def test_3(path, tmpdir, regtest):
# relative path for peakmaps:
from emzed.core.data_types import Table
pm = emzed.io.loadPeakMap(path("data/SHORT_MS2_FILE.mzData"))
t = emzed.utils.toTable("id", (1, 2, 3), type_=int)
t.addColumn("peakmap", pm, type_=object)
folder = tmpdir.join("subfolder")
folder.mkdir()
p2 = folder.join("with_comp.table").strpath
t.store(p2, True, True, "..")
for p in tmpdir.listdir():
# full path varies because the folder is a tmp dir:
print(p.basename, file=regtest)
t2 = Table.load(p2)
# this triggers loading:
t2.peakmap[0].chromatogram(0, 10, 0, 10)
t2.peakmap[0]._path == p.strpath
# now we move and check if proxy still works:
moved = folder.join("..").join("moved")
shutil.move(folder.strpath, moved.strpath)
t2 = Table.load(moved.join("with_comp.table").strpath)
t2.peakmap[0].chromatogram(0, 10, 0, 10)
def test_2(path, tmpdir, regtest):
# same folder as table for peakmaps:
from emzed.core.data_types import Table
pm = emzed.io.loadPeakMap(path("data/SHORT_MS2_FILE.mzData"))
t = emzed.utils.toTable("id", (1, 2, 3), type_=int)
t.addColumn("peakmap", pm, type_=object)
p2 = tmpdir.join("with_comp.table").strpath
t.store(p2, True, True, ".")
# chekc if pm proxy is next ot
file_names = [p.basename for p in tmpdir.listdir()]
print(file_names, file=regtest)
# force loading of data:.
print(len(t.peakmap.values[0]), file=regtest)
s1 = os.stat(p2).st_size
assert s1 < 1000
t = Table.load(p2)
print(len(t.peakmap.values[0]), file=regtest)
subfolder = tmpdir.join("subfolder")
os.makedirs(subfolder.strpath)
for p in file_names:
shutil.move(tmpdir.join(p).strpath, subfolder.strpath)
t2 = Table.load(subfolder.join("with_comp.table").strpath)
print(t2, file=regtest)
print(len(t2.peakmap.values[0]), file=regtest)
print(t2, file=regtest)
dat = pickle.dumps(t)
t = pickle.loads(dat)
run(t, names, [row1, row2, row3])
def j(name):
import os.path
return os.path.join(self.temp_output, name)
t.store(j("test.table"))
try:
Table.storeTable(t, "temp_output/test.table")
assert False, "no exception thrown althoug file should exist!"
except:
pass
t.store(j("test.table"), True)
t = Table.load(j("test.table"))
run(t, names, [row1, row2, row3])
def testSomePredicates(self):
#build table
names = "int long float str object array".split()
types = [
int,
long,
float,
str,
object,
np.ndarray,
]
formats = ["%3d", "%d", "%.3f", "%s", "%r", "'array%r' % (o.shape,)"]
dat = pickle.dumps(t)
t = pickle.loads(dat)
run(t, names, [row1, row2, row3])
def j(name):
import os.path
return os.path.join(self.temp_output, name)
t.store(j("test.table"))
try:
Table.storeTable(t, "temp_output/test.table")
assert False, "no exception thrown althoug file should exist!"
except:
pass
t.store(j("test.table"), True)
t = Table.load(j("test.table"))
run(t, names, [row1, row2, row3])
def testSomePredicates(self):
#build table
names="int long float str object array".split()
types = [int, long, float, str, object, np.ndarray,]
formats = [ "%3d", "%d", "%.3f", "%s", "%r", "'array%r' % (o.shape,)" ]
row1 = [ 1, 12323L, 1.0, "hi", { 1: 1 }, np.array((1,2,3)) ]
row2 = [ 2, 22323L, 2.0, "hi2", [2,3,], np.array(((2,3,4),(1,2,3))) ]
row3 = [ 3, 32323L, 3.0, "hi3", (3,) , np.array(((3,3,4,5),(1,2,3,4))) ]
rows = [row1, row2, row3]
t=Table(names, types, formats, rows, "testtabelle", meta=dict(why=42))
