Merge branch 'v1-misc-fixes' into 'v1.0.0'

Misc bug-fixes towards the v1 release. #709

See merge request !542

gui/public/env.js

 window.nomadEnv = {
   'keycloakBase': 'https://nomad-lab.eu/fairdi/keycloak/auth/',
+  // Use the production API
+  // 'keycloakRealm': 'fairdi_nomad_prod',
+  // 'keycloakClientId': 'nomad_public',
+  // 'appBase': 'https://nomad-lab.eu/prod/v1',
+  // Use the local API
   'keycloakRealm': 'fairdi_nomad_test',
   'keycloakClientId': 'nomad_gui_dev',
   'appBase': 'http://localhost:8000/fairdi/nomad/latest',

gui/src/components/dataset/DatasetsPage.js

@@ -26,7 +26,8 @@ import DeleteIcon from '@material-ui/icons/Delete'
 import DOIIcon from '@material-ui/icons/Bookmark'
 import { DatasetButton } from '../nav/Routes'
 import {
-  addColumnDefaults, combinePagination, Datatable, DatatableLoadMorePagination,
+  addColumnDefaults, combinePagination, Datatable,
+  DatatablePagePagination,
   DatatableTable, DatatableToolbar } from '../datatable/Datatable'
 import Quantity from '../Quantity'
 import DialogContentText from '@material-ui/core/DialogContentText'
@@ -105,7 +106,6 @@ const DatasetActions = React.memo(function VisitDatasetAction({data}) {
     </Tooltip>
     <Dialog
       open={openConfirmDeleteDialog}
-      aria-describedby="alert-dialog-description"
     >
       <DialogContent>
         <DialogContentText id="alert-dialog-description">
@@ -140,7 +140,7 @@ DatasetActions.propTypes = {
 }
 
 function DatasetsPage() {
-  const {api} = useApi()
+  const {api, user} = useApi()
   const errors = useErrors()
   const [apiData, setApiData] = useState(null)
   const data = useMemo(() => apiData?.response, [apiData])
@@ -148,16 +148,19 @@ function DatasetsPage() {
     page_size: 10,
     page: 1,
     order_by: 'dataset_create_time',
-    order: 'asc'
+    order: 'desc'
   })
 
   const load = useCallback(() => {
+    if (!user) {
+      return
+    }
     const {page_size, page, order_by, order} = pagination
-    const url = `/datasets/?page_size=${page_size}&page=${page}&order_by=${order_by}&order=${order}`
+    const url = `/datasets/?page_size=${page_size}&page=${page}&order_by=${order_by}&order=${order}&user_id=${user.sub}`
     api.get(url, null, {returnRequest: true})
       .then(setApiData)
       .catch(errors.raiseError)
-  }, [pagination, setApiData, errors, api])
+  }, [pagination, setApiData, errors, api, user])
 
   useEffect(() => {
     load()
@@ -180,7 +183,7 @@ function DatasetsPage() {
               </SourceApiDialogButton>
             </DatatableToolbar>
             <DatatableTable actions={DatasetActions}>
-              <DatatableLoadMorePagination />
+              <DatatablePagePagination />
             </DatatableTable>
           </Datatable>
         </Paper>

gui/src/components/datatable/Datatable.js

@@ -121,7 +121,7 @@ export const DatatablePagePagination = React.memo(function DatatablePagePaginati
     rowsPerPage={pagination.page_size}
     page={pagination.page - 1}
     onPageChange={handleChangePage}
-    onChangeRowsPerPage={handleChangeRowsPerPage}
+    onRowsPerPageChange={handleChangeRowsPerPage}
   />
 })
 DatatablePagePagination.propTypes = {
@@ -392,7 +392,7 @@ const DatatableRow = React.memo(function DatatableRow({data, selected, uncollaps
   </>
 })
 DatatableRow.propTypes = {
-  data: PropTypes.object.isRequired,
+  data: PropTypes.oneOfType([PropTypes.object, PropTypes.string]).isRequired,
   selected: PropTypes.bool,
   uncollapsed: PropTypes.bool,
   onRowUncollapsed: PropTypes.func.isRequired,
@@ -701,7 +701,7 @@ Datatable.propTypes = {
   shownColumns: PropTypes.arrayOf(PropTypes.string),
   sortingColumns: PropTypes.arrayOf(PropTypes.string),
   /** Optional table data as array of objects. Default is empty table. */
-  data: PropTypes.arrayOf(PropTypes.object),
+  data: PropTypes.arrayOf(PropTypes.oneOfType([PropTypes.object, PropTypes.string])),
   /** Optional pagination object (e.g. from NOMAD API). Used to display current pagination
    * and ordering information. Either based on page (if using DatatablePagePagination) or
    * page_after_value (if using DatatableScrollPagination). */

gui/src/components/uploads/EditMembersDialog.js

@@ -294,7 +294,7 @@ function EditMembersDialog({...props}) {
           <MembersIcon/>
         </Tooltip>
       </IconButton>
-      {open && <Dialog classes={{paper: classes.dialog}} open={open} on disableBackdropClick disableEscapeKeyDown>
+      {open && <Dialog classes={{paper: classes.dialog}} open={open} disableEscapeKeyDown>
         <DialogTitle>Manage upload members</DialogTitle>
         <DialogContent>
           <DialogContentText>

gui/src/components/uploads/EditMetaDataDialog.js

@@ -293,12 +293,13 @@ const ReferencesActions = React.memo((props) => {
   </Box>
 })
 ReferencesActions.propTypes = {
-  data: PropTypes.object.isRequired
+  data: PropTypes.string.isRequired
 }
 
 function EditDatasets() {
-  const {data, api, raiseError, setIsDatasetChanged, setDatasets, defaultDatasets, setDefaultDatasets} = useContext(editMetaDataDialogContext)
-  const [suggestions, setSuggestions] = useState([])
+  const {data, setIsDatasetChanged, setDatasets, defaultDatasets, setDefaultDatasets} = useContext(editMetaDataDialogContext)
+  const {api, user} = useApi()
+  const {raiseError} = useErrors()
   const [validation, setValidation] = useState('')
   const [allDatasets, setAllDatasets] = useState([])
   const [newDataset, setNewDataset] = useState({dataset_id: '', dataset_name: ''})
@@ -312,7 +313,7 @@ function EditDatasets() {
   ]), [])
 
   useEffect(() => {
-    api.get(`/datasets?page_size=${1000}&page=${1}`)
+    api.get(`/datasets/?page_size=${1000}&page=${1}&user_id=${user.sub}`)
       .then(datasets => {
         setAllDatasets(datasets?.data)
       })
@@ -320,7 +321,7 @@ function EditDatasets() {
         setAllDatasets([])
         raiseError(err)
       })
-  }, [api, raiseError])
+  }, [api, user, raiseError, setAllDatasets])
 
   const checkChanges = useCallback((_datasets) => {
     let isSame = defaultDatasets.length === _datasets.length &&
@@ -328,12 +329,6 @@ function EditDatasets() {
     setIsDatasetChanged(!isSame)
   }, [defaultDatasets, setIsDatasetChanged])
 
-  const handleInputChange = useCallback((event, value) => {
-    const query = value.toLowerCase()
-    const withQueryInName = (allDatasets ? allDatasets.filter(dataset => dataset.dataset_name.toLowerCase().indexOf(query) !== -1) : [])
-    setSuggestions(withQueryInName.slice(0, 5))
-  }, [allDatasets])
-
   useEffect(() => {
     if (data?.data?.length > 0) {
       let _datasets = data?.data[0]?.entry_metadata?.datasets
@@ -448,15 +443,16 @@ function EditDatasets() {
       </Box>
       <AutoComplete
         style={{width: '100%'}}
-        options={suggestions}
+        options={allDatasets}
         getOptionLabel={option => option.dataset_name}
-        onInputChange={handleInputChange}
         onChange={handleAutoCompleteChange}
         renderInput={params => (
           <TextField
             {...params}
-            variant='filled' label='Search for an existing dataset' placeholder='Dataset name' argin='normal' fullWidth size='small'
-            error={isDuplicated || apiValidation} helperText={(isDuplicated ? 'The data is already in the selected dataset' : apiValidation)}
+            variant='filled' label='Search for an existing dataset'
+            placeholder='Dataset name' margin='normal' fullWidth size='small'
+            error={isDuplicated || apiValidation !== ''}
+            helperText={(isDuplicated ? 'The data is already in the selected dataset' : apiValidation)}
           />
         )}
       />
@@ -626,8 +622,8 @@ function EditMetaDataDialog({...props}) {
       {!isIcon && <Button onClick={handleOpenDialog} variant='contained' color='primary' disabled={isProcessing}>
         {upload?.entries && (upload?.entries > 1 ? `Edit author metadata of all ${upload?.entries} entries` : `Edit author metadata of all the entries`)}
       </Button>}
-      {open && <Dialog classes={{paper: classes.dialog}} open={open} on disableBackdropClick disableEscapeKeyDown>
-        <DialogTitle>Manage upload meta data</DialogTitle>
+      {open && <Dialog classes={{paper: classes.dialog}} open={open} disableEscapeKeyDown>
+        <DialogTitle>Edit upload meta data</DialogTitle>
         <DialogContent>
           <DialogContentText>
             You can add, remove or edit the meta data for the selected entries.
@@ -670,7 +666,7 @@ function EditMetaDataDialog({...props}) {
 }
 EditMetaDataDialog.propTypes = {
   isIcon: PropTypes.bool,
-  selectedEntries: PropTypes.arrayOf(PropTypes.object)
+  selectedEntries: PropTypes.object
 }
 
 export default EditMetaDataDialog

gui/src/components/uploads/UploadPage.js

@@ -167,6 +167,7 @@ UploadName.propTypes = {
 
 function PublishUpload({upload, onPublish}) {
   const [embargo, setEmbargo] = useState(upload.embargo_length === undefined ? 0 : upload.embargo_length)
+  const [openConfirmDialog, setOpenConfirmDialog] = useState(false)
   const handlePublish = () => {
     onPublish({embargo_length: embargo})
   }
@@ -177,7 +178,25 @@ function PublishUpload({upload, onPublish}) {
     `}</Markdown>
   }
 
+  const buttonLabel = embargo > 0 ? 'Publish with embargo' : 'Publish'
+
   return <React.Fragment>
+    <Dialog
+      open={openConfirmDialog}
+      onClose={() => setOpenConfirmDialog(false)}
+    >
+      <DialogTitle>Confirm that you want to publish the upload</DialogTitle>
+      <DialogContent>
+        <DialogContentText>
+          You are about the publish this upload. The upload cannot be removed and
+          the files and entries in this upload cannot be changed after publication.
+        </DialogContentText>
+      </DialogContent>
+      <DialogActions>
+        <Button onClick={() => setOpenConfirmDialog(false)} autoFocus>Cancel</Button>
+        <Button onClick={handlePublish}>{buttonLabel}</Button>
+      </DialogActions>
+    </Dialog>
     <Markdown>{`
       If you agree this upload will be published and move out of your private staging
       area into the public NOMAD. This step is final. All public data will be made available under the Creative
@@ -224,10 +243,10 @@ function PublishUpload({upload, onPublish}) {
             <Button
               style={{height: 32, minWith: 100}}
               size="small" variant="contained"
-              onClick={() => handlePublish()} color="primary"
+              onClick={() => setOpenConfirmDialog(true)} color="primary"
               disabled={upload.process_running}
             >
-              {embargo > 0 ? 'Publish with embargo' : 'Publish'}
+              {buttonLabel}
             </Button>
           </Box>
         </Grid>

nomad/app/v1/routers/datasets.py

@@ -144,7 +144,7 @@ async def get_datasets(
         request: Request,
         dataset_id: str = FastApiQuery(None),
         dataset_name: str = FastApiQuery(None),
-        user_id: str = FastApiQuery(None),
+        user_id: List[str] = FastApiQuery(None),
         dataset_type: str = FastApiQuery(None),
         doi: str = FastApiQuery(None),
         prefix: str = FastApiQuery(None),
@@ -152,8 +152,9 @@ async def get_datasets(
     '''
     Retrieves all datasets that match the given criteria.
     '''
+
     mongodb_objects = DatasetDefinitionCls.m_def.a_mongo.objects
-    query_params = dict(dataset_id=dataset_id, dataset_name=dataset_name, user_id=user_id, dataset_type=dataset_type, doi=doi)
+    query_params = dict(dataset_id=dataset_id, dataset_name=dataset_name, user_id__in=user_id, dataset_type=dataset_type, doi=doi)
     if prefix is not None and prefix != '':
         query_params.update(dataset_name=re.compile('^%s.*' % prefix, re.IGNORECASE))  # type: ignore
     query_params = {k: v for k, v in query_params.items() if v is not None}