From dce52dadff8c20daa084582cd340aa2a85f8b42b Mon Sep 17 00:00:00 2001
From: alexiswl <8197659+alexiswl@users.noreply.github.com>
Date: Mon, 29 Jan 2024 20:57:02 +1100
Subject: [PATCH] Autocompletion - update python helper scripts to pull in
 cwl-ica module

---
 autocompletion/bash/cwl-ica.bash              | 522 ++++++++++++------
 .../_cwl-ica_list_all_expression_paths.py     |   9 +-
 .../helpers/_cwl-ica_list_all_schema_paths.py |   7 +-
 .../helpers/_cwl-ica_list_all_tool_paths.py   |   7 +-
 ...ca_list_all_typescript_expression_paths.py |   7 +-
 .../_cwl-ica_list_all_workflow_paths.py       |   7 +-
 .../helpers/_cwl-ica_list_category_names.py   |   4 +-
 .../helpers/_cwl-ica_list_project_names.py    |   4 +-
 ...wl-ica_list_registered_expression_paths.py |   7 +-
 .../_cwl-ica_list_registered_schema_paths.py  |   7 +-
 .../_cwl-ica_list_registered_tool_paths.py    |   9 +-
 ..._cwl-ica_list_registered_workflow_paths.py |   9 +-
 .../helpers/_cwl-ica_list_run_instance_ids.py |   5 +-
 .../helpers/_cwl-ica_list_tenant_names.py     |   5 +-
 .../helpers/_cwl-ica_list_tool_names.py       |   5 +-
 ...-ica_list_unregistered_expression_paths.py |   9 +-
 ..._cwl-ica_list_unregistered_schema_paths.py |  10 +-
 .../_cwl-ica_list_unregistered_tool_paths.py  |  10 +-
 ...wl-ica_list_unregistered_workflow_paths.py |  10 +-
 .../helpers/_cwl-ica_list_user_names.py       |   5 +-
 .../helpers/_cwl-ica_list_workflow_names.py   |   5 +-
 autocompletion/run-autocompletion.sh          |   6 +-
 autocompletion/zsh/_cwl-ica                   | 519 +++++++++++------
 23 files changed, 817 insertions(+), 371 deletions(-)

diff --git a/autocompletion/bash/cwl-ica.bash b/autocompletion/bash/cwl-ica.bash
index ff574c2..fa0a03f 100644
--- a/autocompletion/bash/cwl-ica.bash
+++ b/autocompletion/bash/cwl-ica.bash
@@ -78,6 +78,7 @@ Each project is linked to a tenancy id
 '$'\n''tool-sync'$'\t''Sync a tool md5sum in \${CWL_ICA_REPO_PATH}/config/tool.yaml
 and update definition on ICA
 '$'\n''tool-validate'$'\t''Validate a CWL tool ready for initialising on ICA
+'$'\n''typescript-expression-update'$'\t''Update a typescript expression yarn.lock file
 '$'\n''typescript-expression-validate'$'\t''Validate a typescript expression and generate a .cwljs file ready for importation
 '$'\n''validate-api-key-script'$'\t''Confirm your api-key script works for a given project
 '$'\n''validate-config-yamls'$'\t''Confirm all config yamls are legitimate
@@ -1341,6 +1342,26 @@ to workflow names
         ;;
         esac
       ;;
+      typescript-expression-update)
+        OPTIONS+=('--typescript-expression-dir' 'The name of the workflow
+' '--xtrace' 'Set xtrace on the update_yarn_dependencies shell script
+')
+        __cwl-ica_handle_options_flags
+        case ${MYWORDS[$INDEX-1]} in
+          --typescript-expression-dir)
+            _cwl-ica_typescript-expression-update_option_typescript_expression_dir_completion
+          ;;
+          --xtrace)
+          ;;
+
+        esac
+        case $INDEX in
+
+        *)
+            __comp_current_options || return
+        ;;
+        esac
+      ;;
       typescript-expression-validate)
         OPTIONS+=('--typescript-expression-dir' 'The name of the workflow
 ' '--xtrace' 'Set xtrace on the validate_typescript_expressions_directory shell script
@@ -1490,8 +1511,9 @@ python - <<EOF
 """
 List all of the category names in the categories.yaml file
 """
-from utils.repo import get_tool_yaml_path
-from utils.miscell import read_yaml
+# CWL ICA imports
+from cwl_ica.utils.repo import get_tool_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each tool name
 for tool in read_yaml(get_tool_yaml_path())["tools"]:
@@ -1509,8 +1531,8 @@ python - <<EOF
 """
 List all of the category names in the categories.yaml file
 """
-from utils.repo import get_category_yaml_path
-from utils.miscell import read_yaml
+from cwl_ica.utils.repo import get_category_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each project name
 for category in read_yaml(get_category_yaml_path())["categories"]:
@@ -1528,8 +1550,9 @@ python - <<EOF
 """
 List all of the category names in the categories.yaml file
 """
-from utils.repo import get_workflow_yaml_path
-from utils.miscell import read_yaml
+# CWL ICA imports
+from cwl_ica.utils.repo import get_workflow_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each tool name
 for workflow in read_yaml(get_workflow_yaml_path())["workflows"]:
@@ -1547,8 +1570,8 @@ python - <<EOF
 """
 List all of the category names in the categories.yaml file
 """
-from utils.repo import get_category_yaml_path
-from utils.miscell import read_yaml
+from cwl_ica.utils.repo import get_category_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each project name
 for category in read_yaml(get_category_yaml_path())["categories"]:
@@ -1566,8 +1589,8 @@ python - <<EOF
 """
 List all of the project names in the project.yaml file
 """
-from utils.repo import get_project_yaml_path
-from utils.miscell import read_yaml
+from cwl_ica.utils.repo import get_project_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each project name
 for project in read_yaml(get_project_yaml_path())["projects"]:
@@ -1586,13 +1609,16 @@ python - <<EOF
 List the unregistered expression paths
 """
 
-from utils.repo import get_expression_yaml_path
-from utils.repo import get_expressions_dir
-from utils.miscell import read_yaml
+# Externals
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA
+from cwl_ica.utils.repo import get_expression_yaml_path
+from cwl_ica.utils.repo import get_expressions_dir
+from cwl_ica.utils.miscell import read_yaml
+
 # Get the current word value
 if not "${CURRENT_WORD}" == "":
     current_word_value = "${CURRENT_WORD}"
@@ -1682,8 +1708,9 @@ python - <<EOF
 """
 List all of the category names in the categories.yaml file
 """
-from utils.repo import get_user_yaml_path
-from utils.miscell import read_yaml
+# CWL ICA imports
+from cwl_ica.utils.repo import get_user_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each project name
 for user in read_yaml(get_user_yaml_path())["users"]:
@@ -1702,13 +1729,14 @@ python - <<EOF
 List the unregistered tool paths
 """
 
-from utils.repo import get_tool_yaml_path
-from utils.repo import get_tools_dir
-from utils.miscell import read_yaml
+# Externals
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA
+from cwl_ica.utils.repo import get_tools_dir
+
 # Get the current word value
 if not "${CURRENT_WORD}" == "":
     current_word_value = "${CURRENT_WORD}"
@@ -1797,8 +1825,9 @@ python - <<EOF
 """
 List all of the category names in the categories.yaml file
 """
-from utils.repo import get_user_yaml_path
-from utils.miscell import read_yaml
+# CWL ICA imports
+from cwl_ica.utils.repo import get_user_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each project name
 for user in read_yaml(get_user_yaml_path())["users"]:
@@ -1817,13 +1846,14 @@ python - <<EOF
 List the unregistered workflow paths
 """
 
-from utils.repo import get_workflow_yaml_path
-from utils.repo import get_workflows_dir
-from utils.miscell import read_yaml
+# Externals
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA
+from cwl_ica.utils.repo import get_workflows_dir
+
 # Get the current word value
 if not "${CURRENT_WORD}" == "":
     current_word_value = "${CURRENT_WORD}"
@@ -1913,8 +1943,9 @@ python - <<EOF
 """
 List all of the category names in the categories.yaml file
 """
-from utils.repo import get_user_yaml_path
-from utils.miscell import read_yaml
+# CWL ICA imports
+from cwl_ica.utils.repo import get_user_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each project name
 for user in read_yaml(get_user_yaml_path())["users"]:
@@ -1933,13 +1964,16 @@ python - <<EOF
 List the registered tool paths
 """
 
-from utils.repo import get_tool_yaml_path
-from utils.repo import get_tools_dir
-from utils.miscell import read_yaml
+# External imports
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA
+from cwl_ica.utils.repo import get_tool_yaml_path
+from cwl_ica.utils.repo import get_tools_dir
+from cwl_ica.utils.miscell import read_yaml
+
 tool_paths = [
     Path(tool["path"]) / Path(version["path"])
     for tool in read_yaml(get_tool_yaml_path())["tools"]
@@ -2023,8 +2057,8 @@ python - <<EOF
 """
 List all of the project names in the project.yaml file
 """
-from utils.repo import get_project_yaml_path
-from utils.miscell import read_yaml
+from cwl_ica.utils.repo import get_project_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each project name
 for project in read_yaml(get_project_yaml_path())["projects"]:
@@ -2043,13 +2077,16 @@ python - <<EOF
 List the registered workflow paths
 """
 
-from utils.repo import get_workflow_yaml_path
-from utils.repo import get_workflows_dir
-from utils.miscell import read_yaml
+# External imports
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA
+from cwl_ica.utils.repo import get_workflow_yaml_path
+from cwl_ica.utils.repo import get_workflows_dir
+from cwl_ica.utils.miscell import read_yaml
+
 workflow_paths = [
     Path(workflow["path"]) / Path(version["path"])
     for workflow in read_yaml(get_workflow_yaml_path())["workflows"]
@@ -2134,8 +2171,8 @@ python - <<EOF
 """
 List all of the project names in the project.yaml file
 """
-from utils.repo import get_project_yaml_path
-from utils.miscell import read_yaml
+from cwl_ica.utils.repo import get_project_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each project name
 for project in read_yaml(get_project_yaml_path())["projects"]:
@@ -2154,13 +2191,14 @@ python - <<EOF
 List the unregistered tool paths
 """
 
-from utils.repo import get_tool_yaml_path
-from utils.repo import get_tools_dir
-from utils.miscell import read_yaml
+# Externals
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA
+from cwl_ica.utils.repo import get_tools_dir
+
 # Get the current word value
 if not "${CURRENT_WORD}" == "":
     current_word_value = "${CURRENT_WORD}"
@@ -2250,13 +2288,16 @@ python - <<EOF
 List the unregistered expression paths
 """
 
-from utils.repo import get_expression_yaml_path
-from utils.repo import get_expressions_dir
-from utils.miscell import read_yaml
+# Externals
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA
+from cwl_ica.utils.repo import get_expression_yaml_path
+from cwl_ica.utils.repo import get_expressions_dir
+from cwl_ica.utils.miscell import read_yaml
+
 # Get the current word value
 if not "${CURRENT_WORD}" == "":
     current_word_value = "${CURRENT_WORD}"
@@ -2347,13 +2388,14 @@ python - <<EOF
 List the unregistered workflow paths
 """
 
-from utils.repo import get_workflow_yaml_path
-from utils.repo import get_workflows_dir
-from utils.miscell import read_yaml
+# Externals
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA
+from cwl_ica.utils.repo import get_workflows_dir
+
 # Get the current word value
 if not "${CURRENT_WORD}" == "":
     current_word_value = "${CURRENT_WORD}"
@@ -2443,8 +2485,9 @@ python - <<EOF
 """
 List all of the run instance ids in the run.yaml file
 """
-from utils.repo import get_run_yaml_path
-from utils.miscell import read_yaml
+# CWL ICA imports
+from cwl_ica.utils.repo import get_run_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each run instance id
 for run in read_yaml(get_run_yaml_path())["runs"]:
@@ -2462,8 +2505,9 @@ python - <<EOF
 """
 List all of the run instance ids in the run.yaml file
 """
-from utils.repo import get_run_yaml_path
-from utils.miscell import read_yaml
+# CWL ICA imports
+from cwl_ica.utils.repo import get_run_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each run instance id
 for run in read_yaml(get_run_yaml_path())["runs"]:
@@ -2481,8 +2525,9 @@ python - <<EOF
 """
 List all of the category names in the categories.yaml file
 """
-from utils.repo import get_user_yaml_path
-from utils.miscell import read_yaml
+# CWL ICA imports
+from cwl_ica.utils.repo import get_user_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each project name
 for user in read_yaml(get_user_yaml_path())["users"]:
@@ -2500,8 +2545,9 @@ python - <<EOF
 """
 List all of the category names in the categories.yaml file
 """
-from utils.repo import get_user_yaml_path
-from utils.miscell import read_yaml
+# CWL ICA imports
+from cwl_ica.utils.repo import get_user_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each project name
 for user in read_yaml(get_user_yaml_path())["users"]:
@@ -2520,13 +2566,14 @@ python - <<EOF
 List the unregistered tool paths
 """
 
-from utils.repo import get_tool_yaml_path
-from utils.repo import get_tools_dir
-from utils.miscell import read_yaml
+# Externals
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA
+from cwl_ica.utils.repo import get_tools_dir
+
 # Get the current word value
 if not "${CURRENT_WORD}" == "":
     current_word_value = "${CURRENT_WORD}"
@@ -2615,8 +2662,8 @@ python - <<EOF
 """
 List all of the project names in the project.yaml file
 """
-from utils.repo import get_project_yaml_path
-from utils.miscell import read_yaml
+from cwl_ica.utils.repo import get_project_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each project name
 for project in read_yaml(get_project_yaml_path())["projects"]:
@@ -2679,8 +2726,9 @@ python - <<EOF
 """
 List all of the category names in the categories.yaml file
 """
-from utils.repo import get_user_yaml_path
-from utils.miscell import read_yaml
+# CWL ICA imports
+from cwl_ica.utils.repo import get_user_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each project name
 for user in read_yaml(get_user_yaml_path())["users"]:
@@ -2699,13 +2747,14 @@ python - <<EOF
 List the unregistered schema paths
 """
 
-from utils.repo import get_schema_yaml_path
-from utils.repo import get_schemas_dir
-from utils.miscell import read_yaml
+# Externals
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA
+from cwl_ica.utils.repo import get_schemas_dir
+
 # Get the current word value
 if not "${CURRENT_WORD-}" == "":
     current_word_value = "${CURRENT_WORD}"
@@ -2794,8 +2843,9 @@ python - <<EOF
 """
 List all of the category names in the categories.yaml file
 """
-from utils.repo import get_user_yaml_path
-from utils.miscell import read_yaml
+# CWL ICA imports
+from cwl_ica.utils.repo import get_user_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each project name
 for user in read_yaml(get_user_yaml_path())["users"]:
@@ -2814,13 +2864,14 @@ python - <<EOF
 List the unregistered workflow paths
 """
 
-from utils.repo import get_workflow_yaml_path
-from utils.repo import get_workflows_dir
-from utils.miscell import read_yaml
+# Externals
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA
+from cwl_ica.utils.repo import get_workflows_dir
+
 # Get the current word value
 if not "${CURRENT_WORD}" == "":
     current_word_value = "${CURRENT_WORD}"
@@ -2910,8 +2961,8 @@ python - <<EOF
 """
 List all of the project names in the project.yaml file
 """
-from utils.repo import get_project_yaml_path
-from utils.miscell import read_yaml
+from cwl_ica.utils.repo import get_project_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each project name
 for project in read_yaml(get_project_yaml_path())["projects"]:
@@ -3105,13 +3156,16 @@ python - <<EOF
 List the unregistered expression paths
 """
 
-from utils.repo import get_expression_yaml_path
-from utils.repo import get_expressions_dir
-from utils.miscell import read_yaml
+# External
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA imports
+from cwl_ica.utils.repo import get_expression_yaml_path
+from cwl_ica.utils.repo import get_expressions_dir
+from cwl_ica.utils.miscell import read_yaml
+
 registered_expression_paths = [
     Path(expression["path"]) / Path(version["path"])
     for expression in read_yaml(get_expression_yaml_path())["expressions"]
@@ -3213,13 +3267,14 @@ python - <<EOF
 List the registered expression paths
 """
 
-from utils.repo import get_expression_yaml_path
-from utils.repo import get_expressions_dir
-from utils.miscell import read_yaml
+# Externals
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA
+from cwl_ica.utils.repo import get_expression_yaml_path, read_yaml, get_expressions_dir
+
 expression_paths = [
     Path(expression["path"]) / Path(version["path"])
     for expression in read_yaml(get_expression_yaml_path())["expressions"]
@@ -3303,13 +3358,14 @@ python - <<EOF
 List the registered expression paths
 """
 
-from utils.repo import get_expression_yaml_path
-from utils.repo import get_expressions_dir
-from utils.miscell import read_yaml
+# Externals
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA
+from cwl_ica.utils.repo import get_expression_yaml_path, read_yaml, get_expressions_dir
+
 expression_paths = [
     Path(expression["path"]) / Path(version["path"])
     for expression in read_yaml(get_expression_yaml_path())["expressions"]
@@ -3393,13 +3449,14 @@ python - <<EOF
 List the unregistered workflow paths
 """
 
-from utils.repo import get_workflow_yaml_path
-from utils.repo import get_workflows_dir
-from utils.miscell import read_yaml
+# Externals
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA
+from cwl_ica.utils.repo import get_workflows_dir
+
 # Get the current word value
 if not "${CURRENT_WORD}" == "":
     current_word_value = "${CURRENT_WORD}"
@@ -3743,13 +3800,14 @@ python - <<EOF
 List the unregistered workflow paths
 """
 
-from utils.repo import get_workflow_yaml_path
-from utils.repo import get_workflows_dir
-from utils.miscell import read_yaml
+# Externals
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA
+from cwl_ica.utils.repo import get_workflows_dir
+
 # Get the current word value
 if not "${CURRENT_WORD}" == "":
     current_word_value = "${CURRENT_WORD}"
@@ -3836,8 +3894,9 @@ _cwl-ica_list-projects_option_tenant_name_completion() {
 python - <<EOF
 #!/usr/bin/env python
 
-from utils.repo import get_tenant_yaml_path
-from utils.miscell import read_yaml
+# CWL ICA imports
+from cwl_ica.utils.repo import get_tenant_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 for tenant in read_yaml(get_tenant_yaml_path())["tenants"]:
     print(tenant["tenant_name"])
@@ -3855,13 +3914,16 @@ python - <<EOF
 List the registered tool paths
 """
 
-from utils.repo import get_tool_yaml_path
-from utils.repo import get_tools_dir
-from utils.miscell import read_yaml
+# External imports
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA
+from cwl_ica.utils.repo import get_tool_yaml_path
+from cwl_ica.utils.repo import get_tools_dir
+from cwl_ica.utils.miscell import read_yaml
+
 tool_paths = [
     Path(tool["path"]) / Path(version["path"])
     for tool in read_yaml(get_tool_yaml_path())["tools"]
@@ -3945,8 +4007,8 @@ python - <<EOF
 """
 List all of the project names in the project.yaml file
 """
-from utils.repo import get_project_yaml_path
-from utils.miscell import read_yaml
+from cwl_ica.utils.repo import get_project_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each project name
 for project in read_yaml(get_project_yaml_path())["projects"]:
@@ -3973,8 +4035,8 @@ python - <<EOF
 """
 List all of the project names in the project.yaml file
 """
-from utils.repo import get_project_yaml_path
-from utils.miscell import read_yaml
+from cwl_ica.utils.repo import get_project_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each project name
 for project in read_yaml(get_project_yaml_path())["projects"]:
@@ -3989,8 +4051,9 @@ _cwl-ica_project-init_option_tenant_name_completion() {
 python - <<EOF
 #!/usr/bin/env python
 
-from utils.repo import get_tenant_yaml_path
-from utils.miscell import read_yaml
+# CWL ICA imports
+from cwl_ica.utils.repo import get_tenant_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 for tenant in read_yaml(get_tenant_yaml_path())["tenants"]:
     print(tenant["tenant_name"])
@@ -4007,8 +4070,8 @@ python - <<EOF
 """
 List all of the project names in the project.yaml file
 """
-from utils.repo import get_project_yaml_path
-from utils.miscell import read_yaml
+from cwl_ica.utils.repo import get_project_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each project name
 for project in read_yaml(get_project_yaml_path())["projects"]:
@@ -4026,8 +4089,8 @@ python - <<EOF
 """
 List all of the project names in the project.yaml file
 """
-from utils.repo import get_project_yaml_path
-from utils.miscell import read_yaml
+from cwl_ica.utils.repo import get_project_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each project name
 for project in read_yaml(get_project_yaml_path())["projects"]:
@@ -4046,13 +4109,17 @@ python - <<EOF
 List the unregistered schema paths
 """
 
-from utils.repo import get_schema_yaml_path
-from utils.repo import get_schemas_dir
-from utils.miscell import read_yaml
+# External imports
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA imports
+from cwl_ica.utils.repo import get_schema_yaml_path
+from cwl_ica.utils.repo import get_schemas_dir
+from cwl_ica.utils.miscell import read_yaml
+
+
 registered_schema_paths = [
     Path(schema["path"]) / Path(version["path"])
     for schema in read_yaml(get_schema_yaml_path())["schemas"]
@@ -4152,13 +4219,14 @@ python - <<EOF
 List the registered schema paths
 """
 
-from utils.repo import get_schema_yaml_path
-from utils.repo import get_schemas_dir
-from utils.miscell import read_yaml
+# Externals
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA
+from cwl_ica.utils.repo import read_yaml, get_schema_yaml_path, get_schemas_dir
+
 schema_paths = [
     Path(schema["path"]) / Path(version["path"])
     for schema in read_yaml(get_schema_yaml_path())["schemas"]
@@ -4241,13 +4309,14 @@ python - <<EOF
 List the unregistered schema paths
 """
 
-from utils.repo import get_schema_yaml_path
-from utils.repo import get_schemas_dir
-from utils.miscell import read_yaml
+# Externals
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA
+from cwl_ica.utils.repo import get_schemas_dir
+
 # Get the current word value
 if not "${CURRENT_WORD-}" == "":
     current_word_value = "${CURRENT_WORD}"
@@ -4336,8 +4405,8 @@ python - <<EOF
 """
 List all of the project names in the project.yaml file
 """
-from utils.repo import get_project_yaml_path
-from utils.miscell import read_yaml
+from cwl_ica.utils.repo import get_project_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each project name
 for project in read_yaml(get_project_yaml_path())["projects"]:
@@ -4352,8 +4421,9 @@ _cwl-ica_set-default-tenant_option_tenant_name_completion() {
 python - <<EOF
 #!/usr/bin/env python
 
-from utils.repo import get_tenant_yaml_path
-from utils.miscell import read_yaml
+# CWL ICA imports
+from cwl_ica.utils.repo import get_tenant_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 for tenant in read_yaml(get_tenant_yaml_path())["tenants"]:
     print(tenant["tenant_name"])
@@ -4370,8 +4440,9 @@ python - <<EOF
 """
 List all of the category names in the categories.yaml file
 """
-from utils.repo import get_user_yaml_path
-from utils.miscell import read_yaml
+# CWL ICA imports
+from cwl_ica.utils.repo import get_user_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each project name
 for user in read_yaml(get_user_yaml_path())["users"]:
@@ -4390,13 +4461,17 @@ python - <<EOF
 List the unregistered tool paths
 """
 
-from utils.repo import get_tool_yaml_path
-from utils.repo import get_tools_dir
-from utils.miscell import read_yaml
+# External imports
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA imports
+from cwl_ica.utils.repo import get_tool_yaml_path
+from cwl_ica.utils.repo import get_tools_dir
+from cwl_ica.utils.miscell import read_yaml
+
+
 registered_tool_paths = [
     Path(tool["path"]) / Path(version["path"])
     for tool in read_yaml(get_tool_yaml_path())["tools"]
@@ -4496,8 +4571,8 @@ python - <<EOF
 """
 List all of the project names in the project.yaml file
 """
-from utils.repo import get_project_yaml_path
-from utils.miscell import read_yaml
+from cwl_ica.utils.repo import get_project_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each project name
 for project in read_yaml(get_project_yaml_path())["projects"]:
@@ -4512,8 +4587,9 @@ _cwl-ica_tool-init_option_tenants_completion() {
 python - <<EOF
 #!/usr/bin/env python
 
-from utils.repo import get_tenant_yaml_path
-from utils.miscell import read_yaml
+# CWL ICA imports
+from cwl_ica.utils.repo import get_tenant_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 for tenant in read_yaml(get_tenant_yaml_path())["tenants"]:
     print(tenant["tenant_name"])
@@ -4530,8 +4606,8 @@ python - <<EOF
 """
 List all of the category names in the categories.yaml file
 """
-from utils.repo import get_category_yaml_path
-from utils.miscell import read_yaml
+from cwl_ica.utils.repo import get_category_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each project name
 for category in read_yaml(get_category_yaml_path())["categories"]:
@@ -4550,13 +4626,16 @@ python - <<EOF
 List the registered tool paths
 """
 
-from utils.repo import get_tool_yaml_path
-from utils.repo import get_tools_dir
-from utils.miscell import read_yaml
+# External imports
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA
+from cwl_ica.utils.repo import get_tool_yaml_path
+from cwl_ica.utils.repo import get_tools_dir
+from cwl_ica.utils.miscell import read_yaml
+
 tool_paths = [
     Path(tool["path"]) / Path(version["path"])
     for tool in read_yaml(get_tool_yaml_path())["tools"]
@@ -4640,8 +4719,8 @@ python - <<EOF
 """
 List all of the project names in the project.yaml file
 """
-from utils.repo import get_project_yaml_path
-from utils.miscell import read_yaml
+from cwl_ica.utils.repo import get_project_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each project name
 for project in read_yaml(get_project_yaml_path())["projects"]:
@@ -4656,8 +4735,9 @@ _cwl-ica_tool-sync_option_tenants_completion() {
 python - <<EOF
 #!/usr/bin/env python
 
-from utils.repo import get_tenant_yaml_path
-from utils.miscell import read_yaml
+# CWL ICA imports
+from cwl_ica.utils.repo import get_tenant_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 for tenant in read_yaml(get_tenant_yaml_path())["tenants"]:
     print(tenant["tenant_name"])
@@ -4675,13 +4755,14 @@ python - <<EOF
 List the unregistered tool paths
 """
 
-from utils.repo import get_tool_yaml_path
-from utils.repo import get_tools_dir
-from utils.miscell import read_yaml
+# Externals
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA
+from cwl_ica.utils.repo import get_tools_dir
+
 # Get the current word value
 if not "${CURRENT_WORD}" == "":
     current_word_value = "${CURRENT_WORD}"
@@ -4761,6 +4842,122 @@ EOF
 )"
     _cwl-ica_compreply "$param_tool_path"
 }
+_cwl-ica_typescript-expression-update_option_typescript_expression_dir_completion() {
+    local CURRENT_WORD="${words[$cword]}"
+    local param_typescript_expression_dir="$(
+python - <<EOF
+#!/usr/bin/env python3
+
+"""
+List all the typescript expression paths
+"""
+
+# Externals
+from pathlib import Path
+from os import getcwd
+from os.path import relpath
+
+# CWL ICA
+from cwl_ica.utils.repo import get_cwl_ica_repo_path
+
+# Get the current word value
+if not "${CURRENT_WORD}" == "":
+    current_word_value = "${CURRENT_WORD}"
+else:
+    current_word_value = None
+
+if current_word_value is None:
+    current_word_value = ""
+    current_path_resolved = Path(getcwd()).absolute()
+    typescript_expression_paths = [
+        s_file.parent.relative_to(get_cwl_ica_repo_path())
+        for s_file in get_cwl_ica_repo_path().glob("**/*.ts")
+        # We don't want to pull in the typescript test files
+        if not (len(s_file.parent.parts) >= 1 and s_file.parent.parts[-1] == 'tests') and
+        # We also want to make sure it's under the tools, expressions or typescript-expressions directories
+        len(
+            {"tools", "expressions", "typescript-expressions"}.intersection(
+                [
+                    s_file.resolve().absolute().relative_to(get_cwl_ica_repo_path()).parent.parts[0]
+                ]
+            )
+        ) > 0
+    ]
+else:
+    if current_word_value.endswith("/"):
+        current_path_resolved = Path(getcwd()).joinpath(Path(current_word_value)).resolve()
+    else:
+        current_path_resolved = Path(getcwd()).joinpath(Path(current_word_value).parent).resolve()
+
+    typescript_expression_paths = [
+        s_file.parent.relative_to(get_cwl_ica_repo_path())
+        for s_file in current_path_resolved.glob("**/*.ts")
+        # We don't want to pull in the typescript test files
+        if not (len(s_file.parent.parts) >= 1 and s_file.parent.parts[-1] == 'tests') and
+           # We also want to make sure it's under the tools, expressions or typescript-expressions directories
+           len(
+               {"tools", "expressions", "typescript-expressions"}.intersection(
+                   [
+                       s_file.resolve().absolute().relative_to(get_cwl_ica_repo_path()).parent.parts[0]
+                   ]
+               )
+           ) > 0
+    ]
+
+# Resolve the current path
+# If getcwd() is "/c/Users/awluc"
+# 1. Non relative paths: current_word_value = "/etc" -> current_path_resolved = "/etc"
+# 2. Relative parent path: current_word_value = "../../Program Files" -> current_path_resolved = "/c/Program Files"
+# 3. Subfolder: current_word_value = "OneDrive" -> current_path_resolved = "/c/Users/awluc/OneDrive"
+# 4. Subfolder of expressions dir = "OneDrive/GitHub/UMCCR/expressions/contig/" -> current path resolved
+
+# Is the current_path_resolved a subpath of the expressions directory?
+try:
+    _ = current_path_resolved.relative_to(get_cwl_ica_repo_path())
+    in_repo_dir = True
+except ValueError:
+    in_repo_dir = False
+
+if in_repo_dir:
+    current_path_resolved_relative_to_expressions_dir = current_path_resolved.relative_to(get_cwl_ica_repo_path())
+    if current_path_resolved_relative_to_expressions_dir == Path("."):
+        for s_path in typescript_expression_paths:
+            if current_word_value.endswith("/"):
+                print(Path(current_word_value) / s_path)
+            else:
+                print(Path(current_word_value).parent / s_path)
+    else:
+        for s_path in typescript_expression_paths:
+            if str(s_path).startswith(str(current_path_resolved_relative_to_expressions_dir)):
+                if current_word_value.endswith("/"):
+                    print(Path(current_word_value) / s_path.relative_to(
+                        current_path_resolved_relative_to_expressions_dir))
+                else:
+                    print(Path(current_word_value).parent / s_path.relative_to(
+                        current_path_resolved_relative_to_expressions_dir))
+
+else:
+    # Now get the expressions yaml path relative to the current path
+    try:
+        expressions_dir = get_cwl_ica_repo_path().relative_to(current_path_resolved)
+    except ValueError:
+        # We could be in a different mount point OR just in a subdirectory
+        if str(get_cwl_ica_repo_path().absolute()) in str(relpath(get_cwl_ica_repo_path(), current_path_resolved)):
+            # Separate mount point
+            expressions_dir = get_cwl_ica_repo_path().absolute()
+        else:
+            expressions_dir = Path(relpath(get_cwl_ica_repo_path(), current_path_resolved))
+
+    # Now iterate through paths
+    for s_path in typescript_expression_paths:
+        if current_word_value.endswith("/"):
+            print(Path(current_word_value) / expressions_dir.joinpath(s_path))
+        else:
+            print(Path(current_word_value).parent / expressions_dir.joinpath(s_path))
+EOF
+)"
+    _cwl-ica_compreply "$param_typescript_expression_dir"
+}
 _cwl-ica_typescript-expression-validate_option_typescript_expression_dir_completion() {
     local CURRENT_WORD="${words[$cword]}"
     local param_typescript_expression_dir="$(
@@ -4771,13 +4968,14 @@ python - <<EOF
 List all the typescript expression paths
 """
 
-from utils.repo import get_expression_yaml_path
-from utils.repo import get_cwl_ica_repo_path
-from utils.miscell import read_yaml
+# Externals
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA
+from cwl_ica.utils.repo import get_cwl_ica_repo_path
+
 # Get the current word value
 if not "${CURRENT_WORD}" == "":
     current_word_value = "${CURRENT_WORD}"
@@ -4885,8 +5083,8 @@ python - <<EOF
 """
 List all of the project names in the project.yaml file
 """
-from utils.repo import get_project_yaml_path
-from utils.miscell import read_yaml
+from cwl_ica.utils.repo import get_project_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each project name
 for project in read_yaml(get_project_yaml_path())["projects"]:
@@ -4905,13 +5103,17 @@ python - <<EOF
 List the unregistered workflow paths
 """
 
-from utils.repo import get_workflow_yaml_path
-from utils.repo import get_workflows_dir
-from utils.miscell import read_yaml
+# External imports
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA imports
+from cwl_ica.utils.repo import get_workflow_yaml_path
+from cwl_ica.utils.repo import get_workflows_dir
+from cwl_ica.utils.miscell import read_yaml
+
+
 registered_workflow_paths = [
     Path(workflow["path"]) / Path(version["path"])
     for workflow in read_yaml(get_workflow_yaml_path())["workflows"]
@@ -5012,8 +5214,8 @@ python - <<EOF
 """
 List all of the project names in the project.yaml file
 """
-from utils.repo import get_project_yaml_path
-from utils.miscell import read_yaml
+from cwl_ica.utils.repo import get_project_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each project name
 for project in read_yaml(get_project_yaml_path())["projects"]:
@@ -5028,8 +5230,9 @@ _cwl-ica_workflow-init_option_tenants_completion() {
 python - <<EOF
 #!/usr/bin/env python
 
-from utils.repo import get_tenant_yaml_path
-from utils.miscell import read_yaml
+# CWL ICA imports
+from cwl_ica.utils.repo import get_tenant_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 for tenant in read_yaml(get_tenant_yaml_path())["tenants"]:
     print(tenant["tenant_name"])
@@ -5046,8 +5249,8 @@ python - <<EOF
 """
 List all of the category names in the categories.yaml file
 """
-from utils.repo import get_category_yaml_path
-from utils.miscell import read_yaml
+from cwl_ica.utils.repo import get_category_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each project name
 for category in read_yaml(get_category_yaml_path())["categories"]:
@@ -5066,13 +5269,16 @@ python - <<EOF
 List the registered workflow paths
 """
 
-from utils.repo import get_workflow_yaml_path
-from utils.repo import get_workflows_dir
-from utils.miscell import read_yaml
+# External imports
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA
+from cwl_ica.utils.repo import get_workflow_yaml_path
+from cwl_ica.utils.repo import get_workflows_dir
+from cwl_ica.utils.miscell import read_yaml
+
 workflow_paths = [
     Path(workflow["path"]) / Path(version["path"])
     for workflow in read_yaml(get_workflow_yaml_path())["workflows"]
@@ -5157,8 +5363,8 @@ python - <<EOF
 """
 List all of the project names in the project.yaml file
 """
-from utils.repo import get_project_yaml_path
-from utils.miscell import read_yaml
+from cwl_ica.utils.repo import get_project_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each project name
 for project in read_yaml(get_project_yaml_path())["projects"]:
@@ -5173,8 +5379,9 @@ _cwl-ica_workflow-sync_option_tenants_completion() {
 python - <<EOF
 #!/usr/bin/env python
 
-from utils.repo import get_tenant_yaml_path
-from utils.miscell import read_yaml
+# CWL ICA imports
+from cwl_ica.utils.repo import get_tenant_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 for tenant in read_yaml(get_tenant_yaml_path())["tenants"]:
     print(tenant["tenant_name"])
@@ -5192,13 +5399,14 @@ python - <<EOF
 List the unregistered workflow paths
 """
 
-from utils.repo import get_workflow_yaml_path
-from utils.repo import get_workflows_dir
-from utils.miscell import read_yaml
+# Externals
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA
+from cwl_ica.utils.repo import get_workflows_dir
+
 # Get the current word value
 if not "${CURRENT_WORD}" == "":
     current_word_value = "${CURRENT_WORD}"
diff --git a/autocompletion/helpers/_cwl-ica_list_all_expression_paths.py b/autocompletion/helpers/_cwl-ica_list_all_expression_paths.py
index ff55935..e748949 100644
--- a/autocompletion/helpers/_cwl-ica_list_all_expression_paths.py
+++ b/autocompletion/helpers/_cwl-ica_list_all_expression_paths.py
@@ -4,13 +4,16 @@
 List the unregistered expression paths
 """
 
-from utils.repo import get_expression_yaml_path
-from utils.repo import get_expressions_dir
-from utils.miscell import read_yaml
+# Externals
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA
+from cwl_ica.utils.repo import get_expression_yaml_path
+from cwl_ica.utils.repo import get_expressions_dir
+from cwl_ica.utils.miscell import read_yaml
+
 # Get the current word value
 if not "${CURRENT_WORD}" == "":
     current_word_value = "${CURRENT_WORD}"
diff --git a/autocompletion/helpers/_cwl-ica_list_all_schema_paths.py b/autocompletion/helpers/_cwl-ica_list_all_schema_paths.py
index 9d8e02e..cae6fa6 100644
--- a/autocompletion/helpers/_cwl-ica_list_all_schema_paths.py
+++ b/autocompletion/helpers/_cwl-ica_list_all_schema_paths.py
@@ -4,13 +4,14 @@
 List the unregistered schema paths
 """
 
-from utils.repo import get_schema_yaml_path
-from utils.repo import get_schemas_dir
-from utils.miscell import read_yaml
+# Externals
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA
+from cwl_ica.utils.repo import get_schemas_dir
+
 # Get the current word value
 if not "${CURRENT_WORD-}" == "":
     current_word_value = "${CURRENT_WORD}"
diff --git a/autocompletion/helpers/_cwl-ica_list_all_tool_paths.py b/autocompletion/helpers/_cwl-ica_list_all_tool_paths.py
index c095b27..ab4c73f 100644
--- a/autocompletion/helpers/_cwl-ica_list_all_tool_paths.py
+++ b/autocompletion/helpers/_cwl-ica_list_all_tool_paths.py
@@ -4,13 +4,14 @@
 List the unregistered tool paths
 """
 
-from utils.repo import get_tool_yaml_path
-from utils.repo import get_tools_dir
-from utils.miscell import read_yaml
+# Externals
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA
+from cwl_ica.utils.repo import get_tools_dir
+
 # Get the current word value
 if not "${CURRENT_WORD}" == "":
     current_word_value = "${CURRENT_WORD}"
diff --git a/autocompletion/helpers/_cwl-ica_list_all_typescript_expression_paths.py b/autocompletion/helpers/_cwl-ica_list_all_typescript_expression_paths.py
index e2ce79a..bd39ea4 100644
--- a/autocompletion/helpers/_cwl-ica_list_all_typescript_expression_paths.py
+++ b/autocompletion/helpers/_cwl-ica_list_all_typescript_expression_paths.py
@@ -4,13 +4,14 @@
 List all the typescript expression paths
 """
 
-from utils.repo import get_expression_yaml_path
-from utils.repo import get_cwl_ica_repo_path
-from utils.miscell import read_yaml
+# Externals
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA
+from cwl_ica.utils.repo import get_cwl_ica_repo_path
+
 # Get the current word value
 if not "${CURRENT_WORD}" == "":
     current_word_value = "${CURRENT_WORD}"
diff --git a/autocompletion/helpers/_cwl-ica_list_all_workflow_paths.py b/autocompletion/helpers/_cwl-ica_list_all_workflow_paths.py
index c5c70b7..8272986 100644
--- a/autocompletion/helpers/_cwl-ica_list_all_workflow_paths.py
+++ b/autocompletion/helpers/_cwl-ica_list_all_workflow_paths.py
@@ -4,13 +4,14 @@
 List the unregistered workflow paths
 """
 
-from utils.repo import get_workflow_yaml_path
-from utils.repo import get_workflows_dir
-from utils.miscell import read_yaml
+# Externals
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA
+from cwl_ica.utils.repo import get_workflows_dir
+
 # Get the current word value
 if not "${CURRENT_WORD}" == "":
     current_word_value = "${CURRENT_WORD}"
diff --git a/autocompletion/helpers/_cwl-ica_list_category_names.py b/autocompletion/helpers/_cwl-ica_list_category_names.py
index e80b98f..d6a6303 100644
--- a/autocompletion/helpers/_cwl-ica_list_category_names.py
+++ b/autocompletion/helpers/_cwl-ica_list_category_names.py
@@ -3,8 +3,8 @@
 """
 List all of the category names in the categories.yaml file
 """
-from utils.repo import get_category_yaml_path
-from utils.miscell import read_yaml
+from cwl_ica.utils.repo import get_category_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each project name
 for category in read_yaml(get_category_yaml_path())["categories"]:
diff --git a/autocompletion/helpers/_cwl-ica_list_project_names.py b/autocompletion/helpers/_cwl-ica_list_project_names.py
index b17e246..7447c55 100644
--- a/autocompletion/helpers/_cwl-ica_list_project_names.py
+++ b/autocompletion/helpers/_cwl-ica_list_project_names.py
@@ -3,8 +3,8 @@
 """
 List all of the project names in the project.yaml file
 """
-from utils.repo import get_project_yaml_path
-from utils.miscell import read_yaml
+from cwl_ica.utils.repo import get_project_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each project name
 for project in read_yaml(get_project_yaml_path())["projects"]:
diff --git a/autocompletion/helpers/_cwl-ica_list_registered_expression_paths.py b/autocompletion/helpers/_cwl-ica_list_registered_expression_paths.py
index bbf73fa..781ca90 100644
--- a/autocompletion/helpers/_cwl-ica_list_registered_expression_paths.py
+++ b/autocompletion/helpers/_cwl-ica_list_registered_expression_paths.py
@@ -4,13 +4,14 @@
 List the registered expression paths
 """
 
-from utils.repo import get_expression_yaml_path
-from utils.repo import get_expressions_dir
-from utils.miscell import read_yaml
+# Externals
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA
+from cwl_ica.utils.repo import get_expression_yaml_path, read_yaml, get_expressions_dir
+
 expression_paths = [
     Path(expression["path"]) / Path(version["path"])
     for expression in read_yaml(get_expression_yaml_path())["expressions"]
diff --git a/autocompletion/helpers/_cwl-ica_list_registered_schema_paths.py b/autocompletion/helpers/_cwl-ica_list_registered_schema_paths.py
index a982617..f01920f 100644
--- a/autocompletion/helpers/_cwl-ica_list_registered_schema_paths.py
+++ b/autocompletion/helpers/_cwl-ica_list_registered_schema_paths.py
@@ -4,13 +4,14 @@
 List the registered schema paths
 """
 
-from utils.repo import get_schema_yaml_path
-from utils.repo import get_schemas_dir
-from utils.miscell import read_yaml
+# Externals
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA
+from cwl_ica.utils.repo import read_yaml, get_schema_yaml_path, get_schemas_dir
+
 schema_paths = [
     Path(schema["path"]) / Path(version["path"])
     for schema in read_yaml(get_schema_yaml_path())["schemas"]
diff --git a/autocompletion/helpers/_cwl-ica_list_registered_tool_paths.py b/autocompletion/helpers/_cwl-ica_list_registered_tool_paths.py
index f6c13d7..04f227b 100644
--- a/autocompletion/helpers/_cwl-ica_list_registered_tool_paths.py
+++ b/autocompletion/helpers/_cwl-ica_list_registered_tool_paths.py
@@ -4,13 +4,16 @@
 List the registered tool paths
 """
 
-from utils.repo import get_tool_yaml_path
-from utils.repo import get_tools_dir
-from utils.miscell import read_yaml
+# External imports
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA
+from cwl_ica.utils.repo import get_tool_yaml_path
+from cwl_ica.utils.repo import get_tools_dir
+from cwl_ica.utils.miscell import read_yaml
+
 tool_paths = [
     Path(tool["path"]) / Path(version["path"])
     for tool in read_yaml(get_tool_yaml_path())["tools"]
diff --git a/autocompletion/helpers/_cwl-ica_list_registered_workflow_paths.py b/autocompletion/helpers/_cwl-ica_list_registered_workflow_paths.py
index 46e4b89..0ea5dad 100644
--- a/autocompletion/helpers/_cwl-ica_list_registered_workflow_paths.py
+++ b/autocompletion/helpers/_cwl-ica_list_registered_workflow_paths.py
@@ -4,13 +4,16 @@
 List the registered workflow paths
 """
 
-from utils.repo import get_workflow_yaml_path
-from utils.repo import get_workflows_dir
-from utils.miscell import read_yaml
+# External imports
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA
+from cwl_ica.utils.repo import get_workflow_yaml_path
+from cwl_ica.utils.repo import get_workflows_dir
+from cwl_ica.utils.miscell import read_yaml
+
 workflow_paths = [
     Path(workflow["path"]) / Path(version["path"])
     for workflow in read_yaml(get_workflow_yaml_path())["workflows"]
diff --git a/autocompletion/helpers/_cwl-ica_list_run_instance_ids.py b/autocompletion/helpers/_cwl-ica_list_run_instance_ids.py
index 3a34598..5359159 100644
--- a/autocompletion/helpers/_cwl-ica_list_run_instance_ids.py
+++ b/autocompletion/helpers/_cwl-ica_list_run_instance_ids.py
@@ -3,8 +3,9 @@
 """
 List all of the run instance ids in the run.yaml file
 """
-from utils.repo import get_run_yaml_path
-from utils.miscell import read_yaml
+# CWL ICA imports
+from cwl_ica.utils.repo import get_run_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each run instance id
 for run in read_yaml(get_run_yaml_path())["runs"]:
diff --git a/autocompletion/helpers/_cwl-ica_list_tenant_names.py b/autocompletion/helpers/_cwl-ica_list_tenant_names.py
index 7eb8f0a..fba8a2d 100644
--- a/autocompletion/helpers/_cwl-ica_list_tenant_names.py
+++ b/autocompletion/helpers/_cwl-ica_list_tenant_names.py
@@ -1,7 +1,8 @@
 #!/usr/bin/env python
 
-from utils.repo import get_tenant_yaml_path
-from utils.miscell import read_yaml
+# CWL ICA imports
+from cwl_ica.utils.repo import get_tenant_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 for tenant in read_yaml(get_tenant_yaml_path())["tenants"]:
     print(tenant["tenant_name"])
\ No newline at end of file
diff --git a/autocompletion/helpers/_cwl-ica_list_tool_names.py b/autocompletion/helpers/_cwl-ica_list_tool_names.py
index 54cb951..f61ea0c 100644
--- a/autocompletion/helpers/_cwl-ica_list_tool_names.py
+++ b/autocompletion/helpers/_cwl-ica_list_tool_names.py
@@ -3,8 +3,9 @@
 """
 List all of the category names in the categories.yaml file
 """
-from utils.repo import get_tool_yaml_path
-from utils.miscell import read_yaml
+# CWL ICA imports
+from cwl_ica.utils.repo import get_tool_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each tool name
 for tool in read_yaml(get_tool_yaml_path())["tools"]:
diff --git a/autocompletion/helpers/_cwl-ica_list_unregistered_expression_paths.py b/autocompletion/helpers/_cwl-ica_list_unregistered_expression_paths.py
index 6672714..cf37aff 100644
--- a/autocompletion/helpers/_cwl-ica_list_unregistered_expression_paths.py
+++ b/autocompletion/helpers/_cwl-ica_list_unregistered_expression_paths.py
@@ -4,13 +4,16 @@
 List the unregistered expression paths
 """
 
-from utils.repo import get_expression_yaml_path
-from utils.repo import get_expressions_dir
-from utils.miscell import read_yaml
+# External
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA imports
+from cwl_ica.utils.repo import get_expression_yaml_path
+from cwl_ica.utils.repo import get_expressions_dir
+from cwl_ica.utils.miscell import read_yaml
+
 registered_expression_paths = [
     Path(expression["path"]) / Path(version["path"])
     for expression in read_yaml(get_expression_yaml_path())["expressions"]
diff --git a/autocompletion/helpers/_cwl-ica_list_unregistered_schema_paths.py b/autocompletion/helpers/_cwl-ica_list_unregistered_schema_paths.py
index 5369db0..cbb13df 100644
--- a/autocompletion/helpers/_cwl-ica_list_unregistered_schema_paths.py
+++ b/autocompletion/helpers/_cwl-ica_list_unregistered_schema_paths.py
@@ -4,13 +4,17 @@
 List the unregistered schema paths
 """
 
-from utils.repo import get_schema_yaml_path
-from utils.repo import get_schemas_dir
-from utils.miscell import read_yaml
+# External imports
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA imports
+from cwl_ica.utils.repo import get_schema_yaml_path
+from cwl_ica.utils.repo import get_schemas_dir
+from cwl_ica.utils.miscell import read_yaml
+
+
 registered_schema_paths = [
     Path(schema["path"]) / Path(version["path"])
     for schema in read_yaml(get_schema_yaml_path())["schemas"]
diff --git a/autocompletion/helpers/_cwl-ica_list_unregistered_tool_paths.py b/autocompletion/helpers/_cwl-ica_list_unregistered_tool_paths.py
index 4d5c0e1..7907b72 100644
--- a/autocompletion/helpers/_cwl-ica_list_unregistered_tool_paths.py
+++ b/autocompletion/helpers/_cwl-ica_list_unregistered_tool_paths.py
@@ -4,13 +4,17 @@
 List the unregistered tool paths
 """
 
-from utils.repo import get_tool_yaml_path
-from utils.repo import get_tools_dir
-from utils.miscell import read_yaml
+# External imports
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA imports
+from cwl_ica.utils.repo import get_tool_yaml_path
+from cwl_ica.utils.repo import get_tools_dir
+from cwl_ica.utils.miscell import read_yaml
+
+
 registered_tool_paths = [
     Path(tool["path"]) / Path(version["path"])
     for tool in read_yaml(get_tool_yaml_path())["tools"]
diff --git a/autocompletion/helpers/_cwl-ica_list_unregistered_workflow_paths.py b/autocompletion/helpers/_cwl-ica_list_unregistered_workflow_paths.py
index 756816b..4a8fc2c 100644
--- a/autocompletion/helpers/_cwl-ica_list_unregistered_workflow_paths.py
+++ b/autocompletion/helpers/_cwl-ica_list_unregistered_workflow_paths.py
@@ -4,13 +4,17 @@
 List the unregistered workflow paths
 """
 
-from utils.repo import get_workflow_yaml_path
-from utils.repo import get_workflows_dir
-from utils.miscell import read_yaml
+# External imports
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA imports
+from cwl_ica.utils.repo import get_workflow_yaml_path
+from cwl_ica.utils.repo import get_workflows_dir
+from cwl_ica.utils.miscell import read_yaml
+
+
 registered_workflow_paths = [
     Path(workflow["path"]) / Path(version["path"])
     for workflow in read_yaml(get_workflow_yaml_path())["workflows"]
diff --git a/autocompletion/helpers/_cwl-ica_list_user_names.py b/autocompletion/helpers/_cwl-ica_list_user_names.py
index acf0254..4b64399 100644
--- a/autocompletion/helpers/_cwl-ica_list_user_names.py
+++ b/autocompletion/helpers/_cwl-ica_list_user_names.py
@@ -3,8 +3,9 @@
 """
 List all of the category names in the categories.yaml file
 """
-from utils.repo import get_user_yaml_path
-from utils.miscell import read_yaml
+# CWL ICA imports
+from cwl_ica.utils.repo import get_user_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each project name
 for user in read_yaml(get_user_yaml_path())["users"]:
diff --git a/autocompletion/helpers/_cwl-ica_list_workflow_names.py b/autocompletion/helpers/_cwl-ica_list_workflow_names.py
index 67f0adb..6a14613 100644
--- a/autocompletion/helpers/_cwl-ica_list_workflow_names.py
+++ b/autocompletion/helpers/_cwl-ica_list_workflow_names.py
@@ -3,8 +3,9 @@
 """
 List all of the category names in the categories.yaml file
 """
-from utils.repo import get_workflow_yaml_path
-from utils.miscell import read_yaml
+# CWL ICA imports
+from cwl_ica.utils.repo import get_workflow_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each tool name
 for workflow in read_yaml(get_workflow_yaml_path())["workflows"]:
diff --git a/autocompletion/run-autocompletion.sh b/autocompletion/run-autocompletion.sh
index bf26ed3..65ec05d 100644
--- a/autocompletion/run-autocompletion.sh
+++ b/autocompletion/run-autocompletion.sh
@@ -57,8 +57,7 @@ for template in templates/*.evalyaml; do
   docker run \
 	--volume "$PWD:$PWD" \
         --workdir "$PWD" \
-	ghcr.io/umccr/appspec:0.006 \
-	    appspec \
+	 ghcr.io/alexiswl/app-appspec-p5:v0.007-rc \
   		completion \
 			"${template}" \
 		    	--name "${name_root}" \
@@ -78,8 +77,7 @@ for template in templates/*.evalyaml; do
   docker run \
 	--volume "$PWD:$PWD" \
         --workdir "$PWD" \
-	ghcr.io/umccr/appspec:0.006 \
-	    appspec \
+	 ghcr.io/alexiswl/app-appspec-p5:v0.007-rc \
 	  	completion \
         		"${template}" \
             --name "${name_root}" \
diff --git a/autocompletion/zsh/_cwl-ica b/autocompletion/zsh/_cwl-ica
index ba14d7f..515898a 100644
--- a/autocompletion/zsh/_cwl-ica
+++ b/autocompletion/zsh/_cwl-ica
@@ -72,6 +72,7 @@ Each project is linked to a tenancy id
 " tool-sync\:"Sync a tool md5sum in \${CWL_ICA_REPO_PATH}/config/tool.yaml
 and update definition on ICA
 " tool-validate\:"Validate a CWL tool ready for initialising on ICA
+" typescript-expression-update\:"Update a typescript expression yarn.lock file
 " typescript-expression-validate\:"Validate a typescript expression and generate a .cwljs file ready for importation
 " validate-api-key-script\:"Confirm your api-key script works for a given project
 " validate-config-yamls\:"Confirm all config yamls are legitimate
@@ -1061,6 +1062,21 @@ to workflow names
                     && ret=0
 
 
+            ;;
+            typescript-expression-update)
+
+                # ---- Command: typescript-expression-update
+                _arguments -s -C \
+                    '1: :->cmd1' \
+                    '--help[Show command help]' \
+                    '-h[Show command help]' \
+                    '--typescript-expression-dir[The name of the workflow
+]:typescript-expression-dir:_cwl-ica_typescript-expression-update_option_typescript_expression_dir_completion' \
+                    '--xtrace[Set xtrace on the update_yarn_dependencies shell script
+]:xtrace' \
+                    && ret=0
+
+
             ;;
             typescript-expression-validate)
 
@@ -1181,8 +1197,9 @@ python - <<EOF
 """
 List all of the category names in the categories.yaml file
 """
-from utils.repo import get_tool_yaml_path
-from utils.miscell import read_yaml
+# CWL ICA imports
+from cwl_ica.utils.repo import get_tool_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each tool name
 for tool in read_yaml(get_tool_yaml_path())["tools"]:
@@ -1202,8 +1219,8 @@ python - <<EOF
 """
 List all of the category names in the categories.yaml file
 """
-from utils.repo import get_category_yaml_path
-from utils.miscell import read_yaml
+from cwl_ica.utils.repo import get_category_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each project name
 for category in read_yaml(get_category_yaml_path())["categories"]:
@@ -1223,8 +1240,9 @@ python - <<EOF
 """
 List all of the category names in the categories.yaml file
 """
-from utils.repo import get_workflow_yaml_path
-from utils.miscell import read_yaml
+# CWL ICA imports
+from cwl_ica.utils.repo import get_workflow_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each tool name
 for workflow in read_yaml(get_workflow_yaml_path())["workflows"]:
@@ -1244,8 +1262,8 @@ python - <<EOF
 """
 List all of the category names in the categories.yaml file
 """
-from utils.repo import get_category_yaml_path
-from utils.miscell import read_yaml
+from cwl_ica.utils.repo import get_category_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each project name
 for category in read_yaml(get_category_yaml_path())["categories"]:
@@ -1265,8 +1283,8 @@ python - <<EOF
 """
 List all of the project names in the project.yaml file
 """
-from utils.repo import get_project_yaml_path
-from utils.miscell import read_yaml
+from cwl_ica.utils.repo import get_project_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each project name
 for project in read_yaml(get_project_yaml_path())["projects"]:
@@ -1287,13 +1305,16 @@ python - <<EOF
 List the unregistered expression paths
 """
 
-from utils.repo import get_expression_yaml_path
-from utils.repo import get_expressions_dir
-from utils.miscell import read_yaml
+# Externals
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA
+from cwl_ica.utils.repo import get_expression_yaml_path
+from cwl_ica.utils.repo import get_expressions_dir
+from cwl_ica.utils.miscell import read_yaml
+
 # Get the current word value
 if not "${CURRENT_WORD}" == "":
     current_word_value = "${CURRENT_WORD}"
@@ -1385,8 +1406,9 @@ python - <<EOF
 """
 List all of the category names in the categories.yaml file
 """
-from utils.repo import get_user_yaml_path
-from utils.miscell import read_yaml
+# CWL ICA imports
+from cwl_ica.utils.repo import get_user_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each project name
 for user in read_yaml(get_user_yaml_path())["users"]:
@@ -1407,13 +1429,14 @@ python - <<EOF
 List the unregistered tool paths
 """
 
-from utils.repo import get_tool_yaml_path
-from utils.repo import get_tools_dir
-from utils.miscell import read_yaml
+# Externals
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA
+from cwl_ica.utils.repo import get_tools_dir
+
 # Get the current word value
 if not "${CURRENT_WORD}" == "":
     current_word_value = "${CURRENT_WORD}"
@@ -1504,8 +1527,9 @@ python - <<EOF
 """
 List all of the category names in the categories.yaml file
 """
-from utils.repo import get_user_yaml_path
-from utils.miscell import read_yaml
+# CWL ICA imports
+from cwl_ica.utils.repo import get_user_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each project name
 for user in read_yaml(get_user_yaml_path())["users"]:
@@ -1526,13 +1550,14 @@ python - <<EOF
 List the unregistered workflow paths
 """
 
-from utils.repo import get_workflow_yaml_path
-from utils.repo import get_workflows_dir
-from utils.miscell import read_yaml
+# Externals
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA
+from cwl_ica.utils.repo import get_workflows_dir
+
 # Get the current word value
 if not "${CURRENT_WORD}" == "":
     current_word_value = "${CURRENT_WORD}"
@@ -1624,8 +1649,9 @@ python - <<EOF
 """
 List all of the category names in the categories.yaml file
 """
-from utils.repo import get_user_yaml_path
-from utils.miscell import read_yaml
+# CWL ICA imports
+from cwl_ica.utils.repo import get_user_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each project name
 for user in read_yaml(get_user_yaml_path())["users"]:
@@ -1646,13 +1672,16 @@ python - <<EOF
 List the registered tool paths
 """
 
-from utils.repo import get_tool_yaml_path
-from utils.repo import get_tools_dir
-from utils.miscell import read_yaml
+# External imports
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA
+from cwl_ica.utils.repo import get_tool_yaml_path
+from cwl_ica.utils.repo import get_tools_dir
+from cwl_ica.utils.miscell import read_yaml
+
 tool_paths = [
     Path(tool["path"]) / Path(version["path"])
     for tool in read_yaml(get_tool_yaml_path())["tools"]
@@ -1738,8 +1767,8 @@ python - <<EOF
 """
 List all of the project names in the project.yaml file
 """
-from utils.repo import get_project_yaml_path
-from utils.miscell import read_yaml
+from cwl_ica.utils.repo import get_project_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each project name
 for project in read_yaml(get_project_yaml_path())["projects"]:
@@ -1760,13 +1789,16 @@ python - <<EOF
 List the registered workflow paths
 """
 
-from utils.repo import get_workflow_yaml_path
-from utils.repo import get_workflows_dir
-from utils.miscell import read_yaml
+# External imports
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA
+from cwl_ica.utils.repo import get_workflow_yaml_path
+from cwl_ica.utils.repo import get_workflows_dir
+from cwl_ica.utils.miscell import read_yaml
+
 workflow_paths = [
     Path(workflow["path"]) / Path(version["path"])
     for workflow in read_yaml(get_workflow_yaml_path())["workflows"]
@@ -1853,8 +1885,8 @@ python - <<EOF
 """
 List all of the project names in the project.yaml file
 """
-from utils.repo import get_project_yaml_path
-from utils.miscell import read_yaml
+from cwl_ica.utils.repo import get_project_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each project name
 for project in read_yaml(get_project_yaml_path())["projects"]:
@@ -1875,13 +1907,14 @@ python - <<EOF
 List the unregistered tool paths
 """
 
-from utils.repo import get_tool_yaml_path
-from utils.repo import get_tools_dir
-from utils.miscell import read_yaml
+# Externals
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA
+from cwl_ica.utils.repo import get_tools_dir
+
 # Get the current word value
 if not "${CURRENT_WORD}" == "":
     current_word_value = "${CURRENT_WORD}"
@@ -1973,13 +2006,16 @@ python - <<EOF
 List the unregistered expression paths
 """
 
-from utils.repo import get_expression_yaml_path
-from utils.repo import get_expressions_dir
-from utils.miscell import read_yaml
+# Externals
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA
+from cwl_ica.utils.repo import get_expression_yaml_path
+from cwl_ica.utils.repo import get_expressions_dir
+from cwl_ica.utils.miscell import read_yaml
+
 # Get the current word value
 if not "${CURRENT_WORD}" == "":
     current_word_value = "${CURRENT_WORD}"
@@ -2072,13 +2108,14 @@ python - <<EOF
 List the unregistered workflow paths
 """
 
-from utils.repo import get_workflow_yaml_path
-from utils.repo import get_workflows_dir
-from utils.miscell import read_yaml
+# Externals
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA
+from cwl_ica.utils.repo import get_workflows_dir
+
 # Get the current word value
 if not "${CURRENT_WORD}" == "":
     current_word_value = "${CURRENT_WORD}"
@@ -2170,8 +2207,9 @@ python - <<EOF
 """
 List all of the run instance ids in the run.yaml file
 """
-from utils.repo import get_run_yaml_path
-from utils.miscell import read_yaml
+# CWL ICA imports
+from cwl_ica.utils.repo import get_run_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each run instance id
 for run in read_yaml(get_run_yaml_path())["runs"]:
@@ -2191,8 +2229,9 @@ python - <<EOF
 """
 List all of the run instance ids in the run.yaml file
 """
-from utils.repo import get_run_yaml_path
-from utils.miscell import read_yaml
+# CWL ICA imports
+from cwl_ica.utils.repo import get_run_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each run instance id
 for run in read_yaml(get_run_yaml_path())["runs"]:
@@ -2212,8 +2251,9 @@ python - <<EOF
 """
 List all of the category names in the categories.yaml file
 """
-from utils.repo import get_user_yaml_path
-from utils.miscell import read_yaml
+# CWL ICA imports
+from cwl_ica.utils.repo import get_user_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each project name
 for user in read_yaml(get_user_yaml_path())["users"]:
@@ -2233,8 +2273,9 @@ python - <<EOF
 """
 List all of the category names in the categories.yaml file
 """
-from utils.repo import get_user_yaml_path
-from utils.miscell import read_yaml
+# CWL ICA imports
+from cwl_ica.utils.repo import get_user_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each project name
 for user in read_yaml(get_user_yaml_path())["users"]:
@@ -2255,13 +2296,14 @@ python - <<EOF
 List the unregistered tool paths
 """
 
-from utils.repo import get_tool_yaml_path
-from utils.repo import get_tools_dir
-from utils.miscell import read_yaml
+# Externals
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA
+from cwl_ica.utils.repo import get_tools_dir
+
 # Get the current word value
 if not "${CURRENT_WORD}" == "":
     current_word_value = "${CURRENT_WORD}"
@@ -2352,8 +2394,8 @@ python - <<EOF
 """
 List all of the project names in the project.yaml file
 """
-from utils.repo import get_project_yaml_path
-from utils.miscell import read_yaml
+from cwl_ica.utils.repo import get_project_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each project name
 for project in read_yaml(get_project_yaml_path())["projects"]:
@@ -2428,8 +2470,9 @@ python - <<EOF
 """
 List all of the category names in the categories.yaml file
 """
-from utils.repo import get_user_yaml_path
-from utils.miscell import read_yaml
+# CWL ICA imports
+from cwl_ica.utils.repo import get_user_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each project name
 for user in read_yaml(get_user_yaml_path())["users"]:
@@ -2450,13 +2493,14 @@ python - <<EOF
 List the unregistered schema paths
 """
 
-from utils.repo import get_schema_yaml_path
-from utils.repo import get_schemas_dir
-from utils.miscell import read_yaml
+# Externals
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA
+from cwl_ica.utils.repo import get_schemas_dir
+
 # Get the current word value
 if not "${CURRENT_WORD-}" == "":
     current_word_value = "${CURRENT_WORD}"
@@ -2547,8 +2591,9 @@ python - <<EOF
 """
 List all of the category names in the categories.yaml file
 """
-from utils.repo import get_user_yaml_path
-from utils.miscell import read_yaml
+# CWL ICA imports
+from cwl_ica.utils.repo import get_user_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each project name
 for user in read_yaml(get_user_yaml_path())["users"]:
@@ -2569,13 +2614,14 @@ python - <<EOF
 List the unregistered workflow paths
 """
 
-from utils.repo import get_workflow_yaml_path
-from utils.repo import get_workflows_dir
-from utils.miscell import read_yaml
+# Externals
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA
+from cwl_ica.utils.repo import get_workflows_dir
+
 # Get the current word value
 if not "${CURRENT_WORD}" == "":
     current_word_value = "${CURRENT_WORD}"
@@ -2667,8 +2713,8 @@ python - <<EOF
 """
 List all of the project names in the project.yaml file
 """
-from utils.repo import get_project_yaml_path
-from utils.miscell import read_yaml
+from cwl_ica.utils.repo import get_project_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each project name
 for project in read_yaml(get_project_yaml_path())["projects"]:
@@ -2874,13 +2920,16 @@ python - <<EOF
 List the unregistered expression paths
 """
 
-from utils.repo import get_expression_yaml_path
-from utils.repo import get_expressions_dir
-from utils.miscell import read_yaml
+# External
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA imports
+from cwl_ica.utils.repo import get_expression_yaml_path
+from cwl_ica.utils.repo import get_expressions_dir
+from cwl_ica.utils.miscell import read_yaml
+
 registered_expression_paths = [
     Path(expression["path"]) / Path(version["path"])
     for expression in read_yaml(get_expression_yaml_path())["expressions"]
@@ -2984,13 +3033,14 @@ python - <<EOF
 List the registered expression paths
 """
 
-from utils.repo import get_expression_yaml_path
-from utils.repo import get_expressions_dir
-from utils.miscell import read_yaml
+# Externals
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA
+from cwl_ica.utils.repo import get_expression_yaml_path, read_yaml, get_expressions_dir
+
 expression_paths = [
     Path(expression["path"]) / Path(version["path"])
     for expression in read_yaml(get_expression_yaml_path())["expressions"]
@@ -3076,13 +3126,14 @@ python - <<EOF
 List the registered expression paths
 """
 
-from utils.repo import get_expression_yaml_path
-from utils.repo import get_expressions_dir
-from utils.miscell import read_yaml
+# Externals
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA
+from cwl_ica.utils.repo import get_expression_yaml_path, read_yaml, get_expressions_dir
+
 expression_paths = [
     Path(expression["path"]) / Path(version["path"])
     for expression in read_yaml(get_expression_yaml_path())["expressions"]
@@ -3168,13 +3219,14 @@ python - <<EOF
 List the unregistered workflow paths
 """
 
-from utils.repo import get_workflow_yaml_path
-from utils.repo import get_workflows_dir
-from utils.miscell import read_yaml
+# Externals
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA
+from cwl_ica.utils.repo import get_workflows_dir
+
 # Get the current word value
 if not "${CURRENT_WORD}" == "":
     current_word_value = "${CURRENT_WORD}"
@@ -3536,13 +3588,14 @@ python - <<EOF
 List the unregistered workflow paths
 """
 
-from utils.repo import get_workflow_yaml_path
-from utils.repo import get_workflows_dir
-from utils.miscell import read_yaml
+# Externals
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA
+from cwl_ica.utils.repo import get_workflows_dir
+
 # Get the current word value
 if not "${CURRENT_WORD}" == "":
     current_word_value = "${CURRENT_WORD}"
@@ -3631,8 +3684,9 @@ _cwl-ica_list-projects_option_tenant_name_completion() {
 python - <<EOF
 #!/usr/bin/env python
 
-from utils.repo import get_tenant_yaml_path
-from utils.miscell import read_yaml
+# CWL ICA imports
+from cwl_ica.utils.repo import get_tenant_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 for tenant in read_yaml(get_tenant_yaml_path())["tenants"]:
     print(tenant["tenant_name"])
@@ -3652,13 +3706,16 @@ python - <<EOF
 List the registered tool paths
 """
 
-from utils.repo import get_tool_yaml_path
-from utils.repo import get_tools_dir
-from utils.miscell import read_yaml
+# External imports
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA
+from cwl_ica.utils.repo import get_tool_yaml_path
+from cwl_ica.utils.repo import get_tools_dir
+from cwl_ica.utils.miscell import read_yaml
+
 tool_paths = [
     Path(tool["path"]) / Path(version["path"])
     for tool in read_yaml(get_tool_yaml_path())["tools"]
@@ -3744,8 +3801,8 @@ python - <<EOF
 """
 List all of the project names in the project.yaml file
 """
-from utils.repo import get_project_yaml_path
-from utils.miscell import read_yaml
+from cwl_ica.utils.repo import get_project_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each project name
 for project in read_yaml(get_project_yaml_path())["projects"]:
@@ -3776,8 +3833,8 @@ python - <<EOF
 """
 List all of the project names in the project.yaml file
 """
-from utils.repo import get_project_yaml_path
-from utils.miscell import read_yaml
+from cwl_ica.utils.repo import get_project_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each project name
 for project in read_yaml(get_project_yaml_path())["projects"]:
@@ -3794,8 +3851,9 @@ _cwl-ica_project-init_option_tenant_name_completion() {
 python - <<EOF
 #!/usr/bin/env python
 
-from utils.repo import get_tenant_yaml_path
-from utils.miscell import read_yaml
+# CWL ICA imports
+from cwl_ica.utils.repo import get_tenant_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 for tenant in read_yaml(get_tenant_yaml_path())["tenants"]:
     print(tenant["tenant_name"])
@@ -3813,8 +3871,8 @@ python - <<EOF
 """
 List all of the project names in the project.yaml file
 """
-from utils.repo import get_project_yaml_path
-from utils.miscell import read_yaml
+from cwl_ica.utils.repo import get_project_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each project name
 for project in read_yaml(get_project_yaml_path())["projects"]:
@@ -3834,8 +3892,8 @@ python - <<EOF
 """
 List all of the project names in the project.yaml file
 """
-from utils.repo import get_project_yaml_path
-from utils.miscell import read_yaml
+from cwl_ica.utils.repo import get_project_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each project name
 for project in read_yaml(get_project_yaml_path())["projects"]:
@@ -3856,13 +3914,17 @@ python - <<EOF
 List the unregistered schema paths
 """
 
-from utils.repo import get_schema_yaml_path
-from utils.repo import get_schemas_dir
-from utils.miscell import read_yaml
+# External imports
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA imports
+from cwl_ica.utils.repo import get_schema_yaml_path
+from cwl_ica.utils.repo import get_schemas_dir
+from cwl_ica.utils.miscell import read_yaml
+
+
 registered_schema_paths = [
     Path(schema["path"]) / Path(version["path"])
     for schema in read_yaml(get_schema_yaml_path())["schemas"]
@@ -3964,13 +4026,14 @@ python - <<EOF
 List the registered schema paths
 """
 
-from utils.repo import get_schema_yaml_path
-from utils.repo import get_schemas_dir
-from utils.miscell import read_yaml
+# Externals
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA
+from cwl_ica.utils.repo import read_yaml, get_schema_yaml_path, get_schemas_dir
+
 schema_paths = [
     Path(schema["path"]) / Path(version["path"])
     for schema in read_yaml(get_schema_yaml_path())["schemas"]
@@ -4055,13 +4118,14 @@ python - <<EOF
 List the unregistered schema paths
 """
 
-from utils.repo import get_schema_yaml_path
-from utils.repo import get_schemas_dir
-from utils.miscell import read_yaml
+# Externals
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA
+from cwl_ica.utils.repo import get_schemas_dir
+
 # Get the current word value
 if not "${CURRENT_WORD-}" == "":
     current_word_value = "${CURRENT_WORD}"
@@ -4152,8 +4216,8 @@ python - <<EOF
 """
 List all of the project names in the project.yaml file
 """
-from utils.repo import get_project_yaml_path
-from utils.miscell import read_yaml
+from cwl_ica.utils.repo import get_project_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each project name
 for project in read_yaml(get_project_yaml_path())["projects"]:
@@ -4170,8 +4234,9 @@ _cwl-ica_set-default-tenant_option_tenant_name_completion() {
 python - <<EOF
 #!/usr/bin/env python
 
-from utils.repo import get_tenant_yaml_path
-from utils.miscell import read_yaml
+# CWL ICA imports
+from cwl_ica.utils.repo import get_tenant_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 for tenant in read_yaml(get_tenant_yaml_path())["tenants"]:
     print(tenant["tenant_name"])
@@ -4190,8 +4255,9 @@ python - <<EOF
 """
 List all of the category names in the categories.yaml file
 """
-from utils.repo import get_user_yaml_path
-from utils.miscell import read_yaml
+# CWL ICA imports
+from cwl_ica.utils.repo import get_user_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each project name
 for user in read_yaml(get_user_yaml_path())["users"]:
@@ -4212,13 +4278,17 @@ python - <<EOF
 List the unregistered tool paths
 """
 
-from utils.repo import get_tool_yaml_path
-from utils.repo import get_tools_dir
-from utils.miscell import read_yaml
+# External imports
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA imports
+from cwl_ica.utils.repo import get_tool_yaml_path
+from cwl_ica.utils.repo import get_tools_dir
+from cwl_ica.utils.miscell import read_yaml
+
+
 registered_tool_paths = [
     Path(tool["path"]) / Path(version["path"])
     for tool in read_yaml(get_tool_yaml_path())["tools"]
@@ -4319,8 +4389,8 @@ python - <<EOF
 """
 List all of the project names in the project.yaml file
 """
-from utils.repo import get_project_yaml_path
-from utils.miscell import read_yaml
+from cwl_ica.utils.repo import get_project_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each project name
 for project in read_yaml(get_project_yaml_path())["projects"]:
@@ -4337,8 +4407,9 @@ _cwl-ica_tool-init_option_tenants_completion() {
 python - <<EOF
 #!/usr/bin/env python
 
-from utils.repo import get_tenant_yaml_path
-from utils.miscell import read_yaml
+# CWL ICA imports
+from cwl_ica.utils.repo import get_tenant_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 for tenant in read_yaml(get_tenant_yaml_path())["tenants"]:
     print(tenant["tenant_name"])
@@ -4357,8 +4428,8 @@ python - <<EOF
 """
 List all of the category names in the categories.yaml file
 """
-from utils.repo import get_category_yaml_path
-from utils.miscell import read_yaml
+from cwl_ica.utils.repo import get_category_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each project name
 for category in read_yaml(get_category_yaml_path())["categories"]:
@@ -4379,13 +4450,16 @@ python - <<EOF
 List the registered tool paths
 """
 
-from utils.repo import get_tool_yaml_path
-from utils.repo import get_tools_dir
-from utils.miscell import read_yaml
+# External imports
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA
+from cwl_ica.utils.repo import get_tool_yaml_path
+from cwl_ica.utils.repo import get_tools_dir
+from cwl_ica.utils.miscell import read_yaml
+
 tool_paths = [
     Path(tool["path"]) / Path(version["path"])
     for tool in read_yaml(get_tool_yaml_path())["tools"]
@@ -4471,8 +4545,8 @@ python - <<EOF
 """
 List all of the project names in the project.yaml file
 """
-from utils.repo import get_project_yaml_path
-from utils.miscell import read_yaml
+from cwl_ica.utils.repo import get_project_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each project name
 for project in read_yaml(get_project_yaml_path())["projects"]:
@@ -4489,8 +4563,9 @@ _cwl-ica_tool-sync_option_tenants_completion() {
 python - <<EOF
 #!/usr/bin/env python
 
-from utils.repo import get_tenant_yaml_path
-from utils.miscell import read_yaml
+# CWL ICA imports
+from cwl_ica.utils.repo import get_tenant_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 for tenant in read_yaml(get_tenant_yaml_path())["tenants"]:
     print(tenant["tenant_name"])
@@ -4510,13 +4585,14 @@ python - <<EOF
 List the unregistered tool paths
 """
 
-from utils.repo import get_tool_yaml_path
-from utils.repo import get_tools_dir
-from utils.miscell import read_yaml
+# Externals
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA
+from cwl_ica.utils.repo import get_tools_dir
+
 # Get the current word value
 if not "${CURRENT_WORD}" == "":
     current_word_value = "${CURRENT_WORD}"
@@ -4597,6 +4673,124 @@ EOF
  ) )
     compadd -X "tool_path:" $__dynamic_completion
 }
+_cwl-ica_typescript-expression-update_option_typescript_expression_dir_completion() {
+    local __dynamic_completion
+    local CURRENT_WORD="$words[CURRENT]"
+    IFS=$'\n' __dynamic_completion=( $( 
+python - <<EOF
+#!/usr/bin/env python3
+
+"""
+List all the typescript expression paths
+"""
+
+# Externals
+from pathlib import Path
+from os import getcwd
+from os.path import relpath
+
+# CWL ICA
+from cwl_ica.utils.repo import get_cwl_ica_repo_path
+
+# Get the current word value
+if not "${CURRENT_WORD}" == "":
+    current_word_value = "${CURRENT_WORD}"
+else:
+    current_word_value = None
+
+if current_word_value is None:
+    current_word_value = ""
+    current_path_resolved = Path(getcwd()).absolute()
+    typescript_expression_paths = [
+        s_file.parent.relative_to(get_cwl_ica_repo_path())
+        for s_file in get_cwl_ica_repo_path().glob("**/*.ts")
+        # We don't want to pull in the typescript test files
+        if not (len(s_file.parent.parts) >= 1 and s_file.parent.parts[-1] == 'tests') and
+        # We also want to make sure it's under the tools, expressions or typescript-expressions directories
+        len(
+            {"tools", "expressions", "typescript-expressions"}.intersection(
+                [
+                    s_file.resolve().absolute().relative_to(get_cwl_ica_repo_path()).parent.parts[0]
+                ]
+            )
+        ) > 0
+    ]
+else:
+    if current_word_value.endswith("/"):
+        current_path_resolved = Path(getcwd()).joinpath(Path(current_word_value)).resolve()
+    else:
+        current_path_resolved = Path(getcwd()).joinpath(Path(current_word_value).parent).resolve()
+
+    typescript_expression_paths = [
+        s_file.parent.relative_to(get_cwl_ica_repo_path())
+        for s_file in current_path_resolved.glob("**/*.ts")
+        # We don't want to pull in the typescript test files
+        if not (len(s_file.parent.parts) >= 1 and s_file.parent.parts[-1] == 'tests') and
+           # We also want to make sure it's under the tools, expressions or typescript-expressions directories
+           len(
+               {"tools", "expressions", "typescript-expressions"}.intersection(
+                   [
+                       s_file.resolve().absolute().relative_to(get_cwl_ica_repo_path()).parent.parts[0]
+                   ]
+               )
+           ) > 0
+    ]
+
+# Resolve the current path
+# If getcwd() is "/c/Users/awluc"
+# 1. Non relative paths: current_word_value = "/etc" -> current_path_resolved = "/etc"
+# 2. Relative parent path: current_word_value = "../../Program Files" -> current_path_resolved = "/c/Program Files"
+# 3. Subfolder: current_word_value = "OneDrive" -> current_path_resolved = "/c/Users/awluc/OneDrive"
+# 4. Subfolder of expressions dir = "OneDrive/GitHub/UMCCR/expressions/contig/" -> current path resolved
+
+# Is the current_path_resolved a subpath of the expressions directory?
+try:
+    _ = current_path_resolved.relative_to(get_cwl_ica_repo_path())
+    in_repo_dir = True
+except ValueError:
+    in_repo_dir = False
+
+if in_repo_dir:
+    current_path_resolved_relative_to_expressions_dir = current_path_resolved.relative_to(get_cwl_ica_repo_path())
+    if current_path_resolved_relative_to_expressions_dir == Path("."):
+        for s_path in typescript_expression_paths:
+            if current_word_value.endswith("/"):
+                print(Path(current_word_value) / s_path)
+            else:
+                print(Path(current_word_value).parent / s_path)
+    else:
+        for s_path in typescript_expression_paths:
+            if str(s_path).startswith(str(current_path_resolved_relative_to_expressions_dir)):
+                if current_word_value.endswith("/"):
+                    print(Path(current_word_value) / s_path.relative_to(
+                        current_path_resolved_relative_to_expressions_dir))
+                else:
+                    print(Path(current_word_value).parent / s_path.relative_to(
+                        current_path_resolved_relative_to_expressions_dir))
+
+else:
+    # Now get the expressions yaml path relative to the current path
+    try:
+        expressions_dir = get_cwl_ica_repo_path().relative_to(current_path_resolved)
+    except ValueError:
+        # We could be in a different mount point OR just in a subdirectory
+        if str(get_cwl_ica_repo_path().absolute()) in str(relpath(get_cwl_ica_repo_path(), current_path_resolved)):
+            # Separate mount point
+            expressions_dir = get_cwl_ica_repo_path().absolute()
+        else:
+            expressions_dir = Path(relpath(get_cwl_ica_repo_path(), current_path_resolved))
+
+    # Now iterate through paths
+    for s_path in typescript_expression_paths:
+        if current_word_value.endswith("/"):
+            print(Path(current_word_value) / expressions_dir.joinpath(s_path))
+        else:
+            print(Path(current_word_value).parent / expressions_dir.joinpath(s_path))
+EOF
+
+ ) )
+    compadd -X "typescript_expression_dir:" $__dynamic_completion
+}
 _cwl-ica_typescript-expression-validate_option_typescript_expression_dir_completion() {
     local __dynamic_completion
     local CURRENT_WORD="$words[CURRENT]"
@@ -4608,13 +4802,14 @@ python - <<EOF
 List all the typescript expression paths
 """
 
-from utils.repo import get_expression_yaml_path
-from utils.repo import get_cwl_ica_repo_path
-from utils.miscell import read_yaml
+# Externals
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA
+from cwl_ica.utils.repo import get_cwl_ica_repo_path
+
 # Get the current word value
 if not "${CURRENT_WORD}" == "":
     current_word_value = "${CURRENT_WORD}"
@@ -4724,8 +4919,8 @@ python - <<EOF
 """
 List all of the project names in the project.yaml file
 """
-from utils.repo import get_project_yaml_path
-from utils.miscell import read_yaml
+from cwl_ica.utils.repo import get_project_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each project name
 for project in read_yaml(get_project_yaml_path())["projects"]:
@@ -4746,13 +4941,17 @@ python - <<EOF
 List the unregistered workflow paths
 """
 
-from utils.repo import get_workflow_yaml_path
-from utils.repo import get_workflows_dir
-from utils.miscell import read_yaml
+# External imports
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA imports
+from cwl_ica.utils.repo import get_workflow_yaml_path
+from cwl_ica.utils.repo import get_workflows_dir
+from cwl_ica.utils.miscell import read_yaml
+
+
 registered_workflow_paths = [
     Path(workflow["path"]) / Path(version["path"])
     for workflow in read_yaml(get_workflow_yaml_path())["workflows"]
@@ -4855,8 +5054,8 @@ python - <<EOF
 """
 List all of the project names in the project.yaml file
 """
-from utils.repo import get_project_yaml_path
-from utils.miscell import read_yaml
+from cwl_ica.utils.repo import get_project_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each project name
 for project in read_yaml(get_project_yaml_path())["projects"]:
@@ -4873,8 +5072,9 @@ _cwl-ica_workflow-init_option_tenants_completion() {
 python - <<EOF
 #!/usr/bin/env python
 
-from utils.repo import get_tenant_yaml_path
-from utils.miscell import read_yaml
+# CWL ICA imports
+from cwl_ica.utils.repo import get_tenant_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 for tenant in read_yaml(get_tenant_yaml_path())["tenants"]:
     print(tenant["tenant_name"])
@@ -4893,8 +5093,8 @@ python - <<EOF
 """
 List all of the category names in the categories.yaml file
 """
-from utils.repo import get_category_yaml_path
-from utils.miscell import read_yaml
+from cwl_ica.utils.repo import get_category_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each project name
 for category in read_yaml(get_category_yaml_path())["categories"]:
@@ -4915,13 +5115,16 @@ python - <<EOF
 List the registered workflow paths
 """
 
-from utils.repo import get_workflow_yaml_path
-from utils.repo import get_workflows_dir
-from utils.miscell import read_yaml
+# External imports
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA
+from cwl_ica.utils.repo import get_workflow_yaml_path
+from cwl_ica.utils.repo import get_workflows_dir
+from cwl_ica.utils.miscell import read_yaml
+
 workflow_paths = [
     Path(workflow["path"]) / Path(version["path"])
     for workflow in read_yaml(get_workflow_yaml_path())["workflows"]
@@ -5008,8 +5211,8 @@ python - <<EOF
 """
 List all of the project names in the project.yaml file
 """
-from utils.repo import get_project_yaml_path
-from utils.miscell import read_yaml
+from cwl_ica.utils.repo import get_project_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 # Import yaml and print each project name
 for project in read_yaml(get_project_yaml_path())["projects"]:
@@ -5026,8 +5229,9 @@ _cwl-ica_workflow-sync_option_tenants_completion() {
 python - <<EOF
 #!/usr/bin/env python
 
-from utils.repo import get_tenant_yaml_path
-from utils.miscell import read_yaml
+# CWL ICA imports
+from cwl_ica.utils.repo import get_tenant_yaml_path
+from cwl_ica.utils.miscell import read_yaml
 
 for tenant in read_yaml(get_tenant_yaml_path())["tenants"]:
     print(tenant["tenant_name"])
@@ -5047,13 +5251,14 @@ python - <<EOF
 List the unregistered workflow paths
 """
 
-from utils.repo import get_workflow_yaml_path
-from utils.repo import get_workflows_dir
-from utils.miscell import read_yaml
+# Externals
 from pathlib import Path
 from os import getcwd
 from os.path import relpath
 
+# CWL ICA
+from cwl_ica.utils.repo import get_workflows_dir
+
 # Get the current word value
 if not "${CURRENT_WORD}" == "":
     current_word_value = "${CURRENT_WORD}"