CC created two helper scripts for helping re-structure the repo

Author: SHuang-Broad

list_wdl_definitions.sh

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+#!/bin/bash
+
+# Script to list all workflow and task definitions in wdl/tasks folder
+# Outputs a 4-column TSV: name, class, file_path, line_number
+
+set -euo pipefail
+
+WDL_TASKS_DIR="wdl/tasks"
+
+# Function to extract workflows and tasks from a file
+extract_definitions() {
+    local file="$1"
+    
+    # Use grep with line numbers to find workflow and task definitions
+    # Pattern matches: "workflow Name {" or "task Name {"
+    grep -n "^[[:space:]]*\(workflow\|task\)[[:space:]]\+[0-9A-Za-z_-]\+[[:space:]]*{" "$file" 2>/dev/null | while IFS=: read -r line_num match; do
+        # Extract the type (workflow or task) and name
+        local type name
+        type=$(echo "$match" | sed -E 's/^[[:space:]]*(workflow|task)[[:space:]].*/\1/')
+        name=$(echo "$match" | sed -E 's/^[[:space:]]*(workflow|task)[[:space:]]+([0-9A-Za-z_-]+)[[:space:]]*\{.*/\2/')
+        
+        # Output TSV line: name, class, file_path, line_number
+        echo -e "${name}\t${type}\t${file}\t${line_num}"
+    done
+}
+
+# Main execution
+main() {
+    local output_tsv="$1"
+    rm -f "${output_tsv}"
+
+    # Check if WDL tasks directory exists
+    if [[ ! -d "$WDL_TASKS_DIR" ]]; then
+        echo "Error: WDL tasks directory '$WDL_TASKS_DIR' not found" >&2
+        exit 1
+    fi
+    
+    # Print TSV header
+    echo -e "name\tclass\tfile_path\tline_number" > "${output_tsv}"
+    
+    # Find all .wdl files in wdl/tasks and extract definitions
+    find "$WDL_TASKS_DIR" -name "*.wdl" -type f | sort | while read -r file; do
+        extract_definitions "$file" >> "${output_tsv}"
+    done
+}
+
+main "$@" ALL_CALLABLES_IN_TASK_FOLDER.tsv

trace_task_dependencies.sh

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+#!/bin/bash
+
+# Script to trace WDL task dependencies
+# Usage: ./trace_task_dependencies.sh <task_name>
+# Example: ./trace_task_dependencies.sh GetTodayDate
+
+set -euo pipefail
+
+TASK_NAME="$1"
+WDL_DIR="./wdl"
+VISITED=()
+CHAIN=()
+
+# Function to check if a value exists in an array
+contains_element() {
+    local element="$1"
+    shift
+    local array=("$@")
+    for item in "${array[@]}"; do
+        [[ "$item" == "$element" ]] && return 0
+    done
+    return 1
+}
+
+# Function to add visited file to avoid cycles
+add_visited() {
+    local file="$1"
+    VISITED+=("$file")
+}
+
+# Function to check if file was already visited
+is_visited() {
+    local file="$1"
+    if [[ ${#VISITED[@]} -eq 0 ]]; then
+        return 1
+    fi
+    contains_element "$file" "${VISITED[@]}"
+}
+
+# Function to find the file containing a task definition
+find_task_definition() {
+    local task="$1"
+    # Search for task definition pattern: "^task TaskName {"
+    find "${WDL_DIR}" -name "*.wdl" -exec grep -l "^task ${task}\s*{" {} \; 2>/dev/null || true
+}
+
+# Function to find workflows/tasks that call a specific task
+find_callers() {
+    local task="$1"
+    local calling_files=()
+    
+    # Search for "call TaskName" or "call Namespace.TaskName" patterns
+    while IFS= read -r -d '' file; do
+        if grep -q "call.*${task}" "$file" 2>/dev/null; then
+            calling_files+=("$file")
+        fi
+    done < <(find "${WDL_DIR}" -name "*.wdl" -print0)
+    
+    # Only print if array has elements to avoid "unbound variable" error
+    if [[ ${#calling_files[@]} -gt 0 ]]; then
+        printf '%s\n' "${calling_files[@]}"
+    fi
+}
+
+# Function to get workflow/task name from file
+get_workflow_or_task_name() {
+    local file="$1"
+    # Look for workflow or task definition at the top level
+    local name=""
+    name=$(grep -E "^(workflow|task) [0-9A-Za-z_-]+" "$file" | head -1 | awk '{print $2}' | sed 's/{.*$//')
+    echo "$name"
+}
+
+# Function to trace dependencies recursively
+trace_dependencies() {
+    local current_task="$1"
+    local depth="${2:-0}"
+    local indent=$(printf "%*s" $((depth * 2)) "")
+    
+    echo "${indent}Tracing callers of task: $current_task"
+    
+    # Find the task definition file
+    local task_file
+    task_file=$(find_task_definition "$current_task")
+    
+    if [[ -z "$task_file" ]]; then
+        echo "${indent}  Task '$current_task' definition not found"
+        return
+    fi
+    
+    echo "${indent}  Task defined in: $task_file"
+    
+    # Find all files that call this task
+    local callers=()
+    while IFS= read -r line; do
+        [[ -n "$line" ]] && callers+=("$line")
+    done < <(find_callers "$current_task")
+    
+    if [[ ${#callers[@]} -eq 0 ]]; then
+        echo "${indent}  No callers found for task '$current_task'"
+        return
+    fi
+    
+    echo "${indent}  Found ${#callers[@]} caller(s):"
+    
+    for caller_file in "${callers[@]}"; do
+        # Skip if already visited to avoid cycles
+        if is_visited "$caller_file"; then
+            echo "${indent}    $caller_file (already visited, skipping to avoid cycle)"
+            continue
+        fi
+        
+        add_visited "$caller_file"
+        
+        local caller_name
+        caller_name=$(get_workflow_or_task_name "$caller_file")
+        
+        echo "${indent}    $caller_file"
+        echo "${indent}      Contains workflow/task: $caller_name"
+        
+        # Add to current chain
+        CHAIN+=("$caller_name -> $caller_file")
+        
+        # Recursively trace callers of this workflow/task
+        if [[ -n "$caller_name" && "$caller_name" != "$current_task" ]]; then
+            trace_dependencies "$caller_name" $((depth + 1))
+        fi
+    done
+}
+
+# Function to print the full dependency chain
+print_chain() {
+    echo ""
+    echo "=== DEPENDENCY CHAIN SUMMARY ==="
+    if [[ ${#CHAIN[@]} -eq 0 ]]; then
+        echo "No dependency chain found for task '$TASK_NAME'"
+    else
+        echo "Dependency chain for task '$TASK_NAME':"
+        for item in "${CHAIN[@]}"; do
+            echo "  $item"
+        done
+    fi
+}
+
+# Main execution
+main() {
+    if [[ $# -eq 0 ]]; then
+        echo "Usage: $0 <task_name>"
+        echo "Example: $0 GetTodayDate"
+        exit 0
+    fi
+    
+    echo "=================================="
+    echo "=== WDL TASK DEPENDENCY TRACER ==="
+    echo "=================================="
+    echo -e "Searching for workflows that call task: \n\t$TASK_NAME"
+    echo "WDL directory: $WDL_DIR"
+    echo ""
+    
+    # Check if WDL directory exists
+    if [[ ! -d "$WDL_DIR" ]]; then
+        echo "Error: WDL directory '$WDL_DIR' not found"
+        exit 1
+    fi
+    
+    # Start tracing
+    trace_dependencies "$TASK_NAME"
+    
+    # Print summary
+    print_chain
+}
+
+main "$@"