From 72079f2cb99b4456afa36e113bc864c327cf25d4 Mon Sep 17 00:00:00 2001
From: Markus Scheidgen <markus.scheidgen@gmail.com>
Date: Mon, 9 Sep 2019 14:06:45 +0200
Subject: [PATCH] Implemented Dataset page.
---
gui/src/components/App.js | 68 ++--
gui/src/components/DatasetPage.js | 84 +++++
gui/src/components/domains.js | 2 +-
gui/src/components/entry/RepoEntryView.js | 21 +-
gui/src/components/search/Search.js | 272 ++++++++++++++++
.../components/search/SearchAggregations.js | 5 +-
gui/src/components/search/SearchPage.js | 290 ++----------------
gui/src/utils.js | 32 ++
nomad/api/raw.py | 5 +-
nomad/api/repo.py | 47 ++-
nomad/datamodel/base.py | 4 +-
tests/test_api.py | 11 +-
12 files changed, 521 insertions(+), 320 deletions(-)
create mode 100644 gui/src/components/DatasetPage.js
create mode 100644 gui/src/components/search/Search.js
create mode 100644 gui/src/utils.js
diff --git a/gui/src/components/App.js b/gui/src/components/App.js
index 80bbd3fe11..c96d5cc0aa 100644
--- a/gui/src/components/App.js
+++ b/gui/src/components/App.js
@@ -22,13 +22,15 @@ import Calc from './entry/Calc'
import About from './About'
import LoginLogout from './LoginLogout'
import { genTheme, repoTheme, archiveTheme, appBase } from '../config'
-import { DomainProvider } from './domains'
+import { DomainProvider, withDomain } from './domains'
import {help as metainfoHelp, default as MetaInfoBrowser} from './metaInfoBrowser/MetaInfoBrowser'
import packageJson from '../../package.json'
import { Cookies, withCookies } from 'react-cookie'
import Markdown from './Markdown'
import {help as uploadHelp, default as Uploads} from './uploads/Uploads'
-import ResolvePID from './entry/ResolvePID';
+import ResolvePID from './entry/ResolvePID'
+import DatasetPage from './DatasetPage'
+import { capitalize } from '../utils'
export class VersionMismatch extends Error {
constructor(msg) {
@@ -39,27 +41,7 @@ export class VersionMismatch extends Error {
const drawerWidth = 200
-const toolbarTitles = {
- '/': 'About, Documentation, Getting Help',
- '/search': 'Find and Download Data',
- '/uploads': 'Upload and Publish Data',
- '/metainfo': 'The NOMAD Meta Info'
-}
-const toolbarThemes = {
- '/': genTheme,
- '/search': repoTheme,
- '/uploads': repoTheme,
- '/entry': repoTheme,
- '/metainfo': archiveTheme
-}
-
-const toolbarHelp = {
- '/': null,
- '/search': {title: 'How to find and download data', content: searchHelp},
- '/uploads': {title: 'How to upload data', content: uploadHelp},
- '/metainfo': {title: 'About the NOMAD meta-info', content: metainfoHelp}
-}
class NavigationUnstyled extends React.Component {
static propTypes = {
@@ -177,6 +159,31 @@ class NavigationUnstyled extends React.Component {
}
}
+ toolbarTitles = {
+ '/': 'About, Documentation, Getting Help',
+ '/search': 'Find and Download Data',
+ '/uploads': 'Upload and Publish Data',
+ '/metainfo': 'The NOMAD Meta Info',
+ '/entry': capitalize(this.props.domain.entryLabel),
+ '/dataset': 'Dataset'
+ }
+
+ toolbarThemes = {
+ '/': genTheme,
+ '/search': repoTheme,
+ '/uploads': repoTheme,
+ '/entry': repoTheme,
+ '/dataset': repoTheme,
+ '/metainfo': archiveTheme
+ }
+
+ toolbarHelp = {
+ '/': null,
+ '/search': {title: 'How to find and download data', content: searchHelp},
+ '/uploads': {title: 'How to upload data', content: uploadHelp},
+ '/metainfo': {title: 'About the NOMAD meta-info', content: metainfoHelp}
+ }
+
componentDidMount() {
fetch(`${appBase}/meta.json`)
.then((response) => response.json())
@@ -198,6 +205,7 @@ class NavigationUnstyled extends React.Component {
render() {
const { classes, children, location: { pathname }, loading } = this.props
+ const { toolbarThemes, toolbarHelp, toolbarTitles } = this
const selected = dct => {
const key = Object.keys(dct).find(key => {
@@ -299,7 +307,7 @@ class NavigationUnstyled extends React.Component {
}
}
-const Navigation = compose(withRouter, withErrors, withApi(false), withStyles(NavigationUnstyled.styles))(NavigationUnstyled)
+const Navigation = compose(withRouter, withErrors, withApi(false), withDomain, withStyles(NavigationUnstyled.styles))(NavigationUnstyled)
class LicenseAgreementUnstyled extends React.Component {
static propTypes = {
@@ -392,7 +400,7 @@ export default class App extends React.Component {
},
'entry': {
path: '/entry/id/:uploadId/:calcId',
- key: (props) => `entry/${props.match.params.uploadId}/${props.match.params.uploadId}`,
+ key: (props) => `entry/id/${props.match.params.uploadId}/${props.match.params.uploadId}`,
render: props => {
const { match, ...rest } = props
if (match && match.params.uploadId && match.params.calcId) {
@@ -402,6 +410,18 @@ export default class App extends React.Component {
}
}
},
+ 'dataset': {
+ path: '/dataset/id/:datasetId',
+ key: (props) => `dataset/id/${props.match.params.datasetId}`,
+ render: props => {
+ const { match, ...rest } = props
+ if (match && match.params.datasetId) {
+ return (<DatasetPage {...rest} datasetId={match.params.datasetId} />)
+ } else {
+ return ''
+ }
+ }
+ },
'entry_pid': {
path: '/entry/pid/:pid',
key: (props) => `entry/pid/${props.match.params.pid}`,
diff --git a/gui/src/components/DatasetPage.js b/gui/src/components/DatasetPage.js
new file mode 100644
index 0000000000..de9baf5ce3
--- /dev/null
+++ b/gui/src/components/DatasetPage.js
@@ -0,0 +1,84 @@
+import React from 'react'
+import PropTypes from 'prop-types'
+import { withStyles } from '@material-ui/core/styles'
+import { compose } from 'recompose'
+import { withErrors } from './errors'
+import { withApi } from './api'
+import Search from './search/Search'
+import { Typography, Link, Fab } from '@material-ui/core'
+import Download from './entry/Download'
+import DownloadIcon from '@material-ui/icons/CloudDownload'
+
+export const help = `
+This page allows you to **inspect** and **download** NOMAD datasets. It alsow allows you
+to explore a dataset with similar controls that the search page offers.
+`
+
+class DatasetPage extends React.Component {
+ static propTypes = {
+ classes: PropTypes.object.isRequired,
+ api: PropTypes.object.isRequired,
+ datasetId: PropTypes.string.isRequired,
+ raiseError: PropTypes.func.isRequired
+ }
+
+ static styles = theme => ({
+ root: {
+ },
+ description: {
+ padding: theme.spacing.unit * 3
+ },
+ downloadFab: {
+ zIndex: 1,
+ right: 32,
+ top: 56 + 32,
+ position: 'fixed !important'
+ }
+ })
+
+ state = {
+ dataset: {}
+ }
+
+ componentDidMount() {
+ const {datasetId, raiseError, api} = this.props
+ api.search({
+ owner: 'all',
+ dataset_id: datasetId,
+ page: 1, per_page: 1
+ }).then(data => {
+ const entry = data.results[0]
+ const dataset = entry ? entry.datasets.find(ds => ds.id + '' === datasetId) : {}
+ this.setState({dataset: dataset || {}})
+ }).catch(error => {
+ this.setState({dataset: {}})
+ raiseError(error)
+ })
+ }
+
+ render() {
+ const { classes, datasetId } = this.props
+ const { dataset } = this.state
+
+ return (
+ <div className={classes.root}>
+ <div className={classes.description}>
+ <Typography variant="h4">{dataset.name || 'loading ...'}</Typography>
+ <Typography>
+ dataset{dataset.doi ? <span>, with DOI <Link href={dataset.doi}>{dataset.doi}</Link></span> : ''}
+ </Typography>
+ </div>
+ <Search searchParameters={{owner: 'all', dataset_id: datasetId}} />
+ <Download
+ classes={{root: classes.downloadFab}} tooltip="download all rawfiles"
+ component={Fab} className={classes.downloadFab} color="primary" size="medium"
+ url={`raw/query?dataset_id=${datasetId}`} fileName={`${dataset.name}.json`}
+ >
+ <DownloadIcon />
+ </Download>
+ </div>
+ )
+ }
+}
+
+export default compose(withApi(false), withErrors, withStyles(DatasetPage.styles))(DatasetPage)
diff --git a/gui/src/components/domains.js b/gui/src/components/domains.js
index afaa7717fc..58cef56810 100644
--- a/gui/src/components/domains.js
+++ b/gui/src/components/domains.js
@@ -54,7 +54,7 @@ class DomainProviderBase extends React.Component {
still be missing when you are exploring Nomad data using the new search and data
exploring capabilities (menu items on the left).
`,
- entryLabel: 'calculation',
+ entryLabel: 'code run',
searchPlaceholder: 'enter atoms, codes, functionals, or other quantity values',
/**
* A component that is used to render the search aggregations. The components needs
diff --git a/gui/src/components/entry/RepoEntryView.js b/gui/src/components/entry/RepoEntryView.js
index de8d201aba..9319cfaaf2 100644
--- a/gui/src/components/entry/RepoEntryView.js
+++ b/gui/src/components/entry/RepoEntryView.js
@@ -1,6 +1,6 @@
import React from 'react'
import PropTypes from 'prop-types'
-import { withStyles, Divider, Card, CardContent, Grid, CardHeader, Fab, Typography } from '@material-ui/core'
+import { withStyles, Divider, Card, CardContent, Grid, CardHeader, Fab, Typography, Link } from '@material-ui/core'
import { withApi } from '../api'
import { compose } from 'recompose'
import Download from './Download'
@@ -8,6 +8,7 @@ import DownloadIcon from '@material-ui/icons/CloudDownload'
import ApiDialogButton from '../ApiDialogButton'
import Quantity from '../Quantity'
import { withDomain } from '../domains'
+import { Link as RouterLink } from 'react-router-dom'
class RepoEntryView extends React.Component {
static styles = theme => ({
@@ -109,9 +110,11 @@ class RepoEntryView extends React.Component {
<Quantity column>
<Quantity quantity='comment' placeholder='no comment' {...quantityProps} />
<Quantity quantity='references' placeholder='no references' {...quantityProps}>
- {(calcData.references || []).map(ref => <Typography key={ref} noWrap>
- <a href={ref}>{ref}</a>
- </Typography>)}
+ <div>
+ {(calcData.references || []).map(ref => <Typography key={ref} noWrap>
+ <a href={ref}>{ref}</a>
+ </Typography>)}
+ </div>
</Quantity>
<Quantity quantity='authors' {...quantityProps}>
<Typography>
@@ -119,9 +122,13 @@ class RepoEntryView extends React.Component {
</Typography>
</Quantity>
<Quantity quantity='datasets' placeholder='no datasets' {...quantityProps}>
- <Typography>
- {(calcData.datasets || []).map(ds => `${ds.name}${ds.doi ? ` (${ds.doi})` : ''}`).join(', ')}
- </Typography>
+ <div>
+ {(calcData.datasets || []).map(ds => (
+ <Typography key={ds.id}>
+ <Link component={RouterLink} to={`/dataset/id/${ds.id}`}>{ds.name}</Link>
+ {ds.doi ? <span> (<Link href={ds.doi}>{ds.doi}</Link>)</span> : ''}
+ </Typography>))}
+ </div>
</Quantity>
</Quantity>
</CardContent>
diff --git a/gui/src/components/search/Search.js b/gui/src/components/search/Search.js
new file mode 100644
index 0000000000..9f338791ac
--- /dev/null
+++ b/gui/src/components/search/Search.js
@@ -0,0 +1,272 @@
+import React from 'react'
+import PropTypes from 'prop-types'
+import { withStyles } from '@material-ui/core/styles'
+import { IconButton, Typography, Divider, Tooltip, Tabs, Tab } from '@material-ui/core'
+import { compose } from 'recompose'
+import { withErrors } from '../errors'
+import { withApi, DisableOnLoading } from '../api'
+import SearchBar from './SearchBar'
+import EntryList from './EntryList'
+import SearchAggregations from './SearchAggregations'
+import ExpandMoreIcon from '@material-ui/icons/ExpandMore'
+import ExpandLessIcon from '@material-ui/icons/ExpandLess'
+import { withDomain } from '../domains'
+import DatasetList from './DatasetList';
+import { isEquivalent } from '../../utils';
+
+
+/**
+ * Component that comprises all search views: SearchBar, SearchAggregations (aka statistics),
+ * results (EntryList, DatasetList).
+ */
+class Search extends React.Component {
+ static propTypes = {
+ classes: PropTypes.object.isRequired,
+ api: PropTypes.object.isRequired,
+ raiseError: PropTypes.func.isRequired,
+ domain: PropTypes.object,
+ loading: PropTypes.number,
+ searchParameters: PropTypes.object,
+ showDetails: PropTypes.bool
+ }
+
+ static styles = theme => ({
+ root: {
+ },
+ searchContainer: {
+ padding: theme.spacing.unit * 3
+ },
+ resultsContainer: {
+ },
+ searchEntry: {
+ minWidth: 500,
+ maxWidth: 900,
+ margin: 'auto',
+ width: '100%'
+ },
+ search: {
+ marginTop: theme.spacing.unit * 4,
+ marginBottom: theme.spacing.unit * 8,
+ display: 'flex',
+ alignItems: 'center',
+ minWidth: 500,
+ maxWidth: 1000,
+ margin: 'auto',
+ width: '100%'
+ },
+ searchBar: {
+ width: '100%'
+ },
+ searchDivider: {
+ width: 1,
+ height: 28,
+ margin: theme.spacing.unit * 0.5
+ },
+ searchButton: {
+ padding: 10
+ },
+ searchResults: {}
+ })
+
+ static emptySearchData = {
+ results: [],
+ pagination: {
+ total: 0
+ },
+ datasets: {
+ after: null,
+ values: []
+ },
+ statistics: {
+ total: {
+ all: {
+ datasets: 0
+ }
+ }
+ }
+ }
+
+ state = {
+ data: Search.emptySearchData,
+ searchState: {
+ ...SearchAggregations.defaultState
+ },
+ entryListState: {
+ ...EntryList.defaultState
+ },
+ datasetListState: {
+ ...DatasetList.defaultState
+ },
+ showDetails: this.props.showDetails,
+ resultTab: 'entries'
+ }
+
+ constructor(props) {
+ super(props)
+
+ this.updateEntryList = this.updateEntryList.bind(this)
+ this.updateDatasetList = this.updateDatasetList.bind(this)
+ this.updateSearch = this.updateSearch.bind(this)
+ this.handleClickExpand = this.handleClickExpand.bind(this)
+
+ this._mounted = false
+ }
+
+ updateEntryList(changes) {
+ const entryListState = {
+ ...this.state.entryListState, ...changes
+ }
+ this.update({entryListState: entryListState})
+ }
+
+ updateDatasetList(changes) {
+ const datasetListState = {
+ ...this.state.datasetListState, ...changes
+ }
+ this.update({datasetListState: datasetListState})
+ }
+
+ updateSearch(changes) {
+ const searchState = {
+ ...this.state.searchState, ...changes
+ }
+ this.update({searchState: searchState})
+ }
+
+ update(changes) {
+ if (!this._mounted) {
+ return
+ }
+
+ changes = changes || {}
+ const { searchParameters } = this.props
+ const { entryListState, datasetListState, searchState } = {...this.state, ...changes}
+ const { searchValues, ...searchStateRest } = searchState
+ this.setState({...changes})
+
+ this.props.api.search({
+ datasets: true,
+ statistics: true,
+ ...entryListState,
+ ...datasetListState,
+ ...searchValues,
+ ...searchStateRest,
+ ...searchParameters
+ }).then(data => {
+ this.setState({
+ data: data || Search.emptySearchData
+ })
+ }).catch(error => {
+ if (error.name === 'NotAuthorized' && this.props.searchParameters.owner !== 'all') {
+ this.setState({data: Search.emptySearchData})
+ } else {
+ this.setState({data: Search.emptySearchData})
+ this.props.raiseError(error)
+ }
+ })
+ }
+
+ componentDidMount() {
+ this._mounted = true
+ this.update()
+ }
+
+ componentWillUnmount() {
+ this._mounted = false
+ }
+
+ componentDidUpdate(prevProps) {
+ // login/logout or changed search paraemters -> reload results
+ if (prevProps.api !== this.props.api || !isEquivalent(prevProps.searchParameters, this.props.searchParameters)) {
+ this.update()
+ }
+ }
+
+ handleClickExpand() {
+ this.setState({showDetails: !this.state.showDetails})
+ }
+
+ render() {
+ const { classes, domain, loading } = this.props
+ const { data, searchState, entryListState, datasetListState, showDetails, resultTab } = this.state
+ const { searchValues } = searchState
+ const { pagination: { total }, statistics } = data
+
+ const helperText = <span>
+ There are {Object.keys(domain.searchMetrics).filter(key => statistics.total.all[key]).map(key => {
+ return <span key={key}>
+ {domain.searchMetrics[key].renderResultString(!loading && statistics.total.all[key] !== undefined ? statistics.total.all[key] : '...')}
+ </span>
+ })}{Object.keys(searchValues).length ? ' left' : ''}.
+ </span>
+
+ return (
+ <div className={classes.root}>
+ <div className={classes.searchContainer}>
+ <DisableOnLoading>
+ <div className={classes.search}>
+ <SearchBar classes={{autosuggestRoot: classes.searchBar}}
+ fullWidth fullWidthInput={false} helperText={helperText}
+ label="search"
+ placeholder={domain.searchPlaceholder}
+ data={data} searchValues={searchValues}
+ InputLabelProps={{
+ shrink: true
+ }}
+ onChanged={values => this.updateSearch({searchValues: values})}
+ />
+ <Divider className={classes.searchDivider} />
+ <Tooltip title={showDetails ? 'Hide statistics' : 'Show statistics'}>
+ <IconButton className={classes.searchButton} color="secondary" onClick={this.handleClickExpand}>
+ {showDetails ? <ExpandLessIcon/> : <ExpandMoreIcon/>}
+ </IconButton>
+ </Tooltip>
+ </div>
+
+ <div className={classes.searchEntry}>
+ <SearchAggregations
+ data={data} {...searchState} onChange={this.updateSearch}
+ showDetails={showDetails}
+ />
+ </div>
+ </DisableOnLoading>
+ </div>
+ <div className={classes.resultsContainer}>
+ <Tabs
+ value={resultTab}
+ indicatorColor="primary"
+ textColor="primary"
+ onChange={(event, value) => this.setState({resultTab: value})}
+ >
+ <Tab label="Calculations" value="entries" />
+ <Tab label="Datasets" value="datasets" />
+ </Tabs>
+
+ <div className={classes.searchResults} hidden={resultTab !== 'entries'}>
+ <Typography variant="caption" style={{margin: 12}}>
+ About {total.toLocaleString()} results:
+ </Typography>
+
+ <EntryList
+ data={data} total={total}
+ onChange={this.updateEntryList}
+ {...entryListState}
+ />
+ </div>
+ <div className={classes.searchResults} hidden={resultTab !== 'datasets'}>
+ <Typography variant="caption" style={{margin: 12}}>
+ About {statistics.total.all.datasets.toLocaleString()} datasets:
+ </Typography>
+
+ <DatasetList data={data} total={statistics.total.all.datasets}
+ onChange={this.updateDatasetList}
+ {...datasetListState}
+ />
+ </div>
+ </div>
+ </div>
+ )
+ }
+}
+
+export default compose(withApi(false), withErrors, withDomain, withStyles(Search.styles))(Search)
diff --git a/gui/src/components/search/SearchAggregations.js b/gui/src/components/search/SearchAggregations.js
index 794e8801e1..41299810cd 100644
--- a/gui/src/components/search/SearchAggregations.js
+++ b/gui/src/components/search/SearchAggregations.js
@@ -44,7 +44,10 @@ class SearchAggregationsUnstyled extends React.Component {
const firstRealQuantitiy = Object.keys(statistics).find(key => key !== 'total')
if (firstRealQuantitiy) {
const firstValue = Object.keys(statistics[firstRealQuantitiy])[0]
- useMetric = Object.keys(statistics[firstRealQuantitiy][firstValue]).find(metric => metric !== 'code_runs') || 'code_runs'
+ if (firstValue) {
+ useMetric = Object.keys(statistics[firstRealQuantitiy][firstValue])
+ .find(metric => metric !== 'code_runs') || 'code_runs'
+ }
}
const metricsDefinitions = domain.searchMetrics
diff --git a/gui/src/components/search/SearchPage.js b/gui/src/components/search/SearchPage.js
index d79c7b0945..5e47f5556c 100644
--- a/gui/src/components/search/SearchPage.js
+++ b/gui/src/components/search/SearchPage.js
@@ -1,19 +1,12 @@
import React from 'react'
import PropTypes from 'prop-types'
import { withStyles } from '@material-ui/core/styles'
-import { FormControl, FormControlLabel, Checkbox, FormGroup,
- FormLabel, IconButton, Typography, Divider, Tooltip, Tabs, Tab } from '@material-ui/core'
+import { FormControl, FormControlLabel, Checkbox, FormGroup, FormLabel, Tooltip } from '@material-ui/core'
import { compose } from 'recompose'
import { withErrors } from '../errors'
import { withApi, DisableOnLoading } from '../api'
-import SearchBar from './SearchBar'
-import EntryList from './EntryList'
-import SearchAggregations from './SearchAggregations'
-import ExpandMoreIcon from '@material-ui/icons/ExpandMore'
-import ExpandLessIcon from '@material-ui/icons/ExpandLess'
-import { withDomain } from '../domains'
import { appBase } from '../../config'
-import DatasetList from './DatasetList';
+import Search from './Search';
export const help = `
This page allows you to **search** in NOMAD's data. The upper part of this page
@@ -57,181 +50,26 @@ all parsed data. The *log* tab, will show you a log of the entry's processing.
class SearchPage extends React.Component {
static propTypes = {
classes: PropTypes.object.isRequired,
- match: PropTypes.any,
api: PropTypes.object.isRequired,
user: PropTypes.object,
- raiseError: PropTypes.func.isRequired,
- domain: PropTypes.object,
- loading: PropTypes.number
+ raiseError: PropTypes.func.isRequired
}
static styles = theme => ({
root: {
},
- searchContainer: {
- padding: theme.spacing.unit * 3
- },
- resultsContainer: {
- },
searchEntry: {
- minWidth: 500,
- maxWidth: 900,
- margin: 'auto',
- width: '100%'
- },
- search: {
- marginTop: theme.spacing.unit * 4,
- marginBottom: theme.spacing.unit * 8,
- display: 'flex',
- alignItems: 'center',
- minWidth: 500,
- maxWidth: 1000,
- margin: 'auto',
- width: '100%'
- },
- searchBar: {
- width: '100%'
- },
- searchDivider: {
- width: 1,
- height: 28,
- margin: theme.spacing.unit * 0.5
- },
- searchButton: {
- padding: 10
- },
- searchResults: {}
- })
-
- static emptySearchData = {
- results: [],
- pagination: {
- total: 0
- },
- datasets: {
- after: null,
- values: []
- },
- statistics: {
- total: {
- all: {
- datasets: 0
- }
- }
+ padding: theme.spacing.unit * 3
}
- }
+ })
state = {
- data: SearchPage.emptySearchData,
- owner: 'all',
- searchState: {
- ...SearchAggregations.defaultState
- },
- entryListState: {
- ...EntryList.defaultState
- },
- datasetListState: {
- ...DatasetList.defaultState
- },
- showDetails: true,
- resultTab: 'entries'
- }
-
- constructor(props) {
- super(props)
-
- this.updateEntryList = this.updateEntryList.bind(this)
- this.updateDatasetList = this.updateDatasetList.bind(this)
- this.updateSearch = this.updateSearch.bind(this)
- this.handleClickExpand = this.handleClickExpand.bind(this)
-
- this._mounted = false
- }
-
- updateEntryList(changes) {
- const entryListState = {
- ...this.state.entryListState, ...changes
- }
- this.update({entryListState: entryListState})
- }
-
- updateDatasetList(changes) {
- const datasetListState = {
- ...this.state.datasetListState, ...changes
- }
- this.update({datasetListState: datasetListState})
- }
-
- updateSearch(changes) {
- const searchState = {
- ...this.state.searchState, ...changes
- }
- this.update({searchState: searchState})
- }
-
- update(changes) {
- if (!this._mounted) {
- return
- }
-
- changes = changes || {}
- const { owner, entryListState, datasetListState, searchState } = {...this.state, ...changes}
- const { searchValues, ...searchStateRest } = searchState
- this.setState({...changes})
-
- this.props.api.search({
- owner: owner,
- ...entryListState,
- ...datasetListState,
- ...searchValues,
- ...searchStateRest
- }).then(data => {
- this.setState({
- data: data || SearchPage.emptySearchData
- })
- }).catch(error => {
- if (error.name === 'NotAuthorized' && owner !== 'all') {
- this.setState({data: SearchPage.emptySearchData, owner: 'all'})
- } else {
- this.setState({data: SearchPage.emptySearchData, owner: owner})
- this.props.raiseError(error)
- }
- })
- }
-
- componentDidMount() {
- this._mounted = true
- this.update()
- }
-
- componentWillUnmount() {
- this._mounted = false
- }
-
- componentDidUpdate(prevProps) {
- if (prevProps.api !== this.props.api) { // login/logout case, reload results
- this.update()
- } else if (prevProps.match.path !== this.props.match.path) { // navigation case
- // update if we went back to the search
- if (this.props.match.path === '/search' && this.props.match.isExact) {
- this.update()
- }
- }
- }
-
- handleOwnerChange(owner) {
- this.update({owner: owner})
- }
-
- handleClickExpand() {
- this.setState({showDetails: !this.state.showDetails})
+ owner: 'all'
}
render() {
- const { classes, user, domain, loading } = this.props
- const { data, searchState, entryListState, datasetListState, showDetails, resultTab } = this.state
- const { searchValues } = searchState
- const { pagination: { total }, statistics } = data
+ const { classes, user } = this.props
+ const { owner } = this.state
const ownerLabel = {
all: 'All entries',
@@ -249,101 +87,33 @@ class SearchPage extends React.Component {
const withoutLogin = ['all']
- const helperText = <span>
- There are {Object.keys(domain.searchMetrics).filter(key => statistics.total.all[key]).map(key => {
- return <span key={key}>
- {domain.searchMetrics[key].renderResultString(!loading && statistics.total.all[key] !== undefined ? statistics.total.all[key] : '...')}
- </span>
- })}{Object.keys(searchValues).length ? ' left' : ''}.
- </span>
-
return (
<div className={classes.root}>
- <div className={classes.searchContainer}>
- <DisableOnLoading>
- <div className={classes.searchEntry}>
- <FormControl>
- <FormLabel>Filter entries and show: </FormLabel>
- <FormGroup row>
- {['all', 'public', 'user', 'staging']
- .filter(key => user || withoutLogin.indexOf(key) !== -1)
- .map(owner => (
- <Tooltip key={owner} title={ownerTooltips[owner] + (user ? '' : 'You need to be logged-in for more options.')}>
- <FormControlLabel
- control={
- <Checkbox checked={this.state.owner === owner} onChange={() => this.handleOwnerChange(owner)} value="owner" />
- }
- label={ownerLabel[owner]}
- />
- </Tooltip>
- ))}
- </FormGroup>
- </FormControl>
- </div>
-
- <div className={classes.search}>
- <SearchBar classes={{autosuggestRoot: classes.searchBar}}
- fullWidth fullWidthInput={false} helperText={helperText}
- label="search"
- placeholder={domain.searchPlaceholder}
- data={data} searchValues={searchValues}
- InputLabelProps={{
- shrink: true
- }}
- onChanged={values => this.updateSearch({searchValues: values})}
- />
- <Divider className={classes.searchDivider} />
- <Tooltip title={showDetails ? 'Hide statistics' : 'Show statistics'}>
- <IconButton className={classes.searchButton} color="secondary" onClick={this.handleClickExpand}>
- {showDetails ? <ExpandLessIcon/> : <ExpandMoreIcon/>}
- </IconButton>
- </Tooltip>
- </div>
-
- <div className={classes.searchEntry}>
- <SearchAggregations
- data={data} {...searchState} onChange={this.updateSearch}
- showDetails={showDetails}
- />
- </div>
- </DisableOnLoading>
- </div>
- <div className={classes.resultsContainer}>
- <Tabs
- value={resultTab}
- indicatorColor="primary"
- textColor="primary"
- onChange={(event, value) => this.setState({resultTab: value})}
- >
- <Tab label="Calculations" value="entries" />
- <Tab label="Datasets" value="datasets" />
- </Tabs>
-
- <div className={classes.searchResults} hidden={resultTab !== 'entries'}>
- <Typography variant="caption" style={{margin: 12}}>
- About {total.toLocaleString()} results:
- </Typography>
-
- <EntryList
- data={data} total={total}
- onChange={this.updateEntryList}
- {...entryListState}
- />
- </div>
- <div className={classes.searchResults} hidden={resultTab !== 'datasets'}>
- <Typography variant="caption" style={{margin: 12}}>
- About {statistics.total.all.datasets.toLocaleString()} datasets:
- </Typography>
-
- <DatasetList data={data} total={statistics.total.all.datasets}
- onChange={this.updateDatasetList}
- {...datasetListState}
- />
+ <DisableOnLoading>
+ <div className={classes.searchEntry}>
+ <FormControl>
+ <FormLabel>Filter entries and show: </FormLabel>
+ <FormGroup row>
+ {['all', 'public', 'user', 'staging']
+ .filter(key => user || withoutLogin.indexOf(key) !== -1)
+ .map(owner => (
+ <Tooltip key={owner} title={ownerTooltips[owner] + (user ? '' : 'You need to be logged-in for more options.')}>
+ <FormControlLabel
+ control={
+ <Checkbox checked={this.state.owner === owner} onChange={() => this.setState({owner: owner})} value="owner" />
+ }
+ label={ownerLabel[owner]}
+ />
+ </Tooltip>
+ ))}
+ </FormGroup>
+ </FormControl>
</div>
- </div>
+ </DisableOnLoading>
+ <Search searchParameters={{owner: owner}} showDetails />
</div>
)
}
}
-export default compose(withApi(false), withErrors, withDomain, withStyles(SearchPage.styles))(SearchPage)
+export default compose(withApi(false), withErrors, withStyles(SearchPage.styles))(SearchPage)
diff --git a/gui/src/utils.js b/gui/src/utils.js
new file mode 100644
index 0000000000..5d8368caeb
--- /dev/null
+++ b/gui/src/utils.js
@@ -0,0 +1,32 @@
+export const isEquivalent = (a, b) => {
+ // Create arrays of property names
+ var aProps = Object.getOwnPropertyNames(a)
+ var bProps = Object.getOwnPropertyNames(b)
+
+ // If number of properties is different,
+ // objects are not equivalent
+ if (aProps.length !== bProps.length) {
+ return false;
+ }
+
+ for (var i = 0; i < aProps.length; i++) {
+ var propName = aProps[i]
+
+ // If values of same property are not equal,
+ // objects are not equivalent
+ if (a[propName] !== b[propName]) {
+ return false
+ }
+ }
+
+ // If we made it this far, objects
+ // are considered equivalent
+ return true
+}
+
+export const capitalize = (s) => {
+ if (typeof s !== 'string') {
+ return ''
+ }
+ return s.charAt(0).toUpperCase() + s.slice(1)
+}
\ No newline at end of file
diff --git a/nomad/api/raw.py b/nomad/api/raw.py
index 4bfa795046..3ac3869cd2 100644
--- a/nomad/api/raw.py
+++ b/nomad/api/raw.py
@@ -25,7 +25,7 @@ import magic
import sys
import contextlib
-from nomad import search
+from nomad import search, utils
from nomad.files import UploadFiles, Restricted
from nomad.processing import Calc
@@ -383,7 +383,8 @@ class RawFileQueryResource(Resource):
upload_files = UploadFiles.get(
upload_id, create_authorization_predicate(upload_id))
if upload_files is None:
- pass # this should not happen, TODO log error
+ utils.get_logger(__name__).error('upload files do not exist', upload_id=upload_id)
+ continue
if hasattr(upload_files, 'zipfile_cache'):
zipfile_cache = upload_files.zipfile_cache()
diff --git a/nomad/api/repo.py b/nomad/api/repo.py
index d70b40efa4..24323a6722 100644
--- a/nomad/api/repo.py
+++ b/nomad/api/repo.py
@@ -69,7 +69,7 @@ class RepoCalcResource(Resource):
repo_calcs_model = api.model('RepoCalculations', {
- 'pagination': fields.Nested(pagination_model, allow_null=True),
+ 'pagination': fields.Nested(pagination_model, skip_none=True),
'scroll': fields.Nested(allow_null=True, skip_none=True, model=api.model('Scroll', {
'total': fields.Integer(description='The total amount of hits for the search.'),
'scroll_id': fields.String(allow_null=True, description='The scroll_id that can be used to retrieve the next page.'),
@@ -85,7 +85,7 @@ repo_calcs_model = api.model('RepoCalculations', {
'datasets': fields.Raw(api.model('RepoDatasets', {
'after': fields.String(description='The after value that can be used to retrieve the next datasets.'),
'values': fields.Raw(description='A dict with names as key. The values are dicts with "total" and "examples" keys.')
- }), allow_null=True)
+ }), skip_none=True)
})
@@ -125,6 +125,10 @@ repo_request_parser.add_argument(
'metrics', type=str, action='append', help=(
'Metrics to aggregate over all quantities and their values as comma separated list. '
'Possible values are %s.' % ', '.join(datamodel.Domain.instance.metrics_names)))
+repo_request_parser.add_argument(
+ 'datasets', type=bool, help=('Return dataset information.'))
+repo_request_parser.add_argument(
+ 'statistics', type=bool, help=('Return statistics.'))
search_request_parser = api.parser()
@@ -216,6 +220,9 @@ class RepoCalcsResource(Resource):
if bool(request.args.get('date_histogram', False)):
search_request.date_histogram()
metrics: List[str] = request.args.getlist('metrics')
+
+ with_datasets = request.args.get('datasets', False)
+ with_statistics = request.args.get('statistics', False)
except Exception:
abort(400, message='bad parameter types')
@@ -232,31 +239,37 @@ class RepoCalcsResource(Resource):
if metric not in search.metrics_names:
abort(400, message='there is no metric %s' % metric)
- search_request.default_statistics(metrics_to_use=metrics)
- if 'datasets' not in metrics:
- total_metrics = metrics + ['datasets']
- else:
- total_metrics = metrics
- search_request.totals(metrics_to_use=total_metrics)
- search_request.statistic('authors', 1000)
+ if with_statistics:
+ search_request.default_statistics(metrics_to_use=metrics)
+ if 'datasets' not in metrics:
+ total_metrics = metrics + ['datasets']
+ else:
+ total_metrics = metrics
+ search_request.totals(metrics_to_use=total_metrics)
+ search_request.statistic('authors', 1000)
try:
if scroll:
results = search_request.execute_scrolled(scroll_id=scroll_id, size=per_page)
else:
- search_request.quantity(
- 'dataset_ids', size=per_page, examples=1, after=request.args.get('datasets_after', None))
+ if with_datasets:
+ search_request.quantity(
+ 'dataset_id', size=per_page, examples=1,
+ after=request.args.get('datasets_after', None))
+
results = search_request.execute_paginated(
per_page=per_page, page=page, order=order, order_by=order_by)
# TODO just a work around to make things prettier
- statistics = results['statistics']
- if 'code_name' in statistics and 'currupted mainfile' in statistics['code_name']:
- del(statistics['code_name']['currupted mainfile'])
-
- datasets = results.pop('quantities')['dataset_ids']
- results['datasets'] = datasets
+ if with_statistics:
+ statistics = results['statistics']
+ if 'code_name' in statistics and 'currupted mainfile' in statistics['code_name']:
+ del(statistics['code_name']['currupted mainfile'])
+
+ if with_datasets:
+ datasets = results.pop('quantities')['dataset_id']
+ results['datasets'] = datasets
return results, 200
except search.ScrollIdNotFound:
diff --git a/nomad/datamodel/base.py b/nomad/datamodel/base.py
index 62a808bb0d..088d3ea513 100644
--- a/nomad/datamodel/base.py
+++ b/nomad/datamodel/base.py
@@ -267,10 +267,10 @@ class Domain:
calc_id=DomainQuantity(description='Search for the calc_id.'),
pid=DomainQuantity(description='Search for the pid.'),
mainfile=DomainQuantity(description='Search for the mainfile.'),
- datasets=DomainQuantity(
+ dataset=DomainQuantity(
elastic_field='datasets.name', multi=True, elastic_search_type='match',
description='Search for a particular dataset by name.'),
- dataset_ids=DomainQuantity(
+ dataset_id=DomainQuantity(
elastic_field='datasets.id', multi=True,
description='Search for a particular dataset by its id.'),
doi=DomainQuantity(
diff --git a/tests/test_api.py b/tests/test_api.py
index d26c3ea3c9..53ce3b8db7 100644
--- a/tests/test_api.py
+++ b/tests/test_api.py
@@ -718,7 +718,7 @@ class TestRepo():
assert rv.status_code == 404
def test_search_datasets(self, client, example_elastic_calcs, no_warn, other_test_user_auth):
- rv = client.get('/repo/?owner=all', headers=other_test_user_auth)
+ rv = client.get('/repo/?owner=all&datasets=true', headers=other_test_user_auth)
data = self.assert_search(rv, 4)
datasets = data.get('datasets', None)
@@ -790,7 +790,7 @@ class TestRepo():
(0, 'quantities', 'dos')
])
def test_search_parameters(self, client, example_elastic_calcs, no_warn, test_user_auth, calcs, quantity, value):
- query_string = urlencode({quantity: value}, doseq=True)
+ query_string = urlencode({quantity: value, 'statistics': True}, doseq=True)
rv = client.get('/repo/?%s' % query_string, headers=test_user_auth)
logger.debug('run search quantities test', query_string=query_string)
@@ -819,7 +819,7 @@ class TestRepo():
@pytest.mark.parametrize('metrics', metrics_permutations)
def test_search_total_metrics(self, client, example_elastic_calcs, no_warn, metrics):
- rv = client.get('/repo/?%s' % urlencode(dict(metrics=metrics), doseq=True))
+ rv = client.get('/repo/?%s' % urlencode(dict(metrics=metrics, statistics=True, datasets=True), doseq=True))
assert rv.status_code == 200, str(rv.data)
data = json.loads(rv.data)
total_metrics = data.get('statistics', {}).get('total', {}).get('all', None)
@@ -830,7 +830,7 @@ class TestRepo():
@pytest.mark.parametrize('metrics', metrics_permutations)
def test_search_aggregation_metrics(self, client, example_elastic_calcs, no_warn, metrics):
- rv = client.get('/repo/?%s' % urlencode(dict(metrics=metrics), doseq=True))
+ rv = client.get('/repo/?%s' % urlencode(dict(metrics=metrics, statistics=True, datasets=True), doseq=True))
assert rv.status_code == 200
data = json.loads(rv.data)
for name, quantity in data.get('statistics').items():
@@ -844,7 +844,6 @@ class TestRepo():
def test_search_date_histogram(self, client, example_elastic_calcs, no_warn):
rv = client.get('/repo/?date_histogram=true&metrics=total_energies')
- print(rv.data)
assert rv.status_code == 200
data = json.loads(rv.data)
histogram = data.get('statistics').get('date_histogram')
@@ -852,7 +851,7 @@ class TestRepo():
@pytest.mark.parametrize('n_results, page, per_page', [(2, 1, 5), (1, 1, 1), (0, 2, 3)])
def test_search_pagination(self, client, example_elastic_calcs, no_warn, n_results, page, per_page):
- rv = client.get('/repo/?page=%d&per_page=%d' % (page, per_page))
+ rv = client.get('/repo/?page=%d&per_page=%d&statistics=true' % (page, per_page))
assert rv.status_code == 200
data = json.loads(rv.data)
results = data.get('results', None)
--
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