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obi test: minor changes

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This commit is contained in:
Celine Mercier
2017-07-05 14:37:27 +02:00
parent 20c72af697
commit 3f5fef10b9
1 changed files with 27 additions and 20 deletions
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47
python/obitools3/commands/test.pyx
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@ -1,3 +1,5 @@
#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.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.view import View, Line_selection
from obitools3.dms.view.typed_view.view_NUC_SEQS import View_NUC_SEQS from obitools3.dms.view.typed_view.view_NUC_SEQS import View_NUC_SEQS
@ -5,15 +7,19 @@ from obitools3.dms.dms import DMS
from obitools3.dms.column import Column from obitools3.dms.column import Column
from obitools3.dms.taxo.taxo import OBI_Taxonomy from obitools3.dms.taxo.taxo import OBI_Taxonomy
from obitools3.utils cimport str2bytes from obitools3.utils cimport str2bytes
from obitools3.dms.capi.obitypes cimport OBI_INT, \
OBI_FLOAT, \
OBI_BOOL, \
OBI_CHAR, \
OBI_STR, \
OBI_SEQ
import shutil import shutil
import string import string
import random import random
VIEW_TYPES = ["", "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_INT, OBI_FLOAT, OBI_BOOL, OBI_CHAR, OBI_STR, OBI_SEQ]
COL_TYPES = [1, 2, 3, 4, 6, 7]
NUC_SEQUENCE_COLUMN = "NUC_SEQ" NUC_SEQUENCE_COLUMN = "NUC_SEQ"
ID_COLUMN = "ID" ID_COLUMN = "ID"
DEFINITION_COLUMN = "DEFINITION" DEFINITION_COLUMN = "DEFINITION"
@ -31,11 +37,10 @@ MAX_INT = 2147483647 # used to generate random float values
__title__="Tests if the obitools are working properly" __title__="Tests if the obitools are working properly"
default_config = { default_config = {
} }
def test_taxo(config, infos): def test_taxo(config, infos):
tax1 = OBI_Taxonomy.open(infos['dms'], config['obi']['taxo'], taxdump=True) tax1 = OBI_Taxonomy.open(infos['dms'], config['obi']['taxo'], taxdump=True)
tax1.write(TAXTEST) tax1.write(TAXTEST)
@ -229,7 +234,7 @@ def create_random_column(config, infos) :
comments=random_str_with_max_len(COL_COMMENTS_MAX_LEN), comments=random_str_with_max_len(COL_COMMENTS_MAX_LEN),
alias=alias alias=alias
) )
if alias != '' : if alias != '' :
assert infos['view'][alias] == column assert infos['view'][alias] == column
else : else :
@ -284,18 +289,18 @@ def random_new_view(config, infos, first=False):
v_to_clone.close() v_to_clone.close()
if first : if first :
fill_view(config, infos) fill_view(config, infos)
def create_test_obidms(config, infos): def create_test_obidms(config, infos):
infos['dms'] = DMS.new(config['obi']['defaultdms']) infos['dms'] = DMS.new(config['obi']['defaultdms'])
def ini_dms_and_first_view(config, infos): def ini_dms_and_first_view(config, infos):
create_test_obidms(config, infos) create_test_obidms(config, infos)
random_new_view(config, infos, first=True) random_new_view(config, infos, first=True)
infos['view_names'] = [] infos['view_names'] = []
def addOptions(parser): def addOptions(parser):
# TODO put this common group somewhere else but I don't know where # TODO put this common group somewhere else but I don't know where
@ -309,11 +314,12 @@ def addOptions(parser):
help="Name of the default DMS for reading and writing data. " help="Name of the default DMS for reading and writing data. "
"Default: /tmp/test_dms") "Default: /tmp/test_dms")
group.add_argument('--taxo','-t', group.add_argument('--taxo','-t', # TODO I don't understand why the option is not registered if it is not set
action="store", dest="obi:taxo", action="store", dest="obi:taxo",
metavar='<TAXDUMP PATH>', metavar='<TAXDUMP PATH>',
default='', # TODO not None because if it's None, the option is not entered in the option dictionary.
type=str, type=str,
help="Path to a taxdump to test the taxonomy.") # TODO help="Path to a taxdump to test the taxonomy.")
group=parser.add_argument_group('obi test specific options') group=parser.add_argument_group('obi test specific options')
@ -408,7 +414,7 @@ def run(config):
ini_dms_and_first_view(config, infos) ini_dms_and_first_view(config, infos)
print_test(config, repr(infos['view'])) print_test(config, repr(infos['view']))
i = 0 i = 0
for t in range(config['test']['nbtests']): for t in range(config['test']['nbtests']):
random_test(config, infos) random_test(config, infos)
@ -419,12 +425,13 @@ def run(config):
#print(infos) #print(infos)
test_taxo(config, infos) if config['obi']['taxo'] != '' :
test_taxo(config, infos)
infos['view'].close() infos['view'].close()
infos['dms'].close() infos['dms'].close()
shutil.rmtree(config['obi']['defaultdms']+'.obidms', ignore_errors=True) shutil.rmtree(config['obi']['defaultdms']+'.obidms', ignore_errors=True)
print("Done.") print("Done.")