Update write_log_file() so that it put the most recent message on the top; remove duplicate write_log_file()

8 files changed, 32 insertions, 68 deletions

diff --git a/Code/backup_files.py b/Code/backup_files.py
index 6105525..0b044f1 100644
--- a/Code/backup_files.py
+++ b/Code/backup_files.py
@@ -9,21 +9,10 @@
 import os, sys
 from configure import UPDATE_NETWORK_LOG_FILE
 from datetime import datetime
+from log import write_log_file
 
 MINIMUM_SPACE_REQUIREMENT = 1 # Gigabytes
 
-def write_log_file(s, fname):
-    if not os.path.exists(fname):
-        return None
-    f = open(fname, 'a')
-    curr_time = datetime.now().strftime('%Y-%m-%d %H:%M')
-    s = '[' + curr_time + ']: ' + s
-    if not '\n' in s:
-        s += '\n'
-    f.write(s)
-    f.close()
-
-
 def make_paths(s):
     if not os.path.isdir(s):
         os.makedirs(s)
diff --git a/Code/local_network.py b/Code/local_network.py
index 216832f..beb04ac 100644
--- a/Code/local_network.py
+++ b/Code/local_network.py
@@ -30,6 +30,7 @@ import time
 import subprocess
 from datetime import datetime
 from param4net import make_global_param_dict, get_key_value
+from log import write_log_file
 
 FORCE_MAKE_EDGES  = 'NO'
 
@@ -110,15 +111,6 @@ def record_new_or_updated_chip_ids(lst, fname):
         f.write('%s\t%s\n' % (x, curr_time))
     f.close()
     
-def write_log_file(s, fname):
-    f = open(fname, 'a')
-    print(s)
-    curr_time = datetime.now().strftime('%Y-%m-%d %H:%M')
-    s = '[' + curr_time + ']: ' + s
-    if not '\n' in s:
-        s += '\n'
-    f.write(s)
-    f.close()
 
 def write_sample_size_file(sample_size_file, curr_date, tpm_sample_size):
     if not os.path.exists(sample_size_file):
diff --git a/Code/log.py b/Code/log.py
new file mode 100644
index 0000000..396acdd
--- /dev/null
+++ b/Code/log.py
@@ -0,0 +1,19 @@
+import os
+from datetime import datetime
+
+def write_log_file(s, fname):
+    ''' Write s to fname, the most recent on the top'''
+    curr_time = datetime.now().strftime('%Y-%m-%d %H:%M')
+    print('Log at %s: %s' % (curr_time, s.strip()))
+    content = ''
+    if os.path.exists(fname):
+        with open(fname) as f:
+            content = f.read()
+    with open(fname, 'w') as f:
+        f.write('[' + curr_time + ']: ' + s.strip() + '\n' + content)
+
+
+
+if __name__ == '__main__':
+    write_log_file('hello', 'testlog.txt');
+    write_log_file('logger', 'testlog.txt');
diff --git a/Code/make_parameter_rnaseq.py b/Code/make_parameter_rnaseq.py
index 18ef568..f9c7d26 100644
--- a/Code/make_parameter_rnaseq.py
+++ b/Code/make_parameter_rnaseq.py
@@ -9,6 +9,7 @@
 import sys, os, glob, json

 import fnmatch, re

 from datetime import datetime

+from log import write_log_file

 from configure import RNA_SEQ_INFO_FILE, UPDATE_NETWORK_LOG_FILE

 

 NON_ZERO_RATIO = 0.2 # omit *_quant.txt files with too many zeros.

@@ -102,15 +103,6 @@ def read_ena_data_info_json(fname):
     return d

 

 

-def write_log_file(s, fname):

-    f = open(fname, 'a')

-    curr_time = datetime.now().strftime('%Y-%m-%d %H:%M')

-    s = '[' + curr_time + ']: ' + s

-    if not '\n' in s:

-        s += '\n'

-    f.write(s)

-    f.close()

-

 ### main

 if not os.path.exists(RNA_SEQ_INFO_FILE):

     print('make_parameter_rnaseq.py: you must provide %s. See parse_ena_xml.py on how to make it.' % (RNA_SEQ_INFO_FILE))

diff --git a/Code/merge_edges.py b/Code/merge_edges.py
index 3b20468..2fc034c 100644
--- a/Code/merge_edges.py
+++ b/Code/merge_edges.py
@@ -21,22 +21,10 @@
 
 
 import os, operator, sys, math, datetime, glob
+from log import write_log_file
 from configure import EDGE_POOL_DIR, MERGED_EDGE_FILE, UPDATE_NETWORK_LOG_FILE
 import sqlite3
 
-
-def write_log_file(s, fname):
-    if not os.path.exists(fname):
-        return None
-    f = open(fname, 'a')
-    curr_time = datetime.datetime.now().strftime('%Y-%m-%d %H:%M')
-    s = '[' + curr_time + ']: ' + s
-    if not '\n' in s:
-        s += '\n'
-    f.write(s)
-    f.close()
-
-
 def get_number_of_RNAseq_ids(s):
     if s == '.':
         return 1
diff --git a/Code/testlog.txt b/Code/testlog.txt
new file mode 100644
index 0000000..fae738f
--- /dev/null
+++ b/Code/testlog.txt
@@ -0,0 +1,2 @@
+[2024-08-05 14:36]: logger
+[2024-08-05 14:36]: hello
diff --git a/Code/update_network.py b/Code/update_network.py
index e8d5a1d..d5aed9b 100755
--- a/Code/update_network.py
+++ b/Code/update_network.py
@@ -47,6 +47,7 @@ import time
 import subprocess
 from datetime import datetime
 from param4net import make_global_param_dict, get_key_value
+from log import write_log_file
 from configure import HISTORY_DIR, HISTORY_DIR2, FILE_TIMESTAMP, SAMPLE_SIZE_FILE, TEMP_DIR, \
     PARAMETER_FOR_BUILDCMATRIX, PARAMETER_FOR_BUILDRMATRIX, \
     PARAMETER_FOR_NET, PARAMETER_FOR_NET_TRAVADB_STRESS, PARAMETER_FOR_NET_TRAVADB_MAP, PARAMETER_FOR_NET_MILD_DROUGHT, PARAMETER_FOR_NET_WIGGELAB_DIURNAL, \
@@ -123,17 +124,6 @@ def num_ids(fname):
     return len(lines[0].split('\t')) - 1
 
 
-def write_log_file(s, fname):
-    f = open(fname, 'a')
-    curr_time = datetime.now().strftime('%Y-%m-%d %H:%M')
-    s = '[' + curr_time + ']: ' + s
-    if not '\n' in s:
-        s += '\n'
-    f.write(s)
-    f.close()
-    print('Log: %s' % (s.strip()))
-
-
 def write_sample_size_file(sample_size_file, curr_date, tpm_sample_size):
     if not os.path.exists(sample_size_file):
         f = open(sample_size_file, 'w')
diff --git a/Code/update_network_by_force.py b/Code/update_network_by_force.py
index 079f677..fae2965 100644
--- a/Code/update_network_by_force.py
+++ b/Code/update_network_by_force.py
@@ -1,8 +1,9 @@
 # Usage: python3 update_network_by_force.py
-# Purpose: update_network.py could take a few days (even weeks) to run.  Run this script to harvest new edges everyday.
+# Purpose: update_network.py could take a few days (even weeks) to run.  Run this script to harvest new edges before update_network.py finishes.
 #
 # Revision history:
-# Last modified: 24 Nov 2019, hui <lanhui@zjnu.edu.cn>
+# 24 Nov 2019, hui <lanhui@zjnu.edu.cn>
+# Last modified: 5 Aug 2024, hui <lanhui@zjnu.edu.cn>
 
 import os, sys
 import glob
@@ -12,21 +13,11 @@ from configure import HISTORY_DIR, HISTORY_DIR2, UPDATE_NETWORK_LOG_FILE, MERGED
 from configure import PARAMETER_FOR_BUILDCMATRIX, PARAMETER_FOR_BUILDRMATRIX, PARAMETER_FOR_NET
 from configure import DIFF_EDGE_FILE
 from backup_files import copy_and_backup_file
+from log import write_log_file
 from overlap import Overlap
 import utils
 
 ########## Helper functions #######################
-def write_log_file(s, fname):
-    f = open(fname, 'a')
-    curr_time = datetime.now().strftime('%Y-%m-%d %H:%M')
-    s = '[' + curr_time + ']: ' + s
-    if not '\n' in s:
-        s += '\n'
-    f.write(s)
-    f.close()
-    print('Log: %s' % (s.strip()))
-
-
 def num_line(fname):
     ''' Return number of lines in file fname. '''
     if not os.path.exists(fname):
@@ -52,6 +43,7 @@ def age_of_file_in_seconds(fname):
     seconds = time.time() - st.st_mtime
     return seconds
 
+
 def concatenate_edge_files(fname_lst, dir_out, fname_out):
     fout = open(os.path.join(dir_out, fname_out), 'w')
     for fname in fname_lst:
@@ -78,7 +70,7 @@ def concatenate_edge_files(fname_lst, dir_out, fname_out):
         else:
             write_log_file('[update_network_by_force.py] In function concatenate_edge_files(). Check file %s.  It has no rows with 10 fields.' % (fname), UPDATE_NETWORK_LOG_FILE)
     fout.close()
-        
+
 
 def delete_edge_files(fname_lst):
     age_in_hours = 6