Merge branch 'main' into release_blog_202404

delete.ipynb

@@ -0,0 +1,135 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# AiiDAlab QuantumESPRESSO App\n",
+    "\n",
+    "<font color=\"red\"><b>Caution!</b></font> Deleting this job will also remove <b>all associated nodes</b>, including every calculation initiated by this job and their respective results. This action is <b>irreversible</b>.\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import urllib.parse as urlparse\n",
+    "\n",
+    "import ipywidgets as widgets\n",
+    "from aiida import load_profile\n",
+    "from aiida.orm import load_node\n",
+    "from aiida.tools import delete_nodes\n",
+    "from IPython.display import Markdown, display\n",
+    "\n",
+    "# Load AiiDA profile\n",
+    "load_profile()\n",
+    "\n",
+    "# Parse the primary key from the Jupyter notebook URL\n",
+    "url = urlparse.urlsplit(jupyter_notebook_url) # noqa F821\n",
+    "query = urlparse.parse_qs(url.query)\n",
+    "pk = int(query['pk'][0])\n",
+    "\n",
+    "\n",
+    "def display_node_details(pk):\n",
+    "    try:\n",
+    "        node = load_node(pk)\n",
+    "        print(f\"Node ID: {node.pk}\")\n",
+    "        print(f\"Node Type: {node.process_label}\")\n",
+    "        print(f\"Label: {node.label}\")\n",
+    "        print(f\"Description: {node.description}\")\n",
+    "        print(f\"Creation Time: {node.ctime}\")\n",
+    "    except Exception as e:\n",
+    "        print(f\"Error loading node: {str(e)}\")\n",
+    "        return False\n",
+    "    return True\n",
+    "\n",
+    "\n",
+    "def delete_node(pk, dry_run=True):\n",
+    "    if dry_run:\n",
+    "        _, was_deleted = delete_nodes([pk], dry_run=True)\n",
+    "        if was_deleted:\n",
+    "            print(f'Dry run: Node {pk} can be deleted.')\n",
+    "        return\n",
+    "    \n",
+    "    _, was_deleted = delete_nodes([pk], dry_run=False)\n",
+    "    if was_deleted:\n",
+    "        print(f'Node {pk} deleted successfully.')\n",
+    "\n",
+    "\n",
+    "def confirm_deletion(b):\n",
+    "    if delete_confirmation.value.lower() in ['y', 'yes']:\n",
+    "        delete_node(pk, dry_run=False)\n",
+    "    else:\n",
+    "        print('Deletion aborted.')\n",
+    "\n",
+    "\n",
+    "def find_linked_qeapp_jobs(root_node_pk, process_label='QeAppWorkChain'):\n",
+    "    \"\"\"Query all linked node with process_label = QeAppWorkChain.\"\"\"\n",
+    "    from aiida.orm import Node, QueryBuilder\n",
+    "    from aiida.orm.nodes.process.workflow.workchain import WorkChainNode\n",
+    "    qb = QueryBuilder()\n",
+    "    qb.append(WorkChainNode, filters={'id': root_node_pk}, tag='root')\n",
+    "    qb.append(Node, with_incoming='root', tag='calcjob')\n",
+    "    # There are seems a bug with `with_ancestors` in the QueryBuilder, so we have to use `with_incoming` instead.\n",
+    "    # For the moment, it's safe to use `with_incoming` since we check it very time we delete a QEApp \n",
+    "    qb.append(WorkChainNode, filters={'attributes.process_label': 'QeAppWorkChain'}, with_incoming='calcjob')\n",
+    "    results = qb.all()\n",
+    "    if len(results) == 0:\n",
+    "        return None\n",
+    "    return results\n",
+    "\n",
+    "\n",
+    "if display_node_details(pk):\n",
+    "    linked_qeapp_jobs = find_linked_qeapp_jobs(pk)\n",
+    "    if linked_qeapp_jobs:\n",
+    "        warning_html = f\"\"\"\n",
+    "<div style='margin: 10px; padding: 10px; border: 1px solid red; border-radius: 5px; background-color: #ffcccc;'>\n",
+    "    <strong style='color: red;'>Critical:</strong> Unable to delete the requested node due to dependencies.\n",
+    "    There are <strong>{len(linked_qeapp_jobs)}</strong> QEApp jobs linked to this node. Please delete them first:\n",
+    "    <ul>\n",
+    "\"\"\"\n",
+    "        for node in linked_qeapp_jobs[0]:\n",
+    "            warning_html += f\"\"\"<a href=\"./delete.ipynb?pk={node.pk}\" target=\"_blank\">{node.pk}</a><br>\"\"\"\n",
+    "        display(widgets.HTML(value=warning_html))\n",
+    "    else:\n",
+    "        # Ask for confirmation\n",
+    "        nodes, _ = delete_nodes([pk], dry_run=True)\n",
+    "        display(Markdown(f'**YOU ARE ABOUT TO DELETE `{len(nodes)}` NODES! THIS CANNOT BE UNDONE!**'))\n",
+    "        delete_confirmation = widgets.Text(\n",
+    "            value='',\n",
+    "            placeholder='Type \"yes\" to confirm',\n",
+    "            description='Confirm:',\n",
+    "            disabled=False\n",
+    "        )\n",
+    "        confirm_button = widgets.Button(description=\"Delete Node\")\n",
+    "        confirm_button.on_click(confirm_deletion)\n",
+    "        display(delete_confirmation, confirm_button)\n",
+    "else:\n",
+    "    print(\"No valid node found for deletion.\")"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.13"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

job_list.ipynb

@@ -0,0 +1,65 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# AiiDAlab QuantumESPRESSO App"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%%capture\n",
+    "from aiida import load_profile\n",
+    "\n",
+    "load_profile()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from aiidalab_qe.app.utils.search_jobs import QueryInterface\n",
+    "\n",
+    "qi = QueryInterface()\n",
+    "qi.filters_layout"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "qi.table"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.13"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

qe.ipynb

@@ -38,6 +38,8 @@
     "except Exception:\n",
     "    pass\n",
     "\n",
+    "import urllib.parse as urlparse\n",
+    "\n",
     "import ipywidgets as ipw\n",
     "from aiidalab_widgets_base.bug_report import (\n",
     "    install_create_github_issue_exception_handler,\n",
@@ -65,7 +67,15 @@
     "    f'<p style=\"text-align:right;\">Copyright (c) 2023 AiiDAlab team (EPFL)&#8195Version: {__version__}</p>'\n",
     ")\n",
     "\n",
+    "url = urlparse.urlsplit(jupyter_notebook_url) # noqa F821\n",
+    "query = urlparse.parse_qs(url.query)\n",
+    "\n",
+    "\n",
     "app_with_work_chain_selector = App(qe_auto_setup=True)\n",
+    "# if a pk is provided in the query string, set it as the value of the work_chain_selector\n",
+    "if 'pk' in query:\n",
+    "    pk = int(query['pk'][0])\n",
+    "    app_with_work_chain_selector.work_chain_selector.value = pk\n",
     "\n",
     "output = ipw.Output()\n",
     "install_create_github_issue_exception_handler(\n",

src/aiidalab_qe/app/submission/__init__.py

@@ -401,6 +401,7 @@ def submit(self, _=None):
             process.base.extras.set("ui_parameters", serialize(self.ui_parameters))
             # store the workchain name in extras, this will help to filter the workchain in the future
             process.base.extras.set("workchain", self.ui_parameters["workchain"])
+            process.base.extras.set("structure", self.input_structure.get_formula())
             self.process = process
 
         self._update_state()