diff options
Diffstat (limited to 'Code/update_network.py')
| -rwxr-xr-x | Code/update_network.py | 42 |
1 files changed, 19 insertions, 23 deletions
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): |