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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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30
python/obitools3/commands/clean.pyx
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@ -4,13 +4,14 @@ from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport
from obitools3.dms.dms cimport DMS
from obitools3.dms.view import RollbackException
from obitools3.dms.capi.obiclean cimport obi_clean
from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption
from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption, addNoProgressBarOption
from obitools3.uri.decode import open_uri
from obitools3.apps.config import logger
from obitools3.utils cimport tobytes, str2bytes
from obitools3.dms.view.view cimport View
from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS
from io import BufferedWriter
import sys
@ -21,7 +22,8 @@ def addOptions(parser):
addMinimalInputOption(parser)
addMinimalOutputOption(parser)
addNoProgressBarOption(parser)
group = parser.add_argument_group('obi clean specific options')
group.add_argument('--distance', '-d',
@ -88,17 +90,20 @@ def run(config):
if output is None:
raise Exception("Could not create output")
o_dms = output[0]
output_0 = output[0]
final_o_view_name = output[1]
# If the input and output DMS are not the same, run obiclean creating a temporary view that will be exported to
# If stdout output or the input and output DMS are not the same, create a temporary view that will be exported to
# the right DMS and deleted in the other afterwards.
if i_dms != o_dms:
temporary_view_name = final_o_view_name
if i_dms != o_dms or type(output_0)==BufferedWriter:
temporary_view_name = b"temp"
i=0
while temporary_view_name in i_dms: # Making sure view name is unique in input DMS
temporary_view_name = final_o_view_name+b"_"+str2bytes(str(i))
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
@ -116,15 +121,22 @@ def run(config):
# If the input and output DMS are not the same, export result view to output DMS
if i_dms != o_dms:
View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], o_view_name, final_o_view_name)
# stdout output: write to buffer
if type(output_0)==BufferedWriter:
logger("info", "Printing to output...")
o_view = o_dms[o_view_name]
o_view.print_to_output(output_0, noprogressbar=config['obi']['noprogressbar'])
o_view.close()
# Save command config in DMS comments
o_dms.record_command_line(command_line)
#print("\n\nOutput view:\n````````````", file=sys.stderr)
#print(repr(o_dms[final_o_view_name]), file=sys.stderr)
# If the input and the output DMS are different, delete the temporary result view in the input DMS
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)