try to get tests running on new version

This commit is contained in:
Richard Hartmann 2016-09-26 16:57:57 +02:00
parent 662a7c11b5
commit da8281aa70
6 changed files with 6 additions and 1316 deletions

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@ -36,11 +36,6 @@ from . import clients
from . import decorators
from . import servers
from . import ode_wrapper
from . import binfootprint
# persistentData requires sqlitedict
try:
from . import persistentData
except ImportError as e:
warnings.warn("Submodule 'persistentData' is not available. Reason: {}.".format(e))

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@ -46,7 +46,8 @@ import sys
import time
import traceback
import warnings
from . import binfootprint as bf
import binfootprint as bf
import progress
import logging
@ -113,9 +114,6 @@ else:
class JMHostNotReachableError(JMConnectionError):
pass
sys.path.append(os.path.dirname(__file__))
from . import progress
myQueue = mp.Queue
AuthenticationError = mp.AuthenticationError

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@ -1,177 +0,0 @@
# -*- coding: utf-8 -*-
from __future__ import division, print_function
import sys
if sys.version_info.major > 2:
import pathlib
path = pathlib.PosixPath(__file__).absolute()
jobmanager = path.parent.parent# / 'jobmanager'
sys.path.insert(0, str(jobmanager))
else:
from os.path import abspath, dirname, split
# Add parent directory to beginning of path variable
sys.path = [split(dirname(abspath(__file__)))[0]] + sys.path
from jobmanager import binfootprint as bfp
import numpy as np
from collections import namedtuple
import warnings
warnings.filterwarnings('error')
def test_version_tag():
ob = 5
binob = bfp.dump(ob)
assert bfp.byte_to_ord(binob[0]) == bfp._VERS
def test_atom():
atoms = [12345678, 3.141, 'hallo Welt', 'öäüß', True, False, None, 2**65, -3**65, b'\xff\fe\03']
for atom in atoms:
bin_atom = bfp.dump(atom)
atom_prime = bfp.load(bin_atom)
bin_ob_prime = bfp.dump(atom_prime)
assert bin_atom == bin_ob_prime
hash(bin_atom)
def test_tuple():
t = (12345678, 3.141, 'hallo Welt', 'öäüß', True, False, None, (3, tuple(), (4,5,None), 'test'))
bin_tuple = bfp.dump(t)
assert type(bin_tuple) is bfp.BIN_TYPE
t_prime = bfp.load(bin_tuple)
assert t == t_prime
bin_ob_prime = bfp.dump(t_prime)
assert bin_tuple == bin_ob_prime
def test_nparray():
ob = np.random.randn(3,53,2)
bin_ob = bfp.dump(ob)
assert type(bin_ob) is bfp.BIN_TYPE
ob_prime = bfp.load(bin_ob)
assert np.all(ob == ob_prime)
bin_ob_prime = bfp.dump(ob_prime)
assert bin_ob == bin_ob_prime
ob = np.random.randn(3,53,2)
ob = (ob, ob, 4, None)
bin_ob = bfp.dump(ob)
ob_prime = bfp.load(bin_ob)
assert np.all(ob[0] == ob_prime[0])
assert np.all(ob[1] == ob_prime[1])
bin_ob_prime = bfp.dump(ob_prime)
assert bin_ob == bin_ob_prime
def test_list():
ob = [1,2,3]
bin_ob = bfp.dump(ob)
assert type(bin_ob) is bfp.BIN_TYPE
ob_prime = bfp.load(bin_ob)
assert np.all(ob == ob_prime)
bin_ob_prime = bfp.dump(ob_prime)
assert bin_ob == bin_ob_prime
ob = [1, (2,3), np.array([2j,3j])]
bin_ob = bfp.dump(ob)
ob_prime = bfp.load(bin_ob)
bin_ob_prime = bfp.dump(ob_prime)
assert bin_ob == bin_ob_prime
assert np.all(ob[0] == ob_prime[0])
assert np.all(ob[1] == ob_prime[1])
assert np.all(ob[2] == ob_prime[2])
def test_getstate():
class T(object):
def __init__(self, a):
self.a = a
def __getstate__(self):
return [self.a]
def __setstate__(self, state):
self.a = state[0]
ob = T(4)
bin_ob = bfp.dump(ob)
assert type(bin_ob) is bfp.BIN_TYPE
classes = {}
classes['T'] = T
ob_prime = bfp.load(bin_ob, classes)
assert np.all(ob.a == ob_prime.a)
bin_ob_prime = bfp.dump(ob_prime)
assert bin_ob == bin_ob_prime
try:
ob_prime = bfp.load(bin_ob)
except bfp.BFUnkownClassError:
pass
else:
assert False, "binfootprint.BFUnkownClassError should have been raised"
def test_named_tuple():
obj_type = namedtuple('obj_type', ['a','b','c'])
obj = obj_type(12345678, 3.141, 'hallo Welt')
bin_obj = bfp.dump(obj)
assert type(bin_obj) is bfp.BIN_TYPE
obj_prime = bfp.load(bin_obj)
assert obj_prime.__class__.__name__ == obj.__class__.__name__
assert obj_prime._fields == obj._fields
assert obj_prime == obj
bin_ob_prime = bfp.dump(obj_prime)
assert bin_obj == bin_ob_prime
def test_complex():
z = 3+4j
bf = bfp.dump(z)
assert type(bf) is bfp.BIN_TYPE
zr = bfp.load(bf)
assert zr == z
def test_dict():
a = {'a':1, 5:5, 3+4j:'l', False: b'ab4+#'}
bf = bfp.dump(a)
assert type(bf) is bfp.BIN_TYPE
a_restored = bfp.load(bf)
for k in a:
assert a[k] == a_restored[k]
def test_versions():
nt = namedtuple('nt', ['x', 'y'])
n = nt(4,5)
n2 = nt(n, n)
ob = [3, n, n2]
binob = bfp.dump(ob, vers = 0)
try:
bfp.load(binob)
except bfp.BFUnkownClassError:
pass
else:
assert False, "binfootprint.BFUnkownClassError should have been raised"
rest_ob = bfp.load(binob, {'nt': nt})
assert rest_ob == ob
binob = bfp.dump(ob, vers = 0x80)
rest_ob = bfp.load(binob)
assert rest_ob == ob
if __name__ == "__main__":
# test_version_tag()
# test_atom()
# test_tuple()
# test_nparray()
# test_list()
# test_getstate()
# test_named_tuple()
# test_complex()
# test_dict()
test_versions()

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@ -17,7 +17,9 @@ from os.path import abspath, dirname, split
# Add parent directory to beginning of path variable
sys.path = [split(dirname(abspath(__file__)))[0]] + sys.path
from jobmanager import jobmanager, progress, binfootprint
import jobmanager
import binfootprint
import progress
import warnings
warnings.filterwarnings('error')

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@ -1,532 +0,0 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import division, print_function
import sys
import pickle
import os
from os.path import abspath, dirname, split, exists
from shutil import rmtree
import warnings
warnings.filterwarnings('error')
import numpy as np
# Add parent directory to beginning of path variable
sys.path = [split(dirname(abspath(__file__)))[0]] + sys.path
import jobmanager.persistentData as pd
from jobmanager.persistentData import PersistentDataStructure as PDS
VERBOSE = 1
if sys.version_info[0] == 2:
# fixes keyword problems with python 2.x
old_open = open
def new_open(file, mode):
return old_open(name = file, mode = mode)
open = new_open
rmtree('__test_data', ignore_errors=True)
rmtree('__data', ignore_errors=True)
rmtree('__base', ignore_errors=True)
def test_pd():
try:
with PDS(name='test_data', verbose=VERBOSE) as data:
key = 'a'
value = 1
data.setData(key=key, value=value)
assert data.getData(key) == value
assert len(data) == 1
key_sub = 'zz'
with data.getData(key_sub, create_sub_data=True) as sub_data:
sub_data.setData(key=key, value=3)
assert sub_data.getData(key) == 3
assert data.getData(key) == 1
with sub_data.getData(key_sub, create_sub_data=True) as sub_sub_data:
sub_sub_data.setData(key=key, value=4)
assert sub_sub_data.getData(key) == 4
assert sub_data.getData(key) == 3
assert data.getData(key) == 1
with sub_data.getData(key_sub, create_sub_data=True) as sub_sub_data:
assert sub_sub_data.getData(key) == 4
assert sub_data.getData(key) == 3
assert data.getData(key) == 1
finally:
print()
data.erase()
def test_pd_bytes():
t1 = (3.4, 4.5, 5.6, 6.7, 7.8, 8.9)
t2 = (3.4, 4.5, 5.6, 6.7, 7.8, 8.9, 9,1)
b1 = pickle.dumps(t1)
b2 = pickle.dumps(t2)
try:
with PDS(name='base', verbose=VERBOSE) as base_data:
with base_data.getData(key=b1, create_sub_data=True) as sub_data:
for i in range(2, 10):
sub_data[i] = t2
base_data[b2] = t1
if VERBOSE > 1:
print("\nCHECK\n")
with PDS(name='base', verbose=VERBOSE) as base_data:
with base_data.getData(key=b1) as sub_data:
for i in range(2, 10):
assert sub_data[i] == t2
assert base_data[b2] == t1
finally:
print()
base_data.erase()
def test_directory_removal():
try:
with PDS(name='data', verbose=VERBOSE) as data:
with data.newSubData('s1') as s1:
s1['bla'] = 9
f = open(file=data._dirname + '/other_file', mode='w')
f.close()
print("now there should be a warning, because there is an unknown file in the directory!")
finally:
try:
data.erase()
except UserWarning:
pass
assert exists(data._dirname)
os.remove(data._dirname + '/other_file')
os.rmdir(data._dirname)
def test_mp_read_from_sqlite():
import sqlitedict as sqd
import multiprocessing as mp
import time
d = sqd.SqliteDict('test.db', autocommit = True)
def write(arg):
with sqd.SqliteDict('test.db', autocommit = True) as d:
for i in range(100):
d[i] = (i, arg)
def read():
with sqd.SqliteDict('test.db', autocommit = True) as d:
for i in range(len(d)):
print(i, d[i])
p1 = mp.Process(target = write, args=('p1', ))
time.sleep(0.1)
p2 = mp.Process(target = read)
p1.start()
p2.start()
p1.join(10)
p2.join(10)
try:
if p1.is_alive():
raise RuntimeError("write process did not finish on time")
if p2.is_alive():
raise RuntimeError("read process did not finish on time")
finally:
p1.terminate()
p2.terminate()
d.terminate()
def test_from_existing_sub_data():
print()
print('test_from_existing_sub_data')
t1 = (3.4, 4.5, 5.6, 6.7, 7.8, 8.9)
t2 = (3.4, 4.5, 5.6, 6.7, 7.8, 8.9, 9,1)
try:
with PDS(name='base', verbose=VERBOSE) as base_data:
with base_data.getData(key='sub1', create_sub_data = True) as sub_data:
sub_data[100] = t1
sub_data[200] = t2
with sub_data.getData(key = 'subsub1', create_sub_data = True) as sub_sub_data:
sub_sub_data['t'] = 'hallo Welt'
base_data.setDataFromSubData(key='sub2', subData = sub_data)
with PDS(name='base', verbose=VERBOSE) as base_data:
with base_data.getData(key='sub2', create_sub_data = False) as sub_data:
assert sub_data[100] == t1
assert sub_data[200] == t2
with sub_data.getData(key = 'subsub1', create_sub_data = False) as sub_sub_data:
assert sub_sub_data['t'] == 'hallo Welt'
with PDS(name='base', verbose=VERBOSE) as base_data:
with base_data.getData(key='sub1', create_sub_data = True) as sub_data:
base_data['sub2'] = sub_data
with PDS(name='base', verbose=VERBOSE) as base_data:
with base_data.getData(key='sub2', create_sub_data = False) as sub_data:
assert sub_data[100] == t1
assert sub_data[200] == t2
with sub_data.getData(key = 'subsub1', create_sub_data = False) as sub_sub_data:
assert sub_sub_data['t'] == 'hallo Welt'
sub_sub_data['t'] = 'sub2:hallo Welt'
sub_data[100] = "sub2:t1"
sub_data[200] = "sub2:t2"
with PDS(name='base', verbose=VERBOSE) as base_data:
with base_data.getData(key='sub1', create_sub_data = True) as sub_data:
assert sub_data[100] == t1
assert sub_data[200] == t2
with sub_data.getData(key = 'subsub1', create_sub_data = True) as sub_sub_data:
assert sub_sub_data['t'] == 'hallo Welt'
with PDS(name='base', verbose=VERBOSE) as base_data:
with base_data.getData(key='sub2', create_sub_data = False) as sub_data:
with sub_data.getData(key = 'subsub1', create_sub_data = False) as sub_sub_data:
assert sub_sub_data['t'] == 'sub2:hallo Welt'
assert sub_data[100] == "sub2:t1"
assert sub_data[200] == "sub2:t2"
finally:
print()
base_data.erase()
def test_remove_sub_data_and_check_len():
try:
with PDS(name='base', verbose=VERBOSE) as base_data:
with base_data.getData(key='sub1', create_sub_data = True) as sub_data:
sub_data[100] = 't1'
sub_data[200] = 't2'
with sub_data.getData(key = 'subsub1', create_sub_data = True) as sub_sub_data:
sub_sub_data['t'] = 'hallo Welt'
assert len(sub_data) == 3, "len = {}".format(len(sub_data))
assert len(base_data) == 1
base_data['copy_of_sub1'] = sub_data
assert len(base_data) == 2
del base_data['sub1']
assert len(base_data) == 1
with base_data.getData(key='copy_of_sub1', create_sub_data = True) as sub_data:
assert len(sub_data) == 3
assert sub_data[100] == 't1'
assert sub_data[200] == 't2'
with sub_data.getData(key = 'subsub1', create_sub_data = True) as sub_sub_data:
assert sub_sub_data['t'] == 'hallo Welt'
assert ('sub1' not in base_data)
finally:
base_data.erase()
def test_show_stat():
try:
with PDS(name='test_data', verbose=VERBOSE) as data:
key = 'a'
value = 1
data.setData(key=key, value=value)
assert data.getData(key) == value
key_sub = 'zz'
with data.getData(key_sub, create_sub_data=True) as sub_data:
sub_data.setData(key=key, value=3)
assert sub_data.getData(key) == 3
assert data.getData(key) == 1
key_sub_bin = pickle.dumps(key_sub, protocol=2)
with sub_data.getData(key_sub_bin, create_sub_data=True) as sub_sub_data:
sub_sub_data.setData(key=key, value=4)
assert sub_sub_data.getData(key) == 4
assert sub_data.getData(key) == 3
assert data.getData(key) == 1
with sub_data.getData(key_sub_bin, create_sub_data=True) as sub_sub_data:
assert sub_sub_data.getData(key) == 4
assert sub_data.getData(key) == 3
assert data.getData(key) == 1
data.show_stat(recursive=True)
finally:
data.erase()
def slow_len(pd):
n = 0
for k in pd:
n += 1
return n
def test_len():
try:
with PDS(name='data', verbose=VERBOSE) as data:
assert len(data) == 0
assert slow_len(data) == 0
data['a'] = 1
assert len(data) == 1
assert slow_len(data) == 1
for i in range(1, 8):
data[i*10] = i
assert len(data) == 8
assert slow_len(data) == 8
with PDS(name='data', verbose=VERBOSE) as data:
assert len(data) == 8
assert slow_len(data) == 8
data.clear()
assert len(data) == 0
assert slow_len(data) == 0
with PDS(name='data', verbose=VERBOSE) as data:
assert len(data) == 0
assert slow_len(data) == 0
finally:
data.erase()
def test_clear():
try:
with PDS(name='data', verbose=VERBOSE) as data:
data['a'] = 1
data['b'] = 2
with data.newSubData('s1') as s1:
s1['bla'] = 9
with data.newSubData('s2') as s2:
s2['bla2'] = 18
with data['s1'] as s1:
s1['t'] = 'tmp'
s1.clear()
with data['s1'] as s1:
assert len(s1) == 0
assert slow_len(s1) == 0
data.clear()
dir_content = os.listdir(data._dirname)
assert len(dir_content) == 1
assert dir_content[0] == 'data.db'
finally:
data.erase()
def test_not_in():
try:
with PDS(name='data', verbose=VERBOSE) as data:
data['a'] = 1
data['b'] = 2
with data.newSubData('s1') as s1:
s1['bla'] = 9
assert ('a' in data)
assert ('b' in data)
assert ('s1' in data)
assert ('c' not in data)
finally:
data.erase()
def test_npa():
a = np.linspace(0, 1, 100).reshape(10,10)
try:
with PDS(name='data_npa', verbose=VERBOSE) as data:
data['a'] = a
with PDS(name='data_npa', verbose=VERBOSE) as data:
b = data['a']
assert np.all(b == a)
with PDS(name='data_npa', verbose=VERBOSE) as data:
del data['a']
data['a'] = a
finally:
data.erase()
def test_merge():
a = np.random.rand(5)
with PDS(name='d1', verbose=VERBOSE) as d1:
d1.clear()
d1['k1'] = 1
d1['k2'] = 2
d1['k3'] = 3
d1['aa'] = a
with d1.newSubData('sub1') as sub1:
sub1['s1'] = 11
sub1['s2'] = 12
sub1['s3'] = 13
sub1['a'] = a
with PDS(name='d2', verbose=VERBOSE) as d2:
d2.clear()
d2['2k1'] = 1
d2.mergeOtherPDS(other_db_name = "d1", status_interval=0)
with PDS(name='d2', verbose=VERBOSE) as d2:
assert 'k1' in d2
assert d2['k1'] == 1
assert 'k2' in d2
assert d2['k2'] == 2
assert 'k3' in d2
assert d2['k3'] == 3
assert 'aa' in d2
assert np.all(d2['aa'] == a)
assert "sub1" in d2
assert isinstance(d2["sub1"], PDS)
with d2["sub1"] as sub:
assert 's1' in sub
assert sub['s1'] == 11
assert 's2' in sub
assert sub['s2'] == 12
assert 's3' in sub
assert sub['s3'] == 13
assert 'a' in sub
assert np.all(sub['a'] == a)
try:
with PDS(name='d2', verbose=VERBOSE) as d2:
d2.mergeOtherPDS(other_db_name = "d1", update='error', status_interval=0)
except KeyError as e:
print(e)
print("this is ok!")
pass
with PDS(name='d2', verbose=VERBOSE) as d2:
d2['k1'] = 'k1'
d2.mergeOtherPDS(other_db_name = "d1", update='ignore', status_interval=0)
assert d2['k1'] == 'k1'
with PDS(name='d2', verbose=VERBOSE) as d2:
d2['k1'] = 'k1'
d2.mergeOtherPDS(other_db_name = "d1", update='update', status_interval=0)
assert d2['k1'] == 1
def test_merge_fname_conflict():
class PDS_det_fname(PDS):
def newNPA(self, key, nparray):
d = {'fname': 'det_fname.npy',
'magic': pd.MAGIC_SIGN_NPARRAY}
self.db[key] = d
self.db.commit()
full_name = os.path.join(self._dirname, d['fname'])
np.save(full_name, nparray)
return True
def newSubData(self, key):
self.need_open()
dirname = 'subDB'
i = 2
while os.path.exists(os.path.join(self._dirname, '__'+dirname)):
dirname = 'subDB{}'.format(i)
i += 1
print(self._dirname, dirname)
full_name = os.path.join(self._dirname, '__'+dirname)
os.mkdir(full_name)
if not key in self.db:
d = {'name': dirname,
'magic': pd.MAGIC_SIGN}
self.db[key] = d
self.db.commit()
return self.__class__(name = d['name'], path = os.path.join(self._dirname) , verbose = self.verbose)
else:
raise RuntimeError("can NOT create new SubData, key already found!")
a = np.random.rand(5)
b = np.random.rand(5)
with PDS_det_fname(name='d1', verbose=VERBOSE) as d1:
d1.clear()
d1.newNPA('aa', a)
with d1.newSubData('sub1') as sub1:
sub1['s1'] = 11
sub1.newNPA('a', a)
with PDS_det_fname(name='d2', verbose=VERBOSE) as d2:
d2.clear()
d2['2k1'] = 1
d2.newNPA('2aa', b)
with d2.newSubData('sub2') as sub2:
sub2['s2'] = 22
sub2.newNPA('a2', b)
assert np.all(d2['2aa'] == b)
d2.mergeOtherPDS(other_db_name = "d1", update='error', status_interval=0)
assert np.all(d2['2aa'] == b)
assert os.path.exists( os.path.join(d1._path, '__d1', '__subDB'))
assert os.path.exists( os.path.join(d1._path, '__d1', 'det_fname.npy'))
assert os.path.exists( os.path.join(d1._path, '__d2', '__subDB'))
assert os.path.exists( os.path.join(d1._path, '__d2', 'det_fname.npy'))
with PDS_det_fname(name='d2', verbose=VERBOSE) as d2:
assert d2['2k1'] == 1
assert np.all(d2['2aa'] == b)
assert np.all(d2['aa'] == a)
assert d2.has_key('sub1')
with d2['sub1'] as sub1:
assert sub1['s1'] == 11
assert np.all(sub1['a'] == a)
assert d2.has_key('sub2')
with d2['sub2'] as sub2:
assert sub2['s2'] == 22
assert np.all(sub2['a2'] == b)
if __name__ == "__main__":
test_pd()
test_pd_bytes()
test_directory_removal()
test_mp_read_from_sqlite()
test_from_existing_sub_data()
test_remove_sub_data_and_check_len()
test_show_stat()
test_len()
test_clear()
test_not_in()
test_npa()
test_merge()
test_merge_fname_conflict()
pass

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@ -1,596 +0,0 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import division, print_function
import sys
import pickle
import os
from os.path import abspath, dirname, split, exists
from shutil import rmtree
import warnings
warnings.filterwarnings('error')
warnings.filterwarnings(action = "once",
category= DeprecationWarning)
import numpy as np
# Add parent directory to beginning of path variable
sys.path = [split(dirname(abspath(__file__)))[0]] + sys.path
from jobmanager.persistentData import PersistentDataStructure_HDF5 as PDS
from jobmanager.persistentData import PersistentDataStructure as PDS_SQL
from jobmanager.persistentData import mergePDS
VERBOSE = 1
def test_md5_clash():
with PDS(name='test_data', verbose=VERBOSE) as data:
data.clear()
data._md5 = lambda key: str(np.random.randint(0,2))
for i in range(100):
data['a{}'.format(i)] = i
assert len(data) == 100
for i in range(100):
data.newSubData('s{}'.format(i))
assert len(data) == 200
n = 0
for k in data:
n += 1
assert n == 200
def test_pd():
with PDS(name='test_data', verbose=VERBOSE) as data:
data.clear()
key = 'a'
value = 1
try:
data.getData(key)
except KeyError as e:
pass
data.setData(key=key, value=value)
assert data.getData(key) == value
assert len(data) == 1
key_sub = 'zz'
with data.getData(key_sub, create_sub_data=True) as sub_data:
sub_data.setData(key=key, value=3)
assert sub_data.getData(key) == 3
assert data.getData(key) == 1
with sub_data.getData(key_sub, create_sub_data=True) as sub_sub_data:
sub_sub_data.setData(key=key, value=4)
assert sub_sub_data.getData(key) == 4
assert sub_data.getData(key) == 3
assert data.getData(key) == 1
with sub_data.getData(key_sub, create_sub_data=True) as sub_sub_data:
assert sub_sub_data.getData(key) == 4
assert sub_data.getData(key) == 3
assert data.getData(key) == 1
with PDS(name='test_data', verbose=VERBOSE) as data:
data['d1'] = ('ö', 4, [0])
with PDS(name='test_data', verbose=VERBOSE) as data:
d1 = data['d1']
assert d1[0] == 'ö'
assert d1[1] == 4
assert d1[2] == [0]
with PDS(name='test_data', verbose=VERBOSE) as data:
data.clear()
data.newSubData(key='sub_1', overwrite = False)
with PDS(name='test_data', verbose=VERBOSE) as data:
try:
data.newSubData(key='sub_1', overwrite = False)
except KeyError:
pass
data.newSubData(key='sub_1', overwrite = True)
def test_pd_bytes():
t1 = (3.4, 4.5, 5.6, 6.7, 7.8, 8.9)
t2 = (3.4, 4.5, 5.6, 6.7, 7.8, 8.9, 9,1)
b1 = pickle.dumps(t1)
b2 = pickle.dumps(t2)
try:
with PDS(name='base', verbose=VERBOSE) as base_data:
with base_data.getData(key=b1, create_sub_data=True) as sub_data:
for i in range(2, 10):
sub_data[i] = t2
base_data[b2] = t1
if VERBOSE > 1:
print("\nCHECK\n")
with PDS(name='base', verbose=VERBOSE) as base_data:
with base_data.getData(key=b1) as sub_data:
for i in range(2, 10):
assert np.all(sub_data[i] == t2)
assert np.all(base_data[b2] == t1)
finally:
print()
base_data.erase()
def test_mp_read_from_sqlite():
import sqlitedict as sqd
import multiprocessing as mp
import time
d = sqd.SqliteDict('test.db', autocommit = True)
def write(arg):
with sqd.SqliteDict('test.db', autocommit = True) as d:
for i in range(100):
d[i] = (i, arg)
def read():
with sqd.SqliteDict('test.db', autocommit = True) as d:
for i in range(len(d)):
print(i, d[i])
p1 = mp.Process(target = write, args=('p1', ))
time.sleep(0.1)
p2 = mp.Process(target = read)
p1.start()
p2.start()
p1.join(10)
p2.join(10)
try:
if p1.is_alive():
raise RuntimeError("write process did not finish on time")
if p2.is_alive():
raise RuntimeError("read process did not finish on time")
finally:
p1.terminate()
p2.terminate()
d.terminate()
def test_from_existing_sub_data():
print()
print('test_from_existing_sub_data')
t1 = (3.4, 4.5, 5.6, 6.7, 7.8, 8.9)
t2 = (3.4, 4.5, 5.6, 6.7, 7.8, 8.9, 9,1)
with PDS(name='base', verbose=VERBOSE) as base_data:
base_data.clear()
with base_data.getData(key='s1', create_sub_data = True) as s1:
s1['d1'] = 1
s1['d2'] = 'b'
with PDS(name='base', verbose=VERBOSE) as base_data:
assert base_data['s1']['d1'] == 1
assert base_data['s1']['d2'] == 'b'
base_data.setDataFromSubData('s2', base_data['s1'])
assert base_data['s2']['d1'] == 1
assert base_data['s2']['d2'] == 'b'
del base_data['s1']
assert base_data['s2']['d1'] == 1
assert base_data['s2']['d2'] == 'b'
with PDS(name='base', verbose=VERBOSE) as base_data:
with base_data.getData(key='sub1', create_sub_data = True) as sub_data:
sub_data[100] = t1
sub_data[200] = t2
with sub_data.getData(key = 'subsub1', create_sub_data = True) as sub_sub_data:
sub_sub_data['t'] = 'hallo Welt'
base_data.setDataFromSubData(key='sub2', subData = sub_data)
with PDS(name='base', verbose=VERBOSE) as base_data:
with base_data.getData(key='sub2', create_sub_data = False) as sub_data:
assert np.all(sub_data[100] == t1)
assert np.all(sub_data[200] == t2)
with sub_data.getData(key = 'subsub1', create_sub_data = False) as sub_sub_data:
assert sub_sub_data['t'] == 'hallo Welt'
with PDS(name='base', verbose=VERBOSE) as base_data:
with base_data.getData(key='sub1', create_sub_data = True) as sub_data:
base_data['sub2'] = sub_data
with PDS(name='base', verbose=VERBOSE) as base_data:
with base_data.getData(key='sub2', create_sub_data = False) as sub_data:
assert np.all(sub_data[100] == t1)
assert np.all(sub_data[200] == t2)
with sub_data.getData(key = 'subsub1', create_sub_data = False) as sub_sub_data:
assert sub_sub_data['t'] == 'hallo Welt'
sub_sub_data['t'] = 'sub2:hallo Welt'
sub_data[100] = "sub2:t1"
sub_data[200] = "sub2:t2"
with PDS(name='base', verbose=VERBOSE) as base_data:
base_data.clear()
with base_data.getData(key = 'sub1', create_sub_data = True) as sub1:
sub1['npa'] = np.linspace(0,1,10)
sub1['val'] = 'hallo ich bin sub1'
base_data['sub2'] = sub1
with PDS(name='base', verbose=VERBOSE) as base_data:
npa1 = base_data['sub1']['npa']
npa2 = base_data['sub1']['npa']
assert type(npa1) == np.ndarray
assert type(npa2) == np.ndarray
def test_remove_sub_data_and_check_len():
with PDS(name='base', verbose=VERBOSE) as base_data:
base_data.clear()
with base_data.getData(key='sub1', create_sub_data = True) as sub_data:
sub_data[100] = 't1'
sub_data[200] = 't2'
with sub_data.getData(key = 'subsub1', create_sub_data = True) as sub_sub_data:
sub_sub_data['t'] = 'hallo Welt'
assert len(sub_data) == 3, "len = {}".format(len(sub_data))
assert len(base_data) == 1
base_data['copy_of_sub1'] = sub_data
assert len(base_data) == 2
del base_data['sub1']
assert len(base_data) == 1
with base_data.getData(key='copy_of_sub1', create_sub_data = True) as sub_data:
assert len(sub_data) == 3
assert sub_data[100] == 't1'
assert sub_data[200] == 't2'
with sub_data.getData(key = 'subsub1', create_sub_data = True) as sub_sub_data:
assert sub_sub_data['t'] == 'hallo Welt'
assert ('sub1' not in base_data)
def slow_len(pd):
n = 0
for k in pd:
n += 1
return n
def test_len():
with PDS(name='data', verbose=VERBOSE) as data:
data.clear()
assert len(data) == 0
assert slow_len(data) == 0
data['a'] = 1
assert len(data) == 1
assert slow_len(data) == 1
for i in range(1, 8):
data[i*10] = i
assert len(data) == 8
assert slow_len(data) == 8
with PDS(name='data', verbose=VERBOSE) as data:
assert len(data) == 8
assert slow_len(data) == 8
data.clear()
assert len(data) == 0
assert slow_len(data) == 0
with PDS(name='data', verbose=VERBOSE) as data:
assert len(data) == 0
assert slow_len(data) == 0
def test_clear():
with PDS(name='data', verbose=VERBOSE) as data:
data.clear()
data['a'] = 1
data['b'] = 2
with data.newSubData('s1') as s1:
s1['bla'] = 9
with data.newSubData('s2') as s2:
s2['bla2'] = 18
with data['s1'] as s1:
s1['t'] = 'tmp'
s1.clear()
with data['s1'] as s1:
assert len(s1) == 0
assert slow_len(s1) == 0
data.clear()
def test_not_in():
try:
with PDS(name='data', verbose=VERBOSE) as data:
data['a'] = 1
data['b'] = 2
with data.newSubData('s1') as s1:
s1['bla'] = 9
assert ('a' in data)
assert ('b' in data)
assert ('s1' in data)
assert ('c' not in data)
finally:
data.erase()
def test_npa():
a = np.linspace(0, 1, 100).reshape(10,10)
try:
with PDS(name='data_npa', verbose=VERBOSE) as data:
data['a'] = a
with PDS(name='data_npa', verbose=VERBOSE) as data:
b = data['a']
assert np.all(b == a)
with PDS(name='data_npa', verbose=VERBOSE) as data:
del data['a']
data['a'] = a
finally:
data.erase()
def test_merge():
a = np.random.rand(5)
with PDS(name='d1', verbose=VERBOSE) as d1:
d1.clear()
d1['k1'] = 1
d1['k2'] = 2
d1['k3'] = 3
d1['aa'] = a
with d1.newSubData('sub1') as sub1:
sub1['s1'] = 11
sub1['s2'] = 12
sub1['s3'] = 13
sub1['a'] = a
with PDS(name='d2', verbose=VERBOSE) as d2:
d2.clear()
d2['2k1'] = 1
with PDS(name='d1', verbose=VERBOSE) as d1:
d2.mergeOtherPDS(other_db = d1, status_interval=0)
with PDS(name='d2', verbose=VERBOSE) as d2:
assert 'k1' in d2
assert d2['k1'] == 1
assert 'k2' in d2
assert d2['k2'] == 2
assert 'k3' in d2
assert d2['k3'] == 3
assert 'aa' in d2
assert np.all(d2['aa'] == a)
assert "sub1" in d2
assert isinstance(d2["sub1"], PDS)
with d2["sub1"] as sub:
assert 's1' in sub
assert sub['s1'] == 11
assert 's2' in sub
assert sub['s2'] == 12
assert 's3' in sub
assert sub['s3'] == 13
assert 'a' in sub
assert np.all(sub['a'] == a)
try:
with PDS(name='d2', verbose=VERBOSE) as d2:
with PDS(name='d1', verbose=VERBOSE) as d1:
d2.mergeOtherPDS(other_db = d1, update='error', status_interval=0)
except KeyError as e:
print(e)
print("this is ok!")
pass
with PDS(name='d2', verbose=VERBOSE) as d2:
d2['k1'] = 'k1'
with PDS(name='d1', verbose=VERBOSE) as d1:
d2.mergeOtherPDS(other_db = d1, update='ignore', status_interval=0)
assert d2['k1'] == 'k1'
with PDS(name='d2', verbose=VERBOSE) as d2:
d2['k1'] = 'k1'
with PDS(name='d1', verbose=VERBOSE) as d1:
d2.mergeOtherPDS(other_db = d1, update='update', status_interval=0)
assert d2['k1'] == 1
def test_link_vs_copy():
data = np.arange(0,5)
with PDS(name='d', verbose=VERBOSE) as d:
d.clear()
sub = d.getData('sub', create_sub_data = True)
sub['3'] = 3
sub['4'] = 4
h5obj = d.getH5Object('sub')
assert h5obj.attrs['size'] == 2
d.setDataFromSubData('gr1_copy', sub, copy=False)
h5obj = d.getH5Object('gr1_copy')
assert h5obj.attrs['size'] == 2
d.setDataFromSubData('gr1_link', sub, copy=True)
h5obj = d.getH5Object('gr1_link')
assert h5obj.attrs['size'] == 2
assert len(d) == 3
with PDS(name='d', verbose=VERBOSE) as d:
d.clear()
gr1 = d.getData('gr1', create_sub_data=True)
gr1['data'] = data
gr1['str'] = 'gr1'
keys = [k for k in d['gr1']]
assert keys[0] == 'str'
assert keys[1] == 'data'
d.setDataFromSubData('gr1_link', gr1, copy=False)
assert len(d) == d.calc_len()
keys = [k for k in d['gr1']]
assert keys[0] == 'str'
assert keys[1] == 'data'
keys = [k for k in d['gr1_link']]
assert keys[0] == 'str'
assert keys[1] == 'data'
d.setDataFromSubData('gr1_copy', gr1, copy=True)
assert len(d) == d.calc_len()
keys = [k for k in d['gr1']]
assert keys[0] == 'str'
assert keys[1] == 'data'
keys = [k for k in d['gr1_copy']]
assert keys[0] == 'str'
assert keys[1] == 'data'
with PDS(name='d', verbose=VERBOSE) as d:
assert np.all(d['gr1']['data'] == d['gr1_link']['data'])
assert np.all(d['gr1']['data'] == d['gr1_copy']['data'])
d['gr1'].getH5Object('data')[0] = -3
assert d['gr1_link']['data'][0] == -3
assert d['gr1_copy']['data'][0] == 0
keys = [k for k in d['gr1']]
assert keys[0] == 'str'
assert keys[1] == 'data'
def test_merge_fname_conflict():
a = np.random.rand(5)
b = np.random.rand(5)
with PDS(name='d1', verbose=VERBOSE) as d1:
d1.clear()
d1['aa'] = a
with d1.newSubData('sub1') as sub1:
sub1['s1'] = 11
sub1['a'] = a
with PDS(name='d2', verbose=VERBOSE) as d2:
d2.clear()
d2['2k1'] = 1
d2['2aa'] = b
with d2.newSubData('sub2') as sub2:
sub2['s2'] = 22
sub2['a2'] = b
assert np.all(d2['2aa'] == b)
with PDS(name='d1', verbose=VERBOSE) as d1:
d2.mergeOtherPDS(other_db = d1, update='error', status_interval=0)
assert np.all(d2['2aa'] == b)
with PDS(name='d2', verbose=VERBOSE) as d2:
assert d2['2k1'] == 1
assert np.all(d2['2aa'] == b)
assert np.all(d2['aa'] == a)
assert d2.has_key('sub1')
with d2['sub1'] as sub1:
assert sub1['s1'] == 11
assert np.all(sub1['a'] == a)
assert d2.has_key('sub2')
with d2['sub2'] as sub2:
assert sub2['s2'] == 22
assert np.all(sub2['a2'] == b)
def test_convert_SQL_TO_H5():
data = np.empty((10,), dtype='<U2')
data[0] = 'd\U00008000'
data[1] = 'ha'
with PDS_SQL(name='pds_sql') as db:
db.clear()
db['a'] = 5
db[4] = (3, 's', [0])
db['uni'] = data
db[b'\xff\xee'] = np.arange(4)
with db.newSubData('sub') as sub:
sub['d1'] = 1
sub['d2'] = data
with PDS(name='pds_h5') as db_h5:
db_h5.clear()
db_h5['datautest'] = data
with PDS_SQL(name='pds_sql') as db_sql:
mergePDS(db_sql, db_h5, status_interval=0)
with PDS(name='pds_h5') as db_h5:
assert db_h5['a'] == 5
assert db_h5['4'] == (3, 's', [0])
assert np.all(db_h5[b'\xff\xee'] == np.arange(4))
assert np.all(db_h5['uni'] == data)
sub = db_h5['sub']
assert sub['d1'] == 1
assert np.all(sub['d2'] == data)
def test_iterator():
with PDS(name='pds') as db:
db.clear()
db['a'] = 5
db[4] = (3, 's', [0])
db['uni'] = np.arange(10)
db[b'\xff\xee'] = np.arange(4)
with db.newSubData('sub') as sub:
sub['d1'] = 1
sub['d2'] = np.arange(5)
db = PDS(name='pds')
for k in db:
print(k)
db.close()
if __name__ == "__main__":
test_clear()
test_pd()
test_md5_clash()
test_pd_bytes()
test_mp_read_from_sqlite()
test_from_existing_sub_data()
test_remove_sub_data_and_check_len()
test_len()
test_not_in()
test_npa()
test_merge()
test_merge_fname_conflict()
test_link_vs_copy()
test_convert_SQL_TO_H5()
test_iterator()
pass