Physiome Model Repository Platform

This is the Cargo workspace for the PMR project, for building the next generation of Physiome Model Repository.

Build

To build, simply clone this repository, change to that directory, and:

$ cargo build --release

Usage Overview

Once the above command finish successfully, the default binaries will become available.

Currently, only the pmrrepo is of interest, so please run it like so:

$ ./target/release/pmrrepo

Which should automatically create the database file in the Cargo workspace root, using the relative file name defined in the default .env file that also reside there.

To populate that default database file with some useful data for the web application, the sync-pmr2-core.sh helper script may be run to register locally with a selection of real models from the main Physiome Model Repository. Once that completes successfully, build and run the web application using helper script pmrapp.sh, which should replicate this demo instance.

For example:

$ ./sync-pmr2-core.sh
Registering workspace with url ...
...
Syncing commits for workspace with id 17...
$ ./pmrapp.sh
[INFO]: Checking for the Wasm target...
[INFO]: Compiling to Wasm...
...
    Finished release [optimized] target(s) in 46.16s
...
[INFO]: Installing wasm-bindgen...
...
[INFO]: :-) Done in 52.74s
...
    Finished release [optimized] target(s) in 2m 31s
     Running `target/release/pmrapp_server`
serving at: http://0.0.0.0:9380

At this point, open a browser and point it to http://localhost:9380/ and hopefully see the front page of the new prototype demo of the Physiome Model Repository. There is not much to see yet, but hopefully more features will be added in the near future.

Develop

Each member in this workspace are packages that together form the Physiome Model Repository. There will be additional README files within each of them, documenting their use.

One thing of note, the pmrmodel packagemakes use of the sqlx::query! family of macros using offline mode to allow the project to build without requiring a connection to a database. The project will build as normal unless modifications to SQL are required, in which case the sqlx-cli package must be installed, and be used to update the metadata file so that the package may be built with the updated queries.

On systems with sh compatible shell, at the project root, run the following commands instead of cargo sqlx prepare

$ cargo install sqlx-cli
$ ./pmrmodel/sqlx_prepare.sh

Otherwise systems that use batch files (i.e. Windows) will need to replicate those steps manually, or have the database file available.