Autocompletion - update python helper scripts to pull in cwl-ica module

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}"

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}"

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}"

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}"

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}"

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"]:

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"]:

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"]

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"]

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"]

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"]

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"]:

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"])

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"]:

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"]

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"]

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"]

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"]

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"]:

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"]:

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}" \