Address static analyzer issues

compose/build_repo_images_for_compose.sh

@@ -7,10 +7,10 @@ SOURCE=$(dirname "$SCRIPT")
 PROJECT_ROOT=$(realpath "${SOURCE}/../")
 . "${PROJECT_ROOT}/scripts/dependency_versions.sh"
 
-cd ${PROJECT_ROOT}/external/globus-connect-server-deploy/docker
+cd "${PROJECT_ROOT}/external/globus-connect-server-deploy/docker"
 git checkout "$DATAFED_GCS_SUBMODULE_VERSION"
 docker build --progress plain --tag "gcs-ubuntu-base:latest" - < "./docker-files/Dockerfile.ubuntu-20.04"
-cd ${PROJECT_ROOT}
+cd "${PROJECT_ROOT}"
 docker build \
   -f "${PROJECT_ROOT}/docker/Dockerfile.dependencies" \
   "${PROJECT_ROOT}" \

scripts/dependency_install_functions.sh

@@ -7,10 +7,10 @@ source "${SOURCE}/utils.sh"
 
 sudo_command
 # these are the dependencies to be installed by apt
-apt_file_path="${PROJECT_ROOT}/tmp/apt_deps"
-pip_file_path="${PROJECT_ROOT}/tmp/pip_deps"
+export apt_file_path="${PROJECT_ROOT}/tmp/apt_deps"
+export pip_file_path="${PROJECT_ROOT}/tmp/pip_deps"
 # these are the dependencies to be installed and built via cmake
-ext_file_path="${PROJECT_ROOT}/tmp/ext_deps"
+export ext_file_path="${PROJECT_ROOT}/tmp/ext_deps"
 
 if [ ! -d "${PROJECT_ROOT}/tmp" ]; then
     mkdir -p "${PROJECT_ROOT}/tmp" 

scripts/generate_gsi-authz_config.sh

@@ -5,8 +5,8 @@ set -ef -o pipefail
 
 SCRIPT=$(realpath "$0")
 SOURCE=$(dirname "$SCRIPT")
-PROJECT_ROOT=$(realpath ${SOURCE}/..)
-source ${PROJECT_ROOT}/config/datafed.sh
+PROJECT_ROOT=$(realpath "${SOURCE}/..")
+source "${PROJECT_ROOT}/config/datafed.sh"
 
 PATH_TO_CONFIG_DIR=$(realpath "$SOURCE/../config")
 CONFIG_FILE_NAME="gsi-authz.conf"

scripts/globus/create_guest_collection.py

@@ -1,8 +1,6 @@
 import globus_sdk
-import subprocess
+from globus_sdk import AccessTokenAuthorizer
 import utils
-from globus_sdk import AuthClient, AccessTokenAuthorizer
-import json
 import os
 import sys
 
@@ -56,70 +54,21 @@
 if local_username is None:
     raise Exception("DATAFED_REPO_USER is not defined.")
 
-# client = globus_sdk.NativeAppAuthClient(CLIENT_ID)
-
-# manage_projects scope to create a project
-# view_identities to user information for creating GCS server
-# client.oauth2_start_flow(requested_scopes="openid profile email urn:globus:auth:scope:auth.globus.org:manage_projects urn:globus:auth:scope:auth.globus.org:view_identities", refresh_tokens=True)
-#
-# authorize_url = client.oauth2_get_authorize_url(query_params={"prompt": "login"})
-# print("Please go to this URL and login: \n", authorize_url)
-# auth_code = input("Please enter the authorization code: ")
-#
-# token_response = client.oauth2_exchange_code_for_tokens(auth_code)
-## Extract the token
-# refresh_token_auth = token_response.by_resource_server['auth.globus.org']['refresh_token']
-# rt_authorizer = globus_sdk.RefreshTokenAuthorizer(refresh_token_auth, client)
-## auth_client_refresh_token
-# ac_rt = AuthClient(authorizer=rt_authorizer)
-#
-# userinfo = ac_rt.oauth2_userinfo()
-## Will get the primary email and id
-# identity_id = userinfo["sub"]
-# email = userinfo["email"]
-# username = userinfo["preferred_username"]
-# organization = userinfo["identity_provider_display_name"]
-
 if client_id is None:
-    client_id = getClientIdFromCredFile(CRED_FILE_PATH)
+    client_id = utils.getClientIdFromCredFile(CRED_FILE_PATH)
 
 if client_secret is None:
-    client_secret = getCredentialFromFile(CRED_FILE_PATH, client_id)
+    client_secret = utils.getCredentialFromFile(CRED_FILE_PATH, client_id)
 
 client = globus_sdk.ConfidentialAppAuthClient(client_id, client_secret)
 
 scopes = "openid profile email urn:globus:auth:scope:auth.globus.org:manage_projects urn:globus:auth:scope:auth.globus.org:view_identities"
 authorizer = globus_sdk.ClientCredentialsAuthorizer(client, scopes)
-# cc_authorizer = globus_sdk.ClientCredentialsAuthorizer(confidential_client,
-#        scopes)
-
-# token_response = client.oauth2_client_credentials_tokens()
-
-# refresh_token_auth = token_response.by_resource_server['auth.globus.org']['refresh_token']
-# rt_authorizer = globus_sdk.RefreshTokenAuthorizer(refresh_token_auth, client)
-# the useful values that you want at the end of this
-# globus_auth_data = token_response.by_resource_server["auth.globus.org"]
-# globus_transfer_data =
-# token_response.by_resource_server["transfer.api.globus.org"]
-# globus_auth_token = globus_auth_data["access_token"]
-# globus_transfer_token = globus_transfer_data["access_token"]
 
 gcs_client = globus_sdk.GCSClient(DATAFED_GCS_URL, authorizer=authorizer)
 
-
-import globus_sdk
 from globus_sdk import scopes
 
-# client credentials
-# This client identity must have the needed permissions to create a guest
-# collection on the mapped collection, and a valid mapping to a local account
-# on the storage gateway that matches the local_username
-# If using user tokens, the user must be the one with the correct permissions
-# and identity mapping.
-# client_id = "4de65cd7-4363-4510-b652-f8d15a43a0af"
-# client_secret = "*redacted*"
-# local_username = "datafed"
-
 # The scope the client will need, note that primary scope is for the endpoint,
 # but it has a dependency on the mapped collection's data_access scope
 

scripts/globus/globus_cleanup.py

@@ -1,8 +1,7 @@
 import globus_sdk
-from globus_sdk import AuthClient, GroupsClient, AccessTokenAuthorizer
+from globus_sdk import AuthClient, GroupsClient 
 from globus_sdk.scopes import GroupsScopes
 import subprocess
-import json
 import sys
 import os
 import utils

scripts/globus/initialize_globus_endpoint.py

@@ -1,14 +1,11 @@
 import globus_sdk
-import subprocess
 import utils
-from globus_sdk import AuthClient, GroupsClient, AccessTokenAuthorizer
+from globus_sdk import AuthClient, GroupsClient 
 from globus_sdk.scopes import GroupsScopes
 
-import json
 import os
 import sys
 
-
 # Hard coded Native Client ID
 CLIENT_ID = "f8d0afca-7ac4-4a3c-ac05-f94f5d9afce8"