131 lines
4.4 KiB
Cython
Executable File
131 lines
4.4 KiB
Cython
Executable File
#cython: language_level=3
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from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport
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from obitools3.dms import DMS
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from obitools3.dms.view.view cimport View, Line_selection
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from obitools3.uri.decode import open_uri
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from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption, addNoProgressBarOption
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from obitools3.dms.view import RollbackException
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from obitools3.apps.config import logger
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from obitools3.utils cimport str2bytes
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import time
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import sys
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from cpython.exc cimport PyErr_CheckSignals
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from io import BufferedWriter
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__title__="Keep the N last lines of a view."
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def addOptions(parser):
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addMinimalInputOption(parser)
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addMinimalOutputOption(parser)
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addNoProgressBarOption(parser)
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group=parser.add_argument_group('obi tail specific options')
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group.add_argument('-n', '--sequence-count',
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action="store", dest="tail:count",
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metavar='<N>',
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default=10,
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type=int,
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help="Number of last records to keep.")
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def run(config):
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DMS.obi_atexit()
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logger("info", "obi tail")
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# Open the input
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input = open_uri(config["obi"]["inputURI"])
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if input is None:
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raise Exception("Could not read input view")
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i_dms = input[0]
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i_view = input[1]
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# Open the output: only the DMS
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output = open_uri(config['obi']['outputURI'],
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input=False,
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dms_only=True)
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if output is None:
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raise Exception("Could not create output view")
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o_dms = output[0]
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output_0 = output[0]
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final_o_view_name = output[1]
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# If stdout output or the input and output DMS are not the same, create a temporary view that will be exported and deleted.
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if i_dms != o_dms or type(output_0)==BufferedWriter:
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temporary_view_name = b"temp"
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i=0
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while temporary_view_name in i_dms: # Making sure view name is unique in input DMS
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temporary_view_name = temporary_view_name+b"_"+str2bytes(str(i))
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i+=1
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o_view_name = temporary_view_name
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if type(output_0)==BufferedWriter:
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o_dms = i_dms
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else:
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o_view_name = final_o_view_name
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start = max(len(i_view) - config['tail']['count'], 0)
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# Initialize the progress bar
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if config['obi']['noprogressbar'] == False:
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pb = ProgressBar(len(i_view) - start, config)
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else:
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pb = None
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selection = Line_selection(i_view)
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for i in range(start, len(i_view)):
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PyErr_CheckSignals()
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if pb is not None:
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pb(i)
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selection.append(i)
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if pb is not None:
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pb(i, force=True)
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print("", file=sys.stderr)
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# Save command config in View comments
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command_line = " ".join(sys.argv[1:])
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comments = View.get_config_dict(config, "tail", command_line, input_dms_name=[i_dms.name], input_view_name=[i_view.name])
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# Create output view with the line selection
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try:
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o_view = selection.materialize(o_view_name)
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except Exception, e:
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raise RollbackException("obi tail error, rollbacking view: "+str(e), o_view)
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# Save command config in DMS comments
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command_line = " ".join(sys.argv[1:])
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o_view.write_config(config, "tail", command_line, input_dms_name=[i_dms.name], input_view_name=[i_view.name])
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o_dms.record_command_line(command_line)
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# If input and output DMS are not the same, export the temporary view to the output DMS
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# and delete the temporary view in the input DMS
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if i_dms != o_dms:
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o_view.close()
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View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], o_view_name, final_o_view_name)
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o_view = o_dms[final_o_view_name]
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# stdout output: write to buffer
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if type(output_0)==BufferedWriter:
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logger("info", "Printing to output...")
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o_view.print_to_output(output_0, noprogressbar=config['obi']['noprogressbar'])
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o_view.close()
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#print("\n\nOutput view:\n````````````", file=sys.stderr)
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#print(repr(o_view), file=sys.stderr)
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# If the input and the output DMS are different or if stdout output, delete the temporary imported view used to create the final view
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if i_dms != o_dms or type(output_0)==BufferedWriter:
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View.delete_view(i_dms, o_view_name)
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o_dms.close(force=True)
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i_dms.close(force=True)
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logger("info", "Done.")
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