148 lines
4.9 KiB
Cython
Executable File
148 lines
4.9 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
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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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from obitools3.dms.capi.obitypes cimport OBI_BOOL, \
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OBI_CHAR, \
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OBI_FLOAT, \
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OBI_INT, \
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OBI_QUAL, \
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OBI_SEQ, \
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OBI_STR, \
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OBIBool_NA, \
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OBIChar_NA, \
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OBIFloat_NA, \
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OBIInt_NA
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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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NULL_VALUE = {OBI_BOOL: OBIBool_NA,
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OBI_CHAR: OBIChar_NA,
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OBI_FLOAT: OBIFloat_NA,
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OBI_INT: OBIInt_NA,
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OBI_QUAL: [],
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OBI_SEQ: b"",
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OBI_STR: b""}
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__title__="Sort view lines according to the value of a given attribute."
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def addOptions(parser):
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addMinimalInputOption(parser)
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addMinimalOutputOption(parser)
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group=parser.add_argument_group('obi sort specific options')
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group.add_argument('--key', '-k',
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action="append", dest="sort:keys",
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metavar='<TAG NAME>',
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default=[],
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type=str,
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help="Attribute used to sort the sequence records.")
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group.add_argument('--reverse', '-r',
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action="store_true", dest="sort:reverse",
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default=False,
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help="Sort in reverse order.")
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def line_cmp(line, key, pb):
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pb
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if line[key] is None:
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return NULL_VALUE[line.view[key].data_type_int]
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else:
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return line[key]
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def run(config):
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DMS.obi_atexit()
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logger("info", "obi sort")
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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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o_view_name_final = output[1]
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o_view_name = o_view_name_final
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# If the input and output DMS are not the same, create output view in input DMS first, then export it
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# to output DMS, making sure the temporary view name is unique in the input DMS
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if i_dms != o_dms:
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i=0
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while o_view_name in i_dms:
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o_view_name = o_view_name_final+b"_"+str2bytes(str(i))
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i+=1
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# Initialize the progress bar
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pb = ProgressBar(len(i_view), config, seconde=5)
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keys = config['sort']['keys']
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selection = Line_selection(i_view)
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for i in range(len(i_view)): # TODO special function?
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PyErr_CheckSignals()
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selection.append(i)
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for k in keys: # TODO order?
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PyErr_CheckSignals()
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selection.sort(key=lambda line_idx: line_cmp(i_view[line_idx], k, pb(line_idx)), reverse=config['sort']['reverse'])
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pb(len(i_view), force=True)
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print("", file=sys.stderr)
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# Create output view with the sorted 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 sort error, rollbacking view: "+str(e), o_view)
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# Save command config in View and DMS comments
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command_line = " ".join(sys.argv[1:])
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input_dms_name=[input[0].name]
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input_view_name=[input[1].name]
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o_view.write_config(config, "sort", command_line, input_dms_name=input_dms_name, input_view_name=input_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, o_view_name_final)
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o_view = o_dms[o_view_name_final]
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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, delete the temporary imported view used to create the final view
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if i_dms != o_dms:
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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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