configuration

Configuration

There are some environmental variables that peyotl is sensitive to. But, for the most part, configuration is done using config files. The default location for the config file is ~/.peyotl/config, however you can override that by have a variable in your environment called PEYOTL_CONFIG_FILE which holds the full path to the config file that you'd like to use.

The syntax for the config file is the standard INI file format.

Bootstrapping your configuration

The easiest way to get a framework for a config file is to copy the example dot_peyotl directory to the default location:

$ cp extras/dot_peyotl ~/.peyotl

and then edit ~/.peyotl/config in your text editor to reflect the paths to the parent directory of the phylesystem, then the peyotl library can find your local copy of phylesystem repos.

Logging configuration

If PEYOTL_LOGGING_LEVEL is in the environment, then the behavior of the log is determined by environmental variables:

• PEYOTL_LOG_FILE_PATH filepath of log file (StreamHandler if omitted)
• PEYOTL_LOGGING_LEVEL (NotSet, debug, info, warning, error, or critical)
• PEYOTL_LOGGING_FORMAT "rich", "simple" or "None" (None is default)

Otherwise, these logger settings are now controlled by a ~/.peyotl/config or the peyotl/default.conf file (packaged inside the peyotl package. The content to configure the logger looks like:

[logging]
level = debug
filepath = /absolute/path/to/log/file/here
formatter = rich

You probably want to replace the default behavior by specifying PEYOTL_LOGGING_LEVEL or having a ~/.peyotl/config file.

API wrappers

Peyotl has wrappers to make it easier to communicate with Open Tree of Life web services. Because we use peyotl in testing the services as we deploy, the domains where the APIs are configurable:

phylesystem_api = http://api.opentreeoflife.org
oti = http://api.opentreeoflife.org
taxomachine = http://api.opentreeoflife.org
treemachine = http://api.opentreeoflife.org

Phylesystem

If you are performing operations that use a local version of the phylesystem git document store, you need to tell peyotl where to find the phylsystem repo. If the environmental variable PHYLESYSTEM_PARENT is not set then the config file will be used:

[phylesystem]
parent = /home/username/phylesystem/shards

Peyotl will treat any git directory in this parent that has a study subdirectory as if it was a shard of phyleystem.