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Commit e0ca6a9d authored by Markus Scheidgen's avatar Markus Scheidgen
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Merge branch 'v0.8.0-bugfixes' into 'v0.8.0' 

V0.8.0 bugfixes

See merge request !109
parents 5aa6b5c2 cbce84c9
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......@@ -26,3 +26,4 @@ nomad.yaml
build/
dist/
setup.json
parser.osio.log
examples/client.py
View file @ e0ca6a9d
......@@ -3,7 +3,7 @@ from nomad.client import ArchiveQuery
from nomad.metainfo import units
# this will not be necessary, once this is the official NOMAD version
config.client.url = 'https://labdev-nomad.esc.rzg.mpg.de/fairdi/nomad/testing-major/api'
config.client.url = 'http://labdev-nomad.esc.rzg.mpg.de/fairdi/nomad/testing-major/api'
query = ArchiveQuery(
query={
......
gui/src/components/About.js
View file @ e0ca6a9d
......@@ -9,6 +9,26 @@ import { domains } from './domains'
import { Grid, Card, CardContent, Typography, makeStyles, Link } from '@material-ui/core'
import { Link as RouterLink, useHistory } from 'react-router-dom'
export const CodeList = () => {
const {info} = useContext(apiContext)
if (!info) {
return '...'
}
return info.codes.reduce((result, code, index) => {
if (index !== 0) {
result.push(', ')
}
if (code.code_homepage) {
result.push(<Link target="external" key={code.code_name} href={code.code_homepage}>{code.code_name}</Link>)
} else {
result.push(code.code_name)
}
return result
}, [])
}
const useCardStyles = makeStyles(theme => ({
title: {
marginBottom: theme.spacing(1)
......@@ -173,7 +193,7 @@ export default function About() {
You can inspect the Archive form and extracted metadata before
publishing your data.
</p>
<p>NOMAD supports most community codes: {info ? info.codes.join(', ') : '...'}</p>
<p>NOMAD supports most community codes: <CodeList/></p>
<p>
To use NOMAD&apos;s parsers and normalizers outside of NOMAD.
Read <Link href="">here</Link> on how to install
......
gui/src/components/DatasetPage.js
View file @ e0ca6a9d
......@@ -3,8 +3,8 @@ import { errorContext } from './errors'
import { apiContext } from './api'
import Search from './search/Search'
import { Typography, makeStyles } from '@material-ui/core'
import { DatasetActions, DOI } from './search/DatasetList'
import { matchPath, useLocation, useHistory, useRouteMatch } from 'react-router'
import { matchPath, useLocation, useRouteMatch } from 'react-router'
import { DOI } from './search/DatasetList'
export const help = `
This page allows you to **inspect** and **download** NOMAD datasets. It alsow allows you
......@@ -31,7 +31,6 @@ export default function DatasetPage() {
const {raiseError} = useContext(errorContext)
const location = useLocation()
const match = useRouteMatch()
const history = useHistory()
const {datasetId} = matchPath(location.pathname, {
path: `${match.path}/:datasetId`
......@@ -56,18 +55,11 @@ export default function DatasetPage() {
})
}, [location.pathname, api])
const handleChange = dataset => {
if (dataset) {
setDataset({dataset: dataset})
} else {
history.goBack()
}
}
if (!dataset) {
return <div>loading...</div>
}
console.log('### DatasetPage', dataset)
return <div>
<div className={classes.header}>
<div className={classes.description}>
......@@ -76,18 +68,11 @@ export default function DatasetPage() {
dataset{dataset.doi ? <span>, with DOI <DOI doi={dataset.doi} /></span> : ''}
</Typography>
</div>
<div className={classes.actions}>
{dataset && dataset.example && <DatasetActions
dataset={dataset}
onChange={handleChange}/>
}
</div>
</div>
<Search
initialQuery={{owner: 'all'}}
query={{dataset_id: datasetId}}
query={{dataset_id: [datasetId]}}
ownerTypes={['all', 'public']}
initialResultTab="entries"
availableResultTabs={['entries', 'groups', 'datasets']}
......
gui/src/components/api.js
View file @ e0ca6a9d
......@@ -125,7 +125,7 @@ function handleApiError(e) {
let error = null
if (e.response) {
const body = e.response.body
const message = (body && (body.description || body.message)) || e.response.statusText
const message = (body && (body.message || body.description)) || e.response.statusText
const errorMessage = `${message} (${e.response.status})`
if (e.response.status === 404) {
error = new DoesNotExist(errorMessage)
......
gui/src/components/search/DatasetList.js
View file @ e0ca6a9d
......@@ -131,7 +131,7 @@ class DatasetActionsUnstyled extends React.Component {
const canAssignDOI = !doi
const canDelete = !doi
const query = {dataset_id: dataset.id}
const query = {dataset_id: [dataset.dataset_id]}
return <FormGroup row classes={{root: classes.group}}>
{search && <Tooltip title="Open a search page with entries from this dataset only.">
......@@ -180,6 +180,7 @@ class DatasetListUnstyled extends React.Component {
data: PropTypes.object,
total: PropTypes.number,
onChange: PropTypes.func.isRequired,
onEdit: PropTypes.func.isRequired,
history: PropTypes.any.isRequired,
datasets_after: PropTypes.string,
per_page: PropTypes.number,
......@@ -243,8 +244,8 @@ class DatasetListUnstyled extends React.Component {
}
renderEntryActions(entry) {
const {onChange} = this.props
return <DatasetActions search dataset={entry} onChange={() => onChange({})} />
const {onEdit} = this.props
return <DatasetActions search dataset={entry} onChange={onEdit} />
}
render() {
......
gui/src/components/search/EntryList.js
View file @ e0ca6a9d
......@@ -21,7 +21,7 @@ export function Published(props) {
</Tooltip>
} else {
return <Tooltip title="not published yet">
<PrivateIcon color="secondary"/>
<PrivateIcon color="error"/>
</Tooltip>
}
}
......@@ -32,6 +32,7 @@ export class EntryListUnstyled extends React.Component {
data: PropTypes.object.isRequired,
query: PropTypes.object.isRequired,
onChange: PropTypes.func,
onEdit: PropTypes.func,
history: PropTypes.any.isRequired,
order_by: PropTypes.string.isRequired,
order: PropTypes.number.isRequired,
......@@ -236,7 +237,7 @@ export class EntryListUnstyled extends React.Component {
{(row.datasets || []).map(ds => (
<Typography key={ds.dataset_id}>
<Link component={RouterLink} to={`/dataset/id/${ds.dataset_id}`}>{ds.name}</Link>
{ds.doi ? <span>&nbsp; (<Link href={ds.doi}>{ds.doi}</Link>)</span> : <React.Fragment/>}
{ds.doi ? <span>&nbsp; (<Link href={`https://dx.doi.org/${ds.doi}`}>{ds.doi}</Link>)</span> : <React.Fragment/>}
</Typography>))}
</div>
</Quantity>
......@@ -321,7 +322,7 @@ export class EntryListUnstyled extends React.Component {
const createActions = (props, moreActions) => <React.Fragment>
{example && editable ? <EditUserMetadataDialog
example={example} total={selected === null ? totalNumber : selected.length}
onEditComplete={() => this.props.onChange()}
onEditComplete={() => this.props.onEdit()}
{...props}
/> : ''}
<DownloadButton
......
gui/src/components/search/QuantityHistogram.js
View file @ e0ca6a9d
......@@ -5,7 +5,7 @@ import * as d3 from 'd3'
import { scaleBand, scalePow } from 'd3-scale'
import { formatQuantity, nomadPrimaryColor, nomadSecondaryColor, nomadFontFamily } from '../../config.js'
import { searchContext } from './SearchContext.js'
import * as searchQuantities from '../../searchQuantities.json'
import searchQuantities from '../../searchQuantities'
const unprocessedLabel = 'not processed'
const unavailableLabel = 'unavailable'
......
gui/src/components/search/Search.js
View file @ e0ca6a9d
......@@ -549,13 +549,14 @@ const useScroll = (apiGroupName, afterParameterName) => {
}
function SearchEntryList(props) {
const {response, requestParameters, apiQuery} = useContext(searchContext)
const {response, requestParameters, apiQuery, update} = useContext(searchContext)
const setRequestParameters = usePagination()
return <EntryList
query={apiQuery}
editable={apiQuery.owner === 'staging' || apiQuery.owner === 'user'}
data={response}
onChange={setRequestParameters}
onEdit={update}
actions={
<React.Fragment>
<ReRunSearchButton/>
......@@ -568,9 +569,10 @@ function SearchEntryList(props) {
}
function SearchDatasetList(props) {
const {response} = useContext(searchContext)
const {response, update} = useContext(searchContext)
return <DatasetList
data={response}
onEdit={update}
actions={<ReRunSearchButton/>}
{...response} {...props} {...useScroll('datasets')}
/>
......@@ -586,8 +588,9 @@ function SearchGroupList(props) {
}
function SearchUploadList(props) {
const {response} = useContext(searchContext)
const {response, update} = useContext(searchContext)
return <UploadList data={response}
onEdit={update}
actions={<ReRunSearchButton/>}
{...response} {...props} {...useScroll('uploads')}
/>
......
gui/src/components/search/SearchContext.js
View file @ e0ca6a9d
......@@ -150,7 +150,7 @@ export default function SearchContext({initialRequest, initialQuery, query, chil
owner: owner,
...initialQuery,
...requestRef.current.query,
query
...query
}
if (dateHistogram) {
dateHistogramInterval = Dates.intervalSeconds(
......
gui/src/components/search/UploadsList.js
View file @ e0ca6a9d
......@@ -53,7 +53,7 @@ class UploadActionsUnstyled extends React.Component {
classes: PropTypes.object.isRequired,
upload: PropTypes.object.isRequired,
user: PropTypes.object,
onChange: PropTypes.func,
onEdit: PropTypes.func,
history: PropTypes.object.isRequired
}
......@@ -71,9 +71,9 @@ class UploadActionsUnstyled extends React.Component {
}
handleEdit() {
const {onChange, upload} = this.props
if (onChange) {
onChange(upload)
const {onEdit, upload} = this.props
if (onEdit) {
onEdit(upload)
}
}
......@@ -86,7 +86,7 @@ class UploadActionsUnstyled extends React.Component {
const editable = user && upload.example &&
upload.example.authors.find(author => author.user_id === user.sub)
const query = {upload_id: upload.example.upload_id}
const query = {upload_id: [upload.example.upload_id]}
return <FormGroup row classes={{root: classes.group}}>
<Tooltip title="Open this upload on the uploads page">
......@@ -112,6 +112,7 @@ class UploadListUnstyled extends React.Component {
data: PropTypes.object,
total: PropTypes.number,
onChange: PropTypes.func.isRequired,
onEdit: PropTypes.func.isRequired,
history: PropTypes.any.isRequired,
uploads_after: PropTypes.string,
actions: PropTypes.element
......@@ -176,8 +177,8 @@ class UploadListUnstyled extends React.Component {
}
renderEntryActions(entry) {
const {onChange} = this.props
return <UploadActions search upload={entry} onChange={() => onChange({})} />
const {onEdit} = this.props
return <UploadActions search upload={entry} onEdit={onEdit}/>
}
render() {
......
gui/src/components/uploads/Upload.js
View file @ e0ca6a9d
......@@ -171,7 +171,7 @@ class Upload extends React.Component {
cursor: 'pointer'
},
decideIcon: {
color: theme.palette.secondary.main
color: theme.palette.error.main
}
})
......@@ -605,12 +605,13 @@ class Upload extends React.Component {
return <EntryList
title={`Upload with ${data.pagination.total} detected entries`}
query={{upload_id: upload.upload_id}}
query={{upload_id: [upload.upload_id]}}
columns={columns}
selectedColumns={Upload.defaultSelectedColumns}
editable={tasks_status === 'SUCCESS'}
data={data}
onChange={this.handleChange}
onEdit={this.handleChange}
actions={actions}
showEntryActions={entry => entry.processed || !running}
{...this.state.params}
......@@ -634,7 +635,7 @@ class Upload extends React.Component {
} else if (upload.published) {
return render(<PublishedIcon size={32} color="primary"/>, 'This upload is published')
} else {
return render(<UnPublishedIcon size={32} color="secondary"/>, 'This upload is not published yet, and only visible to you')
return render(<UnPublishedIcon size={32} color="error"/>, 'This upload is not published yet, and only visible to you')
}
}
......
gui/src/components/uploads/UploadPage.js
View file @ e0ca6a9d
import React from 'react'
import PropTypes, { instanceOf } from 'prop-types'
import Markdown from '../Markdown'
import { withStyles, Paper, IconButton, FormGroup, FormLabel, Tooltip } from '@material-ui/core'
import { withStyles, Paper, IconButton, FormGroup, FormLabel, Tooltip, Typography } from '@material-ui/core'
import UploadIcon from '@material-ui/icons/CloudUpload'
import Dropzone from 'react-dropzone'
import Upload from './Upload'
......@@ -16,6 +16,7 @@ import Pagination from 'material-ui-flat-pagination'
import { CopyToClipboard } from 'react-copy-to-clipboard'
import { guiBase } from '../../config'
import qs from 'qs'
import { CodeList } from '../About'
export const help = `
NOMAD allows you to upload data. After upload, NOMAD will process your data: it will
......@@ -126,7 +127,8 @@ class UploadPage extends React.Component {
'& svg': {
marginLeft: 'auto',
marginRight: 'auto'
}
},
marginTop: theme.spacing(3)
},
dropzoneAccept: {
background: theme.palette.primary.main,
......@@ -267,6 +269,16 @@ class UploadPage extends React.Component {
return (
<div className={classes.root}>
<Typography>
To prepare your data, simply use <b>zip</b> or <b>tar</b> to create a single file that contains
all your files as they are. These .zip/.tar files can contain subdirectories and additional files.
NOMAD will search through all files and identify the relevant files automatically.
Each uploaded file can be <b>up to 32GB</b> in size, you can have <b>up to 10 unpublished
uploads</b> simultaneously. Your uploaded data is not published right away.
</Typography>
<Typography>
The following codes are supported: <CodeList/>.
</Typography>
<Paper className={classes.dropzoneContainer}>
<Dropzone
accept={[
......@@ -288,7 +300,7 @@ class UploadPage extends React.Component {
rejectClassName={classes.dropzoneReject}
onDrop={this.onDrop.bind(this)}
>
<p>drop .tar.gz or .zip files here</p>
<p>click or drop .tar.gz/.zip files here</p>
<UploadIcon style={{fontSize: 36}}/>
</Dropzone>
</Paper>
......
gui/src/searchQuantities.json
View file @ e0ca6a9d
......@@ -234,7 +234,7 @@
"name": "dft.code_name",
"description": "The name of the used code.",
"many": false,
"statistic_size": 36,
"statistic_size": 34,
"statistic_values": [
"ABINIT",
"ATK",
......@@ -246,30 +246,28 @@
"Crystal",
"DL_POLY",
"DMol3",
"elastic",
"elk",
"exciting",
"FHI-aims",
"fleur",
"GAMESS",
"GPAW",
"GPAW",
"Gaussian",
"GPAW",
"gulp",
"libAtoms",
"MOLCAS",
"NWChem",
"Octopus",
"ONETEP",
"ORCA",
"Octopus",
"Phonopy",
"qbox",
"Quantum Espresso",
"Siesta",
"VASP",
"turbomole",
"VASP",
"WIEN2k",
"elastic",
"elk",
"exciting",
"fleur",
"gulp",
"libAtoms",
"qbox",
"turbomole",
"unavailable",
"not processed"
]
......
nomad/app/api/archive.py
View file @ e0ca6a9d
......@@ -233,19 +233,21 @@ class ArchiveQueryResource(Resource):
See ``/repo`` endpoint for documentation on the search
parameters.
This endpoint uses pagination (see /repo) or id aggregation to handle large result
sets over multiple requests.
Use aggregation.after and aggregation.per_page to request a
certain page with id aggregation.
The actual data are in results and a supplementary python code (curl) to
execute search is in python (curl).
'''
try:
data_in = request.get_json()
scroll = data_in.get('scroll', None)
if scroll:
scroll_id = scroll.get('scroll_id')
scroll = True
aggregation = data_in.get('aggregation', None)
pagination = data_in.get('pagination', {})
page = pagination.get('page', 1)
per_page = pagination.get('per_page', 10 if not scroll else 1000)
per_page = pagination.get('per_page', 10)
query = data_in.get('query', {})
......@@ -270,20 +272,19 @@ class ArchiveQueryResource(Resource):
search_request.owner('all')
apply_search_parameters(search_request, query)
search_request.include('calc_id', 'upload_id', 'with_embargo', 'published', 'parser_name')
if not aggregation:
search_request.include('calc_id', 'upload_id', 'with_embargo', 'published', 'parser_name')
try:
if scroll:
results = search_request.execute_scrolled(
scroll_id=scroll_id, size=per_page, order_by='upload_id')
results['scroll']['scroll'] = True
if aggregation:
results = search_request.execute_aggregated(
after=aggregation.get('after'), per_page=aggregation.get('per_page', 1000),
includes=['with_embargo', 'published', 'parser_name'])
else:
results = search_request.execute_paginated(
per_page=per_page, page=page, order_by='upload_id')
except search.ScrollIdNotFound:
abort(400, 'The given scroll_id does not exist.')
except KeyError as e:
abort(400, str(e))
......@@ -334,7 +335,7 @@ class ArchiveQueryResource(Resource):
except Exception as e:
if raise_errors:
raise e
common.logger(str(e), exc_info=e)
common.logger.error(str(e), upload_id=upload_id, calc_id=calc_id, exc_info=e)
if upload_files is not None:
upload_files.close()
......
nomad/app/api/common.py
View file @ e0ca6a9d
......@@ -65,10 +65,18 @@ scroll_model = api.model('Scroll', {
'total': fields.Integer(default=0, description='The total amount of hits for the search.'),
'scroll_id': fields.String(default=None, allow_null=True, description='The scroll_id that can be used to retrieve the next page.'),
'size': fields.Integer(default=0, help='The size of the returned scroll page.')})
''' Model used in responses with scroll. '''
aggregation_model = api.model('Aggregation', {
'after': fields.String(description='The after key for the current request.', allow_null=True),
'total': fields.Integer(default=0, description='The total amount of hits for the search.'),
'per_page': fields.Integer(default=0, help='The size of the requested page.', allow_null=True)})
''' Model used in responses with id aggregation. '''
search_model_fields = {
'pagination': fields.Nested(pagination_model, allow_null=True, skip_none=True),
'scroll': fields.Nested(scroll_model, allow_null=True, skip_none=True),
'aggregation': fields.Nested(aggregation_model, allow_null=True),
'results': fields.List(fields.Raw(allow_null=True, skip_none=True), description=(
'A list of search results. Each result is a dict with quantitie names as key and '
'values as values'), allow_null=True, skip_none=True),
......
nomad/app/api/info.py
View file @ e0ca6a9d
......@@ -54,10 +54,15 @@ statistics_info_model = api.model('StatisticsInfo', {
# 'archive_file_size': fields.Integer(description='Total amount of binary archive data in TB')
})
code_info_model = api.model('CodeInfo', {
'code_name': fields.String(description='Name of the code or input format', allow_null=True),
'code_homepage': fields.String(description='Homepage of the code or input format', allow_null=True)
}, allow_null=True, skip_none=True)
info_model = api.model('Info', {
'parsers': fields.List(fields.String),
'metainfo_packages': fields.List(fields.String),
'codes': fields.List(fields.String),
'codes': fields.List(fields.Nested(code_info_model)),
'normalizers': fields.List(fields.String),
'domains': fields.List(fields.Nested(model=domain_model)),
'statistics': fields.Nested(model=statistics_info_model, description='General NOMAD statistics'),
......@@ -88,10 +93,14 @@ class InfoResource(Resource):
@api.marshal_with(info_model, skip_none=True, code=200, description='Info send')
def get(self):
''' Return information about the nomad backend and its configuration. '''
codes = [
parser.code_name
for parser in parsing.parser_dict.values()
if isinstance(parser, parsing.MatchingParser) and parser.domain == 'dft']
codes_dict = {}
for parser in parsing.parser_dict.values():
if isinstance(parser, parsing.MatchingParser) and parser.domain == 'dft':
code_name = parser.code_name
if code_name in codes_dict:
continue
codes_dict[code_name] = dict(code_name=code_name, code_homepage=parser.code_homepage)
codes = sorted(list(codes_dict.values()), key=lambda code_info: code_info['code_name'].lower())
return {
'parsers': [
......@@ -100,7 +109,7 @@ class InfoResource(Resource):
'metainfo_packages': ['general', 'general.experimental', 'common', 'public'] + sorted([
key[key.index('/') + 1:]
for key in parsing.parser_dict.keys()]),
'codes': sorted(set(codes), key=lambda x: x.lower()),
'codes': codes,
'normalizers': [normalizer.__name__ for normalizer in normalizing.normalizers],
'statistics': statistics(),
'domains': [
......
nomad/app/api/repo.py
View file @ e0ca6a9d
......@@ -554,7 +554,7 @@ class EditRepoCalcsResource(Resource):
# remove potentially empty old datasets
if removed_datasets is not None:
for dataset in removed_datasets:
if proc.Calc.objects(metadata__dataset_id=dataset).first() is None:
if proc.Calc.objects(metadata__datasets=dataset).first() is None:
Dataset.m_def.a_mongo.objects(dataset_id=dataset).delete()
return json_data, 200
......
nomad/cli/admin/uploads.py
View file @ e0ca6a9d
......@@ -193,7 +193,7 @@ def chown(ctx, username, uploads):
search.refresh()
@uploads.command(help='Change the owner of the upload and all its calcs.')
@uploads.command(help='Reset the processing state.')
@click.argument('UPLOADS', nargs=-1)
@click.option('--with-calcs', is_flag=True, help='Also reset all calculations.')
@click.pass_context
......@@ -209,6 +209,7 @@ def reset(ctx, uploads, with_calcs):
dict(upload_id=upload.upload_id),
{'$set': proc.Calc.reset_pymongo_update()})
upload.process_status = None
upload.reset()
upload.save()
i += 1
......
nomad/client.py
View file @ e0ca6a9d
......@@ -98,6 +98,10 @@ sub-sections return lists of further objects. Here we navigate the sections ``se
sub-section ``section_system`` to access the quantity ``energy_total``. This quantity is a
number with an attached unit (Joule), which can be converted to something else (e.g. Hartree).
The create query object keeps all results in memory. Keep this in mind, when you are
accessing a large amount of query results. You should use :func:`ArchiveQuery.clear`
to remove unnecessary results.