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obi cat: fixed open file descriptor leak and switch to version 3.0.0b34

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Celine Mercier
2020-08-28 10:41:22 +02:00
parent f23c40c905
commit 11a0945a9b
2 changed files with 13 additions and 7 deletions
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18
python/obitools3/commands/cat.pyx
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@ -48,9 +48,9 @@ def run(config):
logger("info", "obi cat") logger("info", "obi cat")
# Open the views to concatenate # Check the views to concatenate
iview_list = []
idms_list = [] idms_list = []
iview_list = []
total_len = 0 total_len = 0
remove_qual = False remove_qual = False
remove_rev_qual = False remove_rev_qual = False
@ -68,8 +68,9 @@ def run(config):
if REVERSE_QUALITY_COLUMN not in i_view: # same as above for reverse quality if REVERSE_QUALITY_COLUMN not in i_view: # same as above for reverse quality
remove_rev_qual = True remove_rev_qual = True
total_len += len(i_view) total_len += len(i_view)
iview_list.append(i_view)
idms_list.append(i_dms) idms_list.append(i_dms)
iview_list.append(i_view.name)
i_view.close()
# Open the output: only the DMS # Open the output: only the DMS
output = open_uri(config['obi']['outputURI'], output = open_uri(config['obi']['outputURI'],
@ -98,8 +99,10 @@ def run(config):
# Initialize multiple elements columns # Initialize multiple elements columns
if type(output_0)==BufferedWriter: if type(output_0)==BufferedWriter:
dict_cols = {} dict_cols = {}
for v in iview_list: for v_uri in config["cat"]["views_to_cat"]:
v = open_uri(v_uri)[1]
for coln in v.keys(): for coln in v.keys():
col = v[coln]
if v[coln].nb_elements_per_line > 1: if v[coln].nb_elements_per_line > 1:
if coln not in dict_cols: if coln not in dict_cols:
dict_cols[coln] = {} dict_cols[coln] = {}
@ -109,6 +112,7 @@ def run(config):
else: else:
dict_cols[coln]['eltnames'] = set(v[coln].elements_names + list(dict_cols[coln]['eltnames'])) dict_cols[coln]['eltnames'] = set(v[coln].elements_names + list(dict_cols[coln]['eltnames']))
dict_cols[coln]['nbelts'] = len(dict_cols[coln]['eltnames']) dict_cols[coln]['nbelts'] = len(dict_cols[coln]['eltnames'])
v.close()
for coln in dict_cols: for coln in dict_cols:
Column.new_column(o_view, coln, dict_cols[coln]['obitype'], Column.new_column(o_view, coln, dict_cols[coln]['obitype'],
nb_elements_per_line=dict_cols[coln]['nbelts'], elements_names=list(dict_cols[coln]['eltnames'])) nb_elements_per_line=dict_cols[coln]['nbelts'], elements_names=list(dict_cols[coln]['eltnames']))
@ -120,7 +124,8 @@ def run(config):
pb = None pb = None
i = 0 i = 0
for v in iview_list: for v_uri in config["cat"]["views_to_cat"]:
v = open_uri(v_uri)[1]
for entry in v: for entry in v:
PyErr_CheckSignals() PyErr_CheckSignals()
if pb is not None: if pb is not None:
@ -131,6 +136,7 @@ def run(config):
else: else:
o_view[i] = entry o_view[i] = entry
i+=1 i+=1
v.close()
# Deletes quality columns if needed # Deletes quality columns if needed
if type(output_0)!=BufferedWriter: if type(output_0)!=BufferedWriter:
@ -145,7 +151,7 @@ def run(config):
# Save command config in DMS comments # Save command config in DMS comments
command_line = " ".join(sys.argv[1:]) command_line = " ".join(sys.argv[1:])
o_view.write_config(config, "cat", command_line, input_dms_name=[d.name for d in idms_list], input_view_name=[v.name for v in iview_list]) o_view.write_config(config, "cat", command_line, input_dms_name=[d.name for d in idms_list], input_view_name=[vname for vname in iview_list])
o_dms.record_command_line(command_line) o_dms.record_command_line(command_line)
#print("\n\nOutput view:\n````````````", file=sys.stderr) #print("\n\nOutput view:\n````````````", file=sys.stderr)

2
python/obitools3/version.py
View File

@ -1,5 +1,5 @@
major = 3 major = 3
minor = 0 minor = 0
serial= '0b33' serial= '0b34'
version ="%d.%d.%s" % (major,minor,serial) version ="%d.%d.%s" % (major,minor,serial)