Fixed patient generation with separate script approach

generate_patients.sh

@@ -0,0 +1,78 @@
+#!/bin/bash
+
+# Script to generate synthetic patients directly using modules created by the pipeline
+# Usage: ./generate_patients.sh <module_name> <output_directory> <population_size>
+
+MODULE_NAME=$1
+OUTPUT_DIR=$2
+POPULATION=${3:-10}
+
+if [ -z "$MODULE_NAME" ] || [ -z "$OUTPUT_DIR" ]; then
+  echo "Usage: $0 <module_name> <output_directory> [population_size]"
+  echo "Example: $0 diabetes /path/to/output 20"
+  exit 1
+fi
+
+# Create output directory
+mkdir -p "$OUTPUT_DIR/m" "$OUTPUT_DIR/f"
+
+# Location of module file
+MODULE_PATH="/data/olamide/synthea-alldiseases/modules/${MODULE_NAME}.json"
+
+if [ ! -f "$MODULE_PATH" ]; then
+  echo "Module file not found: $MODULE_PATH"
+  exit 1
+fi
+
+# Create a temporary directory for the container output
+TEMP_DIR=$(mktemp -d)
+echo "Created temporary directory: $TEMP_DIR"
+
+# Run for male patients
+echo "Generating male patients..."
+docker run --rm \
+  -v "$MODULE_PATH:/app/modules/${MODULE_NAME}.json" \
+  -v "$TEMP_DIR:/app/output" \
+  synthea-module-generator \
+  bash -c "cd /app && ./run_synthea -p $((POPULATION/2)) -g M -m ${MODULE_NAME} Massachusetts"
+
+# Copy male patient files to the output directory
+echo "Copying male patient files..."
+find "$TEMP_DIR/fhir" -name "*.json" ! -name "*hospital*" ! -name "*practitioner*" | while read file; do
+  # Check if it's a patient file by looking for gender field
+  if grep -q '"gender"' "$file"; then
+    cp "$file" "$OUTPUT_DIR/m/"
+  fi
+done
+
+# Clear the temp directory
+rm -rf "$TEMP_DIR/fhir"/*
+
+# Run for female patients
+echo "Generating female patients..."
+docker run --rm \
+  -v "$MODULE_PATH:/app/modules/${MODULE_NAME}.json" \
+  -v "$TEMP_DIR:/app/output" \
+  synthea-module-generator \
+  bash -c "cd /app && ./run_synthea -p $((POPULATION/2)) -g F -m ${MODULE_NAME} Massachusetts"
+
+# Copy female patient files to the output directory
+echo "Copying female patient files..."
+find "$TEMP_DIR/fhir" -name "*.json" ! -name "*hospital*" ! -name "*practitioner*" | while read file; do
+  # Check if it's a patient file by looking for gender field
+  if grep -q '"gender"' "$file"; then
+    cp "$file" "$OUTPUT_DIR/f/"
+  fi
+done
+
+# Count the results
+male_count=$(find "$OUTPUT_DIR/m" -type f -name "*.json" | wc -l)
+female_count=$(find "$OUTPUT_DIR/f" -type f -name "*.json" | wc -l)
+
+# Report results
+echo "Patient generation complete. Results saved to $OUTPUT_DIR"
+echo "Male patients: $male_count"
+echo "Female patients: $female_count"
+
+# Clean up temp directory
+rm -rf "$TEMP_DIR"