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Added the lists of opened columns and arrays in the OBIDMS structure,

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and a counter in the OBIDMS column structure; fixed some bugs and
created tests for referring columns that are bound to disappear anyway.
This commit is contained in:
Celine Mercier
2015-12-02 17:32:07 +01:00
parent b45b496b0e
commit 1586956d57
8 changed files with 331 additions and 142 deletions
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1
python/obitools3/obidms/_obidms.pyx
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@ -79,7 +79,6 @@ cdef class OBIDMS :
cpdef close(self) :
#TODO close all columns (needs to be discussed)
if (obi_close_dms(self.pointer)) < 0 :
raise Exception("Problem closing an OBIDMS")

153
python/obitools3/unit_tests.py
View File

@ -12,7 +12,6 @@ LINE_COUNT_FOR_TEST_COLUMN = 10000 # TODO randomize?
SMALLER_LINE_COUNT_FOR_TEST_COLUMN = 1000 # TODO randomize?
NB_ELEMENTS_PER_LINE = 10 # TODO randomize?
DMS_NAME = "unit_test_dms"
DATA_TYPES = ['OBI_INT', 'OBI_FLOAT', 'OBI_BOOL', 'OBI_CHAR', 'OBI_STR', 'OBI_SEQ']
def create_test_obidms():
@ -22,26 +21,24 @@ def create_test_obidms():
return (dms, dms_name, dms_dir_name)
def create_test_column(dms, data_type_code, multiple_elements_per_line=False):
data_types = DATA_TYPES
data_type_code = data_type_code
data_type_str = data_types[data_type_code-1]
col_name = "unit_test_"+data_type_str
def create_test_column(dms, data_type, multiple_elements_per_line=False):
col_name = "unit_test_"+data_type
if multiple_elements_per_line :
elts_names = elements_names()
col = dms.open_column(col_name,
create=True,
data_type=data_type_code,
type=data_type,
nb_elements_per_line=NB_ELEMENTS_PER_LINE,
elements_names=elts_names)
return (col, col_name, elts_names, data_type_str)
return (col, col_name, elts_names)
else :
col = dms.open_column(col_name,
create=True,
data_type=data_type_code)
return (col, col_name, data_type_str)
type=data_type)
return (col, col_name)
def elements_names():
@ -74,10 +71,10 @@ class OBIDMS_Column_TestCase(unittest.TestCase):
self.dms.close()
shutil.rmtree(self.dms_dir_name, ignore_errors=True)
def test_OBIDMS_column_type(self):
assert self.col.get_data_type() == self.data_type_str, 'Wrong data type associated with column'
assert self.col.get_data_type() == self.data_type, 'Wrong data type associated with column'
def test_OBIDMS_column_cloning(self):
for i in range(LINE_COUNT_FOR_TEST_COLUMN):
self.col[i]= random_obivalue(self.data_type_str)
self.col[i]= random_obivalue(self.data_type)
self.col.close()
clone = self.dms.open_column(self.col_name, clone=True)
self.col = self.dms.open_column(self.col_name)
@ -89,10 +86,21 @@ class OBIDMS_Column_TestCase(unittest.TestCase):
clone.close()
def test_OBIDMS_column_set_and_get(self):
for i in range(LINE_COUNT_FOR_TEST_COLUMN):
v = random_obivalue(self.data_type_str)
v = random_obivalue(self.data_type)
self.col[i] = v
assert self.col[i] == v, "Different value than the set value"
assert self.col[i] is not None, "None value"
def test_OBIDMS_referring_column(self):
for i in range(LINE_COUNT_FOR_TEST_COLUMN):
self.col[i] = random_obivalue(self.data_type)
ref_col = self.dms.open_column(self.col_name, referring=True)
j = 0
for i in range(LINE_COUNT_FOR_TEST_COLUMN):
if i%2 : # TODO randomize
ref_col.grep_line(i)
assert ref_col[j] == self.col[i], "Different value in original column and returned by referring column"
assert ref_col[j] is not None, "None value"
j+=1
class OBIDMS_Column_multiple_elements_TestCase(OBIDMS_Column_TestCase):
@ -101,7 +109,7 @@ class OBIDMS_Column_multiple_elements_TestCase(OBIDMS_Column_TestCase):
for i in range(SMALLER_LINE_COUNT_FOR_TEST_COLUMN):
v = {}
for e in self.elts_names :
v[e] = random_obivalue(self.data_type_str)
v[e] = random_obivalue(self.data_type)
self.col[i] = v
self.col.close()
clone = self.dms.open_column(self.col_name, clone=True)
@ -115,7 +123,7 @@ class OBIDMS_Column_multiple_elements_TestCase(OBIDMS_Column_TestCase):
def test_OBIDMS_column_set_and_get_with_elements_names(self):
for i in range(SMALLER_LINE_COUNT_FOR_TEST_COLUMN):
for e in range(NB_ELEMENTS_PER_LINE) :
v = random_obivalue(self.data_type_str)
v = random_obivalue(self.data_type)
self.col.set_item(i, self.elts_names[e], v)
assert self.col.get_item(i, self.elts_names[e]) == v, "Different value than the set value"
assert self.col.get_item(i, self.elts_names[e]) is not None, "None value"
@ -123,165 +131,168 @@ class OBIDMS_Column_multiple_elements_TestCase(OBIDMS_Column_TestCase):
for i in range(SMALLER_LINE_COUNT_FOR_TEST_COLUMN):
v = {}
for e in self.elts_names :
v[e] = random_obivalue(self.data_type_str)
v[e] = random_obivalue(self.data_type)
self.col[i] = v
assert self.col[i] == v, "Different value than the set value"
assert self.col[i] is not None, "None value"
def test_OBIDMS_referring_column(self):
for i in range(SMALLER_LINE_COUNT_FOR_TEST_COLUMN):
v = {}
for e in self.elts_names :
v[e] = random_obivalue(self.data_type)
self.col[i] = v
ref_col = self.dms.open_column(self.col_name, referring=True)
j = 0
for i in range(SMALLER_LINE_COUNT_FOR_TEST_COLUMN):
if i%2 : # TODO randomize
ref_col.grep_line(i)
assert ref_col[j] == self.col[i], "Different value in original column and returned by referring column"
assert ref_col[j] is not None, "None value"
j+=1
ref_col.close()
class OBIDMS_Column_OBI_INT_TestCase(OBIDMS_Column_TestCase):
def setUp(self):
self.data_type_code = 1
self.data_type = 'OBI_INT'
self.dms, \
self.dms_name, \
self.dms_dir_name = create_test_obidms()
self.col, \
self.col_name, \
self.data_type_str = create_test_column(self.dms,
self.data_type_code)
self.col_name = create_test_column(self.dms,
self.data_type)
class OBIDMS_Column_OBI_INT_multiple_elements_TestCase(OBIDMS_Column_multiple_elements_TestCase):
def setUp(self):
self.data_type_code = 1
self.data_type = 'OBI_INT'
self.dms, \
self.dms_name, \
self.dms_dir_name = create_test_obidms()
self.col, \
self.col_name, \
self.elts_names, \
self.data_type_str = create_test_column(self.dms,
self.data_type_code,
multiple_elements_per_line=True)
self.elts_names = create_test_column(self.dms,
self.data_type,
multiple_elements_per_line=True)
class OBIDMS_Column_OBI_FLOAT_TestCase(OBIDMS_Column_TestCase):
def setUp(self):
self.data_type_code = 2
self.data_type = 'OBI_FLOAT'
self.dms, \
self.dms_name, \
self.dms_dir_name = create_test_obidms()
self.col, \
self.col_name, \
self.data_type_str = create_test_column(self.dms,
self.data_type_code)
self.col_name = create_test_column(self.dms,
self.data_type)
class OBIDMS_Column_OBI_FLOAT_multiple_elements_TestCase(OBIDMS_Column_multiple_elements_TestCase):
def setUp(self):
self.data_type_code = 2
self.data_type = 'OBI_FLOAT'
self.dms, \
self.dms_name, \
self.dms_dir_name = create_test_obidms()
self.col, \
self.col_name, \
self.elts_names, \
self.data_type_str = create_test_column(self.dms,
self.data_type_code,
multiple_elements_per_line=True)
self.elts_names = create_test_column(self.dms,
self.data_type,
multiple_elements_per_line=True)
class OBIDMS_Column_OBI_BOOL_TestCase(OBIDMS_Column_TestCase):
def setUp(self):
self.data_type_code = 3
self.data_type = 'OBI_BOOL'
self.dms, \
self.dms_name, \
self.dms_dir_name = create_test_obidms()
self.col, \
self.col_name, \
self.data_type_str = create_test_column(self.dms,
self.data_type_code)
self.col_name = create_test_column(self.dms,
self.data_type)
class OBIDMS_Column_OBI_BOOL_multiple_elements_TestCase(OBIDMS_Column_multiple_elements_TestCase):
def setUp(self):
self.data_type_code = 3
self.data_type = 'OBI_BOOL'
self.dms, \
self.dms_name, \
self.dms_dir_name = create_test_obidms()
self.col, \
self.col_name, \
self.elts_names, \
self.data_type_str = create_test_column(self.dms,
self.data_type_code,
multiple_elements_per_line=True)
self.elts_names = create_test_column(self.dms,
self.data_type,
multiple_elements_per_line=True)
class OBIDMS_Column_OBI_CHAR_TestCase(OBIDMS_Column_TestCase):
def setUp(self):
self.data_type_code = 4
self.data_type = 'OBI_CHAR'
self.dms, \
self.dms_name, \
self.dms_dir_name = create_test_obidms()
self.col, \
self.col_name, \
self.data_type_str = create_test_column(self.dms,
self.data_type_code)
self.col_name = create_test_column(self.dms,
self.data_type)
class OBIDMS_Column_OBI_CHAR_multiple_elements_TestCase(OBIDMS_Column_multiple_elements_TestCase):
def setUp(self):
self.data_type_code = 4
self.data_type = 'OBI_CHAR'
self.dms, \
self.dms_name, \
self.dms_dir_name = create_test_obidms()
self.col, \
self.col_name, \
self.elts_names, \
self.data_type_str = create_test_column(self.dms,
self.data_type_code,
multiple_elements_per_line=True)
self.elts_names = create_test_column(self.dms,
self.data_type,
multiple_elements_per_line=True)
class OBIDMS_Column_OBI_STR_TestCase(OBIDMS_Column_TestCase):
def setUp(self):
self.data_type_code = 5
self.data_type = 'OBI_STR'
self.dms, \
self.dms_name, \
self.dms_dir_name = create_test_obidms()
self.col, \
self.col_name, \
self.data_type_str = create_test_column(self.dms,
self.data_type_code)
self.col_name = create_test_column(self.dms,
self.data_type)
class OBIDMS_Column_OBI_STR_multiple_elements_TestCase(OBIDMS_Column_multiple_elements_TestCase):
def setUp(self):
self.data_type_code = 5
self.data_type = 'OBI_STR'
self.dms, \
self.dms_name, \
self.dms_dir_name = create_test_obidms()
self.col, \
self.col_name, \
self.elts_names, \
self.data_type_str = create_test_column(self.dms,
self.data_type_code,
multiple_elements_per_line=True)
self.elts_names = create_test_column(self.dms,
self.data_type,
multiple_elements_per_line=True)
class OBIDMS_Column_OBI_SEQ_TestCase(OBIDMS_Column_TestCase):
def setUp(self):
self.data_type_code = 6
self.data_type = 'OBI_SEQ'
self.dms, \
self.dms_name, \
self.dms_dir_name = create_test_obidms()
self.col, \
self.col_name, \
self.data_type_str = create_test_column(self.dms,
self.data_type_code)
self.col_name = create_test_column(self.dms,
self.data_type)
class OBIDMS_Column_OBI_SEQ_multiple_elements_TestCase(OBIDMS_Column_multiple_elements_TestCase):
def setUp(self):
self.data_type_code = 6
self.data_type = 'OBI_SEQ'
self.dms, \
self.dms_name, \
self.dms_dir_name = create_test_obidms()
self.col, \
self.col_name, \
self.elts_names, \
self.data_type_str = create_test_column(self.dms,
self.data_type_code,
multiple_elements_per_line=True)
self.elts_names = create_test_column(self.dms,
self.data_type,
multiple_elements_per_line=True)
if __name__ == '__main__':
unittest.main(verbosity=2, defaultTest=["OBIDMS_Column_OBI_INT_TestCase",