def test_transform(self):
headers, column_cfgs = self.get_complicated_headers()
tr = KeyValueListTransformer(headers, None, column_cfgs)
r = tr.transform(("3", "2", "4", "1a|1b", "x", "5", "6"))
assert len(r) == 6
assert r[0] == ("a1", ["1a", "1b"])
assert r[1] == ("__a2", ["2"])
assert r[2] == ("a3", ["3"])
assert r[3] == ("a4", ["*-4-*"])
assert r[4] == ("a5", ["5"])
assert r[5] == ("a6", ["6"])
def test_transform(self):
headers, column_cfgs = self.get_complicated_headers()
tr = KeyValueListTransformer(headers, None, column_cfgs)
r = tr.transform(("3", "2", "4", "1a|1b", "x", "5", "6"))
assert len(r) == 6
assert r[0] == ("a1", ["1a", "1b"])
assert r[1] == ("__a2", ["2"])
assert r[2] == ("a3", ["3"])
assert r[3] == ("a4", ["*-4-*"])
assert r[4] == ("a5", ["5"])
assert r[5] == ("a6", ["6"])
def test_transform(self):
headers = ["a2", "a4", "a3", "a1"]
output_configs = [
(expected(name="a1", split="|"), 3),
(expected(name="a2", visible=False), 0),
(expected(name="a4", clientvalue="*-{{ value }}-*"), 1),
]
tr = KeyValueListTransformer(headers, output_configs)
r = tr.transform(("2", "4", "x", "1a|1b"))
assert len(r) == 3
assert r[0] == ("a1", ["1a", "1b"])
assert r[1] == ("__a2", ["2"])
assert r[2] == ("a4", ["*-4-*"])
def populate(self, table):
def idcolumn_to_omeroclass(col):
clsname = re.search('::(\w+)Column$', col.ice_staticId()).group(1)
return getattr(omero.model, '%sI' % clsname)
nrows = table.getNumberOfRows()
data = table.readCoordinates(range(nrows))
# Don't create annotations on higher-level objects
# idcoltypes = set(HeaderResolver.screen_keys.values())
idcoltypes = set((ImageColumn, WellColumn))
idcols = []
for n in xrange(len(data.columns)):
col = data.columns[n]
if col.__class__ in idcoltypes:
omeroclass = idcolumn_to_omeroclass(col)
idcols.append((omeroclass, n))
headers = [c.name for c in data.columns]
if self.default_cfg or self.column_cfgs:
tr = KeyValueListTransformer(headers, self.default_cfg,
self.column_cfgs)
else:
tr = KeyValueListPassThrough(headers)
mas = []
for row in izip(*(c.values for c in data.columns)):
rowkvs = tr.transform(row)
targets = []
for omerotype, n in idcols:
if row[n] > 0:
obj = omerotype(row[n], False)
# Josh: disabling to prevent duplication in UI
# targets.append(obj)
targets.extend(self._get_additional_targets(obj))
else:
log.warn("Invalid Id:%d found in row %s", row[n], row)
if targets:
malinks = self.create_map_annotation(targets, rowkvs)
log.debug('Map:\n\t' + ('\n\t'.join(
"%s=%s" % (v.name, v.value)
for v in malinks[0].getChild().getMapValue())))
log.debug('Targets:\n\t' + ('\n\t'.join(
"%s:%d" % (t.ice_staticId().split('::')[-1], t.id._val)
for t in targets)))
mas.extend(malinks)
self.mapannotations = mas
def populate(self, table):
def idcolumn_to_omeroclass(col):
clsname = re.search('::(\w+)Column$', col.ice_staticId()).group(1)
return getattr(omero.model, '%sI' % clsname)
nrows = table.getNumberOfRows()
data = table.readCoordinates(range(nrows))
# Don't create annotations on higher-level objects
# idcoltypes = set(HeaderResolver.screen_keys.values())
idcoltypes = set((ImageColumn, WellColumn))
idcols = []
for n in xrange(len(data.columns)):
col = data.columns[n]
if col.__class__ in idcoltypes:
omeroclass = idcolumn_to_omeroclass(col)
idcols.append((omeroclass, n))
headers = [c.name for c in data.columns]
if self.default_cfg or self.column_cfgs:
tr = KeyValueListTransformer(
headers, self.default_cfg, self.column_cfgs)
else:
tr = KeyValueListPassThrough(headers)
mas = []
for row in izip(*(c.values for c in data.columns)):
rowkvs = tr.transform(row)
targets = []
for omerotype, n in idcols:
if row[n] > 0:
obj = omerotype(row[n], False)
# Josh: disabling to prevent duplication in UI
# targets.append(obj)
targets.extend(self._get_additional_targets(obj))
else:
log.warn("Invalid Id:%d found in row %s", row[n], row)
if targets:
malinks = self.create_map_annotation(targets, rowkvs)
log.debug('Map:\n\t' + ('\n\t'.join("%s=%s" % (
v.name, v.value) for v in
malinks[0].getChild().getMapValue())))
log.debug('Targets:\n\t' + ('\n\t'.join("%s:%d" % (
t.ice_staticId().split('::')[-1], t.id._val)
for t in targets)))
mas.extend(malinks)
self.mapannotations = mas
def test_init_col(self):
headers = ["a1"]
tr = KeyValueListTransformer(headers, None, [{
"name": "a1",
"visible": False
}])
assert tr.default_cfg == expected()
assert len(tr.output_configs) == 1
assert tr.output_configs[0] == (expected(name="a1", visible=False), 0)
def test_init_col_ordered_unordered(self):
headers = ["a2", "a1"]
tr = KeyValueListTransformer(headers, None, [{
"name": "a2",
"visible": False
}, {
"name": "a1",
"position": 1
}])
assert tr.default_cfg == expected()
assert len(tr.output_configs) == 2
assert tr.output_configs[0] == (expected(name="a1", position=1), 1)
assert tr.output_configs[1] == (expected(name="a2", visible=False), 0)
def test_init_col_complicated_order(self):
headers, column_cfgs = self.get_complicated_headers()
tr = KeyValueListTransformer(headers, None, column_cfgs)
assert tr.default_cfg == expected()
assert len(tr.output_configs) == 6
assert tr.output_configs[0] == (expected(name="a1",
position=1,
split="|"), 3)
assert tr.output_configs[1] == (expected(name="a2", visible=False), 1)
assert tr.output_configs[2] == (expected(name="a3"), 0)
assert tr.output_configs[3] == (expected(
name="a4", position=4, clientvalue="*-{{ value }}-*"), 2)
assert tr.output_configs[4] == (expected(name="a5"), 5)
assert tr.output_configs[5] == (expected(name="a6"), 6)
def test_init_col_unincluded(self):
headers = ["a2", "a1"]
tr = KeyValueListTransformer(headers, {
"include": False,
"includeclient": False
}, [{
"name": "a2",
"include": True
}])
assert tr.default_cfg == expected(include=False, includeclient=False)
assert len(tr.output_configs) == 1
assert tr.output_configs[0] == (expected(name="a2",
include=True,
includeclient=False), 0)
def test_transformj2(self):
cfg = expected(name="a1", clientvalue="http://{{ value | urlencode }}")
assert KeyValueListTransformer.transform1("a b",
cfg) == ("a1",
["http://a%20b"])
def test_transform1(self, inout):
cfg = expected(name="a1", **inout[1])
assert KeyValueListTransformer.transform1(inout[0], cfg) == inout[2]
def test_transform1_clientname(self):
cfg = expected(name="a1", clientname="a / 1")
assert KeyValueListTransformer.transform1("ab, c",
cfg) == ("a / 1", ["ab, c"])
def test_transform1(self, inout):
cfg = expected(name="a1", **inout[1])
assert KeyValueListTransformer.transform1(inout[0], cfg) == inout[2]
def test_transform1_clientname(self):
cfg = expected(name="a1", clientname="a / 1")
assert KeyValueListTransformer.transform1("ab, c", cfg) == (
"a / 1", ["ab, c"])