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Configuration

Configuration

Terminology configuration

A single file (web/conf/config_terms.txt) contains all the terminology. The input and search interfaces are completely generated from this definition file, thus defining each of the fields, their input type (checkbox, dropbox, textbox, ...) and the associated controlled vocabulary (ontology and thesaurus by autocompletion, drop-down list according to a list of fixed terms). This is why a configuration and conversion step into JSON format is essential in order to be able to configure all the other modules (example: creation of the MongoDB database schema when starting the application before filling it).

  • Note : The step numbers shown in the figure above are mentioned in brackets in the text below.

TSV to JSON

  • This function is used to generate the terminology definition file in JSON format (config_terms.json) and the corresponding JSON-Schema file (maggot-schema.json) from a tabulated file (1). You can either create a terminology definition file in TSV format from scratch (see below to have more details), or extract the file from the current configuration (see JSON to TSV).

  • Once the terminology definition file has been obtained (2), you can load it and press 'Submit'.

  • Three files are generated (3 & 5):

  • config_terms.json and maggot-schema.json : These files should be placed in the web/conf directory (3). A (re)start of the application must be done in full mode (4) (sh ./run fullstart)
  • config_doc.txt (5) : This file serves as a template for the documentation of the metadata profile. You should edit it with a spreadsheet program, and fill in the description column (6). Then it is used to generate the documentation file in markdown format (see TSV to DOC).

TSV to DOC

  • This function generates the markdown documentation file (doc.md) from the template file (config_doc.txt) which is itself generated from the metadata definition file (config_terms.txt, cf TSV to JSON).

  • Once the template file for the documentation (config_doc.txt) has been edited and documented (6) (see below to have more details), you can load it and press Submit button.

  • The documentation file in markdown format (doc.md) is thus generated (7) and must be placed in the web/docs directory (8). Users will have access to this documentation file via the web interface, in the documentation section, heading "Metadata".

JSON to TSV

  • This function allows you to extract the terminology definition file in TSV format (config_terms.txt) from the current configuration. This allows you to start from this file, either to adapt your own metadata profile or simply to modify it slightly.