class TestLoadRenderingSettings:
def setup_method(self):
self.cli = CLI()
self.cli.register("render", RenderControl, "TEST")
self.render = self.cli.controls['render']
def test_none(self):
with pytest.raises(NonZeroReturnCode):
self.render._load_rendering_settings(None)
def test_non_existing_file(self):
with pytest.raises(NonZeroReturnCode) as e:
self.render._load_rendering_settings(str(uuid.uuid4()) + '.yml')
assert e.value.rv == 103
def test_no_channels(self, tmpdir):
d = {'version': 1}
f = write_yaml(d, tmpdir)
with pytest.raises(NonZeroReturnCode) as e:
self.render._load_rendering_settings(f)
assert e.value.rv == 104
def test_bad_version(self, tmpdir):
d = {'channels': {1: {'label': 'foo'}}}
f = write_yaml(d, tmpdir)
with pytest.raises(NonZeroReturnCode) as e:
self.render._load_rendering_settings(f)
assert e.value.rv == 124
class TestJvmCfg(object):
"""Test template files regeneration"""
@pytest.fixture(autouse=True)
def setup_method(self, tmpadmindir):
self.cli = CLI()
self.cli.dir = path(tmpadmindir)
self.cli.register("admin", AdminControl, "TEST")
self.cli.register("config", PrefsControl, "TEST")
self.args = ["admin", "jvmcfg"]
def testNoTemplatesGeneration(self):
"""Test no template files are generated by the jvmcfg subcommand"""
# Test non-existence of configuration files
for f in GRID_FILES:
assert not os.path.exists(path(self.cli.dir) / "etc" / "grid" / f)
for f in ETC_FILES:
assert not os.path.exists(path(self.cli.dir) / "etc" / f)
# Call the jvmcf command and test file genearation
self.cli.invoke(self.args, strict=True)
for f in GRID_FILES:
assert not os.path.exists(path(self.cli.dir) / "etc" / "grid" / f)
for f in ETC_FILES:
assert not os.path.exists(path(self.cli.dir) / "etc" / f)
@pytest.mark.parametrize(
'suffix', ['', '.blitz', '.indexer', '.pixeldata', '.repository'])
def testInvalidJvmCfgStrategy(self, suffix, tmpdir):
"""Test invalid JVM strategy configuration leads to CLI error"""
key = "omero.jvmcfg.strategy%s" % suffix
self.cli.invoke(["config", "set", key, "bad"], strict=True)
with pytest.raises(NonZeroReturnCode):
self.cli.invoke(self.args, strict=True)
class TestJvmCfg(object):
"""Test template files regeneration"""
@pytest.fixture(autouse=True)
def setup_method(self, tmpadmindir):
self.cli = CLI()
self.cli.register("admin", AdminControl, "TEST")
self.cli.register("config", PrefsControl, "TEST")
self.args = ["admin", "jvmcfg"]
self.cli.dir = path(tmpadmindir)
def testNoTemplatesGeneration(self):
"""Test no template files are generated by the jvmcfg subcommand"""
# Test non-existence of configuration files
for f in GRID_FILES:
assert not os.path.exists(path(self.cli.dir) / "etc" / "grid" / f)
for f in ETC_FILES:
assert not os.path.exists(path(self.cli.dir) / "etc" / f)
# Call the jvmcf command and test file genearation
self.cli.invoke(self.args, strict=True)
for f in GRID_FILES:
assert not os.path.exists(path(self.cli.dir) / "etc" / "grid" / f)
for f in ETC_FILES:
assert not os.path.exists(path(self.cli.dir) / "etc" / f)
@pytest.mark.parametrize("suffix", ["", ".blitz", ".indexer", ".pixeldata", ".repository"])
def testInvalidJvmCfgStrategy(self, suffix, tmpdir):
"""Test invalid JVM strategy configuration leads to CLI error"""
key = "omero.jvmcfg.strategy%s" % suffix
self.cli.invoke(["config", "set", key, "bad"], strict=True)
with pytest.raises(NonZeroReturnCode):
self.cli.invoke(self.args, strict=True)
def testDropBoxArgs(self):
class MockImportControl(ImportControl):
def importer(this, args):
self.assertEquals(args.server, "localhost")
self.assertEquals(args.port, "4064")
self.assertEquals(args.key,
"b0742975-03a1-4f6d-b0ac-639943f1a147")
self.assertEquals(
args.errs,
"/Users/cblackburn/omero/tmp/omero_cblackburn/6915/dropboxuUGl5rerr"
)
self.assertEquals(
args.file,
"/Users/cblackburn/omero/tmp/omero_cblackburn/6915/dropboxaDCjQlout"
)
cmd = [
'-s', 'localhost', '-p', '4064', '-k',
'b0742975-03a1-4f6d-b0ac-639943f1a147'
]
cmd += [
'import',
'---errs=/Users/cblackburn/omero/tmp/omero_cblackburn/6915/dropboxuUGl5rerr'
]
cmd += [
'---file=/Users/cblackburn/omero/tmp/omero_cblackburn/6915/dropboxaDCjQlout'
]
cmd += ['--', '/OMERO/DropBox/root/tinyTest.d3d.dv']
cli = CLI()
cli.register("import", MockImportControl, "HELP")
cli.invoke(cmd)
def import_ln_s(self, host, port):
"""Import file using the ``--transfer=ln_s`` option.
Parameters
----------
host : str
Hostname of OMERO server in which images will be imported.
port : int
Port used to connect to OMERO.server.
Returns
-------
import_status : boolean
True if OMERO import returns a 0 exit status, else False.
"""
cli = CLI()
cli.register('import', ImportControl, '_')
cli.register('sessions', SessionsControl, '_')
cli.invoke([
'import', '-k',
self.conn.getSession().getUuid().val, '-s', host, '-p',
str(port), '--transfer', 'ln_s',
str(self.file_path)
])
if cli.rv == 0:
self.imported = True
print(f'Imported {self.file_path}')
return True
else:
logging.error(f'Import of {self.file_path} has failed!')
return False
def testParametersParsedCorrectly(self):
class TestControl(BaseControl):
def __call__(self2, args):
self.assertEquals("b",args["a"])
cli = CLI()
cli.register("test", TestControl, "HELP")
cli.invoke(["test","a=b"])
self.assertEquals(0, cli.rv)
class TestChgrp(object):
def setup_method(self, method):
self.cli = CLI()
self.cli.register("chgrp", ChgrpControl, "TEST")
self.args = ["chgrp"]
def testHelp(self):
self.args += ["-h"]
self.cli.invoke(self.args, strict=True)
def testNoArgumentsDies(self):
cli = CLI()
cli.register("import", ImportControl, "HELP")
try:
cli.invoke([])
self.assert_(cli.rv != 0)
except NonZeroReturnCode, nzrc:
pass
def testNoArgumentsDies(self):
cli = CLI()
cli.register("import", ImportControl, "HELP")
try:
cli.invoke([])
self.assert_(cli.rv != 0)
except NonZeroReturnCode, nzrc:
pass
def testLineParsedCorrectly(self):
class TestControl(BaseControl):
def __call__(self, args):
if len(*args) != 2:
raise Exc("Args was over parsed! %s" % args)
cli = CLI()
cli.register("test", TestControl, "HELP")
cli.invoke(["test","a","a b c d e"])
self.assertEquals(0, cli.rv)
class TestChgrp(object):
def setup_method(self, method):
self.cli = CLI()
self.cli.register("chgrp", ChgrpControl, "TEST")
self.args = ["chgrp"]
def testHelp(self):
self.args += ["-h"]
self.cli.invoke(self.args, strict=True)
class AbstractCLITest(ITest):
def setup_method(self, method):
super(AbstractCLITest, self).setup_method(method)
self.cli = CLI()
self.cli.register("sessions", SessionsControl, "TEST")
def setup_mock(self):
self.mox = Mox()
def teardown_mock(self):
self.mox.UnsetStubs()
self.mox.VerifyAll()
class AbstractCLITest(ITest):
def setup_method(self, method):
super(AbstractCLITest, self).setup_method(method)
self.cli = CLI()
self.cli.register("sessions", SessionsControl, "TEST")
def setup_mock(self):
self.mox = Mox()
def teardown_mock(self):
self.mox.UnsetStubs()
self.mox.VerifyAll()
class TestTag(object):
def setup_method(self, method):
self.cli = CLI()
self.cli.register("fs", FsControl, "TEST")
self.args = ["fs"]
def testHelp(self):
self.args += ["-h"]
self.cli.invoke(self.args, strict=True)
@pytest.mark.parametrize('subcommand', subcommands)
def testSubcommandHelp(self, subcommand):
self.args += [subcommand, "-h"]
self.cli.invoke(self.args, strict=True)
class TestGroup(object):
def setup_method(self, method):
self.cli = CLI()
self.cli.register("group", GroupControl, "TEST")
self.args = ["group"]
def testHelp(self):
self.args += ["-h"]
self.cli.invoke(self.args, strict=True)
@pytest.mark.parametrize("subcommand", GroupControl().get_subcommands())
def testSubcommandHelp(self, subcommand):
self.args += [subcommand, "-h"]
self.cli.invoke(self.args, strict=True)
class TestTag(object):
def setup_method(self, method):
self.cli = CLI()
self.cli.register("fs", FsControl, "TEST")
self.args = ["fs"]
def testHelp(self):
self.args += ["-h"]
self.cli.invoke(self.args, strict=True)
@pytest.mark.parametrize('subcommand', FsControl().get_subcommands())
def testSubcommandHelp(self, subcommand):
self.args += [subcommand, "-h"]
self.cli.invoke(self.args, strict=True)
def validate_target(self):
"""Check whether an import target can be imported by OMERO
This used the OMERO CLI, but since it is just checking whether
the file can be interpreted by BioFormats, there is no connection
required.
"""
cli = CLI()
cli.register('import', ImportControl, '_')
cli.invoke(['import', '-f', str(self.path_to_target)])
if cli.rv == 0:
self.valid_target = True
else:
self.valid_target = False
class TestUser(object):
def setup_method(self, method):
self.cli = CLI()
self.cli.register("user", UserControl, "TEST")
self.args = ["user"]
# Help subcommands
# ========================================================================
def testHelp(self):
self.args += ["-h"]
self.cli.invoke(self.args, strict=True)
@pytest.mark.parametrize("subcommand", UserControl().get_subcommands())
def testSubcommandHelp(self, subcommand):
self.args += [subcommand, "-h"]
self.cli.invoke(self.args, strict=True)
class TestCli(object):
def testMultipleLoad(self):
"""
In DropBox, the loading of multiple CLIs seems to
lead to the wrong context being assigned to some
controls.
See #4749
"""
import random
from threading import Thread, Event
event = Event()
class T(Thread):
def run(self, *args):
pause = random.random()
event.wait(pause)
self.cli = CLI()
self.cli.loadplugins()
self.con = self.cli.controls["admin"]
self.cmp = self.con.ctx
threads = [T() for x in range(20)]
for t in threads:
t.start()
event.set()
for t in threads:
t.join()
assert len(threads) == len(set([t.cli for t in threads]))
assert len(threads) == len(set([t.con for t in threads]))
assert len(threads) == len(set([t.cmp for t in threads]))
def testLoad(self, tmpdir):
tmpfile = tmpdir.join('test')
tmpfile.write("foo")
self.cli = CLI()
self.cli.register("load", LoadControl, "help")
# replace slashes, otherwise C:\\x becomes C:x
tmpfile = tmpfile.strpath.replace("\\", "/")
with pytest.raises(NonZeroReturnCode):
self.cli.invoke("load %s" % tmpfile, strict=True)
self.cli.invoke("load -k %s" % tmpfile, strict=True)
self.cli.invoke("load --keep-going %s" % tmpfile, strict=True)
class TestHql(object):
def setup_method(self, method):
self.cli = CLI()
self.cli.register("hql", HqlControl, "TEST")
self.args = ["hql"]
def testHelp(self):
self.args += ["-h"]
self.cli.invoke(self.args, strict=True)
@pytest.mark.parametrize("key", BLACKLISTED_KEYS)
def testFilterBlacklist(self, key):
output = self.cli.controls["hql"].filter({key: 1})
assert output == {}
@pytest.mark.parametrize("key", ["rois", "groupExperimenterMap"])
def testFilterLoaded(self, key):
output = self.cli.controls["hql"].filter({"_" + key + "Loaded": 1})
assert output == {}
@pytest.mark.parametrize(
("value", "outcome"),
[("owner=None;group=None", {}),
("owner=1", {"details": "owner=1"})])
def testFilterDetails(self, value, outcome):
output = self.cli.controls["hql"].filter({"_details": value})
assert output == outcome
@pytest.mark.parametrize("multi_value", [[0, 1]])
def testFilterMultiValue(self, multi_value):
output = self.cli.controls["hql"].filter({'key': multi_value})
assert output == {}
@pytest.mark.parametrize("empty_value", [None, [], {}])
def testFilterEmptyValue(self, empty_value):
output = self.cli.controls["hql"].filter({'key': empty_value})
assert output == {}
@pytest.mark.parametrize("value", WHITELISTED_VALUES)
def testFilterWhitelist(self, value):
output = self.cli.controls["hql"].filter({'key': value})
assert output == {'key': value}
def testFilterStrip(self):
output = self.cli.controls["hql"].filter({'_key': 1})
assert output == {'key': 1}
class TestHql(object):
def setup_method(self, method):
self.cli = CLI()
self.cli.register("hql", HqlControl, "TEST")
self.args = ["hql"]
def testHelp(self):
self.args += ["-h"]
self.cli.invoke(self.args, strict=True)
@pytest.mark.parametrize("key", BLACKLISTED_KEYS)
def testFilterBlacklist(self, key):
output = self.cli.controls["hql"].filter({key: 1})
assert output == {}
@pytest.mark.parametrize("key", ["rois", "groupExperimenterMap"])
def testFilterLoaded(self, key):
output = self.cli.controls["hql"].filter({"_" + key + "Loaded": 1})
assert output == {}
@pytest.mark.parametrize(("value", "outcome"),
[("owner=None;group=None", {}),
("owner=1", {
"details": "owner=1"
})])
def testFilterDetails(self, value, outcome):
output = self.cli.controls["hql"].filter({"_details": value})
assert output == outcome
@pytest.mark.parametrize("multi_value", [[0, 1]])
def testFilterMultiValue(self, multi_value):
output = self.cli.controls["hql"].filter({'key': multi_value})
assert output == {}
@pytest.mark.parametrize("empty_value", [None, [], {}])
def testFilterEmptyValue(self, empty_value):
output = self.cli.controls["hql"].filter({'key': empty_value})
assert output == {}
@pytest.mark.parametrize("value", WHITELISTED_VALUES)
def testFilterWhitelist(self, value):
output = self.cli.controls["hql"].filter({'key': value})
assert output == {'key': value}
def testFilterStrip(self):
output = self.cli.controls["hql"].filter({'_key': 1})
assert output == {'key': 1}
def testDropBoxArgs(self):
class MockImportControl(ImportControl):
def importer(this, args):
self.assertEquals(args.server, "localhost")
self.assertEquals(args.port, "4064")
self.assertEquals(args.key, "b0742975-03a1-4f6d-b0ac-639943f1a147")
self.assertEquals(args.errs, "/Users/cblackburn/omero/tmp/omero_cblackburn/6915/dropboxuUGl5rerr")
self.assertEquals(args.file, "/Users/cblackburn/omero/tmp/omero_cblackburn/6915/dropboxaDCjQlout")
cmd = ['-s', 'localhost', '-p', '4064', '-k', 'b0742975-03a1-4f6d-b0ac-639943f1a147']
cmd += ['import', '---errs=/Users/cblackburn/omero/tmp/omero_cblackburn/6915/dropboxuUGl5rerr']
cmd += ['---file=/Users/cblackburn/omero/tmp/omero_cblackburn/6915/dropboxaDCjQlout']
cmd += ['--', '/OMERO/DropBox/root/tinyTest.d3d.dv']
cli = CLI()
cli.register("import", MockImportControl, "HELP")
cli.invoke(cmd)
class TestDownload(object):
def setup_method(self, method):
self.cli = CLI()
self.cli.register("download", DownloadControl, "TEST")
self.args = ["download"]
def testHelp(self):
self.args += ["-h"]
self.cli.invoke(self.args, strict=True)
@pytest.mark.parametrize(
'bad_input',
['-1', 'OriginalFile:-1', 'FileAnnotation:-1', 'Image:-1'])
def testInvalidInput(self, bad_input):
self.args += [bad_input, '-']
with pytest.raises(NonZeroReturnCode):
self.cli.invoke(self.args, strict=True)
class TestScript(object):
def setup_method(self, method):
self.cli = CLI()
self.cli.register("script", ScriptControl, "TEST")
self.args = ["script"]
# Help subcommands
# ========================================================================
def testHelp(self):
self.args += ["-h"]
self.cli.invoke(self.args, strict=True)
@pytest.mark.parametrize("subcommand", ScriptControl().get_subcommands())
def testSubcommandHelp(self, subcommand):
self.args += [subcommand, "-h"]
self.cli.invoke(self.args, strict=True)
class TestCli(object):
def testMultipleLoad(self):
"""
In DropBox, the loading of multiple CLIs seems to
lead to the wrong context being assigned to some
controls.
See #4749
"""
import random
from threading import Thread, Event
event = Event()
class T(Thread):
def run(self, *args):
pause = random.random()
event.wait(pause)
self.cli = CLI()
self.cli.loadplugins()
self.con = self.cli.controls["admin"]
self.cmp = self.con.ctx
threads = [T() for x in range(20)]
for t in threads:
t.start()
event.set()
for t in threads:
t.join()
assert len(threads) == len(set([t.cli for t in threads]))
assert len(threads) == len(set([t.con for t in threads]))
assert len(threads) == len(set([t.cmp for t in threads]))
def testLoad(self):
tmp = create_path()
tmp.write_text("foo")
self.cli = CLI()
self.cli.register("load", LoadControl, "help")
with pytest.raises(NonZeroReturnCode):
self.cli.invoke("load %s" % tmp, strict=True)
self.cli.invoke("load -k %s" % tmp, strict=True)
self.cli.invoke("load --keep-going %s" % tmp, strict=True)
class TestDownload(object):
def setup_method(self, method):
self.cli = CLI()
self.cli.register("download", DownloadControl, "TEST")
self.args = ["download"]
def testHelp(self):
self.args += ["-h"]
self.cli.invoke(self.args, strict=True)
@pytest.mark.parametrize(
'bad_input',
['-1', 'OriginalFile:-1', 'FileAnnotation:-1', 'Image:-1'])
def testInvalidInput(self, bad_input):
self.args += [bad_input, '-']
with pytest.raises(NonZeroReturnCode):
self.cli.invoke(self.args, strict=True)
class TestReadChannels:
def setup_method(self):
self.cli = CLI()
self.cli.register("render", RenderControl, "TEST")
self.render = self.cli.controls['render']
def test_non_integer_channel(self):
d = {'channels': {'GFP': {'label': 'foo'}}}
with pytest.raises(NonZeroReturnCode) as e:
self.render._read_channels(d)
assert e.value.rv == 105
@pytest.mark.parametrize('key', ['min', 'max', 'start', 'end'])
def test_float_keys(self, key):
d = {'channels': {1: {key: 'foo'}}}
with pytest.raises(NonZeroReturnCode) as e:
self.render._read_channels(d)
assert e.value.rv == 105
class TestTag(object):
def setup_method(self, method):
self.cli = CLI()
self.cli.register("tag", TagControl, "TEST")
self.args = ["tag"]
def testHelp(self):
self.args += ["-h"]
self.cli.invoke(self.args, strict=True)
@pytest.mark.parametrize('subcommand', TagControl().get_subcommands())
def testSubcommandHelp(self, subcommand):
self.args += [subcommand, "-h"]
self.cli.invoke(self.args, strict=True)
def testCreateTagsetFails(self):
self.args += ["createset", "--tag", "A"]
with pytest.raises(NonZeroReturnCode):
self.cli.invoke(self.args, strict=True)
def testListFails(self):
self.args += ["list", "--tagset", "tagset"]
with pytest.raises(NonZeroReturnCode):
self.cli.invoke(self.args, strict=True)
def testListsetsFails(self):
self.args += ["listsets", "--tag", "tag"]
with pytest.raises(NonZeroReturnCode):
self.cli.invoke(self.args, strict=True)
@pytest.mark.parametrize(
('object_arg', 'tag_arg'),
[('Image:1', 'test'), ('Image', '1'), ('Image:image', '1'),
('1', '1')])
def testLinkFails(self, object_arg, tag_arg):
self.args += ["link", object_arg, tag_arg]
with pytest.raises(NonZeroReturnCode):
self.cli.invoke(self.args, strict=True)
def users_groups(conn, omero_params):
session_uuid = conn.getSession().getUuid().val
user = omero_params[0]
host = omero_params[2]
port = str(omero_params[3])
cli = CLI()
cli.register('sessions', SessionsControl, 'test')
cli.register('user', UserControl, 'test')
cli.register('group', GroupControl, 'test')
group_info = []
for gname, gperms in GROUPS_TO_CREATE:
cli.invoke([
'group', 'add', gname, '--type', gperms, '-k', session_uuid, '-u',
user, '-s', host, '-p', port
])
gid = ezomero.get_group_id(conn, gname)
group_info.append([gname, gid])
user_info = []
for user, groups_add, groups_own in USERS_TO_CREATE:
# make user while adding to first group
cli.invoke([
'user', 'add', user, 'test', 'tester', '--group-name',
groups_add[0], '-e', '*****@*****.**', '-P', 'abc123', '-k',
session_uuid, '-u', user, '-s', host, '-p', port
])
# add user to rest of groups
if len(groups_add) > 1:
for group in groups_add[1:]:
cli.invoke([
'group', 'adduser', '--user-name', user, '--name', group,
'-k', session_uuid, '-u', user, '-s', host, '-p', port
])
# make user owner of listed groups
if len(groups_own) > 0:
for group in groups_own:
cli.invoke([
'group', 'adduser', '--user-name', user, '--name', group,
'--as-owner', '-k', session_uuid, '-u', user, '-s', host,
'-p', port
])
uid = ezomero.get_user_id(conn, user)
user_info.append([user, uid])
return (group_info, user_info)
self.ctx.die(
197, "Current user is not member of group: %s" % group.id.val)
# Set requests group
for request in req.requests:
request.grp = gid
super(ChgrpControl, self)._process_request(req, args, client)
def create_error_report(self, rsp):
import omero.cmd
if isinstance(rsp, omero.cmd.GraphConstraintERR):
if "Fileset" in rsp.constraints:
fileset = rsp.constraints.get("Fileset")
return "You cannot move part of fileset %s; only complete" \
" filesets can be moved to another group.\n" % \
", ".join(str(x) for x in fileset)
else:
return super(ChgrpControl, self).create_error_report(rsp)
else:
return super(ChgrpControl, self).create_error_report(rsp)
try:
register("chgrp", ChgrpControl, HELP)
except NameError:
if __name__ == "__main__":
cli = CLI()
cli.register("chgrp", ChgrpControl, HELP)
cli.invoke(sys.argv[1:])
else:
self.ctx.out("Experimenter=%s\tomeName=%s"
% (e.getId().getValue(),
e.getOmeName().getValue()))
@admin_only
def create(self, args):
c = self.ctx.conn(args)
ildap = c.sf.getLdapService()
iadmin = c.sf.getAdminService()
import omero
import Ice
try:
exp = ildap.createUser(args.username)
dn = iadmin.lookupLdapAuthExperimenter(exp.id.val)
self.ctx.out("Added user %s (id=%s) with DN=%s" %
(exp.omeName.val, exp.id.val, dn))
except omero.ValidationException as ve:
self.ctx.die(132, ve.message)
except Ice.RequestFailedException as rfe:
self.ctx.die(133, self.exc.handle_failed_request(rfe))
try:
register("ldap", LdapControl, HELP)
except NameError:
if __name__ == "__main__":
cli = CLI()
cli.register("ldap", LdapControl, HELP)
cli.invoke(sys.argv[1:])
help="Read from files or standard in")
parser.set_defaults(func=self.__call__)
parser.add_login_arguments()
def __call__(self, args):
if args.list:
ops = [x[4:] for x in dir(perf_test.Item) if x.startswith("_op_")]
ops.sort()
for op in ops:
print(op)
else:
if not args.file:
self.ctx.die(167, "No files given. Use '-' for stdin.")
client = self.ctx.conn(args)
ctx = perf_test.Context(None, client=client)
self.ctx.out("Saving performance results to %s" % ctx.dir)
ctx.add_reporter(perf_test.CsvReporter(ctx.dir))
# ctx.add_reporter(perf_test.HdfReporter(ctx.dir))
# ctx.add_reporter(perf_test.PlotReporter())
handler = perf_test.PerfHandler(ctx)
perf_test.handle(handler, args.file)
try:
register("perf", PerfControl, HELP)
except NameError:
if __name__ == "__main__":
cli = CLI()
cli.register("perf", PerfControl, HELP)
cli.invoke(sys.argv[1:])
def cli(self):
cli = CLI()
cli.register("upload", UploadControl, "TEST")
cli.register("sessions", SessionsControl, "TEST")
cli.register("s", ScriptControl, "TEST")
return cli
continue
try:
exp = iadmin.lookupExperimenter(omeName)
olddn = iadmin.lookupLdapAuthExperimenter(exp.id.val)
except omero.ApiUsageException:
continue # Unknown user
if olddn:
if olddn != dn:
self.ctx.err("Found different DN for %s: %s" %
(omeName, olddn))
else:
self.ctx.dbg("DN already set for %s: %s" %
(omeName, olddn))
else:
if args.commands:
self.ctx.out("%s ldap setdn %s %s" %
(sys.argv[0], omeName, dn))
else:
self.ctx.out("Experimenter:%s\tomeName=%s\t%s" %
(exp.id.val, omeName, dn))
try:
register("ldap", LdapControl, HELP)
except NameError:
if __name__ == "__main__":
cli = CLI()
cli.register("ldap", LdapControl, HELP)
cli.invoke(sys.argv[1:])
config["omero.config.upgraded"] = "4.2.0"
def handle_line(self, line, config, keys):
line = line.strip()
if not line or line.startswith("#"):
return None
if line.endswith("\\"):
return line[:-1]
parts = line.split("=", 1)
if len(parts[0]) == 0:
return
if len(parts) == 1:
parts.append("")
if keys and parts[0] in keys:
self.ctx.die(502, "Duplicate property: %s (%s => %s)"\
% (parts[0], config[parts[0]], parts[1]))
keys.append(parts[0])
config[parts[0]] = parts[1]
def old(self, args):
self.ctx.out(getprefs(args.target, str(self.ctx.dir / "lib")))
try:
register("config", PrefsControl, HELP)
except NameError:
if __name__ == "__main__":
cli = CLI()
cli.register("config", PrefsControl, HELP)
cli.invoke(sys.argv[1:])
for attr_name, arg_name in java_args.items():
arg_value = getattr(args, attr_name)
if arg_value:
if isinstance(arg_name, tuple):
arg_name = arg_name[0]
login_args.append("%s=%s" % (arg_name, arg_value))
else:
login_args.append(arg_name)
if isinstance(arg_value, (str, unicode)):
login_args.append(arg_value)
a = self.COMMAND + login_args + args.path
p = omero.java.popen(a, debug=False, xargs=xargs, stdout=out, stderr=err)
self.ctx.rv = p.wait()
class TestEngine(ImportControl):
COMMAND = [TEST_CLASS]
try:
register("import", ImportControl, HELP, epilog=EXAMPLES)
register("testengine", TestEngine, TESTHELP)
except NameError:
if __name__ == "__main__":
cli = CLI()
cli.register("import", ImportControl, HELP, epilog=EXAMPLES)
cli.register("testengine", TestEngine, TESTHELP)
cli.invoke(sys.argv[1:])
self.print_usage()
if args.all:
self.print_all_commands_and_topics(args)
elif args.list:
self.print_commands_list(args)
elif args.topic:
self.print_single_command_or_topic(args)
controls = {
"help": (HelpControl, "Syntax help for all commands"),
"quit": (QuitControl, "Quit application"),
"shell": (ShellControl, """Starts an IPython interpreter session
All arguments not understood vi %(prog)s will be passed to the shell.
Use "--" to end parsing, e.g. '%(prog)s -- --help' for IPython help"""),
"version": (VersionControl, "Version number"),
"load": (LoadControl, LOAD_HELP)
}
try:
for k, v in controls.items():
register(k, v[0], v[1])
except NameError:
if __name__ == "__main__":
cli = CLI()
for k, v in controls.items():
cli.register(k, v[0], v[1])
cli.invoke(sys.argv[1:])
class TestRewrite(object):
"""Test template files regeneration"""
@pytest.fixture(autouse=True)
def setup_method(self, tmpadmindir):
self.cli = CLI()
self.cli.dir = path(tmpadmindir)
self.cli.register("admin", AdminControl, "TEST")
self.cli.register("config", PrefsControl, "TEST")
self.args = ["admin", "rewrite"]
def testTemplatesGeneration(self):
"""Test template files are generated by the rewrite subcommand"""
# Test non-existence of configuration files
for f in GRID_FILES:
assert not os.path.exists(
old_div(path(self.cli.dir), "etc" / "grid" / f))
for f in ETC_FILES:
assert not os.path.exists(old_div(path(self.cli.dir), "etc" / f))
# Call the jvmcf command and test file genearation
self.cli.invoke(self.args, strict=True)
for f in GRID_FILES:
assert os.path.exists(
old_div(path(self.cli.dir), "etc" / "grid" / f))
for f in ETC_FILES:
assert os.path.exists(old_div(path(self.cli.dir), "etc" / f))
def testForceRewrite(self, monkeypatch):
"""Test template regeneration while the server is running"""
# Call the jvmcfg command and test file generation
self.cli.invoke(self.args, strict=True)
monkeypatch.setattr(AdminControl, "status", lambda *args, **kwargs: 0)
with pytest.raises(NonZeroReturnCode):
self.cli.invoke(self.args, strict=True)
def testOldTemplates(self):
old_templates = old_div(
path(__file__).dirname(), ".." / "old_templates.xml")
old_templates.copy(
old_div(path(self.cli.dir),
"etc" / "templates" / "grid" / "templates.xml"))
with pytest.raises(NonZeroReturnCode):
self.cli.invoke(self.args, strict=True)
@pytest.mark.parametrize('prefix', [None, 1])
@pytest.mark.parametrize('registry', [None, 111])
@pytest.mark.parametrize('tcp', [None, 222])
@pytest.mark.parametrize('ssl', [None, 333])
@pytest.mark.parametrize('ws_wss_transports', [
(None, None, None),
(444, None, ('ssl', 'tcp', 'wss', 'ws')),
(None, 555, ('ssl', 'tcp', 'wss', 'ws')),
])
def testExplicitPorts(self, registry, ssl, tcp, prefix, ws_wss_transports,
monkeypatch):
"""
Test the omero.ports.xxx and omero.client.icetransports
configuration properties during the generation
of the configuration files
"""
# Skip the JVM settings calculation for this test
ws, wss, transports = ws_wss_transports
kwargs = {}
if prefix:
kwargs["prefix"] = prefix
if registry:
kwargs["registry"] = registry
if tcp:
kwargs["tcp"] = tcp
if ssl:
kwargs["ssl"] = ssl
if ws:
kwargs["ws"] = ws
if wss:
kwargs["wss"] = wss
for (k, v) in list(kwargs.items()):
self.cli.invoke(["config", "set",
"omero.ports.%s" % k,
"%s" % v],
strict=True)
if transports:
self.cli.invoke([
"config", "set", "omero.client.icetransports",
"%s" % ','.join(transports)
],
strict=True)
kwargs["transports"] = transports
self.cli.invoke(self.args, strict=True)
check_ice_config(self.cli.dir, **kwargs)
check_registry(self.cli.dir, **kwargs)
def testGlacier2Icessl(self, monkeypatch):
"""
Test the omero.glacier2.IceSSL.* properties during the generation
of the configuration files
"""
# Skip the JVM settings calculation for this test
# monkeypatch.setattr(omero.install.jvmcfg, "adjust_settings",
# lambda x, y: {})
if sys.platform == "darwin":
expected_ciphers = '(AES)'
else:
expected_ciphers = 'ADH:!LOW:!MD5:!EXP:!3DES:@STRENGTH'
glacier2 = [
("IceSSL.Ciphers", expected_ciphers),
("IceSSL.TestKey", "TestValue"),
]
self.cli.invoke([
"config", "set", "omero.glacier2." + glacier2[1][0], glacier2[1][1]
],
strict=True)
self.cli.invoke(self.args, strict=True)
check_templates_xml(self.cli.dir, glacier2)
"""
Parses who items of the form: "user", "group", "user=1", "group=6"
"""
import omero
WHO_FACTORY = {"user": omero.model.ExperimenterI,
"group": omero.model.ExperimenterGroupI}
WHO_CURRENT = {"user": lambda ec: ec.userId,
"group": lambda ec: ec.groupId}
for key, factory in WHO_FACTORY.items():
if who.startswith(key):
if who == key:
id = WHO_CURRENT[key](self.ctx._event_context)
return factory(id, False)
else:
parts = who.split("=")
if len(parts) != 2:
continue
else:
id = long(parts[1])
return factory(id, False)
try:
register("script", ScriptControl, HELP)
except NameError:
if __name__ == "__main__":
cli = CLI()
cli.register("script", ScriptControl, HELP)
cli.invoke(sys.argv[1:])
WHO_FACTORY = {
"user": omero.model.ExperimenterI,
"group": omero.model.ExperimenterGroupI
}
WHO_CURRENT = {
"user": lambda ec: ec.userId,
"group": lambda ec: ec.groupId
}
for key, factory in list(WHO_FACTORY.items()):
if who.startswith(key):
if who == key:
id = WHO_CURRENT[key](self.ctx.get_event_context())
return factory(id, False)
else:
parts = who.split("=")
if len(parts) != 2:
continue
else:
id = int(parts[1])
return factory(id, False)
try:
register("script", ScriptControl, HELP)
except NameError:
if __name__ == "__main__":
cli = CLI()
cli.register("script", ScriptControl, HELP)
cli.invoke(sys.argv[1:])
def remove(self, args):
import omero
c = self.ctx.conn(args)
a = c.sf.getAdminService()
gid, grp = self.find_group(a, args.GROUP)
uids = [self.find_user(a, x)[0] for x in args.USER]
self.removeusersbyid(c, grp, uids)
def addusersbyid(self, c, group, users):
import omero
a = c.sf.getAdminService()
for add in list(users):
a.addGroups(omero.model.ExperimenterI(add, False), [group])
self.ctx.out("Added %s to group %s" % (add, group.id.val))
def removeusersbyid(self, c, group, users):
import omero
a = c.sf.getAdminService()
for add in list(users):
a.removeGroups(omero.model.ExperimenterI(add, False), [group])
self.ctx.out("Removed %s from group %s" % (add, group.id.val))
try:
register("group", GroupControl, HELP)
except NameError:
if __name__ == "__main__":
cli = CLI()
cli.register("group", GroupControl, HELP)
cli.invoke(sys.argv[1:])
class TestDatabase(object):
def setup_method(self, method):
self.cli = CLI()
self.cli.register("db", DatabaseControl, "TEST")
self.args = ["db"]
dir = path(__file__) / ".." / ".." / ".." / ".." / ".." / ".." /\
".." / "dist" # FIXME: should not be hard-coded
dir = dir.abspath()
cfg = dir / "etc" / "omero.properties"
cfg = cfg.abspath()
self.cli.dir = dir
self.data = {}
for line in cfg.text().split("\n"):
line = line.strip()
for x in ("version", "patch"):
key = "omero.db." + x
if line.startswith(key):
self.data[x] = line[len(key) + 1:]
self.file = create_path()
self.script_file = "%(version)s__%(patch)s.sql" % self.data
if os.path.isfile(self.script_file):
os.rename(self.script_file, self.script_file + '.bak')
assert not os.path.isfile(self.script_file)
self.mox = Mox()
self.mox.StubOutWithMock(getpass, 'getpass')
self.mox.StubOutWithMock(__builtin__, "raw_input")
def teardown_method(self, method):
self.file.remove()
if os.path.isfile(self.script_file):
os.remove(self.script_file)
if os.path.isfile(self.script_file + '.bak'):
os.rename(self.script_file + '.bak', self.script_file)
self.mox.UnsetStubs()
self.mox.VerifyAll()
def password(self, string, strict=True):
self.cli.invoke("db password " + string % self.data, strict=strict)
def testHelp(self):
self.args += ["-h"]
self.cli.invoke(self.args, strict=True)
@pytest.mark.parametrize('subcommand', DatabaseControl().get_subcommands())
def testSubcommandHelp(self, subcommand):
self.args += [subcommand, "-h"]
self.cli.invoke(self.args, strict=True)
def testBadVersionDies(self):
with pytest.raises(NonZeroReturnCode):
self.cli.invoke("db script NONE NONE pw", strict=True)
def testPasswordIsAskedForAgainIfDiffer(self):
self.expectPassword("ome")
self.expectConfirmation("bad")
self.expectPassword("ome")
self.expectConfirmation("ome")
self.mox.ReplayAll()
self.password("")
def testPasswordIsAskedForAgainIfEmpty(self):
self.expectPassword("")
self.expectPassword("ome")
self.expectConfirmation("ome")
self.mox.ReplayAll()
self.password("")
@pytest.mark.parametrize('no_salt', ['', '--no-salt'])
@pytest.mark.parametrize('user_id', ['', '0', '1'])
@pytest.mark.parametrize('password', ['', 'ome'])
def testPassword(self, user_id, password, no_salt, capsys):
args = ""
if user_id:
args += "--user-id=%s " % user_id
if no_salt:
args += "%s " % no_salt
if password:
args += "%s" % password
else:
self.expectPassword("ome", id=user_id)
self.expectConfirmation("ome", id=user_id)
self.mox.ReplayAll()
self.password(args)
out, err = capsys.readouterr()
assert out.strip() == self.password_output(user_id, no_salt)
@pytest.mark.parametrize('file_arg', ['', '-f', '--file'])
@pytest.mark.parametrize('no_salt', ['', '--no-salt'])
@pytest.mark.parametrize('password', ['', '--password ome'])
def testScript(self, no_salt, file_arg, password, capsys):
"""
Recommended usage of db script
"""
args = "db script " + password
if no_salt:
args += " %s" % no_salt
if file_arg:
args += " %s %s" % (file_arg, str(self.file))
output = self.file
else:
output = self.script_file
if not password:
self.expectPassword("ome")
self.expectConfirmation("ome")
self.mox.ReplayAll()
self.cli.invoke(args, strict=True)
out, err = capsys.readouterr()
assert 'Using %s for version' % self.data['version'] in err
assert 'Using %s for patch' % self.data['patch'] in err
if password:
assert 'Using password from commandline' in err
with open(output) as f:
lines = f.readlines()
for line in lines:
if line.startswith('insert into password values (0'):
assert line.strip() == self.script_output(no_salt)
@pytest.mark.parametrize('file_arg', ['', '-f', '--file'])
@pytest.mark.parametrize('no_salt', ['', '--no-salt'])
@pytest.mark.parametrize(
'pos_args', ['%s %s %s', '--version %s --patch %s --password %s'])
def testScriptDeveloperArgs(self, pos_args, no_salt, file_arg, capsys):
"""
Deprecated and developer usage of db script
"""
arg_values = ('VERSION', 'PATCH', 'PASSWORD')
args = "db script " + pos_args % arg_values
if no_salt:
args += " %s" % no_salt
if file_arg:
args += " %s %s" % (file_arg, str(self.file))
self.file
else:
self.script_file
self.mox.ReplayAll()
with pytest.raises(NonZeroReturnCode):
self.cli.invoke(args, strict=True)
out, err = capsys.readouterr()
assert 'Using %s for version' % (arg_values[0]) in err
assert 'Using %s for patch' % (arg_values[1]) in err
assert 'Using password from commandline' in err
assert 'Invalid Database version/patch' in err
def password_ending(self, user, id):
if id and id != '0':
rv = "user %s: " % id
else:
rv = "%s user: "******"password for OMERO " + rv
def expectPassword(self, pw, user="******", id=None):
getpass.getpass("Please enter %s" %
self.password_ending(user, id)).AndReturn(pw)
def expectConfirmation(self, pw, user="******", id=None):
getpass.getpass("Please re-enter %s" %
self.password_ending(user, id)).AndReturn(pw)
def password_output(self, user_id, no_salt):
update_msg = "UPDATE password SET hash = \'%s\'" \
" WHERE experimenter_id = %s;"
if not user_id:
user_id = "0"
return update_msg % (hash_map[(user_id, no_salt)], user_id)
def script_output(self, no_salt):
root_password_msg = "insert into password values (0,\'%s\');"
return root_password_msg % (hash_map[("0", no_salt)])
class TestAdminPorts(object):
def setup_method(self, method):
# # Non-temp directories
ctxdir = path() / ".." / ".." / ".." / "dist"
etc_dir = ctxdir / "etc"
# List configuration files to backup
self.cfg_files = {}
for f in ['internal.cfg', 'master.cfg', 'ice.config']:
self.cfg_files[f] = etc_dir / f
for f in ['windefault.xml', 'default.xml', 'config.xml']:
self.cfg_files[f] = etc_dir / 'grid' / f
# Create temp files for backup
tmp_dir = create_path(folder=True)
self.tmp_cfg_files = {}
for key in self.cfg_files.keys():
if self.cfg_files[key].exists():
self.tmp_cfg_files[key] = tmp_dir / key
self.cfg_files[key].copy(self.tmp_cfg_files[key])
else:
self.tmp_cfg_files[key] = None
# Other setup
self.cli = CLI()
self.cli.dir = ctxdir
self.cli.register("admin", AdminControl, "TEST")
self.args = ["admin", "ports"]
def teardown_method(self, method):
# Restore backups
for key in self.cfg_files.keys():
if self.tmp_cfg_files[key] is not None:
self.tmp_cfg_files[key].copy(self.cfg_files[key])
else:
self.cfg_files[key].remove()
def create_new_ice_config(self):
with open(self.cfg_files['ice.config'], 'w') as f:
f.write('omero.host=localhost')
def check_cfg(self, prefix='', registry=4061, **kwargs):
for key in ['master.cfg', 'internal.cfg']:
s = self.cfg_files[key].text()
assert 'tcp -h 127.0.0.1 -p %s%s' % (prefix, registry) in s
def check_config_xml(self, prefix='', webserver=4080, ssl=4064, **kwargs):
config_text = self.cfg_files["config.xml"].text()
serverport_property = (
'<property name="omero.web.application_server.port"'
' value="%s%s"') % (prefix, webserver)
serverlist_property = (
'<property name="omero.web.server_list"'
' value="[["localhost", %s%s, "omero"]]"'
) % (prefix, ssl)
assert serverport_property in config_text
assert serverlist_property in config_text
def check_ice_config(self, prefix='', webserver=4080, ssl=4064, **kwargs):
config_text = self.cfg_files["ice.config"].text()
pattern = re.compile('^omero.port=\d+$', re.MULTILINE)
matches = pattern.findall(config_text)
assert matches == ["omero.port=%s%s" % (prefix, ssl)]
def check_default_xml(self, prefix='', tcp=4063, ssl=4064, **kwargs):
routerport = (
'<variable name="ROUTERPORT" value="%s%s"/>' % (prefix, ssl))
insecure_routerport = (
'<variable name="INSECUREROUTER" value="OMERO.Glacier2'
'/router:tcp -p %s%s -h @omero.host@"/>' % (prefix, tcp))
client_endpoints = (
'client-endpoints="ssl -p ${ROUTERPORT}:tcp -p %s%s"'
% (prefix, tcp))
for key in ['default.xml', 'windefault.xml']:
s = self.cfg_files[key].text()
assert routerport in s
assert insecure_routerport in s
assert client_endpoints in s
@pytest.mark.parametrize('prefix', [None, 1, 2])
@pytest.mark.parametrize('default', [True, False])
def testRevert(self, prefix, default):
if not default:
self.create_new_ice_config()
kwargs = {}
if prefix:
self.args += ['--prefix', '%s' % prefix]
kwargs['prefix'] = prefix
self.args += ['--skipcheck']
self.cli.invoke(self.args, strict=True)
# Check configuration file ports have been prefixed
self.check_ice_config(**kwargs)
self.check_cfg(**kwargs)
self.check_config_xml(**kwargs)
self.check_default_xml(**kwargs)
# Check revert argument
self.args += ['--revert']
self.cli.invoke(self.args, strict=True)
# Check configuration file ports have been deprefixed
self.check_ice_config()
self.check_cfg()
self.check_config_xml()
self.check_default_xml()
@pytest.mark.parametrize('default', [True, False])
def testFailingRevert(self, default):
if not default:
self.create_new_ice_config()
kwargs = {'prefix': 1}
self.args += ['--skipcheck']
self.args += ['--prefix', '%s' % kwargs['prefix']]
self.cli.invoke(self.args, strict=True)
# Check configuration file ports
self.check_ice_config(**kwargs)
self.check_cfg(**kwargs)
self.check_config_xml(**kwargs)
self.check_default_xml(**kwargs)
# Test revert with a mismatching prefix
self.args[-1] = "2"
self.args += ['--revert']
self.cli.invoke(self.args, strict=True)
# Check configuration file ports have not been modified
self.check_ice_config(**kwargs)
self.check_cfg(**kwargs)
self.check_config_xml(**kwargs)
self.check_default_xml(**kwargs)
@pytest.mark.parametrize('prefix', [None, 1])
@pytest.mark.parametrize('registry', [None, 111])
@pytest.mark.parametrize('tcp', [None, 222])
@pytest.mark.parametrize('ssl', [None, 333])
@pytest.mark.parametrize('webserver', [None, 444])
def testExplicitPorts(self, registry, ssl, tcp, webserver, prefix):
kwargs = {}
if prefix:
self.args += ['--prefix', '%s' % prefix]
kwargs['prefix'] = prefix
if registry:
self.args += ['--registry', '%s' % registry]
kwargs["registry"] = registry
if tcp:
self.args += ['--tcp', '%s' % tcp]
kwargs["tcp"] = tcp
if ssl:
self.args += ['--ssl', '%s' % ssl]
kwargs["ssl"] = ssl
if webserver:
self.args += ['--webserver', '%s' % webserver]
kwargs["webserver"] = webserver
self.args += ['--skipcheck']
self.cli.invoke(self.args, strict=True)
self.check_ice_config(**kwargs)
if out:
out = open(out, "w")
if err:
err = open(err, "w")
p = omero.java.popen(
import_command, debug=False, xargs=xargs, stdout=out,
stderr=err)
self.ctx.rv = p.wait()
finally:
# Make sure file handles are closed
if out:
out.close()
if err:
err.close()
class TestEngine(ImportControl):
COMMAND = [TEST_CLASS]
try:
register("import", ImportControl, HELP, epilog=EXAMPLES)
register("testengine", TestEngine, TESTHELP)
except NameError:
if __name__ == "__main__":
cli = CLI()
cli.register("import", ImportControl, HELP, epilog=EXAMPLES)
cli.register("testengine", TestEngine, TESTHELP)
cli.invoke(sys.argv[1:])
self.ctx.dbg(e)
self.ctx.die(432, "Bad object: %s" % args.type)
c.sf.getUpdateService().indexObject(obj)
else:
search = c.sf.createSearchService()
try:
try:
search.onlyType(args.type)
search.byFullText(args.search_string)
if not search.hasNext():
self.ctx.die(433, "No results found.")
while search.hasNext():
results = search.results()
results = [[x] for x in results]
self.display(results)
except omero.ApiUsageException, aue:
self.ctx.die(434, aue.message)
finally:
search.close()
try:
register("search", SearchControl, HELP)
except NameError:
if __name__ == "__main__":
cli = CLI()
cli.register("search", SearchControl, HELP)
cli.invoke(sys.argv[1:])
return
if len(parts) == 1:
parts.append("")
_key = parts[0]
_new = parts[1]
if _key in config.keys():
_old = config[_key]
else:
self.assert_valid_property_name(_key)
_old = None
if keys and _key in keys and _new != _old:
self.ctx.die(502, "Duplicate property: %s ('%s' => '%s')"
% (_key, _old, _new))
keys.append(_key)
config[_key] = _new
def old(self, args):
self.ctx.out(getprefs(args.target, str(self.ctx.dir / "lib")))
try:
register("config", PrefsControl, HELP)
except NameError:
if __name__ == "__main__":
cli = CLI()
cli.register("config", PrefsControl, HELP)
cli.invoke(sys.argv[1:])
pos = showCols.index(col)
keys.append(pos)
except:
pass
else:
keys = [0]
tb.sort(cols=keys, reverse=args.reverse)
# Format the size column after sorting.
if args.units:
col = tb.get_col("size")
col = [self._to_units(val, args.units) for val in col]
tb.replace_col("size", col)
tb.replace_header("size", "size (%siB)" % args.units)
elif args.human_readable:
col = tb.get_col("size")
col = [filesizeformat(val) for val in col]
tb.replace_col("size", col)
else:
tb.replace_header("size", "size (bytes)")
self.ctx.out(str(tb.build()))
try:
register("fs", FsControl, HELP)
except NameError:
if __name__ == "__main__":
cli = CLI()
cli.register("fs", FsControl, HELP)
cli.invoke(sys.argv[1:])
name = default_name
return server, name, port
def _get_server(self, store, name, port):
defserver = store.last_host()
if not port:
port = str(omero.constants.GLACIER2PORT)
rv = self.ctx.input("Server: [%s:%s]" % (defserver, port))
if not rv:
return defserver, name, port
else:
return self._parse_conn(rv, name)
def _get_username(self, defuser):
if defuser is None:
defuser = get_user("root")
rv = self.ctx.input("Username: [%s]" % defuser)
if not rv:
return defuser
else:
return rv
try:
register("sessions", SessionsControl, HELP)
except NameError:
if __name__ == "__main__":
cli = CLI()
cli.register("sessions", SessionsControl, HELP)
cli.invoke(sys.argv[1:])
else:
return False
def set_environ(self, ice_config=None):
os.environ['ICE_CONFIG'] = ice_config is None and \
str(self.ctx.dir / "etc" / "ice.config") or str(ice_config)
os.environ['PATH'] = str(os.environ.get('PATH', '.') + ':' +
self.ctx.dir / 'bin')
def iis(self, args):
if not (self._isWindows() or self.ctx.isdebug):
self.ctx.die(2, "'iis' command is for Windows only")
self.collectstatic()
if not args.keep_sessions:
self.clearsessions(args)
web_iis = self._get_python_dir() / "omero_web_iis.py"
cmd = [sys.executable, str(web_iis)]
if args.remove:
cmd.append("remove")
self.ctx.call(cmd)
try:
register("web", WebControl, HELP)
except NameError:
if __name__ == "__main__":
cli = CLI()
cli.register("web", WebControl, HELP)
cli.invoke(sys.argv[1:])
" left outer join i.fileset as fs" \
" join fs.usedFiles as uf" \
" join uf.originalFile as f" \
" where i.id = :iid"
query_out = query.projection(sql, params, {'omero.group': '-1'})
if not query_out:
self.ctx.die(602, 'Input image has no associated Fileset')
if len(query_out) > 1:
self.ctx.die(603, 'Input image has more than 1 associated '
'file: %s' % len(query_out))
return unwrap(query_out[0])[0].id.val
self.ctx.die(601, 'Invalid object input')
def parse_object_id(self, object_type, value):
pattern = r'%s:(?P<id>\d+)' % object_type
pattern = re.compile('^' + pattern + '$')
m = pattern.match(value)
if not m:
return
return long(m.group('id'))
try:
register("download", DownloadControl, HELP)
except NameError:
if __name__ == "__main__":
cli = CLI()
cli.register("download", DownloadControl, HELP)
cli.invoke(sys.argv[1:])
class TestPrefs(object):
def setup_method(self, method):
self.cli = CLI()
self.cli.register("config", PrefsControl, HELP)
self.p = create_path()
self.args = ["config", "--source", "%s" % self.p]
def config(self):
return ConfigXml(filename=str(self.p))
def assertStdoutStderr(self, capsys, out='', err=''):
o, e = capsys.readouterr()
assert o.strip() == out
assert e.strip() == err
def invoke(self, s):
self.cli.invoke(self.args + s.split(), strict=True)
def testHelp(self):
self.invoke("-h")
assert 0 == self.cli.rv
@pytest.mark.parametrize('subcommand', subcommands)
def testSubcommandHelp(self, subcommand):
self.invoke("%s -h" % subcommand)
assert 0 == self.cli.rv
def testAll(self, capsys):
config = self.config()
config.default("test")
config.close()
self.invoke("all")
self.assertStdoutStderr(capsys, out="test\ndefault")
def testDefaultInitial(self, capsys):
self.invoke("def")
self.assertStdoutStderr(capsys, out="default")
def testDefaultEnvironment(self, capsys, monkeypatch):
monkeypatch.setenv("OMERO_CONFIG", "testDefaultEnvironment")
self.invoke("def")
self.assertStdoutStderr(capsys, out="testDefaultEnvironment")
def testDefaultSet(self, capsys):
self.invoke("def x")
self.assertStdoutStderr(capsys, out="x")
self.invoke("def")
self.assertStdoutStderr(capsys, out="x")
def testGetSet(self, capsys):
self.invoke("get X")
self.assertStdoutStderr(capsys)
self.invoke("set A B")
self.assertStdoutStderr(capsys)
self.invoke("get A")
self.assertStdoutStderr(capsys, out='B')
self.invoke("get")
self.assertStdoutStderr(capsys, out='A=B')
self.invoke("set A")
self.assertStdoutStderr(capsys)
self.invoke("keys")
self.assertStdoutStderr(capsys)
def testSetFails(self, capsys):
self.invoke("set A=B")
self.assertStdoutStderr(
capsys, err="\"=\" in key name. Did you mean \"...set A B\"?")
def testKeys(self, capsys):
self.invoke("keys")
self.assertStdoutStderr(capsys)
self.invoke("set A B")
self.assertStdoutStderr(capsys)
self.invoke("keys")
self.assertStdoutStderr(capsys, out="A")
def testVersion(self, capsys):
self.invoke("version")
self.assertStdoutStderr(capsys, out=ConfigXml.VERSION)
def testPath(self, capsys):
self.invoke("path")
self.assertStdoutStderr(capsys, out=self.p)
def testLoad(self, capsys):
to_load = create_path()
to_load.write_text("A=B")
self.invoke("load %s" % to_load)
self.assertStdoutStderr(capsys)
self.invoke("get")
self.assertStdoutStderr(capsys, out="A=B")
# Same property/value pairs should pass
self.invoke("load %s" % to_load)
to_load.write_text("A=C")
with pytest.raises(NonZeroReturnCode):
# Different property/value pair should fail
self.invoke("load %s" % to_load)
self.assertStdoutStderr(
capsys, err="Duplicate property: A ('B' => 'C')")
# Quiet load
self.invoke("load -q %s" % to_load)
self.assertStdoutStderr(capsys)
self.invoke("get")
self.assertStdoutStderr(capsys, out="A=C")
def testLoadDoesNotExist(self):
# ticket:7273
pytest.raises(NonZeroReturnCode, self.invoke,
"load THIS_FILE_SHOULD_NOT_EXIST")
def testLoadMultiLine(self, capsys):
to_load = create_path()
to_load.write_text("A=B\\\nC")
self.invoke("load %s" % to_load)
self.invoke("get")
self.assertStdoutStderr(capsys, out="A=BC")
def testSetFromFile(self, capsys):
to_load = create_path()
to_load.write_text("Test")
self.invoke("set -f %s A" % to_load)
self.invoke("get")
self.assertStdoutStderr(capsys, out="A=Test")
def testDrop(self, capsys):
self.invoke("def x")
self.assertStdoutStderr(capsys, out="x")
self.invoke("def")
self.assertStdoutStderr(capsys, out="x")
self.invoke("all")
self.assertStdoutStderr(capsys, out="x\ndefault")
self.invoke("def y")
self.assertStdoutStderr(capsys, out="y")
self.invoke("all")
self.assertStdoutStderr(capsys, out="y\nx\ndefault")
self.invoke("drop x")
self.assertStdoutStderr(capsys)
self.invoke("all")
self.assertStdoutStderr(capsys, 'y\ndefault')
def testDropFails(self, capsys):
self.invoke("drop x")
self.assertStdoutStderr(capsys, err="Unknown configuration: x")
def testEdit(self):
"""
Testing edit is a bit more complex since it wants to
start another process. Rather than using invoke, we
manage things ourselves here.
"""
def fake_edit_path(tmp_file, tmp_text):
pass
args = self.cli.parser.parse_args("config edit".split())
control = self.cli.controls["config"]
config = self.config()
try:
control.edit(args, config, fake_edit_path)
finally:
config.close()
def testNewEnvironment(self, capsys, monkeypatch):
config = self.config()
config.default("default")
config.close()
monkeypatch.setenv("OMERO_CONFIG", "testNewEnvironment")
self.invoke("set A B")
self.assertStdoutStderr(capsys)
self.invoke("get")
self.assertStdoutStderr(capsys, out="A=B")
@pytest.mark.parametrize(
('initval', 'newval'),
[('1', '2'), ('\"1\"', '\"2\"'), ('test', 'test')])
def testAppendFails(self, initval, newval):
self.invoke("set A %s" % initval)
with pytest.raises(NonZeroReturnCode):
self.invoke("append A %s" % newval)
def testRemoveUnsetPropertyFails(self):
with pytest.raises(NonZeroReturnCode):
self.invoke("remove A x")
@pytest.mark.parametrize(
('initval', 'newval'),
[('1', '1'), ('[\"1\"]', '1'), ('[1]', '\"1\"')])
def testRemoveFails(self, initval, newval):
self.invoke("set A %s" % initval)
with pytest.raises(NonZeroReturnCode):
self.invoke("remove A %s" % newval)
def testAppendRemove(self, capsys):
self.invoke("append A 1")
self.invoke("get A")
self.assertStdoutStderr(capsys, out='[1]')
self.invoke("append A \"y\"")
self.invoke("get A")
self.assertStdoutStderr(capsys, out='[1, "y"]')
self.invoke("remove A \"y\"")
self.invoke("get A")
self.assertStdoutStderr(capsys, out='[1]')
self.invoke("remove A 1")
self.invoke("get A")
self.assertStdoutStderr(capsys, out='[]')
def testRemoveIdenticalValues(self, capsys):
self.invoke("set A [1,1]")
self.invoke("remove A 1")
self.invoke("get A")
self.assertStdoutStderr(capsys, out='[1]')
self.invoke("remove A 1")
self.invoke("get A")
self.assertStdoutStderr(capsys, out='[]')
@pytest.mark.usefixtures('configxml')
def testAppendWithDefault(self, monkeypatch, capsys):
import json
monkeypatch.setattr("omeroweb.settings.CUSTOM_SETTINGS_MAPPINGS", {
"omero.web.test": ["TEST", "[1,2,3]", json.loads],
"omero.web.notalist": ["NOTALIST", "abc", str],
})
self.invoke("append omero.web.test 4")
self.invoke("get omero.web.test")
self.assertStdoutStderr(capsys, out='[1, 2, 3, 4]')
self.invoke("append omero.web.unknown 1")
self.invoke("get omero.web.unknown")
self.assertStdoutStderr(capsys, out='[1]')
with pytest.raises(NonZeroReturnCode):
self.invoke("append omero.web.notalist 1")
@pytest.mark.usefixtures('configxml')
def testRemoveWithDefault(self, monkeypatch, capsys):
import json
monkeypatch.setattr("omeroweb.settings.CUSTOM_SETTINGS_MAPPINGS", {
"omero.web.test": ["TEST", "[1,2,3]", json.loads],
})
self.invoke("remove omero.web.test 2")
self.invoke("get omero.web.test")
self.assertStdoutStderr(capsys, out='[1, 3]')
self.invoke("remove omero.web.test 1")
self.invoke("remove omero.web.test 3")
self.invoke("get omero.web.test")
self.assertStdoutStderr(capsys, out='[]')
rv = list()
mapped.append(rv)
if not s.isLoaded():
rv.append("")
rv.append("id=%s" % s.id.val)
rv.append("")
rv.append("")
rv.append("")
rv.append("insufficient privileges")
else:
rv.append(s.node.id)
rv.append(s.uuid)
rv.append(s.started)
rv.append(s.owner.omeName)
if s.userAgent is None:
rv.append("")
else:
rv.append(s.userAgent)
if client.getSessionId() == s.uuid.val:
rv.append("current session")
else:
rv.append("")
self.ctx.controls["hql"].display(mapped, ("node", "session", "started", "owner", "agent", "notes"))
try:
register("admin", AdminControl, HELP)
except NameError:
if __name__ == "__main__":
cli = CLI()
cli.register("admin", AdminControl, HELP)
cli.invoke(sys.argv[1:])
uid, username = self.parse_userid(a, args)
groups = self.list_groups(a, args)
groups = self.filter_groups(groups, uid, args.as_owner, True)
for group in groups:
if args.as_owner:
self.addownersbyid(a, group, [uid])
else:
self.addusersbyid(a, group, [uid])
def leavegroup(self, args):
c = self.ctx.conn(args)
a = c.sf.getAdminService()
uid, username = self.parse_userid(a, args)
groups = self.list_groups(a, args)
groups = self.filter_groups(groups, uid, args.as_owner, False)
for group in list(groups):
if args.as_owner:
self.removeownersbyid(a, group, [uid])
else:
self.removeusersbyid(a, group, [uid])
try:
register("user", UserControl, HELP)
except NameError:
if __name__ == "__main__":
cli = CLI()
cli.register("user", UserControl, HELP)
cli.invoke(sys.argv[1:])
class TestPrefs(object):
def setup_method(self, method):
self.cli = CLI()
self.cli.register("config", PrefsControl, HELP)
self.p = create_path()
self.args = ["-d1", "config", "--source", "%s" % self.p]
def config(self):
return ConfigXml(filename=str(self.p))
def assertStdoutStderr(self, capsys, out='', err='', strip_warning=False):
o, e = capsys.readouterr()
if strip_warning:
assert (e.startswith('WARNING: '))
e = '\n'.join(e.split('\n')[1:])
assert (o.strip() == out and e.strip() == err)
def invoke(self, s):
if isinstance(s, basestring):
s = s.split()
self.cli.invoke(self.args + s, strict=True)
def testHelp(self):
self.invoke("-h")
assert 0 == self.cli.rv
@pytest.mark.parametrize('subcommand', PrefsControl().get_subcommands())
def testSubcommandHelp(self, subcommand):
self.invoke("%s -h" % subcommand)
assert 0 == self.cli.rv
def testAll(self, capsys):
config = self.config()
config.default("test")
config.close()
self.invoke("all")
self.assertStdoutStderr(capsys, out="test\ndefault")
def testDefaultInitial(self, capsys):
self.invoke("def")
self.assertStdoutStderr(capsys, out="default")
def testDefaultEnvironment(self, capsys, monkeypatch):
monkeypatch.setenv("OMERO_CONFIG", "testDefaultEnvironment")
self.invoke("def")
self.assertStdoutStderr(capsys, out="testDefaultEnvironment")
def testDefaultSet(self, capsys):
self.invoke("def x")
self.assertStdoutStderr(capsys, out="x")
self.invoke("def")
self.assertStdoutStderr(capsys, out="x")
def testGetSet(self, capsys):
self.invoke("get X")
self.assertStdoutStderr(capsys)
self.invoke("set A B")
self.assertStdoutStderr(capsys)
self.invoke("get A")
self.assertStdoutStderr(capsys, out='B')
self.invoke("get")
self.assertStdoutStderr(capsys, out='A=B')
self.invoke("set A")
self.assertStdoutStderr(capsys)
self.invoke("keys")
self.assertStdoutStderr(capsys)
def testGetHidePassword(self, capsys):
config = {
"omero.X.mypassword": "******",
"omero.X.pass": "******",
"omero.X.password": "******",
"omero.X.regular": "value",
"omero.Y.MyPassword": "******",
"omero.Y.Pass": "******",
"omero.Y.Password": "******",
"omero.Z.mypassword": "",
"omero.Z.pass": "",
"omero.Z.password": ""
}
output_hidden_password = ('omero.X.mypassword=********\n'
'omero.X.pass=********\n'
'omero.X.password=********\n'
'omero.X.regular=value\n'
'omero.Y.MyPassword=********\n'
'omero.Y.Pass=********\n'
'omero.Y.Password=********\n'
'omero.Z.mypassword=\n'
'omero.Z.pass=\n'
'omero.Z.password='******'omero.X.mypassword=long_password\n'
'omero.X.pass=shortpass\n'
'omero.X.password=medium_password\n'
'omero.X.regular=value\n'
'omero.Y.MyPassword=long_password\n'
'omero.Y.Pass=shortpass\n'
'omero.Y.Password=medium_password\n'
'omero.Z.mypassword=\n'
'omero.Z.pass=\n'
'omero.Z.password='******'argument', ['A=B', 'A= B'])
def testSetFails(self, capsys, argument):
self.invoke("set %s" % argument)
self.assertStdoutStderr(
capsys, err="\"=\" in key name. Did you mean \"...set A B\"?")
def testKeys(self, capsys):
self.invoke("keys")
self.assertStdoutStderr(capsys)
self.invoke("set A B")
self.assertStdoutStderr(capsys)
self.invoke("keys")
self.assertStdoutStderr(capsys, out="A")
self.invoke("set C D=E")
self.assertStdoutStderr(capsys)
self.invoke("keys")
self.assertStdoutStderr(capsys, out="A\nC")
def testVersion(self, capsys):
self.invoke("version")
self.assertStdoutStderr(capsys, out=ConfigXml.VERSION)
def testPath(self, capsys):
self.invoke("path")
self.assertStdoutStderr(capsys, out=self.p)
def testLoad(self, capsys):
to_load = create_path()
to_load.write_text("A=B")
self.invoke("load %s" % to_load)
self.assertStdoutStderr(capsys)
self.invoke("get")
self.assertStdoutStderr(capsys, out="A=B")
# Same property/value pairs should pass
self.invoke("load %s" % to_load)
to_load.write_text("A=C")
with pytest.raises(NonZeroReturnCode):
# Different property/value pair should fail
self.invoke("load %s" % to_load)
self.assertStdoutStderr(capsys,
err="Duplicate property: A ('B' => 'C')")
# Quiet load
self.invoke("load -q %s" % to_load)
self.assertStdoutStderr(capsys)
self.invoke("get")
self.assertStdoutStderr(capsys, out="A=C")
def testLoadDoesNotExist(self):
# ticket:7273
pytest.raises(NonZeroReturnCode, self.invoke,
"load THIS_FILE_SHOULD_NOT_EXIST")
def testLoadMultiLine(self, capsys):
to_load = create_path()
to_load.write_text("A=B\\\nC")
self.invoke("load %s" % to_load)
self.invoke("get")
self.assertStdoutStderr(capsys, out="A=BC")
@pytest.mark.parametrize('validkeyvalue', [('A', 'B'), ('A', 'B=C'),
('A.B', 'C.D'),
('A.B', "'C.D'")])
def testLoadWhitelist(self, capsys, validkeyvalue):
valid_key, valid_value = validkeyvalue
to_load = create_path()
to_load.write_text("%s=%s\n" % (valid_key, valid_value))
self.invoke("load %s" % to_load)
self.invoke("get %s" % valid_key)
self.assertStdoutStderr(capsys, out=valid_value)
@pytest.mark.parametrize(('invalidline', 'invalidkey'),
[('E F G', 'E F G'), ('E!F=G', 'E!F'),
('E = F', 'E')])
def testLoadInvalidKey(self, capsys, invalidline, invalidkey):
self.invoke("set A B")
self.assertStdoutStderr(capsys)
to_load = create_path()
to_load.write_text("C=D\n%s\nH=I\n" % invalidline)
with pytest.raises(NonZeroReturnCode):
self.invoke("load %s" % to_load)
self.assertStdoutStderr(capsys,
err="Illegal property name: %s" % invalidkey)
self.invoke("get")
self.assertStdoutStderr(capsys, out="A=B")
@pytest.mark.parametrize('valid_key_value', [('A', 'B'), ('A', 'B=C'),
('A.B', 'C.D'),
('A.B', "'C.D'")])
def testSetWhitelist(self, capsys, valid_key_value):
valid_key, valid_value = valid_key_value
self.invoke(["set", valid_key, valid_value])
self.invoke(["get", valid_key])
self.assertStdoutStderr(capsys, out=valid_value)
@pytest.mark.parametrize('invalid_key', ['E F', 'E!F', 'E '])
def testSetInvalidKey(self, capsys, invalid_key):
with pytest.raises(NonZeroReturnCode):
self.invoke(["set", invalid_key, "test"])
self.assertStdoutStderr(capsys,
err="Illegal property name: %s" %
invalid_key.strip())
def testSetFromFile(self, capsys):
to_load = create_path()
to_load.write_text("Test")
self.invoke("set -f %s A" % to_load)
self.invoke("get")
self.assertStdoutStderr(capsys, out="A=Test")
def testDrop(self, capsys):
self.invoke("def x")
self.assertStdoutStderr(capsys, out="x")
self.invoke("def")
self.assertStdoutStderr(capsys, out="x")
self.invoke("all")
self.assertStdoutStderr(capsys, out="x\ndefault")
self.invoke("def y")
self.assertStdoutStderr(capsys, out="y")
self.invoke("all")
self.assertStdoutStderr(capsys, out="y\nx\ndefault")
self.invoke("drop x")
self.assertStdoutStderr(capsys)
self.invoke("all")
self.assertStdoutStderr(capsys, 'y\ndefault')
def testDropFails(self, capsys):
self.invoke("drop x")
self.assertStdoutStderr(capsys, err="Unknown configuration: x")
def testEdit(self):
"""
Testing edit is a bit more complex since it wants to
start another process. Rather than using invoke, we
manage things ourselves here.
"""
def fake_edit_path(tmp_file, tmp_text):
pass
args = self.cli.parser.parse_args("config edit".split())
control = self.cli.controls["config"]
config = self.config()
try:
control.edit(args, config, fake_edit_path)
finally:
config.close()
def testNewEnvironment(self, capsys, monkeypatch):
config = self.config()
config.default("default")
config.close()
monkeypatch.setenv("OMERO_CONFIG", "testNewEnvironment")
self.invoke("set A B")
self.assertStdoutStderr(capsys)
self.invoke("get")
self.assertStdoutStderr(capsys, out="A=B")
@pytest.mark.parametrize(('initval', 'newval'), [('1', '2'),
('\"1\"', '\"2\"'),
('test', 'test')])
def testAppendFails(self, initval, newval):
self.invoke("set A %s" % initval)
with pytest.raises(NonZeroReturnCode):
self.invoke("append A %s" % newval)
def testRemoveUnsetPropertyFails(self):
with pytest.raises(NonZeroReturnCode):
self.invoke("remove A x")
@pytest.mark.parametrize(('initval', 'newval'), [('1', '1'),
('[\"1\"]', '1'),
('[1]', '\"1\"')])
def testRemoveFails(self, initval, newval):
self.invoke("set A %s" % initval)
with pytest.raises(NonZeroReturnCode):
self.invoke("remove A %s" % newval)
@pytest.mark.parametrize('report', ['--report', ''])
def testAppendRemove(self, report, capsys):
self.invoke("append %s A 1" % report)
self.assertReportStdout(report, capsys, 'Appended A:1')
self.invoke("get A")
self.assertStdoutStderr(capsys, out='[1]')
self.invoke("append %s A \"y\"" % report)
self.assertReportStdout(report, capsys, 'Appended A:"y"')
self.invoke("get A")
self.assertStdoutStderr(capsys, out='[1, "y"]')
self.invoke("remove %s A \"y\"" % report)
self.assertReportStdout(report, capsys, 'Removed A:"y"')
self.invoke("get A")
self.assertStdoutStderr(capsys, out='[1]')
self.invoke("remove %s A 1" % report)
self.assertReportStdout(report, capsys, 'Removed A:1')
self.invoke("get A")
self.assertStdoutStderr(capsys, out='[]')
def assertReportStdout(self, report, capsys, out):
if report and out:
self.assertStdoutStderr(capsys, out='Changed: %s' % out)
else:
self.assertStdoutStderr(capsys, out='')
@pytest.mark.parametrize('report', ['--report', ''])
def testAppendSet(self, report, capsys):
self.invoke("append %s --set A 1" % report)
self.assertReportStdout(report, capsys, 'Appended A:1')
self.invoke("get A")
self.assertStdoutStderr(capsys, out='[1]')
self.invoke("append %s --set A 2" % report)
self.assertReportStdout(report, capsys, 'Appended A:2')
self.invoke("get A")
self.assertStdoutStderr(capsys, out='[1, 2]')
self.invoke("append %s --set A 1" % report)
self.assertReportStdout(report, capsys, '')
self.invoke("get A")
self.assertStdoutStderr(capsys, out='[1, 2]')
self.invoke("append %s A 1" % report)
self.assertReportStdout(report, capsys, 'Appended A:1')
self.invoke("get A")
self.assertStdoutStderr(capsys, out='[1, 2, 1]')
def testRemoveIdenticalValues(self, capsys):
self.invoke("set A [1,1]")
self.invoke("remove A 1")
self.invoke("get A")
self.assertStdoutStderr(capsys, out='[1]')
self.invoke("remove A 1")
self.invoke("get A")
self.assertStdoutStderr(capsys, out='[]')
@pytest.mark.xfail
@pytest.mark.broken(reason="migrate to omero-web")
@pytest.mark.usefixtures('configxml')
def testAppendWithDefault(self, monkeypatch, capsys):
import json
monkeypatch.setattr(
"omeroweb.settings.CUSTOM_SETTINGS_MAPPINGS", {
"omero.web.test": ["TEST", "[1,2,3]", json.loads],
"omero.web.notalist": ["NOTALIST", "abc", str],
})
self.invoke("append omero.web.test 4")
self.invoke("get omero.web.test")
self.assertStdoutStderr(capsys, out='[1, 2, 3, 4]')
self.invoke("append --set omero.web.test 2")
self.assertStdoutStderr(capsys, out='')
self.invoke("get omero.web.test")
self.assertStdoutStderr(capsys, out='[1, 2, 3, 4]')
self.invoke("append omero.web.unknown 1")
self.invoke("get omero.web.unknown")
self.assertStdoutStderr(capsys, out='[1]')
with pytest.raises(NonZeroReturnCode):
self.invoke("append omero.web.notalist 1")
@pytest.mark.xfail
@pytest.mark.broken(reason="migrate to omero-web")
@pytest.mark.usefixtures('configxml')
def testRemoveWithDefault(self, monkeypatch, capsys):
import json
monkeypatch.setattr("omeroweb.settings.CUSTOM_SETTINGS_MAPPINGS", {
"omero.web.test": ["TEST", "[1,2,3]", json.loads],
})
self.invoke("remove omero.web.test 2")
self.invoke("get omero.web.test")
self.assertStdoutStderr(capsys, out='[1, 3]')
self.invoke("remove omero.web.test 1")
self.invoke("remove omero.web.test 3")
self.invoke("get omero.web.test")
self.assertStdoutStderr(capsys, out='[]')
@pytest.mark.parametrize("data", (
({}, ""),
({
"a": "b"
}, "a=b"),
({
"a": "b",
"a": "d"
}, "a=d"),
({
"a": "b",
"c": "d"
}, "a=b\nc=d"),
({
"c": "d",
"a": "b"
}, "a=b\nc=d"),
))
@pytest.mark.usefixtures('configxml')
def testList(self, data, monkeypatch, capsys):
for k, v in list(data[0].items()):
self.invoke("set %s %s" % (k, v))
self.invoke("list")
self.assertStdoutStderr(capsys, out=data[1], strip_warning=True)
@pytest.mark.xfail
@pytest.mark.broken(reason="needs whitespace fixing")
@pytest.mark.parametrize("data", (
("omero.a=b\nomero.c=d\n##ignore=me\n", "omero.a=b\nomero.c=d",
"a (1)\n\t\nc (1)"),
("omero.whitelist=\\\nome.foo,\\\nome.bar\n### END",
"omero.whitelist=ome.foo,ome.bar", "whitelist (1)"),
("omero.whitelist=\\\nome.foo,\\\nome.bar\n",
"omero.whitelist=ome.foo,ome.bar", "whitelist (1)"),
("omero.whitelist=\\\nome.foo,\\\nome.bar",
"omero.whitelist=ome.foo,ome.bar", "whitelist (1)"),
("omero.user_mapping=\\\na=b,c=d", "omero.user_mapping=a=b,c=d",
"user_mapping (1)"),
("omero.whitelist=ome.foo\nIce.c=d\n",
"Ice.c=d\nomero.whitelist=ome.foo", "whitelist (1)"),
("omero.a=b\nomero.c=d\nomero.e=f\n##ignore=me\n",
"omero.a=b\nomero.c=d\nomero.e=f", "a (1)\n\t\nc (1)\n\t\ne (1)"),
("omero.a=b\nomero.c=d\nomero.e=f\n##ignore=me\n",
"omero.a=b\nomero.c=d\nomero.e=f", "a (1)\n\t\nc (1)\n\t\ne (1)"),
))
def testFileParsing(self, tmpdir, capsys, data):
input, defaults, keys = data
cfg = tmpdir.join("test.cfg")
cfg.write(input)
self.invoke("parse --file=%s --no-web" % cfg)
self.assertStdoutStderr(capsys, out=defaults)
self.invoke("parse --file=%s --defaults --no-web" % cfg)
self.assertStdoutStderr(capsys, out=defaults)
self.invoke("parse --file=%s --keys --no-web" % cfg)
self.assertStdoutStderr(capsys, out=keys)
@pytest.mark.parametrize("data", (
(u"omero.ldap.base=ou=ascii\n", "ascii2"),
(u"omero.ldap.base=ou=ascii\n", "unicodé"),
(u"omero.ldap.base=ou=unicodé\n", "ascii"),
(u"omero.ldap.base=ou=unicodé\n", "unicodé2"),
))
def testUnicode(self, tmpdir, capsys, data):
input, update = data
cfg = tmpdir.join("test.cfg")
cfg.write(input.encode("utf-8"), "wb")
self.invoke("load %s" % cfg) # 3 fail here
self.invoke("get omero.ldap.base")
self.invoke("set omero.ldap.base %s" % update) # 1 here
self.invoke("get omero.ldap.base")
@pytest.mark.xfail
def testConfigPropertyParser(self, tmpdir):
cfg = tmpdir.join("test.properties")
s = "a=1\nb.c=a b <!> c\nd.e=line1\\\nline2\nf.g=\\n\n"
cfg.write(s)
pp = PropertyParser()
props = pp.parse_file(str(cfg))
# Fails, the last two properties are parsed as one:
# 'd.e' = 'line1line2f.g=\\n'
assert len(props) == 4
assert props[0].key == 'a'
assert props[0].val == '1'
assert props[1].key == 'b.c'
assert props[1].val == 'a b <!> c'
assert props[2].key == 'd.e'
assert props[2].val == 'line1line2'
assert props[3].key == 'f.g'
assert props[3].val == '\\n'
rv = dict()
for k, v in values.items():
if k.startswith("_"):
rv[k[1:]] = v
else:
rv[k] = v
return rv
def project(self, querySvc, queryStr, params, ice_map):
import omero
try:
rv = querySvc.projection(queryStr, params, ice_map)
self.ctx.set("last.hql.rv", rv)
return rv
except omero.SecurityViolation, sv:
if "omero.group" in ice_map:
self.ctx.die(53, "SecurityViolation: Current user is not an admin and cannot use '--admin'")
else:
self.ctx.die(54, "SecurityViolation: %s" % sv)
except omero.QueryException, qe:
self.ctx.set("last.hql.rv", [])
self.ctx.die(52, "Bad query: %s" % qe.message)
try:
register("hql", HqlControl, HELP)
except NameError:
if __name__ == "__main__":
cli = CLI()
cli.register("hql", HqlControl, HELP)
cli.invoke(sys.argv[1:])
idx = server.rindex("@")
return server[idx+1:], server[0:idx] # server, user which may also contain an @
except ValueError:
return server, None
def _get_server(self, store):
defserver = store.last_host()
rv = self.ctx.input("Server: [%s]" % defserver)
if not rv:
return defserver, None
else:
return self._parse_conn(rv)
def _get_username(self, defuser):
if defuser is None:
defuser = get_user("root")
rv = self.ctx.input("Username: [%s]" % defuser)
if not rv:
return defuser
else:
return rv
try:
register("sessions", SessionsControl, HELP)
except NameError:
if __name__ == "__main__":
cli = CLI()
cli.register("sessions", SessionsControl, HELP)
cli.invoke(sys.argv[1:])
class TestRewrite(object):
"""Test template files regeneration"""
@pytest.fixture(autouse=True)
def setup_method(self, tmpadmindir):
self.cli = CLI()
self.cli.dir = path(tmpadmindir)
self.cli.register("admin", AdminControl, "TEST")
self.cli.register("config", PrefsControl, "TEST")
self.args = ["admin", "rewrite"]
def testTemplatesGeneration(self):
"""Test template files are generated by the rewrite subcommand"""
# Test non-existence of configuration files
for f in GRID_FILES:
assert not os.path.exists(path(self.cli.dir) / "etc" / "grid" / f)
for f in ETC_FILES:
assert not os.path.exists(path(self.cli.dir) / "etc" / f)
# Call the jvmcf command and test file genearation
self.cli.invoke(self.args, strict=True)
for f in GRID_FILES:
assert os.path.exists(path(self.cli.dir) / "etc" / "grid" / f)
for f in ETC_FILES:
assert os.path.exists(path(self.cli.dir) / "etc" / f)
def testForceRewrite(self, monkeypatch):
"""Test template regeneration while the server is running"""
# Call the jvmcfg command and test file generation
self.cli.invoke(self.args, strict=True)
monkeypatch.setattr(AdminControl, "status", lambda *args, **kwargs: 0)
with pytest.raises(NonZeroReturnCode):
self.cli.invoke(self.args, strict=True)
def testOldTemplates(self):
old_templates = path(__file__).dirname() / ".." / "old_templates.xml"
old_templates.copy(
path(self.cli.dir) / "etc" / "templates" / "grid" /
"templates.xml")
with pytest.raises(NonZeroReturnCode):
self.cli.invoke(self.args, strict=True)
@pytest.mark.parametrize('prefix', [None, 1])
@pytest.mark.parametrize('registry', [None, 111])
@pytest.mark.parametrize('tcp', [None, 222])
@pytest.mark.parametrize('ssl', [None, 333])
def testExplicitPorts(self, registry, ssl, tcp, prefix, monkeypatch):
"""
Test the omero.ports.xxx configuration properties during the generation
of the configuration files
"""
# Skip the JVM settings calculation for this test
monkeypatch.setattr(omero.install.jvmcfg, "adjust_settings",
lambda x, y: {})
kwargs = {}
if prefix:
kwargs["prefix"] = prefix
if registry:
kwargs["registry"] = registry
if tcp:
kwargs["tcp"] = tcp
if ssl:
kwargs["ssl"] = ssl
for (k, v) in kwargs.iteritems():
self.cli.invoke(
["config", "set", "omero.ports.%s" % k, "%s" % v],
strict=True)
self.cli.invoke(self.args, strict=True)
check_ice_config(self.cli.dir, **kwargs)
check_registry(self.cli.dir, **kwargs)
check_default_xml(self.cli.dir, **kwargs)
rv.append("")
rv.append("id=%s" % s.id.val)
rv.append("")
rv.append("")
rv.append("")
rv.append("insufficient privileges")
else:
rv.append(s.node.id)
rv.append(s.uuid)
rv.append(s.started)
rv.append(s.owner.omeName)
if s.userAgent is None:
rv.append("")
else:
rv.append(s.userAgent)
if client.getSessionId() == s.uuid.val:
rv.append("current session")
else:
rv.append("")
self.ctx.controls["hql"].display(
mapped, ("node", "session", "started", "owner", "agent", "notes"))
try:
register("admin", AdminControl, HELP)
except NameError:
if __name__ == "__main__":
cli = CLI()
cli.register("admin", AdminControl, HELP)
cli.invoke(sys.argv[1:])
return
remove = False
offset = 0
while True:
rv = e.read(offset, DEFAULT_READ_LENGTH)
if not rv:
break
rv = rv[:min(DEFAULT_READ_LENGTH, l - offset)]
offset += len(rv)
handle.write(rv)
finally:
try:
if not issysout:
handle.close()
if remove:
os.remove(handle.name)
except Exception, e:
self.ctx.err("Failed to close handle: %s" % e)
e.close()
try:
register("export", ExportControl, HELP)
except NameError:
if __name__ == "__main__":
cli = CLI()
cli.register("export", ExportControl, HELP)
cli.invoke(sys.argv[1:])