Merge branch 'v0.8.9' into 'master'

V0.8.9

See merge request !172

Dockerfile

@@ -77,7 +77,7 @@ RUN \
     find /usr/local/lib/python3.7/site-packages/ -name '*.so' -print -exec sh -c 'file "{}" | grep -q "not stripped" && strip -s "{}"' \;
 
 # Built the GUI in the gui build image
-FROM node:latest as gui_build
+FROM node:14.8 as gui_build
 RUN mkdir -p /app
 WORKDIR /app
 ENV PATH /app/node_modules/.bin:$PATH

gui/package.json

 {
   "name": "nomad-fair-gui",
-  "version": "0.8.8",
+  "version": "0.8.9",
   "commit": "e98694e",
   "private": true,
   "dependencies": {
@@ -19,7 +19,7 @@
     "fetch": "^1.1.0",
     "file-saver": "^2.0.0",
     "html-to-react": "^1.3.3",
-    "keycloak-js": "^6.0.0",
+    "keycloak-js": "^7.0.1",
     "lodash": "^4.17.15",
     "material-ui-chip-input": "^1.0.0-beta.14",
     "material-ui-flat-pagination": "^4.0.0",
@@ -38,7 +38,7 @@
     "react-highlight": "^0.12.0",
     "react-infinite-scroller": "^1.2.4",
     "react-json-view": "^1.19.1",
-    "react-keycloak": "^6.1.0",
+    "react-keycloak": "^7.0.1-191016",
     "react-markdown": "^4.3.1",
     "react-mathjax": "^1.0.1",
     "react-router-dom": "^5.1.2",

gui/src/components/domains.js

@@ -7,13 +7,14 @@ import {
   DFTSystemVisualizations, DFTPropertyVisualizations, DFTMethodVisualizations
 } from './dft/DFTVisualizations'
 import EMSVisualizations from './ems/EMSVisualizations'
+import { Link } from '@material-ui/core'
 
 /* eslint-disable react/display-name */
 
 export const domains = ({
   dft: {
-    name: 'CMS',
-    label: 'Computational material science data (CMS)',
+    name: 'Computational data',
+    label: 'Computational material science data',
     key: 'dft',
     about: 'This include data from many computational material science codes',
     entryLabel: 'entry',
@@ -160,9 +161,9 @@ export const domains = ({
     searchTabs: ['entries', 'materials', 'datasets', 'groups', 'uploads']
   },
   ems: {
-    name: 'EMS',
+    name: 'Experimental data',
     key: 'ems',
-    label: 'Material science experiment data (EMS)',
+    label: 'Experimental material science data',
     about: 'This is metadata from material science experiments',
     entryLabel: 'entry',
     entryLabelPlural: 'entries',
@@ -199,20 +200,29 @@ export const domains = ({
      */
     searchResultColumns: {
       'formula': {
-        label: 'Formula'
+        label: 'Formula',
+        supportsSort: true
+      },
+      'ems.chemical': {
+        label: 'Material name'
       },
       'ems.method': {
-        label: 'Method'
+        label: 'Method',
+        supportsSort: true
+      },
+      'ems.data_type': {
+        label: 'Data'
       },
-      'ems.experiment_location': {
-        label: 'Location'
+      'ems.origin_time': {
+        label: 'Date',
+        render: entry => (entry.ems && entry.ems.origin_time && new Date(entry.ems.origin_time).toLocaleDateString()) || 'unavailable'
       },
-      'ems.experiment_time': {
-        label: 'Date/Time',
-        render: entry => (entry.ems && entry.ems.experiment_time !== 'unavailable') ? new Date(entry.ems.experiment_time * 1000).toLocaleString() : 'unavailable'
+      'ems.repository_url': {
+        label: 'Source',
+        render: entry => <Link target="external" href={entry.ems.entry_repository_url}>{entry.ems.repository_url}</Link>
       }
     },
-    defaultSearchResultColumns: ['formula', 'ems.method', 'ems.experiment_location', 'ems.experiment_time'],
+    defaultSearchResultColumns: ['formula', 'ems.chemical', 'ems.method', 'ems.data_type', 'ems.origin_time', 'ems.repository_url'],
     /**
      * A component to render the domain specific quantities in the metadata card of
      * the entry view. Needs to work with props: data (the entry data from the API),

gui/src/components/ems/EMSEntryCards.js

@@ -27,7 +27,7 @@ class EMSEntryCards extends React.Component {
         <CardContent classes={{root: classes.cardContent}}>
           <Markdown classes={{root: classes.description}}>{`
             The data for this experiment is externally stored and managed. Download the raw experiment data:
-            [${data.ems.repository_url}](${data.ems.repository_url}).
+            [${data.ems && data.ems.repository_url}](${data.ems && data.ems.entry_repository_url}).
 
             The meta data describing this experiment in its original format, can be
             downloaded here directly:

gui/src/components/ems/EMSEntryOverview.js

 import React from 'react'
 import PropTypes from 'prop-types'
 import Quantity from '../Quantity'
-import { Typography } from '@material-ui/core'
+import { Typography, Link } from '@material-ui/core'
 import { apiBase } from '../../config'
 
 export default class EMSEntryOverview extends React.Component {
@@ -45,7 +45,16 @@ export default class EMSEntryOverview extends React.Component {
 
     return (
       <Quantity column>
-        <Quantity quantity="ems.experiment_summary" label="summary" {...this.props} />
+        {data.ems.experiment_summary && <Quantity quantity="ems.experiment_summary" label="summary" {...this.props} />}
+        {this.state.previewBroken
+          ? data.ems.entry_repository_url && <Quantity label="preview" {...this.props}>
+            <Typography noWrap>
+              <a target="external" href={ems.entry_repository_url}>visit this entry on the external database</a>
+            </Typography>
+          </Quantity>
+          : <Quantity label="preview" {...this.props}>
+            <img alt="preview" style={{maxWidth: '100%', height: 'auto'}} src={relative_preview_url} onError={this.handleBrokenPreview}></img>
+          </Quantity>}
         <Quantity row>
           <Quantity column>
             <Quantity row>
@@ -55,27 +64,18 @@ export default class EMSEntryOverview extends React.Component {
                 : ''}
             </Quantity>
             <Quantity quantity="ems.method" label="experimental method" noWrap {...this.props} />
-            <Quantity quantity="ems.experiment_location" label="experiment location" noWrap {...this.props} />
-            <Quantity label="experiment time" {...this.props}>
+            {data.ems.experiment_location && <Quantity quantity="ems.experiment_location" label="experiment location" noWrap {...this.props} />}
+            <Quantity label="experiment or experiment publish date" {...this.props}>
               <Typography noWrap>{
-                data.ems.experiment_time && data.ems.experiment_time !== 'unavailable' ? new Date(data.ems.experiment_time * 1000).toLocaleString() : 'unavailable'
+                (ems && ems.origin_time && new Date(ems.origin_time).toLocaleDateString()) || 'unavailable'
               }</Typography>
             </Quantity>
-            <Quantity label="data" {...this.props}>
+            <Quantity label="data source" {...this.props}>
               <Typography noWrap>
-                <a target="external" href={data.ems.repository_url}>{data.ems.repository_name}</a>
+                <Link target="external" href={ems.entry_repository_url}>{ems.repository_url}</Link>
               </Typography>
             </Quantity>
           </Quantity>
-          {this.state.previewBroken
-            ? data.ems.entry_repository_url && <Quantity label="preview" {...this.props}>
-              <Typography noWrap>
-                <a target="external" href={data.ems.entry_repository_url}>visit this entry on the external database</a>
-              </Typography>
-            </Quantity>
-            : <Quantity label="preview" {...this.props}>
-              <img alt="preview" style={{maxWidth: '100%', height: 'auto'}} src={relative_preview_url} onError={this.handleBrokenPreview}></img>
-            </Quantity>}
         </Quantity>
       </Quantity>
     )

gui/src/components/entry/EntryQuery.js

 import React from 'react'
 import PropTypes from 'prop-types'
-import { withStyles, Typography } from '@material-ui/core'
+import { withStyles, Typography, Link } from '@material-ui/core'
 import { compose } from 'recompose'
 import { withApi, DoesNotExist } from '../api'
 import { withRouter } from 'react-router'
@@ -22,7 +22,8 @@ class EntryQuery extends React.Component {
   }
 
   static defaultState = {
-    doesNotExist: false
+    doesNotExist: false,
+    queryParams: null
   }
 
   state = {...EntryQuery.defaultState}
@@ -43,7 +44,7 @@ class EntryQuery extends React.Component {
       }
     }).catch(error => {
       if (error.name === 'DoesNotExist') {
-        this.setState({doesNotExist: true})
+        this.setState({doesNotExist: true, queryParams: queryParams})
       } else {
         this.props.raiseError(error)
       }
@@ -63,12 +64,19 @@ class EntryQuery extends React.Component {
 
   render() {
     const { classes, api } = this.props
-    const { doesNotExist } = this.state
+    const { doesNotExist, queryParams } = this.state
 
     let message = 'loading ...'
 
     if (doesNotExist) {
-      if (api.isLoggedIn) {
+      console.log(queryParams)
+      if (queryParams && queryParams['external_id'] && queryParams['external_id'].startsWith('mp-')) {
+        message = <React.Fragment>
+          This particular calculation <Link href={`https://materialsproject.org/tasks/${queryParams['external_id']}#`}>
+            {queryParams['external_id']}
+          </Link> has not yet been provided to NOMAD by the Materials Project.
+        </React.Fragment>
+      } else if (api.isLoggedIn) {
         message = `
             This URL points to an entry that either does not exist, or that you are not
             authorized to see.`

gui/src/components/search/Search.js

@@ -410,12 +410,12 @@ DomainSelect.propTypes = {
 }
 
 const ownerLabel = {
-  all: 'All entries',
-  visible: 'Include your private entries',
-  public: 'Only public entries',
-  user: 'Only your entries',
-  shared: 'Incl. shared data',
-  staging: 'Staging area only'
+  all: 'All',
+  visible: 'Include private',
+  public: 'Only public',
+  user: 'Only yours',
+  shared: 'Shared',
+  staging: 'Unpublished'
 }
 
 const ownerTooltips = {

gui/src/index.js

@@ -29,7 +29,7 @@ const keycloak = Keycloak({
 // matomo.push('requireConsent')
 
 ReactDOM.render(
-  <KeycloakProvider keycloak={keycloak} initConfig={{onLoad: 'check-sso'}} LoadingComponent={<div />}>
+  <KeycloakProvider keycloak={keycloak} initConfig={{onLoad: 'check-sso', 'checkLoginIframe': false}} LoadingComponent={<div />}>
     <Router history={matomoEnabled ? matomo.connectToHistory(history) : history}>
       <QueryParamProvider ReactRouterRoute={Route}>
         <App />

gui/yarn.lock

@@ -2580,7 +2580,7 @@ base16@^1.0.0:
   resolved "https://registry.yarnpkg.com/base16/-/base16-1.0.0.tgz#e297f60d7ec1014a7a971a39ebc8a98c0b681e70"
   integrity sha1-4pf2DX7BAUp6lxo568ipjAtoHnA=
-base64-js@^1.0.2:
+base64-js@1.3.1, base64-js@^1.0.2:
   version "1.3.1"
   resolved "https://registry.yarnpkg.com/base64-js/-/base64-js-1.3.1.tgz#58ece8cb75dd07e71ed08c736abc5fac4dbf8df1"
   integrity sha512-mLQ4i2QO1ytvGWFWmcngKO//JXAQueZvwEKtjgQFM4jIK0kU+ytMfplL8j+n5mspOfjHwoAg+9yhb7BwAHm36g==
@@ -4222,11 +4222,6 @@ decode-uri-component@^0.2.0:
   resolved "https://registry.yarnpkg.com/decode-uri-component/-/decode-uri-component-0.2.0.tgz#eb3913333458775cb84cd1a1fae062106bb87545"
   integrity sha1-6zkTMzRYd1y4TNGh+uBiEGu4dUU=
-deep-compare@^0.0.5:
-  version "0.0.5"
-  resolved "https://registry.yarnpkg.com/deep-compare/-/deep-compare-0.0.5.tgz#c38a8f6a834c27dab427dcc496d9d6e1e1b40b67"
-  integrity sha1-w4qPaoNMJ9q0J9zEltnW4eG0C2c=
-
 deep-equal@^1.0.1:
   version "1.1.1"
   resolved "https://registry.yarnpkg.com/deep-equal/-/deep-equal-1.1.1.tgz#b5c98c942ceffaf7cb051e24e1434a25a2e6076a"
@@ -7190,6 +7185,11 @@ jest@24.9.0:
     import-local "^2.0.0"
     jest-cli "^24.9.0"
+js-sha256@0.9.0:
+  version "0.9.0"
+  resolved "https://registry.yarnpkg.com/js-sha256/-/js-sha256-0.9.0.tgz#0b89ac166583e91ef9123644bd3c5334ce9d0966"
+  integrity sha512-sga3MHh9sgQN2+pJ9VYZ+1LPwXOxuBJBA5nrR5/ofPfuiJBE2hnjsaN8se8JznOmGLN2p49Pe5U/ttafcs/apA==
+
 "js-tokens@^3.0.0 || ^4.0.0", js-tokens@^4.0.0:
   version "4.0.0"
   resolved "https://registry.yarnpkg.com/js-tokens/-/js-tokens-4.0.0.tgz#19203fb59991df98e3a287050d4647cdeaf32499"
@@ -7484,10 +7484,13 @@ jsx-ast-utils@^2.4.1:
     array-includes "^3.1.1"
     object.assign "^4.1.0"
-keycloak-js@^6.0.0:
-  version "6.0.1"
-  resolved "https://registry.yarnpkg.com/keycloak-js/-/keycloak-js-6.0.1.tgz#329a5e77210dfc4a7d4acf96f95dd0132455bea3"
-  integrity sha512-p02dBCA9pSH1xvTmRIEMdeMz00eCGKmZF+rjMeqrkiQD4xhXkzu50J9sQjaANolMlLhazOtfql70+N5QWm8Upg==
+keycloak-js@^7.0.1:
+  version "7.0.1"
+  resolved "https://registry.yarnpkg.com/keycloak-js/-/keycloak-js-7.0.1.tgz#490971a2cf404bdbbee87804211f2b4f6561e858"
+  integrity sha512-gefTlb6DjvqH2wTbXCs3o2d54Ot6lvFb0ynF4aU75ucUq9qQ1p1+lm+1OcRRC34nPCG16joPz2QNxNVXi8Bmng==
+  dependencies:
+    base64-js "1.3.1"
+    js-sha256 "0.9.0"
 keycode@^2.1.7:
   version "2.2.0"
@@ -10115,6 +10118,11 @@ react-event-listener@^0.6.0:
     prop-types "^15.6.0"
     warning "^4.0.1"
+react-fast-compare@^2.0.4:
+  version "2.0.4"
+  resolved "https://registry.yarnpkg.com/react-fast-compare/-/react-fast-compare-2.0.4.tgz#e84b4d455b0fec113e0402c329352715196f81f9"
+  integrity sha512-suNP+J1VU1MWFKcyt7RtjiSWUjvidmQSlqu+eHslq+342xCbGTYmC0mEhPCOHxlW0CywylOC1u2DFAT+bv4dBw==
+
 react-highlight@^0.12.0:
   version "0.12.0"
   resolved "https://registry.yarnpkg.com/react-highlight/-/react-highlight-0.12.0.tgz#34de986a0bfdf228904d0c269b69538d95b35802"
@@ -10144,14 +10152,14 @@ react-json-view@^1.19.1:
     react-lifecycles-compat "^3.0.4"
     react-textarea-autosize "^6.1.0"
-react-keycloak@^6.1.0:
-  version "6.1.2"
-  resolved "https://registry.yarnpkg.com/react-keycloak/-/react-keycloak-6.1.2.tgz#7049af20d4229e91c1380a819883ba5f802ae0f7"
-  integrity sha512-KYrB7d1VUmXFSG3hbrwmqr2Jh6mk/hKaMAw1jGB6KSB3BlWe0VPO9tVxbaC5P5JQrQ46aGJnyZXuvn9EqLTQ1Q==
+react-keycloak@^7.0.1-191016:
+  version "7.0.1-191016"
+  resolved "https://registry.yarnpkg.com/react-keycloak/-/react-keycloak-7.0.1-191016.tgz#51236ca71fabeeeaad7970c6fc4ed7717dd9b380"
+  integrity sha512-H0kxrY/klARf09FvcGtGv0pZkaZM8IkUA/43Ie6/jnvpm7oIszeWWnsh2LlsN6nDXv/GTJUs6h7Xt5UZUEsP1w==
   dependencies:
-    deep-compare "^0.0.5"
     hoist-non-react-statics "^3.3.0"
     prop-types "^15.7.2"
+    react-fast-compare "^2.0.4"
 react-lifecycles-compat@^3.0.2, react-lifecycles-compat@^3.0.4:
   version "3.0.4"

nomad/config.py

@@ -266,7 +266,7 @@ datacite = NomadConfig(
 )
 
 meta = NomadConfig(
-    version='0.8.8',
+    version='0.8.9',
     commit=gitinfo.commit,
     release='devel',
     default_domain='dft',

nomad/datamodel/dft.py

@@ -156,7 +156,9 @@ class DFTMetadata(MSection):
     xc_functional = Quantity(
         type=str, default='not processed',
         description='The libXC based xc functional classification used in the simulation.',
-        a_search=Search(statistic_values=list(xc_treatments.values()) + ['unavailable', 'not processed']))
+        a_search=Search(
+            statistic_values=list(xc_treatments.values()) + ['unavailable', 'not processed'],
+            statistic_size=100))
 
     system = Quantity(
         type=str, default='not processed',

nomad/metainfo/search_extension.py

@@ -190,5 +190,6 @@ class Search(Elastic):
     def statistic_values(self, values):
         self._statistic_values = values
         if self._statistic_values is not None:
-            self.statistic_size = len(self._statistic_values)
+            if self.statistic_fixed_size is None:
+                self.statistic_size = len(self._statistic_values)
             self.statistic_fixed_size = len(self._statistic_values)

ops/helm/nomad/Chart.yaml

 apiVersion: v1
-appVersion: "0.8.8"
+appVersion: "0.8.9"
 description: A Helm chart for Kubernetes that only runs nomad services and uses externally hosted databases.
 name: nomad
-version: 0.8.8
+version: 0.8.9

ops/helm/nomad/values.yaml

 ## Default values for nomad@FAIRDI
 version:
-  label: "0.8.8"
+  label: "0.8.9"
   isBeta: false
   usesBetaData: false
   officialUrl: "https://nomad-lab.eu/prod/rae/gui"