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Configuration file - structure and definitions#

MINERVA projects can have a complex structure (read about project structure here) and the accompanying configuration file (always named config.json) allows to integrate them, and pre-define configuration options that will become available on project file (.zip) upload.

The configuration file has the following structure:

• maps - an array of entries, one for each diagram in the project .zip file, both root and submap. Each entry contains the following keys:
  • custom_elements - an array of entries, one for each species alias (read about aliases here) with a defined function. Each entry contains the following keys:
    • element_id (string): species alias of the element in the corresponding map
    • immediate_link (string): an URL to which the user will be redirected on click of this element
    • glyph_file_name (string): a glyph (custom graphics) to be displayed for this element; refers to one of the files in glyphs subdirectory (read more about glyphs)
    • submap (string): a submap to which this element should be linked, submap filename without its extension (read more about submaps).
  • default_center_x, default_center_y (double): default starting X and Y coordinates for this diagram
  • default_zoom_level (integer): default starting zoom level for this diagram; depends on the maximum size of the diagram
  • max_zoom_levels (integer): maximum zoom level allowed for this diagram; depends on the maximum size of the diagram
  • name (string): a diagram name for which this configuration is assigned; filename without its extension
• sbgn (true|false): a flag whether diagrams of this project should be displayed in SBGN style; false means CellDesigner style
• disease (string): an identifiers.org url pointing to a MeSH disease identifier
• organism (string): an identifiers.org url pointing to a Taxonomy identifier
• name (string): name of the project in MINERVA
• version (string): version of the project
• notify_email (string): an email to which project updates are sent about finished project upload and removal
• license: a license object for the contents of the project; a key - value pair with
  • name (string): predefined license string; available license strings are listed below
• custom_license_name (string): a custom license name, if none of the predefined ones are sufficient
• custom_license_url (string): URL to custom license conditions
• source_git_repository (string): link to source git repository if the project was loaded from git
• source_git_branch (string): name of source git repository branch if the project was loaded from a git branch

Available defined licenses#

• “CC0 1.0 Universal”
• “Creative Commons Attribution 4.0 International Public License”
• “Creative Commons Attribution-ShareAlike 4.0 International Public License”
• “Creative Commons Attribution-NonCommercial 4.0 International”
• “Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International Public License”
• “Creative Commons Attribution-NoDerivatives 4.0 International Public License”
• “Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International Public License”

See also https://minerva-service.lcsb.uni.lu/minerva/api/licenses/.

An example configuration file#

Below is a complete JSON structure for an example project. A short summary:

• the project has two maps, named submap_example and advanced_map_example
• submap_example has a default center XY in [100.0,100.0], default zoom of 2, and max zoom level of 2
• advanced_map_example also defines default center and max and default zoom levels; it has four custom elements:
  • glyphs: the element with alias ca1 uses glyph glyphs/g1.png, the element with alias sa11 uses glyph glyphs/g2.png
  • immediate links: the element with alias sa8 redirects to URL “https://disease-maps.io/”
  • submaps: the element with alias sa13 points to the submap submap_example
• the project is displayed in CellDesigner style, and is annotated with disease MeSH D010300, and organism 9606
• name, email and version are provided
• contents are distributed under “Creative Commons Attribution 4.0 International Public License”
• the project was uploaded locally (git repository is null)

{
    "maps": [
        {
            "custom_elements": [],
            "default_center_x": 100.0,
            "default_center_y": 100.0,
            "default_zoom_level": 2,
            "max_zoom_levels": 2,
            "name": "submap_example"
        },
        {
            "custom_elements": [
                {
                    "element_id": "sa11",
                    "immediate_link": null,
                    "glyph_file_name": "glyphs/g2.png",
                    "submap": null
                },
                {
                    "element_id": "ca1",
                    "immediate_link": null,
                    "glyph_file_name": "glyphs/g1.png",
                    "submap": null
                },
                {
                    "element_id": "sa8",
                    "immediate_link": "https://disease-maps.io/",
                    "glyph_file_name": null,
                    "submap": null
                },
                {
                    "element_id": "sa13",
                    "immediate_link": null,
                    "glyph_file_name": null,
                    "submap": "submap_example"
                }
            ],
            "default_center_x": 10.0,
            "default_center_y": 10.0,
            "default_zoom_level": 2,
            "max_zoom_levels": 3,
            "name": "advanced_map_example"
        }
    ],
    "sbgn": false,
    "disease": "https://identifiers.org/mesh:D010300",
    "organism": "https://identifiers.org/taxonomy:9606",
    "name": "advanced_map",
    "version": "v0.1",
    "notify_email": "my@email.com",
    "custom_license_name": "",
    "custom_license_url": "",
    "source_git_repository": null,
    "source_git_branch": null,
    "license": {
        "name": "Creative Commons Attribution 4.0 International Public License"
    }
}