Commit 11a0945a by Celine Mercier

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

parent f23c40c9
......@@ -48,9 +48,9 @@ def run(config):
logger("info", "obi cat")
# Open the views to concatenate
iview_list = []
# Check the views to concatenate
idms_list = []
iview_list = []
total_len = 0
remove_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
remove_rev_qual = True
total_len += len(i_view)
iview_list.append(i_view)
idms_list.append(i_dms)
iview_list.append(i_view.name)
i_view.close()
# Open the output: only the DMS
output = open_uri(config['obi']['outputURI'],
......@@ -98,8 +99,10 @@ def run(config):
# Initialize multiple elements columns
if type(output_0)==BufferedWriter:
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():
col = v[coln]
if v[coln].nb_elements_per_line > 1:
if coln not in dict_cols:
dict_cols[coln] = {}
......@@ -109,6 +112,7 @@ def run(config):
else:
dict_cols[coln]['eltnames'] = set(v[coln].elements_names + list(dict_cols[coln]['eltnames']))
dict_cols[coln]['nbelts'] = len(dict_cols[coln]['eltnames'])
v.close()
for coln in dict_cols:
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']))
......@@ -120,7 +124,8 @@ def run(config):
pb = None
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:
PyErr_CheckSignals()
if pb is not None:
......@@ -131,6 +136,7 @@ def run(config):
else:
o_view[i] = entry
i+=1
v.close()
# Deletes quality columns if needed
if type(output_0)!=BufferedWriter:
......@@ -145,7 +151,7 @@ def run(config):
# Save command config in DMS comments
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)
#print("\n\nOutput view:\n````````````", file=sys.stderr)
......
major = 3
minor = 0
serial= '0b33'
serial= '0b34'
version ="%d.%d.%s" % (major,minor,serial)
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