codtools.cif_cod_deposit

Description

This plugin is specific for cif_cod_deposit script.

Supported codes

• cif_cod_deposit

Inputs

• CifData

  A CIF file.

• Dict

  Contains deposition information, such as user name, password and deposition type:

  • username: depositor’s user name to access the *COD deposition interface;

  • password: depositor’s password to access the *COD deposition interface;

  • deposition-type: determines a type of the deposited CIF file, which can be one of the following:

    • published: CIF file is already published in a scientific paper;

    • prepublication: CIF file is a prepublication material and should not be revealed to the public until the publication of a scientific paper. In this case, a hold_period also has to be specified;

    • personal: CIF file is personal communication.

  • url: URL of *COD deposition API (optional, default URL is http://test.crystallography.net/cgi-bin/cif-deposit.pl);

  • journal: name of the journal, where the CIF is/will be published;

  • user_email: depositor’s e-mail address;

  • author_name: name of the CIF file author;

  • author_email: e-mail of the CIF file author;

  • hold_period: a period (in number months) for the structure to be kept on-hold (only for deposition_type == 'prepublication').

Outputs

• Dict

  Contains the result of deposition:

  • output_messages: lines of output messages and/or errors. For more information refer to outputs for codtools.cif_base plugin.

  • status: a string, one of the following:

    • SUCCESS: a deposition is successful, newly assigned *COD number(s) is/are present in output_messages field;

    • DUPLICATE: submitted data is already in the *COD database thus is not deposited once more;

    • UNCHANGED: the redeposition of the data is unnecessary, as nothing was changed in the contents of file to be replaced;

    • INPUTERROR: an error, related to the input, has occurred, detailed reason may be present in output_messages field;

    • SERVERERROR: an internal server error has occurred, detailed reason may be present in output_messages field;

    • UNKNOWN: the result of the deposition is unknown.

Errors

Run-time errors are returned line-by-line in the output_messages field of Dict object.