1,jamessmith:3empiar-depositor-a~/Applications/Aspera\Connect.app/Contents/Resources/ascp0123456789~/Documents/empiar_deposition_1.json~/Downloads/micrographs-gujohndoe:4,jamessmith:1-gejeremycarpenter@email.com:3-go0000-0000-0000-0001:2,0000-0000-1000-0002:4empiar-depositor-r10ABC123-e~/Downloads/dep_thumb.png0123456789-g01234567-89a-bcde-fghi-jklmnopqrstu~/Documents/empiar_deposition_1.json~/Downloads/micrographsempiar-depositor-a~/Applications/Aspera\Connect.app/Contents/Resources/ascpmy_empiar_user-pmy_empiar_password~/Documents/empiar_deposition_1.json~/Downloads/micrographs