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)
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)
def testNoArgumentsDies(self):
cli = CLI()
cli.register("import", ImportControl, "HELP")
try:
cli.invoke([])
self.assert_(cli.rv != 0)
except NonZeroReturnCode, nzrc:
pass
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 as_stdout(path, readers=""):
path = _to_list(path)
readers = str(readers)
cli = CLI()
cli.loadplugins()
if readers:
cli.invoke(["import", "-l", readers, "-f"]+path)
else:
cli.invoke(["import", "-f"]+path)
if cli.rv != 0:
raise omero.InternalException(None, None, "'import -f' exited with a rc=%s. See console for more information" % cli.rv)
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)
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 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 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)
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)
def hrm_to_omero(conn, id_str, image_file):
"""Upload an image into a specific dataset in OMERO.
In case we know from the suffix that a given file format is not supported
by OMERO, the upload will not be initiated at all (e.g. for SVI-HDF5,
having the suffix '.h5').
The import itself is done by instantiating the CLI class, assembling the
required arguments, and finally running cli.invoke(). This eventually
triggers the importer() method defined in OMERO's Python bindings in
<OMERO.server/lib/python/omero/plugins/import.py>, respectively (source)
<openmicroscopy.git/components/tools/OmeroPy/src/omero/plugins/import.py>.
Parameters
==========
id_str: str - the ID of the target dataset in OMERO (e.g. "G:7:Dataset:23")
image_file: str - the local image file including the full path
Returns
=======
True in case of success, False otherwise.
"""
if image_file.lower().endswith(('.h5', '.hdf5')):
print 'ERROR: HDF5 files are not supported by OMERO!'
return False
# TODO I: group switching required!!
_, gid, obj_type, dset_id = id_str.split(':')
# we have to create the annotations *before* we actually upload the image
# data itself and link them to the image during the upload - the other way
# round is not possible right now as the CLI wrapper (see below) doesn't
# expose the ID of the newly created object in OMERO (confirmed by J-M and
# Sebastien on the 2015 OME Meeting):
namespace = 'deconvolved.hrm'
#### mime = 'text/plain'
# extract the image basename without suffix:
# TODO: is it [0-9a-f] or really [0-9a-z] as in the original PHP code?
basename = re.sub(r'(_[0-9a-f]{13}_hrm)\..*', r'\1', image_file)
comment = gen_parameter_summary(basename + '.parameters.txt')
#### annotations = []
#### # TODO: the list of suffixes should not be hardcoded here!
#### for suffix in ['.hgsb', '.log.txt', '.parameters.txt']:
#### if not os.path.exists(basename + suffix):
#### continue
#### ann = conn.createFileAnnfromLocalFile(
#### basename + suffix, mimetype=mime, ns=namespace, desc=None)
#### annotations.append(ann.getId())
# currently there is no direct "Python way" to import data into OMERO, so
# we have to use the CLI wrapper for this:
from omero.cli import CLI
cli = CLI()
cli.loadplugins()
# NOTE: cli._client should be replaced with cli.set_client() when switching
# to support for OMERO 5.1 and later only:
cli._client = conn.c
import_args = ["import"]
import_args.extend(['-d', dset_id])
if comment is not None:
import_args.extend(['--annotation_ns', namespace])
import_args.extend(['--annotation_text', comment])
#### for ann_id in annotations:
#### import_args.extend(['--annotation_link', str(ann_id)])
import_args.append(image_file)
# print("import_args: " + str(import_args))
try:
cli.invoke(import_args, strict=True)
except:
print('ERROR: uploading "%s" to %s failed!' % (image_file, id_str))
# print(import_args)
return False
return True
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
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):
T = "testDefaultEnvironment"
old = os.environ.get("OMERO_CONFIG", None)
os.environ["OMERO_CONFIG"] = T
try:
self.invoke("def")
self.assertStdoutStderr(capsys, out=T)
finally:
if old:
os.environ["OMERO_CONFIG"] = old
else:
del os.environ["OMERO_CONFIG"]
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 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 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 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):
config = self.config()
config.default("default")
config.close()
os.environ["OMERO_CONFIG"] = "testNewEnvironment"
self.invoke("set A B")
self.assertStdoutStderr(capsys)
self.invoke("get")
self.assertStdoutStderr(capsys, out="A=B")
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
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):
T = "testDefaultEnvironment"
old = os.environ.get("OMERO_CONFIG", None)
os.environ["OMERO_CONFIG"] = T
try:
self.invoke("def")
self.assertStdoutStderr(capsys, out=T)
finally:
if old:
os.environ["OMERO_CONFIG"] = old
else:
del os.environ["OMERO_CONFIG"]
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 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 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 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):
config = self.config()
config.default("default")
config.close()
os.environ["OMERO_CONFIG"] = "testNewEnvironment"
self.invoke("set A B")
self.assertStdoutStderr(capsys)
self.invoke("get")
self.assertStdoutStderr(capsys, out="A=B")
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.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.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 data[0].items():
self.invoke("set %s %s" % (k, v))
self.invoke("list")
self.assertStdoutStderr(capsys, out=data[1], strip_warning=True)
@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)
self.invoke("get omero.ldap.base")
self.invoke("set omero.ldap.base %s" % update)
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'
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)
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)
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 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 hrm_to_omero(conn, id_str, image_file):
"""Upload an image into a specific dataset in OMERO.
In case we know from the suffix that a given file format is not supported
by OMERO, the upload will not be initiated at all (e.g. for SVI-HDF5,
having the suffix '.h5').
The import itself is done by instantiating the CLI class, assembling the
required arguments, and finally running cli.invoke(). This eventually
triggers the importer() method defined in OMERO's Python bindings in
<OMERO.server/lib/python/omero/plugins/import.py>, respectively (source)
<openmicroscopy.git/components/tools/OmeroPy/src/omero/plugins/import.py>.
Parameters
==========
id_str: str - the ID of the target dataset in OMERO (e.g. "G:7:Dataset:23")
image_file: str - the local image file including the full path
Returns
=======
True in case of success, False otherwise.
"""
if image_file.lower().endswith(('.h5', '.hdf5')):
print 'ERROR: HDF5 files are not supported by OMERO!'
return False
# TODO I: group switching required!!
_, gid, obj_type, dset_id = id_str.split(':')
# we have to create the annotations *before* we actually upload the image
# data itself and link them to the image during the upload - the other way
# round is not possible right now as the CLI wrapper (see below) doesn't
# expose the ID of the newly created object in OMERO (confirmed by J-M and
# Sebastien on the 2015 OME Meeting):
namespace = 'deconvolved.hrm'
#### mime = 'text/plain'
# extract the image basename without suffix:
# TODO: is it [0-9a-f] or really [0-9a-z] as in the original PHP code?
basename = re.sub(r'(_[0-9a-f]{13}_hrm)\..*', r'\1', image_file)
comment = gen_parameter_summary(basename + '.parameters.txt')
#### annotations = []
#### # TODO: the list of suffixes should not be hardcoded here!
#### for suffix in ['.hgsb', '.log.txt', '.parameters.txt']:
#### if not os.path.exists(basename + suffix):
#### continue
#### ann = conn.createFileAnnfromLocalFile(
#### basename + suffix, mimetype=mime, ns=namespace, desc=None)
#### annotations.append(ann.getId())
# currently there is no direct "Python way" to import data into OMERO, so
# we have to use the CLI wrapper for this:
from omero.cli import CLI
cli = CLI()
cli.loadplugins()
# NOTE: cli._client should be replaced with cli.set_client() when switching
# to support for OMERO 5.1 and later only:
cli._client = conn.c
import_args = ["import"]
import_args.extend(['-d', dset_id])
if comment is not None:
import_args.extend(['--annotation_ns', namespace])
import_args.extend(['--annotation_text', comment])
#### for ann_id in annotations:
#### import_args.extend(['--annotation_link', str(ann_id)])
import_args.append(image_file)
# print("import_args: " + str(import_args))
try:
cli.invoke(import_args, strict=True)
except:
print('ERROR: uploading "%s" to %s failed!' % (image_file, id_str))
# print(import_args)
return False
return True
def invoke(self, *args):
CLI.invoke(self, *args, strict = True)
def testOne(self):
cli = CLI()
cli.register("t", TestRCode.T, "TEST")
cli.invoke(["t"])
self.assert_(cli.rv == 1, cli.rv)
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)
class TestImport(object):
def setup_method(self, method):
self.cli = CLI()
self.cli.register("import", ImportControl, "TEST")
self.args = ["import"]
def add_client_dir(self):
dist_dir = path(__file__) / ".." / ".." / ".." / ".." / ".." / ".." /\
".." / "dist" # FIXME: should not be hard-coded
dist_dir = dist_dir.abspath()
client_dir = dist_dir / "lib" / "client"
logback = dist_dir / "etc" / "logback-cli.xml"
self.args += ["--clientdir", client_dir]
self.args += ["--logback", logback]
def mkdir(self, parent, name, with_ds_store=False):
child = parent / name
child.mkdir()
if with_ds_store:
ds_store = child / ".DS_STORE"
ds_store.write("")
return child
def mkfakescreen(self,
screen_dir,
nplates=2,
nruns=2,
nwells=2,
nfields=4,
with_ds_store=False):
fieldfiles = []
for iplate in range(nplates):
plate_dir = self.mkdir(screen_dir,
"Plate00%s" % str(iplate),
with_ds_store=with_ds_store)
for irun in range(nruns):
run_dir = self.mkdir(plate_dir,
"Run00%s" % str(irun),
with_ds_store=with_ds_store)
for iwell in range(nwells):
well_dir = self.mkdir(run_dir,
"WellA00%s" % str(iwell),
with_ds_store=with_ds_store)
for ifield in range(nfields):
fieldfile = (well_dir /
("Field00%s.fake" % str(ifield)))
fieldfile.write('')
fieldfiles.append(fieldfile)
return fieldfiles
def mkfakepattern(self, tmpdir, nangles=7, ntimepoints=10):
spim_dir = tmpdir.join("SPIM")
spim_dir.mkdir()
tiffiles = []
for angle in range(1, nangles + 1):
for timepoint in range(1, ntimepoints + 1):
tiffile = (spim_dir / ("spim_TL%s_Angle%s.fake" %
(str(timepoint), str(angle))))
tiffile.write('')
print str(tiffile)
tiffiles.append(tiffile)
patternfile = spim_dir / "spim.pattern"
patternfile.write("spim_TL<1-%s>_Angle<1-%s>.fake" %
(str(ntimepoints), str(nangles)))
assert len(tiffiles) == nangles * ntimepoints
return patternfile, tiffiles
def testDropBoxArgs(self):
class MockImportControl(ImportControl):
def importer(this, args):
assert args.server == "localhost"
assert args.port == "4064"
assert args.key == "b0742975-03a1-4f6d-b0ac-639943f1a147"
assert args.errs == "/tmp/dropbox.err"
assert args.file == "/tmp/dropbox.out"
self.cli.register("mock-import", MockImportControl, "HELP")
self.args = [
'-s', 'localhost', '-p', '4064', '-k',
'b0742975-03a1-4f6d-b0ac-639943f1a147'
]
self.args += ['mock-import', '---errs=/tmp/dropbox.err']
self.args += ['---file=/tmp/dropbox.out']
self.args += ['--', '/OMERO/DropBox/root/test.fake']
self.cli.invoke(self.args)
@pytest.mark.parametrize('help_argument', help_arguments)
def testHelp(self, help_argument):
"""Test help arguments"""
self.args += [help_argument]
self.cli.invoke(self.args)
@pytest.mark.parametrize('clientdir_exists', [True, False])
def testImportNoClientDirFails(self, tmpdir, clientdir_exists):
"""Test fake screen import"""
fakefile = tmpdir.join("test.fake")
fakefile.write('')
if clientdir_exists:
self.args += ["--clientdir", str(tmpdir)]
self.args += [str(fakefile)]
with pytest.raises(NonZeroReturnCode):
self.cli.invoke(self.args, strict=True)
@pytest.mark.parametrize("data", (("1", False), ("3", True)))
def testImportDepth(self, tmpdir, capfd, data):
"""Test import using depth argument"""
dir1 = tmpdir.join("a")
dir1.mkdir()
dir2 = dir1 / "b"
dir2.mkdir()
fakefile = dir2 / "test.fake"
fakefile.write('')
self.add_client_dir()
self.args += ["-f", "--debug=ERROR"]
self.args += [str(dir1)]
def f():
self.cli.invoke(self.args + ["--depth=%s" % depth], strict=True)
depth, result = data
if result:
f()
o, e = capfd.readouterr()
assert str(fakefile) in str(o)
else:
# Now a failure condition
with pytest.raises(NonZeroReturnCode):
f()
def testImportFakeImage(self, tmpdir, capfd):
"""Test fake image import"""
fakefile = tmpdir.join("test.fake")
fakefile.write('')
self.add_client_dir()
self.args += ["-f", "--debug=ERROR"]
self.args += [str(fakefile)]
self.cli.invoke(self.args, strict=True)
o, e = capfd.readouterr()
outputlines = str(o).split('\n')
reader = 'loci.formats.in.FakeReader'
assert outputlines[-2] == str(fakefile)
assert outputlines[-3] == \
"# Group: %s SPW: false Reader: %s" % (str(fakefile), reader)
@pytest.mark.parametrize('params', (
("-l", "only_fakes.txt", True),
("-l", "no_fakes.txt", False),
("--readers", "only_fakes.txt", True),
("--readers", "no_fakes.txt", False),
))
def testImportReaders(self, tmpdir, capfd, params):
"""Test fake image import"""
fakefile = tmpdir.join("test.fake")
fakefile.write('')
flag, filename, status = params
filename = path(__file__).parent / "readers" / filename
self.add_client_dir()
self.args += ["-f", flag, filename]
self.args += [str(fakefile)]
if status:
self.cli.invoke(self.args, strict=True)
o, e = capfd.readouterr()
outputlines = str(o).split('\n')
reader = 'loci.formats.in.FakeReader'
assert outputlines[-2] == str(fakefile)
assert outputlines[-3] == \
"# Group: %s SPW: false Reader: %s" % (str(fakefile), reader)
else:
with pytest.raises(NonZeroReturnCode):
self.cli.invoke(self.args, strict=True)
o, e = capfd.readouterr()
assert "parsed into 0 group" in e
@pytest.mark.parametrize('with_ds_store', (True, False))
def testImportFakeScreen(self, tmpdir, capfd, with_ds_store):
"""Test fake screen import"""
screen_dir = tmpdir.join("screen.fake")
screen_dir.mkdir()
fieldfiles = self.mkfakescreen(screen_dir, with_ds_store=with_ds_store)
self.add_client_dir()
self.args += ["-f", "--debug=ERROR"]
self.args += [str(fieldfiles[0])]
self.cli.invoke(self.args, strict=True)
o, e = capfd.readouterr()
outputlines = str(o).split('\n')
reader = 'loci.formats.in.FakeReader'
assert outputlines[-len(fieldfiles)-2] == \
"# Group: %s SPW: true Reader: %s" % (str(fieldfiles[0]), reader)
for i in range(len(fieldfiles)):
assert outputlines[-1 - len(fieldfiles) + i] == str(fieldfiles[i])
def testImportPattern(self, tmpdir, capfd):
"""Test pattern import"""
patternfile, tiffiles = self.mkfakepattern(tmpdir)
self.add_client_dir()
self.args += ["-f", "--debug=ERROR"]
self.args += [str(patternfile)]
self.cli.invoke(self.args, strict=True)
o, e = capfd.readouterr()
outputlines = str(o).split('\n')
reader = 'loci.formats.in.FilePatternReader'
print o
assert outputlines[-len(tiffiles)-3] == \
"# Group: %s SPW: false Reader: %s" % (str(patternfile), reader)
assert outputlines[-len(tiffiles) - 2] == str(patternfile)
for i in range(len(tiffiles)):
assert outputlines[-1 - len(tiffiles) + i] == str(tiffiles[i])
@pytest.mark.parametrize('hostname', ['localhost', 'servername'])
@pytest.mark.parametrize('port', [None, 4064, 14064])
def testLoginArguments(self, monkeypatch, hostname, port, tmpdir):
self.args += ['test.fake']
sessionid = str(uuid.uuid4())
def new_client(x):
if port:
c = MockClient(hostname, port)
else:
c = MockClient(hostname)
c.setSessionId(sessionid)
return c
monkeypatch.setattr(self.cli, 'conn', new_client)
ice_config = tmpdir / 'ice.config'
ice_config.write('omero.host=%s\nomero.port=%g' % (hostname,
(port or 4064)))
monkeypatch.setenv("ICE_CONFIG", ice_config)
args = self.cli.parser.parse_args(self.args)
command_args = CommandArguments(self.cli, args)
expected_args = ['-s', '%s' % hostname]
expected_args += ['-p', '%s' % (port or 4064)]
expected_args += ['-k', '%s' % sessionid]
expected_args += ['test.fake']
assert command_args.java_args() == expected_args
def testLogPrefix(self, tmpdir, capfd):
fakefile = tmpdir.join("test.fake")
fakefile.write('')
prefix = tmpdir.join("log")
self.add_client_dir()
self.args += [
"-f",
"---logprefix=%s" % prefix, "---file=out", "---errs=errs"
]
self.args += [str(fakefile)]
self.cli.invoke(self.args, strict=True)
o, e = capfd.readouterr()
assert o == ""
assert e == ""
outlines = prefix.join("out").read().split("\n")
reader = 'loci.formats.in.FakeReader'
assert outlines[-2] == str(fakefile)
assert outlines[-3] == \
"# Group: %s SPW: false Reader: %s" % (str(fakefile), reader)
def testYamlOutput(self, tmpdir, capfd):
import yaml
from StringIO import StringIO
fakefile = tmpdir.join("test.fake")
fakefile.write('')
self.add_client_dir()
self.args += ["-f", "--output=yaml", str(fakefile)]
self.cli.invoke(self.args, strict=True)
o, e = capfd.readouterr()
result = yaml.load(StringIO(o))
result = result[0]
assert "fake" in result["group"]
assert 1 == len(result["files"])
assert "reader" in result
assert "spw" in result
def testBulkNoPaths(self):
t = path(__file__) / "bulk_import" / "test_simple"
b = t / "bulk.yml"
self.add_client_dir()
self.args += ["-f", "---bulk=%s" % b, "dne.fake"]
with pytest.raises(NonZeroReturnCode):
self.cli.invoke(self.args, strict=True)
def testBulkSimple(self):
t = path(__file__).parent / "bulk_import" / "test_simple"
b = t / "bulk.yml"
self.add_client_dir()
self.args += ["-f", "---bulk=%s" % b]
self.cli.invoke(self.args, strict=True)
def testBulkInclude(self):
t = path(__file__).parent / "bulk_import" / "test_include" / "inner"
b = t / "bulk.yml"
self.add_client_dir()
self.args += ["-f", "---bulk=%s" % b]
self.cli.invoke(self.args, strict=True)
def testBulkName(self):
# Metadata provided in the yml file will be applied
# to the args
t = path(__file__).parent / "bulk_import" / "test_name"
b = t / "bulk.yml"
class MockImportControl(ImportControl):
def do_import(self, command_args, xargs):
assert "--name=testname" in command_args.java_args()
self.cli.register("mock-import", MockImportControl, "HELP")
self.args = ["mock-import", "-f", "---bulk=%s" % b]
self.add_client_dir()
self.cli.invoke(self.args, strict=True)
def testBulkCols(self):
# Metadata provided about the individual columns in
# the tsv will be used.
t = path(__file__).parent / "bulk_import" / "test_cols"
b = t / "bulk.yml"
class MockImportControl(ImportControl):
def do_import(self, command_args, xargs):
cmd = command_args.java_args()
assert "--name=meta_one" in cmd or \
"--name=meta_two" in cmd
self.cli.register("mock-import", MockImportControl, "HELP")
self.args = ["mock-import", "-f", "---bulk=%s" % b]
self.add_client_dir()
self.cli.invoke(self.args, strict=True)
def testBulkBad(self):
t = path(__file__).parent / "bulk_import" / "test_bad"
b = t / "bulk.yml"
self.add_client_dir()
self.args += ["-f", "---bulk=%s" % b]
with pytest.raises(NonZeroReturnCode):
self.cli.invoke(self.args, strict=True)
def testBulkDry(self, capfd):
t = path(__file__).parent / "bulk_import" / "test_dryrun"
b = t / "bulk.yml"
self.add_client_dir()
self.args += ["-f", "---bulk=%s" % b]
self.cli.invoke(self.args, strict=True)
o, e = capfd.readouterr()
assert o == '"--name=no-op" "1.fake"\n'
def testBulkJavaArgs(self):
"""Test Java arguments"""
t = path(__file__).parent / "bulk_import" / "test_javaargs"
b = t / "bulk.yml"
class MockImportControl(ImportControl):
def do_import(self, command_args, xargs):
assert ("--checksum-algorithm=File-Size-64"
in command_args.java_args())
assert "--parallel-upload=10" in command_args.java_args()
assert "--parallel-fileset=5" in command_args.java_args()
assert "--transfer=ln_s" in command_args.java_args()
assert "--exclude=clientpath" in command_args.java_args()
self.cli.register("mock-import", MockImportControl, "HELP")
self.args = ["mock-import", "-f", "---bulk=%s" % b]
self.add_client_dir()
self.cli.invoke(self.args, strict=True)
@pytest.mark.parametrize('skip', plugin.SKIP_CHOICES)
def testBulkSkip(self, skip):
"""Test skip arguments"""
t = path(__file__).parent / "bulk_import" / "test_skip"
b = t / "%s.yml" % skip
class MockImportControl(ImportControl):
def do_import(self, command_args, xargs):
if skip in ["all", "checksum"]:
assert ("--checksum-algorithm=File-Size-64"
in command_args.java_args())
if skip in ["all", "minmax"]:
assert ("--no-stats-info" in command_args.java_args())
if skip in ["all", "thumbnails"]:
assert ("--no-thumbnails" in command_args.java_args())
if skip in ["all", "upgrade"]:
assert ("--no-upgrade-check" in command_args.java_args())
self.cli.register("mock-import", MockImportControl, "HELP")
self.args = ["mock-import", "-f", "---bulk=%s" % b]
self.add_client_dir()
self.cli.invoke(self.args, strict=True)
class TestDatabase(object):
def setup_method(self, method):
self.cli = CLI()
self.cli.register("db", DatabaseControl, "TEST")
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 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(
'pos_input', ["", "%(version)s", "%(version)s %(patch)s",
"%(version)s %(patch)s ome"])
def testScript(self, pos_input, no_salt, file_arg):
args = "db script "
args += pos_input
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 "version" not in pos_input or "patch" not in pos_input:
self.expectVersion(self.data["version"])
self.expectPatch(self.data["patch"])
if "ome" not in pos_input:
self.expectPassword("ome")
self.expectConfirmation("ome")
self.mox.ReplayAll()
self.cli.invoke(args % self.data, strict=True)
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)
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 expectVersion(self, version):
raw_input("Please enter omero.db.version [%s]: " %
self.data["version"]).AndReturn(version)
def expectPatch(self, patch):
raw_input("Please enter omero.db.patch [%s]: " %
self.data["patch"]).AndReturn(patch)
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)])
"""
m = RE.match(line)
if m:
return self._complete_file(RE.sub('', line))
else:
return BaseControl._complete(self, text, line, begidx, endidx)
def _configure(self, parser):
parser.add_argument("--pytable", action="store_true", help="If set, the following files are interpreted as pytable files" )
parser.add_argument("file", nargs="+")
parser.set_defaults(func=self.upload)
def upload(self, args):
client = self.ctx.conn(args)
for file in args.file:
is_importer, omero_format = omero.util.originalfileutils.getFormat(file)
if (is_importer == omero.util.originalfileutils.IMPORTER):
self.ctx.dir(493, "This file should be imported using omero import")
else:
obj = client.upload(file, type=omero_format)
self.ctx.out("Uploaded %s as " % file + str(obj.id.val))
self.ctx.set("last.upload.id", obj.id.val)
try:
register("upload", UploadControl, HELP)
except NameError:
if __name__ == "__main__":
cli = CLI()
cli.register("upload", UploadControl, HELP)
cli.invoke(sys.argv[1:])
class TestDatabase(object):
def setup_method(self, method):
self.cli = CLI()
self.cli.register("db", DatabaseControl, "TEST")
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 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('pos_input', [
"", "%(version)s", "%(version)s %(patch)s", "%(version)s %(patch)s ome"
])
def testScript(self, pos_input, no_salt, file_arg):
args = "db script "
args += pos_input
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 "version" not in pos_input or "patch" not in pos_input:
self.expectVersion(self.data["version"])
self.expectPatch(self.data["patch"])
if "ome" not in pos_input:
self.expectPassword("ome")
self.expectConfirmation("ome")
self.mox.ReplayAll()
self.cli.invoke(args % self.data, strict=True)
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)
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 expectVersion(self, version):
raw_input("Please enter omero.db.version [%s]: " %
self.data["version"]).AndReturn(version)
def expectPatch(self, patch):
raw_input("Please enter omero.db.patch [%s]: " %
self.data["patch"]).AndReturn(patch)
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 TestSessions(object):
def setup_method(self, method):
self.cli = CLI()
self.cli.register("sessions", SessionsControl, "TEST")
self.args = ["sessions"]
def testHelp(self):
self.args += ["-h"]
self.cli.invoke(self.args, strict=True)
@pytest.mark.parametrize(
"subcommand", SessionsControl().get_subcommands())
def testSubcommandHelp(self, subcommand):
self.args += [subcommand, "-h"]
self.cli.invoke(self.args, strict=True)
def testDefaultSessionsDir(self):
from omero.util import get_user_dir
from path import path
# Default store sessions dir is under user dir
store = self.cli.controls['sessions'].store(None)
assert store.dir == path(get_user_dir()) / 'omero' / 'sessions'
@pytest.mark.parametrize('environment', (
{'OMERO_USERDIR': None,
'OMERO_SESSION_DIR': None,
'OMERO_SESSIONDIR': None},
{'OMERO_USERDIR': None,
'OMERO_SESSION_DIR': 'session_dir',
'OMERO_SESSIONDIR': None},
{'OMERO_USERDIR': None,
'OMERO_SESSION_DIR': None,
'OMERO_SESSIONDIR': 'sessiondir'},
{'OMERO_USERDIR': 'userdir',
'OMERO_SESSION_DIR': None,
'OMERO_SESSIONDIR': None},
{'OMERO_USERDIR': None,
'OMERO_SESSION_DIR': 'session_dir',
'OMERO_SESSIONDIR': 'sessiondir'},
{'OMERO_USERDIR': 'userdir',
'OMERO_SESSION_DIR': 'session_dir',
'OMERO_SESSIONDIR': None},
{'OMERO_USERDIR': 'userdir',
'OMERO_SESSION_DIR': None,
'OMERO_SESSIONDIR': 'sessiondir'},
{'OMERO_USERDIR': 'userdir',
'OMERO_SESSION_DIR': 'session_dir',
'OMERO_SESSIONDIR': 'sessiondir'}))
@pytest.mark.parametrize('session_args', [None, 'session_dir'])
def testCustomSessionsDir(
self, tmpdir, monkeypatch, environment,
session_args):
from argparse import Namespace
from omero.util import get_user_dir
from path import path
for var in environment.keys():
if environment[var]:
monkeypatch.setenv(var, tmpdir / environment.get(var))
else:
monkeypatch.delenv(var, raising=False)
# args.session_dir sets the sessions dir
args = Namespace()
if session_args:
setattr(args, session_args, tmpdir / session_args)
if environment.get('OMERO_SESSION_DIR') or session_args:
pytest.deprecated_call(self.cli.controls['sessions'].store, args)
store = self.cli.controls['sessions'].store(args)
# By order of precedence
if environment.get('OMERO_SESSIONDIR'):
sdir = path(tmpdir) / environment.get('OMERO_SESSIONDIR')
elif environment.get('OMERO_SESSION_DIR'):
sdir = (path(tmpdir) / environment.get('OMERO_SESSION_DIR') /
'omero' / 'sessions')
elif session_args:
sdir = path(getattr(args, session_args)) / 'omero' / 'sessions'
elif environment.get('OMERO_USERDIR'):
sdir = path(tmpdir) / environment.get('OMERO_USERDIR') / 'sessions'
else:
sdir = path(get_user_dir()) / 'omero' / 'sessions'
assert store.dir == sdir
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='[]')
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 and
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', 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):
self.invoke("set omero.X.pass shortpass")
self.cli.invoke(self.args + ["set", "omero.Y.pass", ""], strict=True)
self.invoke("set omero.Y.password long_password")
self.invoke("set omero.Z val")
self.invoke("get")
self.assertStdoutStderr(capsys, out=(
'omero.X.pass=shortpass\n'
'omero.Y.pass=\n'
'omero.Y.password=long_password\n'
'omero.Z=val'))
self.invoke("get --hide-password")
self.assertStdoutStderr(capsys, out=(
'omero.X.pass=********\n'
'omero.Y.pass=\n'
'omero.Y.password=********\n'
'omero.Z=val'))
@pytest.mark.parametrize('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")
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='[]')
@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 data[0].items():
self.invoke("set %s %s" % (k, v))
self.invoke("list")
self.assertStdoutStderr(capsys, out=data[1])
@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)
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)
def invoke(self, *args):
CLI.invoke(self, *args, strict=True)
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 TestImport(object):
def setup_method(self, method):
self.cli = CLI()
self.cli.register("import", ImportControl, "TEST")
self.args = ["import"]
dist_dir = path(__file__) / ".." / ".." / ".." / ".." / ".." / ".." /\
".." / "dist" # FIXME: should not be hard-coded
dist_dir = dist_dir.abspath()
client_dir = dist_dir / "lib" / "client"
self.args += ["--clientdir", client_dir]
def mkdir(self, parent, name, with_ds_store=False):
child = parent / name
child.mkdir()
if with_ds_store:
ds_store = child / ".DS_STORE"
ds_store.write("")
return child
def mkfakescreen(self, screen_dir, nplates=2, nruns=2, nwells=2,
nfields=4, with_ds_store=False):
fieldfiles = []
for iplate in range(nplates):
plate_dir = self.mkdir(
screen_dir, "Plate00%s" % str(iplate),
with_ds_store=with_ds_store)
for irun in range(nruns):
run_dir = self.mkdir(
plate_dir, "Run00%s" % str(irun),
with_ds_store=with_ds_store)
for iwell in range(nwells):
well_dir = self.mkdir(
run_dir, "WellA00%s" % str(iwell),
with_ds_store=with_ds_store)
for ifield in range(nfields):
fieldfile = (well_dir / ("Field00%s.fake" %
str(ifield)))
fieldfile.write('')
fieldfiles.append(fieldfile)
return fieldfiles
def testDropBoxArgs(self):
class MockImportControl(ImportControl):
def importer(this, args):
assert args.server == "localhost"
assert args.port == "4064"
assert args.key == "b0742975-03a1-4f6d-b0ac-639943f1a147"
assert args.errs == "/Users/cblackburn/omero/tmp/\
omero_cblackburn/6915/dropboxuUGl5rerr"
assert args.file == "/Users/cblackburn/omero/tmp/\
omero_cblackburn/6915/dropboxaDCjQlout"
self.cli.register("mock-import", MockImportControl, "HELP")
self.args = ['-s', 'localhost', '-p', '4064', '-k',
'b0742975-03a1-4f6d-b0ac-639943f1a147']
self.args += ['mock-import', '---errs=/Users/cblackburn/omero/tmp/\
omero_cblackburn/6915/dropboxuUGl5rerr']
self.args += ['---file=/Users/cblackburn/omero/tmp/\
omero_cblackburn/6915/dropboxaDCjQlout']
self.args += ['--', '/OMERO/DropBox/root/tinyTest.d3d.dv']
self.cli.invoke(self.args)
@pytest.mark.parametrize('help_argument', help_arguments)
def testHelp(self, help_argument):
"""Test help arguments"""
self.args += [help_argument]
self.cli.invoke(self.args)
@pytest.mark.parametrize("data", (("1", False), ("3", True)))
def testImportDepth(self, tmpdir, capfd, data):
"""Test import using depth argument"""
dir1 = tmpdir.join("a")
dir1.mkdir()
dir2 = dir1 / "b"
dir2.mkdir()
fakefile = dir2 / "test.fake"
fakefile.write('')
self.args += ["-f", "--debug=ERROR"]
self.args += [str(dir1)]
depth, result = data
self.cli.invoke(self.args + ["--depth=%s" % depth], strict=True)
o, e = capfd.readouterr()
if result:
assert str(fakefile) in str(o)
else:
assert str(fakefile) not in str(o)
def testImportFakeImage(self, tmpdir, capfd):
"""Test fake image import"""
fakefile = tmpdir.join("test.fake")
fakefile.write('')
self.args += ["-f", "--debug=ERROR"]
self.args += [str(fakefile)]
self.cli.invoke(self.args, strict=True)
o, e = capfd.readouterr()
outputlines = str(o).split('\n')
reader = 'loci.formats.in.FakeReader'
assert outputlines[-2] == str(fakefile)
assert outputlines[-3] == \
"# Group: %s SPW: false Reader: %s" % (str(fakefile), reader)
@pytest.mark.parametrize('with_ds_store', (True, False))
def testImportFakeScreen(self, tmpdir, capfd, with_ds_store):
"""Test fake screen import"""
screen_dir = tmpdir.join("screen.fake")
screen_dir.mkdir()
fieldfiles = self.mkfakescreen(
screen_dir, with_ds_store=with_ds_store)
self.args += ["-f", "--debug=ERROR"]
self.args += [str(fieldfiles[0])]
self.cli.invoke(self.args, strict=True)
o, e = capfd.readouterr()
outputlines = str(o).split('\n')
reader = 'loci.formats.in.FakeReader'
assert outputlines[-len(fieldfiles)-2] == \
"# Group: %s SPW: true Reader: %s" % (str(fieldfiles[0]), reader)
for i in range(len(fieldfiles)):
assert outputlines[-1-len(fieldfiles)+i] == str(fieldfiles[i])
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])
@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 kwargs.iteritems():
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)
def testOne(self):
cli = CLI()
cli.register("t", TestRCode.T, "TEST")
cli.invoke(["t"])
assert cli.rv == 1, cli.rv
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 TestImport(object):
def setup_method(self, method):
self.cli = CLI()
self.cli.register("import", ImportControl, "TEST")
self.args = ["import"]
def add_client_dir(self):
dist_dir = path(__file__) / ".." / ".." / ".." / ".." / ".." / ".." /\
".." / "dist" # FIXME: should not be hard-coded
dist_dir = dist_dir.abspath()
client_dir = dist_dir / "lib" / "client"
self.args += ["--clientdir", client_dir]
def mkdir(self, parent, name, with_ds_store=False):
child = parent / name
child.mkdir()
if with_ds_store:
ds_store = child / ".DS_STORE"
ds_store.write("")
return child
def mkfakescreen(self, screen_dir, nplates=2, nruns=2, nwells=2,
nfields=4, with_ds_store=False):
fieldfiles = []
for iplate in range(nplates):
plate_dir = self.mkdir(
screen_dir, "Plate00%s" % str(iplate),
with_ds_store=with_ds_store)
for irun in range(nruns):
run_dir = self.mkdir(
plate_dir, "Run00%s" % str(irun),
with_ds_store=with_ds_store)
for iwell in range(nwells):
well_dir = self.mkdir(
run_dir, "WellA00%s" % str(iwell),
with_ds_store=with_ds_store)
for ifield in range(nfields):
fieldfile = (well_dir / ("Field00%s.fake" %
str(ifield)))
fieldfile.write('')
fieldfiles.append(fieldfile)
return fieldfiles
def mkfakepattern(self, tmpdir, nangles=7, ntimepoints=10):
spim_dir = tmpdir.join("SPIM")
spim_dir.mkdir()
tiffiles = []
for angle in range(1, nangles + 1):
for timepoint in range(1, ntimepoints + 1):
tiffile = (spim_dir / ("spim_TL%s_Angle%s.fake" %
(str(timepoint), str(angle))))
tiffile.write('')
print str(tiffile)
tiffiles.append(tiffile)
patternfile = spim_dir / "spim.pattern"
patternfile.write("spim_TL<1-%s>_Angle<1-%s>.fake"
% (str(ntimepoints), str(nangles)))
assert len(tiffiles) == nangles * ntimepoints
return patternfile, tiffiles
def testDropBoxArgs(self):
class MockImportControl(ImportControl):
def importer(this, args):
assert args.server == "localhost"
assert args.port == "4064"
assert args.key == "b0742975-03a1-4f6d-b0ac-639943f1a147"
assert args.errs == "/tmp/dropbox.err"
assert args.file == "/tmp/dropbox.out"
self.cli.register("mock-import", MockImportControl, "HELP")
self.args = ['-s', 'localhost', '-p', '4064', '-k',
'b0742975-03a1-4f6d-b0ac-639943f1a147']
self.args += ['mock-import', '---errs=/tmp/dropbox.err']
self.args += ['---file=/tmp/dropbox.out']
self.args += ['--', '/OMERO/DropBox/root/tinyTest.d3d.dv']
self.cli.invoke(self.args)
@pytest.mark.parametrize('help_argument', help_arguments)
def testHelp(self, help_argument):
"""Test help arguments"""
self.args += [help_argument]
self.cli.invoke(self.args)
@pytest.mark.parametrize('clientdir_exists', [True, False])
def testImportNoClientDirFails(self, tmpdir, clientdir_exists):
"""Test fake screen import"""
fakefile = tmpdir.join("test.fake")
fakefile.write('')
if clientdir_exists:
self.args += ["--clientdir", str(tmpdir)]
self.args += [str(fakefile)]
with pytest.raises(NonZeroReturnCode):
self.cli.invoke(self.args, strict=True)
@pytest.mark.parametrize("data", (("1", False), ("3", True)))
def testImportDepth(self, tmpdir, capfd, data):
"""Test import using depth argument"""
dir1 = tmpdir.join("a")
dir1.mkdir()
dir2 = dir1 / "b"
dir2.mkdir()
fakefile = dir2 / "test.fake"
fakefile.write('')
self.add_client_dir()
self.args += ["-f", "--debug=ERROR"]
self.args += [str(dir1)]
depth, result = data
self.cli.invoke(self.args + ["--depth=%s" % depth], strict=True)
o, e = capfd.readouterr()
if result:
assert str(fakefile) in str(o)
else:
assert str(fakefile) not in str(o)
def testImportFakeImage(self, tmpdir, capfd):
"""Test fake image import"""
fakefile = tmpdir.join("test.fake")
fakefile.write('')
self.add_client_dir()
self.args += ["-f", "--debug=ERROR"]
self.args += [str(fakefile)]
self.cli.invoke(self.args, strict=True)
o, e = capfd.readouterr()
outputlines = str(o).split('\n')
reader = 'loci.formats.in.FakeReader'
assert outputlines[-2] == str(fakefile)
assert outputlines[-3] == \
"# Group: %s SPW: false Reader: %s" % (str(fakefile), reader)
@pytest.mark.parametrize('with_ds_store', (True, False))
def testImportFakeScreen(self, tmpdir, capfd, with_ds_store):
"""Test fake screen import"""
screen_dir = tmpdir.join("screen.fake")
screen_dir.mkdir()
fieldfiles = self.mkfakescreen(
screen_dir, with_ds_store=with_ds_store)
self.add_client_dir()
self.args += ["-f", "--debug=ERROR"]
self.args += [str(fieldfiles[0])]
self.cli.invoke(self.args, strict=True)
o, e = capfd.readouterr()
outputlines = str(o).split('\n')
reader = 'loci.formats.in.FakeReader'
assert outputlines[-len(fieldfiles)-2] == \
"# Group: %s SPW: true Reader: %s" % (str(fieldfiles[0]), reader)
for i in range(len(fieldfiles)):
assert outputlines[-1-len(fieldfiles)+i] == str(fieldfiles[i])
def testImportPattern(self, tmpdir, capfd):
"""Test pattern import"""
patternfile, tiffiles = self.mkfakepattern(tmpdir)
self.add_client_dir()
self.args += ["-f", "--debug=ERROR"]
self.args += [str(patternfile)]
self.cli.invoke(self.args, strict=True)
o, e = capfd.readouterr()
outputlines = str(o).split('\n')
reader = 'loci.formats.in.FilePatternReader'
print o
assert outputlines[-len(tiffiles)-3] == \
"# Group: %s SPW: false Reader: %s" % (str(patternfile), reader)
assert outputlines[-len(tiffiles)-2] == str(patternfile)
for i in range(len(tiffiles)):
assert outputlines[-1-len(tiffiles)+i] == str(tiffiles[i])
@pytest.mark.parametrize('hostname', ['localhost', 'servername'])
@pytest.mark.parametrize('port', [None, 4064, 14064])
def testLoginArguments(self, monkeypatch, hostname, port):
self.args += ['test.fake']
control = self.cli.controls['import']
control.command_args = []
sessionid = str(uuid.uuid4())
def new_client(x):
if port:
c = MockClient(hostname, port)
else:
c = MockClient(hostname)
c.setSessionId(sessionid)
return c
monkeypatch.setattr(self.cli, 'conn', new_client)
control.set_login_arguments(self.cli.parser.parse_args(self.args))
expected_args = ['-s', '%s' % hostname]
expected_args += ['-p', '%s' % (port or 4064)]
expected_args += ['-k', '%s' % sessionid]
assert control.command_args == expected_args