Configuration

The configuration file

Most configuration is in the main configuration file.

Adding a Spotlight

See the main Spotlight configuration docs

Adding a new external reference

At the moment there are two potential files to edit to add a new external reference, the config file and update_generated_files.sh.

Edit the "external_gene_references" section in the main config file and add a new configuration. If the database has an entry in the GO.xrf_abbs file, add a "go_xrf_abbrev" field to the new configuration that matches the "abbreviation" in GO.xrf_abbs. Then add the ID of the external DB to update_generated_files.sh.

If there isn't a GO.xrf_abbs entry add a url field to the new configuration.

See the config file page for more detail.

update_generated_files.sh

Location: https://github.com/pombase/website/blob/master/etc/update_generated_files.sh

The "abbreviation" from the GO.xrf_abbs needs to be added to this line:

ABBREVS="AGI_LocusCode CDD DDJB EC ECOGENE EMBL ...

QuiLT / visualisation tool

The configuration is in the main website config file (pombe-embl/website/pombase_v2_config.json in SVN). Look for:

  "gene_results": {
    "visualisation": {
       "columns": {
       } 
    }
  }

The columns section is a list with one element for each column. The order of the elements is the order the columns are displayed.

The QuiLT columns config

Each column has these settings:

• name - the internal name for this column which is not displayed
• display_name - the name shown in the website
• column_type - can be:
  • "attribute" - for values that are strings
  • "ortholog"
  • "ontology_term" - for data with a term ID and a name
• attr_values - see below

The attr_values config

The attr_values field is a list which specifies the order and colour of values in the tool.

• name - the value from the database, eg. "viable", "depends_on_conditions" or "DNA metabolic process
• display_name - the text to show to the user for this value, eg. if the server returns "depends_on_conditions" we display "viable". This is an optional field. If not set, the name is shown instead.
• color - the colour to use for this block in the tool
• termid - when the column_type is "ontology_term", this is a ontology ID corresponding to the name