# The formatting in this example file is intentionally sloppy to illustrate
# the essential features and to point out what has no effect.
# Lines beginning with "#" are ignored.
# Empty lines are ignored
#
# It is critical to have the term being defined immediately before an equals
# symbol "=". The defining term(s) are to follow the equals symbol.
# Multiple defining terms can be separated with one or more blank characters,
# commas, semicolons, or newline characters. Parentheses may be used for
# readability, but they are ignored.
#
# In many cases the defining term will need to be in quotes because they will
# have characters that would serve to break up the definition into multiple
# tokens. For example http://deepthought:8080/labkey would become a meaningless
# collection of four terms: http, deepthought, 8080, and labkey.
#
# center is a term used to tell the application which features are to be
# available and to allow custom branding with image files.
#
# The rest of the terms are used by the Rlabkey package and the labkey-api-r.
# lkPedColumns are the names of the columns used by the LabKey instance
# being queried.
# mapPedColumns are a one to one mapping of the lkPedColumns to the column
# names used by the nprcgenekeepr package.
#
# Note: lkPedColumns is center-specific. This SNPRC example uses the flat parent
# columns "dam" and "sire", which exist as direct columns on the SNPRC
# demographics table. An ONPRC instance instead uses the lookup-traversal form
# "Id/parents/dam" and "Id/parents/sire", which resolves to the curated
# genetic-preferred parentage. (The package's built-in no-config default uses
# the ONPRC form; see getSiteInfo().) Set lkPedColumns to the form your center's
# LabKey instance exposes; mapPedColumns is unchanged.

# To use this file or one similar, it must be renamed to "_nprcgenekeepr_config"
# for users of Microsoft Windows operating systems and ".nprcgenekeepr_config"
# for other operating systems.
# It must be edited so that the various terms are appropriately defined.
# The file is to be place in the user's home directory.

# Authentication. nprcgenekeepr authenticates to LabKey in one of two ways,
# tried in this order of precedence:
#   1. An API key. Supply it in the environment variable
#      NPRCGENEKEEPR_LABKEY_APIKEY, or as the optional "apiKey" token below.
#      The environment variable wins when both are set. Keep API keys out of
#      shared/version-controlled files. API keys must be enabled by a LabKey
#      site administrator before they can be created.
#   2. A netrc file. If no API key is found, an appropriately configured
#      "_netrc" (Windows) or ".netrc" (non-Windows) file is used, as described
#      at https://www.labkey.org/Documentation/wiki-page.view?name=netrc
# If neither is found, setLabKeyDefaults() stops with a clear error.
#
# Optional API-key token (uncomment and set to use the config-file path):
# apiKey = "paste-your-labkey-api-key-here"

# Optional species reproductive-parameter overrides (issue #73 Part 2).
# By default the Genetic Value Analysis uses the bundled per-species minimum
# breeding ages and gestation windows (the speciesGestation table). A colony
# can override them with up to three optional keys; all are absent by default
# and any that is absent keeps the bundled value.
#
#   speciesOverridesPath -- path to a CSV with a header row and the four
#     columns species, gestation, minMaleBreedingAge, minFemaleBreedingAge
#     (column order is matched by name). List only the species you want to
#     change: each listed species is MERGED onto the bundled table, so every
#     unlisted species keeps its bundled value. gestation is whole days
#     (integer); the breeding-age columns are years (numeric, so 2.5 is exact).
#   minBreedingAgeDefault -- numeric fallback breeding age (years) for a species
#     not found in the table (built-in default 2).
#   gestationDefault -- integer fallback gestation window (days) for a species
#     not found in the table (built-in default 210).
#
# Example (uncomment and edit; keep the CSV path unquoted-friendly, i.e. no
# spaces or commas in the path):
# speciesOverridesPath = "/home/you/colony_species_overrides.csv"
# minBreedingAgeDefault = 2
# gestationDefault = 210


center = "SNPRC"
 baseUrl = "http://deepthought:8080/labkey"
 schemaName = "study"
 folderPath = "/snprcEHR"
 queryName = "demographics"
lkPedColumns = ("Id", "gender", "birth", "death",
              "lastDayAtCenter", "dam", "sire")
mapPedColumns = ("id", "sex", "birth", "death",
  "exit", "dam", "sire")
