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Added properties for the OBIView class and cleaned up deprecated code

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This commit is contained in:
Celine Mercier
2016-09-28 14:26:23 +02:00
parent 03a2c8ef7c
commit b717e8bb8b
3 changed files with 86 additions and 102 deletions
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18
python/obitools3/commands/test.pyx
View File

@ -65,7 +65,7 @@ def random_str_with_max_len(max_len):
def random_column(infos): def random_column(infos):
return random.choice(list(infos['view'].get_columns())) return random.choice(list(infos['view'].columns))
def random_unique_name(infos): def random_unique_name(infos):
@ -117,7 +117,7 @@ def test_add_col(config, infos):
#existing_col = random_bool(config) # TODO doesn't work because of line count problem. See obiview.c line 1737 #existing_col = random_bool(config) # TODO doesn't work because of line count problem. See obiview.c line 1737
#if existing_col and infos["view_names"] != [] : #if existing_col and infos["view_names"] != [] :
# random_view = infos['dms'].open_view(random.choice(infos["view_names"])) # random_view = infos['dms'].open_view(random.choice(infos["view_names"]))
# random_column = random_view[random.choice(list(random_view.get_columns()))] # random_column = random_view[random.choice(list(random_view.columns)]
# random_column_refs = random_column.refs # random_column_refs = random_column.refs
# if random_column_refs['name'] in infos['view'] : # if random_column_refs['name'] in infos['view'] :
# alias = random_unique_name(infos) # alias = random_unique_name(infos)
@ -132,7 +132,7 @@ def test_add_col(config, infos):
def test_delete_col(config, infos): def test_delete_col(config, infos):
print_test(config, ">>> Delete column test") print_test(config, ">>> Delete column test")
if len(list(infos['view'].get_columns())) <= 1 : if len(list(infos['view'].columns)) <= 1 :
print_test(config, "-") print_test(config, "-")
return return
col_name = random_column(infos) col_name = random_column(infos)
@ -218,18 +218,18 @@ def random_new_view(config, infos, first=False):
clone = False clone = False
quality_col = False # TODO quality_col = False # TODO
if not first: if not first:
infos['view_names'].append(infos['view'].get_name()) infos['view_names'].append(infos['view'].name)
infos['view'].save_and_close() infos['view'].save_and_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 = None
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)
if create_line_selection and v_to_clone.get_line_count() > 0: if create_line_selection and v_to_clone.line_count > 0:
print_test(config, "New view with new line selection.") print_test(config, "New view with new line selection.")
line_selection = [] line_selection = []
for i in range(random.randint(1, v_to_clone.get_line_count())) : for i in range(random.randint(1, v_to_clone.line_count)) :
line_selection.append(random.randint(0, v_to_clone.get_line_count()-1)) line_selection.append(random.randint(0, v_to_clone.line_count-1))
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()
@ -242,9 +242,9 @@ def random_new_view(config, infos, first=False):
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:
assert v_to_clone.get_line_count() == infos['view'].get_line_count(), "New view and cloned view don't have the same line count" assert v_to_clone.line_count == infos['view'].line_count, "New view and cloned view don't have the same line count"
else : else :
assert len(line_selection) == infos['view'].get_line_count(), "New view with new line selection does not have the right line count" assert len(line_selection) == infos['view'].line_count, "New view with new line selection does not have the right line count"
v_to_clone.save_and_close() v_to_clone.save_and_close()
if first : if first :
fill_view(config, infos) fill_view(config, infos)

10
python/obitools3/obidms/_obidms.pxd
View File

@ -28,16 +28,14 @@ cdef class OBIDMS_column_multi_elts(OBIDMS_column):
cdef class OBIDMS_column_line: cdef class OBIDMS_column_line:
cdef OBIDMS_column column cdef OBIDMS_column column
cdef index_t index cdef index_t index
cdef class OBIView: cdef class OBIView:
cdef Obiview_p pointer cdef Obiview_p pointer
cdef str name
cdef str comments
cdef dict columns
cdef OBIDMS dms cdef OBIDMS dms
cdef dict columns
cpdef delete_column(self, str column_name) cpdef delete_column(self, str column_name)
cpdef add_column(self, cpdef add_column(self,
@ -57,14 +55,10 @@ 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 save_and_close(self) cpdef save_and_close(self)
cpdef str get_name(self)
cpdef dict get_columns(self)
cpdef int get_line_count(self)
cdef class OBIView_NUC_SEQS(OBIView): cdef class OBIView_NUC_SEQS(OBIView):
cpdef delete_column(self, str column_name)
cpdef align(self, cpdef align(self,
OBIView oview, OBIView oview,
OBIView iview2=*, OBIView iview2=*,

160
python/obitools3/obidms/_obidms.pyx
View File

@ -83,7 +83,7 @@ from cpython.pycapsule cimport PyCapsule_New, PyCapsule_GetPointer
cdef class OBIDMS_column : cdef class OBIDMS_column :
# Should only be initialized through a subclass # Note: should only be initialized through a subclass
def __init__(self, OBIView view, str column_alias): def __init__(self, OBIView view, str column_alias):
cdef OBIDMS_column_p column_p cdef OBIDMS_column_p column_p
@ -94,9 +94,9 @@ cdef class OBIDMS_column :
# Fill structure # Fill structure
self.column_alias = column_alias self.column_alias = column_alias
self.pointer = column_pp self.pointer = column_pp
self.dms = view.dms self.dms = view.dms
self.view = view self.view = view
def __setitem__(self, index_t line_nb, object value): def __setitem__(self, index_t line_nb, object value):
self.set_line(line_nb, value) self.set_line(line_nb, value)
@ -105,20 +105,16 @@ cdef class OBIDMS_column :
return self.get_line(line_nb) return self.get_line(line_nb)
def __len__(self): def __len__(self):
return (self.pointer)[0].header.lines_used return self.lines_used
def __sizeof__(self): def __sizeof__(self):
return ((self.pointer)[0].header.header_size + (self.pointer)[0].header.data_size) return ((self.pointer)[0].header.header_size + (self.pointer)[0].header.data_size)
def __iter__(self): def __iter__(self):
# Declarations # Declarations
cdef index_t lines_used cdef index_t line_nb
cdef index_t line_nb
# Yield each line # Yield each line
lines_used = (self.pointer)[0].header.lines_used for line_nb in range(self.lines_used):
for line_nb in range(lines_used):
yield self.get_line(line_nb) yield self.get_line(line_nb)
def __str__(self) : def __str__(self) :
@ -129,7 +125,7 @@ cdef class OBIDMS_column :
return to_print return to_print
def __repr__(self) : def __repr__(self) :
return (self.column_alias + ", original name: " + self.original_name + ", version " + str((self.pointer)[0].header.version) + ", data type: " + self.data_type) return (self.column_alias + ", original name: " + self.original_name + ", version " + str(self.version) + ", data type: " + self.data_type)
cpdef close(self): cpdef close(self):
if obi_close_column((self.pointer)[0]) < 0 : if obi_close_column((self.pointer)[0]) < 0 :
@ -177,7 +173,6 @@ cdef class OBIDMS_column :
@property @property
def comments(self): def comments(self):
return bytes2str((self.pointer)[0].header.comments) return bytes2str((self.pointer)[0].header.comments)
# TODO setter that concatenates?
# creation_date property getter # creation_date property getter
@property @property
@ -187,11 +182,11 @@ cdef class OBIDMS_column :
@staticmethod @staticmethod
cdef object get_subclass_type(OBIDMS_column_p column_p) : cdef object get_subclass_type(OBIDMS_column_p column_p) :
cdef object subclass cdef object subclass
cdef OBIDMS_column_header_p header cdef OBIDMS_column_header_p header
cdef OBIType_t col_type cdef OBIType_t col_type
cdef bint col_writable cdef bint col_writable
cdef bint col_one_element_per_line cdef bint col_one_element_per_line
header = column_p.header header = column_p.header
col_type = header.returned_data_type col_type = header.returned_data_type
@ -241,6 +236,7 @@ cdef class OBIDMS_column :
###################################################################################################### ######################################################################################################
cdef class OBIDMS_column_multi_elts(OBIDMS_column) : cdef class OBIDMS_column_multi_elts(OBIDMS_column) :
def __getitem__(self, index_t line_nb): def __getitem__(self, index_t line_nb):
@ -250,8 +246,10 @@ cdef class OBIDMS_column_multi_elts(OBIDMS_column) :
for element_name in values : for element_name in values :
self.set_item(line_nb, element_name, values[element_name]) self.set_item(line_nb, element_name, values[element_name])
###################################################################################################### ######################################################################################################
cdef class OBIDMS_column_line : cdef class OBIDMS_column_line :
def __init__(self, OBIDMS_column column, index_t line_nb) : def __init__(self, OBIDMS_column column, index_t line_nb) :
@ -270,22 +268,21 @@ cdef class OBIDMS_column_line :
def __repr__(self) : def __repr__(self) :
return str(self.column.get_line(self.index)) return str(self.column.get_line(self.index))
##########################################
######################################################################################################
cdef class OBIView : cdef class OBIView :
def __init__(self, OBIDMS dms, str view_name, bint new=False, object view_to_clone=None, list 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, list line_selection=None, str comments="", bint quality_column=False):
# TODO quality_column is only here because it's needed for OBIView_NUC_SEQS views, not clean # TODO quality_column is only here because it's needed for OBIView_NUC_SEQS views, not clean?
cdef Obiview_p view = NULL cdef Obiview_p view = NULL
cdef int i cdef index_t* line_selection_p
cdef list col_list cdef int i
cdef str col_name cdef str col_alias
cdef OBIDMS_column column cdef OBIDMS_column_p column_p
cdef OBIDMS_column_p column_p cdef object subclass
cdef OBIDMS_column_header_p header
cdef index_t* line_selection_p
self.dms = dms self.dms = dms
@ -305,46 +302,38 @@ cdef class OBIView :
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))
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), (<OBIView> view_to_clone).pointer, line_selection_p, str2bytes(comments))
elif view_to_clone is None : else :
view = obi_new_view(dms.pointer, str2bytes(view_name), NULL, line_selection_p, str2bytes(comments)) view = obi_new_view(dms.pointer, str2bytes(view_name), NULL, line_selection_p, str2bytes(comments))
# Else, open the existing view # Else, open the existing view
elif not new : else :
if view_name is not None : view = obi_open_view(dms.pointer, str2bytes(view_name))
view = obi_open_view(dms.pointer, str2bytes(view_name))
elif view_name is None :
view = obi_open_view(dms.pointer, NULL) # TODO discuss
if view == NULL : if view == NULL :
raise Exception("Error creating/opening a view") raise Exception("Error creating/opening a view")
self.pointer = view self.pointer = view
self.name = bytes2str(view.infos.name)
# Go through columns to build dictionaries of corresponding python instances # Go through columns to build dictionaries of corresponding python instances # TODO make function?
self.columns = {} self.columns = {}
for i in range(view.infos.column_count) : for i in range(view.infos.column_count) :
column_p = <OBIDMS_column_p> (view.columns)[i] col_alias = bytes2str(view.infos.column_references[i].alias)
header = (column_p).header column_p = <OBIDMS_column_p> (view.columns)[i]
col_name = bytes2str(view.infos.column_references[i].alias) subclass = OBIDMS_column.get_subclass_type(column_p)
subclass = OBIDMS_column.get_subclass_type(column_p) self.columns[col_alias] = subclass(self, col_alias)
self.columns[col_name] = subclass(self, col_name)
def __repr__(self) : def __repr__(self) :
cdef str s cdef str s
s = str(self.name) + "\n" + str(self.comments) + "\n" + str(self.pointer.infos.line_count) + " lines\n" s = str(self.name) + "\n" + str(self.comments) + "\n" + str(self.line_count) + " lines\n"
for column_name in self.columns : for column_name in self.columns :
s = s + self.columns[column_name].__repr__() + '\n' s = s + repr(self.columns[column_name]) + '\n'
return s return s
cpdef delete_column(self, str column_name) : cpdef delete_column(self, str column_name) :
cdef str column_n cdef str column_n
if obi_view_delete_column(self.pointer, str2bytes(column_name)) < 0 : if obi_view_delete_column(self.pointer, str2bytes(column_name)) < 0 :
raise Exception("Problem deleting a column from a view") raise Exception("Problem deleting a column from a view")
# Update the dictionary of column objects: # Update the dictionary of column objects:
(self.columns).pop(column_name) (self.columns).pop(column_name)
self.update_column_pointers() self.update_column_pointers()
@ -382,7 +371,7 @@ cdef class OBIView :
elif nb_elements_per_line == 1 : elif nb_elements_per_line == 1 :
elements_names_b = column_name_b elements_names_b = column_name_b
if type : if type : # TODO make C function that does that
if type == 'OBI_INT' : if type == 'OBI_INT' :
data_type = OBI_INT data_type = OBI_INT
elif type == 'OBI_FLOAT' : elif type == 'OBI_FLOAT' :
@ -400,7 +389,7 @@ cdef class OBIView :
else : else :
raise Exception("Invalid provided data type") raise Exception("Invalid provided data type")
if (obi_view_add_column(self.pointer, column_name_b, version_number, alias_b, # TODO should return pointer on column? if (obi_view_add_column(self.pointer, column_name_b, version_number, alias_b,
data_type, nb_lines, nb_elements_per_line, data_type, nb_lines, nb_elements_per_line,
elements_names_b, str2bytes(indexer_name), elements_names_b, str2bytes(indexer_name),
str2bytes(associated_column_name), associated_column_version, str2bytes(associated_column_name), associated_column_version,
@ -413,8 +402,8 @@ cdef class OBIView :
# Open and store the subclass # Open and store the subclass
subclass = OBIDMS_column.get_subclass_type(column_p) subclass = OBIDMS_column.get_subclass_type(column_p)
(self.columns)[alias] = subclass(self, alias) (self.columns)[alias] = subclass(self, alias)
cpdef change_column_alias(self, str current_alias, str new_alias): cpdef change_column_alias(self, str current_alias, str new_alias):
cdef OBIDMS_column column cdef OBIDMS_column column
if (obi_view_create_column_alias(self.pointer, str2bytes(current_alias), str2bytes(new_alias)) < 0) : if (obi_view_create_column_alias(self.pointer, str2bytes(current_alias), str2bytes(new_alias)) < 0) :
@ -440,17 +429,14 @@ cdef class OBIView :
def __iter__(self): def __iter__(self):
# iter on each line of all columns # Iteration on each line of all columns
# Declarations # Declarations
cdef index_t lines_used
cdef index_t line_nb cdef index_t line_nb
cdef OBIView_line line # TODO Check that this works for NUC SEQ views cdef OBIView_line line
# Yield each line # Yield each line
lines_used = self.pointer.infos.line_count for line_nb in range(self.line_count) :
for line_nb in range(lines_used) :
line = self[line_nb] line = self[line_nb]
yield line yield line
@ -467,29 +453,38 @@ cdef class OBIView :
def __len__(self): def __len__(self):
return(self.pointer.infos.line_count) return(self.line_count)
def __str__(self) : def __str__(self) :
cdef OBIView_line line cdef OBIView_line line
cdef str to_print cdef str to_print
to_print = "" to_print = ""
for line in self.__iter__() : for line in self :
to_print = to_print + str(line) + "\n" to_print = to_print + str(line) + "\n"
return to_print return to_print
cpdef str get_name(self): # line_count property getter
return self.name @property
def line_count(self):
cpdef dict get_columns(self):
return self.columns
cpdef int get_line_count(self) :
return self.pointer.infos.line_count return self.pointer.infos.line_count
# name property getter
@property
def name(self):
return bytes2str(self.pointer.infos.name)
# columns property getter
@property
def columns(self):
return self.columns
# comments property getter
@property
def comments(self):
return bytes2str(self.pointer.infos.comments)
# TODO setter that concatenates new comments?
############################################# #############################################
@ -497,14 +492,12 @@ cdef class OBIView_NUC_SEQS(OBIView):
def __init__(self, OBIDMS dms, str view_name, bint new=False, object view_to_clone=None, list 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, list line_selection=None, str comments="", bint quality_column=False):
cdef Obiview_p view = NULL cdef Obiview_p view = NULL
cdef int i cdef index_t* line_selection_p
cdef list col_list cdef int i
cdef str col_name cdef str col_alias
cdef OBIDMS_column column cdef OBIDMS_column_p column_p
cdef OBIDMS_column_p column_p cdef object subclass
cdef OBIDMS_column_header_p header
cdef index_t* line_selection_p
self.dms = dms self.dms = dms
@ -534,17 +527,14 @@ cdef class OBIView_NUC_SEQS(OBIView):
raise Exception("Error creating/opening view") raise Exception("Error creating/opening view")
self.pointer = view self.pointer = view
self.name = bytes2str(view.infos.name)
self.comments = bytes2str(view.infos.comments)
# Go through columns to build list of corresponding python instances # Go through columns to build dictionaries of corresponding python instances # TODO make function?
self.columns = {} self.columns = {}
for i in range(view.infos.column_count) : for i in range(view.infos.column_count) :
column_p = <OBIDMS_column_p> (view.columns)[i] col_alias = bytes2str(view.infos.column_references[i].alias)
header = (column_p).header column_p = <OBIDMS_column_p> (view.columns)[i]
col_name = bytes2str(view.infos.column_references[i].alias) subclass = OBIDMS_column.get_subclass_type(column_p)
subclass = OBIDMS_column.get_subclass_type(column_p) self.columns[col_alias] = subclass(self, col_alias)
self.columns[col_name] = subclass(self, col_name)
def __getitem__(self, object item) : def __getitem__(self, object item) :
if type(item) == str : if type(item) == str :
@ -557,7 +547,7 @@ cdef class OBIView_NUC_SEQS(OBIView):
self[line_idx][key] = sequence_obj[key] self[line_idx][key] = sequence_obj[key]
# TODO # TODO discuss
cpdef align(self, OBIView oview, OBIView iview2=None, cpdef align(self, OBIView oview, OBIView iview2=None,
double threshold=0.0, bint normalize=True, int reference=0, bint similarity_mode=True) : double threshold=0.0, bint normalize=True, int reference=0, bint similarity_mode=True) :