Feat: adding config in CLI

.github/workflows/ci.yml

@@ -0,0 +1,60 @@
+name: GitHub CI/CD Workflow	
+
+on: [push, pull_request]	
+
+jobs:	
+  build:	
+
+    runs-on: ubuntu-latest	
+    container:	
+      image: ubuntu:24.04	
+    env:	
+      OPENSSL_DIR: /usr/include/openssl	
+      OPENSSL_LIB_DIR: /usr/lib/x86_64-linux-gnu	
+      OPENSSL_INCLUDE_DIR: /usr/include/openssl	
+
+    steps:	
+    - name: Install dependencies	
+      run: |	
+        apt-get update	
+        apt-get install -y curl git build-essential libssl-dev 	
+
+    - uses: actions/checkout@v4 # checkout the repository	
+    - name: Install Rust	
+      run: |
+        curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y
+        echo "$HOME/.cargo/bin" >> $GITHUB_PATH
+
+    - name: Set up JDK 11 # required for build-models.sh	
+      uses: actions/setup-java@v3
+      with:	
+        distribution: 'adopt'	
+        java-version: '11'	
+
+    - name: Install Go	
+      uses: actions/setup-go@v4
+      with:	
+        go-version: '^1.22'  	
+    - name: Install Funnel	
+      run: |	
+          if [ -d "funnel" ]; then rm -Rf funnel; fi	
+          git clone https://github.com/ohsu-comp-bio/funnel.git	
+          cd funnel && make && make install && cd ..	
+    - uses: actions/checkout@v4 # checkout the repository	
+    - name: Build models	
+      run: |	
+        bash ./build-models.sh	
+    - name: Build	
+      run: |	
+        cargo build --verbose	
+    - name: Run tests	
+      run: |	
+        bash ./run-tests.sh	
+    - name: Lint	
+      run: |	
+        cargo clippy -- -D warnings	
+    - name: Format	
+      run: |	
+        cargo fmt -- ./lib/src/serviceinfo/models/*.rs # workaround to fix autogenerated code formatting	
+        cargo fmt -- ./lib/src/tes/models/*.rs	
+        cargo fmt -- --check

.github/workflows/local.yml

@@ -0,0 +1,98 @@
+name: Local CI/CD Workflow	
+
+on: workflow_dispatch
+
+jobs:	
+  build:	
+
+    runs-on: ubuntu-latest	
+    container:	
+      image: ubuntu:24.04	
+    env:	
+      OPENSSL_DIR: /usr/include/openssl	
+      OPENSSL_LIB_DIR: /usr/lib/x86_64-linux-gnu	
+      OPENSSL_INCLUDE_DIR: /usr/include/openssl	
+
+    steps:	
+
+    - name: Cache Rust dependencies	
+      uses: actions/cache@v3
+      with:	
+        path: ~/.cargo	
+        key: ${{ runner.os }}-cargo-${{ hashFiles('**/Cargo.lock') }}	
+        restore-keys: ${{ runner.os }}-cargo-	
+
+    - name: Cache Rust build output	
+      uses: actions/cache@v3
+      with:	
+        path: target	
+        key: ${{ runner.os }}-build-${{ hashFiles('**/Cargo.lock') }}	
+        restore-keys: ${{ runner.os }}-build-		
+
+    - name: Cache Maven dependencies	
+      uses: actions/cache@v3
+      with:	
+        path: ~/.m2/repository	
+        key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}	
+        restore-keys: ${{ runner.os }}-maven-	
+
+    - name: Cache Go modules	
+      uses: actions/cache@v3
+      with:	
+        path: ~/.cache/go-build	
+        key: ${{ runner.os }}-go-${{ hashFiles('**/go.sum') }}	
+        restore-keys: ${{ runner.os }}-go-	
+
+    - name: Cache Funnel dependencies	
+      uses: actions/cache@v3
+      with:	
+        path: ~/funnel/build	
+        key: ${{ runner.os }}-funnel-${{ hashFiles('**/funnel/*') }}	
+        restore-keys: ${{ runner.os }}-funnel-	
+
+    - uses: actions/checkout@v4 # checkout the repository	
+    - name: Install Rust	
+      run: |
+        curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y
+        echo "$HOME/.cargo/bin" >> $GITHUB_PATH
+
+    - name: Set up JDK 11 # required for build-models.sh	
+      uses: actions/setup-java@v3
+      with:	
+        distribution: 'adopt'	
+        java-version: '11'	
+
+    - name: Install Go	
+      uses: actions/setup-go@v4
+      with:	
+        go-version: '^1.22'  	
+    - name: Install Funnel	
+      run: |	
+          if [ -d "funnel" ]; then rm -Rf funnel; fi	
+          git clone https://github.com/ohsu-comp-bio/funnel.git	
+          cd funnel && make && make install && cd ..	
+    - uses: actions/checkout@v4 # checkout the repository	
+    - name: Build models	
+      run: |	
+        . $HOME/.cargo/env	
+        bash ./build-models.sh	
+    - name: Build	
+      run: |	
+        . $HOME/.cargo/env	
+        cargo build --verbose	
+    - name: Run tests	
+      run: |	
+        . $HOME/.cargo/env	
+        bash ./run-tests.sh	
+    - name: Lint	
+      run: |	
+        . $HOME/.cargo/env	
+        cargo clippy -- -D warnings	
+    - name: Format	
+      run: |	
+        . $HOME/.cargo/env	
+        # rustup install nightly – fails for some reason	
+        # rustup default nightly	
+        cargo fmt -- ./lib/src/serviceinfo/models/*.rs # workaround to fix autogenerated code formatting	
+        cargo fmt -- ./lib/src/tes/models/*.rs	
+        cargo fmt -- --check # --config-path ./rustfmt.toml	

.gitignore

@@ -0,0 +1,8 @@
+target/
+debug/
+Cargo.lock
+openapitools.json
+*.log
+funnel-work-dir/
+funnel/
+lib/src/*/models

Cargo.toml

@@ -0,0 +1,13 @@
+[workspace]
+members = [
+    "cli",
+    "lib"
+]
+
+[workspace.package]
+version = "0.1.0"
+authors = ["Aarav Mehta <[email protected]> (Google Summer of Code Participant)", "Pavel Nikonorov <[email protected]> (Google Summer of Code Mentor; GENXT)", "ELIXIR Cloud & AAI <[email protected]> (ELIXIR Europe)"]
+edition = "2021"
+readme = "./README.md"
+license-file = "LICENSE.txt"
+repository = "https://github.com/elixir-cloud-aai/ga4gh-sdk.git"

README.md

@@ -0,0 +1,36 @@
+# A Generic SDK and CLI for GA4GH API services
+
+## Building
+
+First, clone the repository, and then run the following command to automatically generate models using OpenAPI specifications:
+```
+bash ./build-models.sh
+```
+
+To build the project:
+```
+cargo build
+```
+
+## Running the tests
+
+Before running the tests, you need to install Funnel, a task execution system that is compatible with the GA4GH TES API. Follow the instructions in the [Funnel Developer's Guide](https://ohsu-comp-bio.github.io/funnel/docs/development/developers/) to install Funnel.
+
+Once you have installed Funnel, you can run the tests. This will automatically run Funnel as well:
+
+```
+bash ./run-tests.sh
+```
+or, you can run using cargo nextest using
+```
+cargo nextest run
+```
+For checking the unit converage, you can run:
+```
+cargo llvm-cov nextest
+```
+
+To test the CI/CD workflow locally, install `act` and run the following command:
+```
+act -j build --container-architecture linux/amd64 -P ubuntu-latest=ubuntu:24.04 --reuse
+```

build-models.sh

@@ -0,0 +1,77 @@
+# Exit immediately if a command exits with a non-zero status.
+set -e
+
+# Ensure the OpenAPI Generator JAR file is set up
+mkdir -p ~/bin/openapitools
+OPENAPI_GENERATOR_JAR=~/bin/openapitools/openapi-generator-cli.jar
+if [ ! -f "$OPENAPI_GENERATOR_JAR" ]; then
+    curl -L https://repo1.maven.org/maven2/org/openapitools/openapi-generator-cli/7.7.0/openapi-generator-cli-7.7.0.jar -o "$OPENAPI_GENERATOR_JAR"
+fi
+
+get_git_repo_name() {
+    # Extract the URL of the remote "origin"
+    url=$(git config --get remote.origin.url)
+
+    # Extract the repository name from the URL
+    repo_name=$(basename -s .git "$url")
+
+    echo "$repo_name"
+}
+
+SCRIPT_DIR="$(pwd)"
+
+generate_openapi_models() {
+    # Parameters
+    OPENAPI_SPEC_PATH="$1"
+    API_NAME="$2"
+    DESTINATION_DIR="$3"
+
+    # Define the temporary output directory for the OpenAPI generator
+    TEMP_OUTPUT_DIR=$(mktemp -d)
+
+    # Remove the temporary directory at the end of the script
+    trap 'rm -rf "$TEMP_OUTPUT_DIR"' EXIT
+
+    # Run the OpenAPI generator CLI using the JAR file
+    java -jar "$OPENAPI_GENERATOR_JAR" generate -g rust \
+        -i "$OPENAPI_SPEC_PATH" \
+        -o "$TEMP_OUTPUT_DIR" \
+        --additional-properties=useSingleRequestParameter=true 
+
+    # Check if the generation was successful
+    if [ $? -ne 0 ]; then
+        echo "OpenAPI generation failed. Check the verbose output for details."
+        exit 1
+    fi
+
+    # Remove the openapitools.json file
+    rm -f ./openapitools.json
+
+    echo "TEMP_OUTPUT_DIR is $TEMP_OUTPUT_DIR"
+
+    # Modify the import statements in each generated file
+    SED_RULE="s/use crate::models;/#![allow(unused_imports)]\n#![allow(clippy::empty_docs)]\nuse crate::$API_NAME::models;/"
+    for file in $(find "$TEMP_OUTPUT_DIR" -name '*.rs'); do
+        if [[ "$OSTYPE" == "darwin"* ]]; then
+            # macOS (BSD) sed syntax
+            sed -i '' "$SED_RULE" "$file"
+        else
+            # Linux (GNU) sed syntax
+            sed -i "$SED_RULE" "$file"
+        fi
+    done
+
+    rm -rf "$DESTINATION_DIR/models"
+    mkdir -p "$DESTINATION_DIR"
+    cp -r "$TEMP_OUTPUT_DIR/src/models" "$DESTINATION_DIR"
+
+    echo "OpenAPI generation complete. Models copied to $DESTINATION_DIR"
+}
+
+generate_openapi_models \
+    "https://raw.githubusercontent.com/ga4gh-discovery/ga4gh-service-info/develop/service-info.yaml" \
+    "serviceinfo" "$SCRIPT_DIR/lib/src/serviceinfo/"
+
+generate_openapi_models \
+    "https://raw.githubusercontent.com/ga4gh/task-execution-schemas/develop/openapi/task_execution_service.openapi.yaml" \
+    "tes" "$SCRIPT_DIR/lib/src/tes/"

cli/Cargo.toml

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+[package]
+name = "cli"
+description = """
+A cross-platform CLI tool written in Rust to use GA4GH-sdk
+"""
+repository = "https://github.com/elixir-cloud-aai/ga4gh-sdk/tree/main/cli"
+version.workspace = true
+authors.workspace = true
+edition.workspace = true
+readme.workspace = true
+license-file.workspace = true
+
+[dependencies]
+ga4gh-lib = { path = "../lib" }
+clap = "3.0"
+clap_complete = "3.0"
+tokio = { version = "1", features = ["full"] }
+serde_json = "^1.0"
+tempfile = "3.2"
+dirs = "5.0.1"
+
+[[bin]]
+name = "cli"
+path = "src/main.rs"