diff --git a/gui/src/components/APIs.js b/gui/src/components/APIs.js
index 1cd91fc2b7f55e2a4a3fcef16228159908b557e4..4427d6a7d8bad73525085ddc932f761803e42c35 100644
--- a/gui/src/components/APIs.js
+++ b/gui/src/components/APIs.js
@@ -40,7 +40,7 @@ export default function About() {
and functions programatically. For all APIs, we offer dashboards that let you use
each API interactively, right in your browser.
- ## NOMAD's new (Version 1) API
+ ## NOMAD's API
- [API dashboard](${apiBase}/v1/extensions/docs)
- [API documentation](${apiBase}/v1/extensions/redoc)
@@ -50,19 +50,16 @@ export default function About() {
At some point, it will replace it entirely. For new users, we recommend to start
using this API. API Dashboard and documentation contain a tutorial on how to get started.
- ## NOMAD's main (Version 0) API
-
- - [API dashboard](${apiBase}/)
-
- This is NOMAD main REST API. This API the main interface to NOMAD and it also used
- by this web-page to provide all functions. Therefore, everything you do here, can
- also be done by using this API.
-
There is a [tutorial on how to use the API with plain Python](${appBase}/docs/api_tutorial.html).
Another [tutorial covers how to install and use NOMAD's Python client library](${appBase}/docs/archive_tutorial.html).
The [NOMAD Analytics Toolkit](https://nomad-lab.eu/AIToolkit) allows to use
this without installation and directly on NOMAD servers.
+ You can still use NOMAD's old REST API. The data it provides might miss the most
+ recent contributions:
+
+ - [v0 API dashboard](https://nomad-lab.eu/prod/rae/api/)
+
## OPTIMADE
- [OPTIMADE API overview page](${appBase}/optimade/)
diff --git a/gui/src/components/About.js b/gui/src/components/About.js
index 673b50725728cd04621665339ec165ea8f84f8f6..445f527e8a771c61a607d2f637b8cecc7e752536 100644
--- a/gui/src/components/About.js
+++ b/gui/src/components/About.js
@@ -21,7 +21,6 @@ import PropTypes from 'prop-types'
import Markdown from './Markdown'
import { appBase, debug, consent, aitoolkitEnabled, encyclopediaEnabled } from '../config'
import packageJson from '../../package.json'
-import { domainData } from './domainData'
import { Grid, Card, CardContent, Typography, makeStyles, Link, Dialog, DialogTitle, DialogContent, DialogActions, Button } from '@material-ui/core'
import { Link as RouterLink, useHistory } from 'react-router-dom'
import tutorials from '../toolkitMetadata'
@@ -354,10 +353,8 @@ export default function About() {
${debug ? `
### Material science data and domains
Originally NOMAD was build for DFT calculations and data from the respective
- community code. By NOMAD supports multiple materials science domains:
-
- ${info && info.domains.map(domain => domainData[domain.name]).map(domain => `- ${domain.name}: ${domain.about}`).join('\n')}
- ` : ''}
+ community codes. But NOMAD is now extended to support multiple materials science domains,
+ such as experiments, synthesis, and computational methods at different scales.` : ''}
${debug ? `
### Log management with Elastic stack
@@ -381,13 +378,12 @@ export default function About() {
### About this version
- version (API): \`${info ? info.version : 'loading'}/${info ? info.git.commit : 'loading'}\`
- version (GUI): \`${packageJson.version}/${packageJson.commit}\`
- - domains: ${info ? Object.keys(info.domains).map(domain => info.domains[domain].name).join(', ') : 'loading'}
- git: \`${info ? info.git.ref : 'loading'}; ${info ? info.git.version : 'loading'}\`
- last commit message: *${info ? info.git.log : 'loading'}*
- supported codes: ${info ? info.codes.map(code => code.code_name).join(', ') : 'loading'}
- parsers: ${info ? info.parsers.join(', ') : 'loading'}
- normalizers: ${info ? info.normalizers.join(', ') : 'loading'}
- `}</Markdown>
+ `}</Markdown>
</Grid>
</Grid>
</div>
diff --git a/gui/src/components/domainData.js b/gui/src/components/domainData.js
deleted file mode 100644
index 7bebe89f162311cd0c83ca22aa079591cdf2b5c8..0000000000000000000000000000000000000000
--- a/gui/src/components/domainData.js
+++ /dev/null
@@ -1,207 +0,0 @@
-/*
- * Copyright The NOMAD Authors.
- *
- * This file is part of NOMAD. See https://nomad-lab.eu for further info.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-import React from 'react'
-import { Link, Typography } from '@material-ui/core'
-import { amber } from '@material-ui/core/colors'
-
-/* eslint-disable react/display-name */
-
-export const domainData = ({
- dft: {
- name: 'Computational data',
- label: 'Computational materials science data',
- key: 'dft',
- about: 'This include data from many computational materials science codes',
- disclaimer: <Typography>
- First time users can find an introduction to NOMAD, tutorials, and videos <Link href="https://nomad-lab.eu/services/repo-arch" target="nomad-lab">here</Link>.
- </Typography>,
- entryLabel: 'entry',
- entryLabelPlural: 'entries',
- entryHeader: 'DFT Calculation',
- entryTitle: data =>
- data.dft && data.dft.code_name
- ? data.dft.code_name.charAt(0).toUpperCase() + data.dft.code_name.slice(1) + ' run'
- : 'Code run',
- searchPlaceholder: 'enter atoms, codes, functionals, or other quantity values',
- searchMetrics: {
- code_runs: {
- label: 'Entries',
- tooltip: 'The statistics will show the number of database entry. Each set of input/output files that represents a code run is an entry.',
- renderResultString: count => (<span><b>{count.toLocaleString()}</b> entr{count === 1 ? 'y' : 'ies'}</span>)
- },
- unique_entries: {
- label: 'Unique',
- tooltip: 'Counts duplicates only once.',
- renderResultString: count => (<span> and <b>{count.toLocaleString()}</b> unique entr{count === 1 ? 'y' : 'ies'}</span>)
- },
- // total_energies: {
- // label: 'Total energy calculations',
- // tooltip: 'Aggregates the number of total energy calculations as each entry can contain many calculations.',
- // renderResultString: count => (<span> with <b>{count.toLocaleString()}</b> total energy calculation{count === 1 ? '' : 's'}</span>)
- // },
- 'dft.calculations': {
- label: 'Single configuration calculations',
- shortLabel: 'SCC',
- tooltip: 'Aggregates the number of single configuration calculations (e.g. total energy calculations) as each entry can contain many calculations.',
- renderResultString: count => (<span> with <b>{count.toLocaleString()}</b> single configuration calculation{count === 1 ? '' : 's'}</span>)
- },
- // The unique_geometries search aggregates unique geometries based on 10^8 hashes.
- // This takes to long in elastic search for a reasonable user experience.
- // Therefore, we only support geometries without uniqueness check
- 'dft.unique_geometries': {
- label: 'Unique geometries',
- shortLabel: 'Geometries',
- tooltip: 'Aggregates the number of simulated system geometries in all entries.',
- renderResultString: count => (<span> that simulate <b>{count.toLocaleString()}</b> unique geometrie{count === 1 ? '' : 's'}</span>)
- },
- 'encyclopedia.material.materials': {
- label: 'Materials',
- tooltip: 'Shows statistics in terms of materials.',
- renderResultString: count => (<span> of <b>{count.toLocaleString()}</b> material{count === 1 ? '' : 's'}</span>)
- },
- datasets: {
- label: 'Datasets',
- tooltip: 'Shows statistics in terms of datasets that entries belong to.',
- renderResultString: count => (<span> curated in <b>{count.toLocaleString()}</b> dataset{count === 1 ? '' : 's'}</span>)
- }
- },
- defaultSearchMetric: 'code_runs',
- additionalSearchKeys: {
- raw_id: {},
- external_id: {},
- upload_id: {},
- calc_id: {},
- paths: {},
- pid: {},
- mainfile: {},
- calc_hash: {},
- formula: {},
- optimade: {},
- quantities: {},
- 'dft.spacegroup': {},
- 'dft.spacegroup_symbol': {},
- 'dft.labels': {},
- upload_name: {}
- },
- /**
- * An dict where each object represents a column. Possible keys are label, render.
- * Default render
- */
- searchResultColumns: {
- 'formula': {
- label: 'Formula',
- supportsSort: true
- },
- 'dft.code_name': {
- label: 'Code',
- supportsSort: true
- },
- 'dft.basis_set': {
- label: 'Basis set',
- supportsSort: true
- },
- 'dft.xc_functional': {
- label: 'XC functionals',
- supportsSort: true
- },
- 'dft.system': {
- label: 'System',
- supportsSort: true
- },
- 'dft.crystal_system': {
- label: 'Crystal system',
- supportsSort: true
- },
- 'dft.spacegroup_symbol': {
- label: 'Spacegroup',
- supportsSort: true
- },
- 'dft.spacegroup': {
- label: 'Spacegroup (number)',
- supportsSort: true
- }
- },
- defaultSearchResultColumns: ['formula', 'dft.code_name', 'dft.system', 'dft.crystal_system'],
- searchTabs: ['entries', 'materials', 'datasets', 'groups', 'uploads']
- },
- ems: {
- name: 'Experimental data',
- key: 'ems',
- label: 'Experimental data (beta)',
- about: 'This includes first metadata from materials science experiments. This aspect of NOMAD is still in development and mnight change frequently.',
- disclaimer: <Typography style={{color: amber[700]}}>
- This aspect of NOMAD is still under development. The offered functionality and displayed data
- might change frequently, is not necessarely reviewed by NOMAD, and might contain
- errors. Some of the information is taken verbatim from external sources.
- </Typography>,
- entryLabel: 'entry',
- entryLabelPlural: 'entries',
- entryTitle: () => 'Experiment',
- searchPlaceholder: 'enter atoms, experimental methods, or other quantity values',
- /**
- * Metrics are used to show values for aggregations. Each metric has a key (used
- * for API calls), a label (used in the select form), and result string (to show
- * the overall amount in search results).
- */
- searchMetrics: {
- code_runs: {
- label: 'Experiments',
- tooltip: 'Statistics will show the number of entires; usually each entry represents a single experiment.',
- renderResultString: count => (<span><b>{count}</b> entries</span>)
- },
- datasets: {
- label: 'Datasets',
- tooltip: 'Shows statistics in terms of datasets that entries belong to.',
- renderResultString: count => (<span> curated in <b>{count}</b> datasets</span>)
- }
- },
- defaultSearchMetric: 'code_runs',
- /**
- * An dict where each object represents a column. Possible keys are label, render.
- * Default render
- */
- searchResultColumns: {
- 'formula': {
- label: 'Formula',
- supportsSort: true
- },
- 'ems.chemical': {
- label: 'Material name'
- },
- 'ems.method': {
- label: 'Method',
- supportsSort: true
- },
- 'ems.data_type': {
- label: 'Data',
- supportsSort: true
- },
- 'ems.origin_time': {
- label: 'Date',
- supportsSort: true,
- render: entry => (entry.ems && entry.ems.origin_time && new Date(entry.ems.origin_time).toLocaleDateString()) || '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.chemical', 'ems.method', 'ems.data_type', 'ems.origin_time', 'ems.repository_url'],
- searchTabs: ['entries', 'datasets', 'uploads']
- }
-})
diff --git a/gui/src/components/search/EntryList.js b/gui/src/components/search/EntryList.js
index 4c1bcd88215cc750319211c1b23e3defb0a0d545..11891e953d87790e802f50bcb00c8ba5b664d168 100644
--- a/gui/src/components/search/EntryList.js
+++ b/gui/src/components/search/EntryList.js
@@ -30,7 +30,6 @@ import PublicIcon from '@material-ui/icons/Public'
import UploaderIcon from '@material-ui/icons/AccountCircle'
import SharedIcon from '@material-ui/icons/SupervisedUserCircle'
import PrivateIcon from '@material-ui/icons/VisibilityOff'
-import { domainData } from '../domainData'
import { authorList, nameList } from '../../utils'
import EntryDetails from '../entry/EntryDetails'
import { EntryButton } from '../nav/Routes'
@@ -92,12 +91,11 @@ export class EntryListUnstyled extends React.Component {
per_page: PropTypes.number.isRequired,
editable: PropTypes.bool,
editUserMetadataDialogProps: PropTypes.object,
- columns: PropTypes.object,
+ columns: PropTypes.object.isRequired,
title: PropTypes.string,
actions: PropTypes.element,
showEntryActions: PropTypes.func,
- selectedColumns: PropTypes.arrayOf(PropTypes.string),
- domain: PropTypes.object,
+ selectedColumns: PropTypes.arrayOf(PropTypes.string).isRequired,
user: PropTypes.object,
showAccessColumn: PropTypes.bool,
entryPagePathPrefix: PropTypes.string,
@@ -263,7 +261,6 @@ export class EntryListUnstyled extends React.Component {
renderEntryDetails(row) {
const { classes } = this.props
- const domain = (row.domain && domainData[row.domain]) || domainData.dft
return (<div className={classes.entryDetails} style={{width: this.props.entryDetailsWidth}}>
<div className={classes.entryDetailsContents} >
@@ -301,11 +298,11 @@ export class EntryListUnstyled extends React.Component {
<div className={classes.entryDetailsRow} style={{paddingRight: 0}}>
<Quantity column >
{/* <Quantity quantity="pid" label='PID' placeholder="not yet assigned" noWrap data={row} withClipboard /> */}
- <Quantity quantity="calc_id" label={`${domain ? domain.entryLabel : 'entry'} id`} noWrap withClipboard data={row} />
- <Quantity quantity="raw_id" label={`raw id`} noWrap withClipboard data={row} />
- <Quantity quantity="external_id" label={`external id`} noWrap withClipboard data={row} />
- <Quantity quantity='mainfile' noWrap ellipsisFront data={row} withClipboard />
- <Quantity quantity="upload_id" label='upload id' data={row} noWrap withClipboard>
+ <Quantity quantity="calc_id" label="entry id" noWrap withClipboard data={row} />
+ <Quantity quantity="raw_id" label="raw id" noWrap withClipboard data={row} />
+ <Quantity quantity="external_id" label="external id" noWrap withClipboard data={row} />
+ <Quantity quantity="mainfile" noWrap ellipsisFront data={row} withClipboard />
+ <Quantity quantity="upload_id" label="upload id" data={row} noWrap withClipboard>
<Typography style={{flexGrow: 1}}>
<Link component={RouterLink} to={`/uploads/${row.upload_id}`}>{row.upload_id}</Link>
</Typography>
@@ -349,26 +346,15 @@ export class EntryListUnstyled extends React.Component {
}
render() {
- const { classes, data, order, order_by, page, per_page, domain, editable, title, query, actions, user, showAccessColumn, ...rest } = this.props
+ const { classes, data, order, order_by, page, per_page, editable, title, query, actions, user, showAccessColumn, ...rest } = this.props
const { selected } = this.state
const results = data?.results || data?.data || []
const total = data?.pagination.total
const totalNumber = total || 0
- const columns = this.props.columns || {
- ...domain.searchResultColumns,
- ...EntryListUnstyled.defaultColumns
- }
-
- let selectedColumns = this.props.selectedColumns
- if (!selectedColumns) {
- selectedColumns = [...domain.defaultSearchResultColumns]
- if (user !== undefined || showAccessColumn) {
- selectedColumns.push('published')
- }
- selectedColumns.push('authors')
- }
+ const columns = this.props.columns
+ const selectedColumns = this.props.selectedColumns
const pagination = <TablePagination
rowsPerPageOptions={[5, 10, 25, 50, 100]}
@@ -399,7 +385,7 @@ export class EntryListUnstyled extends React.Component {
return (
<div className={classes.root}>
<DataTable
- entityLabels={domain ? [domain.entryLabel, domain.entryLabelPlural] : ['entry', 'entries']}
+ entityLabels={['entry', 'entries']}
selectActions={selectActions}
id={row => row.entry_id}
total={total}
diff --git a/gui/src/components/search/results/SearchResultsEntries.js b/gui/src/components/search/results/SearchResultsEntries.js
index 2857b20f22e94dd423a8aaeeb4e85b54c872be76..28725989fdeec92b71921efdaa1c8558d23e55e5 100644
--- a/gui/src/components/search/results/SearchResultsEntries.js
+++ b/gui/src/components/search/results/SearchResultsEntries.js
@@ -27,7 +27,6 @@ import EditUserMetadataDialog from '../../EditUserMetadataDialog'
import SharedIcon from '@material-ui/icons/SupervisedUserCircle'
import PrivateIcon from '@material-ui/icons/VisibilityOff'
import DownloadButton from '../../DownloadButton'
-import { domainData } from '../../domainData'
import EntryDetails from '../../entry/EntryDetails'
import { authorList, nameList } from '../../../utils'
import NewDataTable from '../../NewDataTable'
@@ -293,8 +292,6 @@ const SearchResultsEntries = React.memo(({
}, [showEntryActions])
const renderEntryDetails = useCallback((row) => {
- const domain = (row.domain && domainData[row.domain]) || domainData.dft
-
return (<div className={styles.entryDetails}>
<div className={styles.entryDetailsContents}>
<div className={styles.entryDetailsRow}>
@@ -331,11 +328,11 @@ const SearchResultsEntries = React.memo(({
<div className={styles.entryDetailsRow} style={{maxWidth: '33%', paddingRight: 0}}>
<Quantity column >
{/* <Quantity quantity="pid" label='PID' placeholder="not yet assigned" noWrap data={row} withClipboard /> */}
- <Quantity quantity="calc_id" label={`${domain ? domain.entryLabel : 'entry'} id`} noWrap withClipboard data={row} />
- <Quantity quantity="raw_id" label={`raw id`} noWrap withClipboard data={row} />
- <Quantity quantity="external_id" label={`external id`} noWrap withClipboard data={row} />
- <Quantity quantity='mainfile' noWrap ellipsisFront data={row} withClipboard />
- <Quantity quantity="upload_id" label='upload id' data={row} noWrap withClipboard>
+ <Quantity quantity="calc_id" label="entry id" noWrap withClipboard data={row} />
+ <Quantity quantity="raw_id" label="raw id" noWrap withClipboard data={row} />
+ <Quantity quantity="external_id" label="external id" noWrap withClipboard data={row} />
+ <Quantity quantity="mainfile" noWrap ellipsisFront data={row} withClipboard />
+ <Quantity quantity="upload_id" label="upload id" data={row} noWrap withClipboard>
<Typography style={{flexGrow: 1}}>
<Link component={RouterLink} to={`/uploads/${row.upload_id}`}>{row.upload_id}</Link>
</Typography>
diff --git a/nomad/app/flask/dcat/mapping.py b/nomad/app/flask/dcat/mapping.py
index fe4e1ab7bf666f75d7573a3dfd1e4aa39829dbc9..4294068f9a7dd04cd6aeae5ea1f35a6ec0cf3a2d 100644
--- a/nomad/app/flask/dcat/mapping.py
+++ b/nomad/app/flask/dcat/mapping.py
@@ -32,7 +32,12 @@ HYDRA = Namespace('http://www.w3.org/ns/hydra/core#')
def get_optional_entry_prop(entry, name):
try:
- return entry[name]
+ value = entry
+ segments = name.split('.')
+ for segment in segments:
+ value = value[segment]
+
+ return value
except (KeyError, AttributeError):
return 'unavailable'
@@ -86,7 +91,7 @@ class Mapping():
self.g.add((dataset, DCT.identifier, Literal(entry['entry_id'])))
self.g.add((dataset, DCT.issued, Literal(entry['upload_time'])))
self.g.add((dataset, DCT.modified, Literal(entry['last_processing'])))
- self.g.add((dataset, DCT.title, Literal(get_optional_entry_prop(entry, 'formula'))))
+ self.g.add((dataset, DCT.title, Literal(get_optional_entry_prop(entry, 'results.material.chemical_formula_descriptive'))))
self.g.add((dataset, DCT.description, Literal(get_optional_entry_prop(entry, 'comment'))))
if slim:
diff --git a/nomad/app/main.py b/nomad/app/main.py
index 9aed3c89363d4a62ea1bb213672b6c818d3b7957..7c9263638c5ab4dbef12e87829921469f42e8aca 100644
--- a/nomad/app/main.py
+++ b/nomad/app/main.py
@@ -96,7 +96,6 @@ async def http_exception_handler(request, exc):
<h2>info</h2>
{'<br/>'.join(f'{key}: {value}' for key, value in config.meta.items())}
<h2>apis</h2>
- <a href="{app_base}/api">NOMAD API v0</a><br/>
<a href="{app_base}/api/v1/extensions/docs">NOMAD API v1</a><br/>
<a href="{app_base}/optimade/v1/extensions/docs">Optimade API</a><br/>
<a href="{app_base}/dcat">DCAT API</a><br/>
@@ -109,10 +108,6 @@ async def http_exception_handler(request, exc):
'info': {
'app': config.meta,
'apis': {
- 'v0': {
- 'root': f'{app_base}/api',
- 'dashboard': f'{app_base}/api',
- },
'v1': {
'root': f'{app_base}/api/v1',
'dashboard': f'{app_base}/api/v1/extensions/docs',
diff --git a/nomad/app/optimade/elasticsearch.py b/nomad/app/optimade/elasticsearch.py
index d8dbea06b7513f3a2262fafde66ffd0a7b1c51a1..4d8941d472927ab092273ecc389eb1f00d89cd37 100644
--- a/nomad/app/optimade/elasticsearch.py
+++ b/nomad/app/optimade/elasticsearch.py
@@ -114,7 +114,7 @@ class StructureCollection(EntryCollection):
super().__init__(
resource_cls=NomadStructureResource,
resource_mapper=StructureMapper,
- transformer=get_transformer(nomad_properties='dft', without_prefix=False))
+ transformer=get_transformer(without_prefix=False))
self.parser = LarkParser(version=(1, 0, 0), variant="default")
diff --git a/nomad/app/optimade/filterparser.py b/nomad/app/optimade/filterparser.py
index 4cfc5a680b899b5c2d4d12622a2ea7c679ed0add..f666cd074c530e1e12c65dbf2a0c98f5364a0e47 100644
--- a/nomad/app/optimade/filterparser.py
+++ b/nomad/app/optimade/filterparser.py
@@ -36,7 +36,7 @@ class FilterException(Exception):
@cached(cache={})
-def _get_transformer(nomad_properties, without_prefix):
+def _get_transformer(without_prefix):
from nomad.datamodel import OptimadeEntry
quantities: Dict[str, Quantity] = {
q.name: Quantity(
@@ -55,35 +55,34 @@ def _get_transformer(nomad_properties, without_prefix):
quantities['elements'].nested_quantity = quantities['elements_ratios']
quantities['elements_ratios'].nested_quantity = quantities['elements_ratios']
- if nomad_properties is not None:
- for name, search_quantity in provider_specific_fields().items():
- names = ['_nmd_' + name]
- if without_prefix:
- names.append(name)
+ for name, search_quantity in provider_specific_fields().items():
+ names = ['_nmd_' + name]
+ if without_prefix:
+ names.append(name)
- for name in names:
- if name not in quantities:
- quantities[name] = Quantity(
- name,
- es_field=search_quantity.search_field,
- elastic_mapping_type=search_quantity.mapping['type'])
+ for name in names:
+ if name not in quantities:
+ quantities[name] = Quantity(
+ name,
+ es_field=search_quantity.search_field,
+ elastic_mapping_type=search_quantity.mapping['type'])
return ElasticTransformer(quantities=quantities.values())
-def parse_filter(filter_str: str, nomad_properties='dft', without_prefix=False) -> Q:
+def parse_filter(filter_str: str, without_prefix=False) -> Q:
''' Parses the given optimade filter str and returns a suitable elastic search query.
Arguments:
filter_str: Can be direct user input with no prior processing.
- nomad_properties: Also include the nomad proprietary properties of the given domain.
+ nomad_properties: Also include the nomad proprietary properties.
without_prefix: Do not prefix the nomad proprietary properties with _nmd_.
Raises:
FilterException: If the given str cannot be parsed, or if there are any semantic
errors in the given expression.
'''
- transformer = _get_transformer(nomad_properties, without_prefix)
+ transformer = _get_transformer(without_prefix)
try:
parse_tree = _parser.parse(filter_str)
diff --git a/nomad/app/v1/routers/info.py b/nomad/app/v1/routers/info.py
index d08ce2fdd4ef39c3190da00b9b15be69dffd2db4..8f834b37140284e9c5cdaf35a7b6e34cf227d0fe 100644
--- a/nomad/app/v1/routers/info.py
+++ b/nomad/app/v1/routers/info.py
@@ -26,7 +26,7 @@ from fastapi.routing import APIRouter
from pydantic.fields import Field
from pydantic.main import BaseModel
-from nomad import config, normalizing, datamodel, gitinfo
+from nomad import config, normalizing, gitinfo
from nomad.utils import strip
from nomad.search import search
from nomad.parsing import parsers, MatchingParser
@@ -48,11 +48,6 @@ class MetainfoModel(BaseModel):
data.'''))
-class DomainModel(BaseModel):
- name: str
- metainfo: MetainfoModel
-
-
class GitInfoModel(BaseModel):
ref: str
version: str
@@ -79,7 +74,6 @@ class InfoModel(BaseModel):
metainfo_packages: List[str]
codes: List[CodeInfoModel]
normalizers: List[str]
- domains: List[DomainModel]
statistics: StatisticsModel = Field(None, description='General NOMAD statistics')
search_quantities: dict
version: str
@@ -130,16 +124,6 @@ async def get_info():
'codes': codes,
'normalizers': [normalizer.__name__ for normalizer in normalizing.normalizers],
'statistics': statistics(),
- 'domains': [
- {
- 'name': domain_name,
- 'metainfo': {
- 'all_package': domain['metainfo_all_package'],
- 'root_section': domain['root_section']
- }
- }
- for domain_name, domain in datamodel.domains.items()
- ],
'search_quantities': {
s.qualified_name: {
'name': s.qualified_name,
diff --git a/nomad/cli/client/__init__.py b/nomad/cli/client/__init__.py
index 3a57199e29e7960ef8c3ecf410834f190698c302..a524ace65264073aba3786116dd40ca9c85353cb 100644
--- a/nomad/cli/client/__init__.py
+++ b/nomad/cli/client/__init__.py
@@ -149,7 +149,7 @@ def local(ctx, entry_id, show_archive, show_metadata, skip_normalizers, not_stri
if show_metadata:
metadata = entry_archive.metadata
- metadata.apply_domain_metadata(entry_archive)
+ metadata.apply_archvie_metadata(entry_archive)
json.dump(metadata.m_to_dict(), sys.stdout, indent=4)
diff --git a/nomad/cli/parse.py b/nomad/cli/parse.py
index 4d1c39875cd7aee2bb285f1a147ef4b8d8c361d9..2e9469fc452f2ddf4dec7c3ffc75914571ccc813 100644
--- a/nomad/cli/parse.py
+++ b/nomad/cli/parse.py
@@ -40,12 +40,12 @@ def _parse(mainfile, show_archive, show_metadata, skip_normalizers, not_strict,
if not skip_normalizers:
normalize_all(entry_archive)
- entry_archive.metadata.apply_domain_metadata(entry_archive)
+ entry_archive.metadata.apply_archvie_metadata(entry_archive)
if show_archive:
json.dump(entry_archive.m_to_dict(), sys.stdout, indent=2)
if show_metadata:
metadata = entry_archive.metadata
- metadata.apply_domain_metadata(entry_archive)
+ metadata.apply_archvie_metadata(entry_archive)
json.dump(metadata.m_to_dict(), sys.stdout, indent=4)
diff --git a/nomad/datamodel/__init__.py b/nomad/datamodel/__init__.py
index 7c905a1c0f4862c5426901a1e544fe5877ea21c3..b93a7170b600647df942c63c439c936b1ec3bce8 100644
--- a/nomad/datamodel/__init__.py
+++ b/nomad/datamodel/__init__.py
@@ -71,12 +71,6 @@ The datamodel supports different *domains*. This means that most domain metadata
entry/calculation is stored in domain-specific sub sections of the :class:`EntryMetadata`
section. We currently have the following domain specific metadata classes/sections:
-.. autoclass:: nomad.datamodel.dft.DFTMetadata
- :members:
-
-.. autoclass:: nomad.datamodel.ems.EMSMetadata
- :members:
-
.. autoclass:: nomad.datamodel.OptimadeEntry
:members:
@@ -87,8 +81,6 @@ import sys
from nomad.metainfo import Environment
-from .dft import DFTMetadata
-from .ems import EMSMetadata
from .datamodel import (
Dataset, User, Author, EditableUserMetadata, UserProvidableMetadata, OasisMetadata,
UploadMetadata, MongoMetadata, EntryMetadata, EntryArchive)
@@ -97,22 +89,5 @@ from .metainfo import m_env
from .results import Results
m_env.m_add_sub_section(Environment.packages, sys.modules['nomad.datamodel.datamodel'].m_package) # type: ignore
-m_env.m_add_sub_section(Environment.packages, sys.modules['nomad.datamodel.dft'].m_package) # type: ignore
-m_env.m_add_sub_section(Environment.packages, sys.modules['nomad.datamodel.ems'].m_package) # type: ignore
m_env.m_add_sub_section(Environment.packages, sys.modules['nomad.datamodel.encyclopedia'].m_package) # type: ignore
m_env.m_add_sub_section(Environment.packages, sys.modules['nomad.datamodel.optimade'].m_package) # type: ignore
-
-domains = {
- 'dft': {
- 'metadata': DFTMetadata,
- 'metainfo_all_package': 'common',
- 'root_section': 'run'
- },
- 'ems': {
- 'metadata': EMSMetadata,
- 'metainfo_all_package': 'common_experimental',
- 'root_section': 'section_measurement'
- }
-}
-
-root_sections = [domain['root_section'] for domain in domains.values()] + ['section_entry_info', 'OptimadeEntry', 'Workflow']
diff --git a/nomad/datamodel/datamodel.py b/nomad/datamodel/datamodel.py
index 803a9b39f91c606e8bf94e6840eac475ee7f8685..a356ed81710ce902943930824727b5599dbf4900 100644
--- a/nomad/datamodel/datamodel.py
+++ b/nomad/datamodel/datamodel.py
@@ -29,16 +29,13 @@ from nomad.datamodel.metainfo.common import FastAccess
from nomad.metainfo.pydantic_extension import PydanticModel
from nomad.metainfo.elasticsearch_extension import Elasticsearch, material_entry_type, entry_type
-from .dft import DFTMetadata
-from .ems import EMSMetadata
-from .optimade import OptimadeEntry
-
# This is usually defined automatically when the first metainfo definition is evaluated, but
# due to the next imports requireing the m_package already, this would be too late.
m_package = metainfo.Package()
from .results import Results # noqa
from .encyclopedia import EncyclopediaMetadata # noqa
+from .optimade import OptimadeEntry # noqa
from .metainfo.simulation.run import Run # noqa
from .metainfo.workflow import Workflow # noqa
from .metainfo.common_experimental import Measurement # noqa
@@ -357,8 +354,6 @@ class EntryMetadata(metainfo.MSection):
calc_hash: The raw file content based checksum/hash of this calculation.
pid: The unique persistent id of this calculation.
mainfile: The upload relative mainfile path.
- domain: Must be the key for a registered domain. This determines which actual
- subclass is instantiated.
files: A list of all files, relative to upload.
processed: Boolean indicating if this calc was successfully processed and archive
@@ -562,23 +557,6 @@ class EntryMetadata(metainfo.MSection):
type=metainfo.Datetime, categories=[MongoMetadata, OasisMetadata],
description='The date and time the user metadata was edited last')
- formula = metainfo.Quantity(
- type=str, categories=[DomainMetadata],
- description='A (reduced) chemical formula')
-
- atoms = metainfo.Quantity(
- type=str, shape=['n_atoms'], default=[], categories=[DomainMetadata],
- description='The atom labels of all atoms of the entry\'s material')
-
- only_atoms = metainfo.Quantity(
- type=str, categories=[DomainMetadata],
- description='The atom labels concatenated in order-number order',
- derived=lambda entry: _only_atoms(entry.atoms))
-
- n_atoms = metainfo.Quantity(
- type=int, categories=[DomainMetadata], default=0,
- description='The number of atoms in the entry\'s material')
-
optimade = metainfo.SubSection(
sub_section=OptimadeEntry,
description='Metadata used for the optimade API.',
@@ -593,29 +571,13 @@ class EntryMetadata(metainfo.MSection):
description='All quantities that are used by this entry.',
a_elasticsearch=QuantitySearch())
- ems = metainfo.SubSection(sub_section=EMSMetadata)
- dft = metainfo.SubSection(sub_section=DFTMetadata, categories=[FastAccess])
encyclopedia = metainfo.SubSection(sub_section=EncyclopediaMetadata, categories=[FastAccess])
def apply_user_metadata(self, metadata: dict):
''' Applies a user provided metadata dict to this calc. '''
self.m_update(**metadata)
- def apply_domain_metadata(self, archive):
- ''' Used to apply metadata that is related to the domain. '''
- assert self.domain is not None, 'all entries must have a domain'
- domain_sub_section_def = self.m_def.all_sub_sections.get(self.domain)
- if domain_sub_section_def is not None:
- domain_section_def = domain_sub_section_def.sub_section
- assert domain_section_def is not None, 'unknown domain %s' % self.domain
-
- # add domain section if not already there
- domain_section = self.m_get_sub_section(domain_sub_section_def, -1)
- if domain_section is None:
- domain_section = self.m_create(domain_section_def.section_cls)
-
- domain_section.apply_domain_metadata(archive)
-
+ def apply_archvie_metadata(self, archive):
quantities = set()
n_quantities = 0
diff --git a/nomad/datamodel/dft.py b/nomad/datamodel/dft.py
deleted file mode 100644
index d9c02f3bb8c8b13e7918ab93da82d232598a6ed7..0000000000000000000000000000000000000000
--- a/nomad/datamodel/dft.py
+++ /dev/null
@@ -1,545 +0,0 @@
-#
-# Copyright The NOMAD Authors.
-#
-# This file is part of NOMAD. See https://nomad-lab.eu for further info.
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-#
-
-'''
-DFT specific metadata
-'''
-
-import re
-
-from nomad import config, utils
-from nomad.metainfo import MSection, Section, Quantity, MEnum, SubSection
-
-from .metainfo.workflow import Workflow
-from .metainfo.common import FastAccess
-from .metainfo.simulation.run import Run
-from .metainfo.simulation.method import Functional
-from .metainfo.simulation.calculation import Energy
-
-
-xc_treatments = {
- 'gga': 'GGA',
- 'hf_': 'HF',
- 'oep': 'OEP',
- 'hyb': 'hybrid',
- 'mgg': 'meta-GGA',
- 'vdw': 'vdW',
- 'lda': 'LDA',
-}
-''' https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/XC-functional '''
-
-basis_sets = {
- 'gaussians': 'gaussians',
- 'realspacegrid': 'real-space grid',
- 'planewaves': 'plane waves'
-}
-
-compound_types = [
- 'unary',
- 'binary',
- 'ternary',
- 'quaternary',
- 'quinary',
- 'sexinary',
- 'septenary',
- 'octanary',
- 'nonary',
- 'decinary'
-]
-
-_electronic_quantities = [
- 'electronic_band_structure',
- 'electronic_dos',
- 'eigenvalues_values',
-]
-
-_mechanical_quantities = [
- 'stress_tensor'
-]
-
-_thermal_quantities = [
- 'heat_capacity_c_v',
- 'helmholtz_free_energy',
- 'phonon_band_structure',
- 'phonon_dos',
-]
-
-_magnetic_quantities = [
- 'spin_S2'
-]
-
-_optical_quantities = [
- 'oscillator_strengths',
- 'transition_dipole_moments'
-]
-
-_searchable_quantities = set(_electronic_quantities + _mechanical_quantities + _thermal_quantities + _magnetic_quantities + _optical_quantities)
-
-version_re = re.compile(r'(\d+(\.\d+(\.\d+)?)?)')
-
-
-def map_functional_name_to_xc_treatment(name):
- if name == config.services.unavailable_value:
- return name
-
- return xc_treatments.get(name[:3].lower(), config.services.unavailable_value)
-
-
-def map_basis_set_to_basis_set_label(name):
- key = name.replace('_', '').replace('-', '').replace(' ', '').lower()
- return basis_sets.get(key, name)
-
-
-def simplify_version(version):
- match = version_re.search(version)
- if match is None:
- return version
- else:
- return match.group(0)
-
-
-def valid_array(array):
- """Checks if the given variable is a non-empty array.
- """
- return array is not None and len(array) > 0
-
-
-class Label(MSection):
- '''
- Label that further classify a structure.
-
- Attributes:
- label: The label as a string
- type: The type of the label
- source: The source that this label was taken from.
-
- '''
- label = Quantity(type=str)
-
- type = Quantity(type=MEnum(
- 'compound_class', 'classification', 'prototype', 'prototype_id'))
-
- source = Quantity(
- type=MEnum('springer', 'aflow_prototype_library'))
-
-
-class DFTMetadata(MSection):
- m_def = Section(a_domain='dft')
-
- basis_set = Quantity(
- type=str, default='not processed',
- description='The used basis set functions.')
-
- xc_functional = Quantity(
- type=str, default='not processed',
- description='The libXC based xc functional classification used in the simulation.')
-
- xc_functional_names = Quantity(
- type=str, default=[], shape=['*'],
- description='The list of libXC functional names that where used in this entry.')
-
- system = Quantity(
- type=str, default='not processed',
- description='The system type of the simulated system.')
-
- compound_type = Quantity(
- type=str, default='not processed',
- description='The compound type of the simulated system.'
- )
-
- crystal_system = Quantity(
- type=str, default='not processed',
- description='The crystal system type of the simulated system.')
-
- spacegroup = Quantity(
- type=int, default=-1,
- description='The spacegroup of the simulated system as number.')
-
- spacegroup_symbol = Quantity(
- type=str, default='not processed',
- description='The spacegroup as international short symbol.')
-
- code_name = Quantity(
- type=str, default='not processed',
- description='The name of the used code.') # in import the parser module is added codes here as statistic_values
-
- code_version = Quantity(
- type=str, default='not processed',
- description='The version of the used code.')
-
- n_geometries = Quantity(
- type=int, default=0, description='Number of unique geometries.')
-
- n_calculations = Quantity(
- type=int, default=0,
- description='Number of single configuration calculation sections')
-
- n_total_energies = Quantity(
- type=int, default=0, description='Number of total energy calculations')
-
- n_quantities = Quantity(
- type=int, default=0, description='Number of metainfo quantities parsed from the entry.')
-
- quantities = Quantity(
- type=str, shape=['0..*'],
- description='All quantities that are used by this entry.')
-
- searchable_quantities = Quantity(
- type=str, shape=['0..*'],
- description='All quantities with existence filters in the search GUI.')
-
- geometries = Quantity(
- type=str, shape=['0..*'],
- description='Hashes for each simulated geometry')
-
- group_hash = Quantity(
- type=str,
- description='Hashes that describe unique geometries simulated by this code run.')
-
- labels = SubSection(
- sub_section=Label, repeats=True, categories=[FastAccess],
- description='The labels taken from AFLOW prototypes and springer.')
-
- labels_springer_compound_class = Quantity(
- type=str, shape=['0..*'],
- description='Springer compund classification.')
-
- labels_springer_classification = Quantity(
- type=str, shape=['0..*'],
- description='Springer classification by property.')
-
- workflow = Quantity(type=Workflow)
-
- def code_name_from_parser(self):
- entry = self.m_parent
- if entry.parser_name is not None:
- from nomad.parsing.parsers import parser_dict
- parser = parser_dict.get(entry.parser_name)
- if hasattr(parser, 'code_name'):
- return parser.code_name
- return config.services.unavailable_value
-
- def update_group_hash(self):
- user_id = None
- uploader = self.m_parent.uploader
- if uploader is not None:
- user_id = uploader.user_id
- self.group_hash = utils.hash(
- self.m_parent.formula,
- self.spacegroup,
- self.basis_set,
- self.xc_functional,
- self.code_name,
- self.code_version,
- self.m_parent.with_embargo,
- user_id)
-
- def apply_domain_metadata(self, entry_archive):
- from nomad.normalizing.system import normalized_atom_labels
- entry = self.m_parent
-
- logger = utils.get_logger(__name__).bind(
- upload_id=entry.upload_id, calc_id=entry.calc_id, mainfile=entry.mainfile)
-
- self.code_name = self.code_name_from_parser()
-
- if entry_archive is None:
- return
-
- section_run = entry_archive.run
- if not section_run:
- logger.warn('no section run found')
- return
- section_run = section_run[0]
-
- # default values
- self.system = config.services.unavailable_value
- self.crystal_system = config.services.unavailable_value
- self.spacegroup_symbol = config.services.unavailable_value
- self.basis_set = config.services.unavailable_value
- self.xc_functional = config.services.unavailable_value
-
- section_system = None
- for section in section_run.system:
- if section.is_representative:
- section_system = section
- break
-
- # code and code specific ids
- try:
- code_name = section_run.program.name
- if code_name:
- self.code_name = code_name
- else:
- raise KeyError
- except KeyError as e:
- logger.warn('archive without program_name', exc_info=e)
-
- try:
- version = section_run.program.version
- if version:
- self.code_version = simplify_version(version)
- else:
- raise KeyError
- except KeyError:
- self.code_version = config.services.unavailable_value
-
- def get_value(value):
- return value if value else config.services.unavailable_value
-
- raw_id = section_run.raw_id
- if raw_id is not None:
- entry.raw_id = raw_id
-
- # metadata (system, method, chemistry)
- atom_labels = section_system.atoms.labels if section_system else []
- atoms = atom_labels if atom_labels else []
- entry.n_atoms = len(atoms)
- atoms = list(set(normalized_atom_labels(set(atoms))))
- atoms.sort()
- entry.atoms = atoms
- self.compound_type = compound_types[len(atoms) - 1] if len(atoms) <= 10 else '>decinary'
-
- self.system = config.services.unavailable_value
- self.crystal_system = config.services.unavailable_value
- self.spacegroup_symbol = config.services.unavailable_value
-
- section_symmetry = None
- if section_system and len(section_system.symmetry) > 0:
- section_symmetry = section_system.symmetry[0]
- self.crystal_system = get_value(section_symmetry.crystal_system)
- spacegroup = section_symmetry.space_group_number
- self.spacegroup = 0 if not spacegroup else int(spacegroup)
- self.spacegroup_symbol = get_value(section_symmetry.international_short_symbol)
-
- if section_run.method and section_run.method[0].basis_set:
- program_basis_set_type = section_run.method[0].basis_set[0].type
- if program_basis_set_type:
- self.basis_set = map_basis_set_to_basis_set_label(program_basis_set_type)
-
- if section_system:
- self.system = get_value(section_system.type)
- if section_system.chemical_composition_reduced is not None:
- entry.formula = get_value(section_system.chemical_composition_reduced)
-
- # metrics and quantities
- quantities = set()
- searchable_quantities = set()
- geometries = set()
- xc_functionals = set()
- xc_functional = None
-
- n_quantities = 0
- n_calculations = 0
- n_total_energies = 0
- n_geometries = 0
-
- for section, property_def, _ in entry_archive.m_traverse():
- property_name = property_def.name
- quantities.add(property_name)
- n_quantities += 1
-
- if property_name in _searchable_quantities:
- searchable_quantities.add(property_name)
-
- if property_def == Functional.name:
- xc_functional = getattr(section, property_name)
- if xc_functional:
- xc_functionals.add(xc_functional)
-
- if property_def == Energy.total:
- n_total_energies += 1
-
- if property_name == 'configuration_raw_gid':
- geometries.add(section.m_get(property_def))
-
- if property_name == Run.calculation:
- n_calculations += 1
-
- if property_def == Run.system:
- n_geometries += 1
-
- # Special handling for electronic/vibrational DOS and band structure:
- # these cannot currently be distinguished through the presence of a
- # single metainfo.
- searchable_quantities.discard("electronic_dos")
- searchable_quantities.discard("electronic_band_structure")
- searchable_quantities.discard("phonon_dos")
- searchable_quantities.discard("phonon_band_structure")
- if self.band_structure_electronic(entry_archive):
- searchable_quantities.add("electronic_band_structure")
- if self.band_structure_phonon(entry_archive):
- searchable_quantities.add("phonon_band_structure")
- if self.dos_electronic(entry_archive):
- searchable_quantities.add("electronic_dos")
- if self.dos_phonon(entry_archive):
- searchable_quantities.add("phonon_dos")
-
- self.xc_functional_names = sorted(xc_functionals)
- if len(self.xc_functional_names) > 0:
- self.xc_functional = map_functional_name_to_xc_treatment(
- get_value(self.xc_functional_names[0]))
- else:
- self.xc_functional = config.services.unavailable_value
-
- self.quantities = list(quantities)
- self.geometries = list(geometries)
- self.searchable_quantities = list(searchable_quantities)
- self.n_quantities = n_quantities
- self.n_calculations = n_calculations
- self.n_total_energies = n_total_energies
- self.n_geometries = n_geometries
-
- # grouping
- self.update_group_hash()
-
- # labels
- compounds = set()
- classifications = set()
- if section_system:
- for section in section_system.springer_material:
- compounds.update(section.compound_class)
- classifications.update(section.classification)
-
- for compound in compounds:
- self.labels.append(Label(label=compound, type='compound_class', source='springer'))
- for classification in classifications:
- self.labels.append(Label(label=classification, type='classification', source='springer'))
- self.labels_springer_compound_class = list(compounds)
- self.labels_springer_classification = list(classifications)
-
- aflow_id, aflow_label = None, None
- section_prototype = section_system.prototype if section_system else []
- if section_prototype:
- aflow_id = get_value(section_prototype[0].aflow_id)
- aflow_label = get_value(section_prototype[0].label)
-
- if aflow_id is not None and aflow_label is not None:
- self.labels.append(Label(label=aflow_label, type='prototype', source='aflow_prototype_library'))
- self.labels.append(Label(label=aflow_id, type='prototype_id', source='aflow_prototype_library'))
-
- if entry_archive.workflow:
- self.workflow = entry_archive.workflow[-1]
-
- def band_structure_electronic(self, entry_archive):
- """Returns whether a valid electronic band structure can be found. In
- the case of multiple valid band structures, only the latest one is
- considered.
-
- Band structure is reported only under the following conditions:
- - There is a non-empty array of band_k_points.
- - There is a non-empty array of band_energies.
- - The reported band_structure_kind is not "vibrational".
- """
- path = ["run", "calculation", "band_structure_electronic"]
- valid = False
- for bs in self.traverse_reversed(entry_archive, path):
- valid = True
- for segment in bs.segment:
- energies = segment.energies
- k_points = segment.kpoints
- if not valid_array(energies) or not valid_array(k_points):
- valid = False
- break
- if valid:
- break
- return valid
-
- def dos_electronic(self, entry_archive):
- """Returns whether a valid electronic DOS can be found. In the case of
- multiple valid DOSes, only the latest one is reported.
-
- DOS is reported only under the following conditions:
- - There is a non-empty array of dos_values_normalized.
- - There is a non-empty array of dos_energies.
- - The reported dos_kind is not "vibrational".
- """
- path = ["run", "calculation", "dos_electronic"]
- for dos in self.traverse_reversed(entry_archive, path):
- energies = dos.energies
- values = dos.total[-1].value
- if valid_array(energies) and valid_array(values):
- return True
-
- return False
-
- def band_structure_phonon(self, entry_archive):
- """Returns whether a valid phonon band structure can be found. In the
- case of multiple valid band structures, only the latest one is
- considered.
-
- Band structure is reported only under the following conditions:
- - There is a non-empty array of band_k_points.
- - There is a non-empty array of band_energies.
- - The reported band_structure_kind is "vibrational".
- """
- path = ["run", "calculation", "band_structure_phonon"]
- valid = False
- for bs in self.traverse_reversed(entry_archive, path):
- valid = True
- for segment in bs.segment:
- energies = segment.energies
- k_points = segment.kpoints
- if not valid_array(energies) or not valid_array(k_points):
- valid = False
- break
- if valid:
- break
-
- return valid
-
- def dos_phonon(self, entry_archive):
- """Returns whether a valid phonon dos can be found. In the case of
- multiple valid data sources, only the latest one is reported.
-
- DOS is reported only under the following conditions:
- - There is a non-empty array of dos_values_normalized.
- - There is a non-empty array of dos_energies.
- - The reported dos_kind is "vibrational".
- """
- path = ["run", "calculation", "dos_phonon"]
- for dos in self.traverse_reversed(entry_archive, path):
- energies = dos.energies
- values = dos.total[-1].value
- if valid_array(energies) and valid_array(values):
- return True
-
- return False
-
- def traverse_reversed(self, entry_archive, path):
- """Traverses the given metainfo path in reverse order. Useful in
- finding the latest reported section or value.
- """
- def traverse(root, path, i):
- sections = getattr(root, path[i])
- if isinstance(sections, list):
- for section in reversed(sections):
- if i == len(path) - 1:
- yield section
- else:
- for s in traverse(section, path, i + 1):
- yield s
- else:
- if i == len(path) - 1:
- yield sections
- else:
- for s in traverse(sections, path, i + 1):
- yield s
- for t in traverse(entry_archive, path, 0):
- if t is not None:
- yield t
diff --git a/nomad/datamodel/ems.py b/nomad/datamodel/ems.py
deleted file mode 100644
index 6a548d9f9357629cae2f87af4ea40ffe2048a30a..0000000000000000000000000000000000000000
--- a/nomad/datamodel/ems.py
+++ /dev/null
@@ -1,140 +0,0 @@
-#
-# Copyright The NOMAD Authors.
-#
-# This file is part of NOMAD. See https://nomad-lab.eu for further info.
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-#
-
-'''
-Experimental material science specific metadata
-'''
-from nomad import config
-from nomad.metainfo import Quantity, MSection, Section, Datetime
-
-
-def _unavailable(value):
- if value is None:
- return config.services.unavailable_value
-
- return value
-
-
-class EMSMetadata(MSection):
- m_def = Section(a_domain='ems')
-
- # sample quantities
- chemical = Quantity(type=str)
- sample_constituents = Quantity(type=str)
- sample_microstructure = Quantity(type=str)
-
- # general metadata
- experiment_summary = Quantity(type=str)
- origin_time = Quantity(type=Datetime)
- experiment_location = Quantity(type=str)
-
- # method
- method = Quantity(type=str)
- data_type = Quantity(type=str)
- probing_method = Quantity(type=str)
-
- # origin metadata
- repository_name = Quantity(type=str)
- repository_url = Quantity(type=str)
- entry_repository_url = Quantity(type=str)
- preview_url = Quantity(type=str)
-
- # TODO move to more a general metadata section
- quantities = Quantity(type=str, shape=['0..*'], default=[])
- group_hash = Quantity(type=str)
-
- def apply_domain_metadata(self, entry_archive):
- from nomad import utils
-
- if entry_archive is None:
- return
-
- entry = self.m_parent
-
- root_section = entry_archive.section_measurement[0]
-
- sample = root_section.section_metadata.section_sample
- entry.formula = config.services.unavailable_value
- if sample:
- # TODO deal with multiple materials
- material = sample.section_material[0] if len(sample.section_material) > 0 else None
- if material:
- entry.formula = _unavailable(material.formula)
- atoms = material.elements
-
- if atoms is None:
- entry.atoms = []
- else:
- if hasattr(atoms, 'tolist'):
- atoms = atoms.tolist()
- entry.n_atoms = len(atoms)
-
- atoms = list(set(atoms))
- atoms.sort()
- entry.atoms = atoms
-
- if material.name:
- self.chemical = _unavailable(material.name)
- else:
- self.chemical = _unavailable(material.formula)
-
- self.sample_microstructure = _unavailable(sample.sample_microstructure)
- self.sample_constituents = _unavailable(sample.sample_constituents)
-
- self.experiment_summary = root_section.section_metadata.section_experiment.notes
- location = root_section.section_metadata.section_experiment.experiment_location
- if location is not None:
- location_str = ', '.join([
- getattr(location, prop)
- for prop in ['facility', 'institution', 'address']
- if getattr(location, prop) is not None])
- self.experiment_location = location_str
-
- if root_section.section_metadata.section_experiment.experiment_start_time:
- self.origin_time = root_section.section_metadata.section_experiment.experiment_start_time
- elif root_section.section_metadata.section_experiment.experiment_publish_time:
- self.origin_time = root_section.section_metadata.section_experiment.experiment_publish_time
- else:
- self.origin_time = self.m_parent.upload_time
-
- # self.data_type = _unavailable(root_section.section_method.data_type)
- self.method = _unavailable(root_section.section_metadata.section_experiment.method_name)
- # self.probing_method = _unavailable(root_section.section_method.probing_method)
-
- self.repository_name = _unavailable(root_section.section_metadata.section_origin.repository_name)
- self.repository_url = root_section.section_metadata.section_origin.repository_url
- self.preview_url = root_section.section_metadata.section_origin.preview_url
- self.entry_repository_url = root_section.section_metadata.section_origin.entry_repository_url
-
- self.group_hash = utils.hash(
- entry.formula,
- self.method,
- self.experiment_location,
- entry.with_embargo,
- entry.uploader)
-
- quantities = set()
-
- quantities.add(root_section.m_def.name)
- for _, property_def, _ in root_section.m_traverse():
- quantities.add(property_def.name)
-
- self.quantities = list(quantities)
-
- if self.m_parent.references is None:
- self.m_parent.references = [self.entry_repository_url]
diff --git a/nomad/normalizing/__init__.py b/nomad/normalizing/__init__.py
index 8d561661c25f5cb7698cbd9e8068c140a6f943a7..8b6fbf9fcd95884c37b326e4c5c44e3248edf537 100644
--- a/nomad/normalizing/__init__.py
+++ b/nomad/normalizing/__init__.py
@@ -41,7 +41,6 @@ from typing import List, Any, Iterable, Type
from .system import SystemNormalizer
from .optimade import OptimadeNormalizer
-from .fhiaims import FhiAimsBaseNormalizer
from .dos import DosNormalizer
from .normalizer import Normalizer
from .band_structure import BandStructureNormalizer
@@ -52,7 +51,6 @@ from .results import ResultsNormalizer
normalizers: Iterable[Type[Normalizer]] = [
SystemNormalizer,
OptimadeNormalizer,
- # FhiAimsBaseNormalizer,
DosNormalizer,
BandStructureNormalizer,
WorkflowNormalizer,
diff --git a/nomad/normalizing/fhiaims.py b/nomad/normalizing/fhiaims.py
deleted file mode 100644
index eea99e3e4546d1a825a77f24b71ae1d1f5466161..0000000000000000000000000000000000000000
--- a/nomad/normalizing/fhiaims.py
+++ /dev/null
@@ -1,125 +0,0 @@
-#
-# Copyright The NOMAD Authors.
-#
-# This file is part of NOMAD. See https://nomad-lab.eu for further info.
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-#
-
-import os.path
-import json
-import numpy as np
-
-from nomad.normalizing.normalizer import Normalizer
-
-controlIn_basis_set = 'x_fhi_aims_section_controlIn_basis_set'
-controlIn_basis_func = 'x_fhi_aims_section_controlIn_basis_func'
-controlIn_nucleus = 'x_fhi_aims_controlIn_nucleus'
-
-pure_types_json = dict()
-
-for pure_types_str in ['light', 'really_tight', 'tight']:
- with open(os.path.join(os.path.dirname(__file__), 'data', pure_types_str + '.json')) as f:
- json_data = json.load(f)
- section_method = json_data['sections']['section_run-0']['sections']['section_method-0']
- pure_types_json[pure_types_str] = section_method[controlIn_basis_set]
-
-
-class FhiAimsBaseNormalizer(Normalizer):
-
- # Finds out if val is in the array
- def compare_val_list(self, val, list):
- if val in list:
- return 0
- return 1
-
- # Comparison between two dicts.
- # List structure:
- def compare_dict_dict(self, d1, d2):
- sum2 = np.zeros(len(d2))
-
- # Loop over the size of dict2
- for k in np.arange(0, len(d2)):
- # Lopp over the elements of each dict2
- for idx, val in d1.items():
- # Excludes the keys that are always different.
- if (idx not in ["gIndex", "references", "uri"]):
- try:
- if (val != d2[k][idx]):
- sum2[k] = sum2[k] + 1
- except KeyError: # this exception case arises if the cut off potential is not a number
- continue
- if (min(sum2) == 0):
- return 0
- else:
- return 1 # sum(sum2)
-
- def compare_to_defaults(self, dict2_default, dict1):
- # first compare the integration grid
- false_hits_integration_grid = 0
- false_hits_basis = 0
-
- for key in dict1:
- if key not in ['gIndex', 'uri', controlIn_basis_func]:
- if np.size(dict1[key]) == 1:
- if(dict1[key] != dict2_default[key]):
- false_hits_integration_grid += 1
- false_hits_integration_grid += abs(np.size(dict1[key]) - np.size(dict2_default[key]))
- if np.size(dict1[key]) > 1:
- for i in dict1[key]:
- false_hits_integration_grid += self.compare_val_list(i, dict2_default[key])
- false_hits_integration_grid += abs(np.size(dict1[key]) - np.size(dict2_default[key]))
-
- elif (key == controlIn_basis_func):
- for i in np.arange(0, len(dict1[key])):
- false_hits_basis += self.compare_dict_dict(
- dict1[key][i], dict2_default[key])
- false_hits_basis += abs(len(dict1[key]) - len(dict2_default[key]))
-
- return [false_hits_integration_grid, false_hits_basis]
-
- def normalize(self, logger=None) -> None:
- super().normalize(logger)
- if not self.section_run or self.section_run.program_name != 'FHI-aims':
- return
-
- for method in self.section_run.section_method:
- to_compare = getattr(method, controlIn_basis_set, None)
- if to_compare is None:
- # not fhi aims data
- continue
-
- matrix_hits_int = dict.fromkeys(pure_types_json, 0)
- matrix_hits_basis = dict.fromkeys(pure_types_json, 0)
-
- for index, data in enumerate(to_compare):
- atom_index = int(data[controlIn_nucleus])
- for key, val in pure_types_json.items():
- results = self.compare_to_defaults(val[atom_index], to_compare[index])
- matrix_hits_int[key] += results[0]
- matrix_hits_basis[key] += results[1]
-
- # matrix_hits[key]=matrix_hits[key]+CompareToDefaults(val[AtomIndex],to_compare[i])
-
- closest_base_int = min(matrix_hits_int, key=matrix_hits_int.get)
- if (matrix_hits_basis[min(matrix_hits_basis, key=matrix_hits_basis.get)] == 0):
- closest_base_base = ''
- else:
- closest_base_base = '+'
-
- if (matrix_hits_int[closest_base_int] == 0):
- method.basis_set = closest_base_int + closest_base_base
- elif(matrix_hits_int[closest_base_int] <= 5):
- method.basis_set = '~' + closest_base_int + closest_base_base
- elif(matrix_hits_int[closest_base_int] > 5):
- method.basis_set = 'custom-' + closest_base_int
diff --git a/nomad/processing/data.py b/nomad/processing/data.py
index 6a10564facd1a861b4ad26c0ed8cd1c9c1b060f2..99973f07b0b1b32df1a095a8686604059fa4e314 100644
--- a/nomad/processing/data.py
+++ b/nomad/processing/data.py
@@ -498,7 +498,7 @@ class Calc(Proc):
'could not apply entry metadata to entry', exc_info=e)
try:
- self._entry_metadata.apply_domain_metadata(self._parser_results)
+ self._entry_metadata.apply_archvie_metadata(self._parser_results)
except Exception as e:
self.get_logger().error(
'could not apply domain metadata to entry', exc_info=e)
@@ -603,9 +603,6 @@ class Calc(Proc):
# new timestamp and method details taken from the referenced
# archive.
self._entry_metadata.last_processing = datetime.utcnow()
- self._entry_metadata.dft.xc_functional = ref_archive.metadata.dft.xc_functional
- self._entry_metadata.dft.basis_set = ref_archive.metadata.dft.basis_set
- self._entry_metadata.dft.update_group_hash()
self._entry_metadata.encyclopedia.status = EncyclopediaMetadata.status.type.success
except Exception as e:
logger.error("Could not retrieve method information for phonon calculation.", exc_info=e)
@@ -666,7 +663,7 @@ class Calc(Proc):
self.set_process_step('archiving')
logger = self.get_logger()
- self._entry_metadata.apply_domain_metadata(self._parser_results)
+ self._entry_metadata.apply_archvie_metadata(self._parser_results)
self._entry_metadata.processed = True
if self.upload.publish_directly:
diff --git a/nomad/search.py b/nomad/search.py
index 500a2ad35fe85ae18ddd5ecf302f33740e3edd1b..7376eac261703e636de350ed11851195ac406888 100644
--- a/nomad/search.py
+++ b/nomad/search.py
@@ -478,8 +478,7 @@ def validate_api_query(
value = str(value)
from nomad.app.optimade import filterparser
try:
- return filterparser.parse_filter(
- value, nomad_properties='dft', without_prefix=True)
+ return filterparser.parse_filter(value, without_prefix=True)
except filterparser.FilterException as e:
raise QueryValidationError(
diff --git a/ops/helm/nomad/deployments/prod-beta-values.yaml b/ops/helm/nomad/deployments/prod-beta-values.yaml
index da831e8a3ee1a50804cf39b01228ea06c1c9a236..14264485e30cbaa5c64a732388ad07af9319fff4 100644
--- a/ops/helm/nomad/deployments/prod-beta-values.yaml
+++ b/ops/helm/nomad/deployments/prod-beta-values.yaml
@@ -41,7 +41,7 @@ mongo:
logstash:
host: logstash.elk.svc.cluster.local
-dbname: fairdi_nomad_prod_v1
+dbname: nomad_prod_v1
uploadurl: 'http://nomad-lab.eu/prod/rae/beta/api/uploads'
diff --git a/ops/helm/nomad/deployments/prod-test-values.yaml b/ops/helm/nomad/deployments/prod-test-values.yaml
index 018f608b83aa552722a7ad7e3b0489e74e562155..8007eea1aea48780f03230e9741cded5273589bf 100644
--- a/ops/helm/nomad/deployments/prod-test-values.yaml
+++ b/ops/helm/nomad/deployments/prod-test-values.yaml
@@ -41,7 +41,7 @@ mongo:
logstash:
host: logstash.elk.svc.cluster.local
-dbname: fairdi_nomad_test_v1
+dbname: nomad_test_v1
uploadurl: 'http://nomad-lab.eu/prod/rae/test/api/uploads'
diff --git a/ops/helm/nomad/templates/nomad-configmap.yml b/ops/helm/nomad/templates/nomad-configmap.yml
index 3360af940082b6e58becf0dfd6a5b3a5351ce792..f13467eaa139491981fb0c62037d18bcb979e59c 100644
--- a/ops/helm/nomad/templates/nomad-configmap.yml
+++ b/ops/helm/nomad/templates/nomad-configmap.yml
@@ -48,8 +48,7 @@ data:
elastic:
host: "{{ .Values.elastic.host }}"
port: {{ .Values.elastic.port }}
- index_name: "{{ .Values.dbname }}_entries"
- materials_index_name: "{{ .Values.dbname }}_materials_v0"
+ entries_index: "{{ .Values.dbname }}_entries_v1"
materials_index: "{{ .Values.dbname }}_materials_v1"
mongo:
host: "{{ .Values.mongo.host }}"
diff --git a/tests/app/flask/test_dcat.py b/tests/app/flask/test_dcat.py
index 78bdbb1cc094332ab543d23a026039665f78f03c..f5878fde7afc06a7009fe759d09885fbc8d2a466 100644
--- a/tests/app/flask/test_dcat.py
+++ b/tests/app/flask/test_dcat.py
@@ -20,6 +20,7 @@ import pytest
from datetime import datetime
from nomad.app.flask.dcat.mapping import Mapping
+from nomad.datamodel.results import Material, Results
from tests.utils import ExampleData
@@ -53,11 +54,11 @@ def data(test_user, other_test_user, elastic_infra):
uploader=test_user,
coauthors=[other_test_user],
comment='this is a calculation comment',
- formula='H20',
published=True)
data = ExampleData()
- data.create_entry(**example_attrs)
+ archive = data.create_entry(**example_attrs)
+ archive.m_create(Results).m_create(Material).chemical_formula_descriptive = 'H2O'
for i in range(1, 11):
example_attrs.update(
diff --git a/tests/app/v1/routers/test_info.py b/tests/app/v1/routers/test_info.py
index 73007bb34e40aef157b7376b6b72435863c48f57..24035f424a7d90c8d9d22974d414c222215cee25 100644
--- a/tests/app/v1/routers/test_info.py
+++ b/tests/app/v1/routers/test_info.py
@@ -26,7 +26,6 @@ def test_info(client, elastic):
assert 'parsers' in data
assert 'statistics' in data
assert len(data['parsers']) >= len(data['codes'])
- assert len(data['domains']) >= 1
assert rv.status_code == 200
rv = client.get('info')
diff --git a/tests/normalizing/test_system.py b/tests/normalizing/test_system.py
index 8ffac7138dfafbbbbaa5e2b4efcbc11ab6bb225d..b3242ae7f3f881f4a23ccffc8fa88874e2d3f1e0 100644
--- a/tests/normalizing/test_system.py
+++ b/tests/normalizing/test_system.py
@@ -120,7 +120,7 @@ def assert_normalized(entry_archive: datamodel.EntryArchive):
metadata = entry_archive.metadata
results = entry_archive.results
- metadata.apply_domain_metadata(entry_archive)
+ metadata.apply_archvie_metadata(entry_archive)
parser_name = metadata.parser_name
exceptions = parser_exceptions.get(parser_name, [])
diff --git a/tests/processing/test_data.py b/tests/processing/test_data.py
index 545379959659d4099466183f5b3ed45607487771..299861f613a823dcb597a285a2dbb0b058582bf9 100644
--- a/tests/processing/test_data.py
+++ b/tests/processing/test_data.py
@@ -16,6 +16,7 @@
# limitations under the License.
#
+from nomad.datamodel.datamodel import EntryArchive
from typing import Generator, Tuple
import pytest
from datetime import datetime
@@ -128,9 +129,6 @@ def assert_processing(upload: Upload, published: bool = False, process='process_
# check some (domain) metadata
assert entry_metadata.quantities
assert len(entry_metadata.quantities) > 0
-
- assert entry_metadata.n_atoms > 0
- assert len(entry_metadata.atoms) > 0
assert len(entry_metadata.processing_errors) == 0
assert upload.get_calc(calc.calc_id) is not None
@@ -382,12 +380,14 @@ def test_re_processing(published: Upload, internal_example_user_metadata, monkey
# assert changed archive files
if with_failure == 'after':
- with published.upload_files.read_archive(first_calc.calc_id) as archive:
- assert list(archive[first_calc.calc_id].keys()) == ['processing_logs', 'metadata']
+ with published.upload_files.read_archive(first_calc.calc_id) as archive_reader:
+ assert list(archive_reader[first_calc.calc_id].keys()) == ['processing_logs', 'metadata']
+ archive = EntryArchive.m_from_dict(archive_reader[first_calc.calc_id].to_dict())
else:
- with published.upload_files.read_archive(first_calc.calc_id) as archive:
- assert len(archive[first_calc.calc_id]) > 2 # contains more then logs and metadata
+ with published.upload_files.read_archive(first_calc.calc_id) as archive_reader:
+ assert len(archive_reader[first_calc.calc_id]) > 2 # contains more then logs and metadata
+ archive = EntryArchive.m_from_dict(archive_reader[first_calc.calc_id].to_dict())
# assert maintained user metadata (mongo+es)
assert_upload_files(published.upload_id, entries, PublicUploadFiles, published=True)
@@ -395,14 +395,13 @@ def test_re_processing(published: Upload, internal_example_user_metadata, monkey
if with_failure not in ['after', 'not-matched']:
assert_processing(Upload.get(published.upload_id, include_published=True), published=True)
- # assert changed calc metadata (mongo)
- entry_metadata = first_calc.full_entry_metadata(published.upload_files)
+ # assert changed calc data
if with_failure not in ['after', 'not-matched']:
- assert entry_metadata.atoms[0] == 'H'
+ assert archive.results.material.elements[0] == 'H'
elif with_failure == 'not-matched':
- assert entry_metadata.atoms[0] == 'Si'
+ assert archive.results.material.elements[0] == 'Si'
else:
- assert entry_metadata.atoms == []
+ assert archive.results is None
@pytest.mark.parametrize('publish,old_staging', [
@@ -542,8 +541,6 @@ def test_process_failure(monkeypatch, uploaded, function, proc_infra, test_user,
with upload.upload_files.read_archive(calc.calc_id) as archive:
calc_archive = archive[calc.calc_id]
assert 'metadata' in calc_archive
- assert calc_archive['metadata']['dft']['code_name'] not in [
- config.services.unavailable_value, config.services.not_processed_value]
if function != 'cleanup':
assert len(calc_archive['metadata']['processing_errors']) > 0
assert 'processing_logs' in calc_archive
diff --git a/tests/test_datamodel.py b/tests/test_datamodel.py
index b27c972d357285d68ee51f80fc145e6485b360b1..7a64c26763bce6a23e6427db51fc7fc5296ba38a 100644
--- a/tests/test_datamodel.py
+++ b/tests/test_datamodel.py
@@ -23,8 +23,6 @@ A generator for random test calculations.
import random
from essential_generators import DocumentGenerator
import datetime
-from ase.data import chemical_symbols
-from ase.spacegroup import Spacegroup
from nomad import datamodel, utils
from nomad.parsing.parsers import parser_dict
@@ -95,24 +93,6 @@ def generate_calc(pid: int = 0, calc_id: str = None, upload_id: str = None, with
_gen_dataset()
for _ in range(0, random.choice(low_numbers_for_refs_and_datasets)))
- entry.atoms = list(random.choices(chemical_symbols[1:], k=random.choice(low_numbers_for_atoms)))
- entry.formula = ''.join('%s%d' % (atom, random.choice(low_numbers_for_atoms)) for atom in entry.atoms)
- entry.formula = entry.formula.replace('1', '')
-
- dft_metadata = entry.m_create(datamodel.DFTMetadata)
- dft_metadata.basis_set = random.choice(basis_sets)
- dft_metadata.xc_functional = random.choice(xc_functionals)
- dft_metadata.system = random.choice(systems)
- dft_metadata.crystal_system = random.choice(crystal_systems)
- spacegroup = random.randint(1, 225)
- dft_metadata.spacegroup = str(spacegroup)
- dft_metadata.spacegroup_symbol = Spacegroup(spacegroup).symbol
- dft_metadata.code_name = random.choice(codes)
- dft_metadata.code_version = '1.0.0'
-
- dft_metadata.n_total_energies = random.choice(range(0, 5))
- dft_metadata.geometries = ['%d' % random.randint(1, 500), '%d' % random.randint(1, 500)]
-
return entry
diff --git a/tests/utils.py b/tests/utils.py
index b003f7be58f97a5d893aa2e180dc4f439f1f6fd7..462a6c433c08aeb40862cafc3e81430bd8fb6094 100644
--- a/tests/utils.py
+++ b/tests/utils.py
@@ -27,7 +27,7 @@ import zipfile
import os.path
from nomad import search, files
-from nomad.datamodel import EntryMetadata, EntryArchive, DFTMetadata, Results
+from nomad.datamodel import EntryMetadata, EntryArchive, Results
from nomad.datamodel.metainfo.simulation.run import Run, Program
from nomad.datamodel.metainfo.simulation.system import System, Atoms
from tests.normalizing.conftest import run_normalize
@@ -260,7 +260,6 @@ class ExampleData:
material_id: str = None,
mainfile: str = None,
results: Union[Results, dict] = None,
- dft: Union[DFTMetadata, dict] = None,
archive: dict = None, **kwargs) -> EntryArchive:
if entry_id is None:
@@ -307,26 +306,6 @@ class ExampleData:
entry_metadata.m_update(**self.entry_defaults)
entry_metadata.m_update(**kwargs)
- # create v0 default data
- if entry_archive.metadata.dft is None:
- if dft is None:
- dft = {
- 'xc_functional': 'GGA',
- 'code_name': 'VASP',
- 'n_calculations': 1,
- 'atoms': ['H', 'O'],
- 'n_atoms': 2
- }
- if isinstance(dft, dict):
- for key in ['atoms', 'n_atoms']:
- if key in dft:
- setattr(entry_metadata, key, dft.pop(key))
- section_dft = DFTMetadata.m_from_dict(dft)
- else:
- section_dft = dft
- assert isinstance(section_dft, DFTMetadata)
- entry_metadata.m_add_sub_section(EntryMetadata.dft, section_dft)
-
# create v1 default data
if entry_archive.results is None:
if results is None:
@@ -426,7 +405,7 @@ class ExampleData:
run_normalize(archive)
entry_metadata = archive.metadata
entry_metadata.domain = 'dft'
- entry_metadata.apply_domain_metadata(archive)
+ entry_metadata.apply_archvie_metadata(archive)
if not optimade:
entry_metadata.optimade = None