def testColumnSpaceNames(self):
grid = self.client.sf.sharedResources()
repoMap = grid.repositories()
repoObj = repoMap.descriptions[0]
table = grid.newTable(repoObj.id.val, "/testColumnSpaceNames")
assert table
cols = []
lc = columns.LongColumnI("Long column", None, [1])
sc = columns.StringColumnI("String column", None, 4)
cols.append(lc)
cols.append(sc)
table.initialize(cols)
lc.values = [1, 2, 3, 4]
sc.values = ["foo", "bar", "foo", "spam"]
table.addData(cols)
assert [1, 2,
3] == table.getWhereList("x>1", {'x': rstring("Long column")},
0, 4, 0)
assert [1] == table.getWhereList("x=='bar'",
{'x': rstring("String column")}, 0, 4,
0)
assert [0, 2] == table.getWhereList("x=='foo'",
{'x': rstring("String column")}, 0,
4, 0)
assert [1, 2] == table.getWhereList("(x>1)&(y!='spam')", {
'x': rstring("Long column"),
'y': rstring("String column")
}, 0, 4, 0)
table.delete()
table.close()
def test2098(self):
"""
Creates and downloads an HDF file and checks
that its size and hash match whats in the db
"""
grid = self.client.sf.sharedResources()
table = grid.newTable(1, "/test")
assert table
lc = columns.LongColumnI('lc', 'desc', [1])
file = None
try:
file = table.getOriginalFile()
assert file
table.initialize([lc])
table.addData([lc])
finally:
# Not deleting since queried
table.close()
# Reload the file
file = self.client.sf.getQueryService().get("OriginalFile",
file.id.val)
# Check values
p = path.path(self.tmpfile())
self.client.download(file, str(p))
assert p.size == file.size.val
def testReadOnlyFile(self):
"""
Create an HDF5 file on the server, and then mark it read-only.
The server should still allow you to load & read that file.
"""
self.testBlankTable() # ofile
filename = self.unique_dir + "/file.txt"
mrepo = self.get_managed_repo()
assert not mrepo.fileExists(filename)
self.create_file(mrepo, filename)
assert mrepo.fileExists(filename)
assert "file.txt" in mrepo.list(self.unique_dir)[0]
grid = self.client.sf.sharedResources()
repoMap = grid.repositories()
repoObj = repoMap.descriptions[0]
table = grid.newTable(repoObj.id.val, "/test")
assert table
lcol = columns.LongColumnI('longcol', 'long col')
table.initialize([lcol])
table.setMetadata('test', wrap('test'))
tid = unwrap(table.getOriginalFile().getId())
table.close()
# Mark the file as read only
# wip: read_only = self.raw("read-only", [file_path])
table = grid.openTable(omero.model.OriginalFileI(tid))
assert table
table.delete()
table.close()
def testCanReadInternalMetadata(self):
grid = self.client.sf.sharedResources()
repoMap = grid.repositories()
repoObj = repoMap.descriptions[0]
table = grid.newTable(repoObj.id.val, "/testInternalMetadata.h5")
table.initialize([columns.LongColumnI('lc')])
assert table.getMetadata("__version")
table.delete()
table.close()
def testGetHeaders(self):
"""
Check all required fields are included in the headers
"""
grid = self.client.sf.sharedResources()
table = grid.newTable(1, "/test")
assert table
cols = [
columns.LongColumnI('no desc'),
columns.LongColumnI('scalar', 'scalar desc'),
columns.LongArrayColumnI('array', 'array desc', 3)
]
table.initialize(cols)
h = table.getHeaders()
assert len(h) == 3
assert (h[0].name, h[0].description) == ('no desc', '')
assert (h[1].name, h[1].description) == ('scalar', 'scalar desc')
assert (h[2].name, h[2].description, h[2].size) == ('array',
'array desc', 3)
table.delete()
table.close()
def test4000TableRead(self):
"""
Tests that empty or zero (ice default) values for stop
are translated appropriately.
"""
grid = self.client.sf.sharedResources()
table = grid.newTable(1, "/test")
assert table
lc = columns.LongColumnI('lc', 'desc', [123])
table.initialize([lc])
table.addData([lc])
assert [123] == table.read([0], 0, 0).columns[0].values
def testCanWriteAlmostInternalMetadata(self, data):
grid = self.client.sf.sharedResources()
repoMap = grid.repositories()
repoObj = repoMap.descriptions[0]
table = grid.newTable(repoObj.id.val, "/testInternalMetadata.h5")
table.initialize([columns.LongColumnI('lc')])
if isinstance(data, dict):
table.setAllMetadata(data)
else:
table.setMetadata(*data)
assert "4" == table.getMetadata("version").val
table.delete()
table.close()
def testCantWriteInternalMetadata(self, data):
grid = self.client.sf.sharedResources()
repoMap = grid.repositories()
repoObj = repoMap.descriptions[0]
table = grid.newTable(repoObj.id.val, "/testInternalMetadata.h5")
table.initialize([columns.LongColumnI('lc')])
with pytest.raises(omero.ApiUsageException):
if isinstance(data, dict):
table.setAllMetadata(data)
else:
table.setMetadata(*data)
table.delete()
table.close()
def test3714GetWhereListVars(self):
"""
Tests that variables are correctly unwrapped
after transport
"""
grid = self.client.sf.sharedResources()
table = grid.newTable(1, "/test")
assert table
lc = columns.LongColumnI('lc', 'desc', [1])
table.initialize([lc])
table.addData([lc])
assert [0] == table.getWhereList('(lc==var)', {"var": rlong(1)}, 0, 0,
0)
def test12606fileSizeCheck(self):
"""
Close may write additional data to a table after a flush, this is
most likely to occur for very small writes such as attribute changes
"""
grid = self.client.sf.sharedResources()
repoMap = grid.repositories()
repoObj = repoMap.descriptions[0]
table = grid.newTable(repoObj.id.val, "/test")
assert table
lcol = columns.LongColumnI('longcol', 'long col')
table.initialize([lcol])
table.setMetadata('test', wrap('test'))
tid = unwrap(table.getOriginalFile().getId())
table.close()
table = grid.openTable(omero.model.OriginalFileI(tid))
assert table
table.close()
def test10431uninitialisedTableReadWrite(self):
"""
Return an error when attempting to read/write an uninitialised table
"""
grid = self.client.sf.sharedResources()
repoMap = grid.repositories()
repoObj = repoMap.descriptions[0]
table = grid.newTable(repoObj.id.val, "/test")
assert table
lcol = columns.LongColumnI('longcol', 'long col')
with pytest.raises(omero.ApiUsageException):
table.addData([lcol])
with pytest.raises(omero.ApiUsageException):
table.read([0], 0, 0)
with pytest.raises(omero.ApiUsageException):
table.slice([], [])
with pytest.raises(omero.ApiUsageException):
table.getWhereList('', None, 0, 0, 0)
def test2855MetadataMethods(self):
"""
Tests the various metadata methods for a table
"""
grid = self.client.sf.sharedResources()
table = grid.newTable(1, "/test")
assert table
def clean(m):
"""
Unwraps the RTypes for easier processing
and gets rid of auto-generated values for
easier testing.
"""
m = unwrap(m)
del m["initialized"]
del m["version"]
return m
try:
print table.getOriginalFile().id.val
lc = columns.LongColumnI('lc', 'desc', [1])
table.initialize([lc])
assert len(clean(table.getAllMetadata())) == 0
# Set a string
table.setMetadata("s", rstring("b"))
assert "b" == unwrap(table.getMetadata("s"))
assert {"s": "b"} == clean(table.getAllMetadata())
# Set an int
table.setMetadata("i", rint(1))
assert 1 == unwrap(table.getMetadata("i"))
assert {"s": "b", "i": 1} == clean(table.getAllMetadata())
# Set a float
table.setMetadata("f", rfloat(1))
assert 1 == unwrap(table.getMetadata("f"))
assert {"s": "b", "i": 1, "f": 1} == clean(table.getAllMetadata())
finally:
table.close()
def testCreateAllColumnsAndMetadata_5_3_4(self):
"""
Call this method to create the reference HDF5 table under a 5.3.4
Python 2.7 server. The OriginalFile ID of the table will be printed,
and can be used to find the file under ${omero.data.dir}/Files/.
Alternatively download it using
``omero download OriginalFile:FileID output.h5``
To run manually goto ``components/tools/OmeroPy``, and run:
``pytest test/integration/tablestest/test_backwards_compatibility.py\
-s -k testCreateAllColumnsAndMetadata_5_3_4``
"""
grid = self.client.sf.sharedResources()
repoMap = grid.repositories()
repoObj = repoMap.descriptions[0]
table = grid.newTable(repoObj.id.val, "/test")
assert table
# Supported metadata types
# https://github.com/ome/omero-py/blob/v5.5.1/src/omero/hdfstorageV2.py#L466
metadata = {
'string': rstring('a'),
'int': rint(1),
'long': rlong(1),
'double': rfloat(0.1),
}
fcol = columns.FileColumnI('filecol', 'file col')
fcol.values = [10, 20]
icol = columns.ImageColumnI('imagecol', 'image col')
icol.values = [30, 40]
rcol = columns.RoiColumnI('roicol', 'roi col')
rcol.values = [50, 60]
wcol = columns.WellColumnI('wellcol', 'well col')
wcol.values = [70, 80]
pcol = columns.PlateColumnI('platecol', 'plate col')
pcol.values = [90, 100]
bcol = columns.BoolColumnI('boolcol', 'bool col')
bcol.values = [True, False]
dcol = columns.DoubleColumnI('doublecol', 'double col')
dcol.values = [0.25, 0.5]
lcol = columns.LongColumnI('longcol', 'long col')
lcol.values = [-1, -2]
scol = columns.StringColumnI('stringcol', 'string col', 3)
scol.values = ["abc", "de"]
larr = columns.LongArrayColumnI('longarr', 'longarr col', 2)
larr.values = [[-2, -1], [1, 2]]
farr = columns.FloatArrayColumnI('floatarr', 'floatarr col', 2)
farr.values = [[-0.25, -0.5], [0.125, 0.0625]]
darr = columns.DoubleArrayColumnI('doublearr', 'doublearr col', 2)
darr.values = [[-0.25, -0.5], [0.125, 0.0625]]
# DatasetColumn is broken!
mask = self.createMaskCol()
cols = [
fcol, icol, rcol, wcol, pcol, bcol, dcol, lcol, scol, mask, larr,
farr, darr
]
table.initialize(cols)
table.setAllMetadata(metadata)
table.addData(cols)
data = table.readCoordinates([0, 1])
testf = data.columns[0].values
assert 10 == testf[0]
assert 20 == testf[1]
testi = data.columns[1].values
assert 30 == testi[0]
assert 40 == testi[1]
testr = data.columns[2].values
assert 50 == testr[0]
assert 60 == testr[1]
testw = data.columns[3].values
assert 70 == testw[0]
assert 80 == testw[1]
testp = data.columns[4].values
assert 90 == testp[0]
assert 100 == testp[1]
testb = data.columns[5].values
assert testb[0]
assert not testb[1]
testd = data.columns[6].values
assert 0.25 == testd[0]
assert 0.5 == testd[1]
testl = data.columns[7].values
assert -1 == testl[0]
assert -2 == testl[1]
tests = data.columns[8].values
assert "abc" == tests[0]
assert "de" == tests[1]
testm = data.columns[9]
self.checkMaskCol(testm)
testla = data.columns[10].values
assert [-2, -1] == testla[0]
assert [1, 2] == testla[1]
testfa = data.columns[11].values
assert [-0.25, -0.5] == testfa[0]
assert [0.125, 0.0625] == testfa[1]
testda = data.columns[12].values
assert [-0.25, -0.5] == testda[0]
assert [0.125, 0.0625] == testda[1]
ofile = table.getOriginalFile()
print("Created OriginalFile:", ofile.getId().val)
table.close()
def test2855MetadataMethods(self):
"""
Tests the various metadata methods for a table
"""
grid = self.client.sf.sharedResources()
table = grid.newTable(1, "/test")
assert table
def clean(m):
"""
Unwraps the RTypes for easier processing
and gets rid of auto-generated values for
easier testing.
"""
m = unwrap(m)
assert "__initialized" in m
assert "__version" in m
del m["__initialized"]
del m["__version"]
return m
try:
print(table.getOriginalFile().id.val)
lc = columns.LongColumnI('lc', 'desc', [1])
table.initialize([lc])
assert len(clean(table.getAllMetadata())) == 0
# Set a string
table.setMetadata("s", rstring("b"))
assert "b" == unwrap(table.getMetadata("s"))
assert {"s": "b"} == clean(table.getAllMetadata())
# Set an int
table.setMetadata("i", rint(1))
assert 1 == unwrap(table.getMetadata("i"))
assert {"s": "b", "i": 1} == clean(table.getAllMetadata())
# Set a float
table.setMetadata("f", rfloat(1))
assert 1 == unwrap(table.getMetadata("f"))
assert {"s": "b", "i": 1, "f": 1} == clean(table.getAllMetadata())
# Replace all user-metadata
table.setAllMetadata({"s2": rstring("b2"), "l2": rlong(3)})
assert {"s2": "b2", "l2": 3} == clean(table.getAllMetadata())
assert table.getMetadata("s") is None
table.setAllMetadata({})
assert {} == clean(table.getAllMetadata())
table.setMetadata("z", rint(1))
with pytest.raises(omero.ApiUsageException):
table.setMetadata("__z", rint(2))
assert {"z": 1} == clean(table.getAllMetadata())
with pytest.raises(omero.ValidationException):
table.setMetadata("z", rint(None))
finally:
table.delete()
table.close()
def testCreateAllColumns_4_4_5(self):
"""
Call this method to create the reference HDF5 table under a 4.4.5
or older server. The OriginalFile ID of the table will be printed,
and can be used to find the file under ${omero.data.dir}/Files/.
To run manually goto ``components/tools/OmeroPy``, and run:
``py.test test/integration/tablestest/test_backwards_compatibility.py\
-s -k testCreateAllColumns_4_4_5``
"""
grid = self.client.sf.sharedResources()
repoMap = grid.repositories()
repoObj = repoMap.descriptions[0]
table = grid.newTable(repoObj.id.val, "/test")
assert table
fcol = columns.FileColumnI('filecol', 'file col')
fcol.values = [10, 20]
icol = columns.ImageColumnI('imagecol', 'image col')
icol.values = [30, 40]
rcol = columns.RoiColumnI('roicol', 'roi col')
rcol.values = [50, 60]
wcol = columns.WellColumnI('wellcol', 'well col')
wcol.values = [70, 80]
pcol = columns.PlateColumnI('platecol', 'plate col')
pcol.values = [90, 100]
bcol = columns.BoolColumnI('boolcol', 'bool col')
bcol.values = [True, False]
dcol = columns.DoubleColumnI('doublecol', 'double col')
dcol.values = [0.25, 0.5]
lcol = columns.LongColumnI('longcol', 'long col')
lcol.values = [-1, -2]
scol = columns.StringColumnI('stringcol', 'string col', 3)
scol.values = ["abc", "de"]
# larr = columns.LongArrayColumnI('longarr', 'longarr col', 2)
# larr.values = [[-2, -1], [1, 2]]
# farr = columns.FloatArrayColumnI('floatarr', 'floatarr col', 2)
# farr.values = [[-0.25, -0.5], [0.125, 0.0625]]
# darr = columns.DoubleArrayColumnI('doublearr', 'doublearr col', 2)
# darr.values = [[-0.25, -0.5], [0.125, 0.0625]]
mask = self.createMaskCol()
cols = [fcol, icol, rcol, wcol, pcol,
bcol, dcol, lcol, scol, mask]
# larr, farr, darr]
table.initialize(cols)
table.addData(cols)
data = table.readCoordinates([0, 1])
testf = data.columns[0].values
assert 10 == testf[0]
assert 20 == testf[1]
testi = data.columns[1].values
assert 30 == testi[0]
assert 40 == testi[1]
testr = data.columns[2].values
assert 50 == testr[0]
assert 60 == testr[1]
testw = data.columns[3].values
assert 70 == testw[0]
assert 80 == testw[1]
testp = data.columns[4].values
assert 90 == testp[0]
assert 100 == testp[1]
testb = data.columns[5].values
assert testb[0]
assert not testb[1]
testd = data.columns[6].values
assert 0.25 == testd[0]
assert 0.5 == testd[1]
testl = data.columns[7].values
assert -1 == testl[0]
assert -2 == testl[1]
tests = data.columns[8].values
assert "abc" == tests[0]
assert "de" == tests[1]
testm = data.columns[9]
self.checkMaskCol(testm)
# testla = data.columns[10].values
# assert [-2, -1] == testla[0]
# assert [1, 2] == testla[1]
# testda = data.columns[11].values
# assert [-0.25, -0.5] == testda[0]
# assert [0.125, 0.0625] == testda[1]
ofile = table.getOriginalFile()
print "Created OriginalFile:", ofile.getId().val
def _testCreateAllColumnsAndMetadata(self):
grid = self.client.sf.sharedResources()
repoMap = grid.repositories()
repoObj = repoMap.descriptions[0]
table = grid.newTable(repoObj.id.val, "/test")
assert table
# Supported metadata types
# https://github.com/ome/omero-py/blob/v5.5.1/src/omero/hdfstorageV2.py#L466
metadata = {
'string': rstring('a'),
'int': rint(1),
'long': rlong(1),
'double': rfloat(0.1),
}
fcol = columns.FileColumnI('filecol', 'file col')
fcol.values = [10, 20]
icol = columns.ImageColumnI('imagecol', 'image col')
icol.values = [30, 40]
rcol = columns.RoiColumnI('roicol', 'roi col')
rcol.values = [50, 60]
wcol = columns.WellColumnI('wellcol', 'well col')
wcol.values = [70, 80]
pcol = columns.PlateColumnI('platecol', 'plate col')
pcol.values = [90, 100]
bcol = columns.BoolColumnI('boolcol', 'bool col')
bcol.values = [True, False]
dcol = columns.DoubleColumnI('doublecol', 'double col')
dcol.values = [0.25, 0.5]
lcol = columns.LongColumnI('longcol', 'long col')
lcol.values = [-1, -2]
scol = columns.StringColumnI('stringcol', 'string col', 3)
scol.values = ["abc", "de"]
larr = columns.LongArrayColumnI('longarr', 'longarr col', 2)
larr.values = [[-2, -1], [1, 2]]
farr = columns.FloatArrayColumnI('floatarr', 'floatarr col', 2)
farr.values = [[-0.25, -0.5], [0.125, 0.0625]]
darr = columns.DoubleArrayColumnI('doublearr', 'doublearr col', 2)
darr.values = [[-0.25, -0.5], [0.125, 0.0625]]
dscol = columns.DatasetColumnI('datasetcol', 'dataset col')
dscol.values = [110, 120]
mask = self.createMaskCol()
cols = [
fcol, icol, rcol, wcol, pcol, bcol, dcol, lcol, scol, mask, larr,
farr, darr, dscol
]
table.initialize(cols)
table.setAllMetadata(metadata)
table.addData(cols)
data = table.readCoordinates([0, 1])
testf = data.columns[0].values
assert 10 == testf[0]
assert 20 == testf[1]
testi = data.columns[1].values
assert 30 == testi[0]
assert 40 == testi[1]
testr = data.columns[2].values
assert 50 == testr[0]
assert 60 == testr[1]
testw = data.columns[3].values
assert 70 == testw[0]
assert 80 == testw[1]
testp = data.columns[4].values
assert 90 == testp[0]
assert 100 == testp[1]
testb = data.columns[5].values
assert testb[0]
assert not testb[1]
testd = data.columns[6].values
assert 0.25 == testd[0]
assert 0.5 == testd[1]
testl = data.columns[7].values
assert -1 == testl[0]
assert -2 == testl[1]
tests = data.columns[8].values
assert "abc" == tests[0]
assert "de" == tests[1]
testm = data.columns[9]
self.checkMaskCol(testm)
testla = data.columns[10].values
assert [-2, -1] == testla[0]
assert [1, 2] == testla[1]
testfa = data.columns[11].values
assert [-0.25, -0.5] == testfa[0]
assert [0.125, 0.0625] == testfa[1]
testda = data.columns[12].values
assert [-0.25, -0.5] == testda[0]
assert [0.125, 0.0625] == testda[1]
testds = data.columns[13].values
assert 110 == testds[0]
assert 120 == testds[1]
ofile = table.getOriginalFile()
print("Created OriginalFile:", ofile.getId().val)
return table
def testAllColumnsSameTable(self):
"""
Check all column types can coexist in the same table
"""
grid = self.client.sf.sharedResources()
repoMap = grid.repositories()
repoObj = repoMap.descriptions[0]
table = grid.newTable(repoObj.id.val, "/test")
assert table
fcol = columns.FileColumnI('filecol', 'file col')
fcol.values = [10, 20]
icol = columns.ImageColumnI('imagecol', 'image col')
icol.values = [30, 40]
rcol = columns.RoiColumnI('roicol', 'roi col')
rcol.values = [50, 60]
wcol = columns.WellColumnI('wellcol', 'well col')
wcol.values = [70, 80]
pcol = columns.PlateColumnI('platecol', 'plate col')
pcol.values = [90, 100]
bcol = columns.BoolColumnI('boolcol', 'bool col')
bcol.values = [True, False]
dcol = columns.DoubleColumnI('doublecol', 'double col')
dcol.values = [0.25, 0.5]
lcol = columns.LongColumnI('longcol', 'long col')
lcol.values = [-1, -2]
scol = columns.StringColumnI('stringcol', 'string col', 46)
scol.values = ["მიკროსკოპის პონი", "de"]
mask = self.createMaskCol()
larr = columns.LongArrayColumnI('longarr', 'longarr col', 2)
larr.values = [[-2, -1], [1, 2]]
farr = columns.FloatArrayColumnI('floatarr', 'floatarr col', 2)
farr.values = [[-8.0, -4.0], [16.0, 32.0]]
darr = columns.DoubleArrayColumnI('doublearr', 'doublearr col', 2)
darr.values = [[-0.25, -0.5], [0.125, 0.0625]]
cols = [
fcol, icol, rcol, wcol, pcol, bcol, dcol, lcol, scol, mask, larr,
farr, darr
]
table.initialize(cols)
table.addData(cols)
data = table.readCoordinates([0, 1])
testf = data.columns[0].values
assert 10 == testf[0]
assert 20 == testf[1]
testi = data.columns[1].values
assert 30 == testi[0]
assert 40 == testi[1]
testr = data.columns[2].values
assert 50 == testr[0]
assert 60 == testr[1]
testw = data.columns[3].values
assert 70 == testw[0]
assert 80 == testw[1]
testp = data.columns[4].values
assert 90 == testp[0]
assert 100 == testp[1]
testb = data.columns[5].values
assert testb[0]
assert not testb[1]
testd = data.columns[6].values
assert 0.25 == testd[0]
assert 0.5 == testd[1]
testl = data.columns[7].values
assert -1 == testl[0]
assert -2 == testl[1]
tests = data.columns[8].values
assert "მიკროსკოპის პონი" == tests[0]
assert "de" == tests[1]
testm = data.columns[9]
self.checkMaskCol(testm)
testla = data.columns[10].values
assert [-2, -1] == testla[0]
assert [1, 2] == testla[1]
testfa = data.columns[11].values
assert [-8.0, -4.0] == testfa[0]
assert [16.0, 32.0] == testfa[1]
testda = data.columns[12].values
assert [-0.25, -0.5] == testda[0]
assert [0.125, 0.0625] == testda[1]
ofile = table.getOriginalFile()
print(("testAllColumnsSameTable", "OriginalFile:", ofile.getId().val))
# Now try an update
updatel = omero.grid.LongColumn('longcol', '', [12345])
updatela = omero.grid.LongArrayColumn('longarr', '', 2, [[654, 321]])
updateData = omero.grid.Data(rowNumbers=[1],
columns=[updatel, updatela])
table.update(updateData)
assert table.getNumberOfRows() == 2
data2 = table.readCoordinates([0, 1])
for n in [0, 1, 2, 3, 4, 5, 6, 8, 11, 12]:
assert data.columns[n].values == data2.columns[n].values
self.checkMaskCol(data2.columns[9])
testl2 = data2.columns[7].values
assert -1 == testl2[0]
assert 12345 == testl2[1]
testla2 = data2.columns[10].values
assert [-2, -1] == testla2[0]
assert [654, 321] == testla2[1]
table.delete()
table.close()
