def test421Upgrade(self):
"""
When upgraded 4.2.0 properties to 4.2.1,
${dn} items in omero.ldap.* properties are
changed to @{dn}
"""
p = create_path()
# How config was written in 4.2.0
XML = Element("icegrid")
active = SubElement(XML, "properties", id="__ACTIVE__")
default = SubElement(XML, "properties", id="default")
for properties in (active, default):
SubElement(
properties, "property", name="omero.config.version",
value="4.2.0")
SubElement(
properties, "property", name="omero.ldap.new_user_group",
value="member=${dn}")
SubElement(
properties, "property", name="omero.ldap.new_user_group_2",
value="member=$${omero.dollar}{dn}")
string = tostring(XML, 'utf-8')
txt = xml.dom.minidom.parseString(string).toprettyxml(" ", "\n", None)
p.write_text(txt)
config = ConfigXml(filename=str(p), env_config="default")
try:
m = config.as_map()
assert "member=@{dn}" == m["omero.ldap.new_user_group"]
assert "member=@{dn}" == m["omero.ldap.new_user_group_2"]
finally:
config.close()
def test421Upgrade(self):
"""
When upgraded 4.2.0 properties to 4.2.1,
${dn} items in omero.ldap.* properties are
changed to @{dn}
"""
p = create_path()
# How config was written in 4.2.0
XML = Element("icegrid")
active = SubElement(XML, "properties", id="__ACTIVE__")
default = SubElement(XML, "properties", id="default")
for properties in (active, default):
SubElement(
properties, "property", name="omero.config.version",
value="4.2.0")
SubElement(
properties, "property", name="omero.ldap.new_user_group",
value="member=${dn}")
SubElement(
properties, "property", name="omero.ldap.new_user_group_2",
value="member=$${omero.dollar}{dn}")
string = tostring(XML, 'utf-8')
txt = xml.dom.minidom.parseString(string).toprettyxml(" ", "\n", None)
p.write_text(txt)
config = ConfigXml(filename=str(p), env_config="default")
try:
m = config.as_map()
assert "member=@{dn}" == m["omero.ldap.new_user_group"]
assert "member=@{dn}" == m["omero.ldap.new_user_group_2"]
finally:
config.close()
def test_4(self, input, output):
p = write_config(input)
config = ConfigXml(filename=str(p), env_config="default")
try:
m = config.as_map()
s = strip_dict(m, suffix="blitz")
assert s == output
finally:
config.close()
def testLocking(self):
p = create_path()
config1 = ConfigXml(filename=str(p))
try:
ConfigXml(filename=str(p))
assert False, "No exception"
except portalocker.LockException:
pass
config1.close()
def testNewVersioning(self):
"""
All property blocks should always have a version set.
"""
p = create_path()
config = ConfigXml(filename=str(p))
m = config.as_map()
for k, v in m.items():
assert "4.2.1" == v
def test_4(self, input, output):
p = write_config(input)
config = ConfigXml(filename=str(p), env_config="default")
try:
m = config.as_map()
s = strip_dict(m, suffix="blitz")
assert s == output
finally:
config.close()
def testLocking(self):
p = create_path()
config1 = ConfigXml(filename=str(p))
try:
ConfigXml(filename=str(p))
assert False, "No exception"
except portalocker.LockException:
pass
config1.close()
def testNewVersioning(self):
"""
All property blocks should always have a version set.
"""
p = create_path()
config = ConfigXml(filename=str(p))
m = config.as_map()
for k, v in m.items():
assert "5.1.0" == v
def test_adjust(self, fixture):
p = write_config(fixture.input)
xml = template_xml()
config = ConfigXml(filename=str(p), env_config="default")
try:
rv = adjust_settings(config, xml, **fixture.kwargs)
fixture.validate(rv)
finally:
config.close()
def test_adjust(self, fixture, monkeypatch):
monkeypatch.setattr(Strategy, "_system_memory_mb_java", lambda x: (2000, 4000))
p = write_config(fixture.input)
xml = template_xml()
config = ConfigXml(filename=str(p), env_config="default")
try:
rv = adjust_settings(config, xml, **fixture.kwargs)
fixture.validate(rv)
finally:
config.close()
def test_adjust(self, fixture, monkeypatch):
monkeypatch.setattr(Strategy, '_system_memory_mb_java', lambda x:
(2000, 4000))
p = write_config(fixture.input)
xml = template_xml()
config = ConfigXml(filename=str(p), env_config="default")
try:
rv = adjust_settings(config, xml, **fixture.kwargs)
fixture.validate(rv)
finally:
config.close()
def testAsDict(self):
p = create_path()
config = ConfigXml(filename=str(p), env_config="DICT")
config["omero.data.dir"] = "HOME"
config.close()
i = initial("DICT")
_ = SubElement(i[0][0], "property", name="omero.data.dir",
value="HOME")
_ = SubElement(i, "properties", id="DICT")
_ = SubElement(_, "property", name="omero.data.dir", value="HOME")
assertXml(i, XML(p.text()))
def testAsDict(self):
p = create_path()
config = ConfigXml(filename=str(p), env_config="DICT")
config["omero.data.dir"] = "HOME"
config.close()
i = initial("DICT")
_ = SubElement(i[0][0], "property", name="omero.data.dir",
value="HOME")
_ = SubElement(i, "properties", id="DICT")
_ = SubElement(_, "property", name="omero.data.dir", value="HOME")
assertXml(i, XML(p.text()))
def testOldVersionDetected(self):
p = create_path()
config = ConfigXml(filename=str(p))
X = config.XML
O = SubElement(X, "properties", {"id": "old"})
SubElement(O, "property", {"omero.ldap.keystore": "/Foo"})
config.close()
try:
config = ConfigXml(filename=str(p))
assert False, "Should throw"
except:
pass
def testSettings510Upgrade(self):
"""
When upgraded 5.0.x properties to 5.1.0 or later,
if omero.web.ui.top_links is set, we need to prepend
'Data', 'History' and 'Help' links
"""
beforeUpdate = '[["Figure", "figure_index"]]'
afterUpdate = '[["Data", "webindex", ' \
'{"title": "Browse Data via Projects, Tags etc"}], ' \
'["History", "history", ' \
'{"title": "History"}], ' \
'["Help", "https://help.openmicroscopy.org/", ' \
'{"target": "new", "title": ' \
'"Open OMERO user guide in a new tab"}], ' \
'["Figure", "figure_index"]]'
p = create_path()
XML = Element("icegrid")
active = SubElement(XML, "properties", id="__ACTIVE__")
default = SubElement(XML, "properties", id="default")
for properties in (active, default):
# Include a property to indicate version is post-4.2.0
SubElement(properties,
"property",
name="omero.config.version",
value="4.2.1")
SubElement(properties,
"property",
name="omero.web.ui.top_links",
value=beforeUpdate)
string = tostring(XML, 'utf-8')
txt = xml.dom.minidom.parseString(string).toprettyxml(" ", "\n", None)
p.write_text(txt)
def compare_json_maps(config, afterUpdate):
m = config.as_map()
beforeUpdate = m["omero.web.ui.top_links"]
assert json.loads(beforeUpdate) == json.loads(afterUpdate)
config = ConfigXml(filename=str(p), env_config="default")
try:
compare_json_maps(config, afterUpdate)
finally:
config.close()
# After config.close() calls config.save() new version should be 5.1.0
config = ConfigXml(filename=str(p), env_config="default")
try:
# Check version has been updated
assert config.version() == "5.1.0"
# And that top_links has not been modified further
compare_json_maps(config, afterUpdate)
finally:
config.close()
def get_config(self, raise_missing=True):
"""
Returns a dictionary of all OMERO config properties
"""
configxml = os.path.join(self.dir, 'etc', 'grid', 'config.xml')
try:
configobj = ConfigXml(configxml, read_only=True)
except Exception as e:
log.warning('config.xml not found: %s', e)
if raise_missing:
raise
return {}
cfgdict = configobj.as_map()
configobj.close()
return cfgdict
def testCannotCreate(self):
d = create_path(folder=True)
d.chmod(0o555)
filename = str(old_div(d, "config.xml"))
with pytest.raises(IOError) as excinfo:
ConfigXml(filename).close()
assert excinfo.value.errno == errno.EACCES
def testSettings510Upgrade(self):
"""
When upgraded 5.0.x properties to 5.1.0 or later,
if omero.web.ui.top_links is set, we need to prepend
'Data', 'History' and 'Help' links
"""
beforeUpdate = '[["Figure", "figure_index"]]'
afterUpdate = '[["Data", "webindex", ' \
'{"title": "Browse Data via Projects, Tags etc"}], ' \
'["History", "history", ' \
'{"title": "History"}], ' \
'["Help", "http://help.openmicroscopy.org/", ' \
'{"target": "new", "title": ' \
'"Open OMERO user guide in a new tab"}], ' \
'["Figure", "figure_index"]]'
p = create_path()
XML = Element("icegrid")
active = SubElement(XML, "properties", id="__ACTIVE__")
default = SubElement(XML, "properties", id="default")
for properties in (active, default):
# Include a property to indicate version is post-4.2.0
SubElement(
properties, "property", name="omero.config.version",
value="4.2.1")
SubElement(
properties, "property", name="omero.web.ui.top_links",
value=beforeUpdate)
string = tostring(XML, 'utf-8')
txt = xml.dom.minidom.parseString(string).toprettyxml(" ", "\n", None)
p.write_text(txt)
config = ConfigXml(filename=str(p), env_config="default")
try:
m = config.as_map()
assert m["omero.web.ui.top_links"] == afterUpdate
finally:
config.close()
# After config.close() calls config.save() new version should be 5.1.0
config = ConfigXml(filename=str(p), env_config="default")
try:
# Check version has been updated
assert config.version() == "5.1.0"
m = config.as_map()
# And that top_links has not been modified further
assert m["omero.web.ui.top_links"] == afterUpdate
finally:
config.close()
def test_12527(self, fixture, monkeypatch):
monkeypatch.setattr(Strategy, '_system_memory_mb_java', lambda x:
(2000, 4000))
p = write_config(fixture.input)
old_templates = old_div(path(__file__).dirname(), "old_templates.xml")
xml = XML(old_templates.abspath().text())
config = ConfigXml(filename=str(p), env_config="default")
with pytest.raises(Exception):
adjust_settings(config, xml, **fixture.kwargs)
def testCannotCreateLock(self):
d = create_path(folder=True)
filename = str(old_div(d, "config.xml"))
lock_filename = "%s.lock" % filename
with open(lock_filename, "w") as fo:
fo.write("dummy\n")
os.chmod(lock_filename, 0o444)
with pytest.raises(IOError) as excinfo:
ConfigXml(filename).close()
assert excinfo.value.errno == errno.EACCES
def update_config(omerodir):
"""
Updates OMERO config with certificate properties if necessary
"""
cfg = ConfigXml(os.path.join(omerodir, "etc", "grid", "config.xml"))
cfgdict = cfg.as_map()
def set_if_empty(cfgkey, default):
if not cfgdict.get(cfgkey):
cfg[cfgkey] = default
log.info("Setting %s=%s", cfgkey, default)
set_if_empty(
"omero.glacier2.IceSSL.DefaultDir",
os.path.join(cfgdict.get("omero.data.dir", "/OMERO"), "certs"),
)
set_if_empty("omero.certificates.commonname", "localhost")
set_if_empty("omero.certificates.owner", "/L=OMERO/O=OMERO.server")
set_if_empty("omero.certificates.key", "server.key")
set_if_empty("omero.glacier2.IceSSL.CertFile", "server.p12")
set_if_empty("omero.glacier2.IceSSL.CAs", "server.pem")
set_if_empty("omero.glacier2.IceSSL.Password", "secret")
set_if_empty("omero.glacier2.IceSSL.Ciphers", "HIGH")
set_if_empty("omero.glacier2.IceSSL.ProtocolVersionMax", "TLS1_2")
set_if_empty("omero.glacier2.IceSSL.Protocols", "TLS1_0,TLS1_1,TLS1_2")
cfgdict = cfg.as_map()
cfg.close()
return cfgdict
def test_create_certificates(self, tmpdir):
(tmpdir / "etc" / "grid").ensure(dir=True)
omerodir = str(tmpdir)
datadir = str(tmpdir / "OMERO")
configxml = ConfigXml(
os.path.join(omerodir, "etc", "grid", "config.xml"))
configxml["omero.data.dir"] = datadir
configxml.close()
m = create_certificates(omerodir)
assert m.startswith("certificates created: ")
cfg = get_config(omerodir)
assert cfg["omero.glacier2.IceSSL.DefaultDir"] == os.path.join(
datadir, "certs")
for filename in ("server.key", "server.p12", "server.pem"):
assert os.path.isfile(os.path.join(datadir, "certs", filename))
out = subprocess.check_output([
"openssl",
"pkcs12",
"-in",
os.path.join(datadir, "certs", "server.p12"),
"-passin",
"pass:secret",
"-passout",
"pass:secret",
])
out = out.decode().splitlines()
for line in (
"subject=L = OMERO, O = OMERO.server, CN = localhost",
"issuer=L = OMERO, O = OMERO.server, CN = localhost",
"-----BEGIN CERTIFICATE-----",
"-----END CERTIFICATE-----",
"-----BEGIN ENCRYPTED PRIVATE KEY-----",
"-----END ENCRYPTED PRIVATE KEY-----",
):
assert line in out
def _get_current_as_json(config: ConfigXml, key: str) -> Optional[DictOrList]:
"""
Get current key value converted from JSON to a list or dict,
taking into account OMERO.web's defaults
"""
if key in config.keys():
current = json.loads(config[key])
if not isinstance(current, (dict, list)):
raise ExternalConfigException(
"Property {} is not a dict or list: {}".format(key, current))
return current
if key.startswith("omero.web."):
return _get_omeroweb_default(key)
return None
def test_config_keep_existing(self, tmpdir):
(tmpdir / "etc" / "grid").ensure(dir=True)
omerodir = str(tmpdir)
configxml = ConfigXml(
os.path.join(omerodir, "etc", "grid", "config.xml"))
configxml["omero.certificates.commonname"] = "omero.example.org"
configxml["omero.certificates.owner"] = "/L=universe/O=42"
configxml.close()
update_config(omerodir)
cfg = get_config(omerodir)
cfg.pop("omero.config.version")
assert cfg == {
"omero.glacier2.IceSSL.CAs": "server.pem",
"omero.glacier2.IceSSL.CertFile": "server.p12",
"omero.glacier2.IceSSL.Ciphers": "HIGH",
"omero.glacier2.IceSSL.DefaultDir": "/OMERO/certs",
"omero.glacier2.IceSSL.Password": "******",
"omero.glacier2.IceSSL.ProtocolVersionMax": "TLS1_2",
"omero.glacier2.IceSSL.Protocols": "TLS1_0,TLS1_1,TLS1_2",
"omero.certificates.commonname": "omero.example.org",
"omero.certificates.key": "server.key",
"omero.certificates.owner": "/L=universe/O=42",
}
def open_config(self, args):
if args.source:
cfg_xml = path(args.source)
if not cfg_xml.exists():
self.ctx.die(124, "File not found: %s" % args.source)
else:
grid_dir = self.ctx.dir / "etc" / "grid"
if grid_dir.exists():
cfg_xml = grid_dir / "config.xml"
else:
userdir = path(get_user_dir())
usr_xml = userdir / "omero" / "config.xml"
self.ctx.err("%s not found; using %s" % (grid_dir, usr_xml))
cfg_xml = usr_xml
try:
return ConfigXml(str(cfg_xml))
except portalocker.LockException:
self.ctx.die(112, "Could not acquire lock on %s" % cfg_xml)
def testOldVersionDetected(self):
p = create_path()
config = ConfigXml(filename=str(p))
X = config.XML
O = SubElement(X, "properties", {"id": "old"})
SubElement(O, "property", {"omero.ldap.keystore": "/Foo"})
config.close()
try:
config = ConfigXml(filename=str(p))
assert False, "Should throw"
except:
pass
def open_config(self, args):
if args.source:
cfg_xml = path(args.source)
if not cfg_xml.exists():
self.ctx.die(124, "File not found: %s" % args.source)
else:
if 'OMERODIR' in os.environ:
base_dir = path(os.environ.get('OMERODIR'))
else:
self.ctx.die(125, 'FATAL: OMERODIR env variable not set')
grid_dir = base_dir / "etc" / "grid"
if not grid_dir.exists():
self.ctx.err("%s not found; creating %s" %
(grid_dir, grid_dir))
os.makedirs(grid_dir)
cfg_xml = grid_dir / "config.xml"
try:
return ConfigXml(str(cfg_xml))
except portalocker.LockException:
self.ctx.die(112, "Could not acquire lock on %s" % cfg_xml)
except Exception as e:
self.ctx.die(113, str(e))
def testReadOnlyConfigSimple(self):
p = create_path()
p.chmod(0444) # r--r--r--
config = ConfigXml(filename=str(p), env_config=None) # Must be None
config.close() # Shouldn't save
def update_config(self, newcfg):
cfg = ConfigXml(os.path.join(self.dir, 'etc', 'grid', 'config.xml'))
for k, v in newcfg.items():
cfg[k] = v
cfg.close()
def testBasic(self):
p = create_path()
config = ConfigXml(filename=str(p))
config.close()
assertXml(initial(), XML(p.text()))
def testWithEnv(self):
p = create_path()
config = ConfigXml(filename=str(p), env_config="FOO")
config.close()
assertXml(initial("FOO"), XML(p.text()))
def get_config(omerodir):
configxml = ConfigXml(os.path.join(omerodir, "etc", "grid", "config.xml"))
try:
return configxml.as_map()
finally:
configxml.close()
def testWithEnv(self):
p = create_path()
config = ConfigXml(filename=str(p), env_config="FOO")
config.close()
assertXml(initial("FOO"), XML(p.text()))
def testCannotRead(self):
p = create_path()
p.chmod(0)
with pytest.raises(IOError) as excinfo:
ConfigXml(str(p)).close()
assert excinfo.value.errno == errno.EACCES
def testWithEnvThenWithoutEnv(self):
"""
This test shows that if you create the config using an env
setting, then without, the __ACTIVE__ block should reflect
"default" and not the intermediate "env" setting.
"""
def get_profile_name(p):
"""
Takes a path object to the config xml
"""
xml = XML(p.text())
props = xml.findall("./properties")
for x in props:
id = x.attrib["id"]
if id == "__ACTIVE__":
for y in x.getchildren():
if y.attrib["name"] == "omero.config.profile":
return y.attrib["value"]
p = create_path()
current = os.environ.get("OMERO_CONFIG", "default")
assert current != "FOO" # Just in case.
config = ConfigXml(filename=str(p))
config.close()
assert current == get_profile_name(p)
config = ConfigXml(filename=str(p), env_config="FOO")
config.close()
assert "FOO" == get_profile_name(p)
# Still foo
config = ConfigXml(filename=str(p))
config.close()
assert "FOO" == get_profile_name(p)
# Re-setting with os.environ won't work
try:
old = os.environ.get("OMERO_CONFIG", None)
os.environ["OMERO_CONFIG"] = "ABC"
config = ConfigXml(filename=str(p))
config.close()
assert "FOO" == get_profile_name(p)
finally:
if old is None:
del os.environ["OMERO_CONFIG"]
else:
os.environ["OMERO_CONFIG"] = old
# But we can reset it with env_config
config = ConfigXml(filename=str(p), env_config="ABC")
config.close()
assert "ABC" == get_profile_name(p)
# or manually. ticket:7343
config = ConfigXml(filename=str(p))
config.default("XYZ")
config.close()
assert "XYZ" == get_profile_name(p)
def testReadOnlyConfigPassesOnExplicitReadOnly(self):
p = create_path()
p.chmod(0444) # r--r--r--
ConfigXml(filename=str(p), env_config="default",
read_only=True).close()
def testWithEnvThenWithoutEnv(self):
"""
This test shows that if you create the config using an env
setting, then without, the __ACTIVE__ block should reflect
"default" and not the intermediate "env" setting.
"""
def get_profile_name(p):
"""
Takes a path object to the config xml
"""
xml = XML(p.text())
props = xml.findall("./properties")
for x in props:
id = x.attrib["id"]
if id == "__ACTIVE__":
for y in x.getchildren():
if y.attrib["name"] == "omero.config.profile":
return y.attrib["value"]
p = create_path()
current = os.environ.get("OMERO_CONFIG", "default")
assert current != "FOO" # Just in case.
config = ConfigXml(filename=str(p))
config.close()
assert current == get_profile_name(p)
config = ConfigXml(filename=str(p), env_config="FOO")
config.close()
assert "FOO" == get_profile_name(p)
# Still foo
config = ConfigXml(filename=str(p))
config.close()
assert "FOO" == get_profile_name(p)
# Re-setting with os.environ won't work
try:
old = os.environ.get("OMERO_CONFIG", None)
os.environ["OMERO_CONFIG"] = "ABC"
config = ConfigXml(filename=str(p))
config.close()
assert "FOO" == get_profile_name(p)
finally:
if old is None:
del os.environ["OMERO_CONFIG"]
else:
os.environ["OMERO_CONFIG"] = old
# But we can reset it with env_config
config = ConfigXml(filename=str(p), env_config="ABC")
config.close()
assert "ABC" == get_profile_name(p)
# or manually. ticket:7343
config = ConfigXml(filename=str(p))
config.default("XYZ")
config.close()
assert "XYZ" == get_profile_name(p)
def testReadOnlyConfigSimple(self):
p = create_path()
p.chmod(0444) # r--r--r--
config = ConfigXml(filename=str(p), env_config=None) # Must be None
config.close() # Shouldn't save
def testBasic(self):
p = create_path()
config = ConfigXml(filename=str(p))
config.close()
assertXml(initial(), XML(p.text()))
def config(self):
return ConfigXml(filename=str(self.p))
def _get_config_xml(omerodir: str) -> ConfigXml:
return ConfigXml(os.path.join(omerodir, "etc", "grid", "config.xml"))