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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
from obitools3.dms.capi.obitypes cimport OBI_BOOL, \
OBI_CHAR, \
OBI_FLOAT, \
OBI_INT, \
OBI_QUAL, \
OBI_SEQ, \
OBI_STR, \
OBIBool_NA, \
OBIChar_NA, \
OBIFloat_NA, \
OBIInt_NA
import time
import sys
from cpython.exc cimport PyErr_CheckSignals
from io import BufferedWriter
NULL_VALUE = {OBI_BOOL: OBIBool_NA,
OBI_CHAR: OBIChar_NA,
OBI_FLOAT: OBIFloat_NA,
OBI_INT: OBIInt_NA,
OBI_QUAL: [],
OBI_SEQ: b"",
OBI_STR: b""}
__title__="Sort view lines according to the value of a given attribute"
def addOptions(parser):
addMinimalInputOption(parser)
addMinimalOutputOption(parser)
addNoProgressBarOption(parser)
group=parser.add_argument_group('obi sort specific options')
group.add_argument('--key', '-k',
action="append", dest="sort:keys",
metavar='<TAG NAME>',
default=[],
type=str,
help="Attribute used to sort the sequence records.")
group.add_argument('--reverse', '-r',
action="store_true", dest="sort:reverse",
default=False,
help="Sort in reverse order.")
def line_cmp(line, key, pb):
pb
if line[key] is None:
return NULL_VALUE[line.view[key].data_type_int]
else:
return line[key]
def run(config):
DMS.obi_atexit()
logger("info", "obi sort")
# 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
# Initialize the progress bar
if config['obi']['noprogressbar'] == False:
pb = ProgressBar(len(i_view), config)
else:
pb = None
keys = config['sort']['keys']
selection = Line_selection(i_view)
for i in range(len(i_view)): # TODO special function?
PyErr_CheckSignals()
selection.append(i)
for k in keys: # TODO order?
PyErr_CheckSignals()
if pb is not None:
selection.sort(key=lambda line_idx: line_cmp(i_view[line_idx], k, pb(line_idx)), reverse=config['sort']['reverse'])
else:
selection.sort(key=lambda line_idx: line_cmp(i_view[line_idx], k, None), reverse=config['sort']['reverse'])
if pb is not None:
pb(len(i_view), force=True)
print("", file=sys.stderr)
# Create output view with the sorted line selection
try:
o_view = selection.materialize(o_view_name)
except Exception, e:
raise RollbackException("obi sort error, rollbacking view: "+str(e), o_view)
# Save command config in View and DMS comments
command_line = " ".join(sys.argv[1:])
input_dms_name=[input[0].name]
input_view_name=[input[1].name]
o_view.write_config(config, "sort", command_line, input_dms_name=input_dms_name, input_view_name=input_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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