Galvalanyser User Guide

For help on setting up the Galv server and Harvesters, see the First Time Quick Setup guide.

Galv server

Once set up, the Galv server instance should not need attending to. To set it up, all you need to do is change the .env file’s VIRTUAL_HOST_ROOT and LETSENCRYPT_EMAIL variables to your domain name and email. When you’ve verified that it works, you can also set LETSENCRYPT_TEST to false to generate real SSL certificates that you do not need to manually accept. It exposes two webservers: the frontend on the main domain and the backend on its api subdomain.

User accounts

User accounts are created via the Web frontend. Users can be assigned to Teams by Lab and Team administrators.

Permissions

Permissions are based on Lab and Team membership.

Users can be assigned to a Team by a Lab administrator or Team administrator. Lab administrators can be appointed by the Galv server administrator or other

Harvester access is based on Lab membership. You are a member of any Lab that you are a member of a Team for. Having access to a Harvester means that you can create Monitored paths on that Harvester for your Team.

Resources, e.g. cells and equipment, are owned by the Team that created them. They use a permission table to determine who can view and edit them.

Permission table (default | alternative) :header: “User role”, “Action”, “Allowed”

Team admin	Create	yes
Team admin	Read	yes
Team admin	Update	yes
Team admin	Delete	yes
Team member	Create	yes
Team member	Read	yes
Team member	Update	yes | no
Team member	Delete	yes | no
Lab user	Create	no
Lab user	Read	yes | no
Lab user	Update	no
Lab user	Delete	no
Approved user	Create	no
Approved user	Read	yes | no
Approved user	Update	yes | no
Approved user	Delete	no
Guest user	Create	no
Guest user	Read	yes | no
Guest user	Update	no
Guest user	Delete	no

An approved user is a user who is a member of any Lab (not necessarily the Lab that the Team belongs to).

REST API

Endpoints are written as absolute paths starting from the Galv server address, so to reach the /harvesters/ endpoint for a Galv server located at http://api.localhost, you would go to http://api.localhost/harvesters/.

API Spec

The REST API provides a browsable interface at /spec/swagger-ui/. Its OpenAPI spec can be downloaded from /spec/. Spec download defaults to .yml format, but .json is available from /spec/?format=json.

Static versions of this spec can be downloaded directly from this website:

• .yml format

• .json format

Browsable API

The browsable API provided by Django REST Framework is not fully functional, but does provide a relatively useful way to browse the raw data on the REST API. It is provided at the base address (endpoint /), and provides its own list of available endpoints.

Web frontend

The primary tool for interacting with the REST API is the web frontend. This is designed to provide a user-friendly way to view and edit Harvesters, Monitored paths, Datasets and their metadata.

The web frontend is accessed via a User account, and allows new user accounts to be created and approved by existing users. Each user’s view of the web frontend is customised to only include information relevant to them.

Datasets page

When first successfully logging in with an (approved) account, the user will land on the Datasets page. This page lists information about any Datasets that have been imported from files in a Monitored path that the user has access to.

The first time you log in, this is likely to be blank. Once some datasets have been imported, you will see them listed here and you will be able to edit their metadata.

Each dataset can be described in terms of its name and type, a purpose selected from a pre-populated list, and may be associated with the particular Cell that generated it, as well as any Equipment that was used.

Data view

Clicking the magnifying glass icon for a dataset allows you to inspect the data. This will bring up two buttons which provide boilerplate code for accessing the data using the Python client or MATLAB, as well as a plot of the voltage and ampage of the cell over the duration of the test.

Additional columns in the data can be added to the preview graph by clicking on their names.

Harvesters page

The Harvesters page lists Harvesters that you have access to, either because you are an administrator of that Harvester, or because you are a user or administrator on one or more of the Harvester’s Monitored paths.

If you are an administrator on the Harvester, you will be able to modify the Harvester properties, changing the Harvester name or the sleep time. Sleep time governs how long the Harvester spends idle between harvest cycles.

There will be an additional section below the monitored paths section that allows you to view or edit the harvester program’s environment variables according to your permissions.

Monitored paths view

Click on the magnifying glass icon to view the selected Harvester’s Paths. The Path view shows the Monitored paths on the Harvester that you can access. If you have sufficient permissions, you will be able to alter Path details, including the directory path, the length of time files must be stable before attempting import, and user permissions.

File view

Click on the magnifying glass icon to view the Files found in the Monitored path. These are read-only because their properties are directly dependent on the actual files in the monitored directory. If any file has failed to import, the last error associated with that import will appear when you mouse-over the IMPORT FAILED state.

If for any reason you want to force the harvester to attempt to import a file that has failed to import correctly, you can do so by clicking the refresh button in the ‘Force Re-import’ column.

Files that have been successfully imported will show at least one linked Datasets. Once you have some, your initial Dataset view will be populated and you can add metadata to your dataset.

Cell page

Each dataset will be generated by a specific cell. The Cell page is where you can provide information about cells, which you can then link to their datasets in the Datasets page.

The majority of cell properties are grouped together in a Cell family. The family contains generic information about name, manufacturer, form factor, chemistry, and capacity and weight statistics. For any cell family that is not currently in use, you can edit its properties. You can also create new cell families.

Once you have a cell family that you would like to create a cell for, click on the magnifying glass icon to view its cells. A cell should have a unique identifier which should be a globally unique value that specifically identifies that cell. A good choice is to use the serial number of the physical cell you are describing. Cells may also have display names so that they are easier to identify when adding metadata to datasets. Where cells are not in use by a dataset, you can edit their unique identifiers and display names.

Equipment page

Equipment can be defined on the equipment page. Equipment has a name and a type, and these can be edited for any equipment that is not in use by a dataset.

Python client

The best way to access the data is via the Python API client. This provides read-only access to datasets and their metadata, and allows you to write reproducible analysis scripts that do not require local storage to run their analyses.

You can download the latest Python API client here.

Harvesters

Harvesters are standalone programs that run continually in Docker containers. Each Harvester has a set of directories called Monitored paths that it watches for changes. When files appear in those paths, the Harvester reports the size to the Galv server. If the file size has been stable for long enough, the Harvester will attempt to import the dataset, sending its metadata and parsed data to the Galv server.

At the beginning of each cycle, the Harvester checks in with the Galv server and updates its configuration if it has been changed.

Monitored paths

Monitored paths are directory paths relative to the Harvester container. It is a good idea to use Docker’s volume mounting to provide easily reachable paths to the Harvester which can then be registered as Monitored paths.

Monitored paths have a Python Regular Expression that is used to match files in the directory (the default is .*). The expression is applied to the filename after the Monitored path itself. If your Monitored path is /data and your regular expression is ^[a-z]+\.csv$, then the Harvester will match files like /data/abc.csv and /data/def.csv. The Monitored path regex can be used to group files with particular extensions, with a particular format to their names, or to identify subdirectories (although the subdirectories could be added as separate Monitored paths).

Datasets

Files that are stable for long enough are parsed by the Harvester. If the file is suitable for parsing, its metadata will be sent to the Galv server and a Dataset will be constructed to house the data.

The file’s data will then be extracted into Galv’s column-value format and sent to the server. The column-value format means that column metadata is abstracted away, allowing every column to be stored as a series of numbers. Columns that contain strings generate an encoding map that is used to restore the values on demand. This method of storing data means that large quantities of data can be stored in the database relatively rapidly.

Datasets’ metadata can be edited in the web frontend’s Datasets page, and the data downloaded directly using the Python client.