Fix: provide correct paths for install shell

packages/cli/Makefile

@@ -4,7 +4,8 @@ VERSION_FILE=../../version.json
 GOBIN=${PWD}/bin/tools
 COVERAGE=coverage.out
 
-DESTINATION=./bin/local/${BINARY_NAME}
+PREFIX=${PWD}/../..
+DESTINATION=${PREFIX}/bin/local/${BINARY_NAME}
 VERSION=$(shell jq .version -r < ${VERSION_FILE})
 
 LINKER_FLAGS=-X github.com/aws/amazon-genomics-cli/internal/pkg/version.Version=${VERSION}

packages/wes_adapter/amazon_genomics/wes/adapters/CromwellWESAdapter.py

@@ -215,7 +215,6 @@ def run_workflow(
         # this is needed for any file downloads
         # once complete the temp dir will be removed and all open files will be closed
         with tempfile.TemporaryDirectory() as tmpdir:
-
             self.logger.debug(f"RUN_WORKFLOW :: tmpdir={tmpdir}")
 
             data = {
@@ -418,7 +417,6 @@ def _translate_from_response_to_state_(self, response):
         return self._get_workflow_state_(status, status_code)
 
     def _get_workflow_state_(self, status, status_code=None):
-
         self.logger.info("_get_workflow_state_(%s, %s)" % (status, status_code))
         if (status_code is not None) and (status_code != 200):
             if (status_code >= 400) and (status_code <= 403):

packages/wes_adapter/install.sh

@@ -1,10 +1,11 @@
 #! /bin/bash
 
-if ! hash python3.9; then
-    echo "python3.9 is not installed"
+
+if ! hash python3; then
+    echo "python3 is not installed"
     exit 1
 fi
 
 rm -rf ./dist && mkdir ./dist
-python3.9 -m pip install -r requirements.txt --target ./dist && (cd ./dist && zip -r ./wes_adapter.zip .)
+python3 -m pip install -r requirements.txt --target ./dist && (cd ./dist && zip -r ./wes_adapter.zip .)
 zip -gr ./dist/wes_adapter.zip ./rest_api ./amazon_genomics ./index.py

packages/wes_adapter/rest_api/controllers/workflow_execution_service_controller.py

@@ -157,7 +157,6 @@ def run_workflow(
     }
 
     for arg in args:
-
         if arg in ("workflow_attachment"):
             # file lists
             args[arg] = request.files.getlist(arg)

scripts/cli/install.sh

@@ -7,6 +7,7 @@ BASE_DIR="$HOME/.agc"
 SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )"
 
 selectArch () {
+    echo "Selecting arch: $(arch)"
     if [[ $(arch) == "arm64" ]]; then
         eval "$1"="arm64"
     else
@@ -17,6 +18,7 @@ selectArch () {
 }
 
 selectCliFile () {
+    echo "Selecting cli File"
     selectArch archKind
     local fileName="agc"
 
@@ -37,28 +39,33 @@ selectCliFile () {
 }
 
 install_cli () {
+    echo "Installing cli"
     selectCliFile cliFile
     if [[ -z "$cliFile" ]]; then
+        echo "$cliFile not found to install"
         exit 1
     fi
 
     mkdir -p "$USER_BIN_DIR"
-    cp "$SCRIPT_DIR/$cliFile" "$USER_BIN_DIR/agc"
+    cp "$SCRIPT_DIR/../../packages/cli/bin/local/$cliFile" "$USER_BIN_DIR/agc"
 
     echo "Please modify your \$PATH variable to include \$HOME/bin directory"
     echo "This can be achieved by running: \"export PATH=\$HOME/bin:\$PATH\""
-    echo "Please append the command above to shell profile to have agc available within every shell instance." 
+    echo "Please append the command above to shell profile to have agc available within every shell instance."
 }
 
 install_cdk () {
+    echo "Installing CDK"
     mkdir -p "$BASE_DIR/cdk"
-    cp "$SCRIPT_DIR/cdk.tgz" "$BASE_DIR/cdk"
+    cp "$SCRIPT_DIR/../../packages/cdk/cdk.tgz" "$BASE_DIR/cdk"
     (cd "$BASE_DIR/cdk" && tar -xzf ./cdk.tgz --strip-components=1 && npm ci --silent)
 }
 
 install_wes () {
+    echo "Installing WES"
     mkdir -p "$BASE_DIR/wes"
-    cp "$SCRIPT_DIR/wes/wes_adapter.zip" "$BASE_DIR/wes"
+    cp "$SCRIPT_DIR/../../packages/wes_adapter/dist/wes_adapter.zip" "$BASE_DIR/wes"
 }
 
+echo "Starting installation"
 install_cli && install_cdk && install_wes && echo "Installation complete. Once \$PATH variable has been adjusted, run 'agc --help' to get started!"

scripts/cli/uninstall.sh

@@ -4,7 +4,7 @@ set -eo pipefail
 
 USER_BIN_DIR="$HOME/bin"
 BASE_DIR="$HOME/.agc"
-SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )"
+SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}/../../" )" &> /dev/null && pwd )"
 
 uninstall_cli () {
     rm -f $USER_BIN_DIR/agc

scripts/run-dev.sh

@@ -27,6 +27,7 @@ run_agc_cli () {
 }
 
 build_wes_adapter() {
+  echo "Building WES Adapter"
   mkdir -p "$HOME/.agc/wes"
   (cd "${SCRIPT_DIR}"/../packages/wes_adapter && ./install.sh)
   mv "${SCRIPT_DIR}"/../packages/wes_adapter/dist/wes_adapter.zip $HOME/.agc/wes/