Cython Column API
This commit is contained in:
Celine Mercier
@ -1 +1 @@
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from .column import column # @UnresolvedImport
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from .column import Column # @UnresolvedImport
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@ -1,7 +1,9 @@
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#cython: language_level=3
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from ..capi.obitypes cimport index_t, \
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obitype_t
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from ..capi.obidmscolumn cimport OBIDMS_column_p
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from ..view.view cimport View
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@ -9,26 +11,41 @@ from ..view.view cimport View
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from ..object cimport OBIWrapper
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cdef dict __OBIDMS_COLUMN_CLASS__
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cdef class Column(OBIWrapper) :
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cdef View _view
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cdef View _view
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cdef bytes _alias
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cdef inline OBIDMS_column_p pointer(self)
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cpdef close(self)
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@staticmethod
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cdef type get_column_class(obitype_t obitype)
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cdef type get_column_class(obitype_t obitype, bint multi_elts)
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@staticmethod
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cdef type get_python_type(obitype_t obitype, bint multi_elts)
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cdef class Column_multi_elts(Column) :
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cpdef set_line(self, index_t line_nb, dict values)
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cdef class Column_line:
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cdef Column _column
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cdef index_t _index
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cpdef update(self, data)
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#
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# cdef class Column_line:
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#
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# cdef Column _column
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# cdef index_t _index
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#
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# cpdef update(self, data)
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#
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#
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cdef register_column_class(obitype_t obitype,
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type classe,
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bint multi_elts,
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type obiclass,
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type python)
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cdef register_all_column_classes()
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@ -1,267 +1,361 @@
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#cython: language_level=3
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from ..capi.obitypes cimport name_data_type
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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_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 ..dms cimport __OBIDMS_COLUMN_CLASS__
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from obitools3.utils cimport bytes2str
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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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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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'''
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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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# Note: should only be initialized through a subclass
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def __init__(self,
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View view,
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int __internalCall__):
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'''
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Create a new OBDMS column objected referring to a already created column
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in the context of a view.
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This constructor is normally only called by subclass constructor.
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@param view: The view object containing the column.
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@type view: OBIView
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'''
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if __internalCall__ != 987654:
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raise RuntimeError('OBIView constructor cannot be called directly')
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OBIWrapper.__init__(self)
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# Check that the class is only created as a subclass instance
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if type(self)==Column or not isinstance(self, Column):
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raise RuntimeError('OBIDMS.Column constructor cannot be called directly')
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# Fill structure
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self._pointer = NULL
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self._view = 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):
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"""
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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][0]
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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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object elements_names=None,
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object comments=b""):
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cdef bytes column_name_b = tobytes(column_name)
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cdef bytes comments_b
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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 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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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 = NULL,
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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, column_name)
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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.change_column_alias(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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# @staticmethod
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# def new(OBIView view,
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# object column_name,
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# index_t nb_elements_per_line=1,
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# object elements_names=None,
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# object comments=b""):
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#
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# cdef bytes column_name_b = tobytes(column_name)
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# cdef bytes comments_b
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# cdef bytes elements_names_b
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# cdef char* elements_names_p
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# cdef OBIDMS_column new_column
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#
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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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#
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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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#
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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 = NULL,
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# data_type = self.pointer.header.returned_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),
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# bytes2str(view.name)))
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#
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# return Column.open(view,column_name)
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#
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#
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# @staticmethod
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# def open(OBIView 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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#
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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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#
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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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#
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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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#
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# column = DMS.get_column_class(column_type)(view, 987654)
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# column._pointer = column_pp
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#
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# return column
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#
|
||||
#
|
||||
# def __len__(self):
|
||||
# '''
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||||
# implements the len() function for the Column class
|
||||
#
|
||||
# @rtype: `int`
|
||||
# '''
|
||||
# return self.lines_used
|
||||
#
|
||||
#
|
||||
# def __sizeof__(self):
|
||||
# '''
|
||||
# returns the size of the C object wrapped by the Column instance
|
||||
# '''
|
||||
# cdef OBIDMS_column_header_p header = self._pointer[0].header
|
||||
# return header.header_size + header.data_size
|
||||
#
|
||||
#
|
||||
# def __iter__(self):
|
||||
# cdef index_t line_nb
|
||||
#
|
||||
# for line_nb in range(self.lines_used):
|
||||
# yield self[line_nb]
|
||||
#
|
||||
#
|
||||
# def __str__(self) :
|
||||
# cdef str to_print
|
||||
# to_print = ''
|
||||
# for line in self :
|
||||
# to_print = to_print + str(line) + "\n"
|
||||
# return to_print
|
||||
#
|
||||
#
|
||||
# def __repr__(self) :
|
||||
# return b"%s, original name: %s, version %d, data type: %d" % (
|
||||
# self._alias,
|
||||
# self.original_name,
|
||||
# self.version,
|
||||
# self.data_type
|
||||
# )
|
||||
#
|
||||
#
|
||||
# cpdef close(self):
|
||||
# if self._pointer != NULL:
|
||||
# if obi_close_column(self._pointer[0]) < 0 :
|
||||
# raise Exception("Problem closing column %s" % bytes2str(self.name))
|
||||
#
|
||||
#
|
||||
# # Column alias property getter and setter
|
||||
# @property
|
||||
# def name(self):
|
||||
# return self._alias
|
||||
# @name.setter
|
||||
# def name(self, new_alias): # @DuplicatedSignature
|
||||
# self._view.change_column_alias(self._alias, new_alias)
|
||||
#
|
||||
# # elements_names property getter
|
||||
# @property
|
||||
# def elements_names(self):
|
||||
# return (((self._pointer)[0].header).elements_names).split(b';')
|
||||
#
|
||||
# # nb_elements_per_line property getter
|
||||
# @property
|
||||
# def nb_elements_per_line(self):
|
||||
# return ((self._pointer)[0].header).nb_elements_per_line
|
||||
#
|
||||
# # data_type property getter
|
||||
# @property
|
||||
# def data_type(self):
|
||||
# return name_data_type(((self._pointer)[0].header).returned_data_type)
|
||||
#
|
||||
# # original_name property getter
|
||||
# @property
|
||||
# def original_name(self):
|
||||
# return ((self._pointer)[0].header).name
|
||||
#
|
||||
# # version property getter
|
||||
# @property
|
||||
# def version(self):
|
||||
# return ((self._pointer)[0].header).version
|
||||
#
|
||||
# # lines_used property getter
|
||||
# @property
|
||||
# def lines_used(self):
|
||||
# return (self._pointer)[0].header.lines_used
|
||||
#
|
||||
# # comments property getter
|
||||
# @property
|
||||
# def comments(self):
|
||||
# return (self._pointer)[0].header.comments
|
||||
#
|
||||
# # creation_date property getter
|
||||
# @property
|
||||
# def creation_date(self):
|
||||
# return obi_format_date((self._pointer)[0].header.creation_date)
|
||||
#
|
||||
#
|
||||
# ######################################################################################################
|
||||
#
|
||||
#
|
||||
# cdef class Column_line :
|
||||
#
|
||||
# def __init__(self, Column column, index_t line_nb) :
|
||||
# self._index = line_nb
|
||||
# self._column = column
|
||||
#
|
||||
# if obi_column_prepare_to_get_value(self._column._pointer[0],line_nb) < 0:
|
||||
# raise IndexError("Cannot access to the line %d" % line_nb)
|
||||
#
|
||||
#
|
||||
# def __contains__(self, str element_name):
|
||||
# pass
|
||||
# #return (element_name in self._column.elements_names)
|
||||
#
|
||||
#
|
||||
# def __repr__(self) :
|
||||
# return str(self._column.get_line(self._index))
|
||||
#
|
||||
#
|
||||
# cpdef update(self, data):
|
||||
# if isinstance(data, dict):
|
||||
# data=data.items()
|
||||
# for key,value in data:
|
||||
# if key in self:
|
||||
# self[key]=value
|
||||
#
|
||||
#
|
||||
# ######################################################################################################
|
||||
#
|
||||
#
|
||||
cdef register_column_class(obitype_t obitype,
|
||||
type classe,
|
||||
type python):
|
||||
"""
|
||||
bint multi_elts,
|
||||
type obiclass,
|
||||
type python_type):
|
||||
'''
|
||||
Each sub class of `OBIDMS_column` needs to be registered after its declaration
|
||||
to declare its relationship with an `OBIType_t`
|
||||
"""
|
||||
'''
|
||||
global __OBIDMS_COLUMN_CLASS__
|
||||
|
||||
assert issubclass(classe,Column)
|
||||
|
||||
__OBIDMS_COLUMN_CLASS__[obitype]=(classe,python)
|
||||
|
||||
assert issubclass(obiclass, Column)
|
||||
|
||||
__OBIDMS_COLUMN_CLASS__[(obitype, multi_elts)] = (obiclass, python_type)
|
||||
|
||||
|
||||
cdef register_all_column_classes() :
|
||||
|
||||
#obi3 = importlib.import_module("obitools3")
|
||||
x = list(pkgutil.walk_packages()) # TODO restrain the walking
|
||||
all_modules = [importlib.import_module(a[1]) for a in x if a[1].startswith("obitools3.dms.column.typed_column.")]
|
||||
for mod in all_modules :
|
||||
getattr(mod, 'register_class')()
|
||||
|
||||
|
||||
register_all_column_classes()
|
||||
|
||||
|
||||
|
||||
|
||||
Reference in New Issue
Block a user