diff --git a/MANIFEST.in b/MANIFEST.in
index 18c39cefaa38740d5fb7d30238e70438b18d8769..fe15e110b79a7b3e7e4c51e35750ebe64b8f8dde 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -8,6 +8,7 @@ include auto_complete_install.sh
include setup.json
recursive-include nomad/app/static/gui/ *.css *.ico *.html *.json *.js *.map *.txt *.svg *.png
recursive-include docs/build/ *.css *.ico *.html *.json *.js *.map *.txt *.svg *.png
+recursive-include dependencies/parsers/ metadata.yaml
recursive-include dependencies/parsers/nexus/nexusparser/definitions/base_classes/ *.xml
recursive-include dependencies/parsers/nexus/nexusparser/definitions/applications/ *.xml
recursive-include dependencies/parsers/nexus/nexusparser/definitions/contributed_definitions/ *.xml
diff --git a/dependencies/parsers/atomistic b/dependencies/parsers/atomistic
index c7fed17419d917ea95d3ab5875916099ade8479e..35eef1fa4705ddd18d3787d4519f08a37f6a8644 160000
--- a/dependencies/parsers/atomistic
+++ b/dependencies/parsers/atomistic
@@ -1 +1 @@
-Subproject commit c7fed17419d917ea95d3ab5875916099ade8479e
+Subproject commit 35eef1fa4705ddd18d3787d4519f08a37f6a8644
diff --git a/dependencies/parsers/database b/dependencies/parsers/database
index 051781cff4d21a8eaf69eb1d992de52dd42eba31..806fda467d037dfcc2d665c5b735650fd3862632 160000
--- a/dependencies/parsers/database
+++ b/dependencies/parsers/database
@@ -1 +1 @@
-Subproject commit 051781cff4d21a8eaf69eb1d992de52dd42eba31
+Subproject commit 806fda467d037dfcc2d665c5b735650fd3862632
diff --git a/dependencies/parsers/eelsdb b/dependencies/parsers/eelsdb
index 79e687d2c83d3240dfa2f399155c4487c94f984f..007ddd3bf4884a09bead33114dda5167b8b51f96 160000
--- a/dependencies/parsers/eelsdb
+++ b/dependencies/parsers/eelsdb
@@ -1 +1 @@
-Subproject commit 79e687d2c83d3240dfa2f399155c4487c94f984f
+Subproject commit 007ddd3bf4884a09bead33114dda5167b8b51f96
diff --git a/dependencies/parsers/electronic b/dependencies/parsers/electronic
index ffe7f5c7105688d38421edb33caa8054d4aee997..5c077f48adcda8e6ec2f5cfb2220adc04100c3e6 160000
--- a/dependencies/parsers/electronic
+++ b/dependencies/parsers/electronic
@@ -1 +1 @@
-Subproject commit ffe7f5c7105688d38421edb33caa8054d4aee997
+Subproject commit 5c077f48adcda8e6ec2f5cfb2220adc04100c3e6
diff --git a/dependencies/parsers/nexus b/dependencies/parsers/nexus
index a866117f5bc61558dba734ee9c91aaf5ddf94522..78b721318cb824e404234702c0aef19a7d8b6dba 160000
--- a/dependencies/parsers/nexus
+++ b/dependencies/parsers/nexus
@@ -1 +1 @@
-Subproject commit a866117f5bc61558dba734ee9c91aaf5ddf94522
+Subproject commit 78b721318cb824e404234702c0aef19a7d8b6dba
diff --git a/dependencies/parsers/workflow b/dependencies/parsers/workflow
index b3565e46b741c6c36c70e233dc55caa444b81fd8..ed2592c0953ebad15e59ca6f60b2b7eb3c2afcd1 160000
--- a/dependencies/parsers/workflow
+++ b/dependencies/parsers/workflow
@@ -1 +1 @@
-Subproject commit b3565e46b741c6c36c70e233dc55caa444b81fd8
+Subproject commit ed2592c0953ebad15e59ca6f60b2b7eb3c2afcd1
diff --git a/gui/src/components/About.js b/gui/src/components/About.js
index fb7a3176d2ca08a421f938c14cfef1636bcd94fd..d5a74561c5a65b2e4ca225f1462770a02014bacd 100644
--- a/gui/src/components/About.js
+++ b/gui/src/components/About.js
@@ -19,13 +19,27 @@ import React, { useLayoutEffect, useRef, useCallback, useEffect, useState } from
import { ReactComponent as AboutSvg } from '../images/about.svg'
import PropTypes from 'prop-types'
import Markdown from './Markdown'
+import { isNil } from 'lodash'
import { appBase, debug, aitoolkitEnabled, encyclopediaBase } from '../config'
import packageJson from '../../package.json'
-import { Grid, Card, CardContent, Typography, makeStyles, Link, Dialog, DialogTitle, DialogContent, DialogActions, Button } from '@material-ui/core'
+import {
+ Button,
+ Card,
+ CardContent,
+ Dialog,
+ DialogTitle,
+ DialogContent,
+ DialogActions,
+ Grid,
+ Link,
+ makeStyles,
+ Typography
+} from '@material-ui/core'
import { Link as RouterLink, useHistory } from 'react-router-dom'
import tutorials from '../toolkitMetadata'
import parserMetadata from '../parserMetadata'
import { useInfo } from './api'
+import { pluralize } from '../utils'
function CodeInfo({code, ...props}) {
if (!code) {
@@ -76,41 +90,84 @@ CodeInfo.propTypes = {
onClose: PropTypes.func
}
-export const CodeList = ({withUploadInstructions}) => {
+export const CodeList = React.memo(({withUploadInstructions}) => {
const [selected, setSelected] = useState(null)
- const codes = Object.keys(parserMetadata).map(code => {
- const metadata = parserMetadata[code]
- if (!metadata) {
- return code
+ // Create lists containing code name and category
+ const codes = []
+ const categorySizes = {}
+ Object.entries(parserMetadata).forEach(([code, metadata]) => {
+ const name = metadata.codeLabel || code
+ const category = metadata.codeCategory
+ if (categorySizes[category]) {
+ categorySizes[category] += 1
+ } else {
+ categorySizes[category] = 1
}
-
- if (withUploadInstructions) {
- return <Link
- href="#" key={code} onClick={() => setSelected(code)}
- >{code.codeLabel || code}</Link>
+ if (!metadata || code === 'example') {
+ return
}
- if (metadata.codeUrl) {
- return <Link href={metadata.codeUrl} key={code} target="code">{code.codeLabel || code}</Link>
- }
+ const link = withUploadInstructions
+ ? [code, category, <Link href="#" key={code} onClick={() => setSelected(code)}>{name}</Link>]
+ : metadata.codeUrl
+ ? [code, category, <Link href={metadata.codeUrl} key={code} target="code">{name}</Link>]
+ : [code, category, name]
- return code
+ codes.push(link)
})
- const toRender = codes.reduce((list, value, index) => {
- if (index !== 0) {
- list.push(', ')
+ // Sort by category size, then by program name. Codes without category go to
+ // the end.
+ codes.sort((a, b) => {
+ const nameA = a[0]
+ const nameB = b[0]
+ const categoryA = a[1]
+ const categoryB = b[1]
+ const sizeA = categorySizes[categoryA]
+ const sizeB = categorySizes[categoryB]
+ if (isNil(categoryA) && !isNil(categoryB)) return 1
+ if (isNil(categoryB) && !isNil(categoryA)) return -1
+ if (sizeA > sizeB) return -1
+ if (sizeA < sizeB) return 1
+ if (nameA > nameB) return 1
+ if (nameA < nameB) return -1
+ return 0
+ })
+
+ // Create a renderable version
+ let currentCategory = null
+ let categoryIndex = 0
+ const codeshtml = codes.reduce((list, value) => {
+ let index = -1
+ const categoryTmp = value[1]
+ const html = value[2]
+ const category = categoryTmp ? pluralize(categoryTmp) : 'Miscellaneous'
+
+ if (currentCategory !== category) {
+ index = 0
+ if (categoryIndex !== 0) {
+ list.push(', ')
+ }
+ list.push(<b> {category}: </b>)
+ categoryIndex += 1
+ currentCategory = category
+ }
+
+ if (html) {
+ if (index !== 0) {
+ list.push(', ')
+ }
+ list.push(html)
}
- list.push(value)
return list
}, [])
- return <React.Fragment>
- {toRender}
+ return <span data-testid="code-list">
+ {codeshtml}
<CodeInfo code={selected} onClose={() => setSelected(null)} />
- </React.Fragment>
-}
+ </span>
+})
CodeList.propTypes = {
withUploadInstructions: PropTypes.bool
}
@@ -370,7 +427,6 @@ export default function About() {
- version (GUI): \`${packageJson.version}/${packageJson.commit}\`
- 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>
diff --git a/gui/src/components/About.spec.js b/gui/src/components/About.spec.js
new file mode 100644
index 0000000000000000000000000000000000000000..6acb6d71c77aeaae05f04a414af8de85eac9f5c1
--- /dev/null
+++ b/gui/src/components/About.spec.js
@@ -0,0 +1,31 @@
+/*
+ * 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 { render, screen } from './conftest.spec'
+import {CodeList} from './About'
+
+test('list of codes renders correctly', async () => {
+ render(<CodeList />)
+ // Check that the list of parsers is printed correctly within the correct categories.
+ // This list should be updated if new codes are added or the code names are updated.
+ // This test value is hardcoded so that any unintentional changes to the code names and
+ // categories can be avoided.
+ const list = /Atomistic codes: ABACUS, ABINIT, AMS, ASAP, Amber, BigDFT, CASTEP, CHARMM, CP2K, CPMD, CRYSTAL, DFTB\+, DL_POLY, DMol3, Elk, FHI-aims, FLEUR, FPLO, GAMESS, GPAW, GROMACS, GROMOS, GULP, Gaussian, LAMMPS, MOPAC, Molcas, NAMD, NWChem, ONETEP, ORCA, Octopus, OpenMX, Psi4, Qball, Qbox, QuantumATK, QuantumESPRESSO, SIESTA, TURBOMOLE, Tinker, VASP, WIEN2k, YAMBO, exciting, libAtoms, Workflow managers: AFLOW, ASR, Atomate, ElaStic, FHI-vibes, LOBSTER, MOFStructures, phonopy, Database managers: EELSDB, NeXus, OpenKIM$/
+ expect(screen.getByTestId('code-list')).toHaveTextContent(list)
+})
diff --git a/gui/src/utils.js b/gui/src/utils.js
index dae17ab559fd7c1042bae17cae0249ac2e09998c..4d1ea21113268920276d3cf4e5b8a6737d7c037f 100644
--- a/gui/src/utils.js
+++ b/gui/src/utils.js
@@ -609,7 +609,7 @@ export function delay(func) {
* Returns the correct form (plural/singular) for the given word. The syntax is
* similar to the "pluralize"-library.
*
- * @param {string} word The word to plurarize
+ * @param {string} word The word to pluralize
* @param {count} number How many of the words exist
* @param {boolean} inclusive Whether to prefix with the number (e.g. 3 ducks)
* @param {boolean} format Whether to format the number.
@@ -627,12 +627,18 @@ export function pluralize(word, count, inclusive, format = true, prefix) {
'material': 'materials',
'dataset': 'datasets',
'item': 'items',
- 'upload': 'uploads'
+ 'upload': 'uploads',
+ 'code': 'codes',
+ 'manager': 'managers'
}
- const plural = dictionary[word]
+ const words = word.trim().split(" ")
+ const lastWord = words[words.length - 1]
+ let plural = dictionary[lastWord]
if (isNil(plural)) {
throw Error(`The word ${word} is not in the dictionary, please add it.`)
}
+ words[words.length - 1] = plural
+ plural = words.join(" ")
const form = count === 1
? word
: plural
diff --git a/nomad/app/v1/routers/info.py b/nomad/app/v1/routers/info.py
index dd799de6ecb220a5d4027cc37e5255274fddc123..8f294ca0810c2d6ace60f052aa841059161dcd19 100644
--- a/nomad/app/v1/routers/info.py
+++ b/nomad/app/v1/routers/info.py
@@ -29,7 +29,8 @@ from pydantic.main import BaseModel
from nomad import config, normalizing, gitinfo
from nomad.utils import strip
from nomad.search import search
-from nomad.parsing import parsers, MatchingParser
+from nomad.parsing import parsers
+from nomad.parsing.parsers import code_metadata
from nomad.app.v1.models import Aggregation, StatisticsAggregation
from nomad.metainfo.elasticsearch_extension import entry_type
@@ -105,15 +106,6 @@ def statistics():
response_model=InfoModel)
async def get_info():
''' Return information about the nomad backend and its configuration. '''
- codes_dict = {}
- for parser in parsers.parser_dict.values():
- if isinstance(parser, MatchingParser) and parser.domain == 'dft':
- code_name = parser.code_name
- if code_name in codes_dict:
- continue
- codes_dict[code_name] = dict(code_name=code_name, code_homepage=parser.code_homepage)
- codes = sorted(list(codes_dict.values()), key=lambda code_info: code_info['code_name'].lower())
-
return {
'parsers': [
key[key.index('/') + 1:]
@@ -121,7 +113,10 @@ async def get_info():
'metainfo_packages': ['general', 'general.experimental', 'common', 'public'] + sorted([
key[key.index('/') + 1:]
for key in parsers.parser_dict.keys()]),
- 'codes': codes,
+ 'codes': [
+ {'code_name': x['codeLabel'], 'code_homepage': x['codeUrl']}
+ for x in sorted(code_metadata.values(), key=lambda info: info['codeLabel'].lower())
+ ],
'normalizers': [normalizer.__name__ for normalizer in normalizing.normalizers],
'statistics': statistics(),
'search_quantities': {
diff --git a/nomad/cli/dev.py b/nomad/cli/dev.py
index 13c8d296f48e3cfa8a60b4c4dc40399d3c3c1aac..278d272e6b398547fcceea32e722dd7c436260e5 100644
--- a/nomad/cli/dev.py
+++ b/nomad/cli/dev.py
@@ -162,23 +162,9 @@ def search_quantities():
@dev.command(help='Generates a JSON file that compiles all the parser metadata from each parser project.')
def parser_metadata():
import json
- import yaml
- import os
- import os.path
- from glob import glob
-
- parsers_metadata = {}
- parsers_path = './dependencies/parsers'
- for parser_metadata_file in sorted(glob(f'{parsers_path}/**/metadata.yaml', recursive=True)):
- with open(parser_metadata_file) as f:
- parser_metadata = yaml.load(f, Loader=yaml.FullLoader)
- parsers_metadata[os.path.basename(os.path.dirname(parser_metadata_file))] = parser_metadata
-
- parsers_metadata = {
- key: parsers_metadata[key]
- for _, key in sorted([(key.lower(), key) for key in parsers_metadata], key=lambda x: x[0])}
+ from nomad.parsing.parsers import code_metadata
- print(json.dumps(parsers_metadata, indent=2))
+ print(json.dumps(code_metadata, indent=2, sort_keys=True))
@dev.command(help='Generates a JSON file from example-uploads metadata in the YAML file.')
diff --git a/nomad/datamodel/metainfo/simulation/calculation.py b/nomad/datamodel/metainfo/simulation/calculation.py
index 8eb6ec93a2ccda46b8123d7707b8978ad4d80271..01f16dea689190964901a8c7e37ea2bdf9227348 100644
--- a/nomad/datamodel/metainfo/simulation/calculation.py
+++ b/nomad/datamodel/metainfo/simulation/calculation.py
@@ -21,7 +21,7 @@ import typing # pylint: disable=unused-import
from nomad.metainfo import ( # pylint: disable=unused-import
MSection, MCategory, Category, Package, Quantity, Section, SubSection, SectionProxy,
Reference, MEnum, derived)
-from nomad.datamodel.metainfo.simulation.system import System
+from nomad.datamodel.metainfo.simulation.system import System, AtomsGroup
from nomad.datamodel.metainfo.simulation.method import Method
from ..common import FastAccess
@@ -178,6 +178,44 @@ class AtomicValues(MSection):
''')
+class AtomicGroup(MSection):
+ '''
+ Generic section containing the values and information reqarding a molecular or sub-molecular
+ quantity that is a function of an atomic group such as radius of gyration...
+ '''
+
+ m_def = Section(validate=False)
+
+ kind = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Kind of the quantity.
+ ''')
+
+
+class AtomicGroupValues(MSection):
+ '''
+ Generic section containing information regarding the values of a trajectory property.
+ '''
+
+ m_def = Section(validate=False)
+
+ label = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Describes the atoms or molecule types involved in determining the property.
+ ''')
+
+ atomsgroup_ref = Quantity(
+ type=Reference(AtomsGroup.m_def),
+ shape=[1],
+ description='''
+ References to the atoms_group section containing the molecule for which Rg was calculated.
+ ''')
+
+
class EnergyEntry(Atomic):
'''
Section describing a type of energy or a contribution to the total energy.
@@ -1538,6 +1576,34 @@ class VibrationalFrequencies(MSection):
infrared = SubSection(sub_section=VibrationalFrequenciesValues.m_def, repeats=False)
+class RadiusOfGyrationValues(AtomicGroupValues):
+ '''
+ Section containing information regarding the values of
+ radius of gyration (Rg).
+ '''
+
+ m_def = Section(validate=False)
+
+ value = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='m',
+ description='''
+ Value of Rg.
+ ''')
+
+
+class RadiusOfGyration(AtomicGroup):
+ '''
+ Section containing information about the calculation of
+ radius of gyration (Rg).
+ '''
+
+ m_def = Section(validate=False)
+
+ radius_of_gyration_values = SubSection(sub_section=RadiusOfGyrationValues.m_def, repeats=True)
+
+
class BaseCalculation(MSection):
'''
Contains computed properties of a configuration as defined by the corresponding
@@ -1675,6 +1741,8 @@ class BaseCalculation(MSection):
density_charge = SubSection(sub_section=Density.m_def, repeats=True)
+ radius_of_gyration = SubSection(sub_section=RadiusOfGyration.m_def, repeats=True)
+
volume = Quantity(
type=np.dtype(np.float64),
shape=[],
diff --git a/nomad/parsing/parser.py b/nomad/parsing/parser.py
index fbe0d530ae5fc767beb1f87991e77301d5db45c2..e488a22d94a807d179430c7c5f02c1f86fdf3aff 100644
--- a/nomad/parsing/parser.py
+++ b/nomad/parsing/parser.py
@@ -16,19 +16,35 @@
# limitations under the License.
#
-from typing import List, Iterable, Dict, Union
+from typing import List, Iterable, Dict, Union, Any, Optional
from abc import ABCMeta, abstractmethod
import re
import os
import os.path
+from enum import Enum
from functools import lru_cache
import importlib
+from pydantic import BaseModel, Extra # pylint: disable=unused-import
+import yaml
from nomad import config, utils
from nomad.datamodel import EntryArchive, EntryMetadata
from nomad.metainfo import Package
+class ParserStatus(Enum):
+ PRODUCTION = "production"
+ BETA = "beta"
+
+
+class ParserMetadata(BaseModel, use_enum_values=True, extra=Extra.allow):
+ codeLabel: str
+ codeUrl: Optional[str]
+ codeCategory: str
+ codeName: str
+ status: ParserStatus
+
+
class Parser(metaclass=ABCMeta):
'''
Instances specify a parser. It allows to find *main files* from given uploaded
@@ -44,6 +60,7 @@ class Parser(metaclass=ABCMeta):
def __init__(self):
self.domain = 'dft'
+ self.metadata = None
@abstractmethod
def is_mainfile(
@@ -161,8 +178,11 @@ class MatchingParser(Parser):
A parser implementation that uses regular expressions to match mainfiles.
Arguments:
- code_name: The name of the code or input format
+ name: The internally used name for the parser. The prefix 'parser/' will
+ be automatically added for legacy reasons.
+ code_name: The displayed name for the parser
code_homepage: The homepage of the code or input format
+ code_catogory: An optional category for the code.
mainfile_mime_re: A regexp that is used to match against a files mime type
mainfile_contents_re: A regexp that is used to match the first 1024 bytes of a
potential mainfile.
@@ -173,7 +193,12 @@ class MatchingParser(Parser):
supported_compressions: A list of [gz, bz2], if the parser supports compressed files
'''
def __init__(
- self, name: str, code_name: str, code_homepage: str = None,
+ self,
+ name: str = None,
+ code_name: str = None,
+ code_homepage: str = None,
+ code_category: str = None,
+ metadata_path: str = None,
mainfile_contents_re: str = None,
mainfile_binary_header: bytes = None,
mainfile_binary_header_re: bytes = None,
@@ -184,14 +209,42 @@ class MatchingParser(Parser):
supported_compressions: List[str] = []) -> None:
super().__init__()
+
self.name = name
self.code_name = code_name
self.code_homepage = code_homepage
+ self.code_category = code_category
+
+ # If a metainfo path is given, read the code metainfo from there.
+ self.metadata_path = metadata_path
+ metadata_keys = {
+ 'code_name': 'codeLabel',
+ 'code_homepage': 'codeUrl',
+ 'code_category': 'codeCategory',
+ 'status': 'status',
+ 'name': 'codeName'
+ }
+ if metadata_path is not None:
+ metadata = ParserMetadata(**self.read_metadata_file(metadata_path))
+ self.metadata = metadata
+ for key_var, key_file in metadata_keys.items():
+ val_local = locals().get(key_var)
+ val_file = getattr(metadata, key_file)
+ if val_local is not None:
+ raise ValueError(
+ f'{key_var} specified both in metadata file ({val_file}) and in '
+ f'parser constructor ({val_local})')
+ if key_file == 'codeName':
+ val_file = f'parsers/{val_file}'
+ setattr(self, key_var, val_file)
+
+ assert self.code_name, f'please provide a code name for {name}'
self.domain = domain
self._mainfile_binary_header = mainfile_binary_header
self._mainfile_mime_re = re.compile(mainfile_mime_re)
self._mainfile_name_re = re.compile(mainfile_name_re)
self._mainfile_alternative = mainfile_alternative
+
# Assign private variable this way to avoid static check issue.
if mainfile_contents_re is not None:
self._mainfile_contents_re = re.compile(mainfile_contents_re)
@@ -205,6 +258,20 @@ class MatchingParser(Parser):
self._ls = lru_cache(maxsize=16)(lambda directory: os.listdir(directory))
+ def read_metadata_file(self, metadata_file: str) -> Dict[str, Any]:
+ '''
+ Read parser metadata from a yaml file.
+ '''
+ logger = utils.get_logger(__name__)
+ try:
+ with open(metadata_file, 'r', encoding='UTF-8') as f:
+ parser_metadata = yaml.load(f, Loader=yaml.FullLoader)
+ except Exception as e:
+ logger.warning('failed to read parser metadata', exc_info=e)
+ raise
+
+ return parser_metadata
+
def is_mainfile(
self, filename: str, mime: str, buffer: bytes, decoded_buffer: str,
compression: str = None) -> Union[bool, Iterable[str]]:
@@ -283,15 +350,17 @@ class MatchingParserInterface(MatchingParser):
self.mainfile_parser.parse(mainfile, archive, logger)
def import_parser_class(self):
+ logger = utils.get_logger(__name__)
try:
module_path, parser_class = self._parser_class_name.rsplit('.', 1)
module = importlib.import_module(module_path)
- return getattr(module, parser_class)
+ parser = getattr(module, parser_class)
except Exception as e:
- logger = utils.get_logger(__name__)
logger.error('cannot import parser', exc_info=e)
raise e
+ return parser
+
class ArchiveParser(MatchingParser):
def __init__(self):
diff --git a/nomad/parsing/parsers.py b/nomad/parsing/parsers.py
index b70f391218f063c3f278f6c8b0189d256008ad98..654623fe3bd3f294bda5b6d9fa72ca90c4ad82f0 100644
--- a/nomad/parsing/parsers.py
+++ b/nomad/parsing/parsers.py
@@ -19,6 +19,8 @@
import os.path
from typing import Tuple, List, Dict
from collections.abc import Iterable
+import pkgutil
+from pathlib import Path
from nomad import config
from nomad.datamodel import EntryArchive, EntryMetadata, results
@@ -196,30 +198,37 @@ def run_parser(
return entry_archives
+# Here we resolve the path of the installation directories of various parsers.
+# Note that this should be done in a way that does not yet import the modules
+# themselves (this takes a while). The parser modules are imported lazily later.
+prefix_electronic = f'{Path(pkgutil.get_loader("electronicparsers").path).parent.absolute()}' # type: ignore
+prefix_atomistic = f'{Path(pkgutil.get_loader("atomisticparsers").path).parent.absolute()}' # type: ignore
+prefix_workflow = f'{Path(pkgutil.get_loader("workflowparsers").path).parent.absolute()}' # type: ignore
+prefix_database = f'{Path(pkgutil.get_loader("databaseparsers").path).parent.absolute()}' # type: ignore
+prefix_eels = f'{Path(pkgutil.get_loader("eelsdbparser").path).parent.absolute()}' # type: ignore
+
parsers = [
GenerateRandomParser(),
TemplateParser(),
ChaosParser(),
MatchingParserInterface(
'electronicparsers.AbinitParser',
- name='parsers/abinit', code_name='ABINIT', code_homepage='https://www.abinit.org/',
+ metadata_path=f'{prefix_electronic}/abinit/metadata.yaml',
mainfile_contents_re=(r'^\n*\.Version\s*[0-9.]*\s*of ABINIT\s*')
),
- MatchingParserInterface(
- 'electronicparsers.ATKParser',
- name='parsers/atk', code_name='AtomistixToolKit',
- code_homepage='https://www.synopsys.com/silicon/quantumatk.html',
- mainfile_name_re=r'^.*\.nc', mainfile_mime_re=r'application/octet-stream'
- ),
MatchingParserInterface(
'electronicparsers.AMSParser',
- name='parsers/ams', code_name='AMS',
- code_homepage='https://www.scm.com',
+ metadata_path=f'{prefix_electronic}/ams/metadata.yaml',
mainfile_contents_re=r'\* +\| +A M S +\| +\*'
),
+ MatchingParserInterface(
+ 'electronicparsers.ATKParser',
+ metadata_path=f'{prefix_electronic}/atk/metadata.yaml',
+ mainfile_name_re=r'^.*\.nc', mainfile_mime_re=r'application/octet-stream'
+ ),
MatchingParserInterface(
'electronicparsers.BigDFTParser',
- name='parsers/bigdft', code_name='BigDFT', code_homepage='http://bigdft.org/',
+ metadata_path=f'{prefix_electronic}/bigdft/metadata.yaml',
mainfile_contents_re=(
# r'__________________________________ A fast and precise DFT wavelet code\s*'
# r'\| \| \| \| \| \|\s*'
@@ -250,18 +259,18 @@ parsers = [
),
MatchingParserInterface(
'electronicparsers.CastepParser',
- name='parsers/castep', code_name='CASTEP', code_homepage='http://www.castep.org/',
+ metadata_path=f'{prefix_electronic}/castep/metadata.yaml',
mainfile_contents_re=(r'\s\|\s*CCC\s*AA\s*SSS\s*TTTTT\s*EEEEE\s*PPPP\s*\|\s*')
),
MatchingParserInterface(
'electronicparsers.CharmmParser',
- name='parsers/charmm', code_name='Charmm', domain='dft',
+ metadata_path=f'{prefix_electronic}/charmm/metadata.yaml',
mainfile_contents_re=r'\s*Chemistry\s*at\s*HARvard\s*Macromolecular\s*Mechanics\s*',
mainfile_mime_re=r'text/.*'
),
MatchingParserInterface(
'electronicparsers.CP2KParser',
- name='parsers/cp2k', code_name='CP2K', code_homepage='https://www.cp2k.org/',
+ metadata_path=f'{prefix_electronic}/cp2k/metadata.yaml',
mainfile_contents_re=(
r'\*\*\*\* \*\*\*\* \*\*\*\*\*\* \*\* PROGRAM STARTED AT\s.*\n'
r' \*\*\*\*\* \*\* \*\*\* \*\*\* \*\* PROGRAM STARTED ON\s*.*\n'
@@ -271,59 +280,52 @@ parsers = [
),
MatchingParserInterface(
'electronicparsers.CPMDParser',
- name='parsers/cpmd', code_name='CPMD',
- code_homepage='https://www.lcrc.anl.gov/for-users/software/available-software/cpmd/',
+ metadata_path=f'{prefix_electronic}/cpmd/metadata.yaml',
mainfile_contents_re=(r'\*\*\* \*\* \*\*\* \*\* \*\*\*\* \*\* \*\* \*\*\*')
),
MatchingParserInterface(
'electronicparsers.CrystalParser',
- name='parsers/crystal',
- code_name='Crystal',
- code_homepage='https://www.crystal.unito.it/',
+ metadata_path=f'{prefix_electronic}/crystal/metadata.yaml',
mainfile_contents_re=(
fr'(\r?\n \*\s+CRYSTAL[\d]+\s+\*\r?\n \*\s*[a-zA-Z]+ : \d+[\.\d+]*)')
),
MatchingParserInterface(
'electronicparsers.Dmol3Parser',
- name='parsers/dmol', code_name='DMol3',
- code_homepage='http://dmol3.web.psi.ch/dmol3.html', domain='dft',
+ metadata_path=f'{prefix_electronic}/dmol3/metadata.yaml',
mainfile_name_re=r'.*\.outmol',
mainfile_contents_re=r'Materials Studio DMol\^3'
),
MatchingParserInterface(
'electronicparsers.ElkParser',
- name='parsers/elk', code_name='elk', code_homepage='http://elk.sourceforge.net/',
+ metadata_path=f'{prefix_electronic}/elk/metadata.yaml',
mainfile_contents_re=r'\| Elk version [0-9.a-zA-Z]+ started \|'
),
MatchingParserInterface(
'electronicparsers.ExcitingParser',
- name='parsers/exciting', code_name='exciting', code_homepage='http://exciting-code.org/',
+ metadata_path=f'{prefix_electronic}/exciting/metadata.yaml',
mainfile_name_re=r'^.*.OUT(\.[^/]*)?$', mainfile_contents_re=(r'EXCITING.*started')
),
MatchingParserInterface(
'electronicparsers.FHIAimsParser',
- name='parsers/fhi-aims', code_name='FHI-aims',
- code_homepage='https://aimsclub.fhi-berlin.mpg.de/',
+ metadata_path=f'{prefix_electronic}/fhiaims/metadata.yaml',
mainfile_contents_re=(
r'^(.*\n)*'
r'?\s*Invoking FHI-aims \.\.\.')
),
MatchingParserInterface(
'electronicparsers.FleurParser',
- name='parsers/fleur', code_name='fleur',
- code_homepage='https://www.flapw.de/', domain='dft',
+ metadata_path=f'{prefix_electronic}/fleur/metadata.yaml',
mainfile_contents_re=r'This output is generated by fleur.'
),
MatchingParserInterface(
'electronicparsers.FploParser',
- name='parsers/fplo', code_name='fplo', domain='dft',
+ metadata_path=f'{prefix_electronic}/fplo/metadata.yaml',
mainfile_contents_re=r'\s*\|\s*FULL-POTENTIAL LOCAL-ORBITAL MINIMUM BASIS BANDSTRUCTURE CODE\s*\|\s*',
mainfile_mime_re=r'text/.*'
),
MatchingParserInterface(
'electronicparsers.GamessParser',
- name='parsers/gamess', code_name='GAMESS',
- code_homepage='https://www.msg.chem.iastate.edu/gamess/versions.html',
+ metadata_path=f'{prefix_electronic}/gamess/metadata.yaml',
mainfile_contents_re=(
r'\s*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\**\s*'
r'\s*\*\s*GAMESS VERSION =\s*(.*)\*\s*'
@@ -331,48 +333,55 @@ parsers = [
),
MatchingParserInterface(
'electronicparsers.GaussianParser',
- name='parsers/gaussian', code_name='Gaussian', code_homepage='http://gaussian.com/',
- mainfile_mime_re=r'.*', mainfile_contents_re=(
+ metadata_path=f'{prefix_electronic}/gaussian/metadata.yaml',
+ mainfile_mime_re=r'.*',
+ mainfile_contents_re=(
r'\s*Cite this work as:'
r'\s*Gaussian [0-9]+, Revision [A-Za-z0-9\.]*,')
),
MatchingParserInterface(
'electronicparsers.GPAWParser',
- name='parsers/gpaw', code_name='GPAW', code_homepage='https://wiki.fysik.dtu.dk/gpaw/',
+ metadata_path=f'{prefix_electronic}/gpaw/metadata.yaml',
mainfile_name_re=(r'^.*\.(gpw2|gpw)$'),
mainfile_mime_re=r'application/(x-tar|octet-stream)'
),
MatchingParserInterface(
'electronicparsers.MolcasParser',
- name='parsers/molcas', code_name='MOLCAS', code_homepage='http://www.molcas.org/',
- domain='dft', mainfile_contents_re=r'M O L C A S'
+ metadata_path=f'{prefix_electronic}/molcas/metadata.yaml',
+ mainfile_contents_re=r'M O L C A S'
+ ),
+ MatchingParserInterface(
+ 'electronicparsers.MopacParser',
+ metadata_path=f'{prefix_electronic}/mopac/metadata.yaml',
+ mainfile_contents_re=r'\s*\*\*\s*MOPAC\s*([0-9a-zA-Z]*)\s*\*\*\s*',
+ mainfile_mime_re=r'text/.*',
),
MatchingParserInterface(
'electronicparsers.NWChemParser',
- name='parsers/nwchem', code_name='NWChem', code_homepage='http://www.nwchem-sw.org/',
+ metadata_path=f'{prefix_electronic}/nwchem/metadata.yaml',
mainfile_contents_re=(
r'Northwest Computational Chemistry Package \(NWChem\) (\d+\.)+\d+')
),
MatchingParserInterface(
'electronicparsers.OctopusParser',
- name='parsers/octopus', code_name='Octopus', code_homepage='https://octopus-code.org/',
+ metadata_path=f'{prefix_electronic}/octopus/metadata.yaml',
mainfile_contents_re=(r'\|0\) ~ \(0\) \|')
),
MatchingParserInterface(
'electronicparsers.OnetepParser',
- name='parsers/onetep', code_name='ONETEP', code_homepage='https://www.onetep.org/',
- domain='dft', mainfile_contents_re=r'####### # # ####### ####### ####### ######'
+ metadata_path=f'{prefix_electronic}/onetep/metadata.yaml',
+ mainfile_contents_re=r'####### # # ####### ####### ####### ######'
),
MatchingParserInterface(
'electronicparsers.OpenmxParser',
- name='parsers/openmx', code_name='OpenMX', code_homepage='http://www.openmx-square.org/',
+ metadata_path=f'{prefix_electronic}/openmx/metadata.yaml',
mainfile_mime_re=r'(text/.*)',
mainfile_name_re=r'.*\.out$',
mainfile_contents_re=(r'^\*{59}\s+\*{59}\s+This calculation was performed by OpenMX'),
),
MatchingParserInterface(
'electronicparsers.OrcaParser',
- name='parsers/orca', code_name='ORCA', code_homepage='https://orcaforum.kofo.mpg.de/',
+ metadata_path=f'{prefix_electronic}/orca/metadata.yaml',
mainfile_contents_re=(
r'\s+\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\**\s*'
r'\s+\* O R C A \*\s*'
@@ -382,45 +391,41 @@ parsers = [
),
MatchingParserInterface(
'electronicparsers.Psi4Parser',
- name='parsers/psi4', code_name='Psi4', code_homepage='https://psicode.org/',
+ metadata_path=f'{prefix_electronic}/psi4/metadata.yaml',
mainfile_contents_re=(r'Psi4: An Open-Source Ab Initio Electronic Structure Package')
),
MatchingParserInterface(
'electronicparsers.QBallParser',
- name='parsers/qball',
- code_name='qball',
+ metadata_path=f'{prefix_electronic}/qball/metadata.yaml',
mainfile_contents_re='qball',
supported_compressions=["gz", "bz2", "xz"]
),
MatchingParserInterface(
'electronicparsers.QboxParser',
- name='parsers/qbox', code_name='qbox', code_homepage='http://qboxcode.org/',
- domain='dft', mainfile_mime_re=r'(application/xml)|(text/.*)',
+ metadata_path=f'{prefix_electronic}/qbox/metadata.yaml',
+ mainfile_mime_re=r'(application/xml)|(text/.*)',
mainfile_contents_re=(r'http://qboxcode.org')
),
MatchingParserInterface(
'electronicparsers.QuantumEspressoParser',
- name='parsers/quantumespresso', code_name='Quantum Espresso',
- code_homepage='https://www.quantum-espresso.org/',
+ metadata_path=f'{prefix_electronic}/quantumespresso/metadata.yaml',
mainfile_contents_re=(r'(Program PWSCF.*starts)|(Current dimensions of program PWSCF are)')
),
MatchingParserInterface(
'electronicparsers.SiestaParser',
- name='parsers/siesta', code_name='Siesta',
- code_homepage='https://departments.icmab.es/leem/siesta/',
+ metadata_path=f'{prefix_electronic}/siesta/metadata.yaml',
mainfile_contents_re=(
r'(Siesta Version: siesta-|SIESTA [0-9]\.[0-9]\.[0-9])|'
r'(\*\s*WELCOME TO SIESTA\s*\*)')
),
MatchingParserInterface(
'electronicparsers.TurbomoleParser',
- name='parsers/turbomole', code_name='turbomole',
- code_homepage='https://www.turbomole.org/',
+ metadata_path=f'{prefix_electronic}/turbomole/metadata.yaml',
mainfile_contents_re=(r'Copyright \(C\) [0-9]+ TURBOMOLE GmbH, Karlsruhe')
),
MatchingParserInterface(
'electronicparsers.VASPParser',
- name='parsers/vasp', code_name='VASP', code_homepage='https://www.vasp.at/',
+ metadata_path=f'{prefix_electronic}/vasp/metadata.yaml',
mainfile_mime_re=r'(application/.*)|(text/.*)',
mainfile_name_re=r'.*[^/]*xml[^/]*', # only the alternative mainfile name should match
mainfile_contents_re=(
@@ -433,56 +438,55 @@ parsers = [
),
MatchingParserInterface(
'electronicparsers.Wien2kParser',
- name='parsers/wien2k', code_name='WIEN2k', code_homepage='http://www.wien2k.at/',
+ metadata_path=f'{prefix_electronic}/wien2k/metadata.yaml',
mainfile_name_re=r'.*\.scf$',
mainfile_alternative=True,
mainfile_contents_re=r'\s*---------\s*:ITE[0-9]+:\s*[0-9]+\.\s*ITERATION\s*---------'
),
MatchingParserInterface(
'electronicparsers.YamboParser',
- name='parsers/yambo', code_name='YAMBO', code_homepage='https://yambo-code.org/',
+ metadata_path=f'{prefix_electronic}/yambo/metadata.yaml',
mainfile_contents_re=(r'Build.+\s+http://www\.yambo-code\.org')
),
MatchingParserInterface(
'electronicparsers.ABACUSParser',
- name='parsers/abacus', code_name='ABACUS', code_homepage='http://abacus.ustc.edu.cn/',
+ metadata_path=f'{prefix_electronic}/abacus/metadata.yaml',
mainfile_contents_re=(r'\s*\n\s*WELCOME TO ABACUS')
),
MatchingParserInterface(
'atomisticparsers.AmberParser',
- name='parsers/amber', code_name='Amber', domain='dft',
+ metadata_path=f'{prefix_atomistic}/amber/metadata.yaml',
mainfile_contents_re=r'\s*Amber\s[0-9]+\s[A-Z]+\s*[0-9]+'
),
MatchingParserInterface(
'atomisticparsers.AsapParser',
- name='parsers/asap', code_name='ASAP', domain='dft',
+ metadata_path=f'{prefix_atomistic}/asap/metadata.yaml',
mainfile_name_re=r'.*.traj$', mainfile_mime_re=r'application/octet-stream'
),
MatchingParserInterface(
'atomisticparsers.DFTBPlusParser',
- name='parsers/dftbplus', code_name='DFTB+', domain='dft',
+ metadata_path=f'{prefix_atomistic}/dftbplus/metadata.yaml',
mainfile_contents_re=r'\| DFTB\+',
mainfile_mime_re=r'text/.*'
),
MatchingParserInterface(
'atomisticparsers.DLPolyParser',
- name='parsers/dl-poly', code_name='DL_POLY',
- code_homepage='https://www.scd.stfc.ac.uk/Pages/DL_POLY.aspx',
+ metadata_path=f'{prefix_atomistic}/dlpoly/metadata.yaml',
mainfile_contents_re=(r'\*\* DL_POLY \*\*'),
),
MatchingParserInterface(
'atomisticparsers.GromacsParser',
- name='parsers/gromacs', code_name='Gromacs', code_homepage='http://www.gromacs.org/',
- domain='dft', mainfile_contents_re=r'gmx mdrun, (VERSION|version)'
+ metadata_path=f'{prefix_atomistic}/gromacs/metadata.yaml',
+ mainfile_contents_re=r'gmx mdrun, (VERSION|version)'
),
MatchingParserInterface(
'atomisticparsers.GromosParser',
- name='parsers/gromos', code_name='Gromos', domain='dft',
+ metadata_path=f'{prefix_atomistic}/gromos/metadata.yaml',
mainfile_contents_re=r'Bugreports to http://www.gromos.net'
),
MatchingParserInterface(
'atomisticparsers.GulpParser',
- name='parsers/gulp', code_name='gulp', code_homepage='http://gulp.curtin.edu.au/gulp/',
+ metadata_path=f'{prefix_atomistic}/gulp/metadata.yaml',
mainfile_contents_re=(
r'\s*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*'
r'\*\*\*\*\*\*\*\*\*\*\*\*\*\s*'
@@ -490,40 +494,28 @@ parsers = [
),
MatchingParserInterface(
'atomisticparsers.LammpsParser',
- name='parsers/lammps', code_name='LAMMPS', code_homepage='https://lammps.sandia.gov/',
- domain='dft', mainfile_contents_re=r'^LAMMPS'
+ metadata_path=f'{prefix_atomistic}/lammps/metadata.yaml',
+ mainfile_contents_re=r'^LAMMPS'
),
MatchingParserInterface(
'atomisticparsers.LibAtomsParser',
- name='parsers/lib-atoms', code_name='libAtoms', code_homepage='https://libatoms.github.io/',
+ metadata_path=f'{prefix_atomistic}/libatoms/metadata.yaml',
mainfile_contents_re=(r'\s*<GAP_params\s'),
),
- MatchingParserInterface(
- 'electronicparsers.MopacParser',
- name='parsers/mopac', code_name='MOPAC', domain='dft',
- mainfile_contents_re=r'\s*\*\*\s*MOPAC\s*([0-9a-zA-Z]*)\s*\*\*\s*',
- mainfile_mime_re=r'text/.*',
- ),
MatchingParserInterface(
'atomisticparsers.NAMDParser',
- name='parsers/namd', code_name='Namd', domain='dft',
+ metadata_path=f'{prefix_atomistic}/namd/metadata.yaml',
mainfile_contents_re=r'\s*Info:\s*NAMD\s*[0-9.]+\s*for\s*',
mainfile_mime_re=r'text/.*',
),
- MatchingParserInterface(
- 'databaseparsers.OpenKIMParser',
- name='parsers/openkim', code_name='OpenKIM', domain='dft',
- mainfile_mime_re=r'(application/json)|(text/.*)',
- mainfile_contents_re=r'openkim|OPENKIM|OpenKIM'
- ),
MatchingParserInterface(
'atomisticparsers.TinkerParser',
- name='parsers/tinker', code_name='TINKER', domain='dft',
+ metadata_path=f'{prefix_atomistic}/tinker/metadata.yaml',
mainfile_contents_re=r'TINKER --- Software Tools for Molecular Design'
),
MatchingParserInterface(
'workflowparsers.AFLOWParser',
- name='parsers/aflow', code_name='AFlow', code_homepage='http://www.aflowlib.org/',
+ metadata_path=f'{prefix_workflow}/aflow/metadata.yaml',
mainfile_mime_re=r'(application/json)|(text/.*)',
mainfile_name_re=r'.*aflowlib\.json.*', # only the alternative mainfile name should match
mainfile_contents_re=(
@@ -541,59 +533,60 @@ parsers = [
),
MatchingParserInterface(
'workflowparsers.ASRParser',
- name='parsers/asr', code_name='ASR',
- code_homepage='https://asr.readthedocs.io/en/latest/index.html',
+ metadata_path=f'{prefix_workflow}/asr/metadata.yaml',
mainfile_mime_re=r'(application/json)|(text/.*)',
mainfile_name_re=r'.*archive_.*\.json',
mainfile_contents_re=(r'"name": "ASR"')
),
MatchingParserInterface(
'workflowparsers.ElasticParser',
- name='parsers/elastic', code_name='elastic', code_homepage='http://exciting-code.org/elastic',
+ metadata_path=f'{prefix_workflow}/elastic/metadata.yaml',
mainfile_contents_re=r'\s*Order of elastic constants\s*=\s*[0-9]+\s*',
mainfile_name_re=(r'.*/INFO_ElaStic')
),
MatchingParserInterface(
'workflowparsers.FHIVibesParser',
- name='parsers/fhi-vibes', code_name='FHI-vibes',
- code_homepage='https://vibes.fhi-berlin.mpg.de/',
+ metadata_path=f'{prefix_workflow}/fhivibes/metadata.yaml',
mainfile_name_re=(r'^.*\.(nc)$'), mainfile_mime_re=r'(application/x-hdf)',
mainfile_binary_header_re=br'^\x89HDF'
),
MatchingParserInterface(
'workflowparsers.LobsterParser',
- name='parsers/lobster', code_name='LOBSTER',
- code_homepage='http://schmeling.ac.rwth-aachen.de/cohp/',
+ metadata_path=f'{prefix_workflow}/lobster/metadata.yaml',
mainfile_name_re=r'.*lobsterout$',
mainfile_contents_re=(r'^LOBSTER\s*v[\d\.]+.*'),
),
MatchingParserInterface(
'workflowparsers.AtomateParser',
- name='parsers/atomate', code_name='Atomate',
- code_homepage='https://materialsproject.org',
+ metadata_path=f'{prefix_workflow}/atomate/metadata.yaml',
mainfile_mime_re=r'(application/json)|(text/.*)',
mainfile_name_re=r'.*mp.+materials\.json',
mainfile_contents_re=(r'"pymatgen_version":')
),
MatchingParserInterface(
'workflowparsers.PhonopyParser',
- name='parsers/phonopy', code_name='Phonopy', code_homepage='https://phonopy.github.io/phonopy/',
+ metadata_path=f'{prefix_workflow}/phonopy/metadata.yaml',
mainfile_name_re=(r'(.*/phonopy-FHI-aims-displacement-0*1/control.in$)|(.*/phon.+yaml)')
),
MatchingParserInterface(
'eelsdbparser.EELSDBParser',
- name='parsers/eels', code_name='eels', code_homepage='https://eelsdb.eu/',
- domain='ems',
+ metadata_path=f'{prefix_eels}/metadata.yaml',
mainfile_mime_re=r'application/json',
mainfile_contents_re=(r'https://eelsdb.eu/spectra')
),
MatchingParserInterface(
'workflowparsers.MOFStructuresParser',
- name='parsers/mofstructures', code_name='MOF Structures',
+ metadata_path=f'{prefix_workflow}/mofstructures/metadata.yaml',
mainfile_mime_re=r'(application/json)|(text/.*)',
mainfile_name_re=r'.*mof_.*\.json',
mainfile_contents_re=r'MOF Structures'
),
+ MatchingParserInterface(
+ 'databaseparsers.OpenKIMParser',
+ metadata_path=f'{prefix_database}/openkim/metadata.yaml',
+ mainfile_mime_re=r'(application/json)|(text/.*)',
+ mainfile_contents_re=r'openkim|OPENKIM|OpenKIM'
+ ),
NexusParser(),
TabularDataParser(),
ArchiveParser()
@@ -602,22 +595,18 @@ parsers = [
empty_parsers = [
EmptyParser(
name='missing/octopus', code_name='Octopus', code_homepage='https://octopus-code.org/',
- domain='dft',
mainfile_name_re=r'(inp)|(.*/inp)'
),
EmptyParser(
- name='missing/crystal', code_name='Crystal', code_homepage='https://www.crystal.unito.it/index.php',
- domain='dft',
+ name='missing/crystal', code_name='CRYSTAL', code_homepage='https://www.crystal.unito.it/index.php',
mainfile_name_re=r'.*\.cryst\.out'
),
EmptyParser(
name='missing/wien2k', code_name='WIEN2k', code_homepage='http://www.wien2k.at/',
- domain='dft',
mainfile_name_re=r'.*\.scf'
),
EmptyParser(
name='missing/fhi-aims', code_name='FHI-aims', code_homepage='https://aimsclub.fhi-berlin.mpg.de/',
- domain='dft',
mainfile_name_re=r'.*\.fhiaims'
)
]
@@ -645,12 +634,15 @@ parser_dict['parser/onetep'] = parser_dict['parsers/onetep']
# register code names as possible statistic value to the dft datamodel
code_names = []
+code_metadata = {}
for parser in parsers:
+ code_name = getattr(parser, 'code_name', None)
if parser.domain == 'dft' and \
- getattr(parser, 'code_name', None) is not None and \
- getattr(parser, 'code_name') != 'currupted mainfile' and \
- getattr(parser, 'code_name') != 'Template':
- code_names.append(getattr(parser, 'code_name'))
+ code_name is not None and \
+ code_name != 'currupted mainfile' and \
+ code_name != 'Template':
+ code_names.append(code_name)
+ code_metadata[code_name] = parser.metadata.dict()
code_names = sorted(set(code_names), key=lambda code_name: code_name.lower())
results.Simulation.program_name.a_elasticsearch[0].values = code_names + [
config.services.unavailable_value, config.services.not_processed_value]
diff --git a/nomad/parsing/tabular.py b/nomad/parsing/tabular.py
index d75307e8e4382b0a647800c6785c61ac8bba5331..a450e595923e2b6652d3cefd3db38f77b92432cf 100644
--- a/nomad/parsing/tabular.py
+++ b/nomad/parsing/tabular.py
@@ -234,6 +234,7 @@ class TabularDataParser(MatchingParser):
def __init__(self) -> None:
super().__init__(
name='parser/tabular', code_name='tabular data',
+ domain=None,
mainfile_mime_re=r'text/.*|application/.*',
mainfile_name_re=r'.*\.archive\.(csv|xlsx?)$')