diff --git a/dependencies/normalizers/simulation/band_structure b/dependencies/normalizers/simulation/band_structure
index 95f42793d8c8babb5b3503ef2b63e3d403a24e4e..9f52ea64d13a0fbc38d40608b34c6b5870fac6b0 160000
--- a/dependencies/normalizers/simulation/band_structure
+++ b/dependencies/normalizers/simulation/band_structure
@@ -1 +1 @@
-Subproject commit 95f42793d8c8babb5b3503ef2b63e3d403a24e4e
+Subproject commit 9f52ea64d13a0fbc38d40608b34c6b5870fac6b0
diff --git a/dependencies/normalizers/simulation/dos b/dependencies/normalizers/simulation/dos
index e47742260dc747b3a8ad00d3a3d5dbe223c125ba..545285f9826a1092015ac9283feafeb04bcbaaf4 160000
--- a/dependencies/normalizers/simulation/dos
+++ b/dependencies/normalizers/simulation/dos
@@ -1 +1 @@
-Subproject commit e47742260dc747b3a8ad00d3a3d5dbe223c125ba
+Subproject commit 545285f9826a1092015ac9283feafeb04bcbaaf4
diff --git a/dependencies/normalizers/simulation/soap b/dependencies/normalizers/simulation/soap
index 06800da2a4c6634dd843d1b66ae5cd5eae9ac9ad..bf413d1c6fcf322b91dd8ca71679ef97e22cc5bd 160000
--- a/dependencies/normalizers/simulation/soap
+++ b/dependencies/normalizers/simulation/soap
@@ -1 +1 @@
-Subproject commit 06800da2a4c6634dd843d1b66ae5cd5eae9ac9ad
+Subproject commit bf413d1c6fcf322b91dd8ca71679ef97e22cc5bd
diff --git a/dependencies/normalizers/simulation/spectra b/dependencies/normalizers/simulation/spectra
index 6e05a3b042c44c86b01cb6b635856c6d49b740f5..95e885fe74aec6b6ef57c255d5eacee1e2728a42 160000
--- a/dependencies/normalizers/simulation/spectra
+++ b/dependencies/normalizers/simulation/spectra
@@ -1 +1 @@
-Subproject commit 6e05a3b042c44c86b01cb6b635856c6d49b740f5
+Subproject commit 95e885fe74aec6b6ef57c255d5eacee1e2728a42
diff --git a/dependencies/normalizers/simulation/system b/dependencies/normalizers/simulation/system
index 7d078267f4a644e7c4ea87740669ea362c60775d..5ed4b3af700dff35e5717cffdf67c8d66df49519 160000
--- a/dependencies/normalizers/simulation/system
+++ b/dependencies/normalizers/simulation/system
@@ -1 +1 @@
-Subproject commit 7d078267f4a644e7c4ea87740669ea362c60775d
+Subproject commit 5ed4b3af700dff35e5717cffdf67c8d66df49519
diff --git a/dependencies/normalizers/simulation/workflow b/dependencies/normalizers/simulation/workflow
index 5ac17eba4a206112753a1fab7c7d548759492d59..dd5f1d2a2c48ed81d509a1a94ba41b18daa8a922 160000
--- a/dependencies/normalizers/simulation/workflow
+++ b/dependencies/normalizers/simulation/workflow
@@ -1 +1 @@
-Subproject commit 5ac17eba4a206112753a1fab7c7d548759492d59
+Subproject commit dd5f1d2a2c48ed81d509a1a94ba41b18daa8a922
diff --git a/gui/src/components/About.js b/gui/src/components/About.js
index 4cb4d3284273d4db83219947ce3b225b47f9540e..38e61b75346d052596c1def4dd00046fef1d7b2b 100644
--- a/gui/src/components/About.js
+++ b/gui/src/components/About.js
@@ -15,7 +15,7 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-import React, { useLayoutEffect, useRef, useCallback, useEffect, useState, useMemo } from 'react'
+import React, { useLayoutEffect, useRef, useCallback, useEffect, useState } from 'react'
import { ReactComponent as AboutSvg } from '../images/about.svg'
import PropTypes from 'prop-types'
import Markdown from './Markdown'
@@ -35,114 +35,9 @@ import {
Typography
} from '@material-ui/core'
import { Link as RouterLink, useHistory } from 'react-router-dom'
-import InputConfig from './search/input/InputConfig'
import { useInfo } from './api'
import { pluralize } from '../utils'
-/**
- * Displays an info dialog.
- */
-function InfoDialog({title, data, DialogProps, onClose}) {
- if (!data) return null
-
- return <Dialog maxWidth='md' fullWidth open={true} {...DialogProps}>
- <DialogTitle>{title}</DialogTitle>
- <DialogContent>
- <InputConfig data={data} format="YAML" readOnly/>
- </DialogContent>
- <DialogActions>
- <Button onClick={() => onClose?.()} color="primary">
- close
- </Button>
- </DialogActions>
- </Dialog>
-}
-InfoDialog.propTypes = {
- title: PropTypes.string,
- data: PropTypes.object,
- DialogProps: PropTypes.object,
- onClose: PropTypes.func
-}
-
-/**
- * Displays a list of information about the version, plugin package and plugin
- * entry points.
- */
-export const DistributionInfo = React.memo(({data}) => {
- const [selected, setSelected] = useState()
- const [title, setTitle] = useState()
-
- const categories = useMemo(() => {
- if (!data) return {}
-
- const categories = {}
- data.plugin_entry_points
- .forEach((entryPoint) => {
- let category = entryPoint.entry_point_type || entryPoint.plugin_type
- // TODO: Schema plugins are recategorized as package plugins. This can be
- // removed once all plugins have been migrated and we remove the old plugin
- // models.
- if (category === 'schema') {
- category = 'schema_package'
- }
- category = category.replace('_', ' ')
- if (categories[category]) {
- categories[category].push(entryPoint)
- } else {
- categories[category] = [entryPoint]
- }
- })
-
- Object.keys(categories).forEach(category => {
- categories[category] = categories[category].sort((a, b) => {
- const nameA = a.name
- const nameB = b.name
- return (nameA > nameB) ? 1 : -1
- })
- })
-
- return categories
- }, [data])
-
- return data
- ? <ul>
- <li>version: {data.version}</li>
- {data.plugin_packages
- ? <li>{"plugin packages: "}
- {data.plugin_packages.map(pluginPackage => <>
- <Link key={pluginPackage.name} href="#" onClick={() => {
- setSelected(pluginPackage)
- setTitle('Plugin package')
- }}>{pluginPackage.name}</Link>
- {", "}
- </>)}
- </li>
- : null
- }
- {Object.keys(categories)
- .sort()
- .map((category) => {
- const entryPoints = categories[category]
- return <li key={category}>
- {`${pluralize(category, 2)}: `}
- {entryPoints.map(entryPoint => <>
- <Link key={entryPoint.id} href="#" onClick={() => {
- setSelected(entryPoint)
- setTitle('Plugin entry point')
- }}>{entryPoint.id}</Link>
- {", "}
- </>)}
- </li>
- })}
- <InfoDialog title={title} data={selected} onClose={() => setSelected(null)} />
- </ul>
- : 'Loading...'
-})
-
-DistributionInfo.propTypes = {
- data: PropTypes.object
-}
-
function CodeInfo({code, ...props}) {
if (!code) {
return null
@@ -312,9 +207,6 @@ const useStyles = makeStyles(theme => ({
maxWidth: 1024,
margin: 'auto',
width: '100%'
- },
- header: {
- margin: '24px 0px'
}
}))
@@ -524,12 +416,13 @@ export default function About() {
with password \`password\`. The user \`sheldon.cooper@nomad-fairdi.tests.de\` is
used for data that has no provenance with the original NOMAD CoE database.
` : ''}
+
+ ### About this version
+ - version: \`${info ? info.version : 'loading'}\`
+ - parsers: ${info ? info.parsers.join(', ') : 'loading'}
+ - normalizers: ${info ? info.normalizers.join(', ') : 'loading'}
`}</Markdown>
</Grid>
- <Grid item xs={12}>
- <Typography variant='h5' className={classes.header}>About this distribution</Typography>
- <DistributionInfo data={info} />
- </Grid>
</Grid>
</div>
}
diff --git a/gui/src/components/nav/Routes.js b/gui/src/components/nav/Routes.js
index 2f2af38223feef9e390fcbff910bae24d56d92cd..abc69391b05cc4697850ed73b268f3851462e9e3 100644
--- a/gui/src/components/nav/Routes.js
+++ b/gui/src/components/nav/Routes.js
@@ -35,7 +35,7 @@ import APIs from '../APIs'
import SearchPage from '../search/SearchPage'
import { SearchContext } from '../search/SearchContext'
import NorthPage, {help as NORTHHelp} from '../north/NorthPage'
-import { aitoolkitEnabled, appBase, oasis, encyclopediaBase, ui, apps } from '../../config'
+import { aitoolkitEnabled, appBase, oasis, encyclopediaBase, ui } from '../../config'
import EntryQuery from '../entry/EntryQuery'
import ResolvePID from '../entry/ResolvePID'
import DatasetPage, { help as datasetHelp } from '../dataset/DatasetPage'
@@ -181,7 +181,7 @@ const toolkitRoute = (!oasis && aitoolkitEnabled)
tooltip: 'Visit the NOMAD Artificial Intelligence Analytics Toolkit'
}
-const searchRoutes = apps
+const searchRoutes = Object.values(ui?.apps?.options || {})
.map((context) => {
const routeMap = {
entries: entryRoutes
diff --git a/gui/src/components/search/input/InputConfig.js b/gui/src/components/search/input/InputConfig.js
index 8fa80536428341c93156edc30ec57c3f229c1918..c151c25c6cce6773e623c6f8a157a004aa204a09 100644
--- a/gui/src/components/search/input/InputConfig.js
+++ b/gui/src/components/search/input/InputConfig.js
@@ -25,7 +25,7 @@ import YAML from 'yaml'
/**
* Form used for editing a YAML or JSON config.
*/
-const InputConfig = React.memo(({data, format, maxRows, minRows, onChange, error, onError, readOnly}) => {
+const InputConfig = React.memo(({data, format, maxRows, minRows, onChange, error, onError}) => {
const controlledError = useRef(error !== undefined)
const [serialized, setSerialized] = useState()
const [errorInternal, setErrorInternal] = useState()
@@ -78,9 +78,6 @@ const InputConfig = React.memo(({data, format, maxRows, minRows, onChange, error
minRows={minRows}
value={serialized}
onChange={handleChange}
- InputProps={{
- readOnly: readOnly
- }}
/>
)
})
@@ -91,8 +88,7 @@ InputConfig.propTypes = {
minRows: PropTypes.number,
onChange: PropTypes.func,
error: PropTypes.string,
- onError: PropTypes.func,
- readOnly: PropTypes.bool
+ onError: PropTypes.func
}
InputConfig.defaultProps = {
diff --git a/gui/src/config.js b/gui/src/config.js
index 05fc3302f37238ab9ca8b715682ad50a4b33f87a..9219bc27b62552e78c600f033589f0c1807d4348 100644
--- a/gui/src/config.js
+++ b/gui/src/config.js
@@ -88,13 +88,6 @@ export const apiBase = `${appBase}/api`
export const northBase = urlAbs(window.nomadEnv.northBase)
export const guiBase = process.env.PUBLIC_URL
export const ui = normalizeConfig(window.nomadEnv.ui)
-export const entry_points = normalizeConfig(window.nomadEnv?.plugins?.entry_points)
-export const apps = Object.values(ui?.apps?.options || [])
-Object.values(entry_points?.options || [])
- .filter(entry_point => entry_point.entry_point_type === 'app')
- .forEach(entry_point => {
- apps.push(entry_point.app)
- })
export const servicesUploadLimit = window.nomadEnv.servicesUploadLimit
export const keycloakBase = window.nomadEnv.keycloakBase
export const keycloakRealm = window.nomadEnv.keycloakRealm
diff --git a/gui/src/utils.js b/gui/src/utils.js
index 9b3b46cb7b5d14aafeb1138de96f9b519cb4361e..c4305bfbebd2e40985616962a758942c342a0e52 100644
--- a/gui/src/utils.js
+++ b/gui/src/utils.js
@@ -825,11 +825,7 @@ export function pluralize(word, count, inclusive, format = true, prefix) {
'mainfile': 'mainfiles',
'folder': 'folders',
'has': 'have',
- 'activity': 'activities',
- 'parser': 'parsers',
- 'normalizer': 'normalizers',
- 'app': 'apps',
- 'package': 'packages'
+ 'activity': 'activities'
}
const words = word.trim().split(" ")
let lastWord = words[words.length - 1]
diff --git a/gui/tests/env.js b/gui/tests/env.js
index 65e35dc5bf93a41821aa50fc06f558eebab0c203..fd78f4ce95adbe6f8f68c6c35592e58aa0c657a5 100644
--- a/gui/tests/env.js
+++ b/gui/tests/env.js
@@ -3810,495 +3810,5 @@ window.nomadEnv = {
"enabled": true
},
"example_uploads": {}
- },
- "plugins": {
- "entry_points": {
- "include": [
- "schema/simulation/run",
- "schema/simulation/workflow",
- "parsers/vasp"
- ],
- "exclude": [],
- "options": {
- "normalizers/simulation/band_structure": {
- "plugin_type": "normalizer",
- "id": "normalizers/simulation/band_structure",
- "name": "bandstructurenormalizer",
- "description": "This is the normalizer for band structure in NOMAD.\n"
- },
- "normalizers/simulation/dos": {
- "plugin_type": "normalizer",
- "id": "normalizers/simulation/dos",
- "name": "dosnormalizer",
- "description": "This is the normalizer for DOS in NOMAD.\n"
- },
- "normalizers/simulation/soap": {
- "plugin_type": "normalizer",
- "id": "normalizers/simulation/soap",
- "name": "soapnormalizer",
- "description": "This is the normalizer for SOAP in NOMAD.\n"
- },
- "normalizers/simulation/spectra": {
- "plugin_type": "normalizer",
- "id": "normalizers/simulation/spectra",
- "name": "spectranormalizer",
- "description": "This is the normalizer for spectra in NOMAD.\n"
- },
- "normalizers/simulation/system": {
- "plugin_type": "normalizer",
- "id": "normalizers/simulation/system",
- "name": "systemnormalizer",
- "description": "This is the normalizer for system in NOMAD.\n"
- },
- "normalizers/simulation/workflow": {
- "plugin_type": "normalizer",
- "id": "normalizers/simulation/workflow",
- "name": "simulationworkflownormalizer",
- "description": "This is the normalizer for simulation workflows in NOMAD.\n"
- },
- "parsers/abacus": {
- "plugin_type": "parser",
- "id": "parsers/abacus",
- "name": "parsers/abacus",
- "plugin_source_code_url": "https://github.com/nomad-coe/electronic-parsers/tree/develop/electronicparsers/abacus"
- },
- "parsers/abinit": {
- "plugin_type": "parser",
- "id": "parsers/abinit",
- "name": "parsers/abinit",
- "plugin_source_code_url": "https://github.com/nomad-coe/electronic-parsers/tree/develop/electronicparsers/abinit"
- },
- "parsers/aflow": {
- "plugin_type": "parser",
- "id": "parsers/aflow",
- "name": "parsers/aflow",
- "plugin_source_code_url": "https://github.com/nomad-coe/workflow-parsers/tree/master/workflowparsers/aflow"
- },
- "parsers/amber": {
- "plugin_type": "parser",
- "id": "parsers/amber",
- "name": "parsers/amber",
- "plugin_source_code_url": "https://github.com/nomad-coe/atomistic-parsers/tree/develop/atomisticparsers/amber"
- },
- "parsers/ams": {
- "plugin_type": "parser",
- "id": "parsers/ams",
- "name": "parsers/ams",
- "plugin_source_code_url": "https://github.com/nomad-coe/electronic-parsers/tree/develop/electronicparsers/ams"
- },
- "parsers/asap": {
- "plugin_type": "parser",
- "id": "parsers/asap",
- "name": "parsers/asap",
- "plugin_source_code_url": "https://github.com/nomad-coe/atomistic-parsers/tree/develop/atomisticparsers/asap"
- },
- "parsers/asr": {
- "plugin_type": "parser",
- "id": "parsers/asr",
- "name": "parsers/asr",
- "plugin_source_code_url": "https://github.com/nomad-coe/workflow-parsers/tree/master/workflowparsers/asr"
- },
- "parsers/atk": {
- "plugin_type": "parser",
- "id": "parsers/atk",
- "name": "parsers/atk",
- "plugin_source_code_url": "https://github.com/nomad-coe/electronic-parsers/tree/develop/electronicparsers/atk"
- },
- "parsers/atomate": {
- "plugin_type": "parser",
- "id": "parsers/atomate",
- "name": "parsers/atomate",
- "plugin_source_code_url": "https://github.com/nomad-coe/workflow-parsers/tree/master/workflowparsers/automate"
- },
- "parsers/bigdft": {
- "plugin_type": "parser",
- "id": "parsers/bigdft",
- "name": "parsers/bigdft",
- "plugin_source_code_url": "https://github.com/nomad-coe/electronic-parsers/tree/develop/electronicparsers/bigdft"
- },
- "parsers/bopfox": {
- "plugin_type": "parser",
- "id": "parsers/bopfox",
- "name": "parsers/bopfox",
- "plugin_source_code_url": "https://github.com/nomad-coe/atomistic-parsers/tree/develop/atomisticparsers/bobfox"
- },
- "parsers/castep": {
- "plugin_type": "parser",
- "id": "parsers/castep",
- "name": "parsers/castep",
- "plugin_source_code_url": "https://github.com/nomad-coe/electronic-parsers/tree/develop/electronicparsers/castep"
- },
- "parsers/charmm": {
- "plugin_type": "parser",
- "id": "parsers/charmm",
- "name": "parsers/charmm",
- "plugin_source_code_url": "https://github.com/nomad-coe/electronic-parsers/tree/develop/electronicparsers/charmm"
- },
- "parsers/chemotion/chemotion": {
- "plugin_type": "parser",
- "id": "parsers/chemotion/chemotion",
- "name": "parsers/chemotion"
- },
- "parsers/cp2k": {
- "plugin_type": "parser",
- "id": "parsers/cp2k",
- "name": "parsers/cp2k",
- "plugin_source_code_url": "https://github.com/nomad-coe/electronic-parsers/tree/develop/electronicparsers/cp2k"
- },
- "parsers/cpmd": {
- "plugin_type": "parser",
- "id": "parsers/cpmd",
- "name": "parsers/cpmd",
- "plugin_source_code_url": "https://github.com/nomad-coe/electronic-parsers/tree/develop/electronicparsers/cpmd"
- },
- "parsers/crystal": {
- "plugin_type": "parser",
- "id": "parsers/crystal",
- "name": "parsers/crystal",
- "plugin_source_code_url": "https://github.com/nomad-coe/electronic-parsers/tree/develop/electronicparsers/crystal"
- },
- "parsers/dftbplus": {
- "plugin_type": "parser",
- "id": "parsers/dftbplus",
- "name": "parsers/dftbplus",
- "plugin_source_code_url": "https://github.com/nomad-coe/atomistic-parsers/tree/develop/atomisticparsers/dftplus"
- },
- "parsers/dlpoly": {
- "plugin_type": "parser",
- "id": "parsers/dlpoly",
- "name": "parsers/dl-poly",
- "plugin_source_code_url": "https://github.com/nomad-coe/atomistic-parsers/tree/develop/atomisticparsers/dlpoly"
- },
- "parsers/dmol3": {
- "plugin_type": "parser",
- "id": "parsers/dmol3",
- "name": "parsers/dmol",
- "plugin_source_code_url": "https://github.com/nomad-coe/electronic-parsers/tree/develop/electronicparsers/dmol3"
- },
- "parsers/edmft": {
- "plugin_type": "parser",
- "id": "parsers/edmft",
- "name": "parsers/edmft",
- "plugin_source_code_url": "https://github.com/nomad-coe/electronic-parsers/tree/develop/electronicparsers/edmft"
- },
- "parsers/eelsdbparser": {
- "plugin_type": "parser",
- "id": "parsers/eelsdbparser",
- "name": "parsers/eels",
- "plugin_source_code_url": "https://github.com/nomad-coe/nomad-parser-eelsdb"
- },
- "parsers/elabftw/elabftw": {
- "plugin_type": "parser",
- "id": "parsers/elabftw/elabftw",
- "name": "parsers/elabftw",
- "plugin_source_code_url": "https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/tree/develop/nomad/parsing/elabftw"
- },
- "parsers/elastic": {
- "plugin_type": "parser",
- "id": "parsers/elastic",
- "name": "parsers/elastic",
- "plugin_source_code_url": "https://github.com/nomad-coe/workflow-parsers/tree/master/workflowparsers/elastic"
- },
- "parsers/elk": {
- "plugin_type": "parser",
- "id": "parsers/elk",
- "name": "parsers/elk",
- "plugin_source_code_url": "https://github.com/nomad-coe/electronic-parsers/tree/develop/electronicparsers/elk"
- },
- "parsers/exciting": {
- "plugin_type": "parser",
- "id": "parsers/exciting",
- "name": "parsers/exciting",
- "plugin_source_code_url": "https://github.com/nomad-coe/electronic-parsers/tree/develop/electronicparsers/exciting"
- },
- "parsers/fhi-aims": {
- "plugin_type": "parser",
- "id": "parsers/fhi-aims",
- "name": "parsers/fhi-aims",
- "plugin_source_code_url": "https://github.com/nomad-coe/electronic-parsers/tree/develop/electronicparsers/fhiaims"
- },
- "parsers/fhivibes": {
- "plugin_type": "parser",
- "id": "parsers/fhivibes",
- "name": "parsers/fhi-vibes",
- "plugin_source_code_url": "https://github.com/nomad-coe/workflow-parsers/tree/master/workflowparsers/fhivibes"
- },
- "parsers/fleur": {
- "plugin_type": "parser",
- "id": "parsers/fleur",
- "name": "parsers/fleur",
- "plugin_source_code_url": "https://github.com/nomad-coe/electronic-parsers/tree/develop/electronicparsers/fleur"
- },
- "parsers/fplo": {
- "plugin_type": "parser",
- "id": "parsers/fplo",
- "name": "parsers/fplo",
- "plugin_source_code_url": "https://github.com/nomad-coe/electronic-parsers/tree/develop/electronicparsers/fplo"
- },
- "parsers/gamess": {
- "plugin_type": "parser",
- "id": "parsers/gamess",
- "name": "parsers/gamess",
- "plugin_source_code_url": "https://github.com/nomad-coe/electronic-parsers/tree/develop/electronicparsers/gamess"
- },
- "parsers/gaussian": {
- "plugin_type": "parser",
- "id": "parsers/gaussian",
- "name": "parsers/gaussian",
- "plugin_source_code_url": "https://github.com/nomad-coe/electronic-parsers/tree/develop/electronicparsers/gaussian"
- },
- "parsers/gpaw": {
- "plugin_type": "parser",
- "id": "parsers/gpaw",
- "name": "parsers/gpaw",
- "plugin_source_code_url": "https://github.com/nomad-coe/electronic-parsers/tree/develop/electronicparsers/gpaw"
- },
- "parsers/gromacs": {
- "plugin_type": "parser",
- "id": "parsers/gromacs",
- "name": "parsers/gromacs",
- "plugin_source_code_url": "https://github.com/nomad-coe/atomistic-parsers/tree/develop/atomisticparsers/gromacs"
- },
- "parsers/gromos": {
- "plugin_type": "parser",
- "id": "parsers/gromos",
- "name": "parsers/gromos",
- "plugin_source_code_url": "https://github.com/nomad-coe/atomistic-parsers/tree/develop/atomisticparsers/gromos"
- },
- "parsers/gulp": {
- "plugin_type": "parser",
- "id": "parsers/gulp",
- "name": "parsers/gulp",
- "plugin_source_code_url": "https://github.com/nomad-coe/atomistic-parsers/tree/develop/atomisticparsers/gulp"
- },
- "parsers/h5md": {
- "plugin_type": "parser",
- "id": "parsers/h5md",
- "name": "parsers/h5md"
- },
- "parsers/lammps": {
- "plugin_type": "parser",
- "id": "parsers/lammps",
- "name": "parsers/lammps",
- "plugin_source_code_url": "https://github.com/nomad-coe/atomistic-parsers/tree/develop/atomisticparsers/lammps"
- },
- "parsers/libatoms": {
- "plugin_type": "parser",
- "id": "parsers/libatoms",
- "name": "parsers/lib-atoms",
- "plugin_source_code_url": "https://github.com/nomad-coe/atomistic-parsers/tree/develop/atomisticparsers/libatoms"
- },
- "parsers/lobster": {
- "plugin_type": "parser",
- "id": "parsers/lobster",
- "name": "parsers/lobster",
- "plugin_source_code_url": "https://github.com/nomad-coe/workflow-parsers/tree/master/workflowparsers/lobster"
- },
- "parsers/magres": {
- "plugin_type": "parser",
- "id": "parsers/magres",
- "name": "parsers/magres",
- "plugin_source_code_url": "https://github.com/nomad-coe/electronic-parsers/tree/develop/electronicparsers/magres"
- },
- "parsers/molcas": {
- "plugin_type": "parser",
- "id": "parsers/molcas",
- "name": "parsers/molcas",
- "plugin_source_code_url": "https://github.com/nomad-coe/electronic-parsers/tree/develop/electronicparsers/molcas"
- },
- "parsers/mopac": {
- "plugin_type": "parser",
- "id": "parsers/mopac",
- "name": "parsers/mopac",
- "plugin_source_code_url": "https://github.com/nomad-coe/electronic-parsers/tree/develop/electronicparsers/mopac"
- },
- "parsers/namd": {
- "plugin_type": "parser",
- "id": "parsers/namd",
- "name": "parsers/namd",
- "plugin_source_code_url": "https://github.com/nomad-coe/atomistic-parsers/tree/develop/atomisticparsers/namd"
- },
- "parsers/nexus": {
- "plugin_type": "parser",
- "id": "parsers/nexus",
- "name": "parsers/nexus",
- "plugin_source_code_url": "https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/tree/develop/nomad/parsing/nexus"
- },
- "parsers/nwchem": {
- "plugin_type": "parser",
- "id": "parsers/nwchem",
- "name": "parsers/nwchem",
- "plugin_source_code_url": "https://github.com/nomad-coe/electronic-parsers/tree/develop/electronicparsers/nwchem"
- },
- "parsers/ocean": {
- "plugin_type": "parser",
- "id": "parsers/ocean",
- "name": "parsers/ocean",
- "plugin_source_code_url": "https://github.com/nomad-coe/electronic-parsers/tree/develop/electronicparsers/ocean"
- },
- "parsers/octopus": {
- "plugin_type": "parser",
- "id": "parsers/octopus",
- "name": "parsers/octopus",
- "plugin_source_code_url": "https://github.com/nomad-coe/electronic-parsers/tree/develop/electronicparsers/octopus"
- },
- "parsers/onetep": {
- "plugin_type": "parser",
- "id": "parsers/onetep",
- "name": "parsers/onetep",
- "plugin_source_code_url": "https://github.com/nomad-coe/electronic-parsers/tree/develop/electronicparsers/onetep"
- },
- "parsers/openkim": {
- "plugin_type": "parser",
- "id": "parsers/openkim",
- "name": "parsers/openkim",
- "plugin_source_code_url": "https://github.com/nomad-coe/electronic-parsers/tree/develop/databaseparsers/openkim"
- },
- "parsers/openmx": {
- "plugin_type": "parser",
- "id": "parsers/openmx",
- "name": "parsers/openmx",
- "plugin_source_code_url": "https://github.com/nomad-coe/electronic-parsers/tree/develop/electronicparsers/openmx"
- },
- "parsers/orca": {
- "plugin_type": "parser",
- "id": "parsers/orca",
- "name": "parsers/orca",
- "plugin_source_code_url": "https://github.com/nomad-coe/electronic-parsers/tree/develop/electronicparsers/orca"
- },
- "parsers/phonopy": {
- "plugin_type": "parser",
- "id": "parsers/phonopy",
- "name": "parsers/phonopy",
- "plugin_source_code_url": "https://github.com/nomad-coe/workflow-parsers/tree/master/workflowparsers/phonopy"
- },
- "parsers/psi4": {
- "plugin_type": "parser",
- "id": "parsers/psi4",
- "name": "parsers/psi4",
- "plugin_source_code_url": "https://github.com/nomad-coe/electronic-parsers/tree/develop/electronicparsers/psi4"
- },
- "parsers/qball": {
- "plugin_type": "parser",
- "id": "parsers/qball",
- "name": "parsers/qball",
- "plugin_source_code_url": "https://github.com/nomad-coe/electronic-parsers/tree/develop/electronicparsers/qball"
- },
- "parsers/qbox": {
- "plugin_type": "parser",
- "id": "parsers/qbox",
- "name": "parsers/qbox",
- "plugin_source_code_url": "https://github.com/nomad-coe/electronic-parsers/tree/develop/electronicparsers/qbox"
- },
- "parsers/quantum_espresso_epw": {
- "plugin_type": "parser",
- "id": "parsers/quantum_espresso_epw",
- "name": "parsers/quantumespressoepw",
- "plugin_source_code_url": "https://github.com/nomad-coe/workflow-parsers/tree/master/workflowparsers/quantum_espresso_epw"
- },
- "parsers/quantum_espresso_phonon": {
- "plugin_type": "parser",
- "id": "parsers/quantum_espresso_phonon",
- "name": "parsers/quantumespressophonon",
- "plugin_source_code_url": "https://github.com/nomad-coe/workflow-parsers/tree/master/workflowparsers/quantum_espresso_phonon"
- },
- "parsers/quantum_espresso_xspectra": {
- "plugin_type": "parser",
- "id": "parsers/quantum_espresso_xspectra",
- "name": "parsers/quantumespressoxspectra",
- "plugin_source_code_url": "https://github.com/nomad-coe/workflow-parsers/tree/master/workflowparsers/quantum_espresso_xpectra"
- },
- "parsers/quantumespresso": {
- "plugin_type": "parser",
- "id": "parsers/quantumespresso",
- "name": "parsers/quantumespresso",
- "plugin_source_code_url": "https://github.com/nomad-coe/electronic-parsers/tree/develop/electronicparsers/quantumespresso"
- },
- "parsers/siesta": {
- "plugin_type": "parser",
- "id": "parsers/siesta",
- "name": "parsers/siesta",
- "plugin_source_code_url": "https://github.com/nomad-coe/electronic-parsers/tree/develop/electronicparsers/siesta"
- },
- "parsers/soliddmft": {
- "plugin_type": "parser",
- "id": "parsers/soliddmft",
- "name": "parsers/soliddmft",
- "plugin_source_code_url": "https://github.com/nomad-coe/electronic-parsers/tree/develop/electronicparsers/soliddmft"
- },
- "parsers/tbstudio": {
- "plugin_type": "parser",
- "id": "parsers/tbstudio",
- "name": "parsers/tbstudio"
- },
- "parsers/tinker": {
- "plugin_type": "parser",
- "id": "parsers/tinker",
- "name": "parsers/tinker",
- "plugin_source_code_url": "https://github.com/nomad-coe/atomistic-parsers/tree/develop/atomisticparsers/tinker"
- },
- "parsers/turbomole": {
- "plugin_type": "parser",
- "id": "parsers/turbomole",
- "name": "parsers/turbomole",
- "plugin_source_code_url": "https://github.com/nomad-coe/electronic-parsers/tree/develop/electronicparsers/turbomole"
- },
- "parsers/vasp": {
- "plugin_type": "parser",
- "id": "parsers/vasp",
- "name": "parsers/vasp",
- "plugin_source_code_url": "https://github.com/nomad-coe/electronic-parsers/tree/develop/electronicparsers/vasp"
- },
- "parsers/w2dynamics": {
- "plugin_type": "parser",
- "id": "parsers/w2dynamics",
- "name": "parsers/w2dynamics",
- "plugin_source_code_url": "https://github.com/nomad-coe/electronic-parsers/tree/develop/electronicparsers/w2dynamics"
- },
- "parsers/wannier90": {
- "plugin_type": "parser",
- "id": "parsers/wannier90",
- "name": "parsers/wannier90",
- "plugin_source_code_url": "https://github.com/nomad-coe/electronic-parsers/tree/develop/electronicparsers/wannier90"
- },
- "parsers/wien2k": {
- "plugin_type": "parser",
- "id": "parsers/wien2k",
- "name": "parsers/wien2k",
- "plugin_source_code_url": "https://github.com/nomad-coe/electronic-parsers/tree/develop/electronicparsers/wien2k"
- },
- "parsers/xtb": {
- "plugin_type": "parser",
- "id": "parsers/xtb",
- "name": "parsers/xtb",
- "plugin_source_code_url": "https://github.com/nomad-coe/atomistic-parsers/tree/develop/atomisticparsers/xtb"
- },
- "parsers/yambo": {
- "plugin_type": "parser",
- "id": "parsers/yambo",
- "name": "parsers/yambo",
- "plugin_source_code_url": "https://github.com/nomad-coe/electronic-parsers/tree/develop/electronicparsers/yambo"
- },
- "schema/nomad-perovskite-solar-cells-database/perovskite_solar_cell_database": {
- "plugin_type": "schema",
- "id": "schema/nomad-perovskite-solar-cells-database/perovskite_solar_cell_database",
- "name": "perovskite_solar_cell_database",
- "description": "A NOMAD plugin containing the schema for the Perovskite Solar Cell Database."
- },
- "schema/simulation/run": {
- "plugin_type": "schema",
- "id": "schema/simulation/run",
- "name": "runschema",
- "description": "Run schema plugin for NOMAD.\n"
- },
- "schema/simulation/workflow": {
- "plugin_type": "schema",
- "id": "schema/simulation/workflow",
- "name": "simulationworkflowschema",
- "description": "This is a collection of schemas for various types of simulation workflows.\n"
- }
- }
- },
- "plugin_packages": {}
}
}
diff --git a/nomad/app/v1/routers/info.py b/nomad/app/v1/routers/info.py
index a44825ecc92ce1d070f717939266b1325b3c34cc..2ded9bafd99323954d4fe2440727462763a064ed 100644
--- a/nomad/app/v1/routers/info.py
+++ b/nomad/app/v1/routers/info.py
@@ -89,14 +89,6 @@ class InfoModel(BaseModel):
metainfo_packages: List[str]
codes: List[CodeInfoModel]
normalizers: List[str]
- plugin_entry_points: List[dict] = Field(
- None,
- desciption='List of plugin entry points that are activated in this deployment.',
- )
- plugin_packages: List[dict] = Field(
- None,
- desciption='List of plugin packages that are installed in this deployment.',
- )
statistics: StatisticsModel = Field(None, description='General NOMAD statistics')
search_quantities: dict
version: str
@@ -160,9 +152,6 @@ async def get_info():
parser_names = sorted(
[re.sub(r'^(parsers?|missing)/', '', key) for key in parsers.parser_dict.keys()]
)
-
- config.load_plugins()
-
return InfoModel(
**{
'parsers': parser_names,
@@ -186,14 +175,6 @@ async def get_info():
'normalizers': [
normalizer.__name__ for normalizer in normalizing.normalizers
],
- 'plugin_entry_points': [
- entry_point.dict_safe()
- for entry_point in config.plugins.entry_points.filtered_values()
- ],
- 'plugin_packages': [
- plugin_package.dict()
- for plugin_package in config.plugins.plugin_packages.values()
- ],
'statistics': statistics(),
'search_quantities': {
s.qualified_name: {
diff --git a/nomad/cli/dev.py b/nomad/cli/dev.py
index 3d6baf264c33ecbba15e9346edfd1110b160f34e..435008cb5202117871470bd188a4b6fe84a67c30 100644
--- a/nomad/cli/dev.py
+++ b/nomad/cli/dev.py
@@ -216,13 +216,6 @@ def get_gui_config() -> str:
"""
from nomad.config import config
- config.load_plugins()
- plugins = config.plugins.dict(exclude_unset=True)
- for key in plugins['entry_points']['options'].keys():
- plugins['entry_points']['options'][key] = config.plugins.entry_points.options[
- key
- ].dict_safe()
-
data = {
'appBase': config.ui.app_base,
'northBase': config.ui.north_base,
@@ -240,7 +233,6 @@ def get_gui_config() -> str:
'servicesUploadLimit': config.services.upload_limit,
'appTokenMaxExpiresIn': config.services.app_token_max_expires_in,
'ui': config.ui.dict(exclude_none=True) if config.ui else {},
- 'plugins': plugins,
}
return f'window.nomadEnv = {json.dumps(data, indent=2)}'
diff --git a/nomad/config/__init__.py b/nomad/config/__init__.py
index c1851e85b2d19550a32be7c242f2af3c9aab2729..e274b5069784f406cbbea26f7a07e5041c60c266 100644
--- a/nomad/config/__init__.py
+++ b/nomad/config/__init__.py
@@ -117,8 +117,7 @@ def _merge(*args) -> Dict[str, Any]:
root = args[0]
for config in args[1:]:
- if config:
- root = merge_dicts(root, config)
+ root = merge_dicts(root, config)
return root
diff --git a/nomad/config/models/config.py b/nomad/config/models/config.py
index 71e2239af4e6488f08faaa8a1410b20253183485..d82252db45ed87f4b20c7bf7c37c4d8f9aeaa41c 100644
--- a/nomad/config/models/config.py
+++ b/nomad/config/models/config.py
@@ -17,14 +17,13 @@
#
import warnings
-import sys
import os
import logging
-from importlib.metadata import version, metadata
+from importlib.metadata import version
import yaml
from typing import List, Union, Optional, Dict, Any
-from pydantic import Field, root_validator, validator
+from pydantic import Field, root_validator, validator, parse_obj_as
import pkgutil
try:
@@ -33,17 +32,11 @@ except Exception: # noqa
# package is not installed
pass
-if sys.version_info < (3, 10):
- from importlib_metadata import entry_points
-else:
- from importlib.metadata import entry_points
-
-
from .common import (
ConfigBaseModel,
Options,
)
-from .plugins import Plugins, EntryPointType, PluginPackage
+from .plugins import Plugins
from .north import NORTH
from .ui import UI
@@ -1008,24 +1001,6 @@ class Config(ConfigBaseModel):
return values
- def get_plugin_entry_point(self, id: str) -> EntryPointType:
- """Returns the plugin entry point with the given id. It will
- contain also any overrides included through nomad.yaml.
-
- Args:
- id: The entry point identifier. Use the identifier given in the
- plugin package pyproject.toml.
- """
- try:
- return self.plugins.entry_points.options[id]
- except KeyError:
- raise KeyError(
- f'Could not find plugin entry point with id "{id}". Make sure that '
- 'the plugin package with an up-to-date pyproject.toml is installed and '
- 'that you are using the entry point id given in the plugin '
- 'pyproject.toml'
- )
-
def load_plugins(self):
"""Used to lazy-load the plugins. We cannot instantiate the plugins
during the initialization of the nomad.config package, because it may
@@ -1038,85 +1013,38 @@ class Config(ConfigBaseModel):
cached_property decorator to the 'plugins' field instead of using this
function.
"""
- from nomad.config import _plugins, _merge
- from nomad.config.models.plugins import Parser, Normalizer, Schema
-
if self.plugins is None:
- # Any plugins defined at the 'plugin' level are lifted to the
- # 'plugin.entry_points'.
- entry_points_config = _plugins.setdefault('entry_points', {})
- include_old = _plugins.get('include')
- include_new = entry_points_config.get('include')
- if include_old is not None:
- if include_new is None:
- entry_points_config['include'] = include_old
- else:
- entry_points_config['include'].extend(include_old)
- entry_points_config.setdefault('exclude', []).extend(
- _plugins.get('exclude', [])
- )
- entry_points_config.setdefault('options', {}).update(
- _plugins.get('options', {})
- )
+ from nomad.config import _plugins
+ from nomad.config.models.plugins import Plugin
- # Handle plugin entry_points (new plugin mechanism)
- plugin_entry_point_ids = set()
- plugin_entry_points = entry_points(group='nomad.plugin')
- plugin_packages = {}
-
- for entry_point in plugin_entry_points:
- key = entry_point.value
- if key in plugin_entry_point_ids:
- raise ValueError(
- f'Could not load plugins due to duplicate entry_point name: "{key}".'
- )
- package_name = entry_point.value.split('.', 1)[0]
- config_override = (
- _plugins.get('entry_points', {}).get('options', {}).get(key, {})
- )
- config_override['id'] = key
- config_instance = entry_point.load()
- package_metadata = metadata(package_name)
- url_list = package_metadata.get_all('Project-URL')
- url_dict = {}
- for url in url_list:
- name, value = url.split(',')
- url_dict[name.lower()] = value.strip()
- if package_name not in plugin_packages:
- plugin_package = PluginPackage(
- name=package_name,
- description=package_metadata.get('Summary'),
- version=version(package_name),
- homepage=url_dict.get('homepage'),
- documentation=url_dict.get('documentation'),
- repository=url_dict.get('repository'),
- entry_points=[key],
- )
- plugin_packages[package_name] = plugin_package
- else:
- plugin_packages[package_name].entry_points.append(key)
- config_default = config_instance.dict(exclude_unset=True)
- config_default['plugin_package'] = package_name
- config_class = config_instance.__class__
- config_final = config_class.parse_obj(
- _merge(config_default, config_override)
- )
- _plugins['entry_points']['options'][key] = config_final
- plugin_entry_point_ids.add(key)
- _plugins['plugin_packages'] = plugin_packages
-
- # Handle plugins defined in nomad.yaml (old plugin mechanism)
- def load_plugin_yaml(name, values: Dict[str, Any]):
+ def load_plugin(values: Dict[str, Any]):
"""Loads plugin metadata from nomad_plugin.yaml"""
python_package = values.get('python_package')
if not python_package:
- raise ValueError(
- f'Could not find python_package for plugin entry point: {name}.'
- )
+ raise ValueError('Python plugins must provide a python_package.')
package_path = values.get('package_path')
if package_path is None:
- package_path = get_package_path(python_package)
+ try:
+ # We try to deduce the package path from the top-level package
+ package_path_segments = python_package.split('.')
+ root_package = package_path_segments[0]
+ package_dirs = package_path_segments[1:]
+ package_path = os.path.join(
+ os.path.dirname(
+ pkgutil.get_loader(root_package).get_filename() # type: ignore
+ ),
+ *package_dirs,
+ )
+ if not os.path.isdir(package_path):
+ # We could not find it this way. Let's try to official way
+ package_path = os.path.dirname(
+ pkgutil.get_loader(python_package).get_filename() # type: ignore
+ )
+ except Exception as e:
+ raise ValueError(
+ f'The python package {python_package} cannot be loaded.', e
+ )
values['package_path'] = package_path
metadata_path = os.path.join(package_path, 'nomad_plugin.yaml')
@@ -1136,41 +1064,5 @@ class Config(ConfigBaseModel):
return values
for key, plugin in _plugins['options'].items():
- if key not in plugin_entry_point_ids:
- plugin_config = load_plugin_yaml(key, plugin)
- plugin_config['id'] = key
- plugin_class = {
- 'parser': Parser,
- 'normalizer': Normalizer,
- 'schema': Schema,
- }.get(plugin_config['plugin_type'])
- _plugins['entry_points']['options'][key] = plugin_class.parse_obj(
- plugin_config
- )
-
+ _plugins['options'][key] = parse_obj_as(Plugin, load_plugin(plugin))
self.plugins = Plugins.parse_obj(_plugins)
-
-
-def get_package_path(package_name: str) -> str:
- """Given a python package name, returns the filepath of the package root folder."""
- package_path = None
- try:
- # We try to deduce the package path from the top-level package
- package_path_segments = package_name.split('.')
- root_package = package_path_segments[0]
- package_dirs = package_path_segments[1:]
- package_path = os.path.join(
- os.path.dirname(
- pkgutil.get_loader(root_package).get_filename() # type: ignore
- ),
- *package_dirs,
- )
- if not os.path.isdir(package_path):
- # We could not find it this way. Let's try to official way
- package_path = os.path.dirname(
- pkgutil.get_loader(python_package).get_filename() # type: ignore
- )
- except Exception as e:
- raise ValueError(f'The python package {package_name} cannot be loaded.', e)
-
- return package_path
diff --git a/nomad/config/models/plugins.py b/nomad/config/models/plugins.py
index d81126bde307d25ddb7927f14786760fb9f46b87..e4797fe8b5247972cf603cebafdd7d82fca9a0a3 100644
--- a/nomad/config/models/plugins.py
+++ b/nomad/config/models/plugins.py
@@ -17,154 +17,12 @@
#
import sys
-from abc import ABCMeta, abstractmethod
import importlib
-from typing import Optional, Dict, Union, List, Literal, TYPE_CHECKING
+from typing_extensions import Annotated
+from typing import Optional, Dict, Union, List, Literal
from pydantic import BaseModel, Field
from .common import Options
-from .ui import App
-
-if TYPE_CHECKING:
- from nomad.metainfo import SchemaPackage
- from nomad.normalizing import Normalizer as NormalizerBaseClass
- from nomad.parsing import Parser as ParserBaseClass
-
-
-class EntryPoint(BaseModel):
- """Base model for a NOMAD plugin entry points."""
-
- id: Optional[str] = Field(
- description='Unique identifier corresponding to the entry point name. Automatically set to the plugin entry point name in pyproject.toml.'
- )
- entry_point_type: str = Field(description='Determines the entry point type.')
- name: Optional[str] = Field(description='Name of the plugin entry point.')
- description: Optional[str] = Field(
- description='A human readable description of the plugin entry point.'
- )
- plugin_package: Optional[str] = Field(
- description='The plugin package from which this entry points comes from.'
- )
-
- def dict_safe(self):
- """Used to serialize the non-confidential parts of a plugin model. This
- function can be overridden in subclasses to expose more information.
- """
- return self.dict(include=EntryPoint.__fields__.keys(), exclude_none=True)
-
-
-class AppEntryPoint(EntryPoint):
- entry_point_type: Literal['app'] = Field(
- 'app', description='Determines the entry point type.'
- )
- app: App = Field(description='The app configuration.')
-
- def dict_safe(self):
- return self.dict(include=AppEntryPoint.__fields__.keys(), exclude_none=True)
-
-
-class SchemaPackageEntryPoint(EntryPoint, metaclass=ABCMeta):
- entry_point_type: Literal['schema_package'] = Field(
- 'schema_package', description='Specifies the entry point type.'
- )
-
- @abstractmethod
- def load(self) -> 'SchemaPackage':
- """Used to lazy-load a schema package instance. You should override this
- method in your subclass. Note that any Python module imports required
- for the schema package should be done within this function as well."""
- pass
-
-
-class NormalizerEntryPoint(EntryPoint, metaclass=ABCMeta):
- entry_point_type: Literal['normalizer'] = Field(
- 'normalizer', description='Determines the entry point type.'
- )
-
- @abstractmethod
- def load(self) -> 'NormalizerBaseClass':
- """Used to lazy-load a normalizer instance. You should override this
- method in your subclass. Note that any Python module imports required
- for the normalizer class should be done within this function as well."""
- pass
-
-
-class ParserEntryPoint(EntryPoint, metaclass=ABCMeta):
- entry_point_type: Literal['parser'] = Field(
- 'parser', description='Determines the entry point type.'
- )
- level: int = Field(
- 0,
- description="""
- The order by which the parser is executed with respect to other parsers.
- """,
- )
-
- mainfile_contents_re: Optional[str] = Field(
- description="""
- A regular expression that is applied the content of a potential mainfile.
- If this expression is given, the parser is only considered for a file, if the
- expression matches.
- """
- )
- mainfile_name_re: str = Field(
- r'.*',
- description="""
- A regular expression that is applied the name of a potential mainfile.
- If this expression is given, the parser is only considered for a file, if the
- expression matches.
- """,
- )
- mainfile_mime_re: str = Field(
- r'.*',
- description="""
- A regular expression that is applied the mime type of a potential
- mainfile. If this expression is given, the parser is only considered
- for a file, if the expression matches.
- """,
- )
- mainfile_binary_header: Optional[bytes] = Field(
- description="""
- Matches a binary file if the given bytes are included in the file.
- """,
- exclude=True,
- )
- mainfile_binary_header_re: Optional[bytes] = Field(
- description="""
- Matches a binary file if the given binary regular expression bytes matches the
- file contents.
- """,
- exclude=True,
- )
- mainfile_alternative: bool = Field(
- False,
- description="""
- If True, the parser only matches a file, if no other file in the same directory
- matches a parser.
- """,
- )
- mainfile_contents_dict: Optional[dict] = Field(
- description="""
- Is used to match structured data files like JSON or HDF5.
- """
- )
- supported_compressions: List[str] = Field(
- [],
- description="""
- Files compressed with the given formats (e.g. xz, gz) are uncompressed and
- matched like normal files.
- """,
- )
-
- @abstractmethod
- def load(self) -> 'ParserBaseClass':
- """Used to lazy-load a parser instance. You should override this method
- in your subclass. Note that any Python module imports required for the
- parser class should be done within this function as well."""
- pass
-
- def dict_safe(self):
- return self.dict(include=ParserEntryPoint.__fields__.keys(), exclude_none=True)
class PluginBase(BaseModel):
@@ -175,10 +33,6 @@ class PluginBase(BaseModel):
Parser or Schema.
"""
- plugin_type: str = Field(
- description='The type of the plugin.',
- )
- id: Optional[str] = Field(description='The unique identifier for this plugin.')
name: str = Field(
description='A short descriptive human readable name for the plugin.'
)
@@ -192,12 +46,6 @@ class PluginBase(BaseModel):
description='The URL of the plugins main source code repository.'
)
- def dict_safe(self):
- """Used to serialize the non-confidential parts of a plugin model. This
- function can be overridden in subclasses to expose more information.
- """
- return self.dict(include=PluginBase.__fields__.keys(), exclude_none=True)
-
class PythonPluginBase(PluginBase):
"""
@@ -325,15 +173,13 @@ class Parser(PythonPluginBase):
mainfile_binary_header: Optional[bytes] = Field(
description="""
Matches a binary file if the given bytes are included in the file.
- """,
- exclude=True,
+ """
)
mainfile_binary_header_re: Optional[bytes] = Field(
description="""
Matches a binary file if the given binary regular expression bytes matches the
file contents.
- """,
- exclude=True,
+ """
)
mainfile_alternative: bool = Field(
False,
@@ -385,7 +231,6 @@ class Parser(PythonPluginBase):
from nomad.parsing.parser import MatchingParserInterface
data = self.dict()
- del data['id']
del data['description']
del data['python_package']
del data['plugin_type']
@@ -396,57 +241,13 @@ class Parser(PythonPluginBase):
return MatchingParserInterface(**data)
-EntryPointType = Union[
- Schema,
- Normalizer,
- Parser,
- SchemaPackageEntryPoint,
- ParserEntryPoint,
- NormalizerEntryPoint,
- AppEntryPoint,
+Plugin = Annotated[
+ Union[Schema, Normalizer, Parser], Field(discriminator='plugin_type')
]
-class EntryPoints(Options):
- options: Dict[str, EntryPointType] = Field(
- dict(), description='The available plugin entry points.'
- )
-
-
-class PluginPackage(BaseModel):
- name: str = Field(
- description='Name of the plugin Python package, read from pyproject.toml.'
- )
- description: Optional[str] = Field(
- description='Package description, read from pyproject.toml.'
- )
- version: Optional[str] = Field(
- description='Plugin package version, read from pyproject.toml.'
- )
- homepage: Optional[str] = Field(
- description='Link to the plugin package homepage, read from pyproject.toml.'
- )
- documentation: Optional[str] = Field(
- description='Link to the plugin package documentation page, read from pyproject.toml.'
- )
- repository: Optional[str] = Field(
- description='Link to the plugin package source code repository, read from pyproject.toml.'
- )
- entry_points: List[str] = Field(
- description='List of entry point ids contained in this package, read form pyproject.toml'
- )
-
-
-class Plugins(BaseModel):
- entry_points: EntryPoints = Field(
- description='Used to control plugin entry points.'
- )
- plugin_packages: Dict[str, PluginPackage] = Field(
- description="""
- Contains the installed installed plugin packages with the package name
- used as a key. This is autogenerated and should not be modified.
- """
- )
+class Plugins(Options):
+ options: Dict[str, Plugin] = Field(dict(), description='The available plugin.')
def add_plugin(plugin: Schema) -> None:
@@ -458,7 +259,7 @@ def add_plugin(plugin: Schema) -> None:
sys.path.insert(0, plugin.package_path)
# Add plugin to config
- config.plugins.entry_points.options[plugin.key] = plugin
+ config.plugins.options[plugin.key] = plugin
# Add plugin to Package registry
package = importlib.import_module(plugin.python_package)
@@ -482,7 +283,7 @@ def remove_plugin(plugin) -> None:
pass
# Remove package as plugin
- del config.plugins.entry_points.options[plugin.key]
+ del config.plugins.options[plugin.key]
# Remove plugin from Package registry
package = importlib.import_module(plugin.python_package).m_package
diff --git a/nomad/datamodel/__init__.py b/nomad/datamodel/__init__.py
index 370ab0775e1845ed24c84a8fa833a0b3a9c62cc5..582a8ed56a5299ad4e834f0c7d058e83a6df79a5 100644
--- a/nomad/datamodel/__init__.py
+++ b/nomad/datamodel/__init__.py
@@ -34,7 +34,6 @@ from .optimade import OptimadeEntry, Species
from .metainfo import m_env
from .results import Results
from .data import EntryData, ArchiveSection
-from nomad.config.models.plugins import SchemaPackageEntryPoint
from .context import Context, ClientContext, ServerContext
m_env.m_add_sub_section(
@@ -63,11 +62,9 @@ def all_metainfo_packages():
from nomad.config import config
config.load_plugins()
- for entry_point in config.plugins.entry_points.filtered_values():
- if isinstance(entry_point, PythonPluginBase):
- entry_point.import_python_package()
- if isinstance(entry_point, SchemaPackageEntryPoint):
- entry_point.load()
+ for plugin in config.plugins.filtered_values():
+ if isinstance(plugin, PythonPluginBase):
+ plugin.import_python_package()
# Importing the parsers will also make sure that related schemas will be imported
# even if they are not part of the plugin's python package as this will import
diff --git a/nomad/datamodel/data.py b/nomad/datamodel/data.py
index 5c4d738df7a446dadcc534f19fccf1fb3b7c7a3c..73595a44ed730023f0e4d86e009777ee32267c9a 100644
--- a/nomad/datamodel/data.py
+++ b/nomad/datamodel/data.py
@@ -257,4 +257,3 @@ class AuthorReference(Reference):
author_reference = AuthorReference()
predefined_datatypes['Author'] = author_reference
-Schema = EntryData
diff --git a/nomad/datamodel/metainfo/__init__.py b/nomad/datamodel/metainfo/__init__.py
index 5df06327f442fab002bdd6318ae66c666f4bd228..d13c4beaf48778cd391dd3ae24b6624a538d009d 100644
--- a/nomad/datamodel/metainfo/__init__.py
+++ b/nomad/datamodel/metainfo/__init__.py
@@ -48,13 +48,13 @@ class SchemaInterface:
simulationworkflowschema, runschema = None, None
config.load_plugins()
-for entry_point in config.plugins.entry_points.filtered_values():
- if isinstance(entry_point, Schema):
- if entry_point.name == 'simulationworkflowschema':
- simulationworkflowschema = SchemaInterface(entry_point.python_package)
- elif entry_point.name == 'runschema':
- runschema = SchemaInterface(entry_point.python_package)
+for plugin in config.plugins.filtered_values():
+ if isinstance(plugin, Schema):
+ if plugin.name == 'simulationworkflowschema':
+ simulationworkflowschema = SchemaInterface(plugin.python_package)
+ elif plugin.name == 'runschema':
+ runschema = SchemaInterface(plugin.python_package)
else:
- importlib.import_module(entry_point.python_package)
+ importlib.import_module(plugin.python_package)
SCHEMA_IMPORT_ERROR = 'Schema not defined.'
diff --git a/nomad/datamodel/metainfo/eln/__init__.py b/nomad/datamodel/metainfo/eln/__init__.py
index 29741b2c4bbd74884639eec8093a724d66131aad..1799f385464984ca4938a23535ba07d381121a54 100644
--- a/nomad/datamodel/metainfo/eln/__init__.py
+++ b/nomad/datamodel/metainfo/eln/__init__.py
@@ -1038,10 +1038,10 @@ class ElnWithStructureFile(ArchiveSection):
if system_normalizer_cls:
system_normalizer = system_normalizer_cls(archive)
system_normalizer.normalize()
- optimade_normalizer = OptimadeNormalizer()
- optimade_normalizer.normalize(archive)
- results_normalizer = ResultsNormalizer()
- results_normalizer.normalize(archive)
+ optimade_normalizer = OptimadeNormalizer(archive)
+ optimade_normalizer.normalize()
+ results_normalizer = ResultsNormalizer(archive)
+ results_normalizer.normalize()
# TODO: rewrite it in a way in which the run section is not needed and System is
# directly added to the archive.data
diff --git a/nomad/files.py b/nomad/files.py
index de4776bf1fed385536f8b5f0d56efae874662da5..7f1e8a2e8169784bf7709d8809bcf6b7d82c863e 100644
--- a/nomad/files.py
+++ b/nomad/files.py
@@ -1520,12 +1520,6 @@ class PublicUploadFiles(UploadFiles):
self._archive_msg_file_object = archive_msg_file_object
self._archive_hdf5_file_object = archive_hdf5_file_object
self._access = access
-
- files_found = True
- self._raw_zip_file_object = raw_zip_file_object
- self._archive_msg_file_object = archive_msg_file_object
- self._archive_hdf5_file_object = archive_hdf5_file_object
- self._access = access
if not files_found:
raise KeyError('Neither public nor restricted files found')
return self._access
diff --git a/nomad/metainfo/__init__.py b/nomad/metainfo/__init__.py
index 382c6e43cc1edcef3b624fcf6fad1a6cefe03645..be07523c0c4e3207e3085d9f4210291978d68199 100644
--- a/nomad/metainfo/__init__.py
+++ b/nomad/metainfo/__init__.py
@@ -42,7 +42,6 @@ from .metainfo import (
Section,
Category,
Package,
- SchemaPackage,
Environment,
MEnum,
Datetime,
diff --git a/nomad/metainfo/elasticsearch_extension.py b/nomad/metainfo/elasticsearch_extension.py
index 422adb9d9cb08c26af30cdf50701d16ffe2874e9..a444a8db962cf890e0435d659474d54fe3010de0 100644
--- a/nomad/metainfo/elasticsearch_extension.py
+++ b/nomad/metainfo/elasticsearch_extension.py
@@ -177,7 +177,6 @@ from elasticsearch_dsl import Q
from nomad import utils
from nomad.config import config
-from nomad.config.models.plugins import Schema, Parser, SchemaPackageEntryPoint
from nomad.metainfo.util import MTypes
from .metainfo import (
@@ -502,27 +501,14 @@ class DocumentType:
# Gather the list of enabled schema plugins. Raise error if duplicate
# package name is encountered.
- package_names = set()
- packages_from_plugins = {}
- for plugin in config.plugins.entry_points.filtered_values():
- if isinstance(plugin, (Schema, Parser)):
- package_name = plugin.python_package
- if package_name in package_names:
+ packages = set()
+ for plugin in config.plugins.filtered_values():
+ if plugin.plugin_type in ['schema', 'parser']:
+ if plugin.python_package in packages:
raise ValueError(
f'Your plugin configuration contains two packages with the same name: {plugin.python_package}.'
)
- package_names.add(package_name)
- elif isinstance(plugin, SchemaPackageEntryPoint):
- packages_from_plugins[plugin.id] = plugin.load()
- for name, package in Package.registry.items():
- if not name:
- logger.warning(
- f'no name defined for package {package}, could not load dynamic quantities'
- )
- continue
- package_name = name.split('.')[0]
- if package_name in package_names:
- packages_from_plugins[name] = package
+ packages.add(plugin.python_package)
# Use to get all quantities from the given definition, TODO: Circular
# definitions are here avoided by simply keeping track of which
@@ -550,21 +536,30 @@ class DocumentType:
yield item
quantities_dynamic = {}
- for package in packages_from_plugins.values():
- for section in package.section_definitions:
- if isinstance(section, Section) and issubclass(
- section.section_cls, EntryData
- ):
- schema_name = section.qualified_name()
- for quantity_def, path, repeats in get_all_quantities(section):
- annotation = create_dynamic_quantity_annotation(quantity_def)
- if not annotation:
- continue
- full_name = f'data.{path}{schema_separator}{schema_name}'
- search_quantity = SearchQuantity(
- annotation, qualified_name=full_name, repeats=repeats
- )
- quantities_dynamic[full_name] = search_quantity
+ for name, package in Package.registry.items():
+ if not name:
+ logger.warning(
+ f'no name defined for package {package}, could not load dynamic quantities'
+ )
+ continue
+ package_name = name.split('.')[0]
+ if package_name in packages:
+ for section in package.section_definitions:
+ if isinstance(section, Section) and issubclass(
+ section.section_cls, EntryData
+ ):
+ schema_name = section.qualified_name()
+ for quantity_def, path, repeats in get_all_quantities(section):
+ annotation = create_dynamic_quantity_annotation(
+ quantity_def
+ )
+ if not annotation:
+ continue
+ full_name = f'data.{path}{schema_separator}{schema_name}'
+ search_quantity = SearchQuantity(
+ annotation, qualified_name=full_name, repeats=repeats
+ )
+ quantities_dynamic[full_name] = search_quantity
self.quantities.update(quantities_dynamic)
def _register(self, annotation, prefix, repeats):
diff --git a/nomad/metainfo/metainfo.py b/nomad/metainfo/metainfo.py
index ae8bcd2bd1ed92652ff045fa115548de0997ea01..3c666b307f9c0405ec5059b76a5b52fb92272f4f 100644
--- a/nomad/metainfo/metainfo.py
+++ b/nomad/metainfo/metainfo.py
@@ -5264,4 +5264,3 @@ class AnnotationModel(Annotation, BaseModel):
AnnotationModel.update_forward_refs()
-SchemaPackage = Package
diff --git a/nomad/mkdocs.py b/nomad/mkdocs.py
index 52941dfdc7387f53fccb510a2edbe0f1b4540b9e..ee06a625d6f719464c8422ccb3b0fed1cc641503 100644
--- a/nomad/mkdocs.py
+++ b/nomad/mkdocs.py
@@ -33,7 +33,7 @@ from markdown.extensions.toc import slugify
from nomad.utils import strip
from nomad.config import config
-from nomad.config.models.plugins import Parser, EntryPointType
+from nomad.config.models.plugins import Parser, Plugin
from nomad.app.v1.models import query_documentation, owner_documentation
from nomad.app.v1.routers.entries import archive_required_documentation
from nomad import utils
@@ -383,7 +383,7 @@ def define_env(env):
def parser_list(): # pylint: disable=unused-variable
parsers = [
plugin
- for _, plugin in config.plugins.entry_points.filtered_items()
+ for _, plugin in config.plugins.filtered_items()
if isinstance(plugin, Parser)
]
@@ -446,21 +446,13 @@ def define_env(env):
@env.macro
def plugin_list(): # pylint: disable=unused-variable
- plugins = [plugin for plugin in config.plugins.entry_points.options.values()]
+ plugins = [plugin for plugin in config.plugins.options.values()]
- def render_plugin(plugin: EntryPointType) -> str:
+ def render_plugin(plugin: Plugin) -> str:
result = plugin.name
- docs_or_code_url = None
- for field in [
- 'plugin_documentation_url',
- 'plugin_source_code_url',
- 'documentation',
- 'repository',
- ]:
- value = getattr(plugin, field, None)
- if value:
- dosc_or_code_url = value
- break
+ docs_or_code_url = (
+ plugin.plugin_documentation_url or plugin.plugin_source_code_url
+ )
if docs_or_code_url:
result = f'[{plugin.name}]({docs_or_code_url})'
if plugin.description:
@@ -470,9 +462,7 @@ def define_env(env):
categories = {}
for plugin in plugins:
- category = getattr(
- plugin, 'plugin_type', getattr(plugin, 'entry_point_type', None)
- )
+ category = plugin.python_package.split('.')[0]
categories.setdefault(category, []).append(plugin)
return '\n\n'.join(
diff --git a/nomad/normalizing/__init__.py b/nomad/normalizing/__init__.py
index 43da668aa0bd223abfcb9d78531ae78a1c4b5e3d..ec5c58b532584b045f0c59d87ce9c5a1b395ddcb 100644
--- a/nomad/normalizing/__init__.py
+++ b/nomad/normalizing/__init__.py
@@ -42,10 +42,7 @@ from collections import UserList
from nomad.config import config
-from nomad.config.models.plugins import (
- Normalizer as OldNormalizerPlugin,
- NormalizerEntryPoint,
-)
+from nomad.config.models.plugins import Normalizer as NormalizerPlugin
from .normalizer import Normalizer
@@ -67,7 +64,6 @@ class NormalizerInterface:
def __init__(self, path: str) -> None:
self._path = path
self._cls = None
- self.archive = None
@property
def normalizer_class(self):
@@ -76,49 +72,21 @@ class NormalizerInterface:
return self._cls
def normalize(self, logger=None):
- self.normalizer.normalize(self.archive, logger)
+ self.normalizer_class.normalize(logger)
def __call__(self, *args: Any) -> Any:
- self.archive = args[0]
- self.normalizer = self.normalizer_class(*args[1:])
- return self
+ return self.normalizer_class(*args)
def __getattr__(self, name: str):
return getattr(self.normalizer_class, name, None)
-class NormalizerInterfaceNew:
- def __init__(self, normalizer: Normalizer) -> None:
- self.normalizer = normalizer
- self.archive = None
-
- def normalize(self, logger=None):
- self.normalizer.normalize(self.archive, logger)
-
- def __call__(self, *args: Any) -> Any:
- self.archive = args[0]
- return self
-
- def __getattr__(self, name: str):
- if name == '__name__':
- return self.normalizer.__class__.__name__
- return getattr(self.normalizer, name, None)
-
-
-config.load_plugins()
-enabled_entry_points = config.plugins.entry_points.filtered_values()
normalizers = SortedNormalizers([])
-# Load normalizers using old plugin mechanism
-for entry_point in enabled_entry_points:
- if isinstance(entry_point, OldNormalizerPlugin):
- normalizers.append(NormalizerInterface(entry_point.normalizer_class_name))
-# Load normalizers using old config mechanism
+for plugin_name, plugin in config.plugins.options.items():
+ if isinstance(plugin, NormalizerPlugin) and config.plugins.filter(plugin_name):
+ normalizers.append(NormalizerInterface(plugin.normalizer_class_name))
+
for normalizer in config.normalize.normalizers.filtered_values():
normalizers.append(NormalizerInterface(normalizer))
-
-# Load normalizers using new plugin mechanism
-for entry_point in enabled_entry_points:
- if isinstance(entry_point, NormalizerEntryPoint):
- normalizers.append(NormalizerInterfaceNew(entry_point.load()))
diff --git a/nomad/normalizing/metainfo.py b/nomad/normalizing/metainfo.py
index 81fdf44b1fbbd54b09b4c86f35d914cae37b0758..7eefb5f9c84414be918875e54b672dd471e17256 100644
--- a/nomad/normalizing/metainfo.py
+++ b/nomad/normalizing/metainfo.py
@@ -16,17 +16,15 @@
# limitations under the License.
#
-from nomad.datamodel import EntryArchive
from nomad.datamodel.data import ArchiveSection
-from nomad.datamodel import EntryArchive
-from typing import Optional
+from typing import List, Optional
from . import Normalizer
class MetainfoNormalizer(Normalizer):
domain: Optional[str] = None
- def normalize_section(self, archive: EntryArchive, section, logger):
+ def normalize_section(self, section, logger):
normalize = None
try:
normalize = getattr(section, 'normalize')
@@ -35,7 +33,7 @@ class MetainfoNormalizer(Normalizer):
if normalize:
try:
- normalize(archive, logger)
+ normalize(self.entry_archive, logger)
except Exception as e:
logger.error(
'could not normalize section',
@@ -43,7 +41,7 @@ class MetainfoNormalizer(Normalizer):
exc_info=e,
)
- def normalize(self, archive: EntryArchive, logger=None) -> None:
+ def normalize(self, logger=None) -> None:
if logger is None:
from nomad import utils
@@ -60,6 +58,6 @@ class MetainfoNormalizer(Normalizer):
)
for sub_section in sub_sections:
_normalize(sub_section)
- self.normalize_section(archive, section, logger)
+ self.normalize_section(section, logger)
- _normalize(archive)
+ _normalize(self.entry_archive)
diff --git a/nomad/normalizing/normalizer.py b/nomad/normalizing/normalizer.py
index 335249b45895fdd0bee82fccae7972a13820972f..145ec4db8e4ac00a7fecc0b64531bbd6f7d0caf5 100644
--- a/nomad/normalizing/normalizer.py
+++ b/nomad/normalizing/normalizer.py
@@ -26,10 +26,11 @@ from nomad.datamodel import EntryArchive
class Normalizer(metaclass=ABCMeta):
"""
- A base class for normalizers. Only one instance of the Normalizer is
- created, and you should perform any heavy initialization in the constructor.
- The normalize method is called on archives, and this function should ideally
- not mutate the state of the shared normalizer instance.
+ A base class for normalizers. Normalizers work on a :class:`EntryArchive` section
+ for read and write. Normalizer instances are reused.
+
+ Arguments:
+ entry_archive: The entry_archive root section of the archive to normalize.
"""
domain: Optional[str] = 'dft'
@@ -38,11 +39,16 @@ class Normalizer(metaclass=ABCMeta):
""" Specifies the order of normalization with respect to other normalizers. Lower level
is executed first."""
- def __init__(self, **kwargs) -> None:
+ def __init__(self, entry_archive: EntryArchive) -> None:
+ self.entry_archive = entry_archive
+ try:
+ self.section_run = entry_archive.run[0]
+ except (AttributeError, IndexError):
+ self.section_run = None
self.logger = get_logger(__name__)
@abstractmethod
- def normalize(self, archive: EntryArchive, logger=None) -> None:
+ def normalize(self, logger=None) -> None:
if logger is not None:
self.logger = logger.bind(normalizer=self.__class__.__name__)
@@ -59,8 +65,8 @@ class SystemBasedNormalizer(Normalizer, metaclass=ABCMeta):
only_representatives: Will only normalize the `representative` systems.
"""
- def __init__(self, only_representatives: bool = False, **kwargs):
- super().__init__(**kwargs)
+ def __init__(self, entry_archive: EntryArchive, only_representatives: bool = False):
+ super().__init__(entry_archive)
self.only_representatives = only_representatives
@property
@@ -74,17 +80,15 @@ class SystemBasedNormalizer(Normalizer, metaclass=ABCMeta):
'configuration_periodic_dimensions',
]
- def _normalize_system(self, archive, system, is_representative):
- return self.normalize_system(archive, system, is_representative)
+ def _normalize_system(self, system, is_representative):
+ return self.normalize_system(system, is_representative)
@abstractmethod
- def normalize_system(
- self, archive: EntryArchive, system: MSection, is_representative: bool
- ) -> bool:
- """Normalize the given section and returns True, if successful"""
+ def normalize_system(self, system: MSection, is_representative: bool) -> bool:
+ """Normalize the given section and returns True, iff successful"""
pass
- def __representative_system(self, archive):
+ def __representative_system(self):
"""Used to select a representative system for this entry.
Attempt to find a single section_system that is representative for the
@@ -95,7 +99,7 @@ class SystemBasedNormalizer(Normalizer, metaclass=ABCMeta):
# Try to find workflow information and select the representative system
# based on it
- workflow = archive.workflow2
+ workflow = self.entry_archive.workflow2
if workflow:
try:
@@ -110,7 +114,7 @@ class SystemBasedNormalizer(Normalizer, metaclass=ABCMeta):
# available in reverse order until a valid one is found.
if system is None:
try:
- sccs = archive.run[0].calculation
+ sccs = self.section_run.calculation
for iscc in reversed(sccs):
isys = iscc.system_ref
if isys is not None:
@@ -123,7 +127,7 @@ class SystemBasedNormalizer(Normalizer, metaclass=ABCMeta):
# If no sccs exist, try to find systems
if system is None:
try:
- system = archive.run[0].system[-1]
+ system = self.section_run.system[-1]
except Exception:
system = None
@@ -142,17 +146,17 @@ class SystemBasedNormalizer(Normalizer, metaclass=ABCMeta):
pass
if scc is not None:
- archive.run[0].m_cache['representative_scc_idx'] = scc.m_parent_index
+ self.section_run.m_cache['representative_scc_idx'] = scc.m_parent_index
if system is not None:
- archive.run[0].m_cache['representative_system_idx'] = system.m_parent_index
+ self.section_run.m_cache['representative_system_idx'] = (
+ system.m_parent_index
+ )
return system.m_resolved() if system is not None else None
- def __normalize_system(
- self, archive: EntryArchive, system, representative, logger=None
- ) -> bool:
+ def __normalize_system(self, system, representative, logger=None) -> bool:
try:
- return self._normalize_system(archive, system, representative)
+ return self._normalize_system(system, representative)
except KeyError as e:
self.logger.error(
@@ -176,22 +180,22 @@ class SystemBasedNormalizer(Normalizer, metaclass=ABCMeta):
)
raise e
- def normalize(self, archive: EntryArchive, logger=None) -> None:
- super().normalize(archive, logger)
+ def normalize(self, logger=None) -> None:
+ super().normalize(logger)
# If no section run detected, do nothing
- if not archive.run:
+ if self.section_run is None:
return
# Process representative system first
repr_sys_idx = None
- repr_sys = self.__representative_system(archive)
+ repr_sys = self.__representative_system()
if repr_sys is not None:
repr_sys_idx = repr_sys.m_parent_index
self.logger.info('chose "representative" section system')
- self.__normalize_system(archive, repr_sys, True, logger)
+ self.__normalize_system(repr_sys, True, logger)
# All the rest if requested
if not self.only_representatives:
- for isys, system in enumerate(archive.run[0].system):
+ for isys, system in enumerate(self.section_run.system):
if isys != repr_sys_idx:
- self.__normalize_system(archive, system, False, logger)
+ self.__normalize_system(system, False, logger)
diff --git a/nomad/normalizing/optimade.py b/nomad/normalizing/optimade.py
index c8f4ea6bc19c826e8a2dd4abfc675fcdeb740c9c..77db87723b3570041bc15c53121a6c15f0f9d218 100644
--- a/nomad/normalizing/optimade.py
+++ b/nomad/normalizing/optimade.py
@@ -23,7 +23,6 @@ import ase.data
import ase.formula
import pint.quantity
-from nomad.datamodel import EntryArchive
from nomad.atomutils import Formula
from nomad.normalizing.normalizer import SystemBasedNormalizer
from nomad.units import ureg
@@ -89,18 +88,18 @@ class OptimadeNormalizer(SystemBasedNormalizer):
It assumes that the :class:`SystemNormalizer` was run before.
"""
- def __init__(self):
- super().__init__(only_representatives=True)
+ def __init__(self, archive):
+ super().__init__(archive, only_representatives=True)
- def add_optimade_data(self, archive: EntryArchive) -> OptimadeEntry:
+ def add_optimade_data(self, index) -> OptimadeEntry:
"""
The 'main' method of this :class:`SystemBasedNormalizer`.
Normalizes the section with the given `index`.
Normalizes geometry, classifies, system_type, and runs symmetry analysis.
"""
- if archive.metadata is None:
- archive.m_create(EntryMetadata)
- optimade = archive.metadata.m_create(OptimadeEntry)
+ if self.entry_archive.metadata is None:
+ self.entry_archive.m_create(EntryMetadata)
+ optimade = self.entry_archive.metadata.m_create(OptimadeEntry)
def get_value(
quantity_def,
@@ -110,7 +109,7 @@ class OptimadeNormalizer(SystemBasedNormalizer):
source: Any = None,
) -> Any:
try:
- source = source if source is not None else archive.run[0].system[-1]
+ source = source if source is not None else self.section_run.system[-1]
value = source.m_get(quantity_def)
if value is None:
return
@@ -129,7 +128,7 @@ class OptimadeNormalizer(SystemBasedNormalizer):
except KeyError:
return default
- system = archive.run[0].system[-1] if archive.run[0].system else None
+ system = self.section_run.system[-1] if self.section_run.system else None
if system is None:
return optimade
@@ -154,9 +153,9 @@ class OptimadeNormalizer(SystemBasedNormalizer):
]
# formulas
- system_cls = (
- archive.run[0].m_def.all_sub_sections['system'].sub_section.section_cls
- )
+ system_cls = self.section_run.m_def.all_sub_sections[
+ 'system'
+ ].sub_section.section_cls
original_formula = get_value(
system_cls.chemical_composition_hill, source=system
)
@@ -199,12 +198,12 @@ class OptimadeNormalizer(SystemBasedNormalizer):
return optimade
- def normalize_system(self, archive: EntryArchive, system, is_representative):
+ def normalize_system(self, system, is_representative):
if not is_representative:
return False
try:
- self.add_optimade_data(archive)
+ self.add_optimade_data(system.m_parent_index)
return True
except Exception as e:
diff --git a/nomad/normalizing/porosity.py b/nomad/normalizing/porosity.py
index d780765f54f4e4951c7ac4227face50fb0caa69b..17ea50d7dcb6fc528f404d8f7b990d222a0dbd1e 100644
--- a/nomad/normalizing/porosity.py
+++ b/nomad/normalizing/porosity.py
@@ -63,8 +63,8 @@ class PorosityNormalizer(SystemBasedNormalizer):
In the future, the it will also compute the rcsr tological code.
"""
- def __init__(self):
- super().__init__(only_representatives=True)
+ def __init__(self, archive):
+ super().__init__(archive, only_representatives=True)
def normalize_system(self, system, is_representative):
if not is_representative:
diff --git a/nomad/normalizing/results.py b/nomad/normalizing/results.py
index edb0ac873cb93a9c3621e938928093009721f7fc..936e91583415e24f4ea425956e7581384e460598 100644
--- a/nomad/normalizing/results.py
+++ b/nomad/normalizing/results.py
@@ -30,7 +30,6 @@ from nomad.atomutils import Formula
from nomad.normalizing.normalizer import Normalizer
from nomad.normalizing.method import MethodNormalizer
from nomad.normalizing.material import MaterialNormalizer
-from nomad.datamodel import EntryArchive
from nomad.datamodel.metainfo.workflow import Workflow
from nomad.datamodel.data import ArchiveSection
from nomad.normalizing.common import structures_2d
@@ -103,10 +102,7 @@ class ResultsNormalizer(Normalizer):
domain = None
normalizer_level = 3
- def normalize(self, archive: EntryArchive, logger=None) -> None:
- self.entry_archive = archive
- self.section_run = archive.run[0] if archive.run else None
-
+ def normalize(self, logger=None) -> None:
# Setup logger
if logger is not None:
self.logger = logger.bind(normalizer=self.__class__.__name__)
@@ -123,9 +119,6 @@ class ResultsNormalizer(Normalizer):
for measurement in self.entry_archive.measurement:
self.normalize_measurement(measurement)
- self.entry_archive = None
- self.section_run = None
-
def normalize_sample(self, sample) -> None:
material = self.entry_archive.m_setdefault('results.material')
diff --git a/nomad/normalizing/topology.py b/nomad/normalizing/topology.py
index a2a7bf774c1d1cb7e7d699ab2f1c159bfce47dfd..00415768d94c996eff10e013405d2b234baa73fb 100644
--- a/nomad/normalizing/topology.py
+++ b/nomad/normalizing/topology.py
@@ -40,6 +40,7 @@ from matid.classification.classifications import (
from nomad import utils
from nomad.config import config
from nomad import atomutils
+from nomad.units import ureg
from nomad.datamodel.results import (
CoreHole,
SymmetryNew as Symmetry,
diff --git a/nomad/parsing/parser.py b/nomad/parsing/parser.py
index 38b671ed2fe40ceab424898aa8e017a8683de06c..513ae79202c8c8bbfea713204c30404d94743d7f 100644
--- a/nomad/parsing/parser.py
+++ b/nomad/parsing/parser.py
@@ -216,7 +216,6 @@ class MatchingParser(Parser):
domain='dft',
metadata: dict = None,
supported_compressions: List[str] = [],
- **kwargs,
) -> None:
super().__init__()
diff --git a/nomad/parsing/parsers.py b/nomad/parsing/parsers.py
index 8b5aa9836fa28854d1ffe9e4bbbd78fdff3d5865..c35340e39884964775b480382e4c434e482068ee 100644
--- a/nomad/parsing/parsers.py
+++ b/nomad/parsing/parsers.py
@@ -21,7 +21,7 @@ from typing import Optional, Tuple, List, Dict
from collections.abc import Iterable
from nomad.config import config
-from nomad.config.models.plugins import Parser as ParserPlugin, ParserEntryPoint
+from nomad.config.models.plugins import Parser as ParserPlugin
from nomad.datamodel import EntryArchive, EntryMetadata, results
from nomad.datamodel.context import Context, ClientContext
@@ -226,27 +226,13 @@ def run_parser(
parsers = [GenerateRandomParser(), TemplateParser(), ChaosParser()]
-config.load_plugins()
-enabled_entry_points = config.plugins.entry_points.filtered_values()
-
-# Load parsers using old plugin mechanism
parsers.extend(
[
- entry_point.create_matching_parser_interface()
- for entry_point in enabled_entry_points
- if isinstance(entry_point, ParserPlugin)
+ plugin.create_matching_parser_interface()
+ for plugin_name, plugin in config.plugins.options.items()
+ if config.plugins.filter(plugin_name) and isinstance(plugin, ParserPlugin)
]
)
-
-# Load parsers using new plugin mechanism. The entry point name is used to
-# identify the parser.
-for entry_point in enabled_entry_points:
- if isinstance(entry_point, ParserEntryPoint):
- entry_point_name = entry_point.id
- instance = entry_point.load()
- instance.name = entry_point_name
- parsers.append(instance)
-
parsers.extend([TabularDataParser(), ArchiveParser()])
# There are some entries with PIDs that have mainfiles which do not match what
@@ -284,10 +270,12 @@ if config.process.use_empty_parsers:
parsers.append(BrokenParser())
-""" A dict to access parsers by name. Usually 'parsers/<...>', e.g. 'parsers/vasp'. """
+
parser_dict: Dict[str, Parser] = {
parser.name: parser for parser in parsers + empty_parsers
-}
+} # type: ignore
+""" A dict to access parsers by name. Usually 'parsers/<...>', e.g. 'parsers/vasp'. """
+
# renamed parsers
_renames = {
diff --git a/pyproject.toml b/pyproject.toml
index 354fbda9a494669a75a7434bef5b5f3bcfa2213f..c21d95504eb7d1f6e50b53c0a96fa307e8e36406 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -24,7 +24,6 @@ dependencies = [
'h5py>=3.6.0',
'hjson>=3.0.2',
'httpx>=0.23.3',
- 'importlib_metadata~=7.1.0',
'jmespath>=0.10.0',
'lxml>=5.2',
'lxml-html-clean>=0.1.0',
diff --git a/requirements-dev.txt b/requirements-dev.txt
index 96429ce7f84175ebdf3276c49fb6bec8d509844e..b6d4a8611c4ed0ccbd38dd381b1042d04eeda9d9 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -22,7 +22,7 @@ async-generator==1.10 # via -r requirements.txt, jupyterhub
atpublic==4.1.0 # via aiosmtpd
attrs==23.2.0 # via -r requirements.txt, aiosmtpd, jsonschema, pytest
babel==2.14.0 # via -r requirements.txt, mkdocs-git-revision-date-localized-plugin, mkdocs-material, sphinx
-backports-tarfile==1.1.0 # via jaraco-context
+backports-tarfile==1.0.0 # via jaraco-context
bagit==1.8.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
basicauth==0.4.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
beautifulsoup4==4.12.3 # via -r requirements.txt, nomad-lab (pyproject.toml)
@@ -33,7 +33,7 @@ blinker==1.7.0 # via -r requirements.txt, flask
blosc2==2.5.1 # via -r requirements.txt, tables
build==1.2.1 # via nomad-lab (pyproject.toml), pip-tools
cachetools==5.3.3 # via -r requirements.txt, nomad-lab (pyproject.toml)
-celery==5.4.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
+celery==5.3.6 # via -r requirements.txt, nomad-lab (pyproject.toml)
certifi==2024.2.2 # via -r requirements.txt, elasticsearch, httpcore, httpx, requests
certipy==0.1.3 # via -r requirements.txt, jupyterhub
cffi==1.16.0 # via -r requirements.txt, cryptography
@@ -63,7 +63,7 @@ dnspython==2.6.1 # via -r requirements.txt, email-validator, pymongo
docker==7.0.0 # via -r requirements.txt, dockerspawner
dockerspawner==13.0.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
docstring-parser==0.16 # via -r requirements.txt, nomad-lab (pyproject.toml)
-docutils==0.21.1 # via -r requirements.txt, m2r, readme-renderer, recommonmark, sphinx
+docutils==0.20.1 # via -r requirements.txt, m2r, readme-renderer, recommonmark, sphinx
elasticsearch==7.17.1 # via -r requirements.txt, elasticsearch-dsl, nomad-lab (pyproject.toml)
elasticsearch-dsl==7.4.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
email-validator==1.3.1 # via -r requirements.txt, optimade
@@ -107,7 +107,7 @@ idna==3.7 # via -r requirements.txt, anyio, email-validator, htt
ifes-apt-tc-data-modeling==0.1 # via -r requirements.txt, pynxtools
imageio==2.27.0 # via -r requirements.txt, hyperspy, kikuchipy, nionswift, nionswift-io, nionui, scikit-image
imagesize==1.4.1 # via -r requirements.txt, sphinx
-importlib-metadata==7.1.0 # via -r requirements.txt, build, dask, flask, hyperspy, jupyter-client, jupyterhub, keyring, markdown, mkdocs, nomad-lab (pyproject.toml), pynxtools, sphinx, twine
+importlib-metadata==7.1.0 # via -r requirements.txt, build, dask, flask, hyperspy, jupyter-client, jupyterhub, keyring, markdown, mkdocs, pynxtools, sphinx, twine
importlib-resources==6.4.0 # via -r requirements.txt, matplotlib, spglib
inflection==0.5.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
ipykernel==6.29.4 # via -r requirements.txt, ipyparallel
@@ -115,7 +115,7 @@ ipyparallel==8.8.0 # via -r requirements.txt, hyperspy
ipython==8.18.1 # via -r requirements.txt, hyperspy, ipykernel, ipyparallel, pynxtools-stm
isodate==0.6.1 # via -r requirements.txt, rdflib
isoduration==20.11.0 # via -r requirements.txt, jsonschema
-itsdangerous==2.2.0 # via -r requirements.txt, flask, nomad-lab (pyproject.toml)
+itsdangerous==2.1.2 # via -r requirements.txt, flask, nomad-lab (pyproject.toml)
jaraco-classes==3.4.0 # via keyring
jaraco-context==5.3.0 # via keyring
jaraco-functools==4.0.0 # via keyring
@@ -165,7 +165,7 @@ mkdocs-redirects==1.2.1 # via nomad-lab (pyproject.toml)
mmtf-python==1.1.3 # via -r requirements.txt, mdanalysis
mongoengine==0.28.2 # via -r requirements.txt, nomad-lab (pyproject.toml)
mongomock==4.1.2 # via -r requirements.txt, optimade
-monty==2024.4.17 # via -r requirements.txt, pymatgen
+monty==2024.3.31 # via -r requirements.txt, pymatgen
more-itertools==10.2.0 # via jaraco-classes, jaraco-functools, pytest
mpmath==1.3.0 # via -r requirements.txt, sympy
mrcfile==1.5.0 # via -r requirements.txt, griddataformats
@@ -213,7 +213,7 @@ pint==0.17 # via -r requirements.txt, hyperspy, nomad-lab (pyproj
pip-tools==7.4.1 # via nomad-lab (pyproject.toml)
pkginfo==1.10.0 # via twine
platformdirs==4.2.0 # via -r requirements.txt, jupyter-core, mkdocs, pooch
-plotly==5.21.0 # via -r requirements.txt, asr, pymatgen
+plotly==5.20.0 # via -r requirements.txt, asr, pymatgen
pluggy==0.13.1 # via pytest
pooch==1.8.1 # via -r requirements.txt, kikuchipy, orix
prettytable==3.10.0 # via -r requirements.txt, hyperspy
@@ -274,7 +274,7 @@ rdflib==5.0.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
rdkit==2023.9.5 # via -r requirements.txt, nomad-lab (pyproject.toml)
readme-renderer==43.0 # via twine
recommonmark==0.7.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
-regex==2024.4.16 # via mkdocs-material
+regex==2023.12.25 # via mkdocs-material
requests==2.31.0 # via -r requirements.txt, docker, hyperspy, jupyterhub, mkdocs-material, nomad-lab (pyproject.toml), oauthenticator, optimade, pooch, pybis, pymatgen, python-gitlab, python-keycloak, requests-toolbelt, rfc3161ng, sphinx, twine
requests-toolbelt==1.0.0 # via -r requirements.txt, python-gitlab, python-keycloak, twine
rfc3161ng==2.1.3 # via -r requirements.txt, nomad-lab (pyproject.toml)
@@ -299,7 +299,7 @@ snowballstemmer==2.2.0 # via -r requirements.txt, sphinx
soupsieve==2.5 # via -r requirements.txt, beautifulsoup4
sparse==0.15.1 # via -r requirements.txt, hyperspy
spglib==2.4.0 # via -r requirements.txt, asr, matid, phonopy, pymatgen
-sphinx==7.3.6 # via -r requirements.txt, recommonmark
+sphinx==7.2.6 # via -r requirements.txt, recommonmark
sphinxcontrib-applehelp==1.0.8 # via -r requirements.txt, sphinx
sphinxcontrib-devhelp==1.0.6 # via -r requirements.txt, sphinx
sphinxcontrib-htmlhelp==2.0.5 # via -r requirements.txt, sphinx
@@ -317,8 +317,8 @@ tenacity==8.2.3 # via -r requirements.txt, plotly
termcolor==2.4.0 # via mkdocs-macros-plugin
texttable==1.7.0 # via -r requirements.txt, pybis
threadpoolctl==3.4.0 # via -r requirements.txt, mdanalysis, scikit-learn
-tifffile==2024.4.18 # via -r requirements.txt, h5grove, hyperspy, scikit-image
-tomli==2.0.1 # via -r requirements.txt, build, mypy, pip-tools, pyproject-hooks, sphinx
+tifffile==2024.2.12 # via -r requirements.txt, h5grove, hyperspy, scikit-image
+tomli==2.0.1 # via build, mypy, pip-tools, pyproject-hooks
toolz==0.12.1 # via -r requirements.txt, dask, hyperspy, partd
toposort==1.10 # via -r requirements.txt, nomad-lab (pyproject.toml)
tornado==6.4 # via -r requirements.txt, ipykernel, ipyparallel, jupyter-client, jupyterhub
diff --git a/requirements.txt b/requirements.txt
index 189c613473a61272643a7bb6fd134d79375f42f0..f5ab4edbc8f85682b94777d8227bad6876635918 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -28,7 +28,7 @@ bitarray==2.9.2 # via nomad-lab (pyproject.toml), nomad_dos_fingerprin
blinker==1.7.0 # via flask
blosc2==2.5.1 # via tables
cachetools==5.3.3 # via nomad-lab (pyproject.toml)
-celery==5.4.0 # via nomad-lab (pyproject.toml)
+celery==5.3.6 # via nomad-lab (pyproject.toml)
certifi==2024.2.2 # via elasticsearch, httpcore, httpx, requests
certipy==0.1.3 # via jupyterhub
cffi==1.16.0 # via cryptography
@@ -55,7 +55,7 @@ dnspython==2.6.1 # via email-validator, pymongo
docker==7.0.0 # via dockerspawner
dockerspawner==13.0.0 # via nomad-lab (pyproject.toml)
docstring-parser==0.16 # via nomad-lab (pyproject.toml)
-docutils==0.21.1 # via m2r, recommonmark, sphinx
+docutils==0.20.1 # via m2r, recommonmark, sphinx
elasticsearch==7.17.1 # via elasticsearch-dsl, nomad-lab (pyproject.toml)
elasticsearch-dsl==7.4.0 # via nomad-lab (pyproject.toml)
email-validator==1.3.1 # via optimade
@@ -96,7 +96,7 @@ idna==3.7 # via anyio, email-validator, httpx, jsonschema, reque
ifes-apt-tc-data-modeling==0.1 # via pynxtools
imageio==2.27.0 # via hyperspy, kikuchipy, nionswift, nionswift-io, nionui, scikit-image
imagesize==1.4.1 # via sphinx
-importlib-metadata==7.1.0 # via dask, flask, hyperspy, jupyter-client, jupyterhub, nomad-lab (pyproject.toml), pynxtools, sphinx
+importlib-metadata==7.1.0 # via dask, flask, hyperspy, jupyter-client, jupyterhub, pynxtools, sphinx
importlib-resources==6.4.0 # via matplotlib, spglib
inflection==0.5.1 # via nomad-lab (pyproject.toml)
ipykernel==6.29.4 # via ipyparallel
@@ -104,7 +104,7 @@ ipyparallel==8.8.0 # via hyperspy
ipython==8.18.1 # via hyperspy, ipykernel, ipyparallel, pynxtools-stm
isodate==0.6.1 # via rdflib
isoduration==20.11.0 # via jsonschema
-itsdangerous==2.2.0 # via flask, nomad-lab (pyproject.toml)
+itsdangerous==2.1.2 # via flask, nomad-lab (pyproject.toml)
jedi==0.19.1 # via ipython
jinja2==3.1.3 # via flask, hyperspy, jupyterhub, sphinx
jmespath==1.0.1 # via nomad-lab (pyproject.toml)
@@ -140,7 +140,7 @@ mistune==3.0.2 # via m2r
mmtf-python==1.1.3 # via mdanalysis
mongoengine==0.28.2 # via nomad-lab (pyproject.toml)
mongomock==4.1.2 # via optimade
-monty==2024.4.17 # via pymatgen
+monty==2024.3.31 # via pymatgen
mpmath==1.3.0 # via sympy
mrcfile==1.5.0 # via griddataformats
msgpack==1.0.8 # via blosc2, mmtf-python, nomad-lab (pyproject.toml)
@@ -179,7 +179,7 @@ phonopy==2.9.1 # via asr
pillow==10.0.1 # via fabio, hyperspy, imageio, matplotlib, nionswift, rdkit, scikit-image
pint==0.17 # via hyperspy, nomad-lab (pyproject.toml), rosettasciio
platformdirs==4.2.0 # via jupyter-core, pooch
-plotly==5.21.0 # via asr, pymatgen
+plotly==5.20.0 # via asr, pymatgen
pooch==1.8.1 # via hyperspy, kikuchipy, orix
prettytable==3.10.0 # via hyperspy
prometheus-client==0.20.0 # via jupyterhub
@@ -247,7 +247,7 @@ snowballstemmer==2.2.0 # via sphinx
soupsieve==2.5 # via beautifulsoup4
sparse==0.15.1 # via hyperspy
spglib==2.4.0 # via asr, matid, phonopy, pymatgen
-sphinx==7.3.6 # via recommonmark
+sphinx==7.2.6 # via recommonmark
sphinxcontrib-applehelp==1.0.8 # via sphinx
sphinxcontrib-devhelp==1.0.6 # via sphinx
sphinxcontrib-htmlhelp==2.0.5 # via sphinx
@@ -264,8 +264,7 @@ tabulate==0.8.9 # via nomad-lab (pyproject.toml), pybis, pymatgen
tenacity==8.2.3 # via plotly
texttable==1.7.0 # via pybis
threadpoolctl==3.4.0 # via mdanalysis, scikit-learn
-tifffile==2024.4.18 # via h5grove, hyperspy, scikit-image
-tomli==2.0.1 # via sphinx
+tifffile==2024.2.12 # via h5grove, hyperspy, scikit-image
toolz==0.12.1 # via dask, hyperspy, partd
toposort==1.10 # via nomad-lab (pyproject.toml)
tornado==6.4 # via ipykernel, ipyparallel, jupyter-client, jupyterhub
diff --git a/tests/normalizing/conftest.py b/tests/normalizing/conftest.py
index b6ae32ecdd060cc539a3594f815f470b504c1646..8f5df250fcd8c39f4d6a45fb3a4cc0b668afef86 100644
--- a/tests/normalizing/conftest.py
+++ b/tests/normalizing/conftest.py
@@ -71,7 +71,7 @@ from nomad.datamodel.metainfo import (
def run_normalize(entry_archive: EntryArchive) -> EntryArchive:
for normalizer_class in normalizers:
normalizer = normalizer_class(entry_archive)
- normalizer.normalize(logger=get_logger(__name__))
+ normalizer.normalize()
return entry_archive
diff --git a/tests/test_config.py b/tests/test_config.py
index b4482e742b47166f718a9adb8d76ae2fb17cd65d..ef167f2bd93a9391ce140ca39d8ebd0189e51f5e 100644
--- a/tests/test_config.py
+++ b/tests/test_config.py
@@ -173,20 +173,18 @@ def test_config_priority(conf_yaml, conf_env, value, mockopen, monkeypatch):
{'plugins': {'include': ['normalizers/simulation/dos']}},
{
'plugins': {
- 'entry_points': {
- 'include': ['normalizers/simulation/dos'],
- 'options': {
- 'normalizers/simulation/dos': {
- 'name': 'yaml',
- 'python_package': 'dosnormalizer',
- 'description': 'This is the normalizer for DOS in NOMAD.\n',
- 'plugin_documentation_url': None,
- 'plugin_source_code_url': None,
- 'normalizer_class_name': 'dosnormalizer.DosNormalizer',
- 'plugin_type': 'normalizer',
- }
- },
- }
+ 'include': ['normalizers/simulation/dos'],
+ 'options': {
+ 'normalizers/simulation/dos': {
+ 'name': 'yaml',
+ 'python_package': 'dosnormalizer',
+ 'description': 'This is the normalizer for DOS in NOMAD.\n',
+ 'plugin_documentation_url': None,
+ 'plugin_source_code_url': None,
+ 'normalizer_class_name': 'dosnormalizer.DosNormalizer',
+ 'plugin_type': 'normalizer',
+ }
+ },
}
},
id='dictionary: merges',
@@ -194,7 +192,7 @@ def test_config_priority(conf_yaml, conf_env, value, mockopen, monkeypatch):
pytest.param(
{'plugins': {'include': ['a']}},
{'plugins': {'include': ['b']}},
- {'plugins': {'entry_points': {'include': ['b']}}},
+ {'plugins': {'include': ['b']}},
id='list: overrides',
),
pytest.param(
@@ -219,9 +217,9 @@ def test_parser_plugins():
config = load_config()
config.load_plugins()
parsers = [
- entry_point
- for entry_point in config.plugins.entry_points.options.values()
- if isinstance(entry_point, Parser)
+ plugin
+ for plugin in config.plugins.options.values()
+ if isinstance(plugin, Parser)
]
assert len(parsers) == 71
@@ -246,5 +244,5 @@ def test_plugin_polymorphism(mockopen, monkeypatch):
}
config = load_test_config(plugins, None, mockopen, monkeypatch)
config.load_plugins()
- assert isinstance(config.plugins.entry_points.options['schema'], Schema)
- assert isinstance(config.plugins.entry_points.options['parser'], Parser)
+ assert isinstance(config.plugins.options['schema'], Schema)
+ assert isinstance(config.plugins.options['parser'], Parser)