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Major update: new type of columns containing indices referring to lines

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in other columns
This commit is contained in:
Celine Mercier
2015-11-29 11:57:07 +01:00
parent 2cf10cb6f0
commit b45b496b0e
15 changed files with 319 additions and 83 deletions
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23
python/obitools3/obidms/_obidms.pyx
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@ -14,6 +14,7 @@ from .capi.obidmscolumn cimport obi_column_get_header_from_name, \
obi_open_column, \
obi_close_column, \
obi_column_format_date, \
obi_grep_line, \
OBIDMS_column_header_p
from .capi.obitypes cimport const_char_p, \
OBIType_t, \
@ -109,7 +110,7 @@ cdef class OBIDMS :
column_name_b = str2bytes(column_name)
dms[column_name] = {}
header = obi_column_get_header_from_name(self.pointer, column_name_b, -1)
data_type = bytes2str(name_data_type(header.data_type))
data_type = bytes2str(name_data_type(header.returned_data_type))
line_count = header.line_count
creation_date = bytes2str(obi_column_format_date(header.creation_date))
obi_unmap_header(header)
@ -127,6 +128,7 @@ cdef class OBIDMS :
str column_name,
bint create=False,
bint clone=False, bint clone_data=True,
bint referring=False,
obiversion_t version_number=-1,
str type='',
index_t nb_lines=0,
@ -157,7 +159,7 @@ cdef class OBIDMS :
if create :
raise Exception("A data type must be specified")
else :
data_type = header.data_type
data_type = header.returned_data_type
else :
if type == 'OBI_INT' :
data_type = OBI_INT
@ -179,7 +181,7 @@ cdef class OBIDMS :
if create : # Set to one if not provided (default value)
nb_elements_per_line = 1
else :
nb_elements_per_line = header.nb_elements_per_line
nb_elements_per_line = header.returned_nb_elements_per_line
if nb_elements_per_line > 1 :
elements_names = bytes2str(header.elements_names).split(';')
@ -258,7 +260,8 @@ cdef class OBIDMS :
raise Exception("Problem with the data type")
column = subclass(self, column_name,
create, clone, clone_data,
create, clone, clone_data,
referring,
version_number, data_type,
nb_lines, nb_elements_per_line,
elements_names, array_name,
@ -276,6 +279,7 @@ cdef class OBIDMS_column :
str column_name,
bint create,
bint clone, bint clone_data,
bint referring,
obiversion_t version_number,
OBIType_t type,
index_t nb_lines,
@ -312,10 +316,14 @@ cdef class OBIDMS_column :
elements_names_b = str2bytes(";".join(elements_names))
self.pointer = obi_create_column(self.dms.pointer, column_name_b, type,
nb_lines, nb_elements_per_line,
elements_names_b, array_name_b, comments_b)
elements_names_b, array_name_b, comments_b,
referring)
else :
if clone :
self.pointer = obi_clone_column(self.dms.pointer, column_name_b, version_number, clone_data)
self.pointer = obi_clone_column(self.dms.pointer, column_name_b, version_number, referring, clone_data)
elif referring :
self.pointer = obi_clone_column(self.dms.pointer, column_name_b, version_number, referring, False)
referred_column_pointer = self.pointer.referred_column
else :
self.pointer = obi_open_column(self.dms.pointer, column_name_b, version_number)
@ -355,6 +363,9 @@ cdef class OBIDMS_column :
# cpdef set_item(self, index_t line_nb, str element_name, object value): TODO
# raise NotImplementedError
cpdef grep_line(self, index_t line_nb):
if obi_grep_line(self.pointer, line_nb) < 0 :
raise Exception("Error grepping line")
cpdef list get_elements_names(self):
return self.elements_names