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OBITools3
Commit a8f03248 authored by Celine Mercier's avatar Celine Mercier
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Major update : views

parent cfaf0690
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python/obitools3/obidms/_obidms.cfiles
View file @ a8f03248
../../../src/obidms.h
../../../src/obidms.c
../../../src/obiview.h
../../../src/obiview.c
../../../src/obidmscolumn.h
../../../src/obidmscolumn.c
../../../src/obidmscolumndir.h
......@@ -15,4 +17,6 @@
../../../src/obiavl.h
../../../src/obiavl.c
../../../src/encode.h
../../../src/encode.c
\ No newline at end of file
../../../src/encode.c
../../../src/obidmscolumn_idx.h
../../../src/obidmscolumn_idx.c
python/obitools3/obidms/_obidms.pxd
View file @ a8f03248
......@@ -2,52 +2,80 @@
from .capi.obidms cimport OBIDMS_p
from .capi.obidmscolumn cimport OBIDMS_column_p
from .capi.obiview cimport Obiview_p
from .capi.obitypes cimport obiversion_t, OBIType_t, index_t
cdef class OBIDMS_column
cdef class OBIDMS:
cdef OBIDMS_p pointer
cdef str dms_name
cpdef dict list(self)
cpdef close(self)
cpdef OBIDMS_column open_column(self,
str column_name,
bint create=*,
bint clone=*, bint clone_data=*,
bint referring=*,
obiversion_t version_number=*,
str type=*,
index_t nb_lines=*,
index_t nb_elements_per_line=*,
list elements_names=*,
str avl_name=*,
str comments=*)
cdef class OBIDMS_column:
cdef OBIDMS_column_p pointer
cdef OBIDMS_column_p* pointer
cdef OBIDMS dms
cdef Obiview_p view
cdef str data_type
cdef str dms_name
cdef str column_name
cdef index_t nb_elements_per_line
cdef list elements_names
cpdef OBIDMS_column_p referred_column_pointer
# cpdef object get_item(self, index_t line_nb, str element_name) TODO can't declare because not the same in all subclasses
# cpdef set_item(self, index_t line_nb, str element_name, object value) TODO can't declare because object value
cpdef grep_line(self, index_t line_nb)
cpdef update_pointer(self)
cpdef list get_elements_names(self)
cpdef str get_data_type(self)
cpdef index_t get_nb_lines_used(self)
cpdef str get_creation_date(self)
cpdef str get_comments(self)
cpdef close(self)
@staticmethod
cdef object get_subclass_type(OBIDMS_column_p column_p)
cdef class OBIDMS_column_multi_elts(OBIDMS_column):
cpdef set_line(self, index_t line_nb, dict values)
cdef class OBIDMS_column_line:
cdef OBIDMS_column column
cdef index_t index
cdef class OBIView:
cdef Obiview_p pointer
cdef str name
cdef dict columns
cdef dict columns_pp # TODO this dict might be unnecessary
cdef OBIDMS dms
cpdef delete_column(self, str column_name)
cpdef add_column(self,
str column_name,
obiversion_t version_number=*,
str type=*,
index_t nb_lines=*,
index_t nb_elements_per_line=*,
list elements_names=*,
str avl_name=*,
str comments=*,
bint create=*
)
cpdef select_line(self, index_t line_nb)
cpdef select_lines(self, list line_selection)
cpdef save_and_close(self)
cdef class OBIView_line :
cdef index_t index
cdef OBIView view
cdef class OBIDMS:
cdef OBIDMS_p pointer
cdef str dms_name
cpdef close(self)
cpdef OBIView open_view(self, str view_name)
cpdef OBIView new_view(self, str view_name, object view_to_clone=*, list line_selection=*)
python/obitools3/obidms/_obidms.pyx
View file @ a8f03248
This diff is collapsed.
python/obitools3/obidms/_obidmscolumn_bool.cfiles
View file @ a8f03248
../../../src/obidmscolumn_bool.c
../../../src/obidmscolumn_bool.h
../../../src/obiview.h
../../../src/obiview.c
../../../src/obidmscolumn.h
../../../src/obidmscolumn.c
../../../src/obidmscolumndir.h
......
python/obitools3/obidms/_obidmscolumn_bool.pxd
View file @ a8f03248
#cython: language_level=3
from .capi.obitypes cimport obibool_t, index_t
from ._obidms cimport OBIDMS_column
from .capi.obitypes cimport index_t
from ._obidms cimport OBIDMS_column, OBIDMS_column_multi_elts
cdef class OBIDMS_column_bool(OBIDMS_column):
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_bool_writable(OBIDMS_column_bool):
cpdef set_line(self, index_t line_nb, object value)
cpdef close(self)
cdef class OBIDMS_column_bool_multi_elts(OBIDMS_column_bool):
cdef class OBIDMS_column_multi_elts_bool(OBIDMS_column_multi_elts):
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, obibool_t value)
cpdef set_line(self, index_t line_nb, object values)
cdef class OBIDMS_column_bool_multi_elts_writable(OBIDMS_column_bool_multi_elts):
cpdef set_item(self, index_t line_nb, str element_name, obibool_t value)
cpdef set_line(self, index_t line_nb, object values)
cpdef close(self)
cpdef set_item(self, index_t line_nb, str element_name, object value)
python/obitools3/obidms/_obidmscolumn_bool.pyx
View file @ a8f03248
#cython: language_level=3
from .capi.obidmscolumn cimport obi_close_column,\
obi_truncate_and_close_column, \
obi_column_get_obibool_with_elt_name, \
obi_column_get_obibool_with_elt_idx, \
obi_column_set_obibool_with_elt_name, \
obi_column_set_obibool_with_elt_idx
from .capi.obidmscolumn cimport obi_truncate_and_close_column, \
obi_column_get_obibool_with_elt_name_in_view, \
obi_column_get_obibool_with_elt_idx_in_view, \
obi_column_set_obibool_with_elt_name_in_view, \
obi_column_set_obibool_with_elt_idx_in_view
from .capi.obierrno cimport obi_errno
from .capi.obitypes cimport OBIBool_NA
from .capi.obitypes cimport OBIBool_NA, obibool_t
from obitools3.utils cimport str2bytes
......@@ -19,7 +18,7 @@ cdef class OBIDMS_column_bool(OBIDMS_column):
cpdef object get_line(self, index_t line_nb):
cdef obibool_t value
cdef object result
value = obi_column_get_obibool_with_elt_idx(self.pointer, line_nb, 0)
value = obi_column_get_obibool_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIBool_NA :
......@@ -27,32 +26,20 @@ cdef class OBIDMS_column_bool(OBIDMS_column):
else :
result = PyBool_FromLong(value)
return result
cpdef set_line(self, index_t line_nb, object value):
raise Exception("Column is read-only")
cpdef close(self):
if obi_close_column(self.pointer) < 0 :
raise Exception("Problem closing a column")
cdef class OBIDMS_column_bool_writable(OBIDMS_column_bool):
cpdef set_line(self, index_t line_nb, object value):
if obi_column_set_obibool_with_elt_idx(self.pointer, line_nb, 0, <obibool_t> value) < 0:
if value is None :
value = OBIBool_NA
if obi_column_set_obibool_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0, <obibool_t> value) < 0:
raise Exception("Problem setting a value in a column")
cpdef close(self):
if obi_truncate_and_close_column(self.pointer) < 0 :
raise Exception("Problem closing a column")
cdef class OBIDMS_column_bool_multi_elts(OBIDMS_column_bool):
cdef class OBIDMS_column_multi_elts_bool(OBIDMS_column_multi_elts):
cpdef object get_item(self, index_t line_nb, str element_name):
cdef obibool_t value
cdef object result
value = obi_column_get_obibool_with_elt_name(self.pointer, line_nb, str2bytes(element_name))
value = obi_column_get_obibool_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name))
if obi_errno > 0 :
raise IndexError(line_nb, element_name)
if value == OBIBool_NA :
......@@ -63,42 +50,29 @@ cdef class OBIDMS_column_bool_multi_elts(OBIDMS_column_bool):
cpdef object get_line(self, index_t line_nb) :
cdef obibool_t value
cdef object result
cdef object value_in_result
cdef dict result
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_obibool_with_elt_idx(self.pointer, line_nb, i)
value = obi_column_get_obibool_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, i)
if obi_errno > 0 :
raise IndexError(line_nb)
result[self.elements_names[i]] = PyBool_FromLong(value)
if all_NA and (value != OBIBool_NA) :
raise IndexError(line_nb)
if value == OBIBool_NA :
value_in_result = None
else :
value_in_result = PyBool_FromLong(value)
result[self.elements_names[i]] = value_in_result
if all_NA and (value_in_result is not None) :
all_NA = False
if all_NA :
result = None
return result
cpdef set_item(self, index_t line_nb, str element_name, obibool_t value):
raise Exception("Column is read-only")
cpdef set_line(self, index_t line_nb, object values):
raise Exception("Column is read-only")
cdef class OBIDMS_column_bool_multi_elts_writable(OBIDMS_column_bool_multi_elts):
cpdef set_item(self, index_t line_nb, str element_name, obibool_t value):
if obi_column_set_obibool_with_elt_name(self.pointer, line_nb, str2bytes(element_name), value) < 0:
cpdef set_item(self, index_t line_nb, str element_name, object value):
if value is None :
value = OBIBool_NA
if obi_column_set_obibool_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name), <obibool_t> value) < 0:
raise Exception("Problem setting a value in a column")
cpdef set_line(self, index_t line_nb, object values):
cdef obibool_t value
for element_name in values :
value = <obibool_t> values[element_name]
self.set_item(line_nb, element_name, value)
cpdef close(self):
if obi_truncate_and_close_column(self.pointer) < 0 :
raise Exception("Problem closing a column")
python/obitools3/obidms/_obidmscolumn_char.cfiles
View file @ a8f03248
../../../src/obidmscolumn_char.c
../../../src/obidmscolumn_char.h
../../../src/obiview.h
../../../src/obiview.c
../../../src/obidmscolumn.h
../../../src/obidmscolumn.c
../../../src/obidmscolumndir.h
......
python/obitools3/obidms/_obidmscolumn_char.pxd
View file @ a8f03248
#cython: language_level=3
from .capi.obitypes cimport obichar_t, index_t
from ._obidms cimport OBIDMS_column
from .capi.obitypes cimport index_t
from ._obidms cimport OBIDMS_column, OBIDMS_column_multi_elts
cdef class OBIDMS_column_char(OBIDMS_column):
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_char_writable(OBIDMS_column_char):
cpdef set_line(self, index_t line_nb, object value)
cpdef close(self)
cdef class OBIDMS_column_char_multi_elts(OBIDMS_column_char):
cdef class OBIDMS_column_multi_elts_char(OBIDMS_column_multi_elts):
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_char_multi_elts_writable(OBIDMS_column_char_multi_elts):
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)
cpdef set_item(self, index_t line_nb, str element_name, object value)
python/obitools3/obidms/_obidmscolumn_char.pyx
View file @ a8f03248
#cython: language_level=3
from .capi.obidmscolumn cimport obi_close_column,\
obi_truncate_and_close_column, \
obi_column_get_obichar_with_elt_name, \
obi_column_get_obichar_with_elt_idx, \
obi_column_set_obichar_with_elt_name, \
obi_column_set_obichar_with_elt_idx
from .capi.obidmscolumn cimport obi_truncate_and_close_column, \
obi_column_get_obichar_with_elt_name_in_view, \
obi_column_get_obichar_with_elt_idx_in_view, \
obi_column_set_obichar_with_elt_name_in_view, \
obi_column_set_obichar_with_elt_idx_in_view
from .capi.obierrno cimport obi_errno
from .capi.obitypes cimport OBIChar_NA
from .capi.obitypes cimport OBIChar_NA, obichar_t
from obitools3.utils cimport str2bytes, bytes2str
......@@ -17,7 +16,7 @@ cdef class OBIDMS_column_char(OBIDMS_column):
cpdef object get_line(self, index_t line_nb):
cdef obichar_t value
cdef object result
value = obi_column_get_obichar_with_elt_idx(self.pointer, line_nb, 0)
value = obi_column_get_obichar_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIChar_NA :
......@@ -27,30 +26,18 @@ cdef class OBIDMS_column_char(OBIDMS_column):
return result
cpdef set_line(self, index_t line_nb, object value):
raise Exception("Column is read-only")
cpdef close(self):
if obi_close_column(self.pointer) < 0 :
raise Exception("Problem closing a column")
cdef class OBIDMS_column_char_writable(OBIDMS_column_char):
cpdef set_line(self, index_t line_nb, object value):
if obi_column_set_obichar_with_elt_idx(self.pointer, line_nb, 0, str2bytes(value)[0]) < 0:
if value is None :
value = OBIChar_NA
if obi_column_set_obichar_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0, str2bytes(value)[0]) < 0:
raise Exception("Problem setting a value in a column")
cpdef close(self):
if obi_truncate_and_close_column(self.pointer) < 0 :
raise Exception("Problem closing a column")
cdef class OBIDMS_column_char_multi_elts(OBIDMS_column_char):
cdef class OBIDMS_column_multi_elts_char(OBIDMS_column_multi_elts):
cpdef object get_item(self, index_t line_nb, str element_name):
cdef obichar_t value
cdef object result
value = obi_column_get_obichar_with_elt_name(self.pointer, line_nb, str2bytes(element_name))
value = obi_column_get_obichar_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name))
if obi_errno > 0 :
raise IndexError(line_nb, element_name)
if value == OBIChar_NA :
......@@ -58,45 +45,33 @@ cdef class OBIDMS_column_char_multi_elts(OBIDMS_column_char):
else :
result = bytes2str(value)
return result
cpdef object get_line(self, index_t line_nb) :
cdef obichar_t value
cdef object result
cdef object value_in_result
cdef dict result
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_obichar_with_elt_idx(self.pointer, line_nb, i)
value = obi_column_get_obichar_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, i)
if obi_errno > 0 :
raise IndexError(line_nb)
result[self.elements_names[i]] = bytes2str(value)
if all_NA and (value != OBIChar_NA) :
raise IndexError(line_nb)
if value == OBIChar_NA :
value_in_result = None
else :
value_in_result = bytes2str(value)
result[self.elements_names[i]] = value_in_result
if all_NA and (value_in_result is not None) :
all_NA = False
if all_NA :
result = None
return result
cpdef set_item(self, index_t line_nb, str element_name, str value):
raise Exception("Column is read-only")
cpdef set_line(self, index_t line_nb, object values):
raise Exception("Column is read-only")
cdef class OBIDMS_column_char_multi_elts_writable(OBIDMS_column_char_multi_elts):
cpdef set_item(self, index_t line_nb, str element_name, str value):
if obi_column_set_obichar_with_elt_name(self.pointer, line_nb, str2bytes(element_name), str2bytes(value)[0]) < 0:
cpdef set_item(self, index_t line_nb, str element_name, object value):
if value is None :
value = OBIChar_NA
if obi_column_set_obichar_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name), str2bytes(value)[0]) < 0:
raise Exception("Problem setting a value in a column")
cpdef set_line(self, index_t line_nb, object values):
cdef str value
for element_name in values :
value = values[element_name]
self.set_item(line_nb, element_name, value)
cpdef close(self):
if obi_truncate_and_close_column(self.pointer) < 0 :
raise Exception("Problem closing a column")
python/obitools3/obidms/_obidmscolumn_float.cfiles
View file @ a8f03248
../../../src/obidmscolumn_float.c
../../../src/obidmscolumn_float.h
../../../src/obiview.h
../../../src/obiview.c
../../../src/obidmscolumn.h
../../../src/obidmscolumn.c
../../../src/obidmscolumndir.h
......
python/obitools3/obidms/_obidmscolumn_float.pxd
View file @ a8f03248
#cython: language_level=3
from .capi.obitypes cimport obifloat_t, index_t
from ._obidms cimport OBIDMS_column
from .capi.obitypes cimport index_t
from ._obidms cimport OBIDMS_column, OBIDMS_column_multi_elts
cdef class OBIDMS_column_float(OBIDMS_column):
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_float_writable(OBIDMS_column_float):
cpdef set_line(self, index_t line_nb, object value)
cpdef close(self)
cdef class OBIDMS_column_float_multi_elts(OBIDMS_column_float):
cdef class OBIDMS_column_multi_elts_float(OBIDMS_column_multi_elts):
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, index_t line_nb, str element_name, obifloat_t value)
cpdef set_line(self, index_t line_nb, object values)
cpdef close(self)
cpdef set_item(self, index_t line_nb, str element_name, object value)
python/obitools3/obidms/_obidmscolumn_float.pyx
View file @ a8f03248
#cython: language_level=3
from .capi.obidmscolumn cimport obi_close_column,\
obi_truncate_and_close_column, \
obi_column_get_obifloat_with_elt_name, \
obi_column_get_obifloat_with_elt_idx, \
obi_column_set_obifloat_with_elt_name, \
obi_column_set_obifloat_with_elt_idx
from .capi.obidmscolumn cimport obi_truncate_and_close_column,\
obi_column_get_obifloat_with_elt_name_in_view, \
obi_column_get_obifloat_with_elt_idx_in_view, \
obi_column_set_obifloat_with_elt_name_in_view, \
obi_column_set_obifloat_with_elt_idx_in_view
from .capi.obierrno cimport obi_errno
from .capi.obitypes cimport OBIFloat_NA
from .capi.obitypes cimport OBIFloat_NA, obifloat_t
from obitools3.utils cimport str2bytes
......@@ -17,7 +16,7 @@ cdef class OBIDMS_column_float(OBIDMS_column):
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)
value = obi_column_get_obifloat_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIFloat_NA :
......@@ -27,30 +26,18 @@ cdef class OBIDMS_column_float(OBIDMS_column):
return result
cpdef set_line(self, index_t line_nb, object value):
raise Exception("Column is read-only")
cpdef close(self):
if obi_close_column(self.pointer) < 0 :
raise Exception("Problem closing a column")
cdef class OBIDMS_column_float_writable(OBIDMS_column_float):
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:
if value is None :
value = OBIFloat_NA
if obi_column_set_obifloat_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0, <obifloat_t> value) < 0:
raise Exception("Problem setting a value in a column")
cpdef close(self):
if obi_truncate_and_close_column(self.pointer) < 0 :
raise Exception("Problem closing a column")
cdef class OBIDMS_column_float_multi_elts(OBIDMS_column_float):
cdef class OBIDMS_column_multi_elts_float(OBIDMS_column_multi_elts):
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))
value = obi_column_get_obifloat_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name))
if obi_errno > 0 :
raise IndexError(line_nb, element_name)
if value == OBIFloat_NA :
......@@ -58,46 +45,33 @@ cdef class OBIDMS_column_float_multi_elts(OBIDMS_column_float):
else :
result = <double> value
return result
cpdef object get_line(self, index_t line_nb) :
cdef obifloat_t value
cdef object result
cdef object value_in_result
cdef dict result
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_obifloat_with_elt_idx(self.pointer, line_nb, i)
value = obi_column_get_obifloat_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, i)
if obi_errno > 0 :
raise IndexError(line_nb)
result[self.elements_names[i]] = <double> value
if all_NA and (value != OBIFloat_NA) :
raise IndexError(line_nb)
if value == OBIFloat_NA :