Sort content of txt files in study dir to make order not important wh…

…ile comparing

test/integration/copy_and_sort.sh

@@ -0,0 +1,45 @@
+#!/bin/bash
+
+# Function to display usage instructions
+usage() {
+    echo "Usage: $0 <source_directory> <destination_directory>"
+    exit 1
+}
+
+# Check if the correct number of arguments is provided
+if [ "$#" -ne 2 ]; then
+    usage
+fi
+
+# Remove trailing slashes from paths if they exist
+SOURCE_DIR="${1%/}"
+DEST_DIR="${2%/}"
+
+# Check if the source directory exists
+if [ ! -d "$SOURCE_DIR" ]; then
+    echo "Error: Source directory does not exist."
+    exit 1
+fi
+
+# Create the destination directory if it does not exist
+mkdir -p "$DEST_DIR"
+
+# Copy files and sort text files
+find "$SOURCE_DIR" -type f | while read -r FILE; do
+    REL_PATH="${FILE#$SOURCE_DIR/}"  # Get relative path
+    DEST_FILE="$DEST_DIR/$REL_PATH"  # Destination file path
+    DEST_DIR_PATH="$(dirname "$DEST_FILE")"  # Destination directory path
+
+    # Create the destination directory if it does not exist
+    mkdir -p "$DEST_DIR_PATH"
+
+    # Check if the file is a text file and sort its contents
+    if file "$FILE" | grep -q "text"; then
+        sort "$FILE" > "$DEST_FILE"
+    else
+        cp "$FILE" "$DEST_FILE"
+    fi
+
+done
+
+echo "Copy and sort operation completed successfully."

test/integration/in_service_import_export_test.sh

@@ -0,0 +1,20 @@
+#!/bin/bash
+
+# exit when any of these fails
+set -e
+
+echo "Importing of the test study with API validation..."
+metaImport.py -v -u http://cbioportal-container:8080 -o -s /cbioportal/test/test_data/study_es_0_import_export/
+
+echo "Exporting of the test study."
+curl -s http://cbioportal-container:8080/export/study/study_es_0_import_export.zip > study_es_0_import_export.zip \
+&& unzip study_es_0_import_export.zip -d ./output_study_es_0_import_export
+
+echo "Sort content of text files from both folders to make order during comparison unimportant."
+./cbioportal/test/integration/copy_and_sort.sh /cbioportal/test/test_data/study_es_0_import_export/ ./input_study_es_0_import_export_sorted/
+./cbioportal/test/integration/copy_and_sort.sh ./output_study_es_0_import_export/ ./output_study_es_0_import_export_sorted/
+
+echo "Comparing the original and exported studies."
+diff --recursive ./input_study_es_0_import_export_sorted/ ./output_study_es_0_import_export_sorted/
+
+exit 0

test/integration/test_import_export.sh

@@ -12,14 +12,6 @@ run_in_service() {
     return $?  # return the exit code of the last command
 }
 
-echo "Importing of the test study with API validation..."
-run_in_service cbioportal 'metaImport.py -v -u http://cbioportal-container:8080 -o -s /cbioportal/test/test_data/study_es_0_import_export/'
-
-echo "Exporting of the test study."
-run_in_service cbioportal 'curl -s http://cbioportal-container:8080/export/study/study_es_0_import_export.zip > study_es_0_import_export.zip && unzip study_es_0_import_export.zip -d ./output_study_es_0_import_export'
-
-echo "Comparing the original and exported studies."
-# TODO ignore order of lines in files
-run_in_service cbioportal 'diff --recursive /cbioportal/test/test_data/study_es_0_import_export/ ./output_study_es_0_import_export'
+run_in_service cbioportal '/cbioportal/test/integration/in_service_import_export_test.sh'
 
 exit 0