Major update: obiarrays with columns containing indices referring to
character strings.
This commit is contained in:
Celine Mercier
@ -2,7 +2,7 @@
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from .capi.obidms cimport OBIDMS_p
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from .capi.obidmscolumn cimport OBIDMS_column_p
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from .capi.obitypes cimport obiversion_t, OBIType_t
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from .capi.obitypes cimport obiversion_t, OBIType_t, index_t
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cdef class OBIDMS_column
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@ -21,8 +21,8 @@ cdef class OBIDMS:
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bint clone=*, bint clone_data=*,
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obiversion_t version_number=*,
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OBIType_t data_type=*,
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size_t nb_lines=*,
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size_t nb_elements_per_line=*,
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index_t nb_lines=*,
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index_t nb_elements_per_line=*,
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list elements_names=*,
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str array_name=*)
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@ -34,14 +34,14 @@ cdef class OBIDMS_column:
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cdef str data_type # TODO keep as OBIType_t? both?
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cdef str dms_name
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cdef str column_name
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cdef size_t nb_elements_per_line
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cdef index_t nb_elements_per_line
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cdef list elements_names
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# cpdef object get_item(self, size_t line_nb, str element_name) TODO can't declare because not the same in all subclasses
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# cpdef set_item(self, size_t line_nb, str element_name, object value) TODO can't declare because object value
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cpdef list get_elements_names(self)
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cpdef str get_data_type(self)
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cpdef size_t get_nb_lines_used(self)
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cpdef str get_creation_date(self)
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cpdef close(self)
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# cpdef object get_item(self, index_t line_nb, str element_name) TODO can't declare because not the same in all subclasses
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# cpdef set_item(self, index_t line_nb, str element_name, object value) TODO can't declare because object value
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cpdef list get_elements_names(self)
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cpdef str get_data_type(self)
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cpdef index_t get_nb_lines_used(self)
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cpdef str get_creation_date(self)
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cpdef close(self)
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@ -80,7 +80,7 @@ cdef class OBIDMS :
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cdef str data_type
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cdef str creation_date
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cdef obiversion_t latest_version
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cdef size_t line_count
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cdef index_t line_count
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cdef OBIDMS_column_header_p header
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p = Path(self.dms_name+'.obidms')
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@ -117,8 +117,8 @@ cdef class OBIDMS :
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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=0,
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index_t nb_lines=0,
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index_t nb_elements_per_line=0,
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list elements_names=None,
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str array_name="default_obiarray"):
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@ -222,7 +222,7 @@ cdef class OBIDMS :
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version_number, data_type,
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nb_lines, nb_elements_per_line,
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elements_names, array_name)
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return column
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@ -237,8 +237,8 @@ cdef class OBIDMS_column :
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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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index_t nb_lines,
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index_t nb_elements_per_line,
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list elements_names,
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str array_name):
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@ -279,8 +279,8 @@ cdef class OBIDMS_column :
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def __iter__(self):
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# Declarations
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cdef size_t lines_used
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cdef size_t line_nb
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cdef index_t lines_used
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cdef index_t line_nb
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# Yield each line
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lines_used = self.pointer.header.lines_used
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@ -288,19 +288,19 @@ cdef class OBIDMS_column :
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yield self.get_line(line_nb)
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def __setitem__(self, size_t line_nb, object value):
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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, size_t line_nb):
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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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# cpdef object get_item(self, size_t line_nb, str element_name): TODO
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# cpdef object get_item(self, index_t line_nb, str element_name): TODO
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# raise NotImplementedError
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# cpdef set_item(self, size_t line_nb, str element_name, object value): TODO
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# cpdef set_item(self, index_t line_nb, str element_name, object value): TODO
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# raise NotImplementedError
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@ -312,7 +312,7 @@ cdef class OBIDMS_column :
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return self.data_type
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cpdef size_t get_nb_lines_used(self):
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cpdef index_t get_nb_lines_used(self):
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return self.pointer.header.lines_used
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@ -1,25 +1,25 @@
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#cython: language_level=3
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from .capi.obitypes cimport obibool_t
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from .capi.obitypes cimport obibool_t, index_t
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from ._obidms cimport OBIDMS_column
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cdef class OBIDMS_column_bool(OBIDMS_column):
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cpdef object get_line(self, size_t line_nb)
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cpdef set_line(self, size_t line_nb, object value)
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cpdef object get_line(self, index_t line_nb)
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cpdef set_line(self, index_t line_nb, object value)
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cpdef close(self)
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cdef class OBIDMS_column_bool_writable(OBIDMS_column_bool):
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cpdef set_line(self, size_t line_nb, object value)
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cpdef set_line(self, index_t line_nb, object value)
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cpdef close(self)
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cdef class OBIDMS_column_bool_multi_elts(OBIDMS_column_bool):
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cpdef object get_item(self, size_t line_nb, str element_name)
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cpdef object get_line(self, size_t line_nb)
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cpdef set_item(self, size_t line_nb, str element_name, obibool_t value)
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cpdef set_line(self, size_t line_nb, object values)
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cpdef object get_item(self, index_t line_nb, str element_name)
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cpdef object get_line(self, index_t line_nb)
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cpdef set_item(self, index_t line_nb, str element_name, obibool_t value)
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cpdef set_line(self, index_t line_nb, object values)
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cdef class OBIDMS_column_bool_multi_elts_writable(OBIDMS_column_bool_multi_elts):
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cpdef set_item(self, size_t line_nb, str element_name, obibool_t value)
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cpdef set_line(self, size_t line_nb, object values)
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cpdef set_item(self, index_t line_nb, str element_name, obibool_t value)
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cpdef set_line(self, index_t line_nb, object values)
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cpdef close(self)
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@ -16,7 +16,7 @@ from cpython.bool cimport PyBool_FromLong
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cdef class OBIDMS_column_bool(OBIDMS_column):
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cpdef object get_line(self, size_t line_nb):
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cpdef object get_line(self, index_t line_nb):
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cdef obibool_t value
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cdef object result
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value = obi_column_get_obibool_with_elt_idx(self.pointer, line_nb, 0)
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@ -28,7 +28,7 @@ cdef class OBIDMS_column_bool(OBIDMS_column):
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result = PyBool_FromLong(value)
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return result
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cpdef set_line(self, size_t line_nb, object value):
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cpdef set_line(self, index_t line_nb, object value):
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raise Exception("Column is read-only")
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cpdef close(self):
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@ -38,7 +38,7 @@ cdef class OBIDMS_column_bool(OBIDMS_column):
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cdef class OBIDMS_column_bool_writable(OBIDMS_column_bool):
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cpdef set_line(self, size_t line_nb, object value):
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cpdef set_line(self, index_t line_nb, object value):
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if obi_column_set_obibool_with_elt_idx(self.pointer, line_nb, 0, <obibool_t> value) < 0:
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raise Exception("Problem setting a value in a column")
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@ -49,7 +49,7 @@ cdef class OBIDMS_column_bool_writable(OBIDMS_column_bool):
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cdef class OBIDMS_column_bool_multi_elts(OBIDMS_column_bool):
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cpdef object get_item(self, size_t line_nb, str element_name):
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cpdef object get_item(self, index_t line_nb, str element_name):
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cdef obibool_t value
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cdef object result
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value = obi_column_get_obibool_with_elt_name(self.pointer, line_nb, str2bytes(element_name))
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@ -61,10 +61,10 @@ cdef class OBIDMS_column_bool_multi_elts(OBIDMS_column_bool):
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result = PyBool_FromLong(value)
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return result
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cpdef object get_line(self, size_t line_nb) :
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cpdef object get_line(self, index_t line_nb) :
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cdef obibool_t value
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cdef object result
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cdef size_t i
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cdef index_t i
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cdef bint all_NA
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result = {}
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all_NA = True
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@ -79,20 +79,20 @@ cdef class OBIDMS_column_bool_multi_elts(OBIDMS_column_bool):
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result = None
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return result
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cpdef set_item(self, size_t line_nb, str element_name, obibool_t value):
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cpdef set_item(self, index_t line_nb, str element_name, obibool_t value):
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raise Exception("Column is read-only")
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cpdef set_line(self, size_t line_nb, object values):
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cpdef set_line(self, index_t line_nb, object values):
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raise Exception("Column is read-only")
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cdef class OBIDMS_column_bool_multi_elts_writable(OBIDMS_column_bool_multi_elts):
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cpdef set_item(self, size_t line_nb, str element_name, obibool_t value):
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cpdef set_item(self, index_t line_nb, str element_name, obibool_t value):
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if obi_column_set_obibool_with_elt_name(self.pointer, line_nb, str2bytes(element_name), value) < 0:
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raise Exception("Problem setting a value in a column")
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cpdef set_line(self, size_t line_nb, object values):
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cpdef set_line(self, index_t line_nb, object values):
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cdef obibool_t value
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for element_name in values :
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value = <obibool_t> values[element_name]
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@ -1,25 +1,25 @@
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#cython: language_level=3
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from .capi.obitypes cimport obichar_t
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from .capi.obitypes cimport obichar_t, index_t
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from ._obidms cimport OBIDMS_column
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cdef class OBIDMS_column_char(OBIDMS_column):
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cpdef object get_line(self, size_t line_nb)
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cpdef set_line(self, size_t line_nb, object value)
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cpdef object get_line(self, index_t line_nb)
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cpdef set_line(self, index_t line_nb, object value)
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cpdef close(self)
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cdef class OBIDMS_column_char_writable(OBIDMS_column_char):
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cpdef set_line(self, size_t line_nb, object value)
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cpdef set_line(self, index_t line_nb, object value)
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cpdef close(self)
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cdef class OBIDMS_column_char_multi_elts(OBIDMS_column_char):
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cpdef object get_item(self, size_t line_nb, str element_name)
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cpdef object get_line(self, size_t line_nb)
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cpdef set_item(self, size_t line_nb, str element_name, bytes value)
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cpdef set_line(self, size_t line_nb, object values)
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cpdef object get_item(self, index_t line_nb, str element_name)
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cpdef object get_line(self, index_t line_nb)
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cpdef set_item(self, index_t line_nb, str element_name, bytes value)
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cpdef set_line(self, index_t line_nb, object values)
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cdef class OBIDMS_column_char_multi_elts_writable(OBIDMS_column_char_multi_elts):
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cpdef set_item(self, size_t line_nb, str element_name, bytes value)
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cpdef set_line(self, size_t line_nb, object values)
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cpdef set_item(self, index_t line_nb, str element_name, bytes value)
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cpdef set_line(self, index_t line_nb, object values)
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cpdef close(self)
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@ -14,7 +14,7 @@ from obitools3.utils cimport str2bytes
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cdef class OBIDMS_column_char(OBIDMS_column):
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cpdef object get_line(self, size_t line_nb):
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cpdef object get_line(self, index_t line_nb):
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cdef obichar_t value
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cdef object result
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value = obi_column_get_obichar_with_elt_idx(self.pointer, line_nb, 0)
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@ -26,7 +26,7 @@ cdef class OBIDMS_column_char(OBIDMS_column):
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result = <bytes> value
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return result
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cpdef set_line(self, size_t line_nb, object value):
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cpdef set_line(self, index_t line_nb, object value):
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raise Exception("Column is read-only")
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cpdef close(self):
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@ -36,7 +36,7 @@ cdef class OBIDMS_column_char(OBIDMS_column):
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cdef class OBIDMS_column_char_writable(OBIDMS_column_char):
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cpdef set_line(self, size_t line_nb, object value):
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cpdef set_line(self, index_t line_nb, object value):
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if obi_column_set_obichar_with_elt_idx(self.pointer, line_nb, 0, <bytes> value[0]) < 0:
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raise Exception("Problem setting a value in a column")
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@ -47,7 +47,7 @@ cdef class OBIDMS_column_char_writable(OBIDMS_column_char):
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cdef class OBIDMS_column_char_multi_elts(OBIDMS_column_char):
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cpdef object get_item(self, size_t line_nb, str element_name):
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cpdef object get_item(self, index_t line_nb, str element_name):
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cdef obichar_t value
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cdef object result
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value = obi_column_get_obichar_with_elt_name(self.pointer, line_nb, str2bytes(element_name))
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@ -59,10 +59,10 @@ cdef class OBIDMS_column_char_multi_elts(OBIDMS_column_char):
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result = <bytes> value
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return result
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cpdef object get_line(self, size_t line_nb) :
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cpdef object get_line(self, index_t line_nb) :
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cdef obichar_t value
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cdef object result
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cdef size_t i
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cdef index_t i
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cdef bint all_NA
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result = {}
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all_NA = True
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@ -77,20 +77,20 @@ cdef class OBIDMS_column_char_multi_elts(OBIDMS_column_char):
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result = None
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return result
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cpdef set_item(self, size_t line_nb, str element_name, bytes value):
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cpdef set_item(self, index_t line_nb, str element_name, bytes value):
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raise Exception("Column is read-only")
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cpdef set_line(self, size_t line_nb, object values):
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cpdef set_line(self, index_t line_nb, object values):
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raise Exception("Column is read-only")
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cdef class OBIDMS_column_char_multi_elts_writable(OBIDMS_column_char_multi_elts):
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cpdef set_item(self, size_t line_nb, str element_name, bytes value):
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cpdef set_item(self, index_t line_nb, str element_name, bytes value):
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if obi_column_set_obichar_with_elt_name(self.pointer, line_nb, str2bytes(element_name), value[0]) < 0:
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raise Exception("Problem setting a value in a column")
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cpdef set_line(self, size_t line_nb, object values):
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cpdef set_line(self, index_t line_nb, object values):
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cdef bytes value
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for element_name in values :
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value = <bytes> values[element_name]
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@ -106,7 +106,7 @@ cdef class OBIDMS_column_char_multi_elts_writable(OBIDMS_column_char_multi_elts)
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# cdef class OBIDMS_column_char(OBIDMS_column) :
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#
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# cpdef object get_item(self, size_t line_nb, str element_name):
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# cpdef object get_item(self, index_t line_nb, str element_name):
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# cdef char value
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# cdef object result
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# value = obi_column_get_obichar_with_elt_name(self.pointer, line_nb, str2bytes(element_name))
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@ -118,7 +118,7 @@ cdef class OBIDMS_column_char_multi_elts_writable(OBIDMS_column_char_multi_elts)
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# result = <bytes> value
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# return result
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#
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# cpdef set_item(self, size_t line_nb, str element_name, bytes value):
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# cpdef set_item(self, index_t line_nb, str element_name, bytes value):
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# raise Exception("Column is read-only")
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#
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# cpdef close(self):
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@ -128,7 +128,7 @@ cdef class OBIDMS_column_char_multi_elts_writable(OBIDMS_column_char_multi_elts)
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#
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# cdef class OBIDMS_column_char_writable(OBIDMS_column_char) :
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#
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# cpdef set_item(self, size_t line_nb, str element_name, bytes value):
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# cpdef set_item(self, index_t line_nb, str element_name, bytes value):
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# if obi_column_set_obichar_with_elt_name(self.pointer, line_nb, str2bytes(element_name), value[0]) < 0:
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# raise Exception("Problem setting a value in a column")
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#
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@ -1,25 +1,25 @@
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#cython: language_level=3
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from .capi.obitypes cimport obifloat_t
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from .capi.obitypes cimport obifloat_t, index_t
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from ._obidms cimport OBIDMS_column
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cdef class OBIDMS_column_float(OBIDMS_column):
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cpdef object get_line(self, size_t line_nb)
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cpdef set_line(self, size_t line_nb, object value)
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cpdef object get_line(self, index_t line_nb)
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cpdef set_line(self, index_t line_nb, object value)
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cpdef close(self)
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|
||||
cdef class OBIDMS_column_float_writable(OBIDMS_column_float):
|
||||
cpdef set_line(self, size_t line_nb, object value)
|
||||
cpdef set_line(self, index_t line_nb, object value)
|
||||
cpdef close(self)
|
||||
|
||||
cdef class OBIDMS_column_float_multi_elts(OBIDMS_column_float):
|
||||
cpdef object get_item(self, size_t line_nb, str element_name)
|
||||
cpdef object get_line(self, size_t line_nb)
|
||||
cpdef set_item(self, size_t line_nb, str element_name, obifloat_t value)
|
||||
cpdef set_line(self, size_t line_nb, object values)
|
||||
cpdef object get_item(self, index_t line_nb, str element_name)
|
||||
cpdef object get_line(self, index_t line_nb)
|
||||
cpdef set_item(self, index_t line_nb, str element_name, obifloat_t value)
|
||||
cpdef set_line(self, index_t line_nb, object values)
|
||||
|
||||
cdef class OBIDMS_column_float_multi_elts_writable(OBIDMS_column_float_multi_elts):
|
||||
cpdef set_item(self, size_t line_nb, str element_name, obifloat_t value)
|
||||
cpdef set_line(self, size_t line_nb, object values)
|
||||
cpdef set_item(self, index_t line_nb, str element_name, obifloat_t value)
|
||||
cpdef set_line(self, index_t line_nb, object values)
|
||||
cpdef close(self)
|
||||
|
||||
@ -14,7 +14,7 @@ from obitools3.utils cimport str2bytes
|
||||
|
||||
cdef class OBIDMS_column_float(OBIDMS_column):
|
||||
|
||||
cpdef object get_line(self, size_t line_nb):
|
||||
cpdef object get_line(self, index_t line_nb):
|
||||
cdef obifloat_t value
|
||||
cdef object result
|
||||
value = obi_column_get_obifloat_with_elt_idx(self.pointer, line_nb, 0)
|
||||
@ -26,7 +26,7 @@ cdef class OBIDMS_column_float(OBIDMS_column):
|
||||
result = <double> value
|
||||
return result
|
||||
|
||||
cpdef set_line(self, size_t line_nb, object value):
|
||||
cpdef set_line(self, index_t line_nb, object value):
|
||||
raise Exception("Column is read-only")
|
||||
|
||||
cpdef close(self):
|
||||
@ -36,7 +36,7 @@ cdef class OBIDMS_column_float(OBIDMS_column):
|
||||
|
||||
cdef class OBIDMS_column_float_writable(OBIDMS_column_float):
|
||||
|
||||
cpdef set_line(self, size_t line_nb, object value):
|
||||
cpdef set_line(self, index_t line_nb, object value):
|
||||
if obi_column_set_obifloat_with_elt_idx(self.pointer, line_nb, 0, <obifloat_t> value) < 0:
|
||||
raise Exception("Problem setting a value in a column")
|
||||
|
||||
@ -47,7 +47,7 @@ cdef class OBIDMS_column_float_writable(OBIDMS_column_float):
|
||||
|
||||
cdef class OBIDMS_column_float_multi_elts(OBIDMS_column_float):
|
||||
|
||||
cpdef object get_item(self, size_t line_nb, str element_name):
|
||||
cpdef object get_item(self, index_t line_nb, str element_name):
|
||||
cdef obifloat_t value
|
||||
cdef object result
|
||||
value = obi_column_get_obifloat_with_elt_name(self.pointer, line_nb, str2bytes(element_name))
|
||||
@ -59,10 +59,10 @@ cdef class OBIDMS_column_float_multi_elts(OBIDMS_column_float):
|
||||
result = <double> value
|
||||
return result
|
||||
|
||||
cpdef object get_line(self, size_t line_nb) :
|
||||
cpdef object get_line(self, index_t line_nb) :
|
||||
cdef obifloat_t value
|
||||
cdef object result
|
||||
cdef size_t i
|
||||
cdef index_t i
|
||||
cdef bint all_NA
|
||||
result = {}
|
||||
all_NA = True
|
||||
@ -77,20 +77,20 @@ cdef class OBIDMS_column_float_multi_elts(OBIDMS_column_float):
|
||||
result = None
|
||||
return result
|
||||
|
||||
cpdef set_item(self, size_t line_nb, str element_name, obifloat_t value):
|
||||
cpdef set_item(self, index_t line_nb, str element_name, obifloat_t value):
|
||||
raise Exception("Column is read-only")
|
||||
|
||||
cpdef set_line(self, size_t line_nb, object values):
|
||||
cpdef set_line(self, index_t line_nb, object values):
|
||||
raise Exception("Column is read-only")
|
||||
|
||||
|
||||
cdef class OBIDMS_column_float_multi_elts_writable(OBIDMS_column_float_multi_elts):
|
||||
|
||||
cpdef set_item(self, size_t line_nb, str element_name, obifloat_t value):
|
||||
cpdef set_item(self, index_t line_nb, str element_name, obifloat_t value):
|
||||
if obi_column_set_obifloat_with_elt_name(self.pointer, line_nb, str2bytes(element_name), value) < 0:
|
||||
raise Exception("Problem setting a value in a column")
|
||||
|
||||
cpdef set_line(self, size_t line_nb, object values):
|
||||
cpdef set_line(self, index_t line_nb, object values):
|
||||
cdef obifloat_t value
|
||||
for element_name in values :
|
||||
value = <obifloat_t> values[element_name]
|
||||
|
||||
@ -1,25 +1,25 @@
|
||||
#cython: language_level=3
|
||||
|
||||
from .capi.obitypes cimport obiint_t
|
||||
from .capi.obitypes cimport obiint_t, index_t
|
||||
from ._obidms cimport OBIDMS_column
|
||||
|
||||
|
||||
cdef class OBIDMS_column_int(OBIDMS_column):
|
||||
cpdef object get_line(self, size_t line_nb)
|
||||
cpdef set_line(self, size_t line_nb, object value)
|
||||
cpdef object get_line(self, index_t line_nb)
|
||||
cpdef set_line(self, index_t line_nb, object value)
|
||||
cpdef close(self)
|
||||
|
||||
cdef class OBIDMS_column_int_writable(OBIDMS_column_int):
|
||||
cpdef set_line(self, size_t line_nb, object value)
|
||||
cpdef set_line(self, index_t line_nb, object value)
|
||||
cpdef close(self)
|
||||
|
||||
cdef class OBIDMS_column_int_multi_elts(OBIDMS_column_int):
|
||||
cpdef object get_item(self, size_t line_nb, str element_name)
|
||||
cpdef object get_line(self, size_t line_nb)
|
||||
cpdef set_item(self, size_t line_nb, str element_name, obiint_t value)
|
||||
cpdef set_line(self, size_t line_nb, object values)
|
||||
cpdef object get_item(self, index_t line_nb, str element_name)
|
||||
cpdef object get_line(self, index_t line_nb)
|
||||
cpdef set_item(self, index_t line_nb, str element_name, obiint_t value)
|
||||
cpdef set_line(self, index_t line_nb, object values)
|
||||
|
||||
cdef class OBIDMS_column_int_multi_elts_writable(OBIDMS_column_int_multi_elts):
|
||||
cpdef set_item(self, size_t line_nb, str element_name, obiint_t value)
|
||||
cpdef set_line(self, size_t line_nb, object values)
|
||||
cpdef set_item(self, index_t line_nb, str element_name, obiint_t value)
|
||||
cpdef set_line(self, index_t line_nb, object values)
|
||||
cpdef close(self)
|
||||
|
||||
@ -16,7 +16,7 @@ from cpython.int cimport PyInt_FromLong
|
||||
|
||||
cdef class OBIDMS_column_int(OBIDMS_column):
|
||||
|
||||
cpdef object get_line(self, size_t line_nb):
|
||||
cpdef object get_line(self, index_t line_nb):
|
||||
cdef obiint_t value
|
||||
cdef object result
|
||||
value = obi_column_get_obiint_with_elt_idx(self.pointer, line_nb, 0)
|
||||
@ -28,7 +28,7 @@ cdef class OBIDMS_column_int(OBIDMS_column):
|
||||
result = PyInt_FromLong(value)
|
||||
return result
|
||||
|
||||
cpdef set_line(self, size_t line_nb, object value):
|
||||
cpdef set_line(self, index_t line_nb, object value):
|
||||
raise Exception("Column is read-only")
|
||||
|
||||
cpdef close(self):
|
||||
@ -38,7 +38,7 @@ cdef class OBIDMS_column_int(OBIDMS_column):
|
||||
|
||||
cdef class OBIDMS_column_int_writable(OBIDMS_column_int):
|
||||
|
||||
cpdef set_line(self, size_t line_nb, object value):
|
||||
cpdef set_line(self, index_t line_nb, object value):
|
||||
if obi_column_set_obiint_with_elt_idx(self.pointer, line_nb, 0, <obiint_t> value) < 0:
|
||||
raise Exception("Problem setting a value in a column")
|
||||
|
||||
@ -49,7 +49,7 @@ cdef class OBIDMS_column_int_writable(OBIDMS_column_int):
|
||||
|
||||
cdef class OBIDMS_column_int_multi_elts(OBIDMS_column_int):
|
||||
|
||||
cpdef object get_item(self, size_t line_nb, str element_name):
|
||||
cpdef object get_item(self, index_t line_nb, str element_name):
|
||||
cdef obiint_t value
|
||||
cdef object result
|
||||
value = obi_column_get_obiint_with_elt_name(self.pointer, line_nb, str2bytes(element_name))
|
||||
@ -61,10 +61,10 @@ cdef class OBIDMS_column_int_multi_elts(OBIDMS_column_int):
|
||||
result = PyInt_FromLong(value)
|
||||
return result
|
||||
|
||||
cpdef object get_line(self, size_t line_nb) :
|
||||
cpdef object get_line(self, index_t line_nb) :
|
||||
cdef obiint_t value
|
||||
cdef object result
|
||||
cdef size_t i
|
||||
cdef index_t i
|
||||
cdef bint all_NA
|
||||
result = {}
|
||||
all_NA = True
|
||||
@ -79,20 +79,20 @@ cdef class OBIDMS_column_int_multi_elts(OBIDMS_column_int):
|
||||
result = None
|
||||
return result
|
||||
|
||||
cpdef set_item(self, size_t line_nb, str element_name, obiint_t value):
|
||||
cpdef set_item(self, index_t line_nb, str element_name, obiint_t value):
|
||||
raise Exception("Column is read-only")
|
||||
|
||||
cpdef set_line(self, size_t line_nb, object values):
|
||||
cpdef set_line(self, index_t line_nb, object values):
|
||||
raise Exception("Column is read-only")
|
||||
|
||||
|
||||
cdef class OBIDMS_column_int_multi_elts_writable(OBIDMS_column_int_multi_elts):
|
||||
|
||||
cpdef set_item(self, size_t line_nb, str element_name, obiint_t value):
|
||||
cpdef set_item(self, index_t line_nb, str element_name, obiint_t value):
|
||||
if obi_column_set_obiint_with_elt_name(self.pointer, line_nb, str2bytes(element_name), value) < 0:
|
||||
raise Exception("Problem setting a value in a column")
|
||||
|
||||
cpdef set_line(self, size_t line_nb, object values):
|
||||
cpdef set_line(self, index_t line_nb, object values):
|
||||
cdef obiint_t value
|
||||
for element_name in values :
|
||||
value = <obiint_t> values[element_name]
|
||||
|
||||
@ -1,24 +1,25 @@
|
||||
#cython: language_level=3
|
||||
|
||||
from .capi.obitypes cimport index_t
|
||||
from ._obidms cimport OBIDMS_column
|
||||
|
||||
|
||||
cdef class OBIDMS_column_str(OBIDMS_column):
|
||||
cpdef object get_line(self, size_t line_nb)
|
||||
cpdef set_line(self, size_t line_nb, object value)
|
||||
cpdef object get_line(self, index_t line_nb)
|
||||
cpdef set_line(self, index_t line_nb, object value)
|
||||
cpdef close(self)
|
||||
|
||||
cdef class OBIDMS_column_str_writable(OBIDMS_column_str):
|
||||
cpdef set_line(self, size_t line_nb, object value)
|
||||
cpdef set_line(self, index_t line_nb, object value)
|
||||
cpdef close(self)
|
||||
|
||||
cdef class OBIDMS_column_str_multi_elts(OBIDMS_column_str):
|
||||
cpdef object get_item(self, size_t line_nb, str element_name)
|
||||
cpdef object get_line(self, size_t line_nb)
|
||||
cpdef set_item(self, size_t line_nb, str element_name, str value)
|
||||
cpdef set_line(self, size_t line_nb, object values)
|
||||
cpdef object get_item(self, index_t line_nb, str element_name)
|
||||
cpdef object get_line(self, index_t line_nb)
|
||||
cpdef set_item(self, index_t line_nb, str element_name, str value)
|
||||
cpdef set_line(self, index_t line_nb, object values)
|
||||
|
||||
cdef class OBIDMS_column_str_multi_elts_writable(OBIDMS_column_str_multi_elts):
|
||||
cpdef set_item(self, size_t line_nb, str element_name, str value)
|
||||
cpdef set_line(self, size_t line_nb, object values)
|
||||
cpdef set_item(self, index_t line_nb, str element_name, str value)
|
||||
cpdef set_line(self, index_t line_nb, object values)
|
||||
cpdef close(self)
|
||||
|
||||
@ -9,42 +9,24 @@ from .capi.obidmscolumn cimport obi_close_column,\
|
||||
from .capi.obierrno cimport obi_errno
|
||||
from .capi.obitypes cimport OBIIdx_NA, const_char_p
|
||||
|
||||
|
||||
from libc.string cimport strlen
|
||||
|
||||
from obitools3.utils cimport str2bytes, bytes2str
|
||||
|
||||
from cpython.int cimport PyInt_FromSsize_t
|
||||
|
||||
|
||||
cdef class OBIDMS_column_str(OBIDMS_column):
|
||||
|
||||
cpdef object get_line(self, size_t line_nb):
|
||||
cdef const_char_p cvalue
|
||||
cpdef object get_line(self, index_t line_nb):
|
||||
cdef bytes value
|
||||
cdef object result
|
||||
|
||||
cvalue = obi_column_get_obistr_with_elt_idx(self.pointer, line_nb, 0)
|
||||
|
||||
print('test 1')
|
||||
|
||||
print(hex(<int> cvalue))
|
||||
|
||||
|
||||
print(strlen(cvalue))
|
||||
print("test")
|
||||
value = <bytes> cvalue
|
||||
print(value)
|
||||
value = <bytes> obi_column_get_obistr_with_elt_idx(self.pointer, line_nb, 0)
|
||||
if obi_errno > 0 :
|
||||
raise IndexError(line_nb)
|
||||
if value == OBIIdx_NA :
|
||||
result = None
|
||||
else :
|
||||
print(value)
|
||||
result = bytes2str(value)
|
||||
return result
|
||||
|
||||
cpdef set_line(self, size_t line_nb, object value):
|
||||
cpdef set_line(self, index_t line_nb, object value):
|
||||
raise Exception("Column is read-only")
|
||||
|
||||
cpdef close(self):
|
||||
@ -54,7 +36,7 @@ cdef class OBIDMS_column_str(OBIDMS_column):
|
||||
|
||||
cdef class OBIDMS_column_str_writable(OBIDMS_column_str):
|
||||
|
||||
cpdef set_line(self, size_t line_nb, object value):
|
||||
cpdef set_line(self, index_t line_nb, object value):
|
||||
if obi_column_set_obistr_with_elt_idx(self.pointer, line_nb, 0, str2bytes(value)) < 0:
|
||||
raise Exception("Problem setting a value in a column")
|
||||
|
||||
@ -65,10 +47,10 @@ cdef class OBIDMS_column_str_writable(OBIDMS_column_str):
|
||||
|
||||
cdef class OBIDMS_column_str_multi_elts(OBIDMS_column_str):
|
||||
|
||||
cpdef object get_item(self, size_t line_nb, str element_name):
|
||||
cpdef object get_item(self, index_t line_nb, str element_name):
|
||||
cdef bytes value
|
||||
cdef object result
|
||||
value = obi_column_get_obistr_with_elt_name(self.pointer, line_nb, str2bytes(element_name))
|
||||
value = <bytes> obi_column_get_obistr_with_elt_name(self.pointer, line_nb, str2bytes(element_name))
|
||||
if obi_errno > 0 :
|
||||
raise IndexError(line_nb, element_name)
|
||||
if value == OBIIdx_NA :
|
||||
@ -77,15 +59,15 @@ cdef class OBIDMS_column_str_multi_elts(OBIDMS_column_str):
|
||||
result = bytes2str(value)
|
||||
return result
|
||||
|
||||
cpdef object get_line(self, size_t line_nb) :
|
||||
cpdef object get_line(self, index_t line_nb) :
|
||||
cdef bytes value
|
||||
cdef object result
|
||||
cdef size_t i
|
||||
cdef index_t i
|
||||
cdef bint all_NA
|
||||
result = {}
|
||||
all_NA = True
|
||||
for i in range(self.nb_elements_per_line) :
|
||||
value = obi_column_get_obistr_with_elt_idx(self.pointer, line_nb, i)
|
||||
value = <bytes> obi_column_get_obistr_with_elt_idx(self.pointer, line_nb, i)
|
||||
if obi_errno > 0 :
|
||||
raise IndexError(line_nb)
|
||||
result[self.elements_names[i]] = bytes2str(value)
|
||||
@ -95,20 +77,20 @@ cdef class OBIDMS_column_str_multi_elts(OBIDMS_column_str):
|
||||
result = None
|
||||
return result
|
||||
|
||||
cpdef set_item(self, size_t line_nb, str element_name, str value):
|
||||
cpdef set_item(self, index_t line_nb, str element_name, str value):
|
||||
raise Exception("Column is read-only")
|
||||
|
||||
cpdef set_line(self, size_t line_nb, object values):
|
||||
cpdef set_line(self, index_t line_nb, object values):
|
||||
raise Exception("Column is read-only")
|
||||
|
||||
|
||||
cdef class OBIDMS_column_str_multi_elts_writable(OBIDMS_column_str_multi_elts):
|
||||
|
||||
cpdef set_item(self, size_t line_nb, str element_name, str value):
|
||||
cpdef set_item(self, index_t line_nb, str element_name, str value):
|
||||
if obi_column_set_obistr_with_elt_name(self.pointer, line_nb, str2bytes(element_name), str2bytes(value)) < 0:
|
||||
raise Exception("Problem setting a value in a column")
|
||||
|
||||
cpdef set_line(self, size_t line_nb, object values):
|
||||
cpdef set_line(self, index_t line_nb, object values):
|
||||
cdef str value
|
||||
for element_name in values :
|
||||
value = values[element_name]
|
||||
|
||||
@ -8,6 +8,7 @@ from ..capi.obitypes cimport const_char_p, \
|
||||
obibool_t, \
|
||||
obichar_t, \
|
||||
obifloat_t, \
|
||||
index_t, \
|
||||
time_t
|
||||
|
||||
|
||||
@ -16,9 +17,9 @@ cdef extern from "obidmscolumn.h" nogil:
|
||||
struct OBIDMS_column_header_t:
|
||||
bint little_endian
|
||||
int header_size
|
||||
size_t line_count
|
||||
size_t lines_used
|
||||
size_t nb_elements_per_line
|
||||
index_t line_count
|
||||
index_t lines_used
|
||||
index_t nb_elements_per_line
|
||||
const_char_p elements_names
|
||||
OBIType_t data_type
|
||||
time_t creation_date
|
||||
@ -38,8 +39,8 @@ cdef extern from "obidmscolumn.h" nogil:
|
||||
OBIDMS_column_p obi_create_column(OBIDMS_p dms,
|
||||
const_char_p column_name,
|
||||
OBIType_t type,
|
||||
size_t nb_lines,
|
||||
size_t nb_elements_per_line,
|
||||
index_t nb_lines,
|
||||
index_t nb_elements_per_line,
|
||||
const_char_p elements_names,
|
||||
const_char_p array_name)
|
||||
|
||||
@ -69,101 +70,101 @@ cdef extern from "obidmscolumn.h" nogil:
|
||||
|
||||
cdef extern from "obidmscolumn_int.h" nogil:
|
||||
int obi_column_set_obiint_with_elt_name(OBIDMS_column_p column,
|
||||
size_t line_nb,
|
||||
index_t line_nb,
|
||||
const_char_p element_name,
|
||||
obiint_t value)
|
||||
|
||||
int obi_column_set_obiint_with_elt_idx(OBIDMS_column_p column,
|
||||
size_t line_nb,
|
||||
size_t element_idx,
|
||||
index_t line_nb,
|
||||
index_t element_idx,
|
||||
obiint_t value)
|
||||
|
||||
obiint_t obi_column_get_obiint_with_elt_name(OBIDMS_column_p column,
|
||||
size_t line_nb,
|
||||
index_t line_nb,
|
||||
const_char_p element_name)
|
||||
|
||||
obiint_t obi_column_get_obiint_with_elt_idx(OBIDMS_column_p column,
|
||||
size_t line_nb,
|
||||
size_t element_idx)
|
||||
index_t line_nb,
|
||||
index_t element_idx)
|
||||
|
||||
|
||||
cdef extern from "obidmscolumn_bool.h" nogil:
|
||||
|
||||
int obi_column_set_obibool_with_elt_name(OBIDMS_column_p column,
|
||||
size_t line_nb,
|
||||
index_t line_nb,
|
||||
const_char_p element_name,
|
||||
obibool_t value)
|
||||
|
||||
int obi_column_set_obibool_with_elt_idx(OBIDMS_column_p column,
|
||||
size_t line_nb,
|
||||
size_t element_idx,
|
||||
index_t line_nb,
|
||||
index_t element_idx,
|
||||
obibool_t value)
|
||||
|
||||
obibool_t obi_column_get_obibool_with_elt_name(OBIDMS_column_p column,
|
||||
size_t line_nb,
|
||||
index_t line_nb,
|
||||
const_char_p element_name)
|
||||
|
||||
obibool_t obi_column_get_obibool_with_elt_idx(OBIDMS_column_p column,
|
||||
size_t line_nb,
|
||||
size_t element_idx)
|
||||
index_t line_nb,
|
||||
index_t element_idx)
|
||||
|
||||
cdef extern from "obidmscolumn_char.h" nogil:
|
||||
|
||||
int obi_column_set_obichar_with_elt_name(OBIDMS_column_p column,
|
||||
size_t line_nb,
|
||||
index_t line_nb,
|
||||
const_char_p element_name,
|
||||
obichar_t value)
|
||||
|
||||
int obi_column_set_obichar_with_elt_idx(OBIDMS_column_p column,
|
||||
size_t line_nb,
|
||||
size_t element_idx,
|
||||
index_t line_nb,
|
||||
index_t element_idx,
|
||||
obichar_t value)
|
||||
|
||||
obichar_t obi_column_get_obichar_with_elt_name(OBIDMS_column_p column,
|
||||
size_t line_nb,
|
||||
index_t line_nb,
|
||||
const_char_p element_name)
|
||||
|
||||
obichar_t obi_column_get_obichar_with_elt_idx(OBIDMS_column_p column,
|
||||
size_t line_nb,
|
||||
size_t element_idx)
|
||||
index_t line_nb,
|
||||
index_t element_idx)
|
||||
|
||||
cdef extern from "obidmscolumn_float.h" nogil:
|
||||
|
||||
int obi_column_set_obifloat_with_elt_name(OBIDMS_column_p column,
|
||||
size_t line_nb,
|
||||
index_t line_nb,
|
||||
const_char_p element_name,
|
||||
obifloat_t value)
|
||||
|
||||
int obi_column_set_obifloat_with_elt_idx(OBIDMS_column_p column,
|
||||
size_t line_nb,
|
||||
size_t element_idx,
|
||||
index_t line_nb,
|
||||
index_t element_idx,
|
||||
obifloat_t value)
|
||||
|
||||
obifloat_t obi_column_get_obifloat_with_elt_name(OBIDMS_column_p column,
|
||||
size_t line_nb,
|
||||
index_t line_nb,
|
||||
const_char_p element_name)
|
||||
|
||||
obifloat_t obi_column_get_obifloat_with_elt_idx(OBIDMS_column_p column,
|
||||
size_t line_nb,
|
||||
size_t element_idx)
|
||||
index_t line_nb,
|
||||
index_t element_idx)
|
||||
|
||||
cdef extern from "obidmscolumn_str.h" nogil:
|
||||
|
||||
int obi_column_set_obistr_with_elt_name(OBIDMS_column_p column,
|
||||
size_t line_nb,
|
||||
index_t line_nb,
|
||||
const_char_p element_name,
|
||||
char* value)
|
||||
|
||||
int obi_column_set_obistr_with_elt_idx(OBIDMS_column_p column,
|
||||
size_t line_nb,
|
||||
size_t element_idx,
|
||||
index_t line_nb,
|
||||
index_t element_idx,
|
||||
char* value)
|
||||
|
||||
const_char_p obi_column_get_obistr_with_elt_name(OBIDMS_column_p column,
|
||||
size_t line_nb,
|
||||
index_t line_nb,
|
||||
const_char_p element_name)
|
||||
|
||||
const_char_p obi_column_get_obistr_with_elt_idx(OBIDMS_column_p column,
|
||||
size_t line_nb,
|
||||
size_t element_idx)
|
||||
index_t line_nb,
|
||||
index_t element_idx)
|
||||
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
#cython: language_level=3
|
||||
|
||||
|
||||
from libc.stdint cimport int32_t
|
||||
from libc.stdint cimport int32_t, int64_t
|
||||
from posix.types cimport time_t
|
||||
|
||||
|
||||
@ -33,10 +33,10 @@ cdef extern from "obitypes.h" nogil:
|
||||
ctypedef int32_t obiint_t
|
||||
ctypedef double obifloat_t
|
||||
ctypedef char obichar_t
|
||||
ctypedef size_t obiidx_t
|
||||
ctypedef int64_t index_t
|
||||
|
||||
extern obiint_t OBIInt_NA
|
||||
extern obiidx_t OBIIdx_NA
|
||||
extern index_t OBIIdx_NA
|
||||
extern obifloat_t OBIFloat_NA
|
||||
extern obichar_t OBIChar_NA
|
||||
extern obibool_t OBIBool_NA
|
||||
|
||||
@ -2,16 +2,17 @@ import os
|
||||
import sys
|
||||
import shutil
|
||||
import unittest
|
||||
from random import randint, uniform
|
||||
from random import randint, uniform, choice
|
||||
import string
|
||||
|
||||
from obitools3.obidms._obidms import OBIDMS
|
||||
|
||||
|
||||
LINE_COUNT_FOR_TEST_COLUMN = 100000 # TODO randomize?
|
||||
SMALLER_LINE_COUNT_FOR_TEST_COLUMN = 10000 # TODO randomize?
|
||||
NB_ELEMENTS_PER_LINE = 50 # TODO randomize?
|
||||
LINE_COUNT_FOR_TEST_COLUMN = 10000 # TODO randomize?
|
||||
SMALLER_LINE_COUNT_FOR_TEST_COLUMN = 1000 # TODO randomize?
|
||||
NB_ELEMENTS_PER_LINE = 20 # TODO randomize?
|
||||
DMS_NAME = "unit_test_dms"
|
||||
DATA_TYPES = ['OBI_INT', 'OBI_FLOAT', 'OBI_BOOL', 'OBI_CHAR']
|
||||
DATA_TYPES = ['OBI_INT', 'OBI_FLOAT', 'OBI_BOOL', 'OBI_CHAR', 'OBI_IDX']
|
||||
|
||||
|
||||
def create_test_obidms():
|
||||
@ -26,7 +27,7 @@ def create_test_column(dms, data_type_code, multiple_elements_per_line=False):
|
||||
data_type_code = data_type_code
|
||||
data_type_str = data_types[data_type_code-1]
|
||||
col_name = "unit_test_"+data_type_str
|
||||
|
||||
|
||||
if multiple_elements_per_line :
|
||||
elts_names = elements_names()
|
||||
col = dms.open_column(col_name,
|
||||
@ -41,7 +42,7 @@ def create_test_column(dms, data_type_code, multiple_elements_per_line=False):
|
||||
create=True,
|
||||
data_type=data_type_code)
|
||||
return (col, col_name, data_type_str)
|
||||
|
||||
|
||||
|
||||
def elements_names():
|
||||
names = [str(i) for i in range(NB_ELEMENTS_PER_LINE)]
|
||||
@ -60,8 +61,9 @@ def random_obivalue(data_type):
|
||||
nucs = 'atgc'
|
||||
return bytes(nucs[randint(0,3)], 'utf-8')
|
||||
elif data_type == "OBI_IDX" :
|
||||
return randint(0,r)
|
||||
|
||||
length = randint(1,500)
|
||||
randoms = ''.join(choice(string.ascii_lowercase) for i in range(length))
|
||||
return randoms
|
||||
|
||||
class OBIDMS_Column_TestCase(unittest.TestCase):
|
||||
def tearDown(self):
|
||||
@ -228,14 +230,42 @@ class OBIDMS_Column_OBI_CHAR_multiple_elements_TestCase(OBIDMS_Column_multiple_e
|
||||
multiple_elements_per_line=True)
|
||||
|
||||
|
||||
class OBIDMS_Column_OBI_STR_TestCase(OBIDMS_Column_TestCase):
|
||||
def setUp(self):
|
||||
self.data_type_code = 5
|
||||
self.dms, \
|
||||
self.dms_name, \
|
||||
self.dms_dir_name = create_test_obidms()
|
||||
self.col, \
|
||||
self.col_name, \
|
||||
self.data_type_str = create_test_column(self.dms,
|
||||
self.data_type_code)
|
||||
|
||||
|
||||
class OBIDMS_Column_OBI_STR_multiple_elements_TestCase(OBIDMS_Column_multiple_elements_TestCase):
|
||||
def setUp(self):
|
||||
self.data_type_code = 5
|
||||
self.dms, \
|
||||
self.dms_name, \
|
||||
self.dms_dir_name = create_test_obidms()
|
||||
self.col, \
|
||||
self.col_name, \
|
||||
self.elts_names, \
|
||||
self.data_type_str = create_test_column(self.dms,
|
||||
self.data_type_code,
|
||||
multiple_elements_per_line=True)
|
||||
|
||||
|
||||
if __name__ == '__main__':
|
||||
unittest.main(verbosity=2, defaultTest=["OBIDMS_Column_OBI_INT_TestCase",
|
||||
"OBIDMS_Column_OBI_INT_multiple_elements_TestCase",
|
||||
"OBIDMS_Column_OBI_FLOAT_TestCase",
|
||||
"OBIDMS_Column_OBI_FLOAT_multiple_elements_TestCase",
|
||||
"OBIDMS_Column_OBI_BOOL_TestCase",
|
||||
"OBIDMS_Column_OBI_BOOL_multiple_elements_TestCase",
|
||||
"OBIDMS_Column_OBI_CHAR_TestCase",
|
||||
"OBIDMS_Column_OBI_CHAR_multiple_elements_TestCase"])
|
||||
unittest.main(verbosity=2, defaultTest=["OBIDMS_Column_OBI_INT_TestCase",
|
||||
"OBIDMS_Column_OBI_INT_multiple_elements_TestCase",
|
||||
"OBIDMS_Column_OBI_FLOAT_TestCase",
|
||||
"OBIDMS_Column_OBI_FLOAT_multiple_elements_TestCase",
|
||||
"OBIDMS_Column_OBI_BOOL_TestCase",
|
||||
"OBIDMS_Column_OBI_BOOL_multiple_elements_TestCase",
|
||||
"OBIDMS_Column_OBI_CHAR_TestCase",
|
||||
"OBIDMS_Column_OBI_CHAR_multiple_elements_TestCase",
|
||||
"OBIDMS_Column_OBI_STR_TestCase",
|
||||
"OBIDMS_Column_OBI_STR_multiple_elements_TestCase"])
|
||||
|
||||
|
||||
|
||||
@ -2,4 +2,4 @@ major = 1
|
||||
minor = 1
|
||||
serial= '16'
|
||||
|
||||
version ="%2d.%02d.%s" % (major,minor,serial)
|
||||
version ="%d.%02d.%s" % (major,minor,serial)
|
||||
|
||||
313
src/obiarray.c
313
src/obiarray.c
@ -13,6 +13,7 @@
|
||||
#include <stdlib.h>
|
||||
#include <stdio.h>
|
||||
#include <stdint.h>
|
||||
#include <string.h>
|
||||
#include <time.h>
|
||||
#include <sys/mman.h>
|
||||
#include <fcntl.h>
|
||||
@ -20,7 +21,9 @@
|
||||
|
||||
#include "obiarray.h"
|
||||
#include "obierrno.h"
|
||||
#include "obitypes.h"
|
||||
#include "obidebug.h"
|
||||
#include "private_at_functions.h"
|
||||
|
||||
|
||||
#define DEBUG_LEVEL 0 // TODO has to be defined somewhere else (cython compil flag?)
|
||||
@ -37,7 +40,7 @@
|
||||
*
|
||||
* @warning The returned pointer has to be freed by the caller.
|
||||
*
|
||||
* @param name The name of the array.
|
||||
* @param array_name The name of the array.
|
||||
*
|
||||
* @returns A pointer to the array file name.
|
||||
* @retval NULL if an error occurred.
|
||||
@ -53,7 +56,7 @@ static char* build_array_file_name(const char* array_name);
|
||||
*
|
||||
* @warning The returned pointer has to be freed by the caller.
|
||||
*
|
||||
* @param name The name of the array.
|
||||
* @param array_name The name of the array.
|
||||
*
|
||||
* @returns A pointer to the array data file name.
|
||||
* @retval NULL if an error occurred.
|
||||
@ -65,62 +68,121 @@ static char* build_array_data_file_name(const char* array_name);
|
||||
|
||||
|
||||
/**
|
||||
* PRIVATE
|
||||
*/
|
||||
static char* build_array_file_path(OBIDMS_p dms, const char* array_name);
|
||||
|
||||
|
||||
/**
|
||||
* PRIVATE
|
||||
* @brief Internal function returning the size of an array header on this platform.
|
||||
*
|
||||
* @returns The size of an array header in bytes.
|
||||
*
|
||||
* @since October 2015
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
size_t get_array_header_size();
|
||||
|
||||
|
||||
/**
|
||||
* PRIVATE
|
||||
* @brief Internal function returning the initial size of an array on this platform.
|
||||
*
|
||||
* @returns The initial size of an array in bytes.
|
||||
*
|
||||
* @since October 2015
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
size_t get_initial_array_size();
|
||||
|
||||
|
||||
/**
|
||||
* PRIVATE
|
||||
* @brief Internal function returning the size of a data array header on this platform.
|
||||
*
|
||||
* @returns The size of a data array header in bytes.
|
||||
*
|
||||
* @since October 2015
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
size_t get_array_data_header_size();
|
||||
|
||||
|
||||
/**
|
||||
* PRIVATE
|
||||
* @brief Internal function returning the initial size of a data array on this platform.
|
||||
*
|
||||
* @returns The initial size of a data array in bytes.
|
||||
*
|
||||
* @since October 2015
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
size_t get_initial_array_data_size();
|
||||
|
||||
|
||||
/**
|
||||
* PRIVATE
|
||||
* @brief Internal function closing a data array structure.
|
||||
*
|
||||
* @param array_data A pointer to the data array.
|
||||
*
|
||||
* @retval 0 if the operation was successfully completed.
|
||||
* @retval -1 if an error occurred.
|
||||
*
|
||||
* @since October 2015
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
int close_array_data(OBIDMS_array_data_p array_data);
|
||||
|
||||
|
||||
/**
|
||||
* PRIVATE
|
||||
* @brief Internal function enlarging an array.
|
||||
*
|
||||
* @param array A pointer to the array structure.
|
||||
*
|
||||
* @retval 0 if the operation was successfully completed.
|
||||
* @retval -1 if an error occurred.
|
||||
*
|
||||
* @since October 2015
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
int grow_array(OBIDMS_array_p array);
|
||||
|
||||
|
||||
/**
|
||||
* PRIVATE
|
||||
* @brief Internal function enlarging a data array.
|
||||
*
|
||||
* @param array A pointer to the array structure.
|
||||
*
|
||||
* @retval 0 if the operation was successfully completed.
|
||||
* @retval -1 if an error occurred.
|
||||
*
|
||||
* @since October 2015
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
int grow_array_data(OBIDMS_array_p array);
|
||||
|
||||
|
||||
/**
|
||||
* PRIVATE
|
||||
* @brief Internal function comparing two byte arrays.
|
||||
*
|
||||
* The encoding is compared first, then the length of the
|
||||
* values, then the values themselves.
|
||||
*
|
||||
* @param value_1 A pointer to the first byte array.
|
||||
* @param value_2 A pointer to the second byte array.
|
||||
*
|
||||
* @returns A value < 0 if value_1 < value_2,
|
||||
* a value > 0 if value_1 > value_2,
|
||||
* and 0 if value_1 == value_2.
|
||||
*
|
||||
* @since October 2015
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
int array_compare(byte_t* value_1, byte_t* value_2);
|
||||
|
||||
|
||||
/**
|
||||
* PRIVATE
|
||||
* @brief Internal function calculating the size in bytes of a byte array.
|
||||
*
|
||||
* @param value A pointer to the byte array.
|
||||
*
|
||||
* @returns The size of the byte array in bytes.
|
||||
*
|
||||
* @since October 2015
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
int32_t array_sizeof(byte_t* value); // TODO not sure about type
|
||||
size_t array_sizeof(byte_t* value); // TODO not sure about type
|
||||
|
||||
|
||||
/************************************************************************
|
||||
@ -170,33 +232,6 @@ static char* build_array_data_file_name(const char* array_name)
|
||||
}
|
||||
|
||||
|
||||
static char* build_array_file_path(OBIDMS_p dms, const char* array_name) // TODO store DIR in dms structure
|
||||
{
|
||||
char* array_file_path;
|
||||
char* array_file_name;
|
||||
|
||||
// Build the array file name
|
||||
array_file_name = build_array_file_name(array_name);
|
||||
if (array_file_name == NULL)
|
||||
return NULL;
|
||||
|
||||
// TODO use get_full_path(int directory_file_descriptor, const char* path_name)
|
||||
array_file_path = (char*) malloc((strlen(dms->directory_name) + strlen("/arrays/") + strlen(array_file_name) + 1) * sizeof(char));
|
||||
if (array_file_path == NULL)
|
||||
{
|
||||
obi_set_errno(OBI_ARRAY_ERROR);
|
||||
obidebug(1, "\nError building an array file path");
|
||||
return NULL;
|
||||
}
|
||||
|
||||
strcpy(array_file_path, dms->directory_name);
|
||||
strcat(array_file_path, "/arrays/");
|
||||
strcat(array_file_path, array_file_name);
|
||||
|
||||
return array_file_path;
|
||||
}
|
||||
|
||||
|
||||
size_t get_array_header_size()
|
||||
{
|
||||
return getpagesize() * 1;
|
||||
@ -272,7 +307,7 @@ int grow_array(OBIDMS_array_p array) // TODO Lock when needed
|
||||
return -1;
|
||||
}
|
||||
|
||||
// Open the array data file
|
||||
// Open the array file
|
||||
array_file_descriptor = openat(array_dir_file_descriptor, array_file_name, O_RDWR);
|
||||
if (array_file_descriptor < 0)
|
||||
{
|
||||
@ -285,7 +320,7 @@ int grow_array(OBIDMS_array_p array) // TODO Lock when needed
|
||||
free(array_file_name);
|
||||
|
||||
// Calculate the new file size
|
||||
old_data_size = ((array->header)->nb_items_max) * sizeof(index_t);
|
||||
old_data_size = (array->header)->array_size;
|
||||
new_data_size = old_data_size * ARRAY_GROWTH_FACTOR;
|
||||
header_size = (array->header)->header_size;
|
||||
file_size = header_size + new_data_size;
|
||||
@ -331,8 +366,11 @@ int grow_array(OBIDMS_array_p array) // TODO Lock when needed
|
||||
// Set new maximum number of items
|
||||
(array->header)->nb_items_max = ceil(((double) new_data_size) / ((double) sizeof(index_t)));
|
||||
|
||||
// Set the new array size
|
||||
(array->header)->array_size = new_data_size;
|
||||
|
||||
// Initialize new data to 0
|
||||
memset((array->first)+old_data_size, 0, new_data_size - old_data_size);
|
||||
memset(((uint8_t*)(array->first))+old_data_size, 0, (new_data_size-old_data_size));
|
||||
|
||||
close(array_file_descriptor);
|
||||
|
||||
@ -343,8 +381,8 @@ int grow_array(OBIDMS_array_p array) // TODO Lock when needed
|
||||
int grow_array_data(OBIDMS_array_p array) // TODO Lock when needed
|
||||
{
|
||||
size_t file_size;
|
||||
size_t old_data_size;
|
||||
size_t new_data_size;
|
||||
index_t old_data_size;
|
||||
index_t new_data_size;
|
||||
size_t header_size;
|
||||
int array_dir_file_descriptor;
|
||||
int array_data_file_descriptor;
|
||||
@ -444,7 +482,7 @@ int array_compare(byte_t* value_1, byte_t* value_2)
|
||||
int32_t len_2;
|
||||
int32_t b;
|
||||
|
||||
obidebug(1, "\nCOMPARING 1=%d,%.*s; 2=%d,%.*s", (int32_t) *(value_1+1), (int32_t) *(value_1+1), value_1+5, (int32_t) *(value_2+1), (int32_t) *(value_2+1), value_2+5);
|
||||
//obidebug(1, "\nCOMPARING 1=%d,%.*s; 2=%d,%.*s", *((int32_t*)(value_1+1)), *((int32_t*)(value_1+1)), value_1+BYTE_ARRAY_HEADER_SIZE, *((int32_t*)(value_2+1)), *((int32_t*)(value_2+1)), value_2+BYTE_ARRAY_HEADER_SIZE);
|
||||
|
||||
size_1 = (uint8_t) *(value_1);
|
||||
size_2 = (uint8_t) *(value_2);
|
||||
@ -452,31 +490,26 @@ int array_compare(byte_t* value_1, byte_t* value_2)
|
||||
if (size_1 != size_2)
|
||||
return (size_1 - size_2);
|
||||
|
||||
len_1 = (int32_t) *(value_1+1);
|
||||
len_2 = (int32_t) *(value_2+1);
|
||||
|
||||
obidebug(1, "\ncomp length = %d - %d = %d", len_1, len_2, (len_1 - len_2));
|
||||
len_1 = *((int32_t*)(value_1+1));
|
||||
len_2 = *((int32_t*)(value_2+1));
|
||||
|
||||
if (len_1 != len_2)
|
||||
return (len_1 - len_2);
|
||||
|
||||
b = 0;
|
||||
b = BYTE_ARRAY_HEADER_SIZE;
|
||||
comp = 0;
|
||||
while (!comp && (b < len_1))
|
||||
while (!comp && (b < len_1+BYTE_ARRAY_HEADER_SIZE))
|
||||
{
|
||||
comp = *(value_1+b) - *(value_2+b);
|
||||
b++;
|
||||
}
|
||||
|
||||
obidebug(1, "\ncomp = %d", comp);
|
||||
|
||||
return comp;
|
||||
}
|
||||
|
||||
|
||||
int32_t array_sizeof(byte_t* value)
|
||||
size_t array_sizeof(byte_t* value)
|
||||
{
|
||||
return (6 + (int32_t) *(value+1));
|
||||
return (BYTE_ARRAY_HEADER_SIZE + *((int32_t*)(value+1)) + 1);
|
||||
}
|
||||
|
||||
|
||||
@ -490,14 +523,39 @@ int obi_array_exists(OBIDMS_p dms, const char* array_name)
|
||||
{
|
||||
struct stat buffer;
|
||||
char* array_file_path;
|
||||
char* array_file_name;
|
||||
int check_dir;
|
||||
int array_dir_file_descriptor;
|
||||
|
||||
// Get the file descriptor of the array directory
|
||||
array_dir_file_descriptor = dirfd(dms->array_directory);
|
||||
if (array_dir_file_descriptor < 0)
|
||||
{
|
||||
obi_set_errno(OBI_ARRAY_ERROR);
|
||||
obidebug(1, "\nError getting the file descriptor for an array directory");
|
||||
return -1;
|
||||
}
|
||||
|
||||
// Build file name
|
||||
array_file_name = build_array_file_name(array_name);
|
||||
if (array_file_name == NULL)
|
||||
{
|
||||
close(array_dir_file_descriptor);
|
||||
return -1;
|
||||
}
|
||||
|
||||
// Build the array file path
|
||||
array_file_path = build_array_file_path(dms, array_name);
|
||||
array_file_path = get_full_path(array_dir_file_descriptor, array_file_name);
|
||||
if (array_file_path == NULL)
|
||||
{
|
||||
obidebug(1, "\nError getting the file path for an array file");
|
||||
return -1;
|
||||
}
|
||||
|
||||
check_dir = stat(array_file_path, &buffer);
|
||||
|
||||
free(array_file_path);
|
||||
free(array_file_name);
|
||||
|
||||
if (check_dir == 0)
|
||||
return 1;
|
||||
@ -549,8 +607,6 @@ OBIDMS_array_p obi_create_array(OBIDMS_p dms, const char* array_name)
|
||||
return NULL;
|
||||
}
|
||||
|
||||
obidebug(1, "\nboom");
|
||||
|
||||
// Build file name
|
||||
array_data_file_name = build_array_data_file_name(array_name);
|
||||
if (array_data_file_name == NULL)
|
||||
@ -559,8 +615,6 @@ OBIDMS_array_p obi_create_array(OBIDMS_p dms, const char* array_name)
|
||||
return NULL;
|
||||
}
|
||||
|
||||
obidebug(1, "\nboom");
|
||||
|
||||
// Create file
|
||||
array_data_file_descriptor = openat(array_dir_file_descriptor, array_data_file_name, O_RDWR | O_CREAT | O_EXCL, 0777);
|
||||
if (array_data_file_descriptor < 0)
|
||||
@ -719,7 +773,7 @@ OBIDMS_array_p obi_create_array(OBIDMS_p dms, const char* array_name)
|
||||
return NULL;
|
||||
}
|
||||
|
||||
array->first = mmap(NULL,
|
||||
array->first = mmap(NULL,
|
||||
data_size,
|
||||
PROT_READ | PROT_WRITE,
|
||||
MAP_SHARED,
|
||||
@ -742,6 +796,7 @@ OBIDMS_array_p obi_create_array(OBIDMS_p dms, const char* array_name)
|
||||
array->directory = dms->array_directory;
|
||||
|
||||
(array->header)->header_size = header_size;
|
||||
(array->header)->array_size = data_size;
|
||||
(array->header)->nb_items = 0;
|
||||
(array->header)->nb_items_max = (index_t) ceil(((double) get_initial_array_size()) / ((double) sizeof(index_t)));
|
||||
(array->header)->creation_date = time(NULL);
|
||||
@ -751,7 +806,6 @@ OBIDMS_array_p obi_create_array(OBIDMS_p dms, const char* array_name)
|
||||
memset(array->first, 0, data_size);
|
||||
|
||||
close(array_file_descriptor);
|
||||
//close(array_dir_file_descriptor); TODO
|
||||
|
||||
return array;
|
||||
}
|
||||
@ -929,7 +983,6 @@ OBIDMS_array_p obi_open_array(OBIDMS_p dms, const char* array_name)
|
||||
array->directory = dms->array_directory;
|
||||
|
||||
close(array_file_descriptor);
|
||||
//close(array_dir_file_descriptor); TODO
|
||||
|
||||
return array;
|
||||
}
|
||||
@ -961,29 +1014,17 @@ int obi_close_array(OBIDMS_array_p array)
|
||||
}
|
||||
|
||||
|
||||
//int obi_delete_array(const char* array_name)
|
||||
//{
|
||||
//
|
||||
//}
|
||||
|
||||
|
||||
index_t obi_array_add(OBIDMS_array_p array, byte_t* value)
|
||||
{
|
||||
index_t idx;
|
||||
index_t nb_items;
|
||||
index_t nb_items_max;
|
||||
index_t* a;
|
||||
byte_t* data;
|
||||
int64_t data_size_used;
|
||||
int64_t* data_size_max_p;
|
||||
int32_t value_size;
|
||||
|
||||
obidebug(1, "\n");
|
||||
index_t idx;
|
||||
index_t nb_items;
|
||||
index_t nb_items_max;
|
||||
index_t data_size_used;
|
||||
index_t* data_size_max_p;
|
||||
size_t value_size;
|
||||
|
||||
nb_items = (array->header)->nb_items;
|
||||
nb_items_max = (array->header)->nb_items_max;
|
||||
a = array->first;
|
||||
data = (array->data)->data;
|
||||
data_size_used = ((array->data)->header)->data_size_used;
|
||||
data_size_max_p = &(((array->data)->header)->data_size_max);
|
||||
|
||||
@ -999,8 +1040,6 @@ index_t obi_array_add(OBIDMS_array_p array, byte_t* value)
|
||||
else // First item
|
||||
idx = 0;
|
||||
|
||||
obidebug(1, "\n");
|
||||
|
||||
// Grow the array if needed
|
||||
if (nb_items == nb_items_max)
|
||||
{
|
||||
@ -1008,37 +1047,22 @@ index_t obi_array_add(OBIDMS_array_p array, byte_t* value)
|
||||
return -1;
|
||||
}
|
||||
|
||||
obidebug(1, "\n");
|
||||
|
||||
// Grow the data if needed
|
||||
value_size = array_sizeof(value);
|
||||
while (*data_size_max_p < (data_size_used + value_size))
|
||||
while (*data_size_max_p < (data_size_used + value_size)) // TODO problem with types
|
||||
{
|
||||
if (grow_array_data(array) < 0)
|
||||
return -1;
|
||||
}
|
||||
|
||||
obidebug(1, "\nidx = %d", idx);
|
||||
// Store the index of the value in the array
|
||||
|
||||
// Add the index of the value in the array
|
||||
memmove((a+idx+1), (a+idx), ((nb_items - idx) * sizeof(index_t)));
|
||||
a[idx] = data_size_used;
|
||||
|
||||
int i;
|
||||
for (i=0; i<nb_items; i++)
|
||||
fprintf(stderr, "\narray[%d] = %d\n", i, a[i]);
|
||||
|
||||
//fprintf(stderr, "\nBEFORE COPY DATA+5=%.5s, DATA+14=%.5s\n", data+5, data+14);
|
||||
//fprintf(stderr, "\nBEFORE COPY DATA+8=%s\n", data+8);
|
||||
|
||||
fprintf(stderr, "\ndata size used = %lld, value size = %d", data_size_used, value_size);
|
||||
if (nb_items > 0)
|
||||
memmove(((array->first)+idx+1), ((array->first)+idx), ((nb_items - idx) * sizeof(index_t)));
|
||||
(array->first)[idx] = data_size_used;
|
||||
|
||||
// Store the value itself at the end of the data
|
||||
memcpy((data+data_size_used), value, value_size);
|
||||
|
||||
//fprintf(stderr, "\nAFTER COPY DATA+8=%s\n", data+8);
|
||||
|
||||
//fprintf(stderr, "\nAFTER COPY DATA+5=%.4s, DATA+14=%.5s\n", data+5, data+14);
|
||||
memcpy((((array->data)->data)+data_size_used), value, value_size);
|
||||
|
||||
// Update the data size
|
||||
((array->data)->header)->data_size_used = data_size_used + value_size;
|
||||
@ -1047,18 +1071,18 @@ index_t obi_array_add(OBIDMS_array_p array, byte_t* value)
|
||||
((array->header)->nb_items)++;
|
||||
(((array->data)->header)->nb_items)++;
|
||||
|
||||
//obidebug(1, "\nSHOULD ++ : %d", (array->header)->nb_items);
|
||||
|
||||
for (i=0; i<(array->header)->nb_items; i++)
|
||||
fprintf(stderr, "\narray[%d] = %d\n", i, a[i]);
|
||||
|
||||
fprintf(stderr, "\nreturning %lld\n", data_size_used);
|
||||
// PRINT ARRAY
|
||||
// fprintf(stderr, "\nARRAY:");
|
||||
// int i;
|
||||
// for (i=0; i<=nb_items; i++)
|
||||
// fprintf(stderr, "\narray[%d] = %d -> %s", i, a[i], data+a[i]+BYTE_ARRAY_HEADER_SIZE);
|
||||
|
||||
// Return the data index of the value
|
||||
return data_size_used;
|
||||
}
|
||||
|
||||
|
||||
byte_t* obi_array_get(OBIDMS_array_p array, index_t idx) // TODO copy?
|
||||
byte_t* obi_array_get(OBIDMS_array_p array, index_t idx)
|
||||
{
|
||||
return (((array->data)->data)+idx);
|
||||
}
|
||||
@ -1080,48 +1104,37 @@ index_t obi_array_search(OBIDMS_array_p array, byte_t* value)
|
||||
data = (array->data)->data;
|
||||
a = array->first;
|
||||
|
||||
obidebug(1, "\nnb items = %d", nb_items);
|
||||
|
||||
if (nb_items == 0)
|
||||
return 0;
|
||||
return -1;
|
||||
|
||||
idx_max = nb_items;
|
||||
idx_max = nb_items-1;
|
||||
idx_min = 0;
|
||||
|
||||
obidebug(1, "\n");
|
||||
|
||||
while (idx_min < idx_max)
|
||||
while (idx_min <= idx_max)
|
||||
{
|
||||
idx_mid = nb_items/2;
|
||||
|
||||
obidebug(1, "\ncomparing with idx = %d, data idx %d", idx_mid, a[idx_mid]);
|
||||
//fprintf(stderr, "\ndata+14=%.5s\n", data+14);
|
||||
|
||||
idx_mid = (idx_min+idx_max)/2;
|
||||
to_compare = obi_array_get(array, a[idx_mid]);
|
||||
|
||||
//fprintf(stderr, "\nto_compare=%.5s\n", to_compare+5);
|
||||
|
||||
comp = array_compare(to_compare, value);
|
||||
|
||||
obidebug(1, "\nCOMP = %d", comp);
|
||||
|
||||
if (!comp)
|
||||
{
|
||||
// Found
|
||||
return a[idx_mid];
|
||||
}
|
||||
else if (comp < 0)
|
||||
{
|
||||
idx = idx_mid + 1;
|
||||
// Search in upper half
|
||||
idx = idx_mid + 1;
|
||||
idx_min = idx_mid + 1;
|
||||
}
|
||||
else
|
||||
idx = idx_mid;
|
||||
{
|
||||
// Search in lower half
|
||||
idx = idx_mid;
|
||||
idx_max = idx_mid - 1;
|
||||
}
|
||||
}
|
||||
|
||||
obidebug(1, "\nNOT FOUND, idx=%d", idx);
|
||||
|
||||
// Not found: return where the value should be
|
||||
// Not found: return where the value should be in the array
|
||||
return -(idx+1);
|
||||
}
|
||||
|
||||
@ -1134,7 +1147,7 @@ byte_t* obi_str_to_obibytes(char* value)
|
||||
|
||||
size = 8;
|
||||
length = strlen(value);
|
||||
value_b = (byte_t*) malloc(length + 6);
|
||||
value_b = (byte_t*) malloc(length + BYTE_ARRAY_HEADER_SIZE + 1);
|
||||
if (value_b == NULL)
|
||||
{
|
||||
obi_set_errno(OBI_ARRAY_ERROR);
|
||||
@ -1143,11 +1156,10 @@ byte_t* obi_str_to_obibytes(char* value)
|
||||
}
|
||||
|
||||
*(value_b) = size;
|
||||
*(value_b+1) = length;
|
||||
|
||||
strcpy(value_b+5, value);
|
||||
*((int32_t*)(value_b+1)) = length;
|
||||
|
||||
// TODO 5 as macro
|
||||
strcpy(value_b+BYTE_ARRAY_HEADER_SIZE, value);
|
||||
|
||||
return value_b;
|
||||
}
|
||||
@ -1157,17 +1169,8 @@ const char* obi_obibytes_to_str(byte_t* value_b)
|
||||
{
|
||||
const char* value;
|
||||
|
||||
value = value_b+5;
|
||||
|
||||
obidebug(1, "\nvalue = %s", value);
|
||||
|
||||
// TODO 5 as macro
|
||||
value = value_b+BYTE_ARRAY_HEADER_SIZE;
|
||||
|
||||
return value;
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
152
src/obiarray.h
152
src/obiarray.h
@ -3,15 +3,15 @@
|
||||
****************************************************************************/
|
||||
|
||||
/**
|
||||
* @file array.h
|
||||
* @file obiarray.h
|
||||
* @author Celine Mercier
|
||||
* @date October 19th 2015
|
||||
* @brief Header file for handling arrays for storing and retrieving data arrays (i.e. character strings).
|
||||
* @brief Header file for handling arrays for storing and retrieving byte arrays (i.e. coding for character strings).
|
||||
*/
|
||||
|
||||
|
||||
#ifndef ARRAY_H_
|
||||
#define ARRAY_H_
|
||||
#ifndef OBIARRAY_H_
|
||||
#define OBIARRAY_H_
|
||||
|
||||
|
||||
#include <stdlib.h>
|
||||
@ -29,9 +29,10 @@
|
||||
*/
|
||||
#define ARRAY_GROWTH_FACTOR (2) /**< The growth factor when an array is enlarged.
|
||||
*/
|
||||
#define BYTE_ARRAY_HEADER_SIZE (5) /**< The size of the header of a byte array.
|
||||
*/
|
||||
|
||||
|
||||
typedef int32_t index_t; /**< Type of the array indices.
|
||||
*/
|
||||
typedef char byte_t; /**< Defining byte type since data is stored in bits
|
||||
* and char (stored on one byte) is the smallest addressable unit.
|
||||
*/
|
||||
@ -43,9 +44,9 @@ typedef char byte_t; /**< Defining byte type since data is stored in bits
|
||||
typedef struct OBIDMS_array_data_header {
|
||||
int header_size; /**< Size of the header in bytes.
|
||||
*/
|
||||
int64_t data_size_used; /**< Size of the data used in bytes. // TODO not sure about type
|
||||
index_t data_size_used; /**< Size of the data used in bytes.
|
||||
*/
|
||||
int64_t data_size_max; /**< Max size of the data in bytes. // TODO not sure about type
|
||||
index_t data_size_max; /**< Max size of the data in bytes.
|
||||
*/
|
||||
index_t nb_items; /**< Number of items.
|
||||
*/
|
||||
@ -73,6 +74,8 @@ typedef struct OBIDMS_array_data {
|
||||
typedef struct OBIDMS_array_header {
|
||||
int header_size; /**< Size of the header in bytes.
|
||||
*/
|
||||
size_t array_size; /**< Size of the array in bytes.
|
||||
*/
|
||||
index_t nb_items; /**< Number of items in the array.
|
||||
*/
|
||||
index_t nb_items_max; /**< Maximum number of items in the array before it has to be enlarged.
|
||||
@ -102,76 +105,181 @@ typedef struct OBIDMS_array {
|
||||
|
||||
|
||||
/**
|
||||
* @brief Checks if an obiarray already exists or not.
|
||||
*
|
||||
* @param dms The OBIDMS to which the obiarray belongs.
|
||||
* @param array_name The name of the obiarray.
|
||||
*
|
||||
* @returns A value indicating whether the obiarray exists or not.
|
||||
* @retval 1 if the obiarray exists.
|
||||
* @retval 0 if the obiarray does not exist.
|
||||
* @retval -1 if an error occurred.
|
||||
*
|
||||
* @since October 2015
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
int obi_array_exists(OBIDMS_p dms, const char* array_name);
|
||||
|
||||
|
||||
/**
|
||||
* @brief Opens an obiarray and creates it if it does not already exist.
|
||||
*
|
||||
* Note: An obiarray is made of two files (referred to by two structures).
|
||||
* One file contains the indices referring to the data, and the other
|
||||
* file contains the data itself. The obiarray as a whole is referred
|
||||
* to via the OBIDMS_array structure.
|
||||
*
|
||||
* @param dms The OBIDMS to which the obiarray belongs.
|
||||
* @param array_name The name of the obiarray.
|
||||
*
|
||||
* @returns A pointer to the obiarray structure.
|
||||
* @retval NULL if an error occurred.
|
||||
*
|
||||
* @since October 2015
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
OBIDMS_array_p obi_array(OBIDMS_p dms, const char* array_name);
|
||||
|
||||
|
||||
/**
|
||||
* @brief Creates an obiarray. Fails if it already exists.
|
||||
*
|
||||
* Note: An obiarray is made of two files (referred to by two structures).
|
||||
* One file contains the indices referring to the data, and the other
|
||||
* file contains the data itself. The obiarray as a whole is referred
|
||||
* to via the OBIDMS_array structure.
|
||||
*
|
||||
* @param dms The OBIDMS to which the obiarray belongs.
|
||||
* @param array_name The name of the obiarray.
|
||||
*
|
||||
* @returns A pointer to the newly created obiarray structure.
|
||||
* @retval NULL if an error occurred.
|
||||
*
|
||||
* @since October 2015
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
OBIDMS_array_p obi_create_array(OBIDMS_p dms, const char* array_name);
|
||||
|
||||
|
||||
/**
|
||||
* @brief Opens an obiarray. Fails if it does not already exist.
|
||||
*
|
||||
* Note: An obiarray is made of two files (referred to by two structures).
|
||||
* One file contains the indices referring to the data, and the other
|
||||
* file contains the data itself. The obiarray as a whole is referred
|
||||
* to via the OBIDMS_array structure.
|
||||
*
|
||||
* @param dms The OBIDMS to which the obiarray belongs.
|
||||
* @param array_name The name of the obiarray.
|
||||
*
|
||||
* @returns A pointer to the obiarray structure.
|
||||
* @retval NULL if an error occurred.
|
||||
*
|
||||
* @since October 2015
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
OBIDMS_array_p obi_open_array(OBIDMS_p dms, const char* array_name);
|
||||
|
||||
|
||||
/**
|
||||
* @brief Closes an obiarray.
|
||||
*
|
||||
* Note: An obiarray is made of two files (referred to by two structures).
|
||||
* One file contains the indices referring to the data, and the other
|
||||
* file contains the data itself. The obiarray as a whole is referred
|
||||
* to via the OBIDMS_array structure.
|
||||
*
|
||||
* @param array A pointer to the obiarray structure to close and free.
|
||||
*
|
||||
* @retval 0 if the operation was successfully completed.
|
||||
* @retval -1 if an error occurred.
|
||||
*
|
||||
* @since October 2015
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
int obi_close_array(OBIDMS_array_p array);
|
||||
|
||||
|
||||
/**
|
||||
* @brief Adds a value (byte array) in an obiarray, checking first if it is already in it.
|
||||
*
|
||||
*/
|
||||
//int obi_delete_array(OBIDMS_p dms, const char* array_name);
|
||||
|
||||
|
||||
/**
|
||||
* The header is already in the byte array
|
||||
* @warning The byte array to add must already be encoded and contain its header.
|
||||
*
|
||||
* @param array A pointer to the obiarray.
|
||||
* @param value The byte array to add in the obiarray.
|
||||
*
|
||||
* @returns The index of the value, whether it was added or already in the obiarray.
|
||||
* @retval -1 if an error occurred.
|
||||
*
|
||||
* @since October 2015
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
index_t obi_array_add(OBIDMS_array_p array, byte_t* value);
|
||||
|
||||
|
||||
/**
|
||||
* Returns the entire array including the header
|
||||
* @brief Recovers a value (byte array) in an obiarray.
|
||||
*
|
||||
* @warning The byte array recovered is encoded and contains its header.
|
||||
*
|
||||
* @param array A pointer to the obiarray.
|
||||
* @param index The index of the value in the data array.
|
||||
*
|
||||
* @returns A pointer to the byte array recovered.
|
||||
*
|
||||
* @since October 2015
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
byte_t* obi_array_get(OBIDMS_array_p array, index_t index);
|
||||
|
||||
|
||||
/**
|
||||
* @brief Searches a value (byte array) in an obiarray performing a binary search.
|
||||
*
|
||||
* @warning The byte array to search must already be encoded and contain its header.
|
||||
*
|
||||
* @param array A pointer to the obiarray.
|
||||
* @param value The byte array to add in the obiarray.
|
||||
*
|
||||
* @returns If the value is found, its data index is returned.
|
||||
* If the value is not found, the array index indicating where the value's data index
|
||||
* should be in the array is returned in the form (- (index + 1)), as data indices in an
|
||||
* obiarray are sorted according to the ascending order of the values (byte arrays) themselves.
|
||||
*
|
||||
* @since October 2015
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
index_t obi_array_search(OBIDMS_array_p array, byte_t* value);
|
||||
|
||||
|
||||
/**
|
||||
* @brief Converts a character string to a byte array with a header.
|
||||
*
|
||||
* @warning The byte array must be freed by the caller.
|
||||
*
|
||||
* @param value The character string to convert.
|
||||
*
|
||||
* @returns A pointer to the byte array created.
|
||||
* @retval NULL if an error occurred.
|
||||
*
|
||||
* @since October 2015
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
byte_t* obi_str_to_obibytes(char* value);
|
||||
|
||||
|
||||
/**
|
||||
* @brief Converts a byte array to a character string.
|
||||
*
|
||||
* @param value_b The byte array to convert.
|
||||
*
|
||||
* @returns A pointer to the character string contained in the byte array.
|
||||
*
|
||||
* @since October 2015
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
const char* obi_obibytes_to_str(byte_t* value_b);
|
||||
|
||||
|
||||
/**
|
||||
* TODO LATER
|
||||
*/
|
||||
// OBIDMS_array_p obi_column_arrayify(FILE, encoding);
|
||||
|
||||
|
||||
#endif /* ARRAY_H_ */
|
||||
#endif /* OBIARRAY_H_ */
|
||||
|
||||
|
||||
@ -163,8 +163,6 @@ OBIDMS_p obi_create_dms(const char* dms_name)
|
||||
return NULL;
|
||||
}
|
||||
|
||||
// TODO close file descriptor?
|
||||
|
||||
free(directory_name);
|
||||
|
||||
return obi_open_dms(dms_name);
|
||||
@ -247,8 +245,6 @@ OBIDMS_p obi_open_dms(const char* dms_name)
|
||||
|
||||
free(directory_name);
|
||||
|
||||
// TODO test if close file descriptor
|
||||
|
||||
return dms;
|
||||
}
|
||||
|
||||
|
||||
@ -72,6 +72,8 @@ int obi_dms_exists(const char* dms_name);
|
||||
* if a directory with this name does not already exist
|
||||
* before creating the new database.
|
||||
*
|
||||
* A directory to store obiarrays is also created.
|
||||
*
|
||||
* @param dms_name A pointer to a C string containing the name of the database.
|
||||
* The actual directory name used to store the DMS will be
|
||||
* `<dms_name>.obidms`.
|
||||
|
||||
@ -143,7 +143,7 @@ static int obi_column_set_elements_names(OBIDMS_column_p column, const char* ele
|
||||
* @since September 2015
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
static size_t get_line_count_per_page(OBIType_t data_type, size_t nb_elements_per_line);
|
||||
static index_t get_line_count_per_page(OBIType_t data_type, index_t nb_elements_per_line);
|
||||
|
||||
|
||||
/************************************************************************
|
||||
@ -463,7 +463,7 @@ int obi_column_set_elements_names(OBIDMS_column_p column, const char* elements_n
|
||||
return 0;
|
||||
}
|
||||
|
||||
size_t get_line_count_per_page(OBIType_t data_type, size_t nb_elements_per_line)
|
||||
index_t get_line_count_per_page(OBIType_t data_type, index_t nb_elements_per_line)
|
||||
{
|
||||
return getpagesize() / (obi_sizeof(data_type) * nb_elements_per_line);
|
||||
}
|
||||
@ -595,15 +595,15 @@ obiversion_t obi_column_get_latest_version_from_name(OBIDMS_p dms, const char* c
|
||||
|
||||
size_t obi_get_platform_header_size()
|
||||
{
|
||||
return getpagesize() * 1;
|
||||
return getpagesize() * 2;
|
||||
}
|
||||
|
||||
|
||||
OBIDMS_column_p obi_create_column(OBIDMS_p dms,
|
||||
const char* column_name,
|
||||
OBIType_t data_type,
|
||||
size_t nb_lines,
|
||||
size_t nb_elements_per_line,
|
||||
index_t nb_lines,
|
||||
index_t nb_elements_per_line,
|
||||
const char* elements_names,
|
||||
const char* array_name)
|
||||
{
|
||||
@ -618,7 +618,7 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
|
||||
int column_dir_file_descriptor;
|
||||
size_t header_size;
|
||||
size_t data_size;
|
||||
size_t minimum_line_count;
|
||||
index_t minimum_line_count;
|
||||
|
||||
new_column = NULL;
|
||||
|
||||
@ -664,7 +664,7 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
|
||||
else if ((elements_names != NULL) && (nb_elements_per_line > 1))
|
||||
{
|
||||
char* token;
|
||||
size_t n = 0;
|
||||
index_t n = 0;
|
||||
token = strdup(elements_names);
|
||||
token = strtok(token, ";");
|
||||
while (token != NULL)
|
||||
@ -989,8 +989,8 @@ OBIDMS_column_p obi_clone_column(OBIDMS_p dms,
|
||||
{
|
||||
OBIDMS_column_p column_to_clone;
|
||||
OBIDMS_column_p new_column;
|
||||
size_t nb_lines;
|
||||
size_t nb_elements_per_line;
|
||||
index_t nb_lines;
|
||||
index_t nb_elements_per_line;
|
||||
size_t data_size;
|
||||
OBIType_t data_type;
|
||||
|
||||
@ -1083,7 +1083,7 @@ int obi_truncate_column_to_lines_used(OBIDMS_column_p column) // TODO is it nece
|
||||
{
|
||||
size_t file_size;
|
||||
size_t data_size;
|
||||
size_t new_line_count;
|
||||
index_t new_line_count;
|
||||
double multiple;
|
||||
int column_dir_file_descriptor;
|
||||
int column_file_descriptor;
|
||||
@ -1180,8 +1180,8 @@ int obi_enlarge_column(OBIDMS_column_p column)
|
||||
size_t old_data_size;
|
||||
size_t new_data_size;
|
||||
size_t header_size;
|
||||
size_t old_line_count;
|
||||
size_t new_line_count;
|
||||
index_t old_line_count;
|
||||
index_t new_line_count;
|
||||
int column_dir_file_descriptor;
|
||||
int column_file_descriptor;
|
||||
char* column_file_name;
|
||||
@ -1316,10 +1316,10 @@ int obi_truncate_and_close_column(OBIDMS_column_p column)
|
||||
|
||||
|
||||
void obi_ini_to_NA_values(OBIDMS_column_p column,
|
||||
size_t first_line_nb,
|
||||
size_t nb_lines)
|
||||
index_t first_line_nb,
|
||||
index_t nb_lines)
|
||||
{
|
||||
size_t i, start, end, nb_elements;
|
||||
index_t i, start, end, nb_elements;
|
||||
|
||||
nb_elements = nb_lines*((column->header)->nb_elements_per_line);
|
||||
start = first_line_nb*((column->header)->nb_elements_per_line);
|
||||
@ -1355,14 +1355,14 @@ void obi_ini_to_NA_values(OBIDMS_column_p column,
|
||||
|
||||
case OBI_IDX: for (i=start;i<end;i++)
|
||||
{
|
||||
*(((obiidx_t*) (column->data)) + i) = OBIIdx_NA;
|
||||
*(((index_t*) (column->data)) + i) = OBIIdx_NA;
|
||||
}
|
||||
break;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
OBIDMS_column_header_p obi_column_get_header_from_name(OBIDMS_p dms, const char* column_name) // ADD VERSION ARGUMENT
|
||||
OBIDMS_column_header_p obi_column_get_header_from_name(OBIDMS_p dms, const char* column_name) // TODO ADD VERSION ARGUMENT
|
||||
{
|
||||
OBIDMS_column_header_p header;
|
||||
OBIDMS_column_directory_p column_directory;
|
||||
@ -1391,7 +1391,7 @@ OBIDMS_column_header_p obi_column_get_header_from_name(OBIDMS_p dms, const char*
|
||||
}
|
||||
|
||||
// Calculate the header size
|
||||
header_size = obi_get_platform_header_size();
|
||||
header_size = obi_get_platform_header_size(); // TODO read in header itself
|
||||
|
||||
// Get the latest version number
|
||||
version_number = obi_get_latest_version_number(column_directory);
|
||||
@ -1458,17 +1458,17 @@ int obi_unmap_header(OBIDMS_column_header_p header)
|
||||
|
||||
|
||||
// TODO to be rewritten in an optimized and safe way
|
||||
size_t obi_column_get_element_index_from_name(OBIDMS_column_p column, const char* element_name)
|
||||
index_t obi_column_get_element_index_from_name(OBIDMS_column_p column, const char* element_name)
|
||||
{
|
||||
char* elements_names;
|
||||
char* name;
|
||||
size_t element_index;
|
||||
index_t element_index;
|
||||
|
||||
elements_names = strdup((column->header)->elements_names);
|
||||
if (elements_names == NULL)
|
||||
{
|
||||
obidebug(1, "\nError strdup-ing the elements names");
|
||||
return SIZE_MAX; //TODO
|
||||
return OBIIdx_NA;
|
||||
}
|
||||
|
||||
element_index = 0;
|
||||
@ -1494,7 +1494,7 @@ size_t obi_column_get_element_index_from_name(OBIDMS_column_p column, const char
|
||||
|
||||
obidebug(1, "\nCan't find an element name");
|
||||
free(elements_names);
|
||||
return SIZE_MAX; //TODO
|
||||
return OBIIdx_NA;
|
||||
}
|
||||
|
||||
|
||||
|
||||
@ -53,13 +53,13 @@ typedef struct OBIDMS_column_header {
|
||||
* - `false` on big endian platforms
|
||||
* @see obi_is_little_endian()
|
||||
*/
|
||||
int header_size; /**< Size of the header in bytes.
|
||||
size_t header_size; /**< Size of the header in bytes.
|
||||
*/
|
||||
size_t line_count; /**< Number of lines of data allocated.
|
||||
index_t line_count; /**< Number of lines of data allocated.
|
||||
*/
|
||||
size_t lines_used; /**< Number of lines of data used.
|
||||
index_t lines_used; /**< Number of lines of data used.
|
||||
*/
|
||||
size_t nb_elements_per_line; /**< Number of elements per line (default: 1).
|
||||
index_t nb_elements_per_line; /**< Number of elements per line (default: 1).
|
||||
*/
|
||||
char elements_names[ELEMENTS_NAMES_MAX+1]; /**< Names of the line elements with ';' as separator
|
||||
* (should be the column name if one element per line).
|
||||
@ -149,7 +149,7 @@ obiversion_t obi_column_get_latest_version_from_name(OBIDMS_p dms, const char* c
|
||||
* The header size is defined as a multiple of the memory page size.
|
||||
* As of now the header size is defined as one time the page size.
|
||||
*
|
||||
* @returns a `size_t` value corresponding to the header size in bytes.
|
||||
* @returns The header size in bytes.
|
||||
*
|
||||
* @since May 2015
|
||||
* @author Eric Coissac (eric.coissac@metabarcoding.org)
|
||||
@ -161,6 +161,7 @@ size_t obi_get_platform_header_size();
|
||||
* @brief Creates a column.
|
||||
*
|
||||
* The minimum data size allocated is one memory page, and the data is initialized to the NA value of the OBIType.
|
||||
* If there is an array associated with the column, it is opened or created if it does not already exist.
|
||||
*
|
||||
* @warning If there is one element per line, elements_names should be equal to column_name. // TODO change this condition?
|
||||
*
|
||||
@ -170,6 +171,7 @@ size_t obi_get_platform_header_size();
|
||||
* @param nb_lines The number of lines to be stored.
|
||||
* @param nb_elements_per_line The number of elements per line.
|
||||
* @param elements_names The names of the elements with ';' as separator.
|
||||
* @param array_name The name of the array if there is one associated with the column.
|
||||
*
|
||||
* @returns A pointer on the newly created column structure.
|
||||
* @retval NULL if an error occurred.
|
||||
@ -180,8 +182,8 @@ size_t obi_get_platform_header_size();
|
||||
OBIDMS_column_p obi_create_column(OBIDMS_p dms,
|
||||
const char* column_name,
|
||||
OBIType_t data_type,
|
||||
size_t nb_lines,
|
||||
size_t nb_elements_per_line,
|
||||
index_t nb_lines,
|
||||
index_t nb_elements_per_line,
|
||||
const char* elements_names,
|
||||
const char* array_name);
|
||||
|
||||
@ -287,7 +289,7 @@ int obi_truncate_and_close_column(OBIDMS_column_p column);
|
||||
* @since August 2015
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
void obi_ini_to_NA_values(OBIDMS_column_p column, size_t first_line_nb, size_t nb_lines); // TO make private?
|
||||
void obi_ini_to_NA_values(OBIDMS_column_p column, index_t first_line_nb, index_t nb_lines); // TO make private?
|
||||
|
||||
|
||||
/**
|
||||
@ -333,7 +335,7 @@ int obi_unmap_header(OBIDMS_column_header_p header);
|
||||
* @since July 2015
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
size_t obi_column_get_element_index_from_name(OBIDMS_column_p column, const char* element_name);
|
||||
index_t obi_column_get_element_index_from_name(OBIDMS_column_p column, const char* element_name);
|
||||
|
||||
|
||||
/**
|
||||
|
||||
@ -28,7 +28,7 @@
|
||||
*
|
||||
**********************************************************************/
|
||||
|
||||
int obi_column_set_obibool_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obibool_t value)
|
||||
int obi_column_set_obibool_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, obibool_t value)
|
||||
{
|
||||
// Check that the line number is not greater than the maximum allowed
|
||||
if (line_nb >= MAXIMUM_LINE_COUNT)
|
||||
@ -57,7 +57,7 @@ int obi_column_set_obibool_with_elt_idx(OBIDMS_column_p column, size_t line_nb,
|
||||
}
|
||||
|
||||
|
||||
obibool_t obi_column_get_obibool_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx)
|
||||
obibool_t obi_column_get_obibool_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx)
|
||||
{
|
||||
if ((line_nb+1) > (column->header)->lines_used)
|
||||
{
|
||||
@ -69,23 +69,23 @@ obibool_t obi_column_get_obibool_with_elt_idx(OBIDMS_column_p column, size_t lin
|
||||
}
|
||||
|
||||
|
||||
int obi_column_set_obibool_with_elt_name(OBIDMS_column_p column, size_t line_nb, const char* element_name, obibool_t value)
|
||||
int obi_column_set_obibool_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, obibool_t value)
|
||||
{
|
||||
size_t element_idx;
|
||||
index_t element_idx;
|
||||
element_idx = obi_column_get_element_index_from_name(column, element_name);
|
||||
if (element_idx == SIZE_MAX) //TODO
|
||||
if (element_idx == OBIIdx_NA)
|
||||
return -1;
|
||||
obi_column_set_obibool_with_elt_idx(column, line_nb, element_idx, value);
|
||||
return 0;
|
||||
}
|
||||
|
||||
|
||||
obibool_t obi_column_get_obibool_with_elt_name(OBIDMS_column_p column, size_t line_nb, const char* element_name)
|
||||
obibool_t obi_column_get_obibool_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name)
|
||||
{
|
||||
size_t element_idx;
|
||||
index_t element_idx;
|
||||
|
||||
element_idx = obi_column_get_element_index_from_name(column, element_name);
|
||||
if (element_idx == SIZE_MAX) //TODO
|
||||
if (element_idx == OBIIdx_NA)
|
||||
return OBIBool_NA;
|
||||
return obi_column_get_obibool_with_elt_idx(column, line_nb, element_idx);
|
||||
}
|
||||
|
||||
@ -38,7 +38,7 @@
|
||||
* @since July 2015
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
int obi_column_set_obibool_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obibool_t value);
|
||||
int obi_column_set_obibool_with_elt_idx(OBIDMS_column_p column, index_t line_nb, size_t element_idx, obibool_t value);
|
||||
|
||||
|
||||
/**
|
||||
@ -54,7 +54,7 @@ int obi_column_set_obibool_with_elt_idx(OBIDMS_column_p column, size_t line_nb,
|
||||
* @since July 2015
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
obibool_t obi_column_get_obibool_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx);
|
||||
obibool_t obi_column_get_obibool_with_elt_idx(OBIDMS_column_p column, index_t line_nb, size_t element_idx);
|
||||
|
||||
|
||||
/**
|
||||
@ -66,7 +66,6 @@ obibool_t obi_column_get_obibool_with_elt_idx(OBIDMS_column_p column, size_t lin
|
||||
* @param column A pointer as returned by obi_create_column() or obi_clone_column().
|
||||
* @param line_nb The number of the line where the value should be set.
|
||||
* @param element_name The name of the element that should be set in the line.
|
||||
* If empty, it is checked that there is only one element per line.
|
||||
* @param value The value that should be set.
|
||||
*
|
||||
* @returns An integer value indicating the success of the operation.
|
||||
@ -76,7 +75,7 @@ obibool_t obi_column_get_obibool_with_elt_idx(OBIDMS_column_p column, size_t lin
|
||||
* @since August 2015
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
int obi_column_set_obibool_with_elt_name(OBIDMS_column_p column, size_t line_nb, const char* element_name, obibool_t value);
|
||||
int obi_column_set_obibool_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, obibool_t value);
|
||||
|
||||
|
||||
/**
|
||||
@ -86,7 +85,6 @@ int obi_column_set_obibool_with_elt_name(OBIDMS_column_p column, size_t line_nb,
|
||||
* @param column A pointer as returned by obi_create_column() or obi_clone_column().
|
||||
* @param line_nb The number of the line where the value should be recovered.
|
||||
* @param element_name The name of the element that should be recovered in the line.
|
||||
* If empty, it is checked that there is only one element per line.
|
||||
*
|
||||
* @returns The recovered value.
|
||||
* @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set.
|
||||
@ -94,7 +92,7 @@ int obi_column_set_obibool_with_elt_name(OBIDMS_column_p column, size_t line_nb,
|
||||
* @since August 2015
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
obibool_t obi_column_get_obibool_with_elt_name(OBIDMS_column_p column, size_t line_nb, const char* element_name);
|
||||
obibool_t obi_column_get_obibool_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name);
|
||||
|
||||
|
||||
#endif /* OBIDMSCOLUMN_BOOL_H_ */
|
||||
|
||||
@ -28,7 +28,7 @@
|
||||
*
|
||||
**********************************************************************/
|
||||
|
||||
int obi_column_set_obichar_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obichar_t value)
|
||||
int obi_column_set_obichar_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, obichar_t value)
|
||||
{
|
||||
// Check that the line number is not greater than the maximum allowed
|
||||
if (line_nb >= MAXIMUM_LINE_COUNT)
|
||||
@ -57,7 +57,7 @@ int obi_column_set_obichar_with_elt_idx(OBIDMS_column_p column, size_t line_nb,
|
||||
}
|
||||
|
||||
|
||||
obichar_t obi_column_get_obichar_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx)
|
||||
obichar_t obi_column_get_obichar_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx)
|
||||
{
|
||||
if ((line_nb+1) > (column->header)->lines_used)
|
||||
{
|
||||
@ -69,23 +69,23 @@ obichar_t obi_column_get_obichar_with_elt_idx(OBIDMS_column_p column, size_t lin
|
||||
}
|
||||
|
||||
|
||||
int obi_column_set_obichar_with_elt_name(OBIDMS_column_p column, size_t line_nb, const char* element_name, obichar_t value)
|
||||
int obi_column_set_obichar_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, obichar_t value)
|
||||
{
|
||||
size_t element_idx;
|
||||
index_t element_idx;
|
||||
element_idx = obi_column_get_element_index_from_name(column, element_name);
|
||||
if (element_idx == SIZE_MAX) //TODO
|
||||
if (element_idx == OBIIdx_NA)
|
||||
return -1;
|
||||
obi_column_set_obichar_with_elt_idx(column, line_nb, element_idx, value);
|
||||
return 0;
|
||||
}
|
||||
|
||||
|
||||
obichar_t obi_column_get_obichar_with_elt_name(OBIDMS_column_p column, size_t line_nb, const char* element_name)
|
||||
obichar_t obi_column_get_obichar_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name)
|
||||
{
|
||||
size_t element_idx;
|
||||
index_t element_idx;
|
||||
|
||||
element_idx = obi_column_get_element_index_from_name(column, element_name);
|
||||
if (element_idx == SIZE_MAX) //TODO
|
||||
if (element_idx == OBIIdx_NA)
|
||||
return OBIChar_NA;
|
||||
return obi_column_get_obichar_with_elt_idx(column, line_nb, element_idx);
|
||||
}
|
||||
|
||||
@ -38,7 +38,7 @@
|
||||
* @since July 2015
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
int obi_column_set_obichar_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obichar_t value);
|
||||
int obi_column_set_obichar_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, obichar_t value);
|
||||
|
||||
|
||||
/**
|
||||
@ -54,7 +54,7 @@ int obi_column_set_obichar_with_elt_idx(OBIDMS_column_p column, size_t line_nb,
|
||||
* @since July 2015
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
obichar_t obi_column_get_obichar_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx);
|
||||
obichar_t obi_column_get_obichar_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx);
|
||||
|
||||
|
||||
/**
|
||||
@ -66,7 +66,6 @@ obichar_t obi_column_get_obichar_with_elt_idx(OBIDMS_column_p column, size_t lin
|
||||
* @param column A pointer as returned by obi_create_column() or obi_clone_column().
|
||||
* @param line_nb The number of the line where the value should be set.
|
||||
* @param element_name The name of the element that should be set in the line.
|
||||
* If empty, it is checked that there is only one element per line.
|
||||
* @param value The value that should be set.
|
||||
*
|
||||
* @returns An integer value indicating the success of the operation.
|
||||
@ -76,7 +75,7 @@ obichar_t obi_column_get_obichar_with_elt_idx(OBIDMS_column_p column, size_t lin
|
||||
* @since August 2015
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
int obi_column_set_obichar_with_elt_name(OBIDMS_column_p column, size_t line_nb, const char* element_name, obichar_t value);
|
||||
int obi_column_set_obichar_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, obichar_t value);
|
||||
|
||||
|
||||
/**
|
||||
@ -86,7 +85,6 @@ int obi_column_set_obichar_with_elt_name(OBIDMS_column_p column, size_t line_nb,
|
||||
* @param column A pointer as returned by obi_create_column() or obi_clone_column().
|
||||
* @param line_nb The number of the line where the value should be recovered.
|
||||
* @param element_name The name of the element that should be recovered in the line.
|
||||
* If empty, it is checked that there is only one element per line.
|
||||
*
|
||||
* @returns The recovered value.
|
||||
* @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set.
|
||||
@ -94,7 +92,7 @@ int obi_column_set_obichar_with_elt_name(OBIDMS_column_p column, size_t line_nb,
|
||||
* @since August 2015
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
obichar_t obi_column_get_obichar_with_elt_name(OBIDMS_column_p column, size_t line_nb, const char* element_name);
|
||||
obichar_t obi_column_get_obichar_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name);
|
||||
|
||||
|
||||
#endif /* OBIDMSCOLUMN_CHAR_H_ */
|
||||
|
||||
@ -28,7 +28,7 @@
|
||||
*
|
||||
**********************************************************************/
|
||||
|
||||
int obi_column_set_obifloat_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obifloat_t value)
|
||||
int obi_column_set_obifloat_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, obifloat_t value)
|
||||
{
|
||||
// Check that the line number is not greater than the maximum allowed
|
||||
if (line_nb >= MAXIMUM_LINE_COUNT)
|
||||
@ -57,7 +57,7 @@ int obi_column_set_obifloat_with_elt_idx(OBIDMS_column_p column, size_t line_nb,
|
||||
}
|
||||
|
||||
|
||||
obifloat_t obi_column_get_obifloat_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx)
|
||||
obifloat_t obi_column_get_obifloat_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx)
|
||||
{
|
||||
if ((line_nb+1) > (column->header)->lines_used)
|
||||
{
|
||||
@ -69,23 +69,23 @@ obifloat_t obi_column_get_obifloat_with_elt_idx(OBIDMS_column_p column, size_t l
|
||||
}
|
||||
|
||||
|
||||
int obi_column_set_obifloat_with_elt_name(OBIDMS_column_p column, size_t line_nb, const char* element_name, obifloat_t value)
|
||||
int obi_column_set_obifloat_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, obifloat_t value)
|
||||
{
|
||||
size_t element_idx;
|
||||
index_t element_idx;
|
||||
element_idx = obi_column_get_element_index_from_name(column, element_name);
|
||||
if (element_idx == SIZE_MAX) //TODO
|
||||
if (element_idx == OBIIdx_NA)
|
||||
return -1;
|
||||
obi_column_set_obifloat_with_elt_idx(column, line_nb, element_idx, value);
|
||||
return 0;
|
||||
}
|
||||
|
||||
|
||||
obifloat_t obi_column_get_obifloat_with_elt_name(OBIDMS_column_p column, size_t line_nb, const char* element_name)
|
||||
obifloat_t obi_column_get_obifloat_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name)
|
||||
{
|
||||
size_t element_idx;
|
||||
index_t element_idx;
|
||||
|
||||
element_idx = obi_column_get_element_index_from_name(column, element_name);
|
||||
if (element_idx == SIZE_MAX) //TODO
|
||||
if (element_idx == OBIIdx_NA)
|
||||
return OBIFloat_NA;
|
||||
return obi_column_get_obifloat_with_elt_idx(column, line_nb, element_idx);
|
||||
}
|
||||
|
||||
@ -38,7 +38,7 @@
|
||||
* @since July 2015
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
int obi_column_set_obifloat_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obifloat_t value);
|
||||
int obi_column_set_obifloat_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, obifloat_t value);
|
||||
|
||||
|
||||
/**
|
||||
@ -54,7 +54,7 @@ int obi_column_set_obifloat_with_elt_idx(OBIDMS_column_p column, size_t line_nb,
|
||||
* @since July 2015
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
obifloat_t obi_column_get_obifloat_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx);
|
||||
obifloat_t obi_column_get_obifloat_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx);
|
||||
|
||||
|
||||
/**
|
||||
@ -66,7 +66,6 @@ obifloat_t obi_column_get_obifloat_with_elt_idx(OBIDMS_column_p column, size_t l
|
||||
* @param column A pointer as returned by obi_create_column() or obi_clone_column().
|
||||
* @param line_nb The number of the line where the value should be set.
|
||||
* @param element_name The name of the element that should be set in the line.
|
||||
* If empty, it is checked that there is only one element per line.
|
||||
* @param value The value that should be set.
|
||||
*
|
||||
* @returns An integer value indicating the success of the operation.
|
||||
@ -76,7 +75,7 @@ obifloat_t obi_column_get_obifloat_with_elt_idx(OBIDMS_column_p column, size_t l
|
||||
* @since August 2015
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
int obi_column_set_obifloat_with_elt_name(OBIDMS_column_p column, size_t line_nb, const char* element_name, obifloat_t value);
|
||||
int obi_column_set_obifloat_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, obifloat_t value);
|
||||
|
||||
|
||||
/**
|
||||
@ -86,7 +85,6 @@ int obi_column_set_obifloat_with_elt_name(OBIDMS_column_p column, size_t line_nb
|
||||
* @param column A pointer as returned by obi_create_column() or obi_clone_column().
|
||||
* @param line_nb The number of the line where the value should be recovered.
|
||||
* @param element_name The name of the element that should be recovered in the line.
|
||||
* If empty, it is checked that there is only one element per line.
|
||||
*
|
||||
* @returns The recovered value.
|
||||
* @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set.
|
||||
@ -94,7 +92,7 @@ int obi_column_set_obifloat_with_elt_name(OBIDMS_column_p column, size_t line_nb
|
||||
* @since August 2015
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
obifloat_t obi_column_get_obifloat_with_elt_name(OBIDMS_column_p column, size_t line_nb, const char* element_name);
|
||||
obifloat_t obi_column_get_obifloat_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name);
|
||||
|
||||
|
||||
#endif /* OBIDMSCOLUMN_FLOAT_H_ */
|
||||
|
||||
@ -28,7 +28,7 @@
|
||||
*
|
||||
**********************************************************************/
|
||||
|
||||
int obi_column_set_obiint_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obiint_t value)
|
||||
int obi_column_set_obiint_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, obiint_t value)
|
||||
{
|
||||
// Check that the line number is not greater than the maximum allowed
|
||||
if (line_nb >= MAXIMUM_LINE_COUNT)
|
||||
@ -57,7 +57,7 @@ int obi_column_set_obiint_with_elt_idx(OBIDMS_column_p column, size_t line_nb, s
|
||||
}
|
||||
|
||||
|
||||
obiint_t obi_column_get_obiint_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx)
|
||||
obiint_t obi_column_get_obiint_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx)
|
||||
{
|
||||
if ((line_nb+1) > (column->header)->lines_used)
|
||||
{
|
||||
@ -69,23 +69,23 @@ obiint_t obi_column_get_obiint_with_elt_idx(OBIDMS_column_p column, size_t line_
|
||||
}
|
||||
|
||||
|
||||
int obi_column_set_obiint_with_elt_name(OBIDMS_column_p column, size_t line_nb, const char* element_name, obiint_t value)
|
||||
int obi_column_set_obiint_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, obiint_t value)
|
||||
{
|
||||
size_t element_idx;
|
||||
index_t element_idx;
|
||||
element_idx = obi_column_get_element_index_from_name(column, element_name);
|
||||
if (element_idx == SIZE_MAX) //TODO
|
||||
if (element_idx == OBIIdx_NA)
|
||||
return -1;
|
||||
obi_column_set_obiint_with_elt_idx(column, line_nb, element_idx, value);
|
||||
return 0;
|
||||
}
|
||||
|
||||
|
||||
obiint_t obi_column_get_obiint_with_elt_name(OBIDMS_column_p column, size_t line_nb, const char* element_name)
|
||||
obiint_t obi_column_get_obiint_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name)
|
||||
{
|
||||
size_t element_idx;
|
||||
index_t element_idx;
|
||||
|
||||
element_idx = obi_column_get_element_index_from_name(column, element_name);
|
||||
if (element_idx == SIZE_MAX) //TODO
|
||||
if (element_idx == OBIIdx_NA)
|
||||
return OBIInt_NA;
|
||||
return obi_column_get_obiint_with_elt_idx(column, line_nb, element_idx);
|
||||
}
|
||||
|
||||
@ -38,7 +38,7 @@
|
||||
* @since July 2015
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
int obi_column_set_obiint_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obiint_t value);
|
||||
int obi_column_set_obiint_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, obiint_t value);
|
||||
|
||||
|
||||
/**
|
||||
@ -54,7 +54,7 @@ int obi_column_set_obiint_with_elt_idx(OBIDMS_column_p column, size_t line_nb, s
|
||||
* @since July 2015
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
obiint_t obi_column_get_obiint_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx);
|
||||
obiint_t obi_column_get_obiint_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx);
|
||||
|
||||
|
||||
/**
|
||||
@ -66,7 +66,6 @@ obiint_t obi_column_get_obiint_with_elt_idx(OBIDMS_column_p column, size_t line_
|
||||
* @param column A pointer as returned by obi_create_column() or obi_clone_column().
|
||||
* @param line_nb The number of the line where the value should be set.
|
||||
* @param element_name The name of the element that should be set in the line.
|
||||
* If empty, it is checked that there is only one element per line.
|
||||
* @param value The value that should be set.
|
||||
*
|
||||
* @returns An integer value indicating the success of the operation.
|
||||
@ -76,7 +75,7 @@ obiint_t obi_column_get_obiint_with_elt_idx(OBIDMS_column_p column, size_t line_
|
||||
* @since August 2015
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
int obi_column_set_obiint_with_elt_name(OBIDMS_column_p column, size_t line_nb, const char* element_name, obiint_t value);
|
||||
int obi_column_set_obiint_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, obiint_t value);
|
||||
|
||||
|
||||
/**
|
||||
@ -86,7 +85,6 @@ int obi_column_set_obiint_with_elt_name(OBIDMS_column_p column, size_t line_nb,
|
||||
* @param column A pointer as returned by obi_create_column() or obi_clone_column().
|
||||
* @param line_nb The number of the line where the value should be recovered.
|
||||
* @param element_name The name of the element that should be recovered in the line.
|
||||
* If empty, it is checked that there is only one element per line.
|
||||
*
|
||||
* @returns The recovered value.
|
||||
* @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set.
|
||||
@ -94,7 +92,7 @@ int obi_column_set_obiint_with_elt_name(OBIDMS_column_p column, size_t line_nb,
|
||||
* @since August 2015
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
obiint_t obi_column_get_obiint_with_elt_name(OBIDMS_column_p column, size_t line_nb, const char* element_name);
|
||||
obiint_t obi_column_get_obiint_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name);
|
||||
|
||||
|
||||
#endif /* OBIDMSCOLUMN_INT_H_ */
|
||||
|
||||
@ -6,7 +6,7 @@
|
||||
* @file obidsmcolumn_str.c
|
||||
* @author Celine Mercier
|
||||
* @date October 28th 2015
|
||||
* @brief Functions handling OBIColumns containing data with the OBIType OBI_IDX.
|
||||
* @brief Functions handling OBIColumns containing data in the form of indices referring to character strings.
|
||||
*/
|
||||
|
||||
|
||||
@ -29,7 +29,7 @@
|
||||
*
|
||||
**********************************************************************/
|
||||
|
||||
int obi_column_set_obistr_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, char* value)
|
||||
int obi_column_set_obistr_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, char* value)
|
||||
{
|
||||
byte_t* value_b;
|
||||
index_t idx;
|
||||
@ -59,31 +59,24 @@ int obi_column_set_obistr_with_elt_idx(OBIDMS_column_p column, size_t line_nb, s
|
||||
if (value_b == NULL)
|
||||
return -1;
|
||||
|
||||
obidebug(1, "\nvalue=%s", value);
|
||||
//obidebug(1, "\nbytes=%s", value_b+5);
|
||||
|
||||
// Add in the obiarray
|
||||
idx = obi_array_add(column->array, value_b);
|
||||
if (idx == -1)
|
||||
return -1;
|
||||
|
||||
obidebug(1, "\nidx=%d", idx);
|
||||
//obidebug(1, "\nbytes 2=%s", obi_array_get(column->array, idx)+5);
|
||||
|
||||
// Add the value's index in the column
|
||||
*(((obiidx_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = idx;
|
||||
*(((index_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = idx;
|
||||
|
||||
// TODO free value_b probably
|
||||
free(value_b);
|
||||
|
||||
return 0;
|
||||
}
|
||||
|
||||
|
||||
const char* obi_column_get_obistr_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx)
|
||||
const char* obi_column_get_obistr_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx)
|
||||
{
|
||||
index_t idx;
|
||||
byte_t* value_b;
|
||||
const char* value;
|
||||
|
||||
if ((line_nb+1) > (column->header)->lines_used)
|
||||
{
|
||||
@ -92,32 +85,22 @@ const char* obi_column_get_obistr_with_elt_idx(OBIDMS_column_p column, size_t li
|
||||
return "\0"; // TODO
|
||||
}
|
||||
|
||||
idx = *(((obiidx_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
|
||||
idx = *(((index_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
|
||||
|
||||
// Check NA
|
||||
if (idx == OBIIdx_NA)
|
||||
return "\0"; // TODO
|
||||
|
||||
obidebug(1, "\nwhy, idx = %d", idx);
|
||||
|
||||
value_b = obi_array_get(column->array, idx);
|
||||
|
||||
obidebug(1, "\nwhyyyy");
|
||||
|
||||
value = obi_obibytes_to_str(value_b);
|
||||
|
||||
obidebug(1, "\nwhyyyyyyyyyyyy, value=%s %p", value, value);
|
||||
obidebug(1, "\nwhyyyyyyyyyyyy, len value=%d", strlen(value));
|
||||
|
||||
return value;
|
||||
return obi_obibytes_to_str(value_b);
|
||||
}
|
||||
|
||||
|
||||
int obi_column_set_obistr_with_elt_name(OBIDMS_column_p column, size_t line_nb, const char* element_name, char* value)
|
||||
int obi_column_set_obistr_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, char* value)
|
||||
{
|
||||
size_t element_idx;
|
||||
index_t element_idx;
|
||||
element_idx = obi_column_get_element_index_from_name(column, element_name);
|
||||
if (element_idx == SIZE_MAX) //TODO
|
||||
if (element_idx == OBIIdx_NA)
|
||||
return -1;
|
||||
if (obi_column_set_obistr_with_elt_idx(column, line_nb, element_idx, value) < 0)
|
||||
return -1;
|
||||
@ -125,12 +108,12 @@ int obi_column_set_obistr_with_elt_name(OBIDMS_column_p column, size_t line_nb,
|
||||
}
|
||||
|
||||
|
||||
const char* obi_column_get_obistr_with_elt_name(OBIDMS_column_p column, size_t line_nb, const char* element_name)
|
||||
const char* obi_column_get_obistr_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name)
|
||||
{
|
||||
size_t element_idx;
|
||||
index_t element_idx;
|
||||
|
||||
element_idx = obi_column_get_element_index_from_name(column, element_name);
|
||||
if (element_idx == SIZE_MAX) //TODO
|
||||
if (element_idx == OBIIdx_NA)
|
||||
return "\0";
|
||||
return obi_column_get_obistr_with_elt_idx(column, line_nb, element_idx);
|
||||
}
|
||||
|
||||
@ -1,17 +1,17 @@
|
||||
/****************************************************************************
|
||||
* OBIDMS_column_idx header file *
|
||||
* OBIDMS_column_str header file *
|
||||
****************************************************************************/
|
||||
|
||||
/**
|
||||
* @file obidsmcolumn_idx.h
|
||||
* @file obidsmcolumn_str.h
|
||||
* @author Celine Mercier
|
||||
* @date August 10th 2015
|
||||
* @brief Header file for the functions handling OBIColumns containing data with the OBIType OBI_IDX.
|
||||
* @date October 28th 2015
|
||||
* @brief Header file for the functions handling OBIColumns containing data in the form of indices referring to character strings.
|
||||
*/
|
||||
|
||||
|
||||
#ifndef OBIDMSCOLUMN_IDX_H_
|
||||
#define OBIDMSCOLUMN_IDX_H_
|
||||
#ifndef OBIDMSCOLUMN_STR_H_
|
||||
#define OBIDMSCOLUMN_STR_H_
|
||||
|
||||
|
||||
#include <stdlib.h>
|
||||
@ -22,7 +22,8 @@
|
||||
|
||||
|
||||
/**
|
||||
* @brief Sets a value in an OBIDMS column containing data with the type OBI_IDX, using the index of the element in the line.
|
||||
* @brief Sets a value in an OBIDMS column containing data in the form of indices referring
|
||||
* to character strings in an obiarray, using the index of the element in the line.
|
||||
*
|
||||
* @warning Pointers returned by obi_open_column() don't allow writing.
|
||||
*
|
||||
@ -35,66 +36,65 @@
|
||||
* @retval 0 on success.
|
||||
* @retval -1 if an error occurred.
|
||||
*
|
||||
* @since July 2015
|
||||
* @since October 2015
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
int obi_column_set_obiidx_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, void* value);
|
||||
int obi_column_set_obistr_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, char* value);
|
||||
|
||||
|
||||
/**
|
||||
* @brief Recovers a value in an OBIDMS column containing data with the type OBI_IDX.
|
||||
* @brief Recovers a value in an OBIDMS column containing data in the form of indices referring
|
||||
* to character strings in an obiarray, using the index of the element in the line.
|
||||
*
|
||||
* @param column A pointer as returned by obi_create_column().
|
||||
* @param line_nb The number of the line where the value should be recovered.
|
||||
* @param element_idx The index of the element that should be recovered in the line.
|
||||
*
|
||||
* @returns The recovered value.
|
||||
* @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set.
|
||||
* @retval '\0' the NA value of the type if an error occurred and obi_errno is set.
|
||||
*
|
||||
* @since July 2015
|
||||
* @since October 2015
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
const char* obi_column_get_obiidx_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx);
|
||||
const char* obi_column_get_obistr_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx);
|
||||
|
||||
|
||||
/**
|
||||
* @brief Sets a value in an OBIDMS column containing data with the type OBI_IDX,
|
||||
* using the name of the element in the line.
|
||||
* @brief Sets a value in an OBIDMS column containing data in the form of indices referring
|
||||
* to character strings in an obiarray, using the name of the element in the line.
|
||||
*
|
||||
* @warning Pointers returned by obi_open_column() don't allow writing.
|
||||
*
|
||||
* @param column A pointer as returned by obi_create_column() or obi_clone_column().
|
||||
* @param line_nb The number of the line where the value should be set.
|
||||
* @param element_name The name of the element that should be set in the line.
|
||||
* If empty, it is checked that there is only one element per line.
|
||||
* @param value The value that should be set.
|
||||
*
|
||||
* @returns An integer value indicating the success of the operation.
|
||||
* @retval 0 on success.
|
||||
* @retval -1 if an error occurred.
|
||||
*
|
||||
* @since August 2015
|
||||
* @since October 2015
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
int obi_column_set_obiidx_with_elt_name(OBIDMS_column_p column, size_t line_nb, const char* element_name, void* value);
|
||||
int obi_column_set_obistr_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, char* value);
|
||||
|
||||
|
||||
/**
|
||||
* @brief Recovers a value in an OBIDMS column containing data with the type OBI_IDX,
|
||||
* using the name of the element in the line.
|
||||
* @brief Recovers a value in an OBIDMS column containing data in the form of indices referring
|
||||
* to character strings in an obiarray, using the name of the element in the line.
|
||||
*
|
||||
* @param column A pointer as returned by obi_create_column() or obi_clone_column().
|
||||
* @param line_nb The number of the line where the value should be recovered.
|
||||
* @param element_name The name of the element that should be recovered in the line.
|
||||
* If empty, it is checked that there is only one element per line.
|
||||
*
|
||||
* @returns The recovered value.
|
||||
* @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set.
|
||||
* @retval '\0' the NA value of the type if an error occurred and obi_errno is set.
|
||||
*
|
||||
* @since August 2015
|
||||
* @since October 2015
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
const char* obi_column_get_obiidx_with_elt_name(OBIDMS_column_p column, size_t line_nb, const char* element_name);
|
||||
const char* obi_column_get_obistr_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name);
|
||||
|
||||
|
||||
#endif /* OBIDMSCOLUMN_IDX_H_ */
|
||||
|
||||
@ -98,7 +98,7 @@ extern int obi_errno;
|
||||
*/
|
||||
#define OBICOL_ACCESS_ERROR (19) /**< Permission error trying to access an OBIDSM column directory
|
||||
*/
|
||||
#define OBI_ARRAY_ERROR (20) /** Error while handling a heap
|
||||
#define OBI_ARRAY_ERROR (20) /** Error while handling an array
|
||||
*/
|
||||
/**@}*/
|
||||
|
||||
|
||||
@ -40,7 +40,7 @@ size_t obi_sizeof(OBIType_t type)
|
||||
case OBI_CHAR: size = sizeof(obichar_t);
|
||||
break;
|
||||
|
||||
case OBI_IDX: size = sizeof(obiidx_t);
|
||||
case OBI_IDX: size = sizeof(index_t);
|
||||
break;
|
||||
|
||||
default: size = 0;
|
||||
@ -50,7 +50,7 @@ size_t obi_sizeof(OBIType_t type)
|
||||
}
|
||||
|
||||
|
||||
size_t obi_array_sizeof(OBIType_t type, size_t nb_lines, size_t nb_elements_per_line)
|
||||
size_t obi_array_sizeof(OBIType_t type, index_t nb_lines, index_t nb_elements_per_line)
|
||||
{
|
||||
size_t size;
|
||||
size_t rsize;
|
||||
|
||||
@ -19,7 +19,7 @@
|
||||
|
||||
|
||||
#define OBIInt_NA (INT32_MIN) /**< NA value for the type OBI_INT */
|
||||
#define OBIIdx_NA (SIZE_MAX) /**< NA value for the type OBI_IDX */
|
||||
#define OBIIdx_NA (INT64_MIN) /**< NA value for indices */
|
||||
#define OBIFloat_NA (float_NA()) /**< NA value for the type OBI_FLOAT */
|
||||
#define OBIChar_NA (0) /**< NA value for the type OBI_CHAR */
|
||||
// TODO not sure about this one as it can be impossible to distinguish from uninitialized values
|
||||
@ -44,14 +44,14 @@ typedef enum OBIType {
|
||||
OBI_FLOAT, /**< a floating value (C type : double) */
|
||||
OBI_BOOL, /**< a boolean true/false value, see obibool_t enum */
|
||||
OBI_CHAR, /**< a character (C type : char) */
|
||||
OBI_IDX /**< an index in a data structure (C type : size_t) */
|
||||
OBI_IDX /**< an index in a data structure (C type : int64_t) */
|
||||
} OBIType_t, *OBIType_p;
|
||||
|
||||
|
||||
typedef int64_t index_t;
|
||||
typedef int32_t obiint_t;
|
||||
typedef double obifloat_t;
|
||||
typedef char obichar_t;
|
||||
typedef size_t obiidx_t;
|
||||
|
||||
|
||||
/**
|
||||
@ -107,7 +107,7 @@ size_t obi_sizeof(OBIType_t type);
|
||||
* @since May 2015
|
||||
* @author Eric Coissac (eric.coissac@metabarcoding.org)
|
||||
*/
|
||||
size_t obi_array_sizeof(OBIType_t data_type, size_t nb_lines, size_t nb_elements_per_line);
|
||||
size_t obi_array_sizeof(OBIType_t data_type, index_t nb_lines, index_t nb_elements_per_line);
|
||||
|
||||
|
||||
/**
|
||||
|
||||
Reference in New Issue
Block a user