365 lines
12 KiB
Cython
365 lines
12 KiB
Cython
#cython: language_level=3
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from obitools3.dms.column import typed_column
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__OBIDMS_COLUMN_CLASS__ = {}
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from ..capi.obitypes cimport name_data_type, \
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obitype_t, \
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OBI_BOOL
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from ..capi.obidmscolumn cimport OBIDMS_column_header_p, \
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obi_close_column, \
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obi_get_elements_names
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from ..capi.obiutils cimport obi_format_date
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from ..capi.obiview cimport obi_view_add_column, \
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obi_view_get_pointer_on_column_in_view, \
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Obiview_p
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from ..object cimport OBIObjectClosedInstance
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from obitools3.utils cimport tobytes, \
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bytes2str, \
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str2bytes
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from obitools3.dms.column import typed_column
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import importlib
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import inspect
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import pkgutil
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cdef class Column(OBIWrapper) :
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'''
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The obitools3.dms.column.Column class wraps a C instance of a column in the context of a View
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'''
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cdef inline OBIDMS_column_p pointer(self) :
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return <OBIDMS_column_p>(<OBIDMS_column_p*>(self._pointer))[0]
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@staticmethod
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cdef type get_column_class(obitype_t obitype, bint multi_elts):
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'''
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Internal function returning the python class representing
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a column for a given obitype.
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'''
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return __OBIDMS_COLUMN_CLASS__[(obitype, multi_elts)][0]
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@staticmethod
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cdef type get_python_type(obitype_t obitype, bint multi_elts): # TODO
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'''
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Internal function returning the python type representing
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an instance for a given obitype.
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'''
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return __OBIDMS_COLUMN_CLASS__[(obitype, multi_elts)][1]
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@staticmethod
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def new_column(View view,
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object column_name,
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obitype_t data_type,
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index_t nb_elements_per_line=1,
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list elements_names=None,
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object comments=b"",
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object alias=b""):
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# TODO indexer_name?
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cdef bytes column_name_b = tobytes(column_name)
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cdef bytes alias_b = tobytes(alias)
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cdef bytes comments_b = tobytes(comments)
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cdef bytes elements_names_b
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cdef char* elements_names_p
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if not view.active() :
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raise OBIObjectClosedInstance()
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if alias_b == b"" :
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alias_b = column_name_b
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if elements_names is not None:
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elements_names_b = b';'.join([tobytes(x) for x in elements_names])
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elements_names_p = elements_names_b
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else:
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elements_names_p = NULL
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if (obi_view_add_column(view = view.pointer(),
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column_name = column_name_b,
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version_number = -1,
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alias = alias_b,
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data_type = <obitype_t>data_type,
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nb_lines = len(view),
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nb_elements_per_line = nb_elements_per_line,
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elements_names = elements_names_p,
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indexer_name = NULL,
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associated_column_name = NULL,
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associated_column_version = -1,
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comments = comments_b,
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create = True)<0):
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raise RuntimeError("Cannot create column %s in view %s" % (bytes2str(column_name_b),
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bytes2str(view.name)))
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return Column.open(view, alias_b)
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@staticmethod
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def open(View view,
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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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cdef type column_class
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if not view.active() :
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raise OBIObjectClosedInstance()
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column_pp = obi_view_get_pointer_on_column_in_view(view.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(view.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_class = Column.get_column_class(column_type, (column_p.header.nb_elements_per_line > 1))
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column = OBIWrapper.new(column_class, column_pp)
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column._view = view
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column._alias = column_name_b
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view.register(column)
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return column
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def add_to_view(self,
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View view,
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object column_name=None) :
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cdef bytes alias
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cdef OBIDMS_column_p column_p = self.pointer()
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if not view.active() :
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raise OBIObjectClosedInstance()
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if (column_name is None):
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alias = self._alias
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else:
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alias = tobytes(column_name)
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if (obi_view_add_column(view = view.pointer(),
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column_name = column_p.header.name,
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version_number = column_p.header.version,
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alias = alias,
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data_type = <obitype_t>0,
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nb_lines = -1,
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nb_elements_per_line = -1,
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elements_names = NULL,
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indexer_name = NULL,
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associated_column_name = NULL,
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associated_column_version = -1,
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comments = NULL,
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create = False) < 0):
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raise RuntimeError("Cannot insert column %s (%s@%d) into view %s" %
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( bytes2str(alias),
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bytes2str(column_p.header.name),
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column_p.header.version,
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bytes2str(view.name)
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))
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view.register(self)
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def __len__(self):
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'''
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implements the len() function for the Column class
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@rtype: `int`
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'''
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return self.lines_used
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def __sizeof__(self):
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'''
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returns the size of the C object wrapped by the Column instance
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'''
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cdef OBIDMS_column_header_p header = self.pointer().header
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return header.header_size + header.data_size
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def __iter__(self):
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cdef index_t line_nb
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for line_nb in range(self.lines_used):
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yield self[line_nb]
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def __setitem__(self, index_t line_nb, object value):
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self.set_line(line_nb, value)
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def __getitem__(self, index_t line_nb):
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return self.get_line(line_nb)
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def __str__(self) :
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cdef str to_print
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cdef Column_line line
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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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def __repr__(self) :
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cdef bytes s
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s = self._alias + b", original name: " + self.original_name + b", version " + str2bytes(str(self.version)) + b", data type: " + self.data_type
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return bytes2str(s) # TODO can't return bytes
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cpdef close(self): # TODO discuss, can't be called bc then bug when closing view that tries to close it in C
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cdef OBIDMS_column_p pointer
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if self.active() :
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pointer = self.pointer()
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self._view.unregister(self)
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OBIWrapper.close(self)
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#if obi_close_column(pointer) < 0 :
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# raise Exception("Problem closing column %s" % bytes2str(self.name))
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# Column alias property getter and setter
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@property
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def name(self):
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return self._alias
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@name.setter
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def name(self, new_alias): # @DuplicatedSignature
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self._view.rename_column(self._alias, new_alias)
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# elements_names property getter
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@property
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def elements_names(self):
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return obi_get_elements_names(self.pointer()).split(b';')
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# nb_elements_per_line property getter
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@property
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def nb_elements_per_line(self):
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return self.pointer().header.nb_elements_per_line
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# data_type property getter
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@property
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def data_type(self):
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return name_data_type(self.pointer().header.returned_data_type)
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# original_name property getter
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@property
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def original_name(self):
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return self.pointer().header.name
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# version property getter
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@property
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def version(self):
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return self.pointer().header.version
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# lines_used property getter
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@property
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def lines_used(self):
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return self.pointer().header.lines_used
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# comments property getter
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@property
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def comments(self):
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return self.pointer().header.comments
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# creation_date property getter
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@property
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def creation_date(self):
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return obi_format_date(self.pointer().header.creation_date)
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######################################################################################################
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cdef class Column_multi_elts(Column) :
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def __getitem__(self, index_t line_nb):
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return Column_line(self, line_nb)
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cpdef set_line(self, index_t line_nb, dict values):
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for element_name in values :
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self.set_item(line_nb, element_name, values[element_name])
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######################################################################################################
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cdef class Column_line :
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def __init__(self, Column column, index_t line_nb) :
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self._index = line_nb
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self._column = column
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def __getitem__(self, object elt_id) :
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return self._column.get_item(self._index, elt_id)
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def __setitem__(self, object elt_id, object value):
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self._column.set_item(self._index, elt_id, value)
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def __contains__(self, str element_name):
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return (element_name in self._column.elements_names)
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def __repr__(self) :
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return str(self._column.get_line(self._index))
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cpdef update(self, data): # TODO ?????
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if isinstance(data, dict):
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data=data.items()
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for key,value in data:
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if key in self:
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self[key]=value
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######################################################################################################
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cdef register_column_class(obitype_t obitype,
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bint multi_elts,
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type obiclass,
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type python_type):
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'''
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Each sub class of `OBIDMS_column` needs to be registered after its declaration
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to declare its relationship with an `OBIType_t`
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'''
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global __OBIDMS_COLUMN_CLASS__
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assert issubclass(obiclass, Column)
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__OBIDMS_COLUMN_CLASS__[(obitype, multi_elts)] = (obiclass, python_type)
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cdef register_all_column_classes() :
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x = list(pkgutil.walk_packages(typed_column.__path__, prefix="obitools3.dms.column.typed_column."))
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all_modules = [importlib.import_module(a[1]) for a in x]
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for mod in all_modules :
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getattr(mod, 'register_class')()
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register_all_column_classes()
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