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Cython API to add an OBI_QUAL column after creating a view

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This commit is contained in:
Celine Mercier
2017-12-19 11:06:24 +01:00
parent b7b8ba7e5a
commit 1a5b499b5c
1 changed files with 20 additions and 5 deletions
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25
python/obitools3/dms/column/column.pyx
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@ -6,8 +6,9 @@ __OBIDMS_COLUMN_CLASS__ = {}
from ..capi.obitypes cimport name_data_type, \ from ..capi.obitypes cimport name_data_type, \
obitype_t, \ obitype_t, \
obiversion_t obiversion_t, \
OBI_QUAL
from ..capi.obidms cimport obi_import_column from ..capi.obidms cimport obi_import_column
from ..capi.obidmscolumn cimport OBIDMS_column_header_p, \ from ..capi.obidmscolumn cimport OBIDMS_column_header_p, \
@ -18,7 +19,8 @@ from ..capi.obiutils cimport obi_format_date
from ..capi.obiview cimport obi_view_add_column, \ from ..capi.obiview cimport obi_view_add_column, \
obi_view_get_pointer_on_column_in_view, \ obi_view_get_pointer_on_column_in_view, \
Obiview_p Obiview_p, \
NUC_SEQUENCE_COLUMN
from ..object cimport OBIDeactivatedInstanceError from ..object cimport OBIDeactivatedInstanceError
@ -85,6 +87,8 @@ cdef class Column(OBIWrapper) :
cdef bytes column_name_b = tobytes(column_name) cdef bytes column_name_b = tobytes(column_name)
cdef bytes alias_b = tobytes(alias) cdef bytes alias_b = tobytes(alias)
cdef bytes comments_b = tobytes(comments) cdef bytes comments_b = tobytes(comments)
cdef char* associated_column_name
cdef int associated_column_version
cdef list elements_names_s cdef list elements_names_s
cdef bytes elements_names_b cdef bytes elements_names_b
cdef char* elements_names_p cdef char* elements_names_p
@ -109,6 +113,17 @@ cdef class Column(OBIWrapper) :
else: else:
elements_names_p = NULL elements_names_p = NULL
# TODO discuss
if data_type == OBI_QUAL:
if NUC_SEQUENCE_COLUMN not in view:
raise RuntimeError("Cannot create column %s in view %s: trying to create quality column but no NUC_SEQ column to associate it with in the view" % (bytes2str(column_name_b),
bytes2str(view.name)))
associated_column_name = NUC_SEQUENCE_COLUMN
associated_column_version = view[NUC_SEQUENCE_COLUMN].version
else:
associated_column_name = NULL
associated_column_version = -1
if (obi_view_add_column(view = view.pointer(), if (obi_view_add_column(view = view.pointer(),
column_name = column_name_b, column_name = column_name_b,
version_number = -1, version_number = -1,
@ -121,8 +136,8 @@ cdef class Column(OBIWrapper) :
tuples = tuples, tuples = tuples,
to_eval = to_eval, to_eval = to_eval,
indexer_name = NULL, indexer_name = NULL,
associated_column_name = NULL, associated_column_name = associated_column_name,
associated_column_version = -1, associated_column_version = associated_column_version,
comments = comments_b, comments = comments_b,
create = True)<0): create = True)<0):
raise RuntimeError("Cannot create column %s in view %s" % (bytes2str(column_name_b), raise RuntimeError("Cannot create column %s in view %s" % (bytes2str(column_name_b),