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Added tuple columns containing immutable indexed data arrays of any type

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This commit is contained in:
Celine Mercier
2017-11-15 13:48:59 +01:00
parent 1684f96b79
commit 9a50803c00
32 changed files with 1097 additions and 284 deletions
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105
python/obitools3/commands/test.pyx
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@ -1,11 +1,11 @@
#cython: language_level=3
from obitools3.apps.progress cimport ProgressBar # TODO I absolutely don't understand why it doesn't work without that line
from obitools3.dms.view.view import View, Line_selection
from obitools3.dms.view import View, Line_selection
from obitools3.dms.view.typed_view.view_NUC_SEQS import View_NUC_SEQS
from obitools3.dms.dms import DMS
from obitools3.dms import DMS
from obitools3.dms.column import Column
from obitools3.dms.taxo.taxo import Taxonomy
from obitools3.dms.taxo import Taxonomy
from obitools3.utils cimport str2bytes
from obitools3.dms.capi.obitypes cimport OBI_INT, \
OBI_FLOAT, \
@ -69,26 +69,68 @@ def random_bool(config):
return random.choice([True, False])
def random_bool_tuples(config):
l=[]
for i in range(random.randint(1, config['test']['tuplemaxlen'])) :
l.append(random.choice([None, random_bool(config)]))
return tuple(l)
def random_char(config):
return str2bytes(random.choice(string.ascii_lowercase))
def random_char_tuples(config):
l=[]
for i in range(random.randint(1, config['test']['tuplemaxlen'])) :
l.append(random.choice([None, random_char(config)]))
return tuple(l)
def random_float(config):
return random.randint(0, MAX_INT) + random.random()
def random_float_tuples(config):
l=[]
for i in range(random.randint(1, config['test']['tuplemaxlen'])) :
l.append(random.choice([None, random_float(config)]))
return tuple(l)
def random_int(config):
return random.randint(0, config['test']['maxlinenb'])
def random_int_tuples(config):
l=[]
for i in range(random.randint(1, config['test']['tuplemaxlen'])) :
l.append(random.choice([None, random_int(config)]))
return tuple(l)
def random_seq(config):
return str2bytes(''.join(random.choice(['a','t','g','c']) for i in range(random_length(config['test']['seqmaxlen']))))
def random_seq_tuples(config):
l=[]
for i in range(random.randint(1, config['test']['tuplemaxlen'])) :
l.append(random.choice([None, random_seq(config)]))
return tuple(l)
def random_bytes(config):
return random_bytes_with_max_len(config['test']['strmaxlen'])
def random_bytes_tuples(config):
l=[]
for i in range(random.randint(1, config['test']['tuplemaxlen'])) :
l.append(random.choice([None, random_bytes(config)]))
return tuple(l)
def random_str_with_max_len(max_len):
return ''.join(random.choice(string.ascii_lowercase) for i in range(random_length(max_len)))
@ -132,11 +174,28 @@ def test_set_and_get(config, infos):
print_test(config, "-")
return
idx = random_int(config)
value = random.choice([None, infos['random_generator'][data_type](config)])
value = random.choice([None, infos['random_generator'][(data_type, col.tuples)](config)])
if col.nb_elements_per_line > 1 :
elt = random.choice(element_names)
col[idx][elt] = value
assert col[idx][elt] == value, "Column: "+repr(col)+"\nSet value != gotten value "+str(value)+" != "+str(col[idx][elt])
elif col.tuples:
col[idx] = value
if value is None:
totest = None
else:
totest = []
for e in value:
if e is not None and e != '':
totest.append(e)
if len(totest) == 0:
totest = None
else:
totest = tuple(totest)
assert col[idx] == totest, "Column: "+repr(col)+"\nSet value != gotten value "+str(totest)+" != "+str(col[idx])
if totest is not None:
for i in range(len(totest)) :
assert col[idx][i] == totest[i], "Column: "+repr(col)+"\nSet value[i] != gotten value[i] "+str(totest[i])+" != "+str(col[idx][i])
else:
col[idx] = value
assert col[idx] == value, "Column: "+repr(col)+"\nSet value != gotten value "+str(value)+" != "+str(col[idx])
@ -210,19 +269,25 @@ def fill_column(config, infos, col) :
if len(element_names) > 1 :
for i in range(random_int(config)) :
for j in range(len(element_names)) :
col[i][element_names[j]] = random.choice([None, infos['random_generator'][data_type](config)])
col[i][element_names[j]] = random.choice([None, infos['random_generator'][(data_type, col.tuples)](config)])
else :
for i in range(random_int(config)) :
col[i] = random.choice([None, infos['random_generator'][data_type](config)])
r = random.choice([None, infos['random_generator'][(data_type, col.tuples)](config)])
col[i] = r
def create_random_column(config, infos) :
alias = random.choice([b'', random_unique_name(infos)])
nb_elements_per_line=random.randint(1, config['test']['maxelts'])
elements_names = []
for i in range(nb_elements_per_line) :
elements_names.append(random_unique_element_name(config, infos))
elements_names = random.choice([None, elements_names])
tuples = random.choice([True, False])
if not tuples :
nb_elements_per_line=random.randint(1, config['test']['maxelts'])
elements_names = []
for i in range(nb_elements_per_line) :
elements_names.append(random_unique_element_name(config, infos))
elements_names = random.choice([None, elements_names])
else :
nb_elements_per_line = 1
elements_names = None
name = random_unique_name(infos)
data_type = random_col_type()
@ -231,6 +296,7 @@ def create_random_column(config, infos) :
data_type,
nb_elements_per_line=nb_elements_per_line,
elements_names=elements_names,
tuples=tuples,
comments=random_str_with_max_len(COL_COMMENTS_MAX_LEN),
alias=alias
)
@ -347,6 +413,14 @@ def addOptions(parser):
type=int,
help="Maximum length of character strings. "
"Default: 200")
group.add_argument('--tuple_max_len','-u',
action="store", dest="test:tuplemaxlen",
metavar='<TUPLE_MAX_LEN>',
default=20,
type=int,
help="Maximum length of tuples. "
"Default: 200")
group.add_argument('--comments_max_len','-c',
action="store", dest="test:commentsmaxlen",
@ -402,7 +476,14 @@ def run(config):
'view': None,
'view_names': None,
'unique_names': [],
'random_generator': {b"OBI_BOOL": random_bool, b"OBI_CHAR": random_char, b"OBI_FLOAT": random_float, b"OBI_INT": random_int, b"OBI_SEQ": random_seq, b"OBI_STR": random_bytes},
'random_generator': {
(b"OBI_BOOL", False): random_bool, (b"OBI_BOOL", True): random_bool_tuples,
(b"OBI_CHAR", False): random_char, (b"OBI_CHAR", True): random_char_tuples,
(b"OBI_FLOAT", False): random_float, (b"OBI_FLOAT", True): random_float_tuples,
(b"OBI_INT", False): random_int, (b"OBI_INT", True): random_int_tuples,
(b"OBI_SEQ", False): random_seq, (b"OBI_SEQ", True): random_seq_tuples,
(b"OBI_STR", False): random_bytes, (b"OBI_STR", True): random_bytes_tuples
},
'tests': [test_set_and_get, test_add_col, test_delete_col, test_col_alias, test_new_view]
}