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When a new view is created with a line selection, the view to clone is

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automatically found + compacted redundant code + fixed potential bug
when cloning a NUC_SEQS view by name
This commit is contained in:
Celine Mercier
2016-10-06 17:55:18 +02:00
parent 399fc2c051
commit 2dcfdc59fc
2 changed files with 56 additions and 82 deletions
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10
python/obitools3/obidms/_obidms.pxd
View File

@ -35,6 +35,16 @@ cdef class OBIView:
cdef Obiview_p _pointer cdef Obiview_p _pointer
cdef dict _columns cdef dict _columns
cdef Obiview_p _open_or_create_view(self,
OBIDMS dms,
str view_name,
bint new=*,
object view_to_clone=*,
index_t* line_selection_p=*,
str comments=*,
bint quality_column=*,
str view_type=*)
cpdef delete_column(self, str column_name) cpdef delete_column(self, str column_name)
cpdef add_column(self, cpdef add_column(self,
str column_name, str column_name,

124
python/obitools3/obidms/_obidms.pyx
View File

@ -273,34 +273,57 @@ cdef class OBIDMS_column_line :
cdef class OBIView : cdef class OBIView :
def __init__(self, OBIDMS dms, str view_name, bint new=False, object view_to_clone=None, OBIView_line_selection line_selection=None, str comments="", bint quality_column=False): def __init__(self, OBIDMS dms, str view_name, bint new=False, object view_to_clone=None, OBIView_line_selection line_selection=None, str comments="", bint quality_column=False, str view_type=None):
# TODO quality_column is only here because it's needed for OBIView_NUC_SEQS views, not clean?
cdef Obiview_p view = NULL cdef index_t* line_selection_p = NULL
cdef index_t* line_selection_p
cdef int i cdef int i
cdef str col_alias cdef str col_alias
cdef OBIDMS_column_p column_p cdef OBIDMS_column_p column_p
cdef object subclass cdef object subclass
# Create the C array for the line selection if needed
if line_selection is not None : if line_selection is not None :
line_selection_p = <index_t*> malloc((len(line_selection) + 1) * sizeof(index_t)) # Get the name of the associated view to clone
view_to_clone = line_selection._view_name # TODO discuss. This makes it possible for the view to clone to be closed. If a view to clone was given it is not checked.
# Build the C array corresponding to the line selection
line_selection_p = <index_t*> malloc((len(line_selection) + 1) * sizeof(index_t)) # +1 for the -1 flagging the end of the array
for i in range(len(line_selection)) : for i in range(len(line_selection)) :
line_selection_p[i] = line_selection[i] line_selection_p[i] = line_selection[i]
line_selection_p[len(line_selection)] = -1 line_selection_p[len(line_selection)] = -1 # flagging the end of the array
else :
line_selection_p = NULL
# Create the view if needed self._pointer = self._open_or_create_view(dms, view_name, new=new, view_to_clone=view_to_clone, line_selection_p=line_selection_p, comments=comments, quality_column=quality_column, view_type=None)
# Go through columns to build dictionaries of corresponding python instances # TODO make function?
self._columns = {}
for i in range(self._pointer.infos.column_count) :
col_alias = bytes2str(self._pointer.infos.column_references[i].alias)
column_p = <OBIDMS_column_p> (self._pointer.columns)[i]
subclass = OBIDMS_column.get_subclass_type(column_p)
self._columns[col_alias] = subclass(self, col_alias)
cdef Obiview_p _open_or_create_view(self, OBIDMS dms, str view_name, bint new=False, object view_to_clone=None, index_t* line_selection_p=NULL, str comments="", bint quality_column=False, str view_type=None):
cdef Obiview_p view = NULL
# Create the view if needed, with the right type
if new : if new :
if view_to_clone is not None : if view_type is None :
if type(view_to_clone) == str : if view_to_clone is not None :
view = obi_new_view_cloned_from_name(dms._pointer, str2bytes(view_name), str2bytes(view_to_clone), line_selection_p, str2bytes(comments)) if type(view_to_clone) == str :
view = obi_new_view_cloned_from_name(dms._pointer, str2bytes(view_name), str2bytes(view_to_clone), line_selection_p, str2bytes(comments))
else :
view = obi_new_view(dms._pointer, str2bytes(view_name), (<OBIView> view_to_clone)._pointer, line_selection_p, str2bytes(comments))
else : else :
view = obi_new_view(dms._pointer, str2bytes(view_name), (<OBIView> view_to_clone)._pointer, line_selection_p, str2bytes(comments)) view = obi_new_view(dms._pointer, str2bytes(view_name), NULL, line_selection_p, str2bytes(comments))
else : elif view_type == VIEW_TYPE_NUC_SEQS :
view = obi_new_view(dms._pointer, str2bytes(view_name), NULL, line_selection_p, str2bytes(comments)) if view_to_clone is not None :
if type(view_to_clone) == str :
view = obi_new_view_nuc_seqs_cloned_from_name(dms._pointer, str2bytes(view_name), str2bytes(view_to_clone), line_selection_p, str2bytes(comments), quality_column)
else :
view = obi_new_view_nuc_seqs(dms._pointer, str2bytes(view_name), (<OBIView> view_to_clone)._pointer, line_selection_p, str2bytes(comments), quality_column)
else :
view = obi_new_view_nuc_seqs(dms._pointer, str2bytes(view_name), NULL, line_selection_p, str2bytes(comments), quality_column)
# Else, open the existing view # Else, open the existing view
else : else :
view = obi_open_view(dms._pointer, str2bytes(view_name)) view = obi_open_view(dms._pointer, str2bytes(view_name))
@ -308,15 +331,7 @@ cdef class OBIView :
if view == NULL : if view == NULL :
raise Exception("Error creating/opening a view") raise Exception("Error creating/opening a view")
self._pointer = view return view
# Go through columns to build dictionaries of corresponding python instances # TODO make function?
self._columns = {}
for i in range(view.infos.column_count) :
col_alias = bytes2str(view.infos.column_references[i].alias)
column_p = <OBIDMS_column_p> (view.columns)[i]
subclass = OBIDMS_column.get_subclass_type(column_p)
self._columns[col_alias] = subclass(self, col_alias)
def __repr__(self) : def __repr__(self) :
@ -491,59 +506,6 @@ cdef class OBIView :
cdef class OBIView_NUC_SEQS(OBIView): cdef class OBIView_NUC_SEQS(OBIView):
def __init__(self, OBIDMS dms, str view_name, bint new=False, object view_to_clone=None, OBIView_line_selection line_selection=None, str comments="", bint quality_column=False):
cdef Obiview_p view = NULL
cdef index_t* line_selection_p
cdef int i
cdef str col_alias
cdef OBIDMS_column_p column_p
cdef object subclass
if line_selection is not None :
# Check that the line selection is associated with the view to clone
if view_to_clone is None :
raise Exception("Error creating a view: there is a new line selection but no associated view to clone")
if type(view_to_clone) == str :
if line_selection._view_name != view_to_clone :
raise Exception("Error creating a view: the new line selection isn't associated with the view to clone")
elif line_selection._view != view_to_clone :
raise Exception("Error creating a view: the new line selection isn't associated with the view to clone")
# Build the C array corresponding to the line selection
line_selection_p = <index_t*> malloc((len(line_selection) + 1) * sizeof(index_t)) # +1 for the -1 flagging the end of the array
for i in range(len(line_selection)) :
line_selection_p[i] = line_selection[i]
line_selection_p[len(line_selection)] = -1 # flagging the end of the array
else :
line_selection_p = NULL
if new :
if view_to_clone is not None :
if type(view_to_clone) == str :
view = obi_new_view_nuc_seqs_cloned_from_name(dms._pointer, str2bytes(view_name), str2bytes(view_to_clone), line_selection_p, str2bytes(comments), quality_column)
else :
view = obi_new_view_nuc_seqs(dms._pointer, str2bytes(view_name), (<OBIView> view_to_clone)._pointer, line_selection_p, str2bytes(comments), quality_column)
elif view_to_clone is None :
view = obi_new_view_nuc_seqs(dms._pointer, str2bytes(view_name), NULL, line_selection_p, str2bytes(comments), quality_column)
elif not new :
if view_name is not None :
view = obi_open_view(dms._pointer, str2bytes(view_name))
elif view_name is None :
view = obi_open_view(dms._pointer, NULL)
if view == NULL :
raise Exception("Error creating/opening view")
self._pointer = view
# Go through columns to build dictionaries of corresponding python instances # TODO make function?
self._columns = {}
for i in range(view.infos.column_count) :
col_alias = bytes2str(view.infos.column_references[i].alias)
column_p = <OBIDMS_column_p> (view.columns)[i]
subclass = OBIDMS_column.get_subclass_type(column_p)
self._columns[col_alias] = subclass(self, col_alias)
def __getitem__(self, object item) : def __getitem__(self, object item) :
if type(item) == str : if type(item) == str :
@ -551,6 +513,7 @@ cdef class OBIView_NUC_SEQS(OBIView):
elif type(item) == int : elif type(item) == int :
return OBI_Nuc_Seq_Stored(self, item) return OBI_Nuc_Seq_Stored(self, item)
def __setitem__(self, index_t line_idx, OBI_Nuc_Seq sequence_obj) : def __setitem__(self, index_t line_idx, OBI_Nuc_Seq sequence_obj) :
for key in sequence_obj : for key in sequence_obj :
self[line_idx][key] = sequence_obj[key] self[line_idx][key] = sequence_obj[key]
@ -753,11 +716,12 @@ cdef class OBIDMS :
view_class = OBIView view_class = OBIView
# Check the type of the view to clone if there is one # TODO make generic for future other view types # Check the type of the view to clone if there is one # TODO make generic for future other view types
if view_to_clone is not None and \ if view_to_clone is not None and \
((type(view_to_clone) == str and self.read_view_infos(view_to_clone)["view_type"] == VIEW_TYPE_NUC_SEQS) or \ ((type(view_to_clone) == str and self.read_view_infos(view_to_clone)["view_type"] == bytes2str(VIEW_TYPE_NUC_SEQS)) or \
isinstance(view_to_clone, OBIView_NUC_SEQS)) : isinstance(view_to_clone, OBIView_NUC_SEQS)) :
view_type = bytes2str(VIEW_TYPE_NUC_SEQS)
view_class = OBIView_NUC_SEQS view_class = OBIView_NUC_SEQS
return view_class(self, view_name, new=True, view_to_clone=view_to_clone, line_selection=line_selection, comments=comments, quality_column=quality_column) return view_class(self, view_name, new=True, view_to_clone=view_to_clone, line_selection=line_selection, comments=comments, quality_column=quality_column, view_type=view_type)
cpdef dict read_view_infos(self, str view_name) : cpdef dict read_view_infos(self, str view_name) :