Merge branch 'v0.9.1' into 'master'

V0.9.1

See merge request !189

exciting @ d9091e62

-Subproject commit 4f08fd0ac2843c3a4763dfb567a3167fd118cb0a
+Subproject commit d9091e62f3180d0d01abdcc75c552b185c6cc8fb

gui/package.json

 {
   "name": "nomad-fair-gui",
-  "version": "0.9.0",
+  "version": "0.9.1",
   "commit": "e98694e",
   "private": true,
   "dependencies": {

gui/public/env.js

@@ -9,7 +9,7 @@ window.nomadEnv = {
   'matomoUrl': 'https://nomad-lab.eu/fairdi/stat',
   'matomoSiteId': '2',
   'version': {
-    'label': '0.9.0',
+    'label': '0.9.1',
     'isBeta': false,
     'isTest': true,
     'usesBetaData': true,

gui/src/components/ErrorHandler.js

@@ -40,11 +40,19 @@ export class ErrorHandler extends React.Component {
     return this.props.children
   }
 }
+ErrorHandler.propTypes = ({
+  children: PropTypes.object,
+  message: PropTypes.string, // Fixed error message. Provide either this or errorHandler
+  errorHandler: PropTypes.func, // Function that is called once an error is caught. It recveives the error object as argument and should return an error message as string.
+  classes: PropTypes.object,
+  className: PropTypes.string
+})
 
 export function ErrorCard({message, className, classes}) {
   const useStyles = makeStyles((theme) => {
     return {
       root: {
+        color: theme.palette.error.main
       },
       content: {
         paddingBottom: '16px'
@@ -73,7 +81,7 @@ export function ErrorCard({message, className, classes}) {
     <CardContent className={[style.content, style['content:last-child']].join(' ')}>
       <Box className={style.container}>
         <Error className={style.errorIcon}/>
-        <Typography className={style.title} color="textSecondary" gutterBottom>
+        <Typography className={style.title} color="error" gutterBottom>
           {message}
         </Typography>
       </Box>
@@ -86,11 +94,3 @@ ErrorCard.propTypes = ({
   classes: PropTypes.object,
   className: PropTypes.string
 })
-
-ErrorHandler.propTypes = ({
-  children: PropTypes.object,
-  message: PropTypes.string, // Fixed error message. Provide either this or errorHandler
-  errorHandler: PropTypes.func, // Function that is called once an error is caught. It recveives the error object as argument and should return an error message as string.
-  classes: PropTypes.object,
-  className: PropTypes.string
-})

gui/src/components/archive/ArchiveBrowser.js

@@ -400,6 +400,10 @@ function Overview({section, def}) {
     let positionsOnly = false
 
     // Do not attempt to perform visualization if size is too big
+    if (!section.atom_species) {
+      // the section is incomplete, we leave the overview empty
+      return ''
+    }
     const nAtoms = section.atom_species.length
     if (nAtoms >= 300) {
       return <ErrorCard
@@ -519,7 +523,9 @@ function Section({section, def}) {
   const filter = config.showCodeSpecific ? def => true : def => !def.name.startsWith('x_')
   return <Content>
     <Title def={def} data={section} kindLabel="section" />
+    <ErrorHandler message="The section overview could not be rendered, due to an unexpected error.">
       <Overview def={def} section={section}></Overview>
+    </ErrorHandler>
     <Compartment title="sub sections">
       {def.sub_sections
         .filter(subSectionDef => section[subSectionDef.name] || config.showAllDefined)

gui/src/components/archive/Browser.js

@@ -8,6 +8,7 @@ import ArrowRightIcon from '@material-ui/icons/ArrowRight'
 import ArrowDownIcon from '@material-ui/icons/ArrowDropDown'
 import classNames from 'classnames'
 import { useLocation, useRouteMatch, Link } from 'react-router-dom'
+import { ErrorHandler } from '../ErrorHandler'
 
 export class Adaptor {
   constructor(e) {
@@ -124,6 +125,9 @@ const useLaneStyles = makeStyles(theme => ({
     display: 'block',
     height: '100%',
     overflowY: 'scroll'
+  },
+  error: {
+    margin: theme.spacing(1)
   }
 }))
 function Lane({lane}) {
@@ -133,7 +137,9 @@ function Lane({lane}) {
   return <div className={classes.root}>
     <div className={classes.container}>
       <laneContext.Provider value={lane}>
+        <ErrorHandler message='This section could not be rendered, due to an unexpected error.' className={classes.error}>
           {adaptor.render()}
+        </ErrorHandler>
       </laneContext.Provider>
     </div>
   </div>

nomad/app/api/archive.py

@@ -307,7 +307,10 @@ class ArchiveQueryResource(Resource):
         upload_files = None
         current_upload_id = None
         required_with_references = compute_required_with_referenced(required)
-        archive_is_complete = required_with_references is not None
+        archive_is_complete = False
+        if required_with_references is not None:
+            archive_is_complete = True
+            required = required_with_references
 
         for entry in calcs:
             with_embargo = entry['with_embargo']
@@ -340,7 +343,7 @@ class ArchiveQueryResource(Resource):
                 try:
                     partial_archive = upload_partial_archives[calc_id]
                     partial_archive = filter_archive(
-                        required_with_references, partial_archive, transform=lambda e: e)
+                        required, partial_archive, transform=lambda e: e)
 
                     data.append({
                         'calc_id': calc_id,

nomad/config.py

@@ -270,7 +270,7 @@ datacite = NomadConfig(
 )
 
 meta = NomadConfig(
-    version='0.9.0',
+    version='0.9.1',
     commit=gitinfo.commit,
     release='devel',
     default_domain='dft',

nomad/normalizing/workflow.py

@@ -15,6 +15,7 @@
 import numpy as np
 
 from nomad.normalizing.normalizer import Normalizer
+from nomad.datamodel import EntryArchive
 from nomad.datamodel.metainfo.public import Workflow, GeometryOptimization, Phonon, Elastic,\
     MolecularDynamics
 
@@ -344,10 +345,6 @@ class WorkflowNormalizer(Normalizer):
         if self.section_run is None:
             return
 
-        workflow = self.entry_archive.section_workflow
-        if not workflow:
-            workflow = self.entry_archive.m_create(Workflow)
-
         workflow_type = None
         if self.entry_archive.section_workflow:
             workflow_type = self.entry_archive.section_workflow.workflow_type
@@ -358,6 +355,10 @@ class WorkflowNormalizer(Normalizer):
         if not workflow_type:
             return
 
+        workflow = self.entry_archive.section_workflow
+        if not workflow:
+            workflow = self.entry_archive.m_create(Workflow)
+
         workflow.workflow_type = workflow_type
 
         if workflow.workflow_type == 'geometry_optimization':
@@ -371,3 +372,7 @@ class WorkflowNormalizer(Normalizer):
 
         elif workflow.workflow_type == 'molecular_dynamics':
             MolecularDynamicsNormalizer(self.entry_archive).normalize()
+
+        # remove the section workflow again, if the parser/normalizer could not produce a result
+        if workflow.calculation_result_ref is None:
+            self.entry_archive.m_remove_sub_section(EntryArchive.section_workflow, -1)

ops/helm/nomad/Chart.yaml

 apiVersion: v1
-appVersion: "0.9.0"
+appVersion: "0.9.1"
 description: A Helm chart for Kubernetes that only runs nomad services and uses externally hosted databases.
 name: nomad
-version: 0.9.0
+version: 0.9.1

ops/helm/nomad/values.yaml

 ## Default values for nomad@FAIRDI
 version:
-  label: "0.9.0"
+  label: "0.9.1"
   isTest: false
   isBeta: false
   usesBetaData: false

tests/normalizing/test_workflow.py

@@ -27,6 +27,12 @@ def workflow_archive():
     return _archive
 
 
+def test_no_workflow(workflow_archive):
+    vasp_archive = workflow_archive(
+        'parsers/vaspoutcar', 'tests/data/parsers/vasp_outcar/OUTCAR')
+    assert vasp_archive.section_workflow is None
+
+
 def test_geometry_optimization_workflow(workflow_archive):
     vasp_archive = workflow_archive(
         'parsers/vasp', 'tests/data/normalizers/workflow/vasp/vasprun.xml')