Backup old RNA_SEQ_INFO_DATABASE_JSON and replace it with an updated one

3 files changed, 29 insertions, 3 deletions

diff --git a/Code/backup_files.py b/Code/backup_files.py
index 1ab3fab..4984a66 100644
--- a/Code/backup_files.py
+++ b/Code/backup_files.py
@@ -7,6 +7,7 @@
 # Created on 7 December 2019 by Hui Lan (lanhui@zjnu.edu.cn)
 
 import os, sys
+import gzip
 from configure import UPDATE_NETWORK_LOG_FILE
 from datetime import datetime
 from log import write_log_file
@@ -34,6 +35,16 @@ def copy_and_backup_file(src_file, dest_dir):
     write_log_file('[backup_files.py] File %s has been backed up to %s and zipped (.gz)' % (src_file, dest_file), UPDATE_NETWORK_LOG_FILE)            
 
 
+def backup_file(src_file):
+    if not os.path.exists(src_file):
+        raise Exception(f'{src_file} does not exists.')
+    curr_date = datetime.now().strftime('%Y%m%d')
+    zip_fname = src_file + '.' + curr_date + '.gz'
+    with gzip.open(zip_fname, 'wb') as gz:
+        with open(src_file) as f:
+            gz.write(f.read().encode('utf-8'))
+    return zip_fname
+
 ## main
 if __name__ == '__main__':
     copy_and_backup_file('../Data/temp/edges.txt', '../Analysis')
diff --git a/Code/parse_ena_xml.py b/Code/parse_ena_xml.py
index 75777a1..4af3a77 100644
--- a/Code/parse_ena_xml.py
+++ b/Code/parse_ena_xml.py
@@ -30,7 +30,9 @@ import os, json, re, operator
 import xml.etree.ElementTree
 import sys
 import string
-from configure import ENA_RECORDS_READ_RUN, ENA_RECORDS_READ_EXPERIMENT, ENA_RECORDS_SAMPLE, ENA_RECORDS_STUDY
+import shutil
+from backup_files import backup_file
+from configure import ENA_RECORDS_READ_RUN, ENA_RECORDS_READ_EXPERIMENT, ENA_RECORDS_SAMPLE, ENA_RECORDS_STUDY, RNA_SEQ_INFO_DATABASE_JSON
 MAX_DESCRIPTION_LENGTH = 6000 # max number to characters to keep in json file
 
 
@@ -326,6 +328,15 @@ if __name__ == '__main__':
     percent = 100*count_tissue/count_transcriptomic
     print(f'%% RNA-seq: {count_transcriptomic}, of which {count_tissue} having tissue info ({percent} percent)')
 
-    fname = '../Data/information/rnaseq_info_database.json.temp'
-    with open(fname, 'w') as f:
+    temp_fname = RNA_SEQ_INFO_DATABASE_JSON + '.temp'
+    with open(temp_fname, 'w') as f:
         json.dump(json_dict, f, indent=4)
+
+    # Use rnaseq_info_database.json.temp to replace the exisiting rnaseq_info_database.json
+    # But make a backup for rnaseq_info_database.json first
+    try:
+        bak_fname = backup_file(RNA_SEQ_INFO_DATABASE_JSON)
+        shutil.move(temp_fname, RNA_SEQ_INFO_DATABASE_JSON)
+        print(f'Made {bak_fname}')
+    except Exception as e:
+        print(f'Backup {RNA_SEQ_INFO_DATABASE_JSON} encountered problem')
diff --git a/Code/test_backup_file.py b/Code/test_backup_file.py
new file mode 100644
index 0000000..d17f60a
--- /dev/null
+++ b/Code/test_backup_file.py
@@ -0,0 +1,4 @@
+from backup_files import backup_file
+from configure import RNA_SEQ_INFO_DATABASE_JSON
+
+backup_file(RNA_SEQ_INFO_DATABASE_JSON)