update branch (#6109)

* Fix #5879 radia cylindrical divisions (#5923) * Fix #5947: move pump_type and rename laser gain tab (#5952) * Fix #5945: add description for thermal lensing (#5957) * fix #5937 omega beam centering and error handling (#5959) * Fix #5944: silas plot units (#5963) Also fixes new drift and lens module names. Replace chirp with tau_0 * fix #5965 omega fixes (#5966) - added default values for simWorkflow - improved layouts - improved genesis error handling * Fix #5931: show error if no epics server on start monitor (#5956) * Fix #5974 radia local cut plane (#5975) * Fix #5974 - adds center to cut point when specified --------- Co-authored-by: mkeilman <mkeilman@radiasoft.net> * fix #3932 include rpnVariables for twissReport cache (#5968) * fix #5414 added more precision and removed quotes from elegant csv output (#5967) * fix #5942 match silas results with notebook (#5964) * Fix #5954: improve silas panel layout (#5960) * Fix #5596 Add file_lock concurrency protection (#5848) * Fix #5596 Add file_lock concurrency protection - Fix #5740 ensure serial greater than incoming and on disk - Fix #5742 restricted critical sections and removed most - Fix #5743 migrate_guest_to_persistent_user locks new and guest uid - Fix #5744 simulation_dir uses lock_user - Fix #5745 validate version in save_simulation_json - Fix #5746 removed lock on auth.unchecked_get_user - Fix #5747 complete_registration passed display_name - Fix #5749 removed auth_db locking, verified all critical sections - Fix #5750 thread locking only in flask - Fix #5751 add auth.create_and_login_user for testing * fix radiasoft/raydata#62: remove unused options (Simulation Documentation URL, Export as Zip, Python Source) in raydata settings submenu (#5891) * Fix #5642 pkuinit.restart_or_fail if `_ping_supervisor` fails (#5643) * fix #5979 fix missing case in plot axis tick formatting (#5987) * Fix #5978: fixed scale bug in hellweg (#5992) * fix #5982 use new hellweg binary output format, gamma vs beta (#5997) * Fix #5983 copy reacts build files into /static (#5984) * fix #5998 improve hellweg source generation, fixed energy scaling (#5999) * Fix #5991 - omit one-time eval (#6006) * Fix #5996: add particles keyword to hellweg (#6001) * Fix #6018 static_files.gen correctly copies react bundle files (#6019) * Fix #5943: error message non premium (#5971) * Fix #5994: make etc/run-jupyterhub.sh work again (#5995) * Fix #5994: make etc/run-jupyterhub.sh work again - notebook must now be installed explicitly - serverextension call is no longer needed with the version of notebook we install - jupyterhub_debug was removed in favor of feature_config.debug but this needed to be cascaded in the jupyterhub conf jinja * fix list * importable package is with an underscore * install deps so users dont have to --------- Co-authored-by: Raven <ravenmarieorourke@gmail.com> * fix #6029 omega qcall work-around (#6030) * fix #5734 fixes for email login on react (#5973) * Fix #5819 radia lock objects (#5969) * fix #6013 work-around hellweg rf fields bug (#6014) * Fix #5948 always calculate n0 and n2 using fenics (#6015) * Fix #6004: change laser pulse units (#6016) * Fix #6032 - try small instead of subscript (#6035) * Fix #6044 - replaced segmentationCylRadius field in view (#6045) Co-authored-by: mkeilman <mkeilman@radiasoft.net> * fix #5588 omega improvements (#6054) * Fix #6055 default to tornado api_server in dev mode (#6072) * Fix #6055 default to tornado api_server in dev mode * Fix #6074 remove google_tag_manager --------- Co-authored-by: Raven <ravenmarieorourke@gmail.com> * Fix #6083: auth.login creates the uid (#6084) In 791364f the api_authEmailAuthorized code was changed from passing the user model we acquired based on searching by the email token to one acquired by searching for the uid into auth.login. Previous behavior: 791364f#diff-109de77eab3047455095be7e4c1f5f1d918083adaa02b87d5c862a8e513e8436L61 Behavior introduced in 791364f: 791364f#diff-109de77eab3047455095be7e4c1f5f1d918083adaa02b87d5c862a8e513e8436R89 But, the uid isn't present on the model. auth.login creates the user and populates the uid. In the case where we have multiple records in auth_email_user_t without a uid the query would return all of the records even though we are looking for just one. This reverts the behavior to what it was previously. * fix #6077 fix to omega for new opal release (#6090) * Fix #5936: beamline named amplifier for silas (#6043) * Fix #6037: replace experimental comparison with new example (#6080) * Fix #6046: "completed reports" instead of "animation" (#6051) * fix #6093 silas crystal UI improvements (#6094) * Fix #6017 improve cloudmc 3d toolbar (#6027) * fix #5829 implement parallel geometry extraction (#6048) * Fix #6049 - all object edges now black (#6050) * Fix #6047 - added axis ratio parameter (#6052) * fix 6095 increase server_test timeout (#6096) * fix #6058: raydata start and stop search times pre-populated (#6082) * Fix #6095 added TestClient.DEFAULT_TIMEOUT_SECS (#6098) * Fix #6101 increase timeouts in file_lock_test (#6102) --------- Co-authored-by: Michael Keilman <30352290+mkeilman@users.noreply.github.com> Co-authored-by: Gurhar Khalsa <49498231+gurhar1133@users.noreply.github.com> Co-authored-by: Paul Moeller <moeller@radiasoft.net> Co-authored-by: mkeilman <mkeilman@radiasoft.net> Co-authored-by: Rob Nagler <github@q33.us> Co-authored-by: Raven <ravenmarieorourke@gmail.com> Co-authored-by: Evan Carlin <evan@carlin.com>
radiasoft · Jul 13, 2023 · 54156ee · 54156ee
1 parent 24fea0f
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Showing 110 changed files with 2,914 additions and 1,774 deletions.
diff --git a/etc/run-jupyterhub.sh b/etc/run-jupyterhub.sh
@@ -38,6 +38,17 @@ END
     rm ~/mail/1
 fi
 
+# POSIT: versions same in container-beamsim-jupyter/build.sh
+# Order is important: jupyterlab-server should be last so it isn't
+# overwritten with a newer version.
+pip install \
+    jupyterhub==1.4.2
+    jupyterhub==1.4.2 \
+    jupyterlab==3.1.14  \
+    notebook==6.5.4 \
+    jupyterlab_server==2.8.2
+ npm install --global configurable-http-proxy
+
 export SIREPO_FEATURE_CONFIG_MODERATED_SIM_TYPES=jupyterhublogin
 export SIREPO_AUTH_ROLE_MODERATION_MODERATOR_EMAIL='vagrant@localhost.localdomain'
 export SIREPO_FROM_EMAIL='$USER+support@localhost.localdomain'

diff --git a/react/src/component/login/email.tsx b/react/src/component/login/email.tsx
@@ -22,20 +22,21 @@ export const LoginEmailConfirm = (props) => {
             headers: {
                 "Content-Type": "application/json"
             }
-        }).then(() => 
+        }).then(() =>
         updateLoginStatusRef(loginStatusRef, appWrapper)
-        .then(() => navigate(`/react/${appName}`))
+        .then(() => navigate(`/${appName}`))
         )
     }
+
     return (
         <Container>
             {
-                needCompleteRegistration ? (
+                needCompleteRegistration === '1' ? (
                     <LoginExtraInfoForm onComplete={(data) => completeLogin(data)}/>
                 ) : (
                     <>
-                        <p>Click the button complete the login process.</p>
-                        <Button onClick={() => completeLogin()}>Continue</Button>
+                        <p>Please click the button below complete the login process.</p>
+                        <Button onClick={() => completeLogin()}>Confirm</Button>
                     </>
                 )
             }
@@ -70,7 +71,7 @@ export const LoginWithEmail = (props) => {
                         <Form.Control placeholder="email@example.com" value={email} onChange={(e) => updateEmail(e.target.value)}/>
                     </Col>
                     <Col sm="2">
-                        <Button variant="primary" onClick={() => doLogin(email)}>Continue</Button>
+                        <Button variant="primary" onClick={() => doLogin(email)} disabled={! (email && email.match(/^.+@.+\..+$/))}>Continue</Button>
                     </Col>
                 </Form.Group>
                 <Row>

diff --git a/react/src/component/login/login.tsx b/react/src/component/login/login.tsx
@@ -42,7 +42,7 @@ export const LoginRouter = (props) => {
             <Routes>
                 <Route path={`${routeHelper.localRoutePattern("logout")}/*`} element={<LogoutRoot/>}/>
                 <Route path={`${routeHelper.localRoutePattern("login")}/*`} element={<LoginRoot/>}/>
-                <Route path={routeHelper.localRoutePattern("loginConfirm")} element={<LoginConfirm/>}/>
+                <Route path={routeHelper.localRoutePattern("loginWithEmailConfirm")} element={<LoginConfirm/>}/>
                 <Route path="*" element={<CatchLoggedOut>{props.children}</CatchLoggedOut>}/>
             </Routes>
         </CLoginStatusRef.Provider>
@@ -191,19 +191,12 @@ export const CatchLoggedOut = (props) => {
 
 type LoginConfirmParams = {
     token: string,
-    method: AuthMethod,
     needCompleteRegistration: "0" | "1"
 }
 
 export const LoginConfirm = (props) => {
-    let { token, method, needCompleteRegistration } = useParams<LoginConfirmParams>();
-
-    switch(method) {
-        case 'email':
-            return <LoginEmailConfirm needCompleteRegistration={needCompleteRegistration} token={token}/>
-        default:
-            throw new Error(`could not handle login method=${method}`)
-    }
+    let { token, needCompleteRegistration } = useParams<LoginConfirmParams>();
+    return <LoginEmailConfirm needCompleteRegistration={needCompleteRegistration} token={token}/>
 }
 
 
@@ -236,11 +229,13 @@ export const LoginExtraInfoForm = (props: { onComplete: ({displayName}) => void
                 <Form.Label column sm="3">
                     Your full name
                 </Form.Label>
-                <Col sm="9">
+                <Col sm="7">
                     <Form.Control value={displayName} onChange={(e) => updateDisplayName(e.target.value)}/>
                 </Col>
+                <Col sm="2">
+                    <Button variant="primary" onClick={() => onComplete({ displayName })} disabled={! displayName}>Continue</Button>
+                </Col>
             </Form.Group>
-            <Button variant="primary" onClick={() => onComplete({ displayName })}>Continue</Button>
         </>
     )
 }
@@ -286,6 +281,7 @@ export function LogoutRoot(props) {
     let navigate = useNavigate();
     let appName = useContext(CAppName);
     let routeHelper = useContext(CRouteHelper);
+    useContext(CLoginStatusRef).current.isLoggedIn = false;
     useEffect(() => {
         fetch(routeHelper.globalRoute("authLogout", { simulation_type: appName })).then(() => navigate(routeHelper.localRoute("root")));
     })

diff --git a/react/src/layout/report.tsx b/react/src/layout/report.tsx
@@ -441,6 +441,10 @@ export class SimulationStartLayout extends Layout<SimulationStartConfig, {}> {
                                 <span>{'Simulation Completed'}</span>
                                 <span>{stopwatch.formatElapsedTime()}</span>
                                 <div>{children}</div>
+                                { simState.alert && <div className="card card-body bg-light">
+                                    <pre>{simState.alert}</pre>
+                                  </div>
+                                }
                                 {startSimulationButton}
                             </Stack>
                         )
@@ -458,6 +462,9 @@ export class SimulationStartLayout extends Layout<SimulationStartConfig, {}> {
                             <Stack gap={2}>
                                 <span>{'Simulation Error'}</span>
                                 <span>{stopwatch.formatElapsedTime()}</span>
+                                <div className="card card-body bg-light">
+                                    <pre>{simState.alert || simState.error}</pre>
+                                </div>
                                 <div>{children}</div>
                                 {startSimulationButton}
                             </Stack>

diff --git a/sirepo/auth/__init__.py b/sirepo/auth/__init__.py
@@ -178,15 +178,11 @@ def complete_registration(self, name=None):
         """Update the database with the user's display_name and sets state to logged-in.
         Guests will have no name.
         """
-        u = self._qcall_bound_user()
-        with sirepo.util.THREAD_LOCK:
-            r = self.user_registration(u)
-            if self._qcall_bound_method() == METHOD_GUEST and name is not None:
-                raise AssertionError(
-                    "user name={name} should be None with method={METHOD_GUEST}",
-                )
-            r.display_name = name
-            r.save()
+        if self._qcall_bound_method() == METHOD_GUEST and name is not None:
+            raise AssertionError(
+                "user name={name} should be None with method={METHOD_GUEST}",
+            )
+        self.user_registration(self._qcall_bound_user(), display_name=name)
         self.qcall.cookie.set_value(_COOKIE_STATE, _STATE_LOGGED_IN)
 
     def cookie_cleaner(self, values):
@@ -313,25 +309,20 @@ def login(
         model=None,
         sim_type=None,
         display_name=None,
-        is_mock=False,
         want_redirect=False,
     ):
         """Login the user
 
         Raises an exception if successful, except in the case of methods
 
         Args:
-            method (module or str): method module (only if is_mock) [None]
+            method (module or str): method module
             uid (str): user to login [None]
             model (auth_db.UserDbBase): user to login (overrides uid) [None]
             sim_type (str): app to redirect to [None]
             display_name (str): to save as the display_name [None]
-            is_mock (bool): simulated login for srunit.quest_start [False]
             want_redirect (bool): http redirect on success [False]
         """
-        if method is None:
-            assert is_mock, "only used by srunit.quest_start"
-            method = METHOD_GUEST
         mm = _METHOD_MODULES[method] if isinstance(method, str) else method
         self._validate_method(mm, sim_type=sim_type)
         guest_uid = None
@@ -373,11 +364,14 @@ def login(
                 model.save()
         if display_name:
             self.complete_registration(self.parse_display_name(display_name))
-        if is_mock:
-            return
         if sim_type:
             if guest_uid and guest_uid != uid:
-                simulation_db.migrate_guest_to_persistent_user(guest_uid, uid)
+                self.qcall.auth_db.commit()
+                simulation_db.migrate_guest_to_persistent_user(
+                    guest_uid,
+                    uid,
+                    qcall=self.qcall,
+                )
             self.login_success_response(sim_type, want_redirect)
         assert not mm.AUTH_METHOD_VISIBLE
 
@@ -418,6 +412,13 @@ def login_success_response(self, sim_type, want_redirect=False):
             sreply=self.qcall.reply_ok(PKDict(authState=self._auth_state())),
         )
 
+    def create_and_login_user(self):
+        """Create a new guest user and log them in
+
+        Only useful for testing.
+        """
+        self._create_user(_METHOD_MODULES[METHOD_GUEST], want_login=True)
+
     def need_complete_registration(self, model_or_uid):
         """Does unauthenticated user need to complete registration?
 
@@ -467,7 +468,7 @@ def require_auth_basic(self):
         if not uid:
             raise sirepo.util.WWWAuthenticate()
         self.qcall.cookie.set_sentinel()
-        self.login(m, uid=uid)
+        self._login_user(m, uid)
 
     def require_email_user(self):
         i = self.require_user()
@@ -514,6 +515,7 @@ def require_user(self):
             if m == METHOD_GUEST:
                 pkdc("guest completeRegistration={}", u)
                 self.complete_registration()
+                self.qcall.auth_db.commit()
                 return u
             r = "completeRegistration"
             e = "uid={} needs to complete registration".format(u)
@@ -535,13 +537,10 @@ def reset_state(self):
         self._set_log_user()
 
     def unchecked_get_user(self, uid):
-        with sirepo.util.THREAD_LOCK:
-            u = self.qcall.auth_db.model("UserRegistration").unchecked_search_by(
-                uid=uid
-            )
-            if u:
-                return u.uid
-            return None
+        u = self.qcall.auth_db.model("UserRegistration").unchecked_search_by(uid=uid)
+        if u:
+            return u.uid
+        return None
 
     def user_dir_not_found(self, user_dir, uid):
         """Called by sirepo.reply when user_dir is not found
@@ -552,17 +551,15 @@ def user_dir_not_found(self, user_dir, uid):
             user_dir (str): directory not found
             uid (str): user
         """
-        with sirepo.util.THREAD_LOCK:
-            for m in _METHOD_MODULES.values():
-                u = self._method_user_model(m, uid)
-                if u:
-                    u.delete()
-            u = self.qcall.auth_db.model("UserRegistration").unchecked_search_by(
-                uid=uid
-            )
+        for m in _METHOD_MODULES.values():
+            u = self._method_user_model(m, uid)
             if u:
                 u.delete()
+        u = self.qcall.auth_db.model("UserRegistration").unchecked_search_by(uid=uid)
+        if u:
+            u.delete()
         self.reset_state()
+        self.qcall.auth_db.commit()
         pkdlog("user_dir={} uid={}", user_dir, uid)
         return self.qcall.reply_redirect_for_app_root()
 
@@ -603,7 +600,11 @@ def user_registration(self, uid, display_name=None):
             auth.UserRegistration: record (potentially blank)
         """
         res = self.qcall.auth_db.model("UserRegistration").unchecked_search_by(uid=uid)
-        if not res:
+        if res:
+            if display_name is not None:
+                res.display_name = display_name
+                res.save()
+        else:
             res = self.qcall.auth_db.model(
                 "UserRegistration",
                 created=datetime.datetime.utcnow(),