# Semsimian Server
A simple web server for the Semsimian project, written in Rust.
## Requirements:
- [Rust](https://www.rust-lang.org/tools/install)
- rustup >= 1.28
- rustc >= 1.89
- cargo >= 1.89
## Installation:
0. Semsimian Server requires a local copy of the Phenio DB.
It will check for the existence of `$HOME/.data.oaklib/phenio.db`, and **automatically download the latest version** if it is missing.
However, if you wish to use a specific version, you may manually download a copy of `phenio.db.gz`
from https://data.monarchinitiative.org and unpack it into `$HOME/.data/oaklib`:
```bash
mkdir -p ~/.data/oaklib
cd ~/.data/oaklib
wget https://data.monarchinitiative.org/monarch-kg/latest/phenio.db.gz
gunzip phenio
```
### From `crates.io`
Semsimian Server is published to [crates.io](https://crates.io/crates/semsimian_server).
To install it for local usage, you can run:
```bash
cargo install semsimian_server
```
This will install the binary to your `~/.cargo/bin` directory,
which can be run from any directory by calling:
```bash
semserver
```
### From Source
1. Clone the repository:
```bash
git clone https://github.com/monarch-initiative/semsimian-server
```
2. Build the project:
```bash
cd semsimian-server
cargo build
```
3. Run the server:
```bash
cargo run
```
### Docker Image
A Dockerfile is provided for convenience. While it is hosted on [Google Cloud Platform](us-central1-docker.pkg.dev/monarch-initiative/monarch-api/semsimian-server:latest),
it can be built locally.
To build the image, run the following command from the root of the repository:
```bash
docker build -t semsimian-server .
```
To run the image, run the following command:
```bash
docker run -p 9999:9999 semsimian-server
```
## Usage:
In debug mode (ie. `cargo build`), the server will be running on `http://localhost:9999`.
The address and port can be configured in the `Rocket.toml` file, or by setting the `ROCKET_ADDRESS` and `ROCKET_PORT` environment variables.
The server exposes two endpoints:
- `/compare/<termset1>/<termset2>/<metric>`:
Returns a JSON object containing the similarity score between the two termsets.
- `termset1` and `termset2`: comma-separated lists of ontology terms.
- `metric`: (optional) the similarity method to use, one of:
- `ancestor_information_content` (**default**)
- `jaccard_similarity`
- `phenodigm_score`
- `cosine_similarity`
- `/search/<termset>/<prefix>/<metric>?<limit>&<direction>`:
Returns a JSON object containing a list of ontology terms that match the search term and prefix.
- `termset`: comma-separated list of ontology terms.
- `prefix`: string that will be used to filter the results.
- `metric`: (optional) the similarity method to use, one of:
- `ancestor_information_content` (**default**)
- `jaccard_similarity`
- `phenodigm_score`
- `cosine_similarity`
- `limit`: number, limit the number of results
- `direction`: the direction of the associations to search for, one of:
`bidirectional`, `subject_to_object`, `object_to_subject`
Example endpoints:
- http://localhost:9999/compare/HP:0000001,HP:0000002/HP:0000003,HP:0000004
- http://localhost:9999/compare/HP:0000001,HP:0000002/HP:0000003,HP:0000004/jaccard_similarity
- http://localhost:9999/search/HP:0000001,HP:0000002/zfin/ancestor_information_content?limit=5&direction=bidirectional
- http://localhost:9999/search/HP:0000001,HP:0000002/zfin?limit=3&direction=bidirectional