entirely reworked cython wrapper
This commit is contained in:
Celine Mercier
@ -1,31 +1,44 @@
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#cython: language_level=3
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from obitools3.utils cimport bytes2str, str2bytes
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from obitools3.obidms.obidmscolumn._obidmscolumn cimport OBIDMS_column
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from pathlib import Path
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# from obitools3.obidms.obidmscolumn.capidmscolumn cimport OBIDMS_column
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# from obitools3.obidms.obidmscolumn.capidmscolumn cimport obiversion_t # TODO pourquoi je peux pas les declarer dans le pxd?
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# from obitools3.obidms.obidmscolumn.capidmscolumn cimport name_data_type
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# from obitools3.obidms.obidmscolumn.capidmscolumn cimport obi_column_get_data_type_from_name
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# from obitools3.obidms.obidmscolumn.capidmscolumn cimport obi_column_get_latest_version_from_name
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# from obitools3.obidms.obidmscolumn.capidmscolumn cimport obi_column_get_line_count_from_name
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#
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from obitools3.obidms.obidmscolumn.obidmscolumn_int.capidmscolumn_int cimport OBIDMS_column_int_writable # TODO pourquoi pas cimport?
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from obitools3.obidms.obidmscolumn.obidmscolumn_int.capidmscolumn_int cimport OBIDMS_column_int_read
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from obitools3.obidms.obidmscolumn.obidmscolumn_float.capidmscolumn_float cimport OBIDMS_column_float_writable
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from obitools3.obidms.obidmscolumn.obidmscolumn_float.capidmscolumn_float cimport OBIDMS_column_float_read
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from obitools3.obidms.obidmscolumn.obidmscolumn_bool.capidmscolumn_bool cimport OBIDMS_column_bool_writable
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from obitools3.obidms.obidmscolumn.obidmscolumn_bool.capidmscolumn_bool cimport OBIDMS_column_bool_read
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from obitools3.obidms.obidmscolumn.obidmscolumn_char.capidmscolumn_char cimport OBIDMS_column_char_writable
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from obitools3.obidms.obidmscolumn.obidmscolumn_char.capidmscolumn_char cimport OBIDMS_column_char_read
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from obitools3.obidms.obidmscolumn.obidmscolumn_idx.capidmscolumn_idx cimport OBIDMS_column_idx_writable
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from obitools3.obidms.obidmscolumn.obidmscolumn_idx.capidmscolumn_idx cimport OBIDMS_column_idx_read
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from obitools3.utils cimport bytes2str, str2bytes
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from .capi.obidms cimport obi_dms
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from .capi.obidmscolumn cimport obi_column_get_data_type_from_name, \
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obi_column_get_latest_version_from_name, \
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obi_column_get_line_count_from_name, \
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obi_column_get_nb_lines_used, \
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obi_column_get_elements_names, \
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obi_create_column, \
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obi_clone_column, \
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obi_open_column, \
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obi_close_column
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from .capi.obitypes cimport const_char_p, name_data_type
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from ._obidms cimport OBIDMS
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from ._obidms cimport OBIDMS_column
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from ._obidmscolumn_int cimport OBIDMS_column_int, \
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OBIDMS_column_int_writable
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from ._obidmscolumn_float cimport OBIDMS_column_float, \
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OBIDMS_column_float_writable
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from ._obidmscolumn_bool cimport OBIDMS_column_bool, \
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OBIDMS_column_bool_writable
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from ._obidmscolumn_char cimport OBIDMS_column_char, \
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OBIDMS_column_char_writable
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from ._obidmscolumn_idx cimport OBIDMS_column_idx, \
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OBIDMS_column_idx_writable
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cdef class OBIDMS :
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def __init__(self, str dms_name) : # TODO
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def __init__(self, str dms_name) :
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# Declarations
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cdef bytes dms_name_b
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@ -61,7 +74,7 @@ cdef class OBIDMS :
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column_name = entry.stem
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column_name_b = str2bytes(column_name)
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dms[column_name] = {}
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data_type = bytes2str((name_data_type(obi_column_get_data_type_from_name(self.pointer, column_name_b)))
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data_type = bytes2str(name_data_type(obi_column_get_data_type_from_name(self.pointer, column_name_b)))
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latest_version = obi_column_get_latest_version_from_name(self.pointer, column_name_b)
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line_count = obi_column_get_line_count_from_name(self.pointer, column_name_b)
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dms[column_name]['data_type'] = data_type
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@ -71,18 +84,18 @@ cdef class OBIDMS :
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return dms
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cpdef OBIDMS_column open_column(self, # TODO j'arrive pas a le passer en cpdef
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str column_name, # TODO
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bint create=False,
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bint clone=False, bint clone_data=True,
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obiversion_t version_number=-1,
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OBIType_t data_type=0, # TODO
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size_t nb_lines=0,
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size_t nb_elements_per_line=1,
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str elements_names=None):
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cpdef OBIDMS_column open_column(self,
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str column_name,
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bint create=False,
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bint clone=False, bint clone_data=True,
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obiversion_t version_number=-1,
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OBIType_t data_type= <OBIType_t> 0,
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size_t nb_lines=0,
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size_t nb_elements_per_line=1,
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str elements_names=None):
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# Declarations
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cdef OBIDMS_column column # TODO not sure object
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cdef OBIDMS_column column
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cdef bytes column_name_b
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# Format the character string to send to C function
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@ -104,7 +117,7 @@ cdef class OBIDMS :
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nb_lines, nb_elements_per_line,
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elements_names)
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else :
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column = OBIDMS_column_int_read(self, column_name,
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column = OBIDMS_column_int(self, column_name,
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create, clone, clone_data,
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version_number, data_type,
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nb_lines, nb_elements_per_line,
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@ -118,7 +131,7 @@ cdef class OBIDMS :
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nb_lines, nb_elements_per_line,
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elements_names)
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else :
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column = OBIDMS_column_float_read(self, column_name,
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column = OBIDMS_column_float(self, column_name,
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create, clone, clone_data,
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version_number, data_type,
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nb_lines, nb_elements_per_line,
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@ -132,7 +145,7 @@ cdef class OBIDMS :
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nb_lines, nb_elements_per_line,
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elements_names)
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else :
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column = OBIDMS_column_bool_read(self, column_name,
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column = OBIDMS_column_bool(self, column_name,
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create, clone, clone_data,
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version_number, data_type,
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nb_lines, nb_elements_per_line,
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@ -146,13 +159,125 @@ cdef class OBIDMS :
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nb_lines, nb_elements_per_line,
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elements_names)
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else :
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column = OBIDMS_column_char_read(self, column_name,
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column = OBIDMS_column_char(self, column_name,
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create, clone, clone_data,
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version_number, data_type,
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nb_lines, nb_elements_per_line,
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elements_names)
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# elif data_type == 5 :
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# if (create or clone) :
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# column = OBIDMS_column_idx_writable(self, column_name,
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# create, clone, clone_data,
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# version_number, data_type,
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# nb_lines, nb_elements_per_line,
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# elements_names)
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# else :
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# column = OBIDMS_column_idx(self, column_name,
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# create, clone, clone_data,
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# version_number, data_type,
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# nb_lines, nb_elements_per_line,
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# elements_names)
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else :
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raise Exception("Problem with the data type")
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return column
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cdef class OBIDMS_column :
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# Should only be initialized through a subclass
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def __init__(self,
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OBIDMS dms,
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str column_name,
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bint create,
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bint clone, bint clone_data,
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obiversion_t version_number,
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OBIType_t type,
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size_t nb_lines,
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size_t nb_elements_per_line,
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str elements_names):
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# Declarations
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cdef bytes column_name_b
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cdef bytes dms_name_b
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cdef bytes elements_names_b
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# Fill structure
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self.dms = dms
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self.data_type = bytes2str(name_data_type(type))
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self.column_name = column_name
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# Format the character strings to send them to C functions
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column_name_b = str2bytes(column_name)
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dms_name_b = str2bytes(self.dms.dms_name)
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# Create, clone or open column
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if create :
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if elements_names == None :
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elements_names_b = column_name_b
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else :
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elements_names_b = str2bytes(elements_names)
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self.pointer = obi_create_column(self.dms.pointer, column_name_b, type, nb_lines, nb_elements_per_line, elements_names_b)
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else :
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if clone :
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self.pointer = obi_clone_column(self.dms.pointer, column_name_b, version_number, clone_data)
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else :
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self.pointer = obi_open_column(self.dms.pointer, column_name_b, version_number)
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def __iter__(self):
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# Declarations
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cdef list elements_names
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cdef str element_name
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cdef bint multiple_elements
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cdef object line # TODO
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cdef size_t lines_used
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cdef size_t line_nb
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# Check if there are multiple elements per line anf if yes, get their names
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elements_names = self.get_elements_names()
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if len(elements_names) > 1 :
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multiple_elements = True
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else :
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element_name = elements_names[0]
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# Yield each line
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lines_used = obi_column_get_nb_lines_used(self.pointer)
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for line_nb in xrange(lines_used):
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if multiple_elements :
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line = []
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for element_name in elements_names :
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line.append(self.get_item(line_nb, element_name))
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else :
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line = self.get_item(line_nb, element_name)
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yield line
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def __setitem__(self, size_t line_nb, object value):
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self.set_item(line_nb, "", value)
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def __getitem__(self, size_t line_nb):
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return self.get_item(line_nb, "")
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cpdef object get_item(self, size_t line_nb, str element_name):
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raise NotImplementedError
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cpdef list get_elements_names(self):
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cdef bytes elements_names
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elements_names = obi_column_get_elements_names(self.pointer)
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return (bytes2str(elements_names)).split(';')
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cpdef str get_data_type(self):
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return self.data_type
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cpdef size_t get_nb_lines_used(self):
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return obi_column_get_nb_lines_used(self.pointer)
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