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all commands (almost): cleaner DMS closing at the end

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This commit is contained in:
Celine Mercier
2020-04-12 17:31:58 +02:00
parent eef5156d95
commit 4d0299904e
16 changed files with 31 additions and 26 deletions
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4
python/obitools3/commands/align.pyx
View File

@ -266,9 +266,9 @@ def run(config):
# If the input and the output DMS are different, delete the temporary result view in the input DMS
if i_dms != o_dms:
View.delete_view(i_dms, o_view_name)
o_dms.close()
o_dms.close(force=True)
i_dms.close()
i_dms.close(force=True)
logger("info", "Done.")

6
python/obitools3/commands/alignpairedend.pyx
View File

@ -247,10 +247,10 @@ def run(config):
#print("\n\nOutput view:\n````````````", file=sys.stderr)
#print(repr(view), file=sys.stderr)
input[0].close()
input[0].close(force=True)
if two_views:
rinput[0].close()
output[0].close()
rinput[0].close(force=True)
output[0].close(force=True)
logger("info", "Done.")

4
python/obitools3/commands/annotate.pyx
View File

@ -379,7 +379,7 @@ def run(config):
# If the input and the output DMS are different, delete the temporary imported view used to create the final view
if i_dms != o_dms:
View.delete_view(o_dms, imported_view_name)
o_dms.close()
i_dms.close()
o_dms.close(force=True)
i_dms.close(force=True)
logger("info", "Done.")

4
python/obitools3/commands/build_ref_db.pyx
View File

@ -97,9 +97,9 @@ def run(config):
# If the input and the output DMS are different, delete the temporary result view in the input DMS
if i_dms != o_dms:
View.delete_view(i_dms, o_view_name)
o_dms.close()
o_dms.close(force=True)
i_dms.close()
i_dms.close(force=True)
logger("info", "Done.")

4
python/obitools3/commands/cat.pyx
View File

@ -133,7 +133,7 @@ def run(config):
#print(repr(view), file=sys.stderr)
for d in idms_list:
d.close()
o_dms.close()
d.close(force=True)
o_dms.close(force=True)
logger("info", "Done.")

4
python/obitools3/commands/clean.pyx
View File

@ -124,8 +124,8 @@ def run(config):
# If the input and the output DMS are different, delete the temporary result view in the input DMS
if i_dms != o_dms:
View.delete_view(i_dms, o_view_name)
o_dms.close()
o_dms.close(force=True)
i_dms.close()
i_dms.close(force=True)
logger("info", "Done.")

2
python/obitools3/commands/count.pyx
View File

@ -56,3 +56,5 @@ def run(config):
print(count2)
else:
print(count1)
input[0].close(force=True)

2
python/obitools3/commands/export.pyx
View File

@ -86,7 +86,7 @@ def run(config):
if not BrokenPipeError and not IOError:
output_object.close()
iview.close()
input[0].close()
input[0].close(force=True)
logger("info", "Done.")

4
python/obitools3/commands/grep.pyx
View File

@ -370,7 +370,7 @@ def run(config):
# If the input and the output DMS are different, delete the temporary imported view used to create the final view
if i_dms != o_dms:
View.delete_view(i_dms, o_view_name)
o_dms.close()
i_dms.close()
o_dms.close(force=True)
i_dms.close(force=True)
logger("info", "Done.")

4
python/obitools3/commands/head.pyx
View File

@ -103,7 +103,7 @@ def run(config):
# If the input and the output DMS are different, delete the temporary imported view used to create the final view
if i_dms != o_dms:
View.delete_view(i_dms, o_view_name)
o_dms.close()
i_dms.close()
o_dms.close(force=True)
i_dms.close(force=True)
logger("info", "Done.")

1
python/obitools3/commands/history.pyx
View File

@ -55,3 +55,4 @@ def run(config):
else:
raise Exception("ASCII history only available for views")
input[0].close(force=True)

2
python/obitools3/commands/less.pyx
View File

@ -46,5 +46,5 @@ def run(config):
process.wait()
iview.close()
input[0].close()
input[0].close(force=True)

2
python/obitools3/commands/ls.pyx
View File

@ -36,6 +36,7 @@ def run(config):
l = []
for view in input[0]:
l.append(tostr(view) + "\t(Date created: " + str(bytes2str_object(dms[view].comments["Date created"]))+")")
dms[view].close()
l.sort()
for v in l:
print(v)
@ -52,3 +53,4 @@ def run(config):
print("\n### Comments:")
print(str(input[1].comments))
input[0].close(force=True)

4
python/obitools3/commands/sort.pyx
View File

@ -141,7 +141,7 @@ def run(config):
# If the input and the output DMS are different, delete the temporary imported view used to create the final view
if i_dms != o_dms:
View.delete_view(i_dms, o_view_name)
o_dms.close()
i_dms.close()
o_dms.close(force=True)
i_dms.close(force=True)
logger("info", "Done.")

4
python/obitools3/commands/tail.pyx
View File

@ -106,7 +106,7 @@ def run(config):
# If the input and the output DMS are different, delete the temporary imported view used to create the final view
if i_dms != o_dms:
View.delete_view(i_dms, o_view_name)
o_dms.close()
i_dms.close()
o_dms.close(force=True)
i_dms.close(force=True)
logger("info", "Done.")

2
python/obitools3/commands/test.pyx
View File

@ -529,7 +529,7 @@ def run(config):
test_taxo(config, infos)
infos['view'].close()
infos['dms'].close()
infos['dms'].close(force=True)
shutil.rmtree(config['obi']['defaultdms']+'.obidms', ignore_errors=True)
print("Done.")