Merge pull request #643 from fractal-analytics-platform/2.9.0-alignment

More fractal-server 2.9.0 alignments
fractal-analytics-platform · Nov 20, 2024 · 2d13474 · 2d13474
2 parents ee08ef0 + a55afd7
commit 2d13474
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,10 +2,15 @@
 
 # Unreleased
 
-* Alignment with fractal-server 2.9.0 (\#640):
+* Alignment with fractal-server 2.9.0 (\#640, \#643):
     * Updated task collections logic and created task-group activities pages for standard users and administrators (\#640);
     * Removed active checkbox from task group edit modal (\#640);
     * Added Manage button to deactivate and reactivate task groups (\#640);
+    * Removed usage of DB_ENGINE and SQLITE_PATH variables (\#643);
+    * Displayed `timestamp_last_used` property in task-group info modal (\#643);
+    * Viewer paths page improvements (\#643);
+    * Added manage buttons on admin task-groups page (\#643);
+    * Added last used timestamp filter to task-group admin page (\#643);
 
 # 1.10.1
 

diff --git a/examples/config_1/fractal_server.md b/examples/config_1/fractal_server.md
@@ -10,8 +10,6 @@ FRACTAL_TASKS_DIR=tasks
 FRACTAL_LOGGING_LEVEL=00
 FRACTAL_RUNNER_BACKEND=local
 FRACTAL_RUNNER_WORKING_BASE_DIR=artifacts
-DB_ENGINE=sqlite
-SQLITE_PATH=fractal_server.db
 ```
 
 Set-up and start-up command:
@@ -24,7 +22,6 @@ Logs include
 ```
 INFO:     Started server process [32331]
 INFO:     Waiting for application startup.
-2023-05-18 07:55:41,391 - fractal_server.app.db - WARNING - SQLite is supported but discouraged in production. Given its partial support for ForeignKey constraints, consistency of the database cannot be guaranteed.
 2023-05-18 07:55:41,742 - fractal_server.main - INFO - User [email protected] created
 INFO:     Application startup complete.
 INFO:     Uvicorn running on http://X.X.X.X:8000 (Press CTRL+C to quit)

diff --git a/examples/config_2_with_domain/fractal_server.md b/examples/config_2_with_domain/fractal_server.md
@@ -11,8 +11,6 @@ FRACTAL_TASKS_DIR=tasks
 FRACTAL_LOGGING_LEVEL=00
 FRACTAL_RUNNER_BACKEND=local
 FRACTAL_RUNNER_WORKING_BASE_DIR=artifacts
-DB_ENGINE=sqlite
-SQLITE_PATH=fractal_server.db
 ```
 
 Set-up and start-up command:
@@ -27,7 +25,6 @@ Logs include
 fractal_server.app.db
 INFO:     Started server process [32375]
 INFO:     Waiting for application startup.
-2023-06-13 08:23:13,678 - fractal_server.app.db - WARNING - SQLite is supported but discouraged in production. Given its partial support for ForeignKey constraints, consistency of the database cannot be guaranteed.
 2023-06-13 08:23:13,736 - fractal_server.main - WARNING - User [email protected] already exists
 INFO:     Application startup complete.
 INFO:     Uvicorn running on http://fractal.XXX.ch:8000 (Press CTRL+C to quit)

diff --git a/examples/config_3_with_domain_and_https/fractal_server.md b/examples/config_3_with_domain_and_https/fractal_server.md
@@ -4,7 +4,6 @@
 DEPLOYMENT_TYPE=testing
 JWT_SECRET_KEY=XXX
 JWT_EXPIRE_SECONDS=80000
-DB_ENGINE=postgres-psycopg
 POSTGRES_USER=XXX
 POSTGRES_HOST=XXX
 POSTGRES_DB=XXX

diff --git a/examples/config_4_with_domain_and_https/fractal_server.md b/examples/config_4_with_domain_and_https/fractal_server.md
@@ -4,7 +4,6 @@
 DEPLOYMENT_TYPE=testing
 JWT_SECRET_KEY=XXX
 JWT_EXPIRE_SECONDS=80000
-DB_ENGINE=postgres-psycopg
 POSTGRES_USER=XXX
 POSTGRES_HOST=XXX
 POSTGRES_DB=XXX

diff --git a/playwright.config.js b/playwright.config.js
@@ -107,7 +107,7 @@ export default defineConfig({
 
 	webServer: [
 		{
-			command: './tests/start-test-server.sh 2.9.0a0',
+			command: './tests/start-test-server.sh 2.9.0a5',
 			port: 8000,
 			waitForPort: true,
 			stdout: 'pipe',

diff --git a/src/lib/components/v2/tasks/TaskGroupActivities.svelte b/src/lib/components/v2/tasks/TaskGroupActivities.svelte
@@ -154,7 +154,7 @@
 		if (activityId && !isNaN(Number(activityId))) {
 			task_group_activity_id = Number(activityId);
 		}
-		if (!admin) {
+		if (!admin || task_group_activity_id !== null) {
 			await searchActivities();
 		}
 		updateTasksCollectionTimeout = setTimeout(

diff --git a/src/lib/components/v2/tasks/TaskGroupInfoModal.svelte b/src/lib/components/v2/tasks/TaskGroupInfoModal.svelte
@@ -1,5 +1,6 @@
 <script>
 	import BooleanIcon from '$lib/components/common/BooleanIcon.svelte';
+	import TimestampCell from '$lib/components/jobs/TimestampCell.svelte';
 	import Modal from '../../common/Modal.svelte';
 
 	/** @type {import('$lib/types').User} */
@@ -61,9 +62,15 @@
 						<li class="list-group-item list-group-item-light fw-bold">Number of files</li>
 						<li class="list-group-item">{taskGroup.venv_file_number || '-'}</li>
 						<li class="list-group-item list-group-item-light fw-bold">Size (MB)</li>
-						<li class="list-group-item">{(taskGroup.venv_size_in_kB / 1000).toFixed(2)}</li>
+						<li class="list-group-item">
+							{taskGroup.venv_size_in_kB ? (taskGroup.venv_size_in_kB / 1000).toFixed(2) : '-'}
+						</li>
 						<li class="list-group-item list-group-item-light fw-bold">Pip extras</li>
 						<li class="list-group-item">{taskGroup.pip_extras || '-'}</li>
+						<li class="list-group-item list-group-item-light fw-bold">Last used</li>
+						<li class="list-group-item">
+							<TimestampCell timestamp={taskGroup.timestamp_last_used} />
+						</li>
 					</ul>
 				</div>
 			</div>

diff --git a/src/lib/components/v2/tasks/TaskGroupManageModal.svelte b/src/lib/components/v2/tasks/TaskGroupManageModal.svelte
@@ -3,6 +3,9 @@
 	import { displayStandardErrorAlert, getAlertErrorFromResponse } from '$lib/common/errors';
 	import Modal from '../../common/Modal.svelte';
 
+	/** @type {boolean} */
+	export let admin;
+
 	/** @type {Modal} */
 	let modal;
 
@@ -36,7 +39,9 @@
 		headers.append('Content-Type', 'application/json');
 
 		const response = await fetch(
-			`/api/v2/task-group/${taskGroup?.id}/${active ? 'reactivate' : 'deactivate'}/`,
+			`/api/${admin ? 'admin/' : ''}v2/task-group/${taskGroup?.id}/${
+				active ? 'reactivate' : 'deactivate'
+			}/`,
 			{
 				method: 'POST',
 				credentials: 'include',
@@ -48,7 +53,8 @@
 
 		if (response.ok) {
 			const result = await response.json();
-			goto(`/v2/tasks/activities?activity_id=${result.id}`);
+			const page = admin ? `/v2/admin/task-groups/activities` : `/v2/tasks/activities`;
+			goto(`${page}?activity_id=${result.id}`);
 			modal.hide();
 		} else {
 			errorAlert = displayStandardErrorAlert(

diff --git a/src/lib/components/v2/tasks/TaskGroupsTable.svelte b/src/lib/components/v2/tasks/TaskGroupsTable.svelte
@@ -268,7 +268,7 @@
 	{updateEditedTaskGroup}
 	groupIdsNames={user.group_ids_names || []}
 />
-<TaskGroupManageModal bind:this={taskGroupManageModal} />
+<TaskGroupManageModal bind:this={taskGroupManageModal} admin={false} />
 <TaskInfoModal bind:this={taskInfoModal} />
 <TaskEditModal bind:this={taskEditModal} {updateEditedTask} />
 

diff --git a/src/lib/types-v2.d.ts b/src/lib/types-v2.d.ts
@@ -166,6 +166,7 @@ export type TaskGroupV2 = {
 	pip_extras: string;
 	active: boolean;
 	timestamp_created: string;
+	timestamp_last_used: string;
 };
 
 export type WorkflowTasksTableRowGroup = {

diff --git a/src/routes/v2/admin/task-groups/+page.svelte b/src/routes/v2/admin/task-groups/+page.svelte
@@ -1,10 +1,13 @@
 <script>
 	import { page } from '$app/stores';
+	import { getTimestamp } from '$lib/common/component_utilities';
 	import { displayStandardErrorAlert, getAlertErrorFromResponse } from '$lib/common/errors';
 	import BooleanIcon from '$lib/components/common/BooleanIcon.svelte';
 	import ConfirmActionButton from '$lib/components/common/ConfirmActionButton.svelte';
 	import Modal from '$lib/components/common/Modal.svelte';
+	import TimestampCell from '$lib/components/jobs/TimestampCell.svelte';
 	import TaskGroupEditModal from '$lib/components/v2/tasks/TaskGroupEditModal.svelte';
+	import TaskGroupManageModal from '$lib/components/v2/tasks/TaskGroupManageModal.svelte';
 
 	/** @type {Array<import('$lib/types').User>} */
 	const users = $page.data.users;
@@ -19,6 +22,10 @@
 	let privateGroup = null;
 	/** @type {boolean|null} */
 	let active = null;
+	let lastUsedDateMin;
+	let lastUsedTimeMin = '';
+	let lastUsedDateMax = '';
+	let lastUsedTimeMax = '';
 
 	let searched = false;
 	let searching = false;
@@ -35,6 +42,8 @@
 
 	/** @type {import('$lib/components/v2/tasks/TaskGroupEditModal.svelte').default} */
 	let taskGroupEditModal;
+	/** @type {import('$lib/components/v2/tasks/TaskGroupManageModal.svelte').default} */
+	let taskGroupManageModal;
 
 	async function searchTaskGroups() {
 		searching = true;
@@ -61,6 +70,14 @@
 			if (active !== null) {
 				url.searchParams.append('active', active.toString());
 			}
+			const lasUsedTimestampMin = getTimestamp(lastUsedDateMin, lastUsedTimeMin);
+			if (lasUsedTimestampMin) {
+				url.searchParams.append('timestamp_last_used_min', lasUsedTimestampMin);
+			}
+			const lasUsedTimestampMax = getTimestamp(lastUsedDateMax, lastUsedTimeMax);
+			if (lasUsedTimestampMax) {
+				url.searchParams.append('timestamp_last_used_max', lasUsedTimestampMax);
+			}
 			const response = await fetch(url);
 			if (!response.ok) {
 				searchErrorAlert = displayStandardErrorAlert(
@@ -84,6 +101,10 @@
 		user_group_id = '';
 		pkg_name = '';
 		origin = '';
+		lastUsedDateMin = '';
+		lastUsedTimeMin = '';
+		lastUsedDateMax = '';
+		lastUsedTimeMax = '';
 		privateGroup = null;
 		active = null;
 		searched = false;
@@ -233,6 +254,48 @@
 				</div>
 			</div>
 		</div>
+
+		<div class="row mt-3">
+			<div class="col-md-3 col-lg-2 mt-2">Last used</div>
+			<div class="col-md-9 col-lg-10">
+				<div class="row row-cols-md-auto">
+					<div class="col-12 mt-1">
+						<div class="input-group">
+							<div class="input-group-text">Min</div>
+							<input
+								type="date"
+								class="form-control"
+								bind:value={lastUsedDateMin}
+								id="last_used_date_min"
+							/>
+							<input
+								type="time"
+								class="form-control"
+								bind:value={lastUsedTimeMin}
+								id="last_used_time_min"
+							/>
+						</div>
+					</div>
+					<div class="col-12 mt-1">
+						<div class="input-group">
+							<div class="input-group-text">Max</div>
+							<input
+								type="date"
+								class="form-control"
+								bind:value={lastUsedDateMax}
+								id="last_used_date_max"
+							/>
+							<input
+								type="time"
+								class="form-control"
+								bind:value={lastUsedTimeMax}
+								id="last_used_time_max"
+							/>
+						</div>
+					</div>
+				</div>
+			</div>
+		</div>
 	</div>
 </div>
 
@@ -266,7 +329,7 @@
 				<col width="90" />
 				<col width="90" />
 				<col width="90" />
-				<col width="270" />
+				<col width="400" />
 			</colgroup>
 			<thead>
 				<tr>
@@ -303,6 +366,10 @@
 								<i class="bi bi-pencil" />
 								Edit
 							</button>
+							<button class="btn btn-info" on:click={() => taskGroupManageModal.open(taskGroup)}>
+								<i class="bi bi-gear" />
+								Manage
+							</button>
 							<ConfirmActionButton
 								modalId="confirmTaskGroupDeleteModal{taskGroup.pkg_name}"
 								style={'danger'}
@@ -330,8 +397,9 @@
 	updateEditedTaskGroup={searchTaskGroups}
 	groupIdsNames={groups.map((g) => [g.id, g.name])}
 />
+<TaskGroupManageModal bind:this={taskGroupManageModal} admin={true} />
 
-<Modal id="taskInfoModal" bind:this={infoModal} size="lg" onClose={onInfoModalClose}>
+<Modal id="taskInfoModal" bind:this={infoModal} size="xl" onClose={onInfoModalClose}>
 	<svelte:fragment slot="header">
 		<h1 class="h5 modal-title flex-grow-1">Task-group info</h1>
 	</svelte:fragment>
@@ -360,8 +428,20 @@
 				<li class="list-group-item">{selectedTaskGroup.path || '-'}</li>
 				<li class="list-group-item list-group-item-light fw-bold">Venv path</li>
 				<li class="list-group-item">{selectedTaskGroup.venv_path || '-'}</li>
+				<li class="list-group-item list-group-item-light fw-bold">Number of files</li>
+				<li class="list-group-item">{selectedTaskGroup.venv_file_number || '-'}</li>
+				<li class="list-group-item list-group-item-light fw-bold">Size (MB)</li>
+				<li class="list-group-item">
+					{selectedTaskGroup.venv_size_in_kB
+						? (selectedTaskGroup.venv_size_in_kB / 1000).toFixed(2)
+						: '-'}
+				</li>
 				<li class="list-group-item list-group-item-light fw-bold">Pip extras</li>
 				<li class="list-group-item">{selectedTaskGroup.pip_extras || '-'}</li>
+				<li class="list-group-item list-group-item-light fw-bold">Last used</li>
+				<li class="list-group-item">
+					<TimestampCell timestamp={selectedTaskGroup.timestamp_last_used} />
+				</li>
 			</ul>
 		{/if}
 	</svelte:fragment>
@@ -384,4 +464,8 @@
 	.row-grey {
 		background-color: #f2f2f2;
 	}
+
+	input[type='date'] {
+		min-width: 190px;
+	}
 </style>
diff --git a/src/routes/viewer-paths/+page.server.js b/src/routes/viewer-paths/+page.server.js
@@ -1,4 +1,4 @@
-import { getCurrentUserViewerPaths } from '$lib/server/api/auth_api.js';
+import { getCurrentUserSettings, getCurrentUserViewerPaths } from '$lib/server/api/auth_api.js';
 import { getLogger } from '$lib/server/logger.js';
 
 const logger = getLogger('viewer paths page');
@@ -7,8 +7,10 @@ export async function load({ fetch }) {
 	logger.trace('Load viewer paths page');
 
 	const viewerPaths = await getCurrentUserViewerPaths(fetch);
+	const settings = await getCurrentUserSettings(fetch);
 
 	return {
-		viewerPaths
+		viewerPaths,
+		settings
 	};
 }
diff --git a/src/routes/viewer-paths/+page.svelte b/src/routes/viewer-paths/+page.svelte
@@ -2,13 +2,40 @@
 	import { page } from '$app/stores';
 
 	/** @type {string[]} */
-	let viewerPaths = $page.data.viewerPaths;
+	const viewerPaths = $page.data.viewerPaths;
+	/** @type {import('$lib/types').UserSettings} */
+	const settings = $page.data.settings;
 </script>
 
 <h1 class="fw-light mb-3">Viewer paths</h1>
 
+<p>
+	This Fractal instance includes an online viewer for OME-Zarrs, based on
+	<a href="https://github.com/hms-dbmi/vizarr" target="_blank">vizarr</a>. Browse to a dataset page,
+	and you will find links to view the available images in the browser.
+</p>
+
+<p>
+	Note that access to image data is restricted to OME-Zarrs within certain paths (and their
+	subfolders).
+	{#if settings.project_dir || viewerPaths.length > 0}
+		The list of paths accessible to the current user includes:
+	{:else}
+		The list of paths accessible to the current user is empty.
+	{/if}
+</p>
+
 <ul>
+	{#if settings.project_dir}
+		<li><code>{settings.project_dir}</code></li>
+	{/if}
 	{#each viewerPaths as viewerPath}
 		<li><code>{viewerPath}</code></li>
 	{/each}
 </ul>
+
+<p>
+	Depending on the Fractal configuration, you may also have access to additional paths.<br />
+	Please contact an admin if you see an error message like <code>403 Forbidden</code> when opening the
+	image viewer.
+</p>
diff --git a/tests/.fractal_server.env b/tests/.fractal_server.env
@@ -1,6 +1,5 @@
 DEPLOYMENT_TYPE=testing
 JWT_SECRET_KEY=somethingverysecret
-DB_ENGINE=postgres-psycopg
 POSTGRES_DB=fractal_test
 POSTGRES_USER=postgres
 POSTGRES_PASSWORD=postgres