Refactoring ...
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412
python/obitools3/dms/view/view.pyx
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412
python/obitools3/dms/view/view.pyx
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#cython: language_level=3
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from libc.stdlib cimport malloc
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from ..capi.obiview cimport Alias_column_pair_p, \
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obi_new_view, \
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obi_open_view, \
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obi_save_and_close_view, \
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obi_view_get_pointer_on_column_in_view, \
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obi_view_delete_column, \
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obi_view_create_column_alias
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from ..capi.obidmscolumn cimport OBIDMS_column_p
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from obitools3.utils cimport tobytes, \
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bytes2str
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cdef class View :
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def __init__(self,dms,int __internalCall__):
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if __internalCall__!=987654:
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raise RuntimeError('OBIView constructor cannot be called directly')
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self._dms = dms
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self._pointer = NULL
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def clone(self,
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object view_name,
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object comments=None):
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cdef bytes view_name_b = tobytes(view_name)
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cdef bytes comments_b
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cdef View view = View(self._dms,
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987654)
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if comments is not None:
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comments_b = tobytes(comments)
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else:
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comments_b = b''
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view._pointer = obi_new_view(self._pointer.dms,
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view_name_b,
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self._pointer,
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NULL,
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comments_b)
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if view._pointer == NULL :
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raise RuntimeError("Error : Cannot clone view %s into view %s"
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% (str(self.name),
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bytes2str(view_name_b))
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)
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return view
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@staticmethod
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def new(DMS dms,
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object view_name,
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object comments=None):
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cdef bytes view_name_b = tobytes(view_name)
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cdef bytes comments_b
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cdef str message
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cdef View view = View(dms,
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987654) # @DuplicatedSignature
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if comments is not None:
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comments_b = tobytes(comments)
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else:
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comments_b = b''
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view._pointer = obi_new_view(dms._pointer,
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view_name_b,
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NULL,
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NULL,
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comments_b)
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if view._pointer == NULL :
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message = "Error : Cannot create view %s" % bytes2str(view_name_b)
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raise RuntimeError(message)
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return view
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@staticmethod
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def open(DMS dms, # @ReservedAssignment
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object view_name):
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cdef bytes view_name_b = tobytes(view_name)
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cdef View view = View(dms,
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987654) # @DuplicatedSignature
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view._pointer = obi_open_view(dms._pointer,
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view_name_b)
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if view._pointer == NULL :
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raise RuntimeError("Error : Cannot open view %s" % bytes2str(view_name_b))
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return view
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def close(self):
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if (self._pointer != NULL
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and obi_save_and_close_view(self._pointer) < 0) :
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raise Exception("Problem closing view %s" %
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bytes2str(self.name))
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def __dealloc__(self):
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self.close()
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def __repr__(self) :
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cdef str s = "{name:s}\n{comments:s}\n{line_count:d} lines\n".format(name = str(self.name),
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comments = str(self.comments),
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line_count = self.line_count)
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#for column_name in self._columns :
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# s = s + repr(self._columns[column_name]) + '\n'
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return s
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def keys(self):
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cdef int i
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cdef int nb_column = self._pointer.infos.column_count
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cdef Alias_column_pair_p column_p = self._pointer.infos.column_references
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for i in range(nb_column) :
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col_alias = bytes2str(self._pointer.infos.column_references[i].alias)
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yield col_alias
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def get_column(self,
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object column_name):
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cdef bytes column_name_b = tobytes(column_name)
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cdef OBIDMS_column_p* column_pp
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cdef OBIDMS_column_p column_p
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cdef Column column
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cdef obitype_t column_type
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column_pp = obi_view_get_pointer_on_column_in_view(self._pointer,
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column_name_b)
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if column_pp == NULL:
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raise KeyError("Cannot access to column %s in view %s" % (
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bytes2str(column_name_b),
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bytes2str(self.name)
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))
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column_p = column_pp[0]
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column_type = column_p.header.returned_data_type
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column = DMS.get_column_class(column_type)(self)
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column._pointer = column_pp
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return column
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cpdef delete_column(self,
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object column_name) :
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cdef bytes column_name_b = tobytes(column_name)
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if obi_view_delete_column(self._pointer, column_name_b) < 0 :
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raise Exception("Problem deleting column %s from a view",
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bytes2str(column_name_b))
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cpdef rename_column(self,
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object current_name,
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object new_name):
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cdef Column column
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cdef bytes current_name_b = tobytes(current_name)
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cdef bytes new_name_b = tobytes(new_name)
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if (obi_view_create_column_alias(self._pointer,
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tobytes(current_name_b),
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tobytes(new_name_b)) < 0) :
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raise Exception("Problem in renaming column %s to %s" % (
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bytes2str(current_name_b),
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bytes2str(new_name_b)))
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cpdef View_line_selection new_selection(self,list lines=None):
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return View_line_selection(self,lines)
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def __iter__(self):
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# Iteration on each line of all columns
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# Declarations
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cdef index_t line_nb
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cdef View_line line
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# Yield each line
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for line_nb in range(self.line_count) :
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line = self[line_nb]
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yield line
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def __getitem__(self, object item) :
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if type(item) == str :
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return (self._columns)[item]
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elif type(item) == int :
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return View_line(self, item)
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def __contains__(self, str column_name):
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return (column_name in self._columns)
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def __len__(self):
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return(self.line_count)
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def __str__(self) :
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cdef View_line line
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cdef str to_print
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to_print = ""
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for line in self :
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to_print = to_print + str(line) + "\n"
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return to_print
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@property
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def dms(self):
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return self._dms
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# line_count property getter
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@property
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def line_count(self):
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return self._pointer.infos.line_count
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# name property getter
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@property
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def name(self):
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return <bytes> self._pointer.infos.name
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# view type property getter
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@property
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def type(self): # @ReservedAssignment
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return bytes2str(self._pointer.infos.view_type)
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# comments property getter
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@property
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def comments(self):
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return <bytes> self._pointer.infos.comments
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# TODO setter that concatenates new comments?
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cdef class Line_selection(list):
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def __init__(self, View view, lines=None) :
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if view._pointer == NULL:
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raise Exception("Error: trying to create a line selection with an invalidated view")
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self._view = view
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self._view_name = view.name
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if lines is not None:
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self.extend(lines)
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def extend(self, iterable):
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cdef index_t i
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cdef index_t max_i = self._view.line_count
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for i in iterable:
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if i > max_i:
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raise RuntimeError("Error: trying to select line %d beyond the line count %d of view %s" %
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(i,
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max_i,
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self._view_name)
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)
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list.append(self,i)
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def append(self, index_t idx) :
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if idx >= self._view.line_count :
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raise IndexError("Error: trying to select line %d beyond the line count %d of view %s" %
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(idx,
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self._view.line_count,
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bytes2str(self.name))
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)
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list.append(self,idx)
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cdef index_t* __build_binary_list__(self):
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cdef index_t* line_selection_p = NULL
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cdef int i
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cdef size_t l_selection = len(self)
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line_selection_p = <index_t*> malloc((l_selection + 1) * sizeof(index_t)) # +1 for the -1 flagging the end of the array
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for i in range(l_selection) :
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line_selection_p[i] = self[i]
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line_selection_p[l_selection] = -1 # flagging the end of the array
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return line_selection_p
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cpdef View materialize(self,
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object view_name,
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object comments=""):
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cdef View view = View(987654)
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cdef bytes view_name_b=tobytes(view_name)
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view._pointer = obi_new_view(self._view._pointer.dms,
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view_name_b,
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self._view._pointer,
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self.__build_binary_list__(),
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tobytes(comments))
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if view._pointer == NULL :
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raise RuntimeError("Error : Cannot clone view %s into view %s"
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% (str(self.name),
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view_name)
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)
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return view
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cdef class Line :
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def __init__(self, View view, index_t line_nb) :
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self._index = line_nb
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self._view = view
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def __getitem__(self, str column_name) :
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return ((self._view)._columns)[column_name][self._index]
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# def __setitem__(self, str column_name, object value):
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# # TODO detect multiple elements (dict type)? put somewhere else? but more risky (in get)
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# # TODO OBI_QUAL ?
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# cdef type value_type
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# cdef str value_obitype
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# cdef bytes value_b
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#
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# if column_name not in self._view :
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# if value == None :
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# raise Exception("Trying to create a column from a None value (can't guess type)")
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# value_type = type(value)
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# if value_type == int :
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# value_obitype = 'OBI_INT'
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# elif value_type == float :
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# value_obitype = 'OBI_FLOAT'
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# elif value_type == bool :
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# value_obitype = 'OBI_BOOL'
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# elif value_type == str or value_type == bytes :
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# if value_type == str :
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# value_b = str2bytes(value)
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# else :
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# value_b = value
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# if only_ATGC(value_b) : # TODO detect IUPAC
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# value_obitype = 'OBI_SEQ'
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# elif len(value) == 1 :
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# value_obitype = 'OBI_CHAR'
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# elif (len(value) > 1) :
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# value_obitype = 'OBI_STR'
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# else :
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# raise Exception("Could not guess the type of a value to create a new column")
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# self._view.add_column(column_name, type=value_obitype)
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#
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# (((self._view)._columns)[column_name]).set_line(self._index, value)
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#
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# def __iter__(self):
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# for column_name in ((self._view)._columns) :
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# yield column_name
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#
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# def __contains__(self, str column_name):
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# return (column_name in self._view._columns)
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def __repr__(self):
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cdef dict line
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cdef str column_name
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line = {}
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# for column_name in self._view._columns :
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# line[column_name] = self[column_name]
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return str(line)
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# cpdef dict get_view_infos(self, str view_name) :
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#
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# cdef Obiview_infos_p view_infos_p
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# cdef dict view_infos_d
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# cdef Alias_column_pair_p column_refs
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# cdef int i, j
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# cdef str column_name
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#
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# view_infos_p = obi_view_map_file(self._pointer,
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# tobytes(view_name))
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# view_infos_d = {}
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# view_infos_d["name"] = bytes2str(view_infos_p.name)
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# view_infos_d["comments"] = bytes2str(view_infos_p.comments)
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# view_infos_d["view_type"] = bytes2str(view_infos_p.view_type)
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# view_infos_d["column_count"] = <int> view_infos_p.column_count
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# view_infos_d["line_count"] = <int> view_infos_p.line_count
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# view_infos_d["created_from"] = bytes2str(view_infos_p.created_from)
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# view_infos_d["creation_date"] = bytes2str(obi_format_date(view_infos_p.creation_date))
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# if (view_infos_p.all_lines) :
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# view_infos_d["line_selection"] = None
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# else :
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# view_infos_d["line_selection"] = {}
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# view_infos_d["line_selection"]["column_name"] = bytes2str((view_infos_p.line_selection).column_name)
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# view_infos_d["line_selection"]["version"] = <int> (view_infos_p.line_selection).version
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# view_infos_d["column_references"] = {}
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# column_references = view_infos_p.column_references
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# for j in range(view_infos_d["column_count"]) :
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# column_name = bytes2str((column_references[j]).alias)
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# view_infos_d["column_references"][column_name] = {}
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# view_infos_d["column_references"][column_name]["original_name"] = bytes2str((column_references[j]).column_refs.column_name)
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# view_infos_d["column_references"][column_name]["version"] = (column_references[j]).column_refs.version
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#
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# obi_view_unmap_file(self._pointer, view_infos_p)
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#
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# return view_infos_d
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