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Python: made all commands handle output to buffer object (e.g. stdout)

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This commit is contained in:
Celine Mercier
2020-07-24 16:09:48 +02:00
parent 46ca693ca9
commit 8aa455ad8a
18 changed files with 511 additions and 213 deletions
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52
python/obitools3/commands/tail.pyx
View File

@ -4,7 +4,7 @@ from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport
from obitools3.dms import DMS
from obitools3.dms.view.view cimport View, Line_selection
from obitools3.uri.decode import open_uri
from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption
from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption, addNoProgressBarOption
from obitools3.dms.view import RollbackException
from obitools3.apps.config import logger
from obitools3.utils cimport str2bytes
@ -12,6 +12,7 @@ from obitools3.utils cimport str2bytes
import time
import sys
from cpython.exc cimport PyErr_CheckSignals
from io import BufferedWriter
__title__="Keep the N last lines of a view."
@ -21,6 +22,7 @@ def addOptions(parser):
addMinimalInputOption(parser)
addMinimalOutputOption(parser)
addNoProgressBarOption(parser)
group=parser.add_argument_group('obi tail specific options')
@ -52,31 +54,41 @@ def run(config):
if output is None:
raise Exception("Could not create output view")
o_dms = output[0]
o_view_name_final = output[1]
o_view_name = o_view_name_final
output_0 = output[0]
final_o_view_name = output[1]
# If the input and output DMS are not the same, create output view in input DMS first, then export it
# to output DMS, making sure the temporary view name is unique in the input DMS
if i_dms != o_dms:
# If stdout output or the input and output DMS are not the same, create a temporary view that will be exported and deleted.
if i_dms != o_dms or type(output_0)==BufferedWriter:
temporary_view_name = b"temp"
i=0
while o_view_name in i_dms:
o_view_name = o_view_name_final+b"_"+str2bytes(str(i))
i+=1
while temporary_view_name in i_dms: # Making sure view name is unique in input DMS
temporary_view_name = temporary_view_name+b"_"+str2bytes(str(i))
i+=1
o_view_name = temporary_view_name
if type(output_0)==BufferedWriter:
o_dms = i_dms
else:
o_view_name = final_o_view_name
start = max(len(i_view) - config['tail']['count'], 0)
# Initialize the progress bar
pb = ProgressBar(len(i_view) - start, config, seconde=5)
if config['obi']['noprogressbar'] == False:
pb = ProgressBar(len(i_view) - start, config)
else:
pb = None
selection = Line_selection(i_view)
for i in range(start, len(i_view)):
PyErr_CheckSignals()
pb(i)
if pb is not None:
pb(i)
selection.append(i)
pb(i, force=True)
print("", file=sys.stderr)
if pb is not None:
pb(i, force=True)
print("", file=sys.stderr)
# Save command config in View comments
command_line = " ".join(sys.argv[1:])
@ -97,14 +109,20 @@ def run(config):
# and delete the temporary view in the input DMS
if i_dms != o_dms:
o_view.close()
View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], o_view_name, o_view_name_final)
o_view = o_dms[o_view_name_final]
View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], o_view_name, final_o_view_name)
o_view = o_dms[final_o_view_name]
# stdout output: write to buffer
if type(output_0)==BufferedWriter:
logger("info", "Printing to output...")
o_view.print_to_output(output_0, noprogressbar=config['obi']['noprogressbar'])
o_view.close()
#print("\n\nOutput view:\n````````````", file=sys.stderr)
#print(repr(o_view), file=sys.stderr)
# 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:
# If the input and the output DMS are different or if stdout output, delete the temporary imported view used to create the final view
if i_dms != o_dms or type(output_0)==BufferedWriter:
View.delete_view(i_dms, o_view_name)
o_dms.close(force=True)
i_dms.close(force=True)