Sparrow for the WiscAr lab

This installation of Sparrow powers the WiscAr lab's instance. It contains customized importers and configurations for the lab's data types.

Installation

Currently, Sparrow is included as a Git Submodule. This pins Sparrow to the particular version that is running for the WiscAr lab.

The installation steps closely follow those for setting up Sparrow with default parameters, but differ slightly because Sparrow is itself a submodule. First, clone this repository from Github. Then, within the created directory, run git submodule update --init --recursive. This will check out Sparrow and all of its submodules in a single step.

As in the general instructions, linking the sparrow command-line executable onto your path with sudo ln -s Sparrow/bin/sparrow /usr/local/bin will allow you to run the Sparrow command-line application.

The sparrow-config.sh file in this repository contains configuration for WiscAr's version of Sparrow. It will be automatically sourced anytime you run sparrow in this repository's directory or a subdirectory. You will need to create a file sparrow-config.overrides.sh in this directory containing application secrets:

export MAPBOX_API_TOKEN=<your-api-token>
export SPARROW_SECRET_KEY=<example>

You can also override other Sparrow environment variables in this file.

Updating Sparrow

Sparrow can be updated by checking out the desired version within the Sparrow submodule, and running git submodule update --init --recursive to make sure any dependencies stay in sync. When updating, you may need to run a database migration [more info on that soon].

Getting data

Restoring from a database dump

The state of an existing Sparrow installation can be restored using the command sparrow db-import <your-database.pg-dump>.

Importing MAP spectrometer data

MAP spectrometer data can be imported using the sparrow import-map command. The MAP spectrometer data archive is expected to be available within this directory at Data/MAP-Irradiations.

Bulk metadata import

Metadata can be imported using the command sparrow import-metadata. This currently expects a file Data/WiscAr_metadata.xlsx within this repository.

Todo

• Implement Noblesse spectrometer import
• Implement importer for PyChron interpreted ages
• Switch to number-based versioning instead of including the Sparrow submodule