Put the definition of make_paths() in utils.py because multiple places use it

4 files changed, 27 insertions, 32 deletions

diff --git a/Code/backup_files.py b/Code/backup_files.py
index 0b044f1..1ab3fab 100644
--- a/Code/backup_files.py
+++ b/Code/backup_files.py
@@ -10,14 +10,10 @@ import os, sys
 from configure import UPDATE_NETWORK_LOG_FILE
 from datetime import datetime
 from log import write_log_file
+from utils import make_paths
 
 MINIMUM_SPACE_REQUIREMENT = 1 # Gigabytes
 
-def make_paths(s):
-    if not os.path.isdir(s):
-        os.makedirs(s)
-
-
 def disk_has_enough_space():
     available_G = 4 * os.statvfs('/home').f_bavail / (1024*1024) # compute available space (in Gigabytes).  Each block has 4k bytes, work for Linux/UNIX systems only
     if available_G < MINIMUM_SPACE_REQUIREMENT:
diff --git a/Code/local_network.py b/Code/local_network.py
index beb04ac..e05e7a0 100644
--- a/Code/local_network.py
+++ b/Code/local_network.py
@@ -31,6 +31,7 @@ import subprocess
 from datetime import datetime
 from param4net import make_global_param_dict, get_key_value
 from log import write_log_file
+from utils import make_paths
 
 FORCE_MAKE_EDGES  = 'NO'
 
@@ -71,10 +72,7 @@ def ok_webapp_dir(para_for_net):
         print('genes.json not here, make one')
         cmd = 'python text2json.py %s > ../Webapp/static/json/genes.json' % (glb_param_dict['GENE_ID_AND_GENE_NAME'])
         os.system(cmd)
-    
-def make_paths(s):
-    if not os.path.isdir(s):
-        os.makedirs(s)
+
     
 def make_important_dirs():
     make_paths('../Data/history/edges/many_targets')
diff --git a/Code/update_network.py b/Code/update_network.py
index 7b26f58..74e5599 100755
--- a/Code/update_network.py
+++ b/Code/update_network.py
@@ -48,6 +48,7 @@ import subprocess
 from datetime import datetime
 from param4net import make_global_param_dict, get_key_value
 from log import write_log_file
+from utils import make_paths
 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, \
@@ -62,33 +63,12 @@ from configure import HISTORY_DIR, HISTORY_DIR2, FILE_TIMESTAMP, SAMPLE_SIZE_FIL
 
 ## Helper functions
 
-def get_value(s, delimit):
-    lst = s.split(delimit, 1) # only split at the first delimit    
-    return lst[1].strip()
-
-
-def validate_webapp_dir(para_for_net):
-    ''' Make sure this function is executed under the directory Code. '''
-    glb_param_dict = make_global_param_dict(para_for_net)
-    # if genes.json is not present, create one
-    if not os.path.exists('../Webapp/static/json/genes.json'):
-        print('[update_network.py]: cannot find genes.json, make one ...')
-        cmd = 'python3 text2json.py %s > ../Webapp/static/json/genes.json' % (glb_param_dict['GENE_ID_AND_GENE_NAME'])
-        os.system(cmd)
-
-    
-def make_paths(s):
-    if not os.path.isdir(s):
-        os.makedirs(s)
-
-
 def make_important_dirs():
     make_paths('../Data/history/edges/many_targets')
     make_paths('../Data/history/edges/one_target')
     make_paths('../Data/log')
     make_paths('../Data/information')    
-    make_paths('../Data/temp')
-    make_paths('../Data/upload')        
+    make_paths('../Data/temp')    
     make_paths('../Data/parameter')
     make_paths('../Data/R/Mapped')
     make_paths('../Data/R/Mapped/public')
@@ -96,14 +76,30 @@ def make_important_dirs():
     make_paths('../Data/R/Mapped/other')
     make_paths('../Data/R/Raw')
     make_paths('../Data/C/Mapped')
+    make_paths('../Data/C/Mapped/Columns')    
     make_paths('../Data/C/Raw')    
     make_paths('../Data/history/edges')
-    make_paths(EDGE_POOL_DIR)    
     make_paths('../Data/history/bind')
     make_paths('../Data/history/expr')
     make_paths('../Webapp/static/json')
     make_paths('../Webapp/static/edges')    
     make_paths('../Webapp/templates')    
+    make_paths(EDGE_POOL_DIR)
+
+
+def get_value(s, delimit):
+    lst = s.split(delimit, 1) # only split at the first delimit    
+    return lst[1].strip()
+
+
+def validate_webapp_dir(para_for_net):
+    ''' Make sure this function is executed under the directory Code. '''
+    glb_param_dict = make_global_param_dict(para_for_net)
+    # if genes.json is not present, create one
+    if not os.path.exists('../Webapp/static/json/genes.json'):
+        print('[update_network.py]: cannot find genes.json, make one ...')
+        cmd = 'python3 text2json.py %s > ../Webapp/static/json/genes.json' % (glb_param_dict['GENE_ID_AND_GENE_NAME'])
+        os.system(cmd)
 
     
 def num_line(fname):
diff --git a/Code/utils.py b/Code/utils.py
index 3a89a8e..27922d0 100644
--- a/Code/utils.py
+++ b/Code/utils.py
@@ -37,6 +37,11 @@ def make_new_edges_file(Sold, Snew, fname_new, output_file):
         f.write('*** Number of newly added edges: %d.  Last modification date: %s. ***\n' % (len(result), datetime.now().strftime('%Y-%m-%d %H:%M')))
 
 
+def make_paths(s):
+    if not os.path.isdir(s):
+        os.makedirs(s)
+
+
 if __name__ == '__main__':
     S2 = get_edge_set('/home/lanhui/brain/Data/temp/edges.txt')
     S1 = get_edge_set('/home/lanhui/brain/Data/temp/edges.txt.old')