def testWithEnvThenWithoutEnv(self):
"""
This test shows that if you create the config using an env
setting, then without, the __ACTIVE__ block should reflect
"default" and not the intermediate "env" setting.
"""
def get_profile_name(p):
"""
Takes a path object to the config xml
"""
xml = XML(p.text())
props = xml.findall("./properties")
for x in props:
id = x.attrib["id"]
if id == "__ACTIVE__":
for y in x.getchildren():
if y.attrib["name"] == "omero.config.profile":
return y.attrib["value"]
p = create_path()
current = os.environ.get("OMERO_CONFIG", "default")
assert current != "FOO" # Just in case.
config = ConfigXml(filename=str(p))
config.close()
assert current == get_profile_name(p)
config = ConfigXml(filename=str(p), env_config="FOO")
config.close()
assert "FOO" == get_profile_name(p)
# Still foo
config = ConfigXml(filename=str(p))
config.close()
assert "FOO" == get_profile_name(p)
# Re-setting with os.environ won't work
try:
old = os.environ.get("OMERO_CONFIG", None)
os.environ["OMERO_CONFIG"] = "ABC"
config = ConfigXml(filename=str(p))
config.close()
assert "FOO" == get_profile_name(p)
finally:
if old is None:
del os.environ["OMERO_CONFIG"]
else:
os.environ["OMERO_CONFIG"] = old
# But we can reset it with env_config
config = ConfigXml(filename=str(p), env_config="ABC")
config.close()
assert "ABC" == get_profile_name(p)
# or manually. ticket:7343
config = ConfigXml(filename=str(p))
config.default("XYZ")
config.close()
assert "XYZ" == get_profile_name(p)
def testLoadTagset(self, capfd):
ts_name = self.uuid()
ts_desc = self.uuid()
tag_names = ["tagset %s - %s" % (ts_name, x) for x in [1, 2]]
p = create_path(suffix=".json")
p.write_text("""
[{
"name" : "%s",
"desc" : "%s",
"set" : [{
"name" : "%s",
"desc" : ""},
{
"name" : "%s",
"desc" : ""}]
}]""" % (ts_name, ts_desc, tag_names[0], tag_names[1]))
self.args += ["load", str(p)]
self.cli.invoke(self.args, strict=True)
o, e = capfd.readouterr()
# Check tagset is created
tagset = self.get_object(o)
assert tagset.textValue.val == ts_name
assert tagset.ns.val == NSINSIGHTTAGSET
assert tagset.description.val == ts_desc
# Check all tags are linked to the tagset
tags = self.get_tags_in_tagset(tagset.id.val)
assert sorted([x.textValue.val for x in tags]) == sorted(tag_names)
def create_script(self):
path = create_path()
for x in ("Screen", "Plate", "Project", "Dataset"):
path.write_text("new %s name=test\n" % x, append=True)
path.write_text("new %s name=test description=foo\n" % x,
append=True)
return path
def run(self, args):
if not os.path.exists(args.file):
self.ctx.die(670, "No such file: %s" % args.file)
else:
client = self.ctx.conn(args)
store = SessionsStore()
srv, usr, uuid = store.get_current()
props = store.get(srv, usr, uuid)
from omero.scripts import parse_file
from omero.util.temp_files import create_path
path = create_path()
text = """
omero.host=%(omero.host)s
omero.user=%(omero.sess)s
omero.pass=%(omero.sess)s
"""
path.write_text(text % props)
params = parse_file(args.file)
m = self._parse_inputs(args, params)
for k, v in m.items():
if v is not None:
client.setInput(k, v)
p = self.ctx.popen([sys.executable, args.file], stdout=sys.stdout,
stderr=sys.stderr, ICE_CONFIG=str(path))
p.wait()
if p.poll() != 0:
self.ctx.die(p.poll(), "Execution failed.")
def testCannotCreate(self):
d = create_path(folder=True)
d.chmod(0555)
filename = str(d / "config.xml")
with pytest.raises(IOError) as excinfo:
ConfigXml(filename).close()
assert excinfo.value.errno == errno.EACCES
def setup_method(self, method):
# Non-temp directories
build_dir = path() / "build"
top_dir = path() / ".." / ".." / ".."
etc_dir = top_dir / "etc"
# Necessary fiels
prefs_file = build_dir / "prefs.class"
internal_cfg = etc_dir / "internal.cfg"
master_cfg = etc_dir / "master.cfg"
# Temp directories
tmp_dir = create_path(folder=True)
tmp_etc_dir = tmp_dir / "etc"
tmp_grid_dir = tmp_etc_dir / "grid"
tmp_lib_dir = tmp_dir / "lib"
tmp_var_dir = tmp_dir / "var"
# Setup tmp dir
[x.makedirs() for x in (tmp_grid_dir, tmp_lib_dir, tmp_var_dir)]
prefs_file.copy(tmp_lib_dir)
master_cfg.copy(tmp_etc_dir)
internal_cfg.copy(tmp_etc_dir)
# Other setup
self.cli = MockCLI()
self.cli.dir = tmp_dir
self.cli.register("admin", AdminControl, "TEST")
self.cli.register("config", PrefsControl, "TEST")
def testImport(self):
import time
s1 = time.time()
client = self.new_client()
mrepo = self.getManagedRepo(client)
folder = create_path(folder=True)
for x in range(200):
name = "%s.unknown" % x
(folder / name).touch()
paths = folder.files()
proc = mrepo.importPaths(paths)
hashes = self.upload_folder(proc, folder)
handle = proc.verifyUpload(hashes)
req = handle.getRequest()
fs = req.activity.getParent()
cb = CmdCallbackI(client, handle)
self.assertError(cb, loops=200)
delete = omero.cmd.Delete2()
delete.targetObjects = {'Fileset': [fs.id.val]}
s2 = time.time()
print s2 - s1,
t1 = time.time()
client.submit(delete, loops=200)
t2 = time.time()
print " ", t2-t1,
def test421Upgrade(self):
"""
When upgraded 4.2.0 properties to 4.2.1,
${dn} items in omero.ldap.* properties are
changed to @{dn}
"""
p = create_path()
# How config was written in 4.2.0
XML = Element("icegrid")
active = SubElement(XML, "properties", id="__ACTIVE__")
default = SubElement(XML, "properties", id="default")
for properties in (active, default):
SubElement(
properties, "property", name="omero.config.version",
value="4.2.0")
SubElement(
properties, "property", name="omero.ldap.new_user_group",
value="member=${dn}")
SubElement(
properties, "property", name="omero.ldap.new_user_group_2",
value="member=$${omero.dollar}{dn}")
string = tostring(XML, 'utf-8')
txt = xml.dom.minidom.parseString(string).toprettyxml(" ", "\n", None)
p.write_text(txt)
config = ConfigXml(filename=str(p), env_config="default")
try:
m = config.as_map()
assert "member=@{dn}" == m["omero.ldap.new_user_group"]
assert "member=@{dn}" == m["omero.ldap.new_user_group_2"]
finally:
config.close()
def testAutoFillTicket2326(self):
SCRIPT = """if True:
import omero.scripts
import omero.rtypes
client = omero.scripts.client("ticket2326", omero.scripts.Long("width", optional=True))
width = client.getInput("width")
print width
client.setOutput("noWidthKey", omero.rtypes.rbool("width" not in client.getInputKeys()))
client.setOutput("widthIsNull", omero.rtypes.rbool(width is None))
"""
impl = omero.processor.usermode_processor(self.client)
svc = self.client.sf.getScriptService()
try:
scriptID = svc.uploadScript("/test/testAutoFillTicket2326", SCRIPT)
process = svc.runScript(scriptID, {}, None)
cb = omero.scripts.ProcessCallbackI(self.client, process)
while cb.block(500) is None:
pass
results = process.getResults(0)
stdout = results["stdout"].val
downloaded = create_path()
self.client.download(ofile=stdout, filename=str(downloaded))
text = downloaded.text().strip()
self.assertEquals("None", text)
self.assertTrue(results["widthIsNull"].val)
self.assertTrue(results["noWidthKey"].val)
self.assertTrue("stderr" not in results)
finally:
impl.cleanup()
def demo(self, args):
from omero.util.temp_files import create_path
t = create_path("Demo_Script", ".py")
try:
from hashlib import sha1 as sha_new
except ImportError:
from sha import new as sha_new
digest = sha_new()
digest.update(DEMO_SCRIPT)
sha1 = digest.hexdigest()
self.ctx.out("\nExample script writing session")
self.ctx.out("="*80)
def msg(title, method=None, *arguments):
self.ctx.out("\n")
self.ctx.out("\t+" + ("-"*68) + "+")
title = "\t| %-66.66s | " % title
self.ctx.out(title)
if method:
cmd = "%s %s" % (method.__name__, " ".join(arguments))
cmd = "\t| COMMAND: bin/omero script %-40.40s | " % cmd
self.ctx.out(cmd)
self.ctx.out("\t+" + ("-"*68) + "+")
self.ctx.out(" ")
if method:
try:
self.ctx.invoke(['script', method.__name__] +
list(arguments))
except Exception, e:
import traceback
self.ctx.out("\nEXECUTION FAILED: %s" % e)
self.ctx.dbg(traceback.format_exc())
def testWithEnvThenWithoutEnv(self):
"""
This test shows that if you create the config using an env
setting, then without, the __ACTIVE__ block should reflect
"default" and not the intermediate "env" setting.
"""
def get_profile_name(p):
"""
Takes a path object to the config xml
"""
xml = XML(p.text())
props = xml.findall("./properties")
for x in props:
id = x.attrib["id"]
if id == "__ACTIVE__":
for y in x.getchildren():
if y.attrib["name"] == "omero.config.profile":
return y.attrib["value"]
p = create_path()
current = os.environ.get("OMERO_CONFIG", "default")
config = ConfigXml(filename=str(p))
config.close()
self.assertEquals(current, get_profile_name(p))
config = ConfigXml(filename=str(p), env_config="FOO")
config.close()
self.assertEquals("FOO", get_profile_name(p))
config = ConfigXml(filename=str(p))
config.close()
self.assertEquals(current, get_profile_name(p))
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 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 test_get_unit_and_value(self):
# units defaults to MICROMETER
fake = create_path("image", "&physicalSizeX=1.0.fake")
pixIds = self.import_image(filename=fake.abspath())
self.args = self.login_args() + [
"obj", "get", "Pixels:%s" % pixIds[0], "physicalSizeX"]
state = self.go()
assert state.get_row(0) == "1.0 MICROMETER"
def prep_directory(client, mrepo):
"""
Create an empty FS directory by performing an import and
then deleting the created fileset.
"""
from omero.cmd import Delete2, DoAll
from omero.grid import ImportSettings
from omero.model import ChecksumAlgorithmI
from omero.model import FilesetI
from omero.model import FilesetEntryI
from omero.model import UploadJobI
fs = FilesetI()
fs.linkJob(UploadJobI())
entry = FilesetEntryI()
entry.clientPath = rstring("README.txt")
fs.addFilesetEntry(entry)
settings = ImportSettings()
settings.checksumAlgorithm = ChecksumAlgorithmI()
settings.checksumAlgorithm.value = rstring("SHA1-160")
proc = mrepo.importFileset(fs, settings)
try:
tmp = create_path()
prx = proc.getUploader(0)
try:
tmp.write_text("THIS IS A PLACEHOLDER")
hash = client.sha1(tmp)
with open(tmp, "r") as source:
client.write_stream(source, prx)
finally:
prx.close()
tmp.remove()
handle = proc.verifyUpload([hash])
try:
req = handle.getRequest()
fs = req.activity.parent
finally:
handle.close()
dir = unwrap(mrepo.treeList(fs.templatePrefix.val))
oid = dir.items()[0][1].get("id")
ofile = client.sf.getQueryService().get("OriginalFile", oid)
delete1 = Delete2(targetObjects={"Fileset": [fs.id.val]})
delete2 = Delete2(targetObjects={"OriginalFile": [ofile.id.val]})
doall = DoAll()
doall.requests = [delete1, delete2]
cb = client.submit(doall)
cb.close(True)
finally:
proc.close()
return fs.templatePrefix.val
def preMethod(self):
self.dir = create_path("bin_test", folder=True)
self.bin = self.dir / "bin"
self.bin.makedirs()
self.omero = self.bin / "omero"
self.omero.write_text( orig.text() )
self.exe = """sh -c "python '%s' '' " """ % self.omero.abspath()
self.mkdir = """sudo sh -c "mkdir '%s/var'" """ % self.dir.abspath() # Always sudo
self.chmod = """sudo sh -c "chmod %%s '%s/var'" """ % self.dir.abspath() # "
def __init__(self, *args, **kwargs):
CLI.__init__(self, *args, **kwargs)
self.DIR = create_path(folder=True)
self.REQRESP = {}
self.STORE = MyStore(self.DIR)
self.STORE.clear(testhost, testuser)
self.register("s", SessionsControl, "TEST")
self.controls["s"].FACTORY = lambda ignore: self.STORE
assert self.STORE.count(testhost, testuser) == 0
def setUp(self):
self.cli = MockCLI()
self.cli.register("db", DatabaseControl, "TEST")
db = self.cli.controls["db"]
data = db.loaddefaults()
self.data = {}
for x in ("version", "patch"):
self.data[x] = data.properties.getProperty("omero.db."+x)
self.file = create_path()
def testLocking(self):
p = create_path()
config1 = ConfigXml(filename=str(p))
try:
config2 = ConfigXml(filename=str(p))
self.fail("No exception")
except portalocker.LockException:
pass
config1.close()
def testNewVersioning(self):
"""
All property blocks should always have a version set.
"""
p = create_path()
config = ConfigXml(filename=str(p))
m = config.as_map()
for k, v in list(m.items()):
assert "5.1.0" == v
def testLocking(self):
p = create_path()
config1 = ConfigXml(filename=str(p))
try:
ConfigXml(filename=str(p))
assert False, "No exception"
except portalocker.LockException:
pass
config1.close()
def setUp(self):
self.cli = MockCLI()
self.cli.register("db", DatabaseControl, "TEST")
db = self.cli.controls["db"]
data = db.loaddefaults()
self.data = {}
for x in ("version", "patch"):
self.data[x] = data.properties.getProperty("omero.db." + x)
self.file = create_path()
def testLocking(self):
p = create_path()
config1 = ConfigXml(filename=str(p))
try:
config2 = ConfigXml(filename=str(p))
self.fail("No exception")
except portalocker.LockException:
pass
config1.close()
def testNewVersioning(self):
"""
All property blocks should always have a version set.
"""
p = create_path()
config = ConfigXml(filename=str(p))
m = config.as_map()
for k, v in m.items():
self.assertEquals("4.2.1", v)
def testLocking(self):
p = create_path()
config1 = ConfigXml(filename=str(p))
try:
ConfigXml(filename=str(p))
assert False, "No exception"
except portalocker.LockException:
pass
config1.close()
def pingfile(self):
pingfile = create_path()
pingfile.write_text("""if True:
import omero
import omero.scripts as OS
import omero.grid as OG
OS.client("ping-%s")
""" % self.uuid())
return pingfile
def test_upload_multiple_files(self, capfd, ln_s):
f1 = create_path(suffix=".txt")
f2 = create_path(suffix=".txt")
self.args += [str(f1), str(f2)]
if ln_s:
self.args += ["--data-dir", "/OMERO"]
out = self.upload(capfd)
assert out.startswith("OriginalFile:")
objects = self.get_objects(out)
assert len(objects) == 2
assert objects[0].name.val == f1.name
assert objects[1].name.val == f2.name
if ln_s:
assert self.is_symlink(objects[0])
assert self.is_symlink(objects[1])
else:
assert not self.is_symlink(objects[0])
assert not self.is_symlink(objects[1])
def __init__(self, *args, **kwargs):
CLI.__init__(self, *args, **kwargs)
self.DIR = create_path(folder=True)
self.REQRESP = {}
self.STORE = MyStore(self.DIR)
self.STORE.clear(testhost, testuser)
self.register("s", SessionsControl, "TEST")
self.controls["s"].FACTORY = lambda ignore: self.STORE
assert self.STORE.count(testhost, testuser) == 0
def pingfile(self):
pingfile = create_path()
pingfile.write_text("""if True:
import omero
import omero.scripts as OS
import omero.grid as OG
OS.client("ping-%s")
""" % self.uuid())
return pingfile
def testNewVersioning(self):
"""
All property blocks should always have a version set.
"""
p = create_path()
config = ConfigXml(filename=str(p))
m = config.as_map()
for k, v in m.items():
assert "5.1.0" == v
def test_guessed_mimetype(self, capfd):
f = create_path(suffix=".txt")
self.args += [str(f)]
out = self.upload(capfd)
assert out.startswith("OriginalFile:")
objects = self.get_objects(out)
assert len(objects) == 1
assert objects[0].name.val == f.name
assert objects[0].mimetype.val == "text/plain"
def edit(self, args, config, edit_path = edit_path):
from omero.util.temp_files import create_path, remove_path
start_text = "# Edit your preferences below. Comments are ignored\n"
for k in sorted(config.keys()):
start_text += ("%s=%s\n" % (k, config[k]))
temp_file = create_path()
try:
edit_path(temp_file, start_text)
except RuntimeError, re:
self.ctx.die(954, "%s: Failed to edit %s" % (getattr(re, "pid", "Unknown"), temp_file))
def testAsDict(self):
p = create_path()
config = ConfigXml(filename=str(p), env_config="DICT")
config["omero.data.dir"] = "HOME"
config.close()
initial = self.initial("DICT")
_ = SubElement(initial[0][0], "property", name="omero.data.dir", value="HOME")
_ = SubElement(initial, "properties", id="DICT")
_ = SubElement(_, "property", name="omero.data.dir", value="HOME")
self.assertXml(initial, XML(p.text()))
def test_get_unit_and_value(self):
# units defaults to MICROMETER
fake = create_path("image", "&physicalSizeX=1.0.fake")
pixIds = self.import_image(filename=fake.abspath())
self.args = self.login_args() + [
"obj", "get",
"Pixels:%s" % pixIds[0], "physicalSizeX"
]
state = self.go()
assert state.get_row(0) == "1.0 MICROMETER"
def write_config(data):
p = create_path()
i = initial()
for k, v in data.items():
for x in i[0:2]: # __ACTIVE__ & default
SubElement(x, "property", name=k, value=v)
string = tostring(i, "utf-8")
txt = xml.dom.minidom.parseString(string).toprettyxml(" ", "\n", None)
p.write_text(txt)
return p
def testCannotCreateLock(self):
d = create_path(folder=True)
filename = str(d / "config.xml")
lock_filename = "%s.lock" % filename
with open(lock_filename, "w") as fo:
fo.write("dummy\n")
os.chmod(lock_filename, 0444)
with pytest.raises(IOError) as excinfo:
ConfigXml(filename).close()
assert excinfo.value.errno == errno.EACCES
def write_config(data):
p = create_path()
i = initial()
for k, v in list(data.items()):
for x in i[0:2]: # __ACTIVE__ & default
SubElement(x, "property", name=k, value=v)
string = tostring(i, 'utf-8')
txt = xml.dom.minidom.parseString(string).toprettyxml(" ", "\n", None)
p.write_text(txt)
return p
def __init__(self, client, user):
self.client = client
self.user = user
self.admin = self.client.sf.getAdminService()
self.query = self.client.sf.getQueryService()
self.update = self.client.sf.getUpdateService()
self.context = self.admin.getEventContext()
self.img = create_path("cliimportfixture.", ".png")
i = Image.new(mode="1", size=[8, 8])
i.save(self.img)
def edit(self, args, config, edit_path = edit_path):
from omero.util.temp_files import create_path, remove_path
start_text = "# Edit your preferences below. Comments are ignored\n"
for k in sorted(config.keys()):
start_text += ("%s=%s\n" % (k, config[k]))
temp_file = create_path()
try:
edit_path(temp_file, start_text)
except RuntimeError, re:
self.ctx.die(954, "%s: Failed to edit %s" % (getattr(re, "pid", "Unknown"), temp_file))
def testCannotCreateLock(self):
d = create_path(folder=True)
filename = str(old_div(d, "config.xml"))
lock_filename = "%s.lock" % filename
with open(lock_filename, "w") as fo:
fo.write("dummy\n")
os.chmod(lock_filename, 0o444)
with pytest.raises(IOError) as excinfo:
ConfigXml(filename).close()
assert excinfo.value.errno == errno.EACCES
def testSettings510Upgrade(self):
"""
When upgraded 5.0.x properties to 5.1.0 or later,
if omero.web.ui.top_links is set, we need to prepend
'Data', 'History' and 'Help' links
"""
beforeUpdate = '[["Figure", "figure_index"]]'
afterUpdate = '[["Data", "webindex", ' \
'{"title": "Browse Data via Projects, Tags etc"}], ' \
'["History", "history", ' \
'{"title": "History"}], ' \
'["Help", "https://help.openmicroscopy.org/", ' \
'{"target": "new", "title": ' \
'"Open OMERO user guide in a new tab"}], ' \
'["Figure", "figure_index"]]'
p = create_path()
XML = Element("icegrid")
active = SubElement(XML, "properties", id="__ACTIVE__")
default = SubElement(XML, "properties", id="default")
for properties in (active, default):
# Include a property to indicate version is post-4.2.0
SubElement(properties,
"property",
name="omero.config.version",
value="4.2.1")
SubElement(properties,
"property",
name="omero.web.ui.top_links",
value=beforeUpdate)
string = tostring(XML, 'utf-8')
txt = xml.dom.minidom.parseString(string).toprettyxml(" ", "\n", None)
p.write_text(txt)
def compare_json_maps(config, afterUpdate):
m = config.as_map()
beforeUpdate = m["omero.web.ui.top_links"]
assert json.loads(beforeUpdate) == json.loads(afterUpdate)
config = ConfigXml(filename=str(p), env_config="default")
try:
compare_json_maps(config, afterUpdate)
finally:
config.close()
# After config.close() calls config.save() new version should be 5.1.0
config = ConfigXml(filename=str(p), env_config="default")
try:
# Check version has been updated
assert config.version() == "5.1.0"
# And that top_links has not been modified further
compare_json_maps(config, afterUpdate)
finally:
config.close()
def testAsDict(self):
p = create_path()
config = ConfigXml(filename=str(p), env_config="DICT")
config["omero.data.dir"] = "HOME"
config.close()
i = initial("DICT")
_ = SubElement(i[0][0], "property", name="omero.data.dir",
value="HOME")
_ = SubElement(i, "properties", id="DICT")
_ = SubElement(_, "property", name="omero.data.dir", value="HOME")
assertXml(i, XML(p.text()))
def testReplace(self):
p = create_path(suffix=".py")
p.write_text(scriptText)
# test replace with user script (not official)
# Sets current script
self.cli.invoke(self.args + ["upload", str(p)], strict=True)
newId = self.cli.get("script.file.id")
self.cli.invoke(self.args + ["list", "user"], strict=True)
replaceArgs = self.args + ["replace", str(newId), str(p)]
self.cli.invoke(replaceArgs, strict=True)
def test_upload_file(self):
"""Test the upload of the file, the creation is tested above"""
f = create_path()
f.write_text("""Test test_upload_file %s """ % self.uuid())
update_service = self.client.sf.getUpdateService()
of = scriptUtil.create_file(update_service, str(f))
store = self.client.sf.createRawFileStore()
try:
scriptUtil.upload_file(store, of, f)
finally:
store.close()
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 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 as_dictionary(path, readers="", extra_args=None):
"""Run as_stdout, parses the output and returns a dictionary of the form::
{
some_file_in_group :
[
some_file_in_group
some_other_file_in_group
...
last_file_in_group
],
some_file_in_second_group : ...
}
you can pass more arguments to the `import` command through the
extra_args argument in the form of a list.
to_import = as_dictionary("/my/dir/with_tifs", extra_args=["--depth", "6"])
will go through the directories with a depth level of 6 instead of
the default 4. Arguments of interest might be: `debugging`,
`report`, `logback`. Note that the command runs locally so options
such as `--exclude` will not work as they need information from the server.
"""
t = create_path("candidates", "err")
path = _to_list(path)
path.insert(0, "---file=%s" % t)
try:
as_stdout(path, readers=readers, extra_args=extra_args)
f = open(str(t), "r")
output = f.readlines()
f.close()
finally:
remove_path(t)
gline = -1
key = None
groups = {}
for line in output:
line = line.strip()
if len(line) == 0:
continue
if line.startswith("#"):
gline = -1
else:
if gline == -1:
gline = 1
key = line
groups[key] = [line]
else:
groups[key].append(line)
return groups
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")
def importMIF(self,
seriesCount=0,
name=None,
client=None,
with_companion=False,
skip="all",
**kwargs):
if client is None:
client = self.client
if name is None:
name = "importMIF"
try:
globalMetadata = kwargs.pop("GlobalMetadata")
except:
globalMetadata = None
if globalMetadata:
with_companion = True
append = ""
# Only include series count if enabled; in the case of plates,
# this will be unused
if seriesCount >= 1:
append = "series=%d%s" % (seriesCount, append)
if kwargs:
for k, v in kwargs.items():
append += "&%s=%s" % (k, v)
query = client.sf.getQueryService()
fake = create_path(name, "&%s.fake" % append)
if with_companion:
ini = open(fake.abspath() + ".ini", "w")
if globalMetadata:
ini.write("[GlobalMetadata]\n")
for k, v in globalMetadata.items():
ini.write("%s=%s\n" % (k, v))
ini.close()
pixelIds = self.import_image(filename=fake.abspath(),
client=client,
skip=skip,
**kwargs)
if seriesCount >= 1:
assert seriesCount == len(pixelIds)
images = []
for pixIdStr in pixelIds:
pixels = query.get("Pixels", long(pixIdStr))
images.append(pixels.getImage())
return images
def testReadOnlyConfigFailsOnEnv2(self):
old = os.environ.get("OMERO_CONFIG")
os.environ["OMERO_CONFIG"] = "default"
try:
p = create_path()
p.chmod(0444) # r--r--r--
pytest.raises(Exception, ConfigXml, filename=str(p))
finally:
if old is None:
del os.environ["OMERO_CONFIG"]
else:
os.environ["OMERO_CONFIG"] = old
def uploadFileset(self, proc, files):
tmp = create_path()
hashes = []
for idx, file in enumerate(files):
prx = proc.getUploader(idx)
self.client.download(file, filename=tmp)
hashes.append(self.client.sha1(tmp))
with open(tmp, "r") as source:
self.client.write_stream(source, prx)
prx.close()
tmp.remove()
return proc.verifyUpload(hashes)
def _checkstd(self, output, which):
rfile = output.val[which]
ofile = rfile.val
assert ofile
tmppath = create_path("clitest")
try:
self.client.download(ofile, str(tmppath))
assert os.path.getsize(str(tmppath))
return tmppath.text()
finally:
remove_path(tmppath)
def _checkstd(self, output, which):
rfile = output.val[which]
ofile = rfile.val
assert ofile
tmppath = create_path("pingtest")
try:
self.client.download(ofile, str(tmppath))
assert os.path.getsize(str(tmppath))
return tmppath.text()
finally:
remove_path(tmppath)
def testReplaceOfficial(self):
p = create_path(suffix=".py")
p.write_text(scriptText)
# test replace with official script
self.args = self.root_login_args() + ["script"]
uploadArgs = self.args + ["upload", str(p), "--official"]
self.cli.invoke(uploadArgs, strict=True) # Sets current script
newId = self.cli.get("script.file.id")
self.cli.invoke(self.args + ["list"], strict=True)
replaceArgs = self.args + ["replace", str(newId), str(p)]
self.cli.invoke(replaceArgs, strict=True)
def uploadFileset(self, proc, files):
tmp = create_path()
hashes = []
for idx, file in enumerate(files):
prx = proc.getUploader(idx)
self.client.download(file, filename=tmp)
hashes.append(self.client.sha1(tmp))
with open(tmp, "r") as source:
self.client.write_stream(source, prx)
prx.close()
tmp.remove()
return proc.verifyUpload(hashes)
def testOldVersionDetected(self):
p = create_path()
config = ConfigXml(filename=str(p))
X = config.XML
O = SubElement(X, "properties", {"id": "old"})
SubElement(O, "property", {"omero.ldap.keystore": "/Foo"})
config.close()
try:
config = ConfigXml(filename=str(p))
assert False, "Should throw"
except:
pass
def testUploadDownload(self):
uploaded = tmpfile()
downloaded = create_path()
ofile = self.client.upload(str(uploaded), type="text/plain")
self.client.download(ofile, str(downloaded))
lines = downloaded.lines()
self.assert_("abc\n" == lines[0], lines[0])
self.assert_("def\n" == lines[1], lines[1])
self.assert_("123\n" == lines[2], lines[2])
sha1_upload = self.client.sha1(str(uploaded))
sha1_download = self.client.sha1(str(downloaded))
self.assertEquals(sha1_upload, sha1_download,
"%s!=%s" % (sha1_upload, sha1_download))
def createCsv(self,
colNames="Well,Well Type,Concentration",
rowData=("A1,Control,0", "A2,Treatment,10")):
csvFileName = create_path("test", ".csv")
csvFile = open(csvFileName, 'w')
try:
csvFile.write(colNames)
csvFile.write("\n")
csvFile.write("\n".join(rowData))
finally:
csvFile.close()
return str(csvFileName)