Merge pull request #27 from umccr/filemanager

FileManager microservice

.gitignore

@@ -46,3 +46,7 @@ cdk.context.json
 !.yarn/versions
 
 *.sqlite3
+
+# SQL dumps, data, etc...
+
+data/

docker-compose.yml

@@ -53,64 +53,75 @@ services:
     image: stoplight/prism:4
     platform: linux/amd64
     container_name: orcabus_wes
-    command: mock -d -h 0.0.0.0 "/openapi/wes.json"
+    command: mock -d -h 0.0.0.0 "/openapi/ica/v1/wes.json"
     restart: always
     ports:
       - "4010:4010"
     volumes:
-      - ./openapi:/openapi
+      - ./openapi/ica:/openapi/ica
 
   tes:
     image: stoplight/prism:4
     platform: linux/amd64
     container_name: orcabus_tes
-    command: mock -d -h 0.0.0.0 "/openapi/tes.json"
+    command: mock -d -h 0.0.0.0 "/openapi/ica/v1/tes.json"
     restart: always
     ports:
       - "4011:4010"
     volumes:
-      - ./openapi:/openapi
+      - ./openapi/ica:/openapi/ica
 
   gds:
     image: stoplight/prism:4
     platform: linux/amd64
     container_name: orcabus_gds
-    command: mock -d -h 0.0.0.0 "/openapi/gds.json"
+    command: mock -d -h 0.0.0.0 "/openapi/ica/v1/gds.json"
     restart: always
     ports:
       - "4012:4010"
     volumes:
-      - ./openapi:/openapi
+      - ./openapi/ica:/openapi/ica
 
   ens:
     image: stoplight/prism:4
     platform: linux/amd64
     container_name: orcabus_ens
-    command: mock -d -h 0.0.0.0 "/openapi/ens.json"
+    command: mock -d -h 0.0.0.0 "/openapi/ica/v1/ens.json"
     restart: always
     ports:
       - "4013:4010"
     volumes:
-      - ./openapi:/openapi
+      - ./openapi/ica:/openapi/ica
 
   console:
     image: stoplight/prism:4
     platform: linux/amd64
     container_name: orcabus_console
-    command: mock -d -h 0.0.0.0 "/openapi/console.json"
+    command: mock -d -h 0.0.0.0 "/openapi/ica/v1/console.json"
     restart: always
     ports:
       - "4014:4010"
     volumes:
-      - ./openapi:/openapi
+      - ./openapi/ica:/openapi/ica
 
   v2:
     image: stoplight/prism:4
     platform: linux/amd64
     container_name: orcabus_ica_v2
-    command: mock -d -h 0.0.0.0 "/openapi/openapi_public.yaml"
+    command: mock -d -h 0.0.0.0 "/openapi/ica/v2/openapi_public.yaml"
     restart: always
     ports:
       - "4015:4010"
     volumes:
-      - ./openapi:/openapi
+      - ./openapi/ica:/openapi/ica
+
+  filemanager:
+    image: stoplight/prism:4
+    platform: linux/amd64
+    container_name: orcabus_filemanager
+    command: mock -d -h 0.0.0.0 "/openapi/orcabus/filemanager.json"
+    restart: always
+    ports:
+      - "4016:4010"
+    volumes:
+      - ./openapi/orcabus:/openapi/orcabus

docs/developer/RUST_API.md

@@ -0,0 +1,54 @@
+# 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:
+
+```bash
+curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh
+```
+
+For development edit and compile loop, use the [`cargo-watch`](https://crates.io/crates/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 rust_api: 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:
+
+```bash
+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'
+```
+
+# 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:
+
+- [Google 3-day Rust course](https://github.com/google/comprehensive-rust)
+- [SQLx quickstart](https://www.youtube.com/watch?v=TCERYbgvbq0)
+- [Rust Axum full course](https://www.youtube.com/watch?v=XZtlD_m59sM)

openapi/README.md

@@ -1,16 +1,6 @@
-# OpenAPI
+# Orcabus microservices OpenAPI client definitions
 
-This directory contains OpenAPI/Swagger JSON files. They are generated/obtained as follows.
+Each language implementation should make sure to expose an `api-docs` and `swagger-ui` url routes that expose the APIs for a given microservice, i.e:
 
-## ICA
-
-Sync of https://github.com/umccr-illumina/libica/tree/dev/swagger
-
-```
-wget https://raw.githubusercontent.com/umccr-illumina/libica/dev/swagger/console.json -O console.json
-wget https://raw.githubusercontent.com/umccr-illumina/libica/dev/swagger/ens.json -O ens.json
-wget https://raw.githubusercontent.com/umccr-illumina/libica/dev/swagger/gds.json -O gds.json
-wget https://raw.githubusercontent.com/umccr-illumina/libica/dev/swagger/tes.json -O tes.json
-wget https://raw.githubusercontent.com/umccr-illumina/libica/dev/swagger/wes.json -O wes.json
-wget https://raw.githubusercontent.com/umccr-illumina/libica/main/swagger/openapi_public.yaml -O openapi_public.yaml
-```
+http://localhost:8080/swagger-ui/
+http://localhost:8080/api-docs/filemanager.json

openapi/ica/v1/README.md

@@ -0,0 +1,15 @@
+# OpenAPI
+
+This directory contains OpenAPI/Swagger JSON files. They are generated/obtained as follows.
+
+## ICA
+
+Sync of https://github.com/umccr-illumina/libica/tree/dev/swagger
+
+```
+wget https://raw.githubusercontent.com/umccr-illumina/libica/dev/swagger/console.json -O console.json
+wget https://raw.githubusercontent.com/umccr-illumina/libica/dev/swagger/ens.json -O ens.json
+wget https://raw.githubusercontent.com/umccr-illumina/libica/dev/swagger/gds.json -O gds.json
+wget https://raw.githubusercontent.com/umccr-illumina/libica/dev/swagger/tes.json -O tes.json
+wget https://raw.githubusercontent.com/umccr-illumina/libica/dev/swagger/wes.json -O wes.json
+```

openapi/ica/v2/README.md

@@ -0,0 +1,3 @@
+This is the OpenAPI ICA v2 definition, obtained from upstream:
+
+wget https://raw.githubusercontent.com/umccr-illumina/libica/main/swagger/openapi_public.yaml -O openapi_public.yaml

openapi/orcabus/filemanager.json

@@ -0,0 +1 @@
+{"openapi":"3.0.3","info":{"title":"rust-api","description":"","license":{"name":""},"version":"0.1.0"},"paths":{"/file/":{"get":{"tags":["file"],"summary":"Search query","description":"Search query\nSearch files","operationId":"search","parameters":[{"name":"id","in":"query","required":true,"schema":{"type":"integer","format":"int32"}},{"name":"name","in":"query","required":true,"schema":{"type":"string"}},{"name":"size","in":"query","required":true,"schema":{"type":"integer","format":"int64","minimum":0.0}},{"name":"hash","in":"query","required":true,"schema":{"type":"string"}}],"responses":{"200":{"description":"List matching objects","content":{"application/json":{"schema":{"type":"array","items":{"$ref":"#/components/schemas/File"}}}}}}}}},"components":{"schemas":{"File":{"type":"object","description":"Item to do.","required":["id","name","size","hash"],"properties":{"hash":{"type":"string"},"id":{"type":"integer","format":"int32"},"name":{"type":"string","example":"foo.bam"},"size":{"type":"integer","format":"int64","minimum":0.0}}},"FileError":{"oneOf":[{"type":"object","required":["NotFound"],"properties":{"NotFound":{"type":"string","description":"File not found by id."}},"example":"id = 1"},{"type":"object","required":["Unauthorized"],"properties":{"Unauthorized":{"type":"string","description":"File operation unauthorized"}},"example":"missing api key"}],"description":"File operation errors"}},"securitySchemes":{"api_key":{"type":"apiKey","in":"header","name":"File_apikey"}}},"tags":[{"name":"File","description":"File manager API"}]}

skel/rust-api/.gitignore

@@ -0,0 +1,2 @@
+target/
+*.swp