Task/DES-3065: Use cloud.data system for HPC work directories (#1423)

* use cloud.data system for HPC work directories

* fix issues with tests

* Rename 'HPC Work' to 'Work'; consolidate hard-coded system names

* add project title as a subtitle in datacite, prefixed with 'in' (#1428)

* deep-copy entity values before inserting them into the project tree (#1427)

* Log DOIs for each file when multiple are selected, even if there are duplicates (#1430)

* Bug/wc 84 metrics modal error (#1431)

* commit to main

* prevent blank or null values from causing metrics page to crash

* remove those type coercions and fix the type errors

* Refactor MetricsModalBody component to improve readability and maintainability

* remove docker compose changes

---------

Co-authored-by: Jake Rosenberg <[email protected]>

* Task/WC-95: Clear file selection when changing publication version (#1432)

* Log DOIs for each file when multiple are selected, even if there are duplicates

* Unset file selections when changing the selected publication version

* Show up to 3 keywords in the publication listing (#1429)

* task/WC-91: Directories in Publication Preview should open in the Curation listing (#1425)

* Directories in Publication Preview open in the Curation listing

* fix links inside the publication pipeline

* revert link _target change

* Task/WC-96: Log views of non-Other type publications as listings on the root dir (#1433)

* log views of non-Other type projects as listings on the root dir

* fix hook dependencies

* bump setfacls app to v0.0.2 (#1434)

* improve DOI support in Publication search (#1437)

* Ensure correct publication dates after subsequent publish (#1436)

* update wording in Copy modal

* task/WP-685: user work workspace file select (#1426)

* handle error in revoke method

* handle cloud.data work system in workspace select modal

---------

Co-authored-by: Sal Tijerina <[email protected]>
Co-authored-by: Van Go <[email protected]>

client/modules/_common_components/src/datafiles/DatafilesBreadcrumb/DatafilesBreadcrumb.tsx

@@ -1,7 +1,12 @@
 import { Breadcrumb, BreadcrumbProps } from 'antd';
 import React from 'react';
 import styles from './DatafilesBreadcrumb.module.css';
-import { getSystemRootDisplayName, useAuthenticatedUser } from '@client/hooks';
+import {
+  getSystemRootDisplayName,
+  useAuthenticatedUser,
+  USER_MYDATA_SYSTEM,
+  USER_WORK_SYSTEM,
+} from '@client/hooks';
 
 function getPathRoutes(
   baseRoute: string,
@@ -50,13 +55,6 @@ export const DatafilesBreadcrumb: React.FC<
   );
 };
 
-function isUserHomeSystem(system: string) {
-  return [
-    'designsafe.storage.default',
-    'designsafe.storage.frontera.work',
-  ].includes(system);
-}
-
 export const BaseFileListingBreadcrumb: React.FC<
   {
     api: string;
@@ -78,7 +76,10 @@ export const BaseFileListingBreadcrumb: React.FC<
   const { user } = useAuthenticatedUser();
   const rootAlias =
     systemRootAlias || getSystemRootDisplayName(api, system, systemLabel);
-  const systemRoot = isUserHomeSystem(system) ? '/' + user?.username : '';
+  let systemRoot = '';
+  if (system === USER_MYDATA_SYSTEM) systemRoot = '/' + user?.username;
+  if (system === USER_WORK_SYSTEM) systemRoot = '/work/' + user?.homedir;
+
   return (
     <DatafilesBreadcrumb
       initialBreadcrumbs={[
@@ -90,7 +91,7 @@ export const BaseFileListingBreadcrumb: React.FC<
       ]}
       path={path}
       baseRoute={`/${api}/${system}`}
-      systemRoot={isUserHomeSystem(system) ? '/' + user?.username : ''}
+      systemRoot={systemRoot}
       systemRootAlias={systemRootAlias || getSystemRootDisplayName(api, system)}
       {...props}
     />

client/modules/_hooks/src/datafiles/index.ts

@@ -22,10 +22,7 @@ export { useUploadFile } from './useUploadFile';
 export { useUploadFolder } from './useUploadFolder';
 export { useFileDetail } from './useFileDetail';
 
-export {
-  usePathDisplayName,
-  getSystemRootDisplayName,
-} from './usePathDisplayName';
+export * from './usePathDisplayName';
 
 export * from './nees';
 export * from './projects';

client/modules/_hooks/src/datafiles/usePathDisplayName.ts

@@ -1,6 +1,9 @@
 import { useCallback } from 'react';
 import { useAuthenticatedUser } from '../useAuthenticatedUser';
 
+export const USER_MYDATA_SYSTEM = 'designsafe.storage.default';
+export const USER_WORK_SYSTEM = 'cloud.data';
+
 export function getSystemRootDisplayName(
   api: string,
   system: string,
@@ -9,10 +12,11 @@ export function getSystemRootDisplayName(
   if (api === 'googledrive') return 'Google Drive';
   if (api === 'box') return 'Box';
   if (api === 'dropbox') return 'Dropbox';
+
   return (
     {
-      'designsafe.storage.default': 'My Data',
-      'designsafe.storage.frontera.work': 'HPC Work',
+      [USER_MYDATA_SYSTEM]: 'My Data',
+      [USER_WORK_SYSTEM]: 'Work',
       'designsafe.storage.community': 'Community Data',
     }[system] ?? label
   );
@@ -23,20 +27,22 @@ function _getPathDisplayName(
   system: string,
   path: string,
   label: string,
-  username?: string
+  username?: string,
+  homedir?: string
 ) {
   const usernamePath = encodeURIComponent('/' + username);
+  const workdirPath = `/work/${homedir}`;
 
   if (!path) return getSystemRootDisplayName(api, system, label);
   if (api === 'googledrive' && !path) return 'Google Drive';
   if (api === 'dropbox' && !path) return 'Dropbox';
   if (api === 'box' && !path) return 'Box';
 
-  if (system === 'designsafe.storage.default' && path === usernamePath) {
+  if (system === USER_MYDATA_SYSTEM && path === usernamePath) {
     return 'My Data';
   }
-  if (system === 'designsafe.storage.frontera.work' && path === usernamePath) {
-    return 'HPC Work';
+  if (system === USER_WORK_SYSTEM && path === workdirPath) {
+    return 'Work';
   }
 
   return decodeURIComponent(path).split('/').slice(-1)[0] || label;
@@ -47,7 +53,14 @@ export function usePathDisplayName() {
 
   const getPathDisplayName = useCallback(
     (api: string, system: string, path: string, label: string = 'Data Files') =>
-      _getPathDisplayName(api, system, path, label, user?.username),
+      _getPathDisplayName(
+        api,
+        system,
+        path,
+        label,
+        user?.username,
+        user?.homedir
+      ),
     [user]
   );
 

client/modules/_hooks/src/systems/types.ts

@@ -61,6 +61,7 @@ export type TTapisSystem = {
     label?: string;
     keyservice?: boolean;
     isMyData?: boolean;
+    hasWork?: boolean;
     portalNames: string[];
   };
   importRefId?: string;

client/modules/_hooks/src/useAuthenticatedUser.ts

@@ -4,6 +4,7 @@ export type TUser = {
   lastName: string;
   email: string;
   institution: string;
+  homedir: string;
 };
 
 declare global {

client/modules/datafiles/src/DatafilesModal/CopyModal/CopyModal.tsx

@@ -154,8 +154,8 @@ export const CopyModal: React.FC<{
         setShowProjects(false);
         setDest({
           destApi: 'tapis',
-          destSystem: 'designsafe.storage.frontera.work',
-          destPath: encodeURIComponent('/' + user?.username),
+          destSystem: 'cloud.data',
+          destPath: encodeURIComponent('/work/' + user?.homedir),
         });
         break;
       case 'myprojects':
@@ -250,7 +250,7 @@ export const CopyModal: React.FC<{
             <Select
               options={[
                 { label: 'My Data', value: 'mydata' },
-                { label: 'HPC Work', value: 'hpcwork' },
+                { label: 'Work', value: 'hpcwork' },
                 { label: 'My Projects', value: 'myprojects' },
               ]}
               style={{ marginBottom: '12px' }}

client/modules/datafiles/src/DatafilesSideNav/DatafilesSideNav.tsx

@@ -38,10 +38,10 @@ export const DatafilesSideNav: React.FC = () => {
           </DataFilesNavLink>
 
           <DataFilesNavLink
-            to={`/tapis/designsafe.storage.frontera.work`}
+            to={`/tapis/cloud.data/`}
             tooltip="Work directory on TACC HPC machines for use with Jupyter"
           >
-            HPC Work
+            Work
           </DataFilesNavLink>
           <DataFilesNavLink
             to="/projects"

client/modules/datafiles/src/DatafilesToolbar/DatafilesToolbar.tsx

@@ -4,6 +4,7 @@ import {
   useAuthenticatedUser,
   useFileListingRouteParams,
   useProjectDetail,
+  USER_WORK_SYSTEM,
   useSelectedFiles,
   useSelectedFilesForSystem,
 } from '@client/hooks';
@@ -103,7 +104,7 @@ export const DatafilesToolbar: React.FC<{ searchInput?: React.ReactNode }> = ({
         // Disable downloads from frontera.work until we have a non-flaky mount on ds-download.
         canDownload:
           selectedFiles.length >= 1 &&
-          system !== 'designsafe.storage.frontera.work' &&
+          system !== USER_WORK_SYSTEM &&
           !selectedFiles[0].path.endsWith('.hazmapper'),
       };
     },

client/modules/workspace/src/SelectModal/SelectModal.tsx

@@ -103,9 +103,13 @@ const getSystemRootPath = (
   storageSystem: TTapisSystem | undefined,
   user: TUser | undefined
 ): string => {
-  return storageSystem?.notes?.isMyData
-    ? encodeURIComponent('/' + user?.username)
-    : '';
+  if (storageSystem?.notes?.isMyData) {
+    return encodeURIComponent('/' + user?.username);
+  }
+  if (storageSystem?.notes?.hasWork) {
+    return encodeURIComponent('/work/' + user?.homedir);
+  }
+  return '';
 };
 
 const getBackPath = (
@@ -298,7 +302,7 @@ export const SelectModal: React.FC<{
       return (a.notes?.isMyData ? 0 : 1) - (b.notes?.isMyData ? 0 : 1);
     })
     .map((system) => ({
-      label: system.notes.label,
+      label: system.notes?.hasWork ? 'Work' : system.notes.label ?? system.id,
       value: system.id,
     }));
   systemOptions.push({ label: 'My Projects', value: 'myprojects' });
@@ -363,7 +367,9 @@ export const SelectModal: React.FC<{
       selectedPath: getSystemRootPath(system, user),
       scheme: getScheme(system),
     });
-    setSystemLabel(system.notes.label ?? system.id);
+    setSystemLabel(
+      system.notes?.hasWork ? 'Work' : system.notes.label ?? system.id
+    );
   };
 
   const onProjectSelect = (uuid: string, projectId: string) => {

client/src/datafiles/layouts/FileListingLayout.tsx

@@ -1,6 +1,11 @@
 import { DatafilesToolbar, FileListing } from '@client/datafiles';
 import { BaseFileListingBreadcrumb } from '@client/common-components';
-import { useAuthenticatedUser, useFileListingRouteParams } from '@client/hooks';
+import {
+  useAuthenticatedUser,
+  useFileListingRouteParams,
+  USER_MYDATA_SYSTEM,
+  USER_WORK_SYSTEM,
+} from '@client/hooks';
 import { Button, Form, Input, Layout } from 'antd';
 import React from 'react';
 import { Link, Navigate, useSearchParams } from 'react-router-dom';
@@ -37,13 +42,11 @@ export const FileListingLayout: React.FC = () => {
   const { api, path, scheme, system } = useFileListingRouteParams();
   const { user } = useAuthenticatedUser();
 
-  const isUserHomeSystem = [
-    'designsafe.storage.default',
-    'designsafe.storage.frontera.work',
-  ].includes(system);
-
   const redirectHome =
-    user?.username && !path && api === 'tapis' && isUserHomeSystem;
+    user?.username && !path && api === 'tapis' && system === USER_MYDATA_SYSTEM;
+
+  const redirectWork =
+    user?.username && !path && api === 'tapis' && system === USER_WORK_SYSTEM;
   return (
     <Layout style={{ gap: '5px', minWidth: '500px' }}>
       <DatafilesToolbar searchInput={<FileListingSearchBar />} />
@@ -69,6 +72,12 @@ export const FileListingLayout: React.FC = () => {
               replace
             />
           )}
+          {redirectWork && (
+            <Navigate
+              to={`../${encodeURIComponent('/work/' + user.homedir)}`}
+              replace
+            />
+          )}
           <FileListing api={api} system={system} path={path} scheme={scheme} />
         </div>
       </Layout.Content>

designsafe/apps/accounts/forms.py

@@ -333,7 +333,7 @@ def clean_website(self):
 
     class Meta:
         model = DesignSafeProfile
-        exclude = ['user', 'ethnicity', 'gender', 'update_required', 'institution']
+        exclude = ['user', 'ethnicity', 'gender', 'update_required', 'institution', 'homedir']
 
 
 class UserRegistrationForm(UserProfileForm, ProfessionalProfileForm):

designsafe/apps/accounts/migrations/0021_designsafeprofile_homedir.py

@@ -0,0 +1,17 @@
+# Generated by Django 4.2.11 on 2024-08-29 21:19
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("designsafe_accounts", "0020_designsafeprofile_institution"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="designsafeprofile",
+            name="homedir",
+            field=models.CharField(default=None, max_length=256, null=True),
+        ),
+    ]

designsafe/apps/accounts/models.py

@@ -3,6 +3,7 @@
 from django.db import connections, DatabaseError
 from django.utils.translation import gettext_lazy as _
 from django.core.mail import send_mail
+from pytas.http import TASClient
 import logging
 import six
 
@@ -74,6 +75,7 @@ class DesignSafeProfile(models.Model):
     professional_level = models.CharField(max_length=256, default=None, null=True)
     research_activities = models.ManyToManyField(DesignSafeProfileResearchActivities)
     institution = models.CharField(max_length=256, default=None, null=True)
+    homedir = models.CharField(max_length=256, default=None, null=True)
     update_required = models.BooleanField(default=True)
     last_updated = models.DateTimeField(auto_now=True, null=True)
 
@@ -84,6 +86,22 @@ def send_mail(self, subject, body=None):
                   [self.user.email],
                   html_message=body)
 
+    def get_homedir(self):
+        """
+        Get a user's homedir.
+        If it does not exist in the database yet, retrieve and cache it.
+        """
+        if self.homedir:
+            return self.homedir
+
+        tas = TASClient()
+        tas_user = tas.get_user(username=self.user.username)
+
+        homedir = tas_user.get("homeDirectory", "")
+        self.homedir = homedir
+        self.save()
+        return homedir
+
 
 class NotificationPreferences(models.Model):
     user = models.OneToOneField(settings.AUTH_USER_MODEL,

designsafe/apps/auth/backends.py

@@ -36,7 +36,8 @@ def on_user_logged_out(sender, request, user, **kwargs):
         login_provider = "TACC"
 
     logger.info(
-        "Revoking tapis token: %s", TapisOAuthToken().get_masked_token(user.tapis_oauth.access_token)
+        "Revoking tapis token: %s",
+        TapisOAuthToken().get_masked_token(user.tapis_oauth.access_token),
     )
     backend = TapisOAuthBackend()
     TapisOAuthBackend.revoke(backend, user.tapis_oauth.access_token)
@@ -139,7 +140,8 @@ def authenticate(self, *args, **kwargs):
             token = kwargs["token"]
 
             logger.info(
-                'Attempting login via Tapis with token "%s"' % TapisOAuthToken().get_masked_token(token)
+                'Attempting login via Tapis with token "%s"'
+                % TapisOAuthToken().get_masked_token(token)
             )
             client = Tapis(base_url=settings.TAPIS_TENANT_BASEURL, access_token=token)
 
@@ -188,9 +190,13 @@ def authenticate(self, *args, **kwargs):
 
     def revoke(self, token):
         logger.info(
-            "Attempting to revoke Tapis token %s" % TapisOAuthToken().get_masked_token(token)
+            "Attempting to revoke Tapis token %s"
+            % TapisOAuthToken().get_masked_token(token)
         )
 
-        client = Tapis(base_url=settings.TAPIS_TENANT_BASEURL, access_token=token)
-        response = client.authenticator.revoke_token(token=token)
-        logger.info("revoke response is %s" % response)
+        try:
+            client = Tapis(base_url=settings.TAPIS_TENANT_BASEURL, access_token=token)
+            response = client.authenticator.revoke_token(token=token)
+            logger.info("revoke response is %s" % response)
+        except BaseTapyException as e:
+            logger.error("Error revoking token: %s", e.message)

designsafe/context_processors.py

@@ -53,3 +53,10 @@ def site_verification(request):
     if google_verification_id:
         context['GOOGLE_SITE_VERIFICATION_ID'] = google_verification_id
     return context
+
+def tas_homedir(request):
+    """Retrieve user's TAS homedir."""
+    if getattr(settings, "TEST", None) or not request.user.is_authenticated:
+        return {}
+
+    return {"tas_homedir": request.user.profile.get_homedir()}

designsafe/settings/common_settings.py

@@ -181,6 +181,7 @@
                 'designsafe.context_processors.site_verification',
                 'designsafe.context_processors.debug',
                 'designsafe.context_processors.messages',
+                'designsafe.context_processors.tas_homedir',
                 'designsafe.apps.cms_plugins.context_processors.cms_section',
             ],
         },