a718081ebd
function handling errors and exceptions, as it can't read the right value of the global obi_errno (Cython configuration problem?)
154 lines
4.4 KiB
Cython
154 lines
4.4 KiB
Cython
#cython: language_level=3
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from obitools3.dms.capi.obitypes cimport is_a_DNA_seq, \
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OBI_VOID, \
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OBI_BOOL, \
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OBI_CHAR, \
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OBI_FLOAT, \
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OBI_INT, \
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OBI_QUAL, \
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OBI_SEQ, \
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OBI_STR, \
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index_t
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from obitools3.dms.capi.obierrno cimport OBI_LINE_IDX_ERROR, \
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OBI_ELT_IDX_ERROR
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#obi_errno
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cdef obi_errno_to_exception(int obi_errno, index_t line_nb=-1, object elt_id=None, str error_message=None) :
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global obi_errno
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if obi_errno > 0 :
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if obi_errno == OBI_LINE_IDX_ERROR :
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raise IndexError(line_nb, None or error_message)
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elif obi_errno == OBI_ELT_IDX_ERROR :
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raise IndexError(elt_id, None or error_message)
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else :
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raise Exception(None or error_message)
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cdef bytes str2bytes(str string):
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"""
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Short cut to convert ascii encoded python string (str) to bytes
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which can be easily converted to C-strings.
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@param string: the python string to be converted.
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@type string: str
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@return a transcoded string
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@rtype: bytes
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"""
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return string.encode('ascii')
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cdef str bytes2str(bytes string):
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"""
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Short cut to convert bytes (C-strings) to ascii encoded python string (str).
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@param string: the binary (C-string) string to be converted.
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@type string: bytes
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@return an ascii transcoded string
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@rtype: str
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"""
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return string.decode('ascii')
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cdef bytes tobytes(object string):
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"""
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Short cut to convert ascii encoded string (str or bytes) to bytes
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which can be easily converted to C-strings.
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@param string: the python string to be converted.
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@type string: bytes or str
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@return a transcoded string
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@rtype: bytes
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"""
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if isinstance(string, bytes):
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return string
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return str2bytes(string)
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cdef str tostr(object string):
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"""
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Short cut to convert ascii encoded string (str or bytes) to bytes
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which can be easily converted to C-strings.
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@param string: the python string to be converted.
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@type string: bytes or str
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@return a transcoded string
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@rtype: bytes
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"""
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if isinstance(string, str):
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return string
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return bytes2str(string)
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cdef obitype_t get_obitype_single_value(object value) :
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cdef type value_type
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cdef obitype_t value_obitype
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if value is None :
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return OBI_VOID
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value_type = type(value)
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value_obitype = OBI_VOID
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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 is_a_DNA_seq(tobytes(value)) :
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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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value_obitype = OBI_VOID
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return value_obitype
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cdef obitype_t update_obitype(obitype_t obitype, object new_value) :
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cdef type new_type
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new_type = type(new_value)
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if obitype == OBI_INT :
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if new_type == float :
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return OBI_FLOAT
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# TODO BOOL vers INT/FLOAT
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elif new_type == str or new_type == bytes :
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if obitype == OBI_SEQ and is_a_DNA_seq(tobytes(new_value)) :
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pass
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else :
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return OBI_STR
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return obitype
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cdef obitype_t get_obitype_iterable_value(object value) :
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cdef obitype_t value_obitype
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value_obitype = OBI_VOID
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for k in value :
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if value_obitype == OBI_VOID :
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value_obitype = get_obitype_single_value(value[k])
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else :
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value_obitype = update_obitype(value_obitype, value[k])
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return value_obitype
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cdef obitype_t get_obitype(object value) :
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if type(value) == dict or type(value) == list or type(value) == tuple :
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return get_obitype_iterable_value(value)
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else :
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return get_obitype_single_value(value)
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