Minor upload gui fixes. #709

gui/src/components/api.js

@@ -52,8 +52,15 @@ export class ApiError extends Error {
   }
 }
 
+export class ApiRequestError extends Error {
+  constructor(msg) {
+    super(msg)
+    this.name = 'BadRequest'
+  }
+}
+
 function handleApiError(e) {
-  if (e.name === 'CannotReachApi' || e.name === 'NotAuthorized' || e.name === 'DoesNotExist') {
+  if (e.name === 'CannotReachApi' || e.name === 'NotAuthorized' || e.name === 'DoesNotExist' || e.name === 'BadRequest') {
     throw e
   }
 
@@ -66,6 +73,8 @@ function handleApiError(e) {
       error = new DoesNotExist(errorMessage)
     } else if (e.response.status === 401) {
       error = new NotAuthorized(errorMessage)
+    } else if (e.response.status === 400) {
+      error = new ApiRequestError(errorMessage)
     } else if (e.response.status === 502) {
       error = new ApiError(errorMessage)
     } else {

gui/src/components/dataset/DatasetsPage.js

@@ -17,7 +17,7 @@
  */
 import React, { useCallback, useContext, useEffect, useState, useMemo } from 'react'
 import PropTypes from 'prop-types'
-import {Paper, IconButton, Tooltip, DialogContent, Button, Dialog} from '@material-ui/core'
+import {Paper, IconButton, Tooltip, DialogContent, Button, Dialog, DialogTitle} from '@material-ui/core'
 import { useApi, withLoginRequired } from '../api'
 import Page from '../Page'
 import { useErrors } from '../errors'
@@ -67,33 +67,33 @@ const DatasetActions = React.memo(function VisitDatasetAction({data}) {
   const {api} = useApi()
   const {raiseError} = useErrors()
   const {refresh} = useContext(PageContext)
-  const [openConfirmDialog, setOpenConfirmDialog] = useState(false)
+  const [openConfirmDeleteDialog, setOpenConfirmDeleteDialog] = useState(false)
+  const [openConfirmDoiDialog, setOpenConfirmDoiDialog] = useState(false)
 
   const handleDelete = useCallback(() => {
+    setOpenConfirmDeleteDialog(false)
     api.delete(`/datasets/${data.dataset_id}`)
       .then(refresh).catch(raiseError)
-  }, [api, raiseError, data.dataset_id, refresh])
+  }, [api, raiseError, data.dataset_id, refresh, setOpenConfirmDeleteDialog])
 
   const handleAssignDoi = useCallback(() => {
+    setOpenConfirmDoiDialog(false)
     api.post(`/datasets/${data.dataset_id}/action/doi`)
-      .then(refresh).catch(raiseError)
-  }, [api, raiseError, data.dataset_id, refresh])
-
-  const onConfirm = () => {
-    setOpenConfirmDialog(true)
-  }
+      .then(refresh)
+      .catch(raiseError)
+  }, [api, raiseError, data.dataset_id, refresh, setOpenConfirmDoiDialog])
 
   return <React.Fragment>
     <Tooltip title="Assign a DOI">
       <span>
-        <IconButton onClick={handleAssignDoi} disabled={!!data.doi}>
+        <IconButton onClick={() => setOpenConfirmDoiDialog(true)} disabled={!!data.doi}>
           <DOIIcon />
         </IconButton>
       </span>
     </Tooltip>
     <Tooltip title={(data.doi ? 'The dataset cannot be deleted. A DOI has been assigned to the dataset.' : 'Delete the dataset')}>
       <span>
-        <IconButton onClick={onConfirm} disabled={!!data.doi} style={{pointerEvents: 'auto'}}>
+        <IconButton onClick={() => setOpenConfirmDeleteDialog(true)} disabled={!!data.doi} style={{pointerEvents: 'auto'}}>
           <DeleteIcon />
         </IconButton>
       </span>
@@ -104,7 +104,7 @@ const DatasetActions = React.memo(function VisitDatasetAction({data}) {
       </DatasetButton>
     </Tooltip>
     <Dialog
-      open={openConfirmDialog}
+      open={openConfirmDeleteDialog}
       aria-describedby="alert-dialog-description"
     >
       <DialogContent>
@@ -113,10 +113,26 @@ const DatasetActions = React.memo(function VisitDatasetAction({data}) {
         </DialogContentText>
       </DialogContent>
       <DialogActions>
-        <Button onClick={() => setOpenConfirmDialog(false)} autoFocus>Cancel</Button>
+        <Button onClick={() => setOpenConfirmDeleteDialog(false)} autoFocus>Cancel</Button>
         <Button onClick={handleDelete}>Delete</Button>
       </DialogActions>
     </Dialog>
+    <Dialog
+      open={openConfirmDoiDialog}
+      onClose={() => setOpenConfirmDoiDialog(false)}
+    >
+      <DialogTitle>Confirm that you want to assign a DOI</DialogTitle>
+      <DialogContent>
+        <DialogContentText>
+          Assigning a DOI is permanent. You will not be able to remove entries from
+          datasets with a DOI. You cannot delete datasets with a DOI.
+        </DialogContentText>
+      </DialogContent>
+      <DialogActions>
+        <Button onClick={() => setOpenConfirmDoiDialog(false)} autoFocus>Cancel</Button>
+        <Button onClick={handleAssignDoi}>Assign DOI</Button>
+      </DialogActions>
+    </Dialog>
   </React.Fragment>
 })
 DatasetActions.propTypes = {

gui/src/components/errors.js

@@ -56,7 +56,9 @@ class ErrorSnacksUnstyled extends React.Component {
   onError(error) {
     let errorStr = 'Unexpected error. Please try again and let us know, if this error keeps happening.'
     if (error instanceof Error) {
-      if (error.name === 'CannotReachApi') {
+      if (error.name === 'BadRequest') {
+        errorStr = error.message
+      } else if (error.name === 'CannotReachApi') {
         errorStr = 'Cannot reach NOMAD, please try again later.'
       } else if (error.name === 'NotAuthorized') {
         errorStr = error.message

gui/src/components/uploads/UploadPage.js

@@ -224,7 +224,7 @@ function PublishUpload({upload, onPublish}) {
             <Button
               style={{height: 32, minWith: 100}}
               size="small" variant="contained"
-              onClick={() => handlePublish()} color="primary" autoFocus
+              onClick={() => handlePublish()} color="primary"
               disabled={upload.process_running}
             >
               {embargo > 0 ? 'Publish with embargo' : 'Publish'}
@@ -499,7 +499,7 @@ function UploadPage() {
           </Dialog>
         </Grid>
       </Grid>
-      <Stepper classes={{root: classes.stepper}} orientation="vertical" nonLinear>
+      <Stepper classes={{root: classes.stepper}} orientation="vertical" >
         <Step expanded active={false}>
           <StepLabel>Prepare and upload your files</StepLabel>
           <StepContent>
@@ -529,7 +529,7 @@ function UploadPage() {
             <FilesBrower className={classes.stepContent} uploadId={uploadId} disabled={isProcessing || deleteClicked} />
           </StepContent>
         </Step>
-        <Step expanded={!isEmpty}>
+        <Step expanded={!isEmpty} active={false}>
           <StepLabel>Process data</StepLabel>
           <StepContent>
             <ProcessingStatus data={data} />
@@ -540,7 +540,7 @@ function UploadPage() {
               onPaginationChanged={setPagination}/>
           </StepContent>
         </Step>
-        {(isAuthenticated && isWriter) && <Step expanded={!isEmpty}>
+        {(isAuthenticated && isWriter) && <Step expanded={!isEmpty} active={false}>
           <StepLabel>Edit author metadata</StepLabel>
           <StepContent>
             <Typography className={classes.stepContent}>
@@ -556,7 +556,7 @@ function UploadPage() {
             {!isEmpty && <EditMetaDataDialog selectedEntries={{'upload_id': upload.upload_id}}/>}
           </StepContent>
         </Step>}
-        {(isAuthenticated && isWriter) && <Step expanded={!isEmpty}>
+        {(isAuthenticated && isWriter) && <Step expanded={!isEmpty} active={false}>
           <StepLabel>Publish</StepLabel>
           <StepContent>
             {isPublished && <Typography className={classes.stepContent}>

gui/src/components/uploads/UploadsPage.js

@@ -253,7 +253,7 @@ function UploadsPage() {
     page_size: 10,
     page: 1,
     order_by: 'upload_create_time',
-    order: 'asc'
+    order: 'desc'
   })
 
   const fetchData = useCallback(() => {

nomad/app/v1/routers/datasets.py

@@ -24,19 +24,19 @@ from pydantic import BaseModel, Field, validator
 from datetime import datetime
 import enum
 
-from nomad import utils, datamodel, processing
+from nomad import utils, datamodel, processing, config
 from nomad.metainfo.elasticsearch_extension import entry_type
 from nomad.utils import strip, create_uuid
 from nomad.datamodel import Dataset as DatasetDefinitionCls
 from nomad.doi import DOI
-from nomad.search import update_by_query
+from nomad.search import search, update_by_query
 
 from .auth import create_user_dependency
 from .entries import _do_exaustive_search
 from ..utils import create_responses, parameter_dependency_from_model
 from ..models import (
-    Pagination, PaginationResponse, Query, HTTPExceptionModel, User,
-    Direction, Owner, Any_)
+    Pagination, PaginationResponse, MetadataPagination, Query, HTTPExceptionModel,
+    User, Direction, Owner, Any_)
 
 
 router = APIRouter()
@@ -76,6 +76,20 @@ _dataset_is_fixed_response = status.HTTP_400_BAD_REQUEST, {
         The dataset already has a DOI and cannot be changed anymore.
     ''')}
 
+_dataset_has_unpublished_contents = status.HTTP_400_BAD_REQUEST, {
+    'model': HTTPExceptionModel,
+    'description': strip('''
+        The dataset has unpublished contents. No DOI can be assigned at the moment.
+        Publish the dataset contents first.
+    ''')}
+
+_dataset_is_empty = status.HTTP_400_BAD_REQUEST, {
+    'model': HTTPExceptionModel,
+    'description': strip('''
+        The dataset is empty. No DOI can be assigned at this moment. Add some published
+        contents to the dataset first.
+    ''')}
+
 
 Dataset = datamodel.Dataset.m_def.a_pydantic.model
 
@@ -336,7 +350,9 @@ async def delete_dataset(
     '/{dataset_id}/action/doi', tags=[default_tag],
     summary='Assign a DOI to a dataset',
     response_model=DatasetResponse,
-    responses=create_responses(_bad_id_response, _dataset_is_fixed_response, _bad_user_response),
+    responses=create_responses(
+        _bad_id_response, _dataset_is_fixed_response, _dataset_has_unpublished_contents,
+        _bad_user_response, _dataset_is_empty),
     response_model_exclude_unset=True,
     response_model_exclude_none=True)
 async def assign_doi(
@@ -362,6 +378,27 @@ async def assign_doi(
             status_code=_bad_user_response[0],
             detail=_bad_user_response[1]['description'])
 
+    response = search(
+        owner='admin',
+        query={'datasets.dataset_id': dataset_id},
+        pagination=MetadataPagination(page_size=0),
+        user_id=config.services.admin_user_id)
+    if response.pagination.total == 0:
+        raise HTTPException(
+            status_code=_dataset_is_empty[0],
+            detail=_dataset_is_empty[1]['description'])
+
+    response = search(
+        owner='admin',
+        query={'datasets.dataset_id': dataset_id, 'published': False},
+        pagination=MetadataPagination(page_size=0),
+        user_id=config.services.admin_user_id)
+
+    if response.pagination.total > 0:
+        raise HTTPException(
+            status_code=_dataset_has_unpublished_contents[0],
+            detail=_dataset_has_unpublished_contents[1]['description'])
+
     doi = DOI.create(title='NOMAD dataset: %s' % dataset.dataset_name, user=user)
     doi.create_draft()
     doi.make_findable()

tests/app/v1/routers/test_datasets.py

@@ -43,13 +43,14 @@ to assert for certain aspects in the responses.
 '''
 
 
+def create_dataset(**kwargs):
+    dataset = Dataset(dataset_create_time=datetime.now(), dataset_modified_time=datetime.now(), **kwargs)
+    dataset.m_get_annotations('mongo').save()
+    return dataset
+
+
 @pytest.fixture(scope='function')
 def data(elastic, raw_files, mongo, test_user, other_test_user):
-    def create_dataset(**kwargs):
-        dataset = Dataset(dataset_create_time=datetime.now(), dataset_modified_time=datetime.now(), **kwargs)
-        dataset.m_get_annotations('mongo').save()
-        return dataset
-
     data = ExampleData(main_author=test_user)
     data.create_upload(upload_id='upload_1', published=True)
     data.create_entry(
@@ -276,9 +277,28 @@ def test_delete_dataset(client, data, test_user_auth, other_test_user_auth, data
     pytest.param('dataset_1', 'test_user', 200, id='plain'),
     pytest.param('dataset_1', None, 401, id='no-user'),
     pytest.param('dataset_1', 'other_test_user', 401, id='wrong-user'),
-    pytest.param('dataset_doi', 'test_user', 400, id='with-doi')
+    pytest.param('dataset_doi', 'test_user', 400, id='with-doi'),
+    pytest.param('unpublished', 'test_user', 400, id='unpublished'),
+    pytest.param('empty', 'test_user', 400, id='empty')
 ])
 def test_assign_doi_dataset(client, data, test_user, test_user_auth, other_test_user_auth, dataset_id, user, status_code):
+    more_data = ExampleData(main_author=test_user)
+    more_data.create_upload(upload_id='unpublished', published=False)
+    more_data.create_entry(
+        upload_id='unpublished', entry_id='unpublished',
+        mainfile='test_content/1/mainfile.json',
+        datasets=[create_dataset(
+            dataset_id='unpublished', user_id=test_user.user_id,
+            dataset_name='test unpublished entries',
+            dataset_type='owned')])
+
+    create_dataset(
+        dataset_id='empty', user_id=test_user.user_id,
+        dataset_name='test empty dataset',
+        dataset_type='owned')
+
+    more_data.save(with_files=False)
+
     auth = None
     if user == 'test_user':
         auth = test_user_auth