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Changed the cython API to create new views so as to have different

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functions for the different cases
This commit is contained in:
Celine Mercier
2016-12-07 14:17:57 +01:00
parent 936be64c34
commit fa4e4ffaff
4 changed files with 64 additions and 51 deletions
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2
python/obitools3/commands/grep.pyx
View File

@ -77,7 +77,7 @@ def run(config):
selection.append(i) selection.append(i)
# Create output view with the line selection # Create output view with the line selection
oview = d.new_view(config['obi']['outputview'], line_selection=selection, comments="obi grep: "+str(config['grep']['predicates'])+"\n") oview = d.clone_view_with_line_selection(config['obi']['outputview'], selection, comments="obi grep: "+str(config['grep']['predicates'])+"\n")
#print("\n") #print("\n")
#print(repr(oview)) #print(repr(oview))

19
python/obitools3/commands/test.pyx
View File

@ -8,7 +8,7 @@ import string
import random import random
VIEW_TYPES = [None, "NUC_SEQS_VIEW"] VIEW_TYPES = ["", "NUC_SEQS_VIEW"]
COL_TYPES = ["OBI_BOOL", "OBI_CHAR", "OBI_FLOAT", "OBI_INT", "OBI_SEQ", "OBI_STR"] COL_TYPES = ["OBI_BOOL", "OBI_CHAR", "OBI_FLOAT", "OBI_INT", "OBI_SEQ", "OBI_STR"]
NUC_SEQUENCE_COLUMN = "NUC_SEQ" NUC_SEQUENCE_COLUMN = "NUC_SEQ"
ID_COLUMN = "ID" ID_COLUMN = "ID"
@ -212,13 +212,12 @@ def fill_view(config, infos):
def random_new_view(config, infos, first=False): def random_new_view(config, infos, first=False):
v_to_clone = None v_to_clone = None
line_selection = None line_selection = None
clone = False
quality_col = False # TODO quality_col = False # TODO
if not first: if not first:
infos['view_names'].append(infos['view'].name) infos['view_names'].append(infos['view'].name)
infos['view'].close() infos['view'].close()
v_to_clone = infos['dms'].open_view(random.choice(infos["view_names"])) v_to_clone = infos['dms'].open_view(random.choice(infos["view_names"]))
v_type = None v_type = ""
print_test(config, "View to clone: ") print_test(config, "View to clone: ")
print_test(config, repr(v_to_clone)) print_test(config, repr(v_to_clone))
create_line_selection = random_bool(config) create_line_selection = random_bool(config)
@ -230,12 +229,14 @@ def random_new_view(config, infos, first=False):
#print_test(config, "New line selection: "+str(line_selection)) #print_test(config, "New line selection: "+str(line_selection))
else : else :
v_type = random_view_type() v_type = random_view_type()
infos['view'] = infos['dms'].new_view(random_unique_name(infos),
view_to_clone=v_to_clone, if line_selection is not None :
line_selection=line_selection, infos['view'] = infos['dms'].clone_view_with_line_selection(random_unique_name(infos), line_selection, comments=random_str_with_max_len(config['test']['commentsmaxlen']))
view_type=v_type, elif v_to_clone is not None :
comments=random_str_with_max_len(config['test']['commentsmaxlen']), infos['view'] = infos['dms'].clone_view(random_unique_name(infos), v_to_clone, comments=random_str_with_max_len(config['test']['commentsmaxlen']))
quality_column=quality_col) else :
infos['view'] = infos['dms'].new_view(random_unique_name(infos), view_type=v_type, comments=random_str_with_max_len(config['test']['commentsmaxlen']), quality_column=quality_col)
print_test(config, repr(infos['view'])) print_test(config, repr(infos['view']))
if v_to_clone is not None : if v_to_clone is not None :
if line_selection is None: if line_selection is None:

24
python/obitools3/obidms/_obidms.pxd
View File

@ -36,14 +36,14 @@ cdef class OBIView:
cdef dict _columns cdef dict _columns
cdef Obiview_p _open_or_create_view(self, cdef Obiview_p _open_or_create_view(self,
OBIDMS dms, OBIDMS dms,
str view_name, str view_name,
bint new=*, bint new=*,
object view_to_clone=*, object view_to_clone=*,
index_t* line_selection_p=*, index_t* line_selection_p=*,
str comments=*, str comments=*,
bint quality_column=*, bint quality_column=*,
str view_type=*) 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,
@ -63,6 +63,8 @@ cdef class OBIView:
cpdef change_column_alias(self, str current_alias, str new_alias) cpdef change_column_alias(self, str current_alias, str new_alias)
cpdef update_column_pointers(self) cpdef update_column_pointers(self)
cpdef close(self) cpdef close(self)
@staticmethod
cdef object get_view_subclass(str view_type)
cdef class OBIView_NUC_SEQS(OBIView): cdef class OBIView_NUC_SEQS(OBIView):
@ -96,7 +98,11 @@ cdef class OBIDMS:
cpdef close(self) cpdef close(self)
cpdef OBI_Taxonomy open_taxonomy(self, str taxo_name) cpdef OBI_Taxonomy open_taxonomy(self, str taxo_name)
cpdef OBIView open_view(self, str view_name) cpdef OBIView open_view(self, str view_name)
cpdef OBIView new_view(self, str view_name, object view_to_clone=*, OBIView_line_selection line_selection=*, str view_type=*, str comments=*, bint quality_column=*)
cpdef OBIView new_view(self, str view_name, str view_type=*, bint quality_column=*, str comments=*)
cpdef OBIView clone_view(self, str view_name, object view_to_clone, str comments=*)
cpdef OBIView clone_view_with_line_selection(self, str view_name, OBIView_line_selection line_selection, str comments=*)
cpdef dict read_view_infos(self, str view_name) cpdef dict read_view_infos(self, str view_name)
# cpdef dict read_views(self) TODO # cpdef dict read_views(self) TODO

64
python/obitools3/obidms/_obidms.pyx
View File

@ -272,7 +272,7 @@ 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, str view_type=None): 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=""):
cdef index_t* line_selection_p = NULL cdef index_t* line_selection_p = NULL
cdef int i cdef int i
@ -300,13 +300,13 @@ cdef class OBIView :
self._columns[col_alias] = subclass(self, col_alias) 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 _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=""):
cdef Obiview_p view = NULL cdef Obiview_p view = NULL
# Create the view if needed, with the right type # Create the view if needed, with the right type
if new : if new :
if view_type is None : if view_type == "" :
if view_to_clone is not None : if view_to_clone is not None :
if type(view_to_clone) == str : 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)) view = obi_new_view_cloned_from_name(dms._pointer, str2bytes(view_name), str2bytes(view_to_clone), line_selection_p, str2bytes(comments))
@ -507,6 +507,16 @@ cdef class OBIView :
# TODO setter that concatenates new comments? # TODO setter that concatenates new comments?
@staticmethod
cdef object get_view_subclass(str view_type) :
cdef object subclass
if view_type == bytes2str(VIEW_TYPE_NUC_SEQS) :
view_class = OBIView_NUC_SEQS
else :
view_class = OBIView
return view_class
###################################################################################################### ######################################################################################################
@ -685,39 +695,35 @@ cdef class OBIDMS :
cpdef OBIView open_view(self, str view_name) : cpdef OBIView open_view(self, str view_name) :
cdef object view_class cdef object view_class
cdef dict view_infos view_class = OBIView.get_view_subclass(self.read_view_infos(view_name)["view_type"])
view_infos = self.read_view_infos(view_name)
if view_infos["view_type"] == bytes2str(VIEW_TYPE_NUC_SEQS) :
view_class = OBIView_NUC_SEQS
else :
view_class = OBIView
return view_class(self, view_name) return view_class(self, view_name)
cpdef OBIView new_view(self, str view_name, object view_to_clone=None, OBIView_line_selection line_selection=None, str view_type=None, str comments="", bint quality_column=False) : cpdef OBIView new_view(self, str view_name, str view_type="", bint quality_column=False, str comments="") :
cdef object view_class cdef object view_class
# Get right subclass depending on view type # Get right subclass depending on view type
if view_type is not None : view_class = OBIView.get_view_subclass(view_type)
if view_type == bytes2str(VIEW_TYPE_NUC_SEQS) : return view_class(self, view_name, new=True, comments=comments, quality_column=quality_column, view_type=view_type)
view_class = OBIView_NUC_SEQS
else :
view_class = OBIView
# 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 \
((type(view_to_clone) == str and self.read_view_infos(view_to_clone)["view_type"] == bytes2str(VIEW_TYPE_NUC_SEQS)) or \
(type(view_to_clone) != str and view_to_clone.type == bytes2str(VIEW_TYPE_NUC_SEQS)))) or \
(line_selection is not None and (line_selection._view.type == bytes2str(VIEW_TYPE_NUC_SEQS))) :
view_type = bytes2str(VIEW_TYPE_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, view_type=view_type)
cpdef OBIView clone_view(self, str view_name, object view_to_clone, str comments="") :
cdef object view_class
cdef str view_type
# Get right subclass depending on view type
if type(view_to_clone) == str :
view_type = self.read_view_infos(view_to_clone)["view_type"]
else :
view_type = view_to_clone.type
view_class = OBIView.get_view_subclass(view_type)
return view_class(self, view_name, new=True, view_to_clone=view_to_clone, comments=comments, view_type=view_type)
cpdef OBIView clone_view_with_line_selection(self, str view_name, OBIView_line_selection line_selection, str comments="") :
cdef object view_class
# Get right subclass depending on view type
view_class = OBIView.get_view_subclass(line_selection._view.type)
return view_class(self, view_name, new=True, view_to_clone=line_selection._view, line_selection=line_selection, comments=comments)
cpdef dict read_view_infos(self, str view_name) : cpdef dict read_view_infos(self, str view_name) :