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RUST_API.md

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Rust API Profile

  • Use this profile if your microservice needs: ORM, API, LAMBDA, SQS

App

  • Consider building a microservice: rust-api

Quickstart

Assuming you already have the Rust toolchain installed on your system, otherwise install it via:

curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh

For development edit and compile loop, use the cargo-watch crate:

$ cargo install cargo-watch     # if not installed previously
$ cargo watch -c -w src -x run  # Watches "src" dir, eXecutes "cargo run"

   Compiling rust-api v0.1.0 (/Users/rvalls/dev/umccr/orcabus/skel/rust-api)
    Finished dev [unoptimized + debuginfo] target(s) in 1.74s
     Running `target/debug/rust-api`
2023-06-13T00:56:41.621002Z  INFO filemanager: listening on 0.0.0.0:8080

Then:

$ curl localhost:8080/file/moo.bam

And to access the builtin Swagger playground, visit http://localhost:8080/swagger-ui/ on your browser.

Database

Since this microservice is reliant on (meta)data present on the former "Data Portal" database, we'll have to load those tables in on the orcabus_db container and inner MySQL DB like so:

aws s3 cp s3://<data-portal-dev-bucket>/data_portal.sql.gz data/
docker cp data/data_portal.sql.gz orcabus_db:/
docker exec -i -e MYSQL_PWD=orcabus orcabus_db mysql -u orcabus -e "DROP DATABASE IF EXISTS orcabus; CREATE DATABASE IF NOT EXISTS orcabus;"
docker exec -i -e MYSQL_PWD=orcabus orcabus_db /bin/bash -c 'zcat data_portal.sql.gz | mysql -uorcabus orcabus'

One off mysql SQL commands can be interactively launched, i.e (assuming make up command has succeeded and database container(s) are up and running):

docker exec -it orcabus_db mysql -h 0.0.0.0 -D orcabus -u root -proot
mysql> show tables;
+----------------------------------+
| Tables_in_orcabus                |
+----------------------------------+
| data_portal_gdsfile              |
| data_portal_s3lims               |
| data_portal_s3object             |
(...)
mysql> describe orcabus.data_portal_gdsfile;
+----------------+--------------+------+-----+---------+----------------+
| Field          | Type         | Null | Key | Default | Extra          |
+----------------+--------------+------+-----+---------+----------------+
| id             | bigint       | NO   | PRI | NULL    | auto_increment |
| file_id        | varchar(255) | NO   |     | NULL    |                |
| name           | longtext     | NO   |     | NULL    |                |
(...)
| presigned_url  | longtext     | YES  |     | NULL    |                |
| unique_hash    | varchar(64)  | NO   | UNI | NULL    |                |
+----------------+--------------+------+-----+---------+----------------+
22 rows in set (0.00 sec)

mysql> describe orcabus.data_portal_s3object;
+--------------------+--------------+------+-----+---------+----------------+
| Field              | Type         | Null | Key | Default | Extra          |
+--------------------+--------------+------+-----+---------+----------------+
| id                 | bigint       | NO   | PRI | NULL    | auto_increment |
| bucket             | varchar(255) | NO   |     | NULL    |                |
| key                | longtext     | NO   |     | NULL    |                |
| size               | bigint       | NO   |     | NULL    |                |
| last_modified_date | datetime(6)  | NO   |     | NULL    |                |
| e_tag              | varchar(255) | NO   |     | NULL    |                |
| unique_hash        | varchar(64)  | NO   | UNI | NULL    |                |
+--------------------+--------------+------+-----+---------+----------------+

Rust learning

While at first Rust can seem intimidating (as a language), there's plenty of materials online that can help you get up to speed with this microservice codebase, check this out: