Merge branch 'release_20.09' into dev

Author: mvdbeek

client/src/components/User/ExternalIdentities/ExternalIdentities.vue

@@ -89,7 +89,7 @@ import Vue from "vue";
 import BootstrapVue from "bootstrap-vue";
 import { getGalaxyInstance } from "app";
 import svc from "./service";
-import { logoutClick } from "layout/menu";
+import { userLogout } from "layout/menu";
 import ExternalLogin from "components/User/ExternalIdentities/ExternalLogin.vue";
 
 Vue.use(BootstrapVue);
@@ -180,7 +180,7 @@ export default {
         disconnectAndReset() {
             // Disconnects the user's final ext id and logouts of current session
             this.disconnectID();
-            logoutClick();
+            userLogout();
         },
         removeItem(item) {
             this.items = this.items.filter((o) => o != item);

client/src/components/User/UserPreferences.vue

@@ -88,6 +88,7 @@ import _l from "utils/localization";
 import axios from "axios";
 import QueryStringParsing from "utils/query-string-parsing";
 import { getUserPreferencesModel } from "components/User/UserPreferencesModel";
+import { userLogoutAll, userLogoutClient } from "layout/menu";
 import "@fortawesome/fontawesome-svg-core";
 
 Vue.use(BootstrapVue);
@@ -217,11 +218,7 @@ export default {
                     Cancel: function () {
                         Galaxy.modal.hide();
                     },
-                    "Sign out": function () {
-                        window.location.href = `${getAppRoot()}user/logout?session_csrf_token=${
-                            Galaxy.session_csrf_token
-                        }`;
-                    },
+                    "Sign out": userLogoutAll,
                 },
             });
         },
@@ -241,23 +238,21 @@ export default {
             this.handleSubmit();
         },
         async handleSubmit() {
-            const Galaxy = getGalaxyInstance();
-            const userId = Galaxy.user.id;
             if (!this.checkFormValidity()) {
                 return false;
             }
             if (this.email === this.name) {
                 this.nameState = true;
                 try {
-                    await axios.delete(`${getAppRoot()}api/users/${userId}`);
+                    await axios.delete(`${getAppRoot()}api/users/${this.userId}`);
                 } catch (e) {
                     if (e.response.status === 403) {
                         this.deleteError =
                             "User deletion must be configured on this instance in order to allow user self-deletion.  Please contact an administrator for assistance.";
                         return false;
                     }
                 }
-                window.location.href = `${getAppRoot()}user/logout?session_csrf_token=${Galaxy.session_csrf_token}`;
+                userLogoutClient();
             } else {
                 this.nameState = false;
                 return false;

client/src/layout/menu.js

@@ -3,10 +3,16 @@ import { getGalaxyInstance } from "app";
 import _l from "utils/localization";
 import { CommunicationServerView } from "layout/communication-server-view";
 
-export function logoutClick() {
+const POST_LOGOUT_URL = "root/login?is_logout_redirect=true";
+
+/**
+ * Handles user logout.  Invalidates the current session, checks to see if we
+ * need to log out of OIDC too, and goes to our POST_LOGOUT_URL (or some other
+ * configured redirect). */
+export function userLogout(logoutAll = false) {
     const galaxy = getGalaxyInstance();
     const session_csrf_token = galaxy.session_csrf_token;
-    const url = `${galaxy.root}user/logout?session_csrf_token=${session_csrf_token}`;
+    const url = `${galaxy.root}user/logout?session_csrf_token=${session_csrf_token}&logout_all=${logoutAll}`;
     axios
         .get(url)
         .then(() => {
@@ -21,14 +27,29 @@ export function logoutClick() {
             }
         })
         .then((response) => {
-            if (response.data && response.data.redirect_uri) {
+            if (response.data?.redirect_uri) {
                 window.top.location.href = response.data.redirect_uri;
             } else {
-                window.top.location.href = `${galaxy.root}root/login?is_logout_redirect=true`;
+                window.top.location.href = `${galaxy.root}${POST_LOGOUT_URL}`;
             }
         });
 }
 
+/** User logout with 'log out all sessions' flag set.  This will invalidate all
+ * active sessions a user might have. */
+export function userLogoutAll() {
+    return userLogout(true);
+}
+
+/** Purely clientside logout, dumps session and redirects without invalidating
+ * serverside. Currently only used when marking an account deleted -- any
+ * subsequent navigation after the deletion API request would fail otherwise */
+export function userLogoutClient() {
+    const galaxy = getGalaxyInstance();
+    galaxy.user?.clearSessionStorage();
+    window.top.location.href = `${galaxy.root}${POST_LOGOUT_URL}`;
+}
+
 export function fetchMenu(options = {}) {
     const Galaxy = getGalaxyInstance();
     const menu = [];
@@ -244,7 +265,7 @@ export function fetchMenu(options = {}) {
                 {
                     title: _l("Logout"),
                     divider: true,
-                    onclick: logoutClick,
+                    onclick: userLogout,
                 },
                 {
                     title: _l("Datasets"),

lib/galaxy/jobs/runners/kubernetes.py

@@ -2,7 +2,6 @@
 Offload jobs to a Kubernetes cluster.
 """
 
-import errno
 import logging
 import math
 import os
@@ -459,30 +458,14 @@ def check_watched_item(self, job_state):
             # there is no job responding to this job_id, it is either lost or something happened.
             log.error("No Jobs are available under expected selector app=%s", job_state.job_id)
             self.mark_as_failed(job_state)
-            try:
-                with open(job_state.error_file, 'w') as error_file:
-                    error_file.write("No Kubernetes Jobs are available under expected selector app=%s\n" % job_state.job_id)
-            except OSError as e:
-                # Python 2/3 compatible handling of FileNotFoundError
-                if e.errno == errno.ENOENT:
-                    log.error("Job directory already cleaned up. Assuming already handled for selector app=%s", job_state.job_id)
-                else:
-                    raise
-            return job_state
+            # job is no longer viable - remove from watched jobs
+            return None
         else:
             # there is more than one job associated to the expected unique job id used as selector.
             log.error("More than one Kubernetes Job associated to job id '%s'", job_state.job_id)
             self.mark_as_failed(job_state)
-            try:
-                with open(job_state.error_file, 'w') as error_file:
-                    error_file.write("More than one Kubernetes Job associated with job id '%s'\n" % job_state.job_id)
-            except OSError as e:
-                # Python 2/3 compatible handling of FileNotFoundError
-                if e.errno == errno.ENOENT:
-                    log.error("Job directory already cleaned up. Assuming already handled for selector app=%s", job_state.job_id)
-                else:
-                    raise
-            return job_state
+            # job is no longer viable - remove from watched jobs
+            return None
 
     def _handle_job_failure(self, job, job_state):
         # Figure out why job has failed

lib/galaxy/tool_util/cwl/util.py

@@ -338,7 +338,7 @@ def __init__(self, contents, path=None, **kwargs):
         self.path = path
 
     def __str__(self):
-        return "FileLiteralTarget[path={}] with {}".format(self.path, self.properties)
+        return "FileLiteralTarget[contents={}] with {}".format(self.contents, self.properties)
 
 
 class FileUploadTarget:

lib/galaxy/tools/repositories.py

@@ -29,6 +29,7 @@ def __init__(self, app_name,
         self.temporary_path = tempfile.mkdtemp(prefix='tool_validation_')
         self.config.tool_data_table_config = os.path.join(self.temporary_path, 'tool_data_table_conf.xml')
         self.config.shed_tool_data_table_config = os.path.join(self.temporary_path, 'shed_tool_data_table_conf.xml')
+        self.config.interactivetools_enable = True
         self.tool_data_tables = tool_data_tables
         self.tool_shed_registry = Bunch(tool_sheds={})
         self.datatypes_registry = registry

lib/galaxy/webapps/galaxy/controllers/tool_runner.py

@@ -47,6 +47,9 @@ def __tool_404__():
         # tool id not available, redirect to main page
         if tool_id is None:
             return trans.response.send_redirect(url_for(controller='root', action='welcome'))
+        if tool_id.endswith('/'):
+            # Probably caused by a redirect
+            tool_id = tool_id[:-1]
         tool = self.__get_tool(tool_id)
         # tool id is not matching, display an error
         if not tool:

lib/galaxy/webapps/galaxy/controllers/user.py

@@ -200,7 +200,7 @@ def resend_activation_email(self, trans, email, username):
         """
         if email is None:  # User is coming from outside registration form, load email from trans
             if not trans.user:
-                trans.show_error_message("No session found, cannot send activation email.")
+                return "No session found, cannot send activation email.", None
             email = trans.user.email
         if username is None:  # User is coming from outside registration form, load email from trans
             username = trans.user.username

lib/galaxy_test/selenium/test_sign_out.py

@@ -18,4 +18,5 @@ def test_sign_out(self):
         self.assertTrue(email == new_email)
         self.components.preferences.sign_out.wait_for_and_click()
         self.components.sign_out.sign_out_button.wait_for_and_click()
+        self.sleep_for(self.wait_types.UX_TRANSITION)
         assert not self.is_logged_in()

test/integration/test_kubernetes_runner.py

@@ -216,6 +216,17 @@ def test_job_environment(self):
         job_env = self._run_and_get_environment_properties()
         assert job_env.some_env == '42'
 
+    @staticmethod
+    def _wait_for_external_state(sa_session, job, expected):
+        # Not checking the state here allows the change from queued to running to overwrite
+        # the change from queued to deleted_new in the API thread - this is a problem because
+        # the job will still run. See issue https://github.com/galaxyproject/galaxy/issues/4960.
+        max_tries = 60
+        while max_tries > 0 and job.job_runner_external_id is None or job.state != expected:
+            sa_session.refresh(job)
+            time.sleep(1)
+            max_tries -= 1
+
     @skip_without_tool('cat_data_and_sleep')
     def test_kill_process(self):
         with self.dataset_populator.test_history() as history_id:
@@ -234,22 +245,12 @@ def test_kill_process(self):
 
             app = self._app
             sa_session = app.model.context.current
-            external_id = None
-            state = False
-
-            job = sa_session.query(app.model.Job).filter_by(tool_id="cat_data_and_sleep").one()
-            # Not checking the state here allows the change from queued to running to overwrite
-            # the change from queued to deleted_new in the API thread - this is a problem because
-            # the job will still run. See issue https://github.com/galaxyproject/galaxy/issues/4960.
-            max_tries = 60
-            while max_tries > 0 and external_id is None or state != app.model.Job.states.RUNNING:
-                sa_session.refresh(job)
-                assert not job.finished
-                external_id = job.job_runner_external_id
-                state = job.state
-                time.sleep(1)
-                max_tries -= 1
+            job = sa_session.query(app.model.Job).get(app.security.decode_id(job_dict["id"]))
+
+            self._wait_for_external_state(sa_session, job, app.model.Job.states.RUNNING)
+            assert not job.finished
 
+            external_id = job.job_runner_external_id
             output = unicodify(subprocess.check_output(['kubectl', 'get', 'job', external_id, '-o', 'json']))
             status = json.loads(output)
             assert status['status']['active'] == 1
@@ -264,6 +265,42 @@ def test_kill_process(self):
                 subprocess.check_output(['kubectl', 'get', 'job', external_id, '-o', 'json'], stderr=subprocess.STDOUT)
             assert "not found" in unicodify(excinfo.value.output)
 
+    @skip_without_tool('cat_data_and_sleep')
+    def test_external_job_delete(self):
+        with self.dataset_populator.test_history() as history_id:
+            hda1 = self.dataset_populator.new_dataset(history_id, content="1 2 3")
+            running_inputs = {
+                "input1": {"src": "hda", "id": hda1["id"]},
+                "sleep_time": 240,
+            }
+            running_response = self.dataset_populator.run_tool(
+                "cat_data_and_sleep",
+                running_inputs,
+                history_id,
+                assert_ok=False,
+            )
+            job_dict = running_response.json()["jobs"][0]
+
+            app = self._app
+            sa_session = app.model.context.current
+            job = sa_session.query(app.model.Job).get(app.security.decode_id(job_dict["id"]))
+
+            self._wait_for_external_state(sa_session, job, app.model.Job.states.RUNNING)
+
+            external_id = job.job_runner_external_id
+            output = unicodify(subprocess.check_output(['kubectl', 'get', 'job', external_id, '-o', 'json']))
+            status = json.loads(output)
+            assert status['status']['active'] == 1
+
+            output = unicodify(subprocess.check_output(['kubectl', 'delete', 'job', external_id, '-o', 'name']))
+            assert 'job.batch/%s' % external_id in output
+
+            result = self.dataset_populator.wait_for_tool_run(run_response=running_response, history_id=history_id,
+                                                              assert_ok=False).json()
+            details = self.dataset_populator.get_job_details(result['jobs'][0]['id'], full=True).json()
+
+            assert details['state'] == app.model.Job.states.ERROR, details
+
     @skip_without_tool('job_properties')
     def test_exit_code_127(self):
         inputs = {