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#cython: language_level=3
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, addNoProgressBarOption
from obitools3.dms.view import RollbackException
from obitools3.apps.config import logger
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"
def addOptions(parser):
addMinimalInputOption(parser)
addMinimalOutputOption(parser)
addNoProgressBarOption(parser)
group=parser.add_argument_group('obi tail specific options')
group.add_argument('-n', '--sequence-count',
action="store", dest="tail:count",
metavar='<N>',
default=10,
type=int,
help="Number of last records to keep.")
def run(config):
DMS.obi_atexit()
logger("info", "obi tail")
# Open the input
input = open_uri(config["obi"]["inputURI"])
if input is None:
raise Exception("Could not read input view")
i_dms = input[0]
i_view = input[1]
# Open the output: only the DMS
output = open_uri(config['obi']['outputURI'],
input=False,
dms_only=True)
if output is None:
raise Exception("Could not create output view")
o_dms = output[0]
output_0 = output[0]
final_o_view_name = output[1]
# 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 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
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()
if pb is not None:
pb(i)
selection.append(i)
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:])
comments = View.get_config_dict(config, "tail", command_line, input_dms_name=[i_dms.name], input_view_name=[i_view.name])
# Create output view with the line selection
try:
o_view = selection.materialize(o_view_name)
except Exception, e:
raise RollbackException("obi tail error, rollbacking view: "+str(e), o_view)
# Save command config in DMS comments
command_line = " ".join(sys.argv[1:])
o_view.write_config(config, "tail", command_line, input_dms_name=[i_dms.name], input_view_name=[i_view.name])
o_dms.record_command_line(command_line)
# If input and output DMS are not the same, export the temporary view to the output DMS
# 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, 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 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)
logger("info", "Done.")
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