Merge pull request #15958 from mvdbeek/dev

Merge 23.0 into dev
galaxyproject · Apr 20, 2023 · 6f7def1 · 6f7def1
2 parents da6f448 + 3d836f0
commit 6f7def1
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Showing 16 changed files with 98 additions and 17 deletions.
diff --git a/client/src/components/ClientError.vue b/client/src/components/ClientError.vue
@@ -6,7 +6,6 @@
 // (AdminRequired), but could be used for other client errors that need to be
 // presented to the user interrupting the normal flow and context of the app.
 
-import { defineProps } from "vue";
 import Alert from "@/components/Alert.vue";
 
 const props = defineProps<{

diff --git a/client/src/components/providers/UserHistories.js b/client/src/components/providers/UserHistories.js
@@ -28,7 +28,9 @@ export default {
             return null;
         },
         historyModels() {
-            return this.histories.map((h) => Object.assign({}, h));
+            return this.histories
+                .map((h) => Object.assign({}, h))
+                .filter((h) => !h.user_id || h.user_id === this.user.id);
         },
     },
     methods: {

diff --git a/client/src/composables/toast.ts b/client/src/composables/toast.ts
@@ -30,7 +30,7 @@ export const Toast = {
     },
 
     error(message: string, title = "Error") {
-        toastRef.value?.showToast(message, title, "error");
+        toastRef.value?.showToast(message, title, "danger");
     },
 };
 

diff --git a/client/src/entry/analysis/router.js b/client/src/entry/analysis/router.js
@@ -504,18 +504,41 @@ export function getRouter(Galaxy) {
         ],
     });
 
-    router.beforeEach(async (to, from, next) => {
-        // TODO: merge anon redirect functionality here for more standard handling
-
+    function checkAdminAccessRequired(to) {
         // Check parent route hierarchy to see if we require admin access here.
         // Access is required if *any* component in the hierarchy requires it.
         if (to.matched.some((record) => record.meta.requiresAdmin === true)) {
-            const isAdmin = getGalaxyInstance()?.user?.isAdmin() || false;
-            if (!isAdmin) {
-                const error = new Error(`Administrator Access Required for '${to.path}'.`);
-                error.name = "AdminRequired";
-                next(error);
-            }
+            const isAdmin = getGalaxyInstance()?.user?.isAdmin();
+            return !isAdmin;
+        }
+        return false;
+    }
+
+    function checkRegisteredUserAccessRequired(to) {
+        // Check parent route hierarchy to see if we require registered user access here.
+        // Access is required if *any* component in the hierarchy requires it.
+        if (to.matched.some((record) => record.meta.requiresRegisteredUser === true)) {
+            const isAnonymous = getGalaxyInstance()?.user?.isAnonymous();
+            return isAnonymous;
+        }
+        return false;
+    }
+
+    router.beforeEach(async (to, from, next) => {
+        // TODO: merge anon redirect functionality here for more standard handling
+
+        const isAdminAccessRequired = checkAdminAccessRequired(to);
+        if (isAdminAccessRequired) {
+            const error = new Error(`Admin access required for '${to.path}'.`);
+            error.name = "AdminRequired";
+            next(error);
+        }
+
+        const isRegisteredUserAccessRequired = checkRegisteredUserAccessRequired(to);
+        if (isRegisteredUserAccessRequired) {
+            const error = new Error(`Registered user access required for '${to.path}'.`);
+            error.name = "RegisteredUserRequired";
+            next(error);
         }
         next();
     });

diff --git a/client/src/entry/analysis/routes/storageDashboardRoutes.ts b/client/src/entry/analysis/routes/storageDashboardRoutes.ts
@@ -6,6 +6,7 @@ export default [
     {
         path: "/storage",
         component: Base,
+        meta: { requiresRegisteredUser: true },
         children: [
             {
                 path: "",

diff --git a/client/src/store/historyStore/historyStore.js b/client/src/store/historyStore/historyStore.js
@@ -16,7 +16,7 @@ import {
 const state = {
     // selected history
     currentHistoryId: null,
-    // histories for current user
+    // histories for current user, can also have other user histories loaded for HistoryView
     histories: {},
     historiesLoading: false,
 };
@@ -98,7 +98,7 @@ let isLoadingHistories = false;
 const actions = {
     async copyHistory({ dispatch }, { history, name, copyAll }) {
         const newHistory = await cloneHistory(history, name, copyAll);
-        return dispatch("selectHistory", newHistory);
+        return dispatch("setCurrentHistory", newHistory.id);
     },
     async createNewHistory({ dispatch }) {
         // create history, then select it as current at the same time

diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst
@@ -2915,6 +2915,18 @@
 :Type: float
 
 
+~~~~~~~~~~~~~~~~~~~
+``sentry_ca_certs``
+~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Use this option to provide the path to location of the CA
+    (Certificate Authority) certificate file if the sentry server uses
+    a self-signed certificate.
+:Default: ``None``
+:Type: str
+
+
 ~~~~~~~~~~~~~~~
 ``statsd_host``
 ~~~~~~~~~~~~~~~

diff --git a/lib/galaxy/app.py b/lib/galaxy/app.py
@@ -202,6 +202,7 @@ def configure_sentry_client(self):
                 release=f"{self.config.version_major}.{self.config.version_minor}",
                 integrations=[sentry_logging],
                 traces_sample_rate=self.config.sentry_traces_sample_rate,
+                ca_certs=self.config.sentry_ca_certs,
             )
 
 

diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample
@@ -1670,6 +1670,11 @@ galaxy:
   # to Sentry. A value higher than 0 is required to analyze performance.
   #sentry_traces_sample_rate: 0.0
 
+  # Use this option to provide the path to location of the CA
+  # (Certificate Authority) certificate file if the sentry server uses a
+  # self-signed certificate.
+  #sentry_ca_certs: null
+
   # Log to statsd Statsd is an external statistics aggregator
   # (https://github.com/etsy/statsd) Enabling the following options will
   # cause galaxy to log request timing and other statistics to the

diff --git a/lib/galaxy/config/sample/tool_shed.yml.sample b/lib/galaxy/config/sample/tool_shed.yml.sample
@@ -316,6 +316,11 @@ tool_shed:
   # to Sentry. A value higher than 0 is required to analyze performance.
   #sentry_traces_sample_rate: 0.0
 
+  # Use this option to provide the path to location of the CA
+  # (Certificate Authority) certificate file if the sentry server uses a
+  # self-signed certificate.
+  #sentry_ca_certs: null
+
   # Galaxy Session Timeout This provides a timeout (in minutes) after
   # which a user will have to log back in. A duration of 0 disables this
   # feature.

diff --git a/lib/galaxy/config/schemas/config_schema.yml b/lib/galaxy/config/schemas/config_schema.yml
@@ -2108,6 +2108,13 @@ mapping:
           will have that percentage chance of being sent to Sentry. A value higher than 0
           is required to analyze performance.
 
+      sentry_ca_certs:
+        type: str
+        required: False
+        desc: |
+          Use this option to provide the path to location of the CA (Certificate Authority)
+          certificate file if the sentry server uses a self-signed certificate.
+
       statsd_host:
         type: str
         required: false

diff --git a/lib/galaxy/config/schemas/tool_shed_config_schema.yml b/lib/galaxy/config/schemas/tool_shed_config_schema.yml
@@ -566,6 +566,13 @@ mapping:
           will have that percentage chance of being sent to Sentry. A value higher than 0
           is required to analyze performance.
 
+      sentry_ca_certs:
+        type: str
+        required: False
+        desc: |
+          Use this option to provide the path to location of the CA (Certificate Authority)
+          certificate file if the sentry server uses a self-signed certificate.
+
       session_duration:
         type: int
         default: 0

diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt
@@ -73,7 +73,7 @@ fsspec==2023.1.0 ; python_version >= "3.7" and python_version < "3.12"
 future==0.18.3 ; python_version >= "3.7" and python_version < "3.12"
 galaxy-sequence-utils==1.1.5 ; python_version >= "3.7" and python_version < "3.12"
 galaxy2cwl==0.1.4 ; python_version >= "3.7" and python_version < "3.12"
-gravity==1.0.2 ; python_version >= "3.7" and python_version < "3.12"
+gravity==1.0.3 ; python_version >= "3.7" and python_version < "3.12"
 greenlet==2.0.2 ; python_version >= "3.7" and platform_machine == "aarch64" and python_version < "3.12" or python_version >= "3.7" and platform_machine == "ppc64le" and python_version < "3.12" or python_version >= "3.7" and platform_machine == "x86_64" and python_version < "3.12" or python_version >= "3.7" and platform_machine == "amd64" and python_version < "3.12" or python_version >= "3.7" and platform_machine == "AMD64" and python_version < "3.12" or python_version >= "3.7" and platform_machine == "win32" and python_version < "3.12" or python_version >= "3.7" and platform_machine == "WIN32" and python_version < "3.12"
 gunicorn==20.1.0 ; python_version >= "3.7" and python_version < "3.12"
 gxformat2==0.17.0 ; python_version >= "3.7" and python_version < "3.12"

diff --git a/lib/galaxy/jobs/runners/__init__.py b/lib/galaxy/jobs/runners/__init__.py
@@ -36,6 +36,7 @@
 )
 from galaxy.tool_util.output_checker import DETECTED_JOB_STATE
 from galaxy.util import (
+    asbool,
     DATABASE_MAX_STRING_SIZE,
     ExecutionTimer,
     in_directory,
@@ -342,7 +343,7 @@ def get_work_dir_outputs(
         output_paths = {}
         for dataset_path in job_wrapper.job_io.get_output_fnames():
             path = dataset_path.real_path
-            if job_wrapper.get_destination_configuration("outputs_to_working_directory", False):
+            if asbool(job_wrapper.get_destination_configuration("outputs_to_working_directory", False)):
                 path = dataset_path.false_path
             output_paths[dataset_path.dataset_id] = path
 

diff --git a/lib/galaxy/model/security.py b/lib/galaxy/model/security.py
@@ -1536,7 +1536,6 @@ def check_folder_contents(self, user, roles, folder, hidden_folder_ids=""):
             return True, ""
         action = self.permitted_actions.DATASET_ACCESS
 
-        raise
         lddas = (
             self.sa_session.query(self.model.LibraryDatasetDatasetAssociation)
             .join("library_dataset")

diff --git a/lib/galaxy_test/api/test_folders.py b/lib/galaxy_test/api/test_folders.py
@@ -19,6 +19,20 @@ def setUp(self):
     def test_create(self):
         folder = self._create_folder("Test Create Folder")
         self._assert_valid_folder(folder)
+        # assert that listing items in folder works.
+        # this is a regression test
+        response = self._get(f"libraries/{folder['parent_library_id']}/contents")
+        response.raise_for_status()
+
+    @requires_new_library
+    def test_list_library(self):
+        library, _ = self.library_populator.fetch_single_url_to_folder()
+        library = self._list_library(library["id"])
+        assert len(library) == 2
+        folders = [folder for folder in library if folder["type"] == "folder"]
+        assert len(folders) == 1
+        files = [file for file in library if file["type"] == "file"]
+        assert len(files) == 1
 
     @requires_new_library
     def test_create_without_name_raises_400(self):
@@ -117,6 +131,11 @@ def test_update_deleted_raise_403(self):
         put_response = self._put(f"folders/{folder_id}", data=data, admin=True, json=True)
         self._assert_status_code_is(put_response, 403)
 
+    def _list_library(self, library_id):
+        response = self._get(f"libraries/{library_id}/contents")
+        response.raise_for_status()
+        return response.json()
+
     def _create_folder(self, name: str):
         root_folder_id = self.library["root_folder_id"]
         data = {