Exemplo n.º 1
0
    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()
Exemplo n.º 2
0
    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()
Exemplo n.º 3
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 def test_4(self, input, output):
     p = write_config(input)
     config = ConfigXml(filename=str(p), env_config="default")
     try:
         m = config.as_map()
         s = strip_dict(m, suffix="blitz")
         assert s == output
     finally:
         config.close()
Exemplo n.º 4
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 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()
Exemplo n.º 5
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 def testNewVersioning(self):
     """
     All property blocks should always have a version set.
     """
     p = create_path()
     config = ConfigXml(filename=str(p))
     m = config.as_map()
     for k, v in m.items():
         assert "4.2.1" == v
Exemplo n.º 6
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 def test_4(self, input, output):
     p = write_config(input)
     config = ConfigXml(filename=str(p), env_config="default")
     try:
         m = config.as_map()
         s = strip_dict(m, suffix="blitz")
         assert s == output
     finally:
         config.close()
Exemplo n.º 7
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 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()
Exemplo n.º 8
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 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
Exemplo n.º 9
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 def test_adjust(self, fixture):
     p = write_config(fixture.input)
     xml = template_xml()
     config = ConfigXml(filename=str(p), env_config="default")
     try:
         rv = adjust_settings(config, xml, **fixture.kwargs)
         fixture.validate(rv)
     finally:
         config.close()
Exemplo n.º 10
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 def test_adjust(self, fixture, monkeypatch):
     monkeypatch.setattr(Strategy, "_system_memory_mb_java", lambda x: (2000, 4000))
     p = write_config(fixture.input)
     xml = template_xml()
     config = ConfigXml(filename=str(p), env_config="default")
     try:
         rv = adjust_settings(config, xml, **fixture.kwargs)
         fixture.validate(rv)
     finally:
         config.close()
Exemplo n.º 11
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 def test_adjust(self, fixture, monkeypatch):
     monkeypatch.setattr(Strategy, '_system_memory_mb_java', lambda x:
                         (2000, 4000))
     p = write_config(fixture.input)
     xml = template_xml()
     config = ConfigXml(filename=str(p), env_config="default")
     try:
         rv = adjust_settings(config, xml, **fixture.kwargs)
         fixture.validate(rv)
     finally:
         config.close()
Exemplo n.º 12
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 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()))
Exemplo n.º 13
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 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()))
Exemplo n.º 14
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    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
Exemplo n.º 15
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    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()
Exemplo n.º 16
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 def get_config(self, raise_missing=True):
     """
     Returns a dictionary of all OMERO config properties
     """
     configxml = os.path.join(self.dir, 'etc', 'grid', 'config.xml')
     try:
         configobj = ConfigXml(configxml, read_only=True)
     except Exception as e:
         log.warning('config.xml not found: %s', e)
         if raise_missing:
             raise
         return {}
     cfgdict = configobj.as_map()
     configobj.close()
     return cfgdict
Exemplo n.º 17
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 def testCannotCreate(self):
     d = create_path(folder=True)
     d.chmod(0o555)
     filename = str(old_div(d, "config.xml"))
     with pytest.raises(IOError) as excinfo:
         ConfigXml(filename).close()
     assert excinfo.value.errno == errno.EACCES
Exemplo n.º 18
0
    def testSettings510Upgrade(self):
        """
        When upgraded 5.0.x properties to 5.1.0 or later,
        if omero.web.ui.top_links is set, we need to prepend
        'Data', 'History' and 'Help' links
        """

        beforeUpdate = '[["Figure", "figure_index"]]'
        afterUpdate = '[["Data", "webindex", ' \
            '{"title": "Browse Data via Projects, Tags etc"}], ' \
            '["History", "history", ' \
            '{"title": "History"}], ' \
            '["Help", "http://help.openmicroscopy.org/", ' \
            '{"target": "new", "title": ' \
            '"Open OMERO user guide in a new tab"}], ' \
            '["Figure", "figure_index"]]'
        p = create_path()

        XML = Element("icegrid")
        active = SubElement(XML, "properties", id="__ACTIVE__")
        default = SubElement(XML, "properties", id="default")
        for properties in (active, default):
            # Include a property to indicate version is post-4.2.0
            SubElement(
                properties, "property", name="omero.config.version",
                value="4.2.1")
            SubElement(
                properties, "property", name="omero.web.ui.top_links",
                value=beforeUpdate)
        string = tostring(XML, 'utf-8')
        txt = xml.dom.minidom.parseString(string).toprettyxml("  ", "\n", None)
        p.write_text(txt)

        config = ConfigXml(filename=str(p), env_config="default")
        try:
            m = config.as_map()
            assert m["omero.web.ui.top_links"] == afterUpdate
        finally:
            config.close()

        # After config.close() calls config.save() new version should be 5.1.0
        config = ConfigXml(filename=str(p), env_config="default")
        try:
            # Check version has been updated
            assert config.version() == "5.1.0"
            m = config.as_map()
            # And that top_links has not been modified further
            assert m["omero.web.ui.top_links"] == afterUpdate
        finally:
            config.close()
Exemplo n.º 19
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 def test_12527(self, fixture, monkeypatch):
     monkeypatch.setattr(Strategy, '_system_memory_mb_java', lambda x:
                         (2000, 4000))
     p = write_config(fixture.input)
     old_templates = old_div(path(__file__).dirname(), "old_templates.xml")
     xml = XML(old_templates.abspath().text())
     config = ConfigXml(filename=str(p), env_config="default")
     with pytest.raises(Exception):
         adjust_settings(config, xml, **fixture.kwargs)
Exemplo n.º 20
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 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
Exemplo n.º 21
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def update_config(omerodir):
    """
    Updates OMERO config with certificate properties if necessary
    """

    cfg = ConfigXml(os.path.join(omerodir, "etc", "grid", "config.xml"))
    cfgdict = cfg.as_map()

    def set_if_empty(cfgkey, default):
        if not cfgdict.get(cfgkey):
            cfg[cfgkey] = default
            log.info("Setting %s=%s", cfgkey, default)

    set_if_empty(
        "omero.glacier2.IceSSL.DefaultDir",
        os.path.join(cfgdict.get("omero.data.dir", "/OMERO"), "certs"),
    )
    set_if_empty("omero.certificates.commonname", "localhost")
    set_if_empty("omero.certificates.owner", "/L=OMERO/O=OMERO.server")
    set_if_empty("omero.certificates.key", "server.key")
    set_if_empty("omero.glacier2.IceSSL.CertFile", "server.p12")
    set_if_empty("omero.glacier2.IceSSL.CAs", "server.pem")
    set_if_empty("omero.glacier2.IceSSL.Password", "secret")

    set_if_empty("omero.glacier2.IceSSL.Ciphers", "HIGH")
    set_if_empty("omero.glacier2.IceSSL.ProtocolVersionMax", "TLS1_2")
    set_if_empty("omero.glacier2.IceSSL.Protocols", "TLS1_0,TLS1_1,TLS1_2")

    cfgdict = cfg.as_map()
    cfg.close()
    return cfgdict
Exemplo n.º 22
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    def test_create_certificates(self, tmpdir):
        (tmpdir / "etc" / "grid").ensure(dir=True)
        omerodir = str(tmpdir)
        datadir = str(tmpdir / "OMERO")
        configxml = ConfigXml(
            os.path.join(omerodir, "etc", "grid", "config.xml"))
        configxml["omero.data.dir"] = datadir
        configxml.close()

        m = create_certificates(omerodir)
        assert m.startswith("certificates created: ")

        cfg = get_config(omerodir)
        assert cfg["omero.glacier2.IceSSL.DefaultDir"] == os.path.join(
            datadir, "certs")

        for filename in ("server.key", "server.p12", "server.pem"):
            assert os.path.isfile(os.path.join(datadir, "certs", filename))

        out = subprocess.check_output([
            "openssl",
            "pkcs12",
            "-in",
            os.path.join(datadir, "certs", "server.p12"),
            "-passin",
            "pass:secret",
            "-passout",
            "pass:secret",
        ])
        out = out.decode().splitlines()
        for line in (
                "subject=L = OMERO, O = OMERO.server, CN = localhost",
                "issuer=L = OMERO, O = OMERO.server, CN = localhost",
                "-----BEGIN CERTIFICATE-----",
                "-----END CERTIFICATE-----",
                "-----BEGIN ENCRYPTED PRIVATE KEY-----",
                "-----END ENCRYPTED PRIVATE KEY-----",
        ):
            assert line in out
def _get_current_as_json(config: ConfigXml, key: str) -> Optional[DictOrList]:
    """
    Get current key value converted from JSON to a list or dict,
    taking into account OMERO.web's defaults
    """
    if key in config.keys():
        current = json.loads(config[key])
        if not isinstance(current, (dict, list)):
            raise ExternalConfigException(
                "Property {} is not a dict or list: {}".format(key, current))
        return current
    if key.startswith("omero.web."):
        return _get_omeroweb_default(key)
    return None
Exemplo n.º 24
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    def test_config_keep_existing(self, tmpdir):
        (tmpdir / "etc" / "grid").ensure(dir=True)
        omerodir = str(tmpdir)
        configxml = ConfigXml(
            os.path.join(omerodir, "etc", "grid", "config.xml"))
        configxml["omero.certificates.commonname"] = "omero.example.org"
        configxml["omero.certificates.owner"] = "/L=universe/O=42"
        configxml.close()

        update_config(omerodir)
        cfg = get_config(omerodir)
        cfg.pop("omero.config.version")
        assert cfg == {
            "omero.glacier2.IceSSL.CAs": "server.pem",
            "omero.glacier2.IceSSL.CertFile": "server.p12",
            "omero.glacier2.IceSSL.Ciphers": "HIGH",
            "omero.glacier2.IceSSL.DefaultDir": "/OMERO/certs",
            "omero.glacier2.IceSSL.Password": "******",
            "omero.glacier2.IceSSL.ProtocolVersionMax": "TLS1_2",
            "omero.glacier2.IceSSL.Protocols": "TLS1_0,TLS1_1,TLS1_2",
            "omero.certificates.commonname": "omero.example.org",
            "omero.certificates.key": "server.key",
            "omero.certificates.owner": "/L=universe/O=42",
        }
Exemplo n.º 25
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 def open_config(self, args):
     if args.source:
         cfg_xml = path(args.source)
         if not cfg_xml.exists():
             self.ctx.die(124, "File not found: %s" % args.source)
     else:
         grid_dir = self.ctx.dir / "etc" / "grid"
         if grid_dir.exists():
             cfg_xml = grid_dir / "config.xml"
         else:
             userdir = path(get_user_dir())
             usr_xml = userdir / "omero" / "config.xml"
             self.ctx.err("%s not found; using %s" % (grid_dir, usr_xml))
             cfg_xml = usr_xml
     try:
         return ConfigXml(str(cfg_xml))
     except portalocker.LockException:
         self.ctx.die(112, "Could not acquire lock on %s" % cfg_xml)
Exemplo n.º 26
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    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
Exemplo n.º 27
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 def open_config(self, args):
     if args.source:
         cfg_xml = path(args.source)
         if not cfg_xml.exists():
             self.ctx.die(124, "File not found: %s" % args.source)
     else:
         if 'OMERODIR' in os.environ:
             base_dir = path(os.environ.get('OMERODIR'))
         else:
             self.ctx.die(125, 'FATAL: OMERODIR env variable not set')
         grid_dir = base_dir / "etc" / "grid"
         if not grid_dir.exists():
             self.ctx.err("%s not found; creating %s" %
                          (grid_dir, grid_dir))
             os.makedirs(grid_dir)
         cfg_xml = grid_dir / "config.xml"
     try:
         return ConfigXml(str(cfg_xml))
     except portalocker.LockException:
         self.ctx.die(112, "Could not acquire lock on %s" % cfg_xml)
     except Exception as e:
         self.ctx.die(113, str(e))
Exemplo n.º 28
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 def testReadOnlyConfigSimple(self):
     p = create_path()
     p.chmod(0444)  # r--r--r--
     config = ConfigXml(filename=str(p), env_config=None)  # Must be None
     config.close()  # Shouldn't save
Exemplo n.º 29
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 def update_config(self, newcfg):
     cfg = ConfigXml(os.path.join(self.dir, 'etc', 'grid', 'config.xml'))
     for k, v in newcfg.items():
         cfg[k] = v
     cfg.close()
Exemplo n.º 30
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 def testBasic(self):
     p = create_path()
     config = ConfigXml(filename=str(p))
     config.close()
     assertXml(initial(), XML(p.text()))
Exemplo n.º 31
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 def testWithEnv(self):
     p = create_path()
     config = ConfigXml(filename=str(p), env_config="FOO")
     config.close()
     assertXml(initial("FOO"), XML(p.text()))
Exemplo n.º 32
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def get_config(omerodir):
    configxml = ConfigXml(os.path.join(omerodir, "etc", "grid", "config.xml"))
    try:
        return configxml.as_map()
    finally:
        configxml.close()
Exemplo n.º 33
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 def testWithEnv(self):
     p = create_path()
     config = ConfigXml(filename=str(p), env_config="FOO")
     config.close()
     assertXml(initial("FOO"), XML(p.text()))
Exemplo n.º 34
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 def testCannotRead(self):
     p = create_path()
     p.chmod(0)
     with pytest.raises(IOError) as excinfo:
         ConfigXml(str(p)).close()
     assert excinfo.value.errno == errno.EACCES
Exemplo n.º 35
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    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)
Exemplo n.º 36
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 def testReadOnlyConfigPassesOnExplicitReadOnly(self):
     p = create_path()
     p.chmod(0444)  # r--r--r--
     ConfigXml(filename=str(p), env_config="default",
               read_only=True).close()
Exemplo n.º 37
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    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)
Exemplo n.º 38
0
 def testReadOnlyConfigSimple(self):
     p = create_path()
     p.chmod(0444)  # r--r--r--
     config = ConfigXml(filename=str(p), env_config=None)  # Must be None
     config.close()  # Shouldn't save
Exemplo n.º 39
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 def testBasic(self):
     p = create_path()
     config = ConfigXml(filename=str(p))
     config.close()
     assertXml(initial(), XML(p.text()))
Exemplo n.º 40
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 def config(self):
     return ConfigXml(filename=str(self.p))
def _get_config_xml(omerodir: str) -> ConfigXml:
    return ConfigXml(os.path.join(omerodir, "etc", "grid", "config.xml"))