Basic obi grep with new Cython API
This commit is contained in:
Celine Mercier
@ -1,100 +1,96 @@
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# from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport
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# from obitools3.dms.dms import OBIDMS # TODO cimport doesn't work
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# #, OBIView, OBIView_line_selection # TODO cimport doesn't work
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#
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# from functools import reduce
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# import time
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#
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# __title__="Grep view lines that match the given predicates"
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#
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#cython: language_level=3
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from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport
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from obitools3.dms.dms import DMS # TODO cimport doesn't work
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from obitools3.dms.view.view import View, Line_selection # TODO cimport doesn't work
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from functools import reduce
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import time
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__title__="Grep view lines that match the given predicates"
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default_config = { 'inputview' : None,
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'outputview' : None
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}
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def addOptions(parser):
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# TODO put this common group somewhere else but I don't know where
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group=parser.add_argument_group('DMS and view options')
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group.add_argument('--default-dms','-d',
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action="store", dest="obi:defaultdms",
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metavar='<DMS NAME>',
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default=None,
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type=str,
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help="Name of the default DMS for reading and writing data.")
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group.add_argument('--input-view','-i',
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action="store", dest="obi:inputview",
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metavar='<INPUT VIEW NAME>',
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default=None,
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type=str,
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help="Name of the input view, either raw if the view is in the default DMS,"
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" or in the form 'dms:view' if it is in another DMS.")
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group.add_argument('--output-view','-o',
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action="store", dest="obi:outputview",
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metavar='<OUTPUT VIEW NAME>',
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default=None,
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type=str,
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help="Name of the output view, either raw if the view is in the default DMS,"
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" or in the form 'dms:view' if it is in another DMS.")
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group=parser.add_argument_group('obi grep specific options')
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group.add_argument('--predicate','-p',
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action="append", dest="grep:predicates",
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metavar='<PREDICATE>',
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default=None,
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type=str,
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help="Grep lines that match the given python expression on <line> or <sequence>.")
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def run(config):
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pass
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# default_config = { 'inputview' : None,
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# 'outputview' : None
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# }
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#
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# def addOptions(parser):
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#
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# # TODO put this common group somewhere else but I don't know where
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# group=parser.add_argument_group('DMS and view options')
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#
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# group.add_argument('--default-dms','-d',
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# action="store", dest="obi:defaultdms",
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# metavar='<DMS NAME>',
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# default=None,
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# type=str,
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# help="Name of the default DMS for reading and writing data.")
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#
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# group.add_argument('--input-view','-i',
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# action="store", dest="obi:inputview",
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# metavar='<INPUT VIEW NAME>',
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# default=None,
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# type=str,
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# help="Name of the input view, either raw if the view is in the default DMS,"
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# " or in the form 'dms:view' if it is in another DMS.")
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#
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# group.add_argument('--output-view','-o',
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# action="store", dest="obi:outputview",
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# metavar='<OUTPUT VIEW NAME>',
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# default=None,
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# type=str,
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# help="Name of the output view, either raw if the view is in the default DMS,"
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# " or in the form 'dms:view' if it is in another DMS.")
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#
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#
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# group=parser.add_argument_group('obi grep specific options')
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#
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# group.add_argument('--predicate','-p',
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# action="append", dest="grep:predicates",
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# metavar='<PREDICATE>',
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# default=None,
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# type=str,
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# help="Grep lines that match the given python expression on <line> or <sequence>.")
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#
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#
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# def run(config):
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#
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# # Open DMS
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# d = OBIDMS(config['obi']['defaultdms'])
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#
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# # Open input view 1
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# # iview = d.open_view(config['obi']['inputview'])
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# #
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# # # Initialize the progress bar
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# # pb = ProgressBar(len(iview), config, seconde=5)
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# #
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# # # Apply filter
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# # selection = OBIView_line_selection(iview)
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# # for i in range(len(iview)) :
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# # pb(i)
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# # line = iview[i]
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# #
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# # loc_env = {'sequence': line, 'line': line} # TODO add taxonomy
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# #
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# # good = (reduce(lambda bint x, bint y: x and y,
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# # (bool(eval(p, loc_env, line))
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# # for p in config['grep']['predicates']), True))
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# #
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# # if good :
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# # selection.append(i)
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# #
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# # # Create output view with the line selection
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# # oview = d.clone_view_with_line_selection(config['obi']['outputview'], selection, comments="obi grep: "+str(config['grep']['predicates'])+"\n")
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# #
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# # #print("\n")
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# # #print(repr(oview))
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# #
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# # iview.close()
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# # oview.close()
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# d.close()
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#
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#
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#
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#
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#
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#
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#
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#
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#
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# Open DMS
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d = DMS.open(config['obi']['defaultdms'])
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# Open input view 1
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iview = View.open(d, config['obi']['inputview'])
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# Initialize the progress bar
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pb = ProgressBar(len(iview), config, seconde=5)
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# Apply filter
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selection = Line_selection(iview)
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for i in range(len(iview)) :
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pb(i)
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line = iview[i]
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loc_env = {'sequence': line, 'line': line} # TODO add taxonomy
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good = (reduce(lambda bint x, bint y: x and y,
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(bool(eval(p, loc_env, line))
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for p in config['grep']['predicates']), True))
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if good :
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selection.append(i)
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# Create output view with the line selection
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oview = selection.materialize(config['obi']['outputview'], comments="obi grep: "+str(config['grep']['predicates'])+"\n")
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print("\n")
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print(repr(oview))
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d.close()
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