diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index ca7d3e3d8eb2ba2ad07f1a74314414a41174f334..5bdad66c816a37bfd80fd18bfc1729c3389442a4 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -236,6 +236,20 @@ deploy prod test:
- /^dev-.*$/
when: manual
+deploy prod util:
+ stage: release
+ before_script:
+ - mkdir -p /etc/deploy
+ - echo ${CI_K8S_PROD_CONFIG} | base64 -d > ${KUBECONFIG}
+ script:
+ - helm dependency update ops/helm/nomad
+ - helm upgrade --install nomad-util-v1 ops/helm/nomad -f ops/helm/nomad/deployments/prod-util-values.yaml --set image.tag=$CI_COMMIT_REF_NAME,roll=true --wait
+ - docker pull $TEST_IMAGE
+ - docker run -t -e NOMAD_KEYCLOAK_REALM_NAME=fairdi_nomad_prod $TEST_IMAGE python -m nomad.cli client -n https://nomad-lab.eu/prod/v1/util/api -u test -w $CI_NOMAD_TEST_PASSWORD integrationtests --skip-publish --skip-doi
+ except:
+ - /^dev-.*$/
+ when: manual
+
release latest image:
stage: release
script:
diff --git a/dependencies/parsers/atomistic b/dependencies/parsers/atomistic
index 7a57120d6b4845f471577af75ad3e205ee503ea5..5f18ce5289026a01856ea1741c62b09fd0c0ea8a 160000
--- a/dependencies/parsers/atomistic
+++ b/dependencies/parsers/atomistic
@@ -1 +1 @@
-Subproject commit 7a57120d6b4845f471577af75ad3e205ee503ea5
+Subproject commit 5f18ce5289026a01856ea1741c62b09fd0c0ea8a
diff --git a/dependencies/parsers/electronic b/dependencies/parsers/electronic
index eee9bd051c3c52e3560cdb8092f79488dee05009..0161e491222515f06d79a690cbdd56f109ac0ed0 160000
--- a/dependencies/parsers/electronic
+++ b/dependencies/parsers/electronic
@@ -1 +1 @@
-Subproject commit eee9bd051c3c52e3560cdb8092f79488dee05009
+Subproject commit 0161e491222515f06d79a690cbdd56f109ac0ed0
diff --git a/dependencies/parsers/workflow b/dependencies/parsers/workflow
index 4050431cce67d80793e548e7f79e44de7e95ecb8..557e880015153eabe05fd0c13e3efce73e6c5e97 160000
--- a/dependencies/parsers/workflow
+++ b/dependencies/parsers/workflow
@@ -1 +1 @@
-Subproject commit 4050431cce67d80793e548e7f79e44de7e95ecb8
+Subproject commit 557e880015153eabe05fd0c13e3efce73e6c5e97
diff --git a/gui/materia b/gui/materia
index 8089b06fc35d23e0ef5a39e9c6943ef7f876defe..b2016c324335605c7bc8a73966f3c39db68c87ff 160000
--- a/gui/materia
+++ b/gui/materia
@@ -1 +1 @@
-Subproject commit 8089b06fc35d23e0ef5a39e9c6943ef7f876defe
+Subproject commit b2016c324335605c7bc8a73966f3c39db68c87ff
diff --git a/gui/package.json b/gui/package.json
index 1f5282998e562b62ddf2d51cf4f419c1f9147e75..585415aa7737faba041e5d29df51f38a39f6b380 100644
--- a/gui/package.json
+++ b/gui/package.json
@@ -1,6 +1,6 @@
{
"name": "nomad-fair-gui",
- "version": "1.0.7",
+ "version": "1.0.8",
"commit": "e98694e",
"private": true,
"workspaces": [
diff --git a/gui/public/env.js b/gui/public/env.js
index e522694959bb1c8c8be0bbc2dcb788489ecbdf16..bc042beec2b5a3190fce5229f29332a1e5bc9881 100644
--- a/gui/public/env.js
+++ b/gui/public/env.js
@@ -11,7 +11,7 @@ window.nomadEnv = {
'encyclopediaBase': 'https://nomad-lab.eu/prod/rae/encyclopedia/#',
'debug': false,
'version': {
- 'label': '1.0.7',
+ 'label': '1.0.8',
'isBeta': false,
'isTest': true,
'usesBetaData': true,
diff --git a/gui/src/components/aitoolkit/CoursePage.js b/gui/src/components/aitoolkit/CoursePage.js
new file mode 100644
index 0000000000000000000000000000000000000000..4c1300f1e5d2dd064b67cd48259098a273d88926
--- /dev/null
+++ b/gui/src/components/aitoolkit/CoursePage.js
@@ -0,0 +1,454 @@
+/*
+ * 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 {
+ Button,
+ Grid,
+ Typography,
+ Divider,
+ IconButton,
+ makeStyles,
+ AccordionActions
+
+} from '@material-ui/core'
+import { Link } from 'react-router-dom'
+import { StringParam, useQueryParam } from 'use-query-params'
+import TutorialsIcon from '../../images/AIT_ico_bp_tutorial.svg'
+import ArrowIcon from '../../images/AIT_ico_bd_link_go_to.svg'
+import FigureAI from '../../images/AIT_illu_AIT.svg'
+import tutorials from '../../courseAI.json'
+import { aitoolkitEnabled } from '../../config'
+import MuiAccordion from '@material-ui/core/Accordion'
+import MuiAccordionSummary from '@material-ui/core/AccordionSummary'
+import MuiAccordionDetails from '@material-ui/core/AccordionDetails'
+import { styled } from '@material-ui/core/styles'
+import ArrowForwardIosSharpIcon from '@material-ui/icons/ArrowForwardIosSharp'
+import ExpandMoreIcon from '@material-ui/icons/ExpandMore'
+import Markdown from '../Markdown'
+import AccessIcon from '../../images/AIT_ico_bd_link_external_big.svg'
+import WatchIcon from '../../images/AIT_ico_bd_youtube.svg'
+import PdfIcon from '../../images/AIT_ico_bd_link_pdf.svg'
+import DoiIcon from '../../images/AIT_ico_bd_link_doi.svg'
+
+export const useStyles = makeStyles(theme => ({
+ root: {
+ margin: theme.spacing(3),
+ width: '100%',
+ marginLeft: 'auto',
+ marginRight: 'auto',
+ maxWidth: '1052px',
+ marginBottom: '150px'
+ },
+ sectionIcon: {
+ marginTop: theme.spacing(3)
+ },
+ sectionTitle: {
+ marginBottom: theme.spacing(1),
+ marginLeft: theme.spacing(2),
+ marginTop: '105px'
+ },
+ title: {
+ color: '#2A3C67',
+ fontSize: '35px',
+ marginLeft: '-10px',
+ fontWeight: theme.typography.fontWeightMedium,
+ marginTop: '-70px'
+ },
+ deck: {
+ color: '#2A3C67',
+ fontSize: '22px',
+ marginTop: '20px',
+ lineHeight: '30px',
+ marginLeft: '-10px',
+ width: '518px'
+ },
+ icon: {
+ height: '371px',
+ marginTop: '-20px',
+ marginLeft: '100px'
+ },
+ filter: {
+ fontWeight: theme.typography.fontWeightMedium,
+ color: '#2A3C67',
+ fontSize: '20px',
+ marginTop: '60px',
+ marginLeft: '0px'
+ },
+ autocomplete: {
+ height: 'auto',
+ color: '#2A3C67',
+ border: '3px solid #00DFE0',
+ borderRadius: '10px 10px 10px 10px',
+ marginTop: '10px',
+ marginLeft: '0px',
+ width: '240px'
+ },
+ tutorialsList: {
+ marginTop: '50px'
+ },
+ textLevel: {
+ textAlign: 'left',
+ color: '#2A3C67',
+ fontSize: '22px',
+ height: '22px',
+ marginTop: '-16px'
+ },
+ titleSecondary: {
+ fontWeight: 'bold',
+ color: '#00DFE0',
+ fontSize: '35px',
+ marginLeft: '-10px'
+ },
+ bottomButton: {
+ color: '#F3F2F5',
+ backgroundColor: '#F3F2F5',
+ borderRadius: '30px',
+ width: '242px',
+ height: '70px',
+ textAlign: 'center',
+ align: 'center',
+ marginTop: '40px',
+ textTransform: 'none',
+ fontSize: '12pt',
+ lineHeight: '20px'
+ },
+ bottomButtonText: {
+ color: '#2A3C67',
+ fontWeight: theme.typography.fontWeightMedium
+ },
+ bottomIcon: {
+ marginTop: '80px',
+ marginLeft: '120px'
+ },
+ tutorialTitleGrid: {
+ marginRight: '40px'
+ },
+ tutorialTitleText: {
+ fontWeight: theme.typography.fontWeightMedium,
+ fontSize: '28px',
+ color: '#2A3C67',
+ lineHeight: '30px'
+ },
+ fieldText: {
+ color: '#2A3C67'
+ },
+ linkAuthors: {
+ color: '#2A3C67',
+ cursor: 'pointer',
+ lineHeight: '20px',
+ fontSize: '16px'
+ },
+ tutorialDescriptionGrid: {
+ marginLeft: '50px'
+ },
+ tutorialDescriptionText: {
+ color: '#2A3C67',
+ fontSize: '18px'
+ },
+ keywordsGrid: {
+ marginLeft: '80px'
+ },
+ linkKeywords: {
+ border: '1.5px solid #00DFE0',
+ lineHeight: '35px',
+ color: '#2A3C67',
+ cursor: 'pointer',
+ fontStyle: 'normal',
+ fontSize: '16px'
+ },
+ tutorialActions: {
+ marginLeft: '50px'
+ },
+ tutorialResources: {
+ marginTop: '-17px',
+ marginLeft: '-6px'
+ }
+}))
+
+const Accordion = styled((props) => (
+ <MuiAccordion {...props} />
+))(({ theme }) => ({
+ backgroundColor: theme.palette.background.default,
+ borderBottom: '13px solid #7FEFEF'
+}))
+
+const AccordionSummary = styled((props) => (
+ <MuiAccordionSummary
+ expandIcon={<ArrowForwardIosSharpIcon sx={{ fontSize: '0.9rem' }} />}
+ {...props}
+ />
+))(({ theme }) => ({
+ flexDirection: 'row-reverse',
+ '& .MuiAccordionSummary-expandIconWrapper.Mui-expanded': {
+ transform: 'rotate(90deg)'
+ },
+ '& .MuiAccordionSummary-content': {
+ marginLeft: theme.spacing(1),
+ marginTop: '20px',
+ marginBottom: '20px'
+ }
+}))
+
+const AccordionDetails = styled(MuiAccordionDetails)(({ theme }) => ({
+ padding: theme.spacing(2)
+}))
+
+export default function TutorialsPage() {
+ const styles = useStyles()
+
+ const tutorials_list = tutorials.tutorials
+
+ tutorials_list.forEach(tutorial => {
+ tutorial.key = tutorial.title.replace(/\W/gm, '_').toLowerCase()
+ })
+
+ function AccordionsList() {
+ const [expanded, setExpanded] = useQueryParam('expanded', StringParam)
+ return (
+ tutorials_list.map(tutorial => (
+ <div key={tutorial.title} >
+ <Accordion
+ key={tutorial.key}
+ expanded={expanded === tutorial.key}
+ onChange={() => setExpanded(expanded === tutorial.key ? null : tutorial.key)}
+ elevation={0}
+ >
+ <AccordionSummary expandIcon={<ExpandMoreIcon />}>
+ <Grid container spacing={1} >
+ <Grid item xs={7} className={styles.tutorialTitleGrid} >
+ <Typography className={styles.tutorialTitleText}>
+ {tutorial.title}
+ </Typography>
+ </Grid>
+ <Grid item xs={4}>
+ <Typography className={styles.fieldText}>
+ {<b>Lecturer: </b> }
+ {tutorial.lecturer
+
+ }
+ </Typography>
+ </Grid>
+ </Grid>
+ </AccordionSummary>
+ <AccordionDetails >
+ <Grid container spacing={4}>
+ <Grid item xs={6} className={styles.tutorialDescriptionGrid}>
+ <Markdown className={styles.tutorialDescriptionText}>
+ {tutorial.description}
+ </Markdown>
+ </Grid>
+ <Grid item xs={4} className={styles.keywordsGrid}>
+
+ {tutorial.notebook_name_1 && <><Typography className={styles.fieldText}>
+ <b>Notebook authors:</b>
+ </Typography><Typography>
+ {tutorial.authors_notebook_1
+ .map(name => {
+ const label = name.split(',').reverse().join(' ')
+ return label
+ }).reduce((prev, curr) => [prev, ' | ', curr])}
+ </Typography>
+ <Button
+ href={tutorial.link_notebook_1}
+ target="tutorial"
+ startIcon={<img alt='Access icon' src={AccessIcon}></img>}
+ >
+ <Typography className={styles.fieldText} >
+ <b>Access notebook</b>
+ </Typography>
+ </Button>
+ </>}
+ {tutorial.notebook_name_2 && <><Typography className={styles.fieldText}>
+ <b>Notebook authors:</b>
+ </Typography><Typography>
+ {tutorial.authors_notebook_2
+ .map(name => {
+ const label = name.split(',').reverse().join(' ')
+ return label
+ }).reduce((prev, curr) => [prev, ' | ', curr])}
+ </Typography>
+ <Button
+ href={tutorial.link_notebook_2}
+ target="tutorial"
+ startIcon={<img alt='Access icon' src={AccessIcon}></img>}
+ >
+ <Typography className={styles.fieldText} >
+ <b>Access notebook</b>
+ </Typography>
+ </Button>
+ </>}
+ </Grid>
+ </Grid>
+ </AccordionDetails>
+ <AccordionActions>
+ <Grid container spacing={4}>
+ <Grid item xs={7} className={styles.tutorialActions}>
+ <Grid container spacing={0}>
+ <Grid item xs={5}>
+ <Button
+ href={tutorial.link_video_1}
+ target="tutorial"
+ startIcon={<img alt='Watch icon' src={WatchIcon}></img>}
+ >
+ <Typography className={styles.fieldText} >
+ <b>Watch video 1</b>
+ </Typography>
+ </Button>
+ </Grid>
+ <Grid item xs={5} >
+ <div>
+ { tutorial.link_video_2 && <Button
+ width='10px'
+ color='#2A3C67'
+ href={tutorial.link_video_2}
+ target="tutorial"
+ startIcon={<img alt='Watch icon' src={WatchIcon}></img>}
+ >
+ <Typography className={styles.fieldText} >
+ <b>Watch video 2</b>
+ </Typography>
+ </Button>}
+ </div>
+ </Grid>
+ </Grid>
+ </Grid>
+ {tutorial.link_paper &&
+ <Grid item xs={4} className={styles.tutorialResources}>
+ <Grid item xs={12}>
+ <Typography className={styles.fieldText}>
+ <b>Additional Resources</b>:
+ </Typography>
+ </Grid>
+ <Grid container spacing={0}>
+ <Grid item xs={2} >
+ <div>
+ {tutorial.link_paper && <Button
+ color='#2A3C67'
+ href={tutorial.link_paper}
+ target="tutorial"
+ startIcon={<img alt='DOI icon' src={DoiIcon}></img>}>
+ </Button>}
+ </div>
+ </Grid>
+ <Grid item xs={2}>
+ <div>
+ {tutorial.link_paper && <Button
+ color='#2A3C67'
+ href={tutorial.link_paper}
+ target="tutorial"
+ startIcon={<img alt='PDF icon' src={PdfIcon}/>}>
+ </Button>}
+ </div>
+ </Grid>
+ </Grid>
+ </Grid>
+ }
+ </Grid>
+ </AccordionActions>
+ <Divider />
+ </Accordion>
+ </div>
+ )))
+ }
+
+ return <Grid container spacing={1} className={styles.root}>
+ <Grid container spacing={0} className={styles.Heading}>
+ <Grid item xs={6} className={styles.sectionTitle}>
+ <Grid container spacing={0}>
+ <Grid item xs={4} style={{marginTop: '-100px', marginLeft: '-20px'}}>
+ <IconButton
+ {...(aitoolkitEnabled ? ({to: 'aitoolkit', component: Link}) : ({href: 'https://nomad-lab.eu/AIToolkit', component: 'a'}))}
+ >
+ <img alt='AI toolkit logo' src={FigureAI} style={{width: '120px'}}/>
+ </IconButton>
+ </Grid>
+ <Grid item xs={8}>
+ <Typography className={styles.title}>
+ AI lectures
+ </Typography>
+ </Grid>
+ </Grid>
+ <Typography className={styles.deck}>
+ We present a virtual course in artificial intelligence, by proposing a path through some of the tutorial notebooks from the AI-toolkit. Each topic is presented via a video lecture and accompanied by one or more notebooks that allow for putting your hand on the explained methods. </Typography>
+ </Grid>
+ <Grid item xs={4} className={styles.sectionIcon}>
+ <img alt='Tutorials icon' src={TutorialsIcon} className={styles.icon}/>
+ </Grid>
+ </Grid>
+
+ <Grid container spacing={1} className={styles.tutorialsList}>
+ <Grid item xs={12}>
+ <Divider
+ style={{
+ backgroundColor: '#7FEFEF',
+ height: '13px',
+ borderRadius: '4px',
+ marginBottom: '-8px'
+ }}
+ />
+ </Grid>
+ <Grid item xs={12}>
+ <AccordionsList/>
+ </Grid>
+
+ </Grid>
+ <Grid item xs={6} className={styles.sectionTitle}>
+ <Typography className={styles.titleSecondary}>
+ Next intermediate level
+ </Typography>
+ <Typography className={styles.deck}>
+ If you are still curious about applications of artificial intelligence to materials science, you can find
+ more lectures and more notebooks in our tutorials section.
+ </Typography>
+ <Grid container spacing={1}>
+ <Grid item xs={4}>
+ <IconButton
+ component={Link}
+ {...(aitoolkitEnabled ? ({to: 'aitoolkit', component: Link}) : ({href: 'https://nomad-lab.eu/AIToolkit', component: 'a'}))}
+ style={{marginRight: '0px', marginTop: '20px'}}
+ >
+ <img alt='AI toolkit logo' src={FigureAI} style={{width: '120px'}}/>
+ </IconButton>
+ </Grid>
+ <Grid item xs={8}>
+ <Button
+ width='10px'
+ color='#2A3C67'
+ component={Link}
+ to="tutorials"
+ className={styles.bottomButton}
+ endIcon={<img alt='Arrow icon' src={ArrowIcon}/>}
+ >
+ <Typography className={styles.bottomButtonText}>
+ More AI tutorials
+ </Typography>
+ </Button>
+ </Grid>
+ </Grid>
+ </Grid>
+ <Grid item xs={4} className={styles.sectionIcon}>
+ <IconButton
+ component={Link}
+ to="tutorials"
+ className={styles.bottomIcon}
+ >
+ <img alt='Tutorials icon' src={TutorialsIcon} style={{width: '300px'}}/>
+ </IconButton>
+ </Grid>
+ </Grid>
+}
diff --git a/gui/src/components/nav/Routes.js b/gui/src/components/nav/Routes.js
index a8b230301718ce2d6aadf41cf5be23d1080ff940..9d3ead48a533ac23e563bc5329d24abe622a806f 100644
--- a/gui/src/components/nav/Routes.js
+++ b/gui/src/components/nav/Routes.js
@@ -26,6 +26,7 @@ import About from '../About'
import AIToolkitPage from '../aitoolkit/AIToolkitPage'
import TutorialsPage from '../aitoolkit/TutorialsPage'
import ReproducePage from '../aitoolkit/ReproducePage'
+import CoursePage from '../aitoolkit/CoursePage'
import { MetainfoPage, help as metainfoHelp } from '../archive/MetainfoBrowser'
import EntryPage, { help as entryHelp } from '../entry/EntryPage'
import UploadPage from '../uploads/UploadPage'
@@ -296,6 +297,11 @@ export const routes = [
path: 'reproduce',
title: 'Artificial Intelligence Toolkit',
component: ReproducePage
+ },
+ {
+ path: 'course',
+ title: 'Artificial Intelligence Toolkit',
+ component: CoursePage
}
]
},
diff --git a/gui/src/courseAI.json b/gui/src/courseAI.json
new file mode 100644
index 0000000000000000000000000000000000000000..b5f88b7e3736bcedbd43a465d04fd083bbf0bfec
--- /dev/null
+++ b/gui/src/courseAI.json
@@ -0,0 +1,136 @@
+ {
+ "tutorials": [
+ {
+ "lecturer": "Luca Ghiringhelli",
+ "title": "Introduction to artificial intelligence and machine-learning methods",
+ "description": "This introductory lecture covers a general overview of artificial intelligence methods, including machine-learning and data-mining methods. There is no hands-on notebook specifically associated to this lectures, but the concepts introduced therein can be useful to link together the various techniques presented in the next lectures.",
+ "link_video_1": "https://www.youtube.com/watch?v=z_Q0yXGHPDE",
+ "link_video_2": "https://www.youtube.com/watch?v=7m0vfdK716I",
+ "notebook_1": "true",
+ "authors_notebook_1": [
+ "Ahmetcik, Emre",
+ "Ziletti, Angelo",
+ "Ouyang, Runhai",
+ "Sbail\u00f2, Luigi",
+ "Scheffler, Matthias",
+ "Ghiringhelli, Luca M."]
+ },
+ {
+ "lecturer": "Santiago Rigamonti",
+ "title": "Regularized regression and kernel methods",
+ "description": "In this tutorial, we will explore the application of kernel ridge regression to the prediction of materials properties.",
+ "link_video_1": "https://www.youtube.com/watch?v=QHfcpuYfDtI",
+ "link_video_2": "https://www.youtube.com/watch?v=A6c_QJmMAqE",
+ "notebook_name_1": "krr4mat.ipynb",
+ "link_notebook_1": "https://analytics-toolkit.nomad-coe.eu/public/user-redirect/notebooks/tutorials/krr4mat.ipynb",
+ "authors_notebook_1": [
+ "Langer, Marcel"
+ ]
+ },
+ {
+ "lecturer": "Daniel Speckhard",
+ "title": "Decision trees and random forests",
+ "description": "In this tutorial, we will introduce decision trees. We go through a toy model introducing the SKLearn API. We then discuss step by step the different theoretical aspects of trees. We then move to training a regression tree and classification tree on different datasets related to materials science. We end the tutorial by covering random forests and bagging classfiers.",
+ "link_video_1": "https://www.youtube.com/watch?v=lUdCB6cqpvo",
+ "link_video_2": "https://www.youtube.com/watch?v=rwxE35URuF8",
+ "authors_notebook_1": [
+ "Speckhard, Daniel",
+ "Leitherer, Andreas",
+ "Ghiringhelli, Luca M."
+ ],
+ "notebook_name_1": "decision_tree.ipynb",
+ "link_notebook_1": "https://analytics-toolkit.nomad-coe.eu/public/user-redirect/notebooks/tutorials/decision_tree.ipynb"
+ },
+ {
+ "lecturer": "Angelo Ziletti",
+ "title": "Artificial neural networks and deep learning",
+ "link_video_1": "https://www.youtube.com/watch?v=-_-2ESB4Ag0",
+ "link_video_2": "https://www.youtube.com/watch?v=qRqIU3kYF80",
+ "description": "In these tutorials, we introduce the basic of deep learning, via tranditional multilayer perceptrons and modern convolutional neural networks.",
+ "notebook_name_1": "nn_regression.ipynb",
+ "link_notebook_1": "https://nomad-lab.eu/prod/analytics/public/user-redirect/notebooks/tutorials/nn_regression.ipynb",
+ "authors_notebook_1": [
+ "Leitherer, Andreas",
+ "Sbail\u00f2, Luigi",
+ "Ghiringhelli, Luca M."
+ ],
+ "notebook_name_2": "convolutional_nn.ipynb",
+ "link_notebook_2": "https://analytics-toolkit.nomad-coe.eu/public/user-redirect/notebooks/tutorials/convolutional_nn.ipynb",
+ "authors_notebook_2": [
+ "Ziletti, Angelo",
+ "Leitherer, Andreas",
+ "Ghiringhelli, Luca M."
+ ]
+ },
+ {
+ "lecturer": "Luigi Sbail\u00f2",
+ "title": "Unsupervised learning",
+ "link_video_1": "https://www.youtube.com/watch?v=Ozu-QCBB2bg",
+ "link_video_2": "https://www.youtube.com/watch?v=hnB5B7Iu6Ds",
+ "description": "In this tutorial, we introduce to the most popular clustering algorithms. We focus on partitioning, hierarchical and density-based clustering algorithms. The methods are tested on synthetic datasets of increasing complexity.",
+ "notebook_name_1": "clustering_tutorial.ipynb",
+ "link_notebook_1": "https://analytics-toolkit.nomad-coe.eu/public/user-redirect/notebooks/tutorials/clustering_tutorial.ipynb",
+ "authors_notebook_1": [
+ "Sbail\u00f2, Luigi",
+ "Ghiringhelli, Luca M."
+ ],
+ "notebook_name_2": "exploratory_analysis.ipynb",
+ "link_notebook_2": "https://analytics-toolkit.nomad-coe.eu/public/user-redirect/notebooks/tutorials/exploratory_analysis.ipynb",
+ "authors_notebook_2": [
+ "Sbail\u00f2, Luigi",
+ "Ghiringhelli, Luca M."
+ ]
+ },
+ {
+ "lecturer": "Luca Ghiringhelli",
+ "title": "Compressed sensing meets symbolic regression: SISSO",
+ "description": "In this tutorial, we will show how to find descriptive parameters to predict materials properties using symbolic regrression combined with compressed sensing tools. The relative stability of the zincblende (ZB) versus rocksalt (RS) structure of binary materials is predicted and compared against a model trained with kernel ridge regression.",
+ "link_video_1": "https://www.youtube.com/watch?v=YJZm4xot4bM",
+ "link_video_2": "https://www.youtube.com/watch?v=KjPCMdWikBg",
+ "notebook_name_1": "compressed_sensing.ipynb",
+ "authors_notebook_1": [
+ "Ahmetcik, Emre",
+ "Ziletti, Angelo",
+ "Ouyang, Runhai",
+ "Sbail\u00f2, Luigi",
+ "Scheffler, Matthias",
+ "Ghiringhelli, Luca M."
+ ],
+ "link_notebook_1": "https://analytics-toolkit.nomad-coe.eu/public/user-redirect/notebooks/tutorials/compressed_sensing.ipynb"
+ },
+ {
+ "lecturer": "Matthias Scheffler",
+ "title": "Subgroup discovery, rare-phenomena challenge, and domain of applicability",
+ "link_video_1": "https://www.youtube.com/watch?v=cizNEJypwao",
+ "link_video_2": "https://www.youtube.com/watch?v=uKEzs6koTcs",
+ "description": "In these tutorials, we introduce the subgroup discovery (SGD) method, which identifies rules (Boolean statements involving selected features among the given candidates) describing exceptional subsets of data. SGD is an exploratory analysis tools and allows for identifying local structure in the data, while most ML tools focus on global models. A notable application of SGD is to locate the domain of applicability of ML models, i.e., identifying the property of data that are expected to yield significantly lower errors than the overall dataset. A notebook on this specific application is also linked.",
+ "authors_notebook_1":[
+ "Foppa, Lucas",
+ "Ghiringhelli, Luca M."
+ ],
+
+ "notebook_name_1": "sgd_alloys_oxygen_reduction_evolution.ipynb",
+ "link_notebook_1": "https://nomad-lab.eu/prod/analytics/public/user-redirect/notebooks/tutorials/sgd_alloys_oxygen_reduction_evolution.ipynb",
+ "notebook_name_2": "domain_of_applicability.ipynb",
+ "link_notebook_2": "https://analytics-toolkit.nomad-coe.eu/public/user-redirect/notebooks/tutorials/domain_of_applicability.ipynb",
+ "authors_notebook_2": [
+ "Arif, Mohammad-Yasin",
+ "Sbail\u00f2, Luigi",
+ "Ghiringhelli, Luca M."
+ ]
+ },
+ {
+ "lecturer": "Lucas Foppa",
+ "title": "Fusion of experimental and computational data by AI",
+ "description": "In this tutorial, we provide an example of AI techniques combined to experiments, in such a way that the AI is trained on an initial set of data and the predictions of the trained model is used to guide the experiment in a similar but distinct class of materials.",
+ "link_video_1": "https://www.youtube.com/watch?v=8wbITgsDNqE",
+ "authors_notebook_1": [
+ "Foppa, Lucas",
+ "Ghiringhelli, Luca M.",
+ "Scheffler, Matthias"
+ ],
+ "notebook_name_1": "sgd_propylene_oxidation_hte.ipynb",
+ "link_notebook_1": "https://analytics-toolkit.nomad-coe.eu/public/user-redirect/notebooks/tutorials/sgd_propylene_oxidation_hte.ipynb"
+ }
+ ]
+ }
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diff --git a/gui/src/setupTests.js b/gui/src/setupTests.js
index 03ed708b22ae79f9acc96ffb2b352f83b7ddb08c..0dd4457ebe36487a18eb375aebc1da4c45f4d85b 100644
--- a/gui/src/setupTests.js
+++ b/gui/src/setupTests.js
@@ -11,7 +11,7 @@ global.nomadEnv = {
'appBase': 'http://nomad-lab.eu/prod/rae/beta',
'debug': false,
'version': {
- 'label': '1.0.7',
+ 'label': '1.0.8',
'isBeta': false,
'isTest': true,
'usesBetaData': true,
diff --git a/gui/yarn.lock b/gui/yarn.lock
index e5fc8cd173fb9f641a6772c161f31a87681ce44b..0c1e3aa0a863bafc30101ae354dd5dfde35c7e8c 100644
--- a/gui/yarn.lock
+++ b/gui/yarn.lock
@@ -1695,6 +1695,11 @@
dependencies:
type-detect "4.0.8"
+"@socket.io/component-emitter@~3.1.0":
+ version "3.1.0"
+ resolved "https://registry.yarnpkg.com/@socket.io/component-emitter/-/component-emitter-3.1.0.tgz#96116f2a912e0c02817345b3c10751069920d553"
+ integrity sha512-+9jVqKhRSpsc591z5vX+X5Yyw+he/HCB4iQ/RYxw35CEPaY1gnsNE43nf9n9AaYjAQrTiI/mOwKUKdUs9vf7Xg==
+
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version "4.2.0"
resolved "https://registry.npmjs.org/@svgr/babel-plugin-add-jsx-attribute/-/babel-plugin-add-jsx-attribute-4.2.0.tgz"
@@ -1883,16 +1888,52 @@
dependencies:
"@babel/types" "^7.3.0"
+"@types/component-emitter@^1.2.10":
+ version "1.2.11"
+ resolved "https://registry.yarnpkg.com/@types/component-emitter/-/component-emitter-1.2.11.tgz#50d47d42b347253817a39709fef03ce66a108506"
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resolved "https://registry.npmjs.org/@types/cookie/-/cookie-0.3.3.tgz"
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+"@types/cookie@^0.4.1":
+ version "0.4.1"
+ resolved "https://registry.yarnpkg.com/@types/cookie/-/cookie-0.4.1.tgz#bfd02c1f2224567676c1545199f87c3a861d878d"
+ integrity sha512-XW/Aa8APYr6jSVVA1y/DEIZX0/GMKLEVekNG727R8cs56ahETkRAy/3DR7+fJyh7oUgGwNQaRfXCun0+KbWY7Q==
+
+"@types/cors@^2.8.12":
+ version "2.8.12"
+ resolved "https://registry.yarnpkg.com/@types/cors/-/cors-2.8.12.tgz#6b2c510a7ad7039e98e7b8d3d6598f4359e5c080"
+ integrity sha512-vt+kDhq/M2ayberEtJcIN/hxXy1Pk+59g2FV/ZQceeaTyCtCucjL2Q7FXlFjtWn4n15KCr1NE2lNNFhp0lEThw==
+
+"@types/eslint-scope@^3.7.3":
+ version "3.7.3"
+ resolved "https://registry.yarnpkg.com/@types/eslint-scope/-/eslint-scope-3.7.3.tgz#125b88504b61e3c8bc6f870882003253005c3224"
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+ dependencies:
+ "@types/eslint" "*"
+ "@types/estree" "*"
+
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version "1.0.0"
resolved "https://registry.npmjs.org/@types/eslint-visitor-keys/-/eslint-visitor-keys-1.0.0.tgz"
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+"@types/eslint@*":
+ version "8.4.2"
+ resolved "https://registry.yarnpkg.com/@types/eslint/-/eslint-8.4.2.tgz#48f2ac58ab9c631cb68845c3d956b28f79fad575"
+ integrity sha512-Z1nseZON+GEnFjJc04sv4NSALGjhFwy6K0HXt7qsn5ArfAKtb63dXNJHf+1YW6IpOIYRBGUbu3GwJdj8DGnCjA==
+ dependencies:
+ "@types/estree" "*"
+ "@types/json-schema" "*"
+
+"@types/estree@*", "@types/estree@^0.0.51":
+ version "0.0.51"
+ resolved "https://registry.yarnpkg.com/@types/estree/-/estree-0.0.51.tgz#cfd70924a25a3fd32b218e5e420e6897e1ac4f40"
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+
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version "7.2.0"
resolved "https://registry.npmjs.org/@types/glob/-/glob-7.2.0.tgz"
@@ -1936,6 +1977,11 @@
dependencies:
"@types/istanbul-lib-report" "*"
+"@types/json-schema@*", "@types/json-schema@^7.0.8":
+ version "7.0.11"
+ resolved "https://registry.yarnpkg.com/@types/json-schema/-/json-schema-7.0.11.tgz#d421b6c527a3037f7c84433fd2c4229e016863d3"
+ integrity sha512-wOuvG1SN4Us4rez+tylwwwCV1psiNVOkJeM3AUWUNWg/jDQY2+HE/444y5gc+jBmRqASOm2Oeh5c1axHobwRKQ==
+
"@types/json-schema@^7.0.3", "@types/json-schema@^7.0.5", "@types/json-schema@^7.0.6", "@types/json-schema@^7.0.7":
version "7.0.9"
resolved "https://registry.npmjs.org/@types/json-schema/-/json-schema-7.0.9.tgz"
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+"@types/node@>=10.0.0":
+ version "17.0.31"
+ resolved "https://registry.yarnpkg.com/@types/node/-/node-17.0.31.tgz#a5bb84ecfa27eec5e1c802c6bbf8139bdb163a5d"
+ integrity sha512-AR0x5HbXGqkEx9CadRH3EBYx/VkiUgZIhP4wvPn/+5KIsgpNoyFaRlVe0Zlx9gRtg8fA06a9tskE2MSN7TcG4Q==
+
"@types/object-assign@^4.0.30":
version "4.0.30"
resolved "https://registry.npmjs.org/@types/object-assign/-/object-assign-4.0.30.tgz"
@@ -2234,6 +2285,14 @@
"@typescript-eslint/types" "4.33.0"
eslint-visitor-keys "^2.0.0"
+"@webassemblyjs/ast@1.11.1":
+ version "1.11.1"
+ resolved "https://registry.yarnpkg.com/@webassemblyjs/ast/-/ast-1.11.1.tgz#2bfd767eae1a6996f432ff7e8d7fc75679c0b6a7"
+ integrity sha512-ukBh14qFLjxTQNTXocdyksN5QdM28S1CxHt2rdskFyL+xFV7VremuBLVbmCePj+URalXBENx/9Lm7lnhihtCSw==
+ dependencies:
+ "@webassemblyjs/helper-numbers" "1.11.1"
+ "@webassemblyjs/helper-wasm-bytecode" "1.11.1"
+
"@webassemblyjs/ast@1.8.5":
version "1.8.5"
resolved "https://registry.npmjs.org/@webassemblyjs/ast/-/ast-1.8.5.tgz"
@@ -2243,45 +2302,36 @@
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"@webassemblyjs/wast-parser" "1.8.5"
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- version "1.9.0"
- resolved "https://registry.npmjs.org/@webassemblyjs/ast/-/ast-1.9.0.tgz"
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- "@webassemblyjs/wast-parser" "1.9.0"
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+ resolved "https://registry.yarnpkg.com/@webassemblyjs/floating-point-hex-parser/-/floating-point-hex-parser-1.11.1.tgz#f6c61a705f0fd7a6aecaa4e8198f23d9dc179e4f"
+ integrity sha512-iGRfyc5Bq+NnNuX8b5hwBrRjzf0ocrJPI6GWFodBFzmFnyvrQ83SHKhmilCU/8Jv67i4GJZBMhEzltxzcNagtQ==
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version "1.8.5"
resolved "https://registry.npmjs.org/@webassemblyjs/helper-code-frame/-/helper-code-frame-1.8.5.tgz"
@@ -2289,23 +2339,11 @@
dependencies:
"@webassemblyjs/wast-printer" "1.8.5"
-"@webassemblyjs/helper-code-frame@1.9.0":
- version "1.9.0"
- resolved "https://registry.npmjs.org/@webassemblyjs/helper-code-frame/-/helper-code-frame-1.9.0.tgz"
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- dependencies:
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resolved "https://registry.npmjs.org/@webassemblyjs/helper-fsm/-/helper-fsm-1.8.5.tgz"
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resolved "https://registry.npmjs.org/@webassemblyjs/helper-module-context/-/helper-module-context-1.8.5.tgz"
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mamacro "^0.0.3"
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- resolved "https://registry.npmjs.org/@webassemblyjs/helper-module-context/-/helper-module-context-1.9.0.tgz"
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+ resolved "https://registry.yarnpkg.com/@webassemblyjs/helper-numbers/-/helper-numbers-1.11.1.tgz#64d81da219fbbba1e3bd1bfc74f6e8c4e10a62ae"
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dependencies:
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+
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+ resolved "https://registry.yarnpkg.com/@webassemblyjs/helper-wasm-bytecode/-/helper-wasm-bytecode-1.11.1.tgz#f328241e41e7b199d0b20c18e88429c4433295e1"
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+"@webassemblyjs/helper-wasm-section@1.11.1":
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+ resolved "https://registry.yarnpkg.com/@webassemblyjs/helper-wasm-section/-/helper-wasm-section-1.11.1.tgz#21ee065a7b635f319e738f0dd73bfbda281c097a"
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+ dependencies:
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+ "@webassemblyjs/helper-buffer" "1.11.1"
+ "@webassemblyjs/helper-wasm-bytecode" "1.11.1"
+ "@webassemblyjs/wasm-gen" "1.11.1"
"@webassemblyjs/helper-wasm-section@1.8.5":
version "1.8.5"
@@ -2341,15 +2391,12 @@
"@webassemblyjs/helper-wasm-bytecode" "1.8.5"
"@webassemblyjs/wasm-gen" "1.8.5"
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+"@webassemblyjs/ieee754@1.11.1":
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+ resolved "https://registry.yarnpkg.com/@webassemblyjs/ieee754/-/ieee754-1.11.1.tgz#963929e9bbd05709e7e12243a099180812992614"
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dependencies:
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- "@webassemblyjs/helper-buffer" "1.9.0"
- "@webassemblyjs/helper-wasm-bytecode" "1.9.0"
- "@webassemblyjs/wasm-gen" "1.9.0"
+ "@xtuc/ieee754" "^1.2.0"
"@webassemblyjs/ieee754@1.8.5":
version "1.8.5"
@@ -2358,12 +2405,12 @@
dependencies:
"@xtuc/ieee754" "^1.2.0"
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- resolved "https://registry.npmjs.org/@webassemblyjs/ieee754/-/ieee754-1.9.0.tgz"
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+"@webassemblyjs/leb128@1.11.1":
+ version "1.11.1"
+ resolved "https://registry.yarnpkg.com/@webassemblyjs/leb128/-/leb128-1.11.1.tgz#ce814b45574e93d76bae1fb2644ab9cdd9527aa5"
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dependencies:
- "@xtuc/ieee754" "^1.2.0"
+ "@xtuc/long" "4.2.2"
"@webassemblyjs/leb128@1.8.5":
version "1.8.5"
@@ -2372,22 +2419,29 @@
dependencies:
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- dependencies:
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+"@webassemblyjs/utf8@1.11.1":
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+ resolved "https://registry.yarnpkg.com/@webassemblyjs/utf8/-/utf8-1.11.1.tgz#d1f8b764369e7c6e6bae350e854dec9a59f0a3ff"
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resolved "https://registry.npmjs.org/@webassemblyjs/utf8/-/utf8-1.8.5.tgz"
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- resolved "https://registry.npmjs.org/@webassemblyjs/utf8/-/utf8-1.9.0.tgz"
- integrity sha512-GZbQlWtopBTP0u7cHrEx+73yZKrQoBMpwkGEIqlacljhXCkVM1kMQge/Mf+csMJAjEdSwhOyLAS0AoR3AG5P8w==
+"@webassemblyjs/wasm-edit@1.11.1":
+ version "1.11.1"
+ resolved "https://registry.yarnpkg.com/@webassemblyjs/wasm-edit/-/wasm-edit-1.11.1.tgz#ad206ebf4bf95a058ce9880a8c092c5dec8193d6"
+ integrity sha512-g+RsupUC1aTHfR8CDgnsVRVZFJqdkFHpsHMfJuWQzWU3tvnLC07UqHICfP+4XyL2tnr1amvl1Sdp06TnYCmVkA==
+ dependencies:
+ "@webassemblyjs/ast" "1.11.1"
+ "@webassemblyjs/helper-buffer" "1.11.1"
+ "@webassemblyjs/helper-wasm-bytecode" "1.11.1"
+ "@webassemblyjs/helper-wasm-section" "1.11.1"
+ "@webassemblyjs/wasm-gen" "1.11.1"
+ "@webassemblyjs/wasm-opt" "1.11.1"
+ "@webassemblyjs/wasm-parser" "1.11.1"
+ "@webassemblyjs/wast-printer" "1.11.1"
"@webassemblyjs/wasm-edit@1.8.5":
version "1.8.5"
@@ -2403,19 +2457,16 @@
"@webassemblyjs/wasm-parser" "1.8.5"
"@webassemblyjs/wast-printer" "1.8.5"
-"@webassemblyjs/wasm-edit@1.9.0":
- version "1.9.0"
- resolved "https://registry.npmjs.org/@webassemblyjs/wasm-edit/-/wasm-edit-1.9.0.tgz"
- integrity sha512-FgHzBm80uwz5M8WKnMTn6j/sVbqilPdQXTWraSjBwFXSYGirpkSWE2R9Qvz9tNiTKQvoKILpCuTjBKzOIm0nxw==
+"@webassemblyjs/wasm-gen@1.11.1":
+ version "1.11.1"
+ resolved "https://registry.yarnpkg.com/@webassemblyjs/wasm-gen/-/wasm-gen-1.11.1.tgz#86c5ea304849759b7d88c47a32f4f039ae3c8f76"
+ integrity sha512-F7QqKXwwNlMmsulj6+O7r4mmtAlCWfO/0HdgOxSklZfQcDu0TpLiD1mRt/zF25Bk59FIjEuGAIyn5ei4yMfLhA==
dependencies:
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- "@webassemblyjs/helper-buffer" "1.9.0"
- "@webassemblyjs/helper-wasm-bytecode" "1.9.0"
- "@webassemblyjs/helper-wasm-section" "1.9.0"
- "@webassemblyjs/wasm-gen" "1.9.0"
- "@webassemblyjs/wasm-opt" "1.9.0"
- "@webassemblyjs/wasm-parser" "1.9.0"
- "@webassemblyjs/wast-printer" "1.9.0"
+ "@webassemblyjs/ast" "1.11.1"
+ "@webassemblyjs/helper-wasm-bytecode" "1.11.1"
+ "@webassemblyjs/ieee754" "1.11.1"
+ "@webassemblyjs/leb128" "1.11.1"
+ "@webassemblyjs/utf8" "1.11.1"
"@webassemblyjs/wasm-gen@1.8.5":
version "1.8.5"
@@ -2428,16 +2479,15 @@
"@webassemblyjs/leb128" "1.8.5"
"@webassemblyjs/utf8" "1.8.5"
-"@webassemblyjs/wasm-gen@1.9.0":
- version "1.9.0"
- resolved "https://registry.npmjs.org/@webassemblyjs/wasm-gen/-/wasm-gen-1.9.0.tgz"
- integrity sha512-cPE3o44YzOOHvlsb4+E9qSqjc9Qf9Na1OO/BHFy4OI91XDE14MjFN4lTMezzaIWdPqHnsTodGGNP+iRSYfGkjA==
+"@webassemblyjs/wasm-opt@1.11.1":
+ version "1.11.1"
+ resolved "https://registry.yarnpkg.com/@webassemblyjs/wasm-opt/-/wasm-opt-1.11.1.tgz#657b4c2202f4cf3b345f8a4c6461c8c2418985f2"
+ integrity sha512-VqnkNqnZlU5EB64pp1l7hdm3hmQw7Vgqa0KF/KCNO9sIpI6Fk6brDEiX+iCOYrvMuBWDws0NkTOxYEb85XQHHw==
dependencies:
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- "@webassemblyjs/helper-wasm-bytecode" "1.9.0"
- "@webassemblyjs/ieee754" "1.9.0"
- "@webassemblyjs/leb128" "1.9.0"
- "@webassemblyjs/utf8" "1.9.0"
+ "@webassemblyjs/ast" "1.11.1"
+ "@webassemblyjs/helper-buffer" "1.11.1"
+ "@webassemblyjs/wasm-gen" "1.11.1"
+ "@webassemblyjs/wasm-parser" "1.11.1"
"@webassemblyjs/wasm-opt@1.8.5":
version "1.8.5"
@@ -2449,15 +2499,17 @@
"@webassemblyjs/wasm-gen" "1.8.5"
"@webassemblyjs/wasm-parser" "1.8.5"
-"@webassemblyjs/wasm-opt@1.9.0":
- version "1.9.0"
- resolved "https://registry.npmjs.org/@webassemblyjs/wasm-opt/-/wasm-opt-1.9.0.tgz"
- integrity sha512-Qkjgm6Anhm+OMbIL0iokO7meajkzQD71ioelnfPEj6r4eOFuqm4YC3VBPqXjFyyNwowzbMD+hizmprP/Fwkl2A==
+"@webassemblyjs/wasm-parser@1.11.1":
+ version "1.11.1"
+ resolved "https://registry.yarnpkg.com/@webassemblyjs/wasm-parser/-/wasm-parser-1.11.1.tgz#86ca734534f417e9bd3c67c7a1c75d8be41fb199"
+ integrity sha512-rrBujw+dJu32gYB7/Lup6UhdkPx9S9SnobZzRVL7VcBH9Bt9bCBLEuX/YXOOtBsOZ4NQrRykKhffRWHvigQvOA==
dependencies:
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- "@webassemblyjs/helper-buffer" "1.9.0"
- "@webassemblyjs/wasm-gen" "1.9.0"
- "@webassemblyjs/wasm-parser" "1.9.0"
+ "@webassemblyjs/ast" "1.11.1"
+ "@webassemblyjs/helper-api-error" "1.11.1"
+ "@webassemblyjs/helper-wasm-bytecode" "1.11.1"
+ "@webassemblyjs/ieee754" "1.11.1"
+ "@webassemblyjs/leb128" "1.11.1"
+ "@webassemblyjs/utf8" "1.11.1"
"@webassemblyjs/wasm-parser@1.8.5":
version "1.8.5"
@@ -2471,18 +2523,6 @@
"@webassemblyjs/leb128" "1.8.5"
"@webassemblyjs/utf8" "1.8.5"
-"@webassemblyjs/wasm-parser@1.9.0":
- version "1.9.0"
- resolved "https://registry.npmjs.org/@webassemblyjs/wasm-parser/-/wasm-parser-1.9.0.tgz"
- integrity sha512-9+wkMowR2AmdSWQzsPEjFU7njh8HTO5MqO8vjwEHuM+AMHioNqSBONRdr0NQQ3dVQrzp0s8lTcYqzUdb7YgELA==
- dependencies:
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- "@webassemblyjs/helper-api-error" "1.9.0"
- "@webassemblyjs/helper-wasm-bytecode" "1.9.0"
- "@webassemblyjs/ieee754" "1.9.0"
- "@webassemblyjs/leb128" "1.9.0"
- "@webassemblyjs/utf8" "1.9.0"
-
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version "1.8.5"
resolved "https://registry.npmjs.org/@webassemblyjs/wast-parser/-/wast-parser-1.8.5.tgz"
@@ -2495,16 +2535,12 @@
"@webassemblyjs/helper-fsm" "1.8.5"
"@xtuc/long" "4.2.2"
-"@webassemblyjs/wast-parser@1.9.0":
- version "1.9.0"
- resolved "https://registry.npmjs.org/@webassemblyjs/wast-parser/-/wast-parser-1.9.0.tgz"
- integrity sha512-qsqSAP3QQ3LyZjNC/0jBJ/ToSxfYJ8kYyuiGvtn/8MK89VrNEfwj7BPQzJVHi0jGTRK2dGdJ5PRqhtjzoww+bw==
+"@webassemblyjs/wast-printer@1.11.1":
+ version "1.11.1"
+ resolved "https://registry.yarnpkg.com/@webassemblyjs/wast-printer/-/wast-printer-1.11.1.tgz#d0c73beda8eec5426f10ae8ef55cee5e7084c2f0"
+ integrity sha512-IQboUWM4eKzWW+N/jij2sRatKMh99QEelo3Eb2q0qXkvPRISAj8Qxtmw5itwqK+TTkBuUIE45AxYPToqPtL5gg==
dependencies:
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- "@webassemblyjs/floating-point-hex-parser" "1.9.0"
- "@webassemblyjs/helper-api-error" "1.9.0"
- "@webassemblyjs/helper-code-frame" "1.9.0"
- "@webassemblyjs/helper-fsm" "1.9.0"
+ "@webassemblyjs/ast" "1.11.1"
"@xtuc/long" "4.2.2"
"@webassemblyjs/wast-printer@1.8.5":
@@ -2516,15 +2552,6 @@
"@webassemblyjs/wast-parser" "1.8.5"
"@xtuc/long" "4.2.2"
-"@webassemblyjs/wast-printer@1.9.0":
- version "1.9.0"
- resolved "https://registry.npmjs.org/@webassemblyjs/wast-printer/-/wast-printer-1.9.0.tgz"
- integrity sha512-2J0nE95rHXHyQ24cWjMKJ1tqB/ds8z/cyeOZxJhcb+rW+SQASVjuznUSmdz5GpVJTzU8JkhYut0D3siFDD6wsA==
- dependencies:
- "@webassemblyjs/ast" "1.9.0"
- "@webassemblyjs/wast-parser" "1.9.0"
- "@xtuc/long" "4.2.2"
-
"@welldone-software/why-did-you-render@^6.2.1":
version "6.2.3"
resolved "https://registry.npmjs.org/@welldone-software/why-did-you-render/-/why-did-you-render-6.2.3.tgz"
@@ -2576,6 +2603,11 @@ acorn-globals@^6.0.0:
acorn "^7.1.1"
acorn-walk "^7.1.1"
+acorn-import-assertions@^1.7.6:
+ version "1.8.0"
+ resolved "https://registry.yarnpkg.com/acorn-import-assertions/-/acorn-import-assertions-1.8.0.tgz#ba2b5939ce62c238db6d93d81c9b111b29b855e9"
+ integrity sha512-m7VZ3jwz4eK6A4Vtt8Ew1/mNbP24u0FhdyfA7fSvnJR6LMdfOYnmuIrrJAgrYfYJ10F/otaHTtrtrtmHdMNzEw==
+
acorn-jsx@^5.2.0, acorn-jsx@^5.3.1:
version "5.3.2"
resolved "https://registry.npmjs.org/acorn-jsx/-/acorn-jsx-5.3.2.tgz"
@@ -2596,7 +2628,7 @@ acorn@^5.5.3:
resolved "https://registry.npmjs.org/acorn/-/acorn-5.7.4.tgz"
integrity sha512-1D++VG7BhrtvQpNbBzovKNc1FLGGEE/oGe7b9xJm/RFHMBeUaUGpluV9RLjZa47YFdPcDAenEYuq9pQPcMdLJg==
-acorn@^6.0.1, acorn@^6.0.4, acorn@^6.2.1, acorn@^6.4.1:
+acorn@^6.0.1, acorn@^6.0.4, acorn@^6.2.1:
version "6.4.2"
resolved "https://registry.npmjs.org/acorn/-/acorn-6.4.2.tgz"
integrity sha512-XtGIhXwF8YM8bJhGxG5kXgjkEuNGLTkoYqVE+KMR+aspr4KGYmKYg7yUe3KghyQ9yheNwLnjmzh/7+gfDBmHCQ==
@@ -2611,6 +2643,11 @@ acorn@^8.2.4:
resolved "https://registry.npmjs.org/acorn/-/acorn-8.6.0.tgz"
integrity sha512-U1riIR+lBSNi3IbxtaHOIKdH8sLFv3NYfNv8sg7ZsNhcfl4HF2++BfqqrNAxoCLQW1iiylOj76ecnaUxz+z9yw==
+acorn@^8.4.1, acorn@^8.5.0:
+ version "8.7.1"
+ resolved "https://registry.yarnpkg.com/acorn/-/acorn-8.7.1.tgz#0197122c843d1bf6d0a5e83220a788f278f63c30"
+ integrity sha512-Xx54uLJQZ19lKygFXOWsscKUbsBZW0CPykPhVQdhIeIwrbPmJzqeASDInc8nKBnp/JT6igTs82qPXz069H8I/A==
+
address@1.1.2, address@^1.0.1:
version "1.1.2"
resolved "https://registry.npmjs.org/address/-/address-1.1.2.tgz"
@@ -2627,11 +2664,6 @@ adjust-sourcemap-loader@2.0.0:
object-path "0.11.4"
regex-parser "2.2.10"
-after@0.8.2:
- version "0.8.2"
- resolved "https://registry.npmjs.org/after/-/after-0.8.2.tgz"
- integrity sha1-/ts5T58OAqqXaOcCvaI7UF+ufh8=
-
agent-base@6:
version "6.0.2"
resolved "https://registry.npmjs.org/agent-base/-/agent-base-6.0.2.tgz"
@@ -2667,7 +2699,7 @@ ajv@6.5.3:
json-schema-traverse "^0.4.1"
uri-js "^4.2.2"
-ajv@^6.1.0, ajv@^6.10.0, ajv@^6.10.2, ajv@^6.12.3, ajv@^6.12.4:
+ajv@^6.1.0, ajv@^6.10.0, ajv@^6.10.2, ajv@^6.12.3, ajv@^6.12.4, ajv@^6.12.5:
version "6.12.6"
resolved "https://registry.npmjs.org/ajv/-/ajv-6.12.6.tgz"
integrity sha512-j3fVLgvTo527anyYyJOGTYJbG+vnnQYvE0m5mmkc1TK+nxAppkCLMIL0aZ4dblVCNoGShhm+kzE4ZUykBoMg4g==
@@ -2994,11 +3026,6 @@ array.prototype.flatmap@^1.2.5:
define-properties "^1.1.3"
es-abstract "^1.19.0"
-arraybuffer.slice@~0.0.7:
- version "0.0.7"
- resolved "https://registry.npmjs.org/arraybuffer.slice/-/arraybuffer.slice-0.0.7.tgz"
- integrity sha512-wGUIVQXuehL5TCqQun8OW81jGzAWycqzFF8lFp+GOM5BXLYj3bKNsYC4daB7n6XjCqxQA/qgTJ+8ANR3acjrog==
-
arrify@^1.0.1:
version "1.0.1"
resolved "https://registry.npmjs.org/arrify/-/arrify-1.0.1.tgz"
@@ -3365,11 +3392,6 @@ bach@^1.0.0:
async-settle "^1.0.0"
now-and-later "^2.0.0"
-backo2@1.0.2:
- version "1.0.2"
- resolved "https://registry.npmjs.org/backo2/-/backo2-1.0.2.tgz"
- integrity sha1-MasayLEpNjRj41s+u2n038+6eUc=
-
bail@^1.0.0:
version "1.0.5"
resolved "https://registry.npmjs.org/bail/-/bail-1.0.5.tgz"
@@ -3390,11 +3412,6 @@ base16@^1.0.0:
resolved "https://registry.npmjs.org/base16/-/base16-1.0.0.tgz"
integrity sha1-4pf2DX7BAUp6lxo568ipjAtoHnA=
-base64-arraybuffer@0.1.4:
- version "0.1.4"
- resolved "https://registry.npmjs.org/base64-arraybuffer/-/base64-arraybuffer-0.1.4.tgz"
- integrity sha1-mBjHngWbE1X5fgQooBfIOOkLqBI=
-
base64-js@1.3.1:
version "1.3.1"
resolved "https://registry.npmjs.org/base64-js/-/base64-js-1.3.1.tgz"
@@ -3405,9 +3422,9 @@ base64-js@^1.0.2:
resolved "https://registry.npmjs.org/base64-js/-/base64-js-1.5.1.tgz"
integrity sha512-AKpaYlHn8t4SVbOHCy+b5+KKgvR4vrsD8vbvrbiQJps7fKDTkjkDry6ji0rUJjC0kzbNePLwzxq8iypo41qeWA==
-base64id@2.0.0:
+base64id@2.0.0, base64id@~2.0.0:
version "2.0.0"
- resolved "https://registry.npmjs.org/base64id/-/base64id-2.0.0.tgz"
+ resolved "https://registry.yarnpkg.com/base64id/-/base64id-2.0.0.tgz#2770ac6bc47d312af97a8bf9a634342e0cd25cb6"
integrity sha512-lGe34o6EHj9y3Kts9R4ZYs/Gr+6N7MCaMlIFA3F1R2O5/m7K06AxfSeO5530PEERE6/WyEg3lsuyw4GHlPZHog==
base@^0.11.1:
@@ -3469,11 +3486,6 @@ bit-twiddle@^1.0.0:
resolved "https://registry.npmjs.org/bit-twiddle/-/bit-twiddle-1.0.2.tgz"
integrity sha1-DGwfq+KyPRcXPZpht7cJPrnhdp4=
-blob@0.0.5:
- version "0.0.5"
- resolved "https://registry.npmjs.org/blob/-/blob-0.0.5.tgz"
- integrity sha512-gaqbzQPqOoamawKg0LGVd7SzLgXS+JH61oWprSLH+P+abTczqJbhTR8CmJ2u9/bUYNmHTGJx/UEmn6doAvvuig==
-
bluebird@^3.5.5:
version "3.7.2"
resolved "https://registry.npmjs.org/bluebird/-/bluebird-3.7.2.tgz"
@@ -3583,35 +3595,35 @@ browser-resolve@^1.11.3:
dependencies:
resolve "1.1.7"
-browser-sync-client@^2.27.7:
- version "2.27.7"
- resolved "https://registry.npmjs.org/browser-sync-client/-/browser-sync-client-2.27.7.tgz"
- integrity sha512-wKg9UP9a4sCIkBBAXUdbkdWFJzfSAQizGh+nC19W9y9zOo9s5jqeYRFUUbs7x5WKhjtspT+xetVp9AtBJ6BmWg==
+browser-sync-client@^2.27.9:
+ version "2.27.9"
+ resolved "https://registry.yarnpkg.com/browser-sync-client/-/browser-sync-client-2.27.9.tgz#3a4bff71d1d657dff6106ac234a6bf24c724a9d3"
+ integrity sha512-FHW8kydp7FXo6jnX3gXJCpHAHtWNLK0nx839nnK+boMfMI1n4KZd0+DmTxHBsHsF3OHud4V4jwoN8U5HExMIdQ==
dependencies:
etag "1.8.1"
fresh "0.5.2"
mitt "^1.1.3"
rxjs "^5.5.6"
-browser-sync-ui@^2.27.7:
- version "2.27.7"
- resolved "https://registry.npmjs.org/browser-sync-ui/-/browser-sync-ui-2.27.7.tgz"
- integrity sha512-Bt4OQpx9p18OIzk0KKyu7jqlvmjacasUlk8ARY3uuIyiFWSBiRgr2i6XY8dEMF14DtbooaEBOpHEu9VCYvMcCw==
+browser-sync-ui@^2.27.9:
+ version "2.27.9"
+ resolved "https://registry.yarnpkg.com/browser-sync-ui/-/browser-sync-ui-2.27.9.tgz#53253383a6d8cbc921c85f290fa330fdb449d76b"
+ integrity sha512-rsduR2bRIwFvM8CX6iY/Nu5aWub0WB9zfSYg9Le/RV5N5DEyxJYey0VxdfWCnzDOoelassTDzYQo+r0iJno3qw==
dependencies:
async-each-series "0.1.1"
connect-history-api-fallback "^1"
immutable "^3"
server-destroy "1.0.1"
- socket.io-client "^2.4.0"
+ socket.io-client "^4.4.1"
stream-throttle "^0.1.3"
-browser-sync@^2.27.7:
- version "2.27.7"
- resolved "https://registry.npmjs.org/browser-sync/-/browser-sync-2.27.7.tgz"
- integrity sha512-9ElnnA/u+s2Jd+IgY+2SImB+sAEIteHsMG0NR96m7Ph/wztpvJCUpyC2on1KqmG9iAp941j+5jfmd34tEguGbg==
+browser-sync@^2.27.9:
+ version "2.27.9"
+ resolved "https://registry.yarnpkg.com/browser-sync/-/browser-sync-2.27.9.tgz#e0555cb44bd5ede00685e70e108b393d2966874a"
+ integrity sha512-3zBtggcaZIeU9so4ja9yxk7/CZu9B3DOL6zkxFpzHCHsQmkGBPVXg61jItbeoa+WXgNLnr1sYES/2yQwyEZ2+w==
dependencies:
- browser-sync-client "^2.27.7"
- browser-sync-ui "^2.27.7"
+ browser-sync-client "^2.27.9"
+ browser-sync-ui "^2.27.9"
bs-recipes "1.3.4"
bs-snippet-injector "^2.0.1"
chokidar "^3.5.1"
@@ -3637,9 +3649,9 @@ browser-sync@^2.27.7:
serve-index "1.9.1"
serve-static "1.13.2"
server-destroy "1.0.1"
- socket.io "2.4.0"
+ socket.io "^4.4.1"
ua-parser-js "1.0.2"
- yargs "^15.4.1"
+ yargs "^17.3.1"
browserify-aes@^1.0.0, browserify-aes@^1.0.4:
version "1.2.0"
@@ -3723,6 +3735,17 @@ browserslist@^4.0.0, browserslist@^4.12.0, browserslist@^4.17.5, browserslist@^4
node-releases "^2.0.1"
picocolors "^1.0.0"
+browserslist@^4.14.5:
+ version "4.20.3"
+ resolved "https://registry.yarnpkg.com/browserslist/-/browserslist-4.20.3.tgz#eb7572f49ec430e054f56d52ff0ebe9be915f8bf"
+ integrity sha512-NBhymBQl1zM0Y5dQT/O+xiLP9/rzOIQdKM/eMJBAq7yBgaB6krIYLGejrwVYnSHZdqjscB1SPuAjHwxjvN6Wdg==
+ dependencies:
+ caniuse-lite "^1.0.30001332"
+ electron-to-chromium "^1.4.118"
+ escalade "^3.1.1"
+ node-releases "^2.0.3"
+ picocolors "^1.0.0"
+
bs-recipes@1.3.4:
version "1.3.4"
resolved "https://registry.npmjs.org/bs-recipes/-/bs-recipes-1.3.4.tgz"
@@ -3955,6 +3978,11 @@ caniuse-lite@^1.0.0, caniuse-lite@^1.0.30000981, caniuse-lite@^1.0.30001035, can
resolved "https://registry.npmjs.org/caniuse-lite/-/caniuse-lite-1.0.30001283.tgz"
integrity sha512-9RoKo841j1GQFSJz/nCXOj0sD7tHBtlowjYlrqIUS812x9/emfBLBt6IyMz1zIaYc/eRL8Cs6HPUVi2Hzq4sIg==
+caniuse-lite@^1.0.30001332:
+ version "1.0.30001339"
+ resolved "https://registry.yarnpkg.com/caniuse-lite/-/caniuse-lite-1.0.30001339.tgz#f9aece4ea8156071613b27791547ba0b33f176cf"
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resolved "https://registry.npmjs.org/cliui/-/cliui-7.0.4.tgz"
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+ resolved "https://registry.yarnpkg.com/cors/-/cors-2.8.5.tgz#eac11da51592dd86b9f06f6e7ac293b3df875d29"
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+ dependencies:
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+ vary "^1"
+
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resolved "https://registry.npmjs.org/cosmiconfig/-/cosmiconfig-5.2.1.tgz"
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dependencies:
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+ ms "2.1.2"
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+ version "1.4.137"
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+
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resolved "https://registry.npmjs.org/elliptic/-/elliptic-6.5.4.tgz"
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+engine.io-client@~6.2.1:
+ version "6.2.2"
+ resolved "https://registry.yarnpkg.com/engine.io-client/-/engine.io-client-6.2.2.tgz#c6c5243167f5943dcd9c4abee1bfc634aa2cbdd0"
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- arraybuffer.slice "~0.0.7"
- base64-arraybuffer "0.1.4"
- blob "0.0.5"
- has-binary2 "~1.0.2"
+ "@socket.io/component-emitter" "~3.1.0"
+ debug "~4.3.1"
+ engine.io-parser "~5.0.3"
+ ws "~8.2.3"
+ xmlhttprequest-ssl "~2.0.0"
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+engine.io-parser@~5.0.3:
+ version "5.0.4"
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+
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+ version "6.2.0"
+ resolved "https://registry.yarnpkg.com/engine.io/-/engine.io-6.2.0.tgz#003bec48f6815926f2b1b17873e576acd54f41d0"
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dependencies:
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+ "@types/cors" "^2.8.12"
+ "@types/node" ">=10.0.0"
accepts "~1.3.4"
base64id "2.0.0"
cookie "~0.4.1"
- debug "~4.1.0"
- engine.io-parser "~2.2.0"
- ws "~7.4.2"
+ cors "~2.8.5"
+ debug "~4.3.1"
+ engine.io-parser "~5.0.3"
+ ws "~8.2.3"
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+enhanced-resolve@^4.1.0, enhanced-resolve@^4.1.1:
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resolved "https://registry.npmjs.org/enhanced-resolve/-/enhanced-resolve-4.5.0.tgz"
integrity sha512-Nv9m36S/vxpsI+Hc4/ZGRs0n9mXqSWGGq49zxb/cJfPAQMbUtttJAlNPS4AQzaBdw/pKskw5bMbekT/Y7W/Wlg==
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memory-fs "^0.5.0"
tapable "^1.0.0"
+enhanced-resolve@^5.9.2:
+ version "5.9.3"
+ resolved "https://registry.yarnpkg.com/enhanced-resolve/-/enhanced-resolve-5.9.3.tgz#44a342c012cbc473254af5cc6ae20ebd0aae5d88"
+ integrity sha512-Bq9VSor+kjvW3f9/MiiR4eE3XYgOl7/rS8lnSxbRbF3kS0B2r+Y9w5krBWxZgDxASVZbdYrn5wT4j/Wb0J9qow==
+ dependencies:
+ graceful-fs "^4.2.4"
+ tapable "^2.2.0"
+
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version "2.3.6"
resolved "https://registry.npmjs.org/enquirer/-/enquirer-2.3.6.tgz"
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string.prototype.trimstart "^1.0.4"
unbox-primitive "^1.0.1"
+es-module-lexer@^0.9.0:
+ version "0.9.3"
+ resolved "https://registry.yarnpkg.com/es-module-lexer/-/es-module-lexer-0.9.3.tgz#6f13db00cc38417137daf74366f535c8eb438f19"
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+
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version "1.2.1"
resolved "https://registry.npmjs.org/es-to-primitive/-/es-to-primitive-1.2.1.tgz"
@@ -6248,6 +6263,14 @@ eslint-plugin-testing-library@^3.10.1:
dependencies:
"@typescript-eslint/experimental-utils" "^3.10.1"
+eslint-scope@5.1.1, eslint-scope@^5.0.0, eslint-scope@^5.1.1:
+ version "5.1.1"
+ resolved "https://registry.npmjs.org/eslint-scope/-/eslint-scope-5.1.1.tgz"
+ integrity sha512-2NxwbF/hZ0KpepYN0cNbo+FN6XoK7GaHlQhgx/hIZl6Va0bF45RQOOwhLIy8lQDbuCiadSLCBnH2CFYquit5bw==
+ dependencies:
+ esrecurse "^4.3.0"
+ estraverse "^4.1.1"
+
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version "4.0.3"
resolved "https://registry.npmjs.org/eslint-scope/-/eslint-scope-4.0.3.tgz"
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esrecurse "^4.1.0"
estraverse "^4.1.1"
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- dependencies:
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- estraverse "^4.1.1"
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resolved "https://registry.npmjs.org/eslint-utils/-/eslint-utils-1.4.3.tgz"
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resolved "https://registry.npmjs.org/events/-/events-3.3.0.tgz"
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@@ -6920,7 +6935,7 @@ find-cache-dir@^3.2.0:
make-dir "^3.0.2"
pkg-dir "^4.1.0"
-find-up@4.1.0, find-up@^4.0.0, find-up@^4.1.0:
+find-up@4.1.0, find-up@^4.0.0:
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resolved "https://registry.npmjs.org/find-up/-/find-up-4.1.0.tgz"
integrity sha512-PpOwAdQ/YlXQ2vj8a3h8IipDuYRi3wceVQQGYWxNINccq40Anw7BlsEXCMbt1Zt+OLA6Fq9suIpIWD0OsnISlw==
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resolved "https://registry.npmjs.org/glob-to-regexp/-/glob-to-regexp-0.3.0.tgz"
integrity sha1-jFoUlNIGbFcMw7/kSWF1rMTVAqs=
+glob-to-regexp@^0.4.1:
+ version "0.4.1"
+ resolved "https://registry.yarnpkg.com/glob-to-regexp/-/glob-to-regexp-0.4.1.tgz#c75297087c851b9a578bd217dd59a92f59fe546e"
+ integrity sha512-lkX1HJXwyMcprw/5YUZc2s7DrpAiHB21/V+E1rHUrVNokkvB6bqMzT0VfV6/86ZNabt1k14YOIaT7nDvOX3Iiw==
+
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version "5.0.5"
resolved "https://registry.npmjs.org/glob-watcher/-/glob-watcher-5.0.5.tgz"
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+graceful-fs@^4.2.9:
+ version "4.2.10"
+ resolved "https://registry.yarnpkg.com/graceful-fs/-/graceful-fs-4.2.10.tgz#147d3a006da4ca3ce14728c7aefc287c367d7a6c"
+ integrity sha512-9ByhssR2fPVsNZj478qUUbKfmL0+t5BDVyjShtyZZLiK7ZDAArFFfopyOTj0M05wE2tJPisA4iTnnXl2YoPvOA==
+
growly@^1.3.0:
version "1.3.0"
resolved "https://registry.npmjs.org/growly/-/growly-1.3.0.tgz"
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- resolved "https://registry.npmjs.org/has-binary2/-/has-binary2-1.0.3.tgz"
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- dependencies:
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-
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resolved "https://registry.npmjs.org/has-flag/-/has-flag-3.0.0.tgz"
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resolved "https://registry.npmjs.org/indexes-of/-/indexes-of-1.0.1.tgz"
integrity sha1-8w9xbI4r00bHtn0985FVZqfAVgc=
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- integrity sha1-gtwzbSMrkGIXnQWrMpOmYFn9Q10=
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resolved "https://registry.npmjs.org/infer-owner/-/infer-owner-1.0.4.tgz"
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integrity sha1-u5NdSFgsuhaMBoNJV6VKPgcSTxE=
-isarray@2.0.1:
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- integrity sha1-o32U7ZzaLVmGXJ92/llu4fM4dB4=
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version "2.0.0"
resolved "https://registry.npmjs.org/isexe/-/isexe-2.0.0.tgz"
@@ -9203,6 +9206,15 @@ jest-worker@^25.1.0:
merge-stream "^2.0.0"
supports-color "^7.0.0"
+jest-worker@^27.4.5:
+ version "27.5.1"
+ resolved "https://registry.yarnpkg.com/jest-worker/-/jest-worker-27.5.1.tgz#8d146f0900e8973b106b6f73cc1e9a8cb86f8db0"
+ integrity sha512-7vuh85V5cdDofPyxn58nrPjBktZo0u9x1g8WtjQol+jZDaE+fhN+cIvTj11GndBnMnyfrUOG1sZQxCdjKh+DKg==
+ dependencies:
+ "@types/node" "*"
+ merge-stream "^2.0.0"
+ supports-color "^8.0.0"
+
jest@24.9.0:
version "24.9.0"
resolved "https://registry.npmjs.org/jest/-/jest-24.9.0.tgz"
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+loader-runner@^4.2.0:
+ version "4.3.0"
+ resolved "https://registry.yarnpkg.com/loader-runner/-/loader-runner-4.3.0.tgz#c1b4a163b99f614830353b16755e7149ac2314e1"
+ integrity sha512-3R/1M+yS3j5ou80Me59j7F9IMs4PXs3VqRrm0TU3AbKPxlmpoY1TNscJV/oGJXo8qCatFGTfDbY6W6ipGOYXfg==
+
loader-utils@1.2.3:
version "1.2.3"
resolved "https://registry.npmjs.org/loader-utils/-/loader-utils-1.2.3.tgz"
@@ -10213,6 +10230,11 @@ mime-db@1.51.0, "mime-db@>= 1.43.0 < 2":
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integrity sha512-5y8A56jg7XVQx2mbv1lu49NR4dokRnhZYTtL+KGfaa27uq4pSTXkwQkFJl4pkRMyNFz/EtYDSkiiEHx3F7UN6g==
+mime-db@1.52.0:
+ version "1.52.0"
+ resolved "https://registry.yarnpkg.com/mime-db/-/mime-db-1.52.0.tgz#bbabcdc02859f4987301c856e3387ce5ec43bf70"
+ integrity sha512-sPU4uV7dYlvtWJxwwxHD0PuihVNiE7TyAbQ5SWxDCB9mUYvOgroQOwYQQOKPJ8CIbE+1ETVlOoK1UC2nU3gYvg==
+
mime-db@~1.33.0:
version "1.33.0"
resolved "https://registry.npmjs.org/mime-db/-/mime-db-1.33.0.tgz"
@@ -10232,6 +10254,13 @@ mime-types@^2.1.12, mime-types@~2.1.17, mime-types@~2.1.19, mime-types@~2.1.24:
dependencies:
mime-db "1.51.0"
+mime-types@^2.1.27:
+ version "2.1.35"
+ resolved "https://registry.yarnpkg.com/mime-types/-/mime-types-2.1.35.tgz#381a871b62a734450660ae3deee44813f70d959a"
+ integrity sha512-ZDY+bPm5zTTF+YpCrAU9nK0UgICYPT0QtT1NZWFv4s++TNkcgVaT0g6+4R2uI4MjQjzysHB1zxuWL50hzaeXiw==
+ dependencies:
+ mime-db "1.52.0"
+
mime@1.4.1:
version "1.4.1"
resolved "https://registry.npmjs.org/mime/-/mime-1.4.1.tgz"
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-neo-async@^2.5.0, neo-async@^2.6.1:
+neo-async@^2.5.0, neo-async@^2.6.1, neo-async@^2.6.2:
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resolved "https://registry.npmjs.org/neo-async/-/neo-async-2.6.2.tgz"
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+node-releases@^2.0.3:
+ version "2.0.4"
+ resolved "https://registry.yarnpkg.com/node-releases/-/node-releases-2.0.4.tgz#f38252370c43854dc48aa431c766c6c398f40476"
+ integrity sha512-gbMzqQtTtDz/00jQzZ21PQzdI9PyLYqUSvD0p3naOhX4odFji0ZxYdnVwPTxmSwkmxhcFImpozceidSG+AgoPQ==
+
"nomad-fair-gui@file:.":
- version "1.0.4"
+ version "1.0.8"
dependencies:
"@date-io/date-fns" "1.x"
"@fontsource/material-icons" "^4.2.1"
@@ -10621,7 +10655,7 @@ node-releases@^2.0.1:
mathjs "^7.1.0"
muuri "^0.9.5"
muuri-react "^3.1.6"
- nomad-fair-gui "file:../../../.cache/yarn/v6/npm-nomad-fair-gui-1.0.4-242748d1-d2ee-4abb-b990-62653a75e0a2-1646650639665/node_modules/nomad-fair-gui"
+ nomad-fair-gui "file:../../../../Library/Caches/Yarn/v6/npm-nomad-fair-gui-1.0.8-27db3b4d-61a1-4f19-827a-50b28cd081d0-1652177602070/node_modules/nomad-fair-gui"
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integrity sha1-m+3VygiXlJvKR+f/QIBi1Un1h/I=
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resolved "https://registry.npmjs.org/object-assign/-/object-assign-4.1.1.tgz"
integrity sha1-IQmtx5ZYh8/AXLvUQsrIv7s2CGM=
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version "1.3.3"
resolved "https://registry.npmjs.org/parseurl/-/parseurl-1.3.3.tgz"
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ajv "^6.12.4"
ajv-keywords "^3.5.2"
+schema-utils@^3.1.0, schema-utils@^3.1.1:
+ version "3.1.1"
+ resolved "https://registry.yarnpkg.com/schema-utils/-/schema-utils-3.1.1.tgz#bc74c4b6b6995c1d88f76a8b77bea7219e0c8281"
+ integrity sha512-Y5PQxS4ITlC+EahLuXaY86TXfR7Dc5lw294alXOq86JAHCihAIZfqv8nNCWvaEJvaC51uN9hbLGeV0cFBdH+Fw==
+ dependencies:
+ "@types/json-schema" "^7.0.8"
+ ajv "^6.12.5"
+ ajv-keywords "^3.5.2"
+
section-iterator@^2.0.0:
version "2.0.0"
resolved "https://registry.npmjs.org/section-iterator/-/section-iterator-2.0.0.tgz"
@@ -13880,6 +13913,13 @@ serialize-javascript@^4.0.0:
dependencies:
randombytes "^2.1.0"
+serialize-javascript@^6.0.0:
+ version "6.0.0"
+ resolved "https://registry.yarnpkg.com/serialize-javascript/-/serialize-javascript-6.0.0.tgz#efae5d88f45d7924141da8b5c3a7a7e663fefeb8"
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+ dependencies:
+ randombytes "^2.1.0"
+
serialize-query-params@^0.3.0:
version "0.3.0"
resolved "https://registry.npmjs.org/serialize-query-params/-/serialize-query-params-0.3.0.tgz"
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source-map-resolve "^0.5.0"
use "^3.1.0"
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-
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+socket.io-adapter@~2.4.0:
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- resolved "https://registry.npmjs.org/socket.io-client/-/socket.io-client-2.4.0.tgz"
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+ resolved "https://registry.yarnpkg.com/socket.io-adapter/-/socket.io-adapter-2.4.0.tgz#b50a4a9ecdd00c34d4c8c808224daa1a786152a6"
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+
+socket.io-client@^4.4.1:
+ version "4.5.0"
+ resolved "https://registry.yarnpkg.com/socket.io-client/-/socket.io-client-4.5.0.tgz#3858b6183bab31c5c4eaf3efd0fa50840ebb4504"
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- debug "~3.1.0"
- engine.io-client "~3.5.0"
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+ "@socket.io/component-emitter" "~3.1.0"
+ debug "~4.3.2"
+ engine.io-client "~6.2.1"
+ socket.io-parser "~4.2.0"
+
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+ version "4.0.4"
+ resolved "https://registry.yarnpkg.com/socket.io-parser/-/socket.io-parser-4.0.4.tgz#9ea21b0d61508d18196ef04a2c6b9ab630f4c2b0"
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+ "@types/component-emitter" "^1.2.10"
component-emitter "~1.3.0"
- debug "~3.1.0"
- isarray "2.0.1"
+ debug "~4.3.1"
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- resolved "https://registry.npmjs.org/socket.io-parser/-/socket.io-parser-3.4.1.tgz"
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+socket.io-parser@~4.2.0:
+ version "4.2.0"
+ resolved "https://registry.yarnpkg.com/socket.io-parser/-/socket.io-parser-4.2.0.tgz#3f01e5bc525d94aa52a97ed5cbc12e229bbc4d6b"
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dependencies:
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- debug "~4.1.0"
- isarray "2.0.1"
+ "@socket.io/component-emitter" "~3.1.0"
+ debug "~4.3.1"
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- resolved "https://registry.npmjs.org/socket.io/-/socket.io-2.4.0.tgz"
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+socket.io@^4.4.1:
+ version "4.5.0"
+ resolved "https://registry.yarnpkg.com/socket.io/-/socket.io-4.5.0.tgz#78ae2e84784c29267086a416620c18ef95b37186"
+ integrity sha512-slTYqU2jCgMjXwresG8grhUi/cC6GjzmcfqArzaH3BN/9I/42eZk9yamNvZJdBfTubkjEdKAKs12NEztId+bUA==
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- has-binary2 "~1.0.2"
- socket.io-adapter "~1.1.0"
- socket.io-client "2.4.0"
- socket.io-parser "~3.4.0"
+ accepts "~1.3.4"
+ base64id "~2.0.0"
+ debug "~4.3.2"
+ engine.io "~6.2.0"
+ socket.io-adapter "~2.4.0"
+ socket.io-parser "~4.0.4"
sockjs-client@1.4.0:
version "1.4.0"
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source-map-url "^0.4.0"
urix "^0.1.0"
-source-map-support@^0.5.6, source-map-support@~0.5.12:
+source-map-support@^0.5.6, source-map-support@~0.5.12, source-map-support@~0.5.20:
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resolved "https://registry.npmjs.org/source-map-support/-/source-map-support-0.5.21.tgz"
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integrity sha512-CkCj6giN3S+n9qrYiBTX5gystlENnRW5jZeNLHpe6aue+SrHcG5VYwujhW9s4dY31mEGsxBDrHR6oI69fTXsaQ==
+source-map@~0.8.0-beta.0:
+ version "0.8.0-beta.0"
+ resolved "https://registry.yarnpkg.com/source-map/-/source-map-0.8.0-beta.0.tgz#d4c1bb42c3f7ee925f005927ba10709e0d1d1f11"
+ integrity sha512-2ymg6oRBpebeZi9UUNsgQ89bhx01TcTkmNTGnNO88imTmbSgy4nfujrgVEFKWpMTEGA11EDkTt7mqObTPdigIA==
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+
sparkles@^1.0.0:
version "1.0.1"
resolved "https://registry.npmjs.org/sparkles/-/sparkles-1.0.1.tgz"
@@ -14737,6 +14776,13 @@ supports-color@^7.0.0, supports-color@^7.1.0:
dependencies:
has-flag "^4.0.0"
+supports-color@^8.0.0:
+ version "8.1.1"
+ resolved "https://registry.yarnpkg.com/supports-color/-/supports-color-8.1.1.tgz#cd6fc17e28500cff56c1b86c0a7fd4a54a73005c"
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+ dependencies:
+ has-flag "^4.0.0"
+
sver-compat@^1.5.0:
version "1.5.0"
resolved "https://registry.npmjs.org/sver-compat/-/sver-compat-1.5.0.tgz"
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+tapable@^2.1.1, tapable@^2.2.0:
+ version "2.2.1"
+ resolved "https://registry.yarnpkg.com/tapable/-/tapable-2.2.1.tgz#1967a73ef4060a82f12ab96af86d52fdb76eeca0"
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+
term-size@^1.2.0:
version "1.2.0"
resolved "https://registry.npmjs.org/term-size/-/term-size-1.2.0.tgz"
@@ -14866,6 +14917,17 @@ terser-webpack-plugin@^1.4.3:
webpack-sources "^1.4.0"
worker-farm "^1.7.0"
+terser-webpack-plugin@^5.1.3:
+ version "5.3.1"
+ resolved "https://registry.yarnpkg.com/terser-webpack-plugin/-/terser-webpack-plugin-5.3.1.tgz#0320dcc270ad5372c1e8993fabbd927929773e54"
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+ dependencies:
+ jest-worker "^27.4.5"
+ schema-utils "^3.1.1"
+ serialize-javascript "^6.0.0"
+ source-map "^0.6.1"
+ terser "^5.7.2"
+
terser@^4.1.2, terser@^4.4.3, terser@^4.6.3:
version "4.8.0"
resolved "https://registry.npmjs.org/terser/-/terser-4.8.0.tgz"
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source-map "~0.6.1"
source-map-support "~0.5.12"
+terser@^5.7.2:
+ version "5.13.1"
+ resolved "https://registry.yarnpkg.com/terser/-/terser-5.13.1.tgz#66332cdc5a01b04a224c9fad449fc1a18eaa1799"
+ integrity sha512-hn4WKOfwnwbYfe48NgrQjqNOH9jzLqRcIfbYytOXCOv46LBfWr9bDS17MQqOi+BWGD0sJK3Sj5NC/gJjiojaoA==
+ dependencies:
+ acorn "^8.5.0"
+ commander "^2.20.0"
+ source-map "~0.8.0-beta.0"
+ source-map-support "~0.5.20"
+
test-exclude@^5.2.3:
version "5.2.3"
resolved "https://registry.npmjs.org/test-exclude/-/test-exclude-5.2.3.tgz"
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chalk "^1.1.3"
dlv "^1.1.3"
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+three.meshline@1.4.0:
+ version "1.4.0"
+ resolved "https://registry.yarnpkg.com/three.meshline/-/three.meshline-1.4.0.tgz#2a483cbd99cd5f74cf6ee5c253a9a4b4a8169178"
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+three@^0.135.0:
+ version "0.135.0"
+ resolved "https://registry.yarnpkg.com/three/-/three-0.135.0.tgz#cff4ec8edd3c51ce9bc7e88d13e8eafed4d0ddfc"
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throat@^4.0.0:
version "4.1.0"
@@ -15015,11 +15087,6 @@ to-absolute-glob@^2.0.0:
is-absolute "^1.0.0"
is-negated-glob "^1.0.0"
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resolved "https://registry.npmjs.org/to-arraybuffer/-/to-arraybuffer-1.0.1.tgz"
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integrity sha1-HCQ6ULWVwb5Up1S/7OhWO5/42BM=
-vary@~1.1.2:
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resolved "https://registry.npmjs.org/vary/-/vary-1.1.2.tgz"
integrity sha1-IpnwLG3tMNSllhsLn3RSShj2NPw=
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-voronoi-diagram@^1.0.1:
+voronoi-diagram@1.0.1:
version "1.0.1"
- resolved "https://registry.npmjs.org/voronoi-diagram/-/voronoi-diagram-1.0.1.tgz"
+ resolved "https://registry.yarnpkg.com/voronoi-diagram/-/voronoi-diagram-1.0.1.tgz#4741e1e8e3184d2cdf49222adf377f062c50edfb"
integrity sha1-R0Hh6OMYTSzfSSIq3zd/BixQ7fs=
dependencies:
circumcenter "^1.0.0"
@@ -15887,7 +15954,7 @@ watchpack-chokidar2@^2.0.1:
dependencies:
chokidar "^2.1.8"
-watchpack@^1.6.0, watchpack@^1.7.4:
+watchpack@^1.6.0:
version "1.7.5"
resolved "https://registry.npmjs.org/watchpack/-/watchpack-1.7.5.tgz"
integrity sha512-9P3MWk6SrKjHsGkLT2KHXdQ/9SNkyoJbabxnKOoJepsvJjJG8uYTR3yTPxPQvNDI3w4Nz1xnE0TLHK4RIVe/MQ==
@@ -15898,6 +15965,14 @@ watchpack@^1.6.0, watchpack@^1.7.4:
chokidar "^3.4.1"
watchpack-chokidar2 "^2.0.1"
+watchpack@^2.3.1:
+ version "2.3.1"
+ resolved "https://registry.yarnpkg.com/watchpack/-/watchpack-2.3.1.tgz#4200d9447b401156eeca7767ee610f8809bc9d25"
+ integrity sha512-x0t0JuydIo8qCNctdDrn1OzH/qDzk2+rdCOC3YzumZ42fiMqmQ7T3xQurykYMhYfHaPHTp4ZxAx2NfUo1K6QaA==
+ dependencies:
+ glob-to-regexp "^0.4.1"
+ graceful-fs "^4.1.2"
+
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version "1.7.3"
resolved "https://registry.npmjs.org/wbuf/-/wbuf-1.7.3.tgz"
@@ -16018,6 +16093,11 @@ webpack-sources@^1.1.0, webpack-sources@^1.4.0, webpack-sources@^1.4.1, webpack-
source-list-map "^2.0.0"
source-map "~0.6.1"
+webpack-sources@^3.2.3:
+ version "3.2.3"
+ resolved "https://registry.yarnpkg.com/webpack-sources/-/webpack-sources-3.2.3.tgz#2d4daab8451fd4b240cc27055ff6a0c2ccea0cde"
+ integrity sha512-/DyMEOrDgLKKIG0fmvtz+4dUX/3Ghozwgm6iPp8KRhvn+eQf9+Q7GWxVNMk3+uCPWfdXYC4ExGBckIXdFEfH1w==
+
webpack@4.42.0:
version "4.42.0"
resolved "https://registry.npmjs.org/webpack/-/webpack-4.42.0.tgz"
@@ -16047,34 +16127,35 @@ webpack@4.42.0:
watchpack "^1.6.0"
webpack-sources "^1.4.1"
-webpack@^4.46.0:
- version "4.46.0"
- resolved "https://registry.npmjs.org/webpack/-/webpack-4.46.0.tgz"
- integrity sha512-6jJuJjg8znb/xRItk7bkT0+Q7AHCYjjFnvKIWQPkNIOyRqoCGvkOs0ipeQzrqz4l5FtN5ZI/ukEHroeX/o1/5Q==
- dependencies:
- "@webassemblyjs/ast" "1.9.0"
- "@webassemblyjs/helper-module-context" "1.9.0"
- "@webassemblyjs/wasm-edit" "1.9.0"
- "@webassemblyjs/wasm-parser" "1.9.0"
- acorn "^6.4.1"
- ajv "^6.10.2"
- ajv-keywords "^3.4.1"
+webpack@^5.72.0:
+ version "5.72.0"
+ resolved "https://registry.yarnpkg.com/webpack/-/webpack-5.72.0.tgz#f8bc40d9c6bb489a4b7a8a685101d6022b8b6e28"
+ integrity sha512-qmSmbspI0Qo5ld49htys8GY9XhS9CGqFoHTsOVAnjBdg0Zn79y135R+k4IR4rKK6+eKaabMhJwiVB7xw0SJu5w==
+ dependencies:
+ "@types/eslint-scope" "^3.7.3"
+ "@types/estree" "^0.0.51"
+ "@webassemblyjs/ast" "1.11.1"
+ "@webassemblyjs/wasm-edit" "1.11.1"
+ "@webassemblyjs/wasm-parser" "1.11.1"
+ acorn "^8.4.1"
+ acorn-import-assertions "^1.7.6"
+ browserslist "^4.14.5"
chrome-trace-event "^1.0.2"
- enhanced-resolve "^4.5.0"
- eslint-scope "^4.0.3"
+ enhanced-resolve "^5.9.2"
+ es-module-lexer "^0.9.0"
+ eslint-scope "5.1.1"
+ events "^3.2.0"
+ glob-to-regexp "^0.4.1"
+ graceful-fs "^4.2.9"
json-parse-better-errors "^1.0.2"
- loader-runner "^2.4.0"
- loader-utils "^1.2.3"
- memory-fs "^0.4.1"
- micromatch "^3.1.10"
- mkdirp "^0.5.3"
- neo-async "^2.6.1"
- node-libs-browser "^2.2.1"
- schema-utils "^1.0.0"
- tapable "^1.1.3"
- terser-webpack-plugin "^1.4.3"
- watchpack "^1.7.4"
- webpack-sources "^1.4.1"
+ loader-runner "^4.2.0"
+ mime-types "^2.1.27"
+ neo-async "^2.6.2"
+ schema-utils "^3.1.0"
+ tapable "^2.1.1"
+ terser-webpack-plugin "^5.1.3"
+ watchpack "^2.3.1"
+ webpack-sources "^3.2.3"
websocket-driver@>=0.5.1:
version "0.7.4"
@@ -16347,15 +16428,6 @@ wrap-ansi@^5.1.0:
string-width "^3.0.0"
strip-ansi "^5.0.0"
-wrap-ansi@^6.2.0:
- version "6.2.0"
- resolved "https://registry.npmjs.org/wrap-ansi/-/wrap-ansi-6.2.0.tgz"
- integrity sha512-r6lPcBGxZXlIcymEu7InxDMhdW0KDxpLgoFLcguasxCaJ/SOIZwINatK9KY/tf+ZrlywOKU0UDj3ATXUBfxJXA==
- dependencies:
- ansi-styles "^4.0.0"
- string-width "^4.1.0"
- strip-ansi "^6.0.0"
-
wrap-ansi@^7.0.0:
version "7.0.0"
resolved "https://registry.npmjs.org/wrap-ansi/-/wrap-ansi-7.0.0.tgz"
@@ -16405,10 +16477,10 @@ ws@^7.4.6:
resolved "https://registry.npmjs.org/ws/-/ws-7.5.6.tgz"
integrity sha512-6GLgCqo2cy2A2rjCNFlxQS6ZljG/coZfZXclldI8FB/1G3CCI36Zd8xy2HrFVACi8tfk5XrgLQEk+P0Tnz9UcA==
-ws@~7.4.2:
- version "7.4.6"
- resolved "https://registry.npmjs.org/ws/-/ws-7.4.6.tgz"
- integrity sha512-YmhHDO4MzaDLB+M9ym/mDA5z0naX8j7SIlT8f8z+I0VtzsRbekxEutHSme7NPS2qE8StCYQNUnfWdXta/Yu85A==
+ws@~8.2.3:
+ version "8.2.3"
+ resolved "https://registry.yarnpkg.com/ws/-/ws-8.2.3.tgz#63a56456db1b04367d0b721a0b80cae6d8becbba"
+ integrity sha512-wBuoj1BDpC6ZQ1B7DWQBYVLphPWkm8i9Y0/3YdHjHKHiohOJ1ws+3OccDWtH+PoC9DZD5WOTrJvNbWvjS6JWaA==
x-is-string@^0.1.0:
version "0.1.0"
@@ -16425,10 +16497,10 @@ xmlchars@^2.1.1, xmlchars@^2.2.0:
resolved "https://registry.npmjs.org/xmlchars/-/xmlchars-2.2.0.tgz"
integrity sha512-JZnDKK8B0RCDw84FNdDAIpZK+JuJw+s7Lz8nksI7SIuU3UXJJslUthsi+uWBUYOwPFwW7W7PRLRfUKpxjtjFCw==
-xmlhttprequest-ssl@~1.6.2:
- version "1.6.3"
- resolved "https://registry.npmjs.org/xmlhttprequest-ssl/-/xmlhttprequest-ssl-1.6.3.tgz"
- integrity sha512-3XfeQE/wNkvrIktn2Kf0869fC0BN6UpydVasGIeSm2B1Llihf7/0UfZM+eCkOw3P7bP4+qPgqhm7ZoxuJtFU0Q==
+xmlhttprequest-ssl@~2.0.0:
+ version "2.0.0"
+ resolved "https://registry.yarnpkg.com/xmlhttprequest-ssl/-/xmlhttprequest-ssl-2.0.0.tgz#91360c86b914e67f44dce769180027c0da618c67"
+ integrity sha512-QKxVRxiRACQcVuQEYFsI1hhkrMlrXHPegbbd1yn9UHOmRxY+si12nQYzri3vbzt8VdTTRviqcKxcyllFas5z2A==
xregexp@^4.3.0:
version "4.4.1"
@@ -16493,19 +16565,16 @@ yargs-parser@^13.1.2:
camelcase "^5.0.0"
decamelize "^1.2.0"
-yargs-parser@^18.1.2:
- version "18.1.3"
- resolved "https://registry.npmjs.org/yargs-parser/-/yargs-parser-18.1.3.tgz"
- integrity sha512-o50j0JeToy/4K6OZcaQmW6lyXXKhq7csREXcDwk2omFPJEwUNOVtJKvmDr9EI1fAJZUyZcRF7kxGBWmRXudrCQ==
- dependencies:
- camelcase "^5.0.0"
- decamelize "^1.2.0"
-
yargs-parser@^20.2.2, yargs-parser@^20.2.7:
version "20.2.9"
resolved "https://registry.npmjs.org/yargs-parser/-/yargs-parser-20.2.9.tgz"
integrity sha512-y11nGElTIV+CT3Zv9t7VKl+Q3hTQoT9a1Qzezhhl6Rp21gJ/IVTW7Z3y9EWXhuUBC2Shnf+DX0antecpAwSP8w==
+yargs-parser@^21.0.0:
+ version "21.0.1"
+ resolved "https://registry.yarnpkg.com/yargs-parser/-/yargs-parser-21.0.1.tgz#0267f286c877a4f0f728fceb6f8a3e4cb95c6e35"
+ integrity sha512-9BK1jFpLzJROCI5TzwZL/TU4gqjK5xiHV/RfWLOahrjAko/e4DJkRDZQXfvqAsiZzzYhgAzbgz6lg48jcm4GLg==
+
yargs-parser@^5.0.1:
version "5.0.1"
resolved "https://registry.npmjs.org/yargs-parser/-/yargs-parser-5.0.1.tgz"
@@ -16561,23 +16630,6 @@ yargs@^13.3.0, yargs@^13.3.2:
y18n "^4.0.0"
yargs-parser "^13.1.2"
-yargs@^15.4.1:
- version "15.4.1"
- resolved "https://registry.npmjs.org/yargs/-/yargs-15.4.1.tgz"
- integrity sha512-aePbxDmcYW++PaqBsJ+HYUFwCdv4LVvdnhBy78E57PIor8/OVvhMrADFFEDh8DHDFRv/O9i3lPhsENjO7QX0+A==
- dependencies:
- cliui "^6.0.0"
- decamelize "^1.2.0"
- find-up "^4.1.0"
- get-caller-file "^2.0.1"
- require-directory "^2.1.1"
- require-main-filename "^2.0.0"
- set-blocking "^2.0.0"
- string-width "^4.2.0"
- which-module "^2.0.0"
- y18n "^4.0.0"
- yargs-parser "^18.1.2"
-
yargs@^16.2.0:
version "16.2.0"
resolved "https://registry.npmjs.org/yargs/-/yargs-16.2.0.tgz"
@@ -16591,6 +16643,19 @@ yargs@^16.2.0:
y18n "^5.0.5"
yargs-parser "^20.2.2"
+yargs@^17.3.1:
+ version "17.4.1"
+ resolved "https://registry.yarnpkg.com/yargs/-/yargs-17.4.1.tgz#ebe23284207bb75cee7c408c33e722bfb27b5284"
+ integrity sha512-WSZD9jgobAg3ZKuCQZSa3g9QOJeCCqLoLAykiWgmXnDo9EPnn4RPf5qVTtzgOx66o6/oqhcA5tHtJXpG8pMt3g==
+ dependencies:
+ cliui "^7.0.2"
+ escalade "^3.1.1"
+ get-caller-file "^2.0.5"
+ require-directory "^2.1.1"
+ string-width "^4.2.3"
+ y18n "^5.0.5"
+ yargs-parser "^21.0.0"
+
yargs@^7.1.0:
version "7.1.2"
resolved "https://registry.npmjs.org/yargs/-/yargs-7.1.2.tgz"
@@ -16610,11 +16675,6 @@ yargs@^7.1.0:
y18n "^3.2.1"
yargs-parser "^5.0.1"
-yeast@0.1.2:
- version "0.1.2"
- resolved "https://registry.npmjs.org/yeast/-/yeast-0.1.2.tgz"
- integrity sha1-AI4G2AlDIMNy28L47XagymyKxBk=
-
yocto-queue@^0.1.0:
version "0.1.0"
resolved "https://registry.npmjs.org/yocto-queue/-/yocto-queue-0.1.0.tgz"
diff --git a/nomad/app/v1/routers/entries.py b/nomad/app/v1/routers/entries.py
index a3bf7bdac4a32ddcd0078e7dafc4862bd4ad786b..e17b9ecebf0cc554d37ec17defe61a87ac2134ba 100644
--- a/nomad/app/v1/routers/entries.py
+++ b/nomad/app/v1/routers/entries.py
@@ -17,6 +17,10 @@
#
from datetime import datetime
+import functools
+from itertools import zip_longest
+import multiprocessing
+import operator
from typing import Optional, Set, Union, Dict, Iterator, Any, List
from fastapi import (
@@ -38,7 +42,6 @@ from nomad.datamodel import EditableUserMetadata
from nomad.files import StreamedFile, create_zipstream
from nomad.utils import strip
from nomad.archive import RequiredReader, RequiredValidationError, ArchiveQueryError
-from nomad.archive import ArchiveQueryError
from nomad.search import AuthenticationRequiredError, SearchError, update_metadata as es_update_metadata
from nomad.search import search, QueryValidationError
from nomad.metainfo.elasticsearch_extension import entry_type
@@ -69,7 +72,7 @@ archive_required_documentation = strip('''
The `required` part allows you to specify what parts of the requested archives
should be returned. The NOMAD Archive is a hierarchical data format and
you can *require* certain branches (i.e. *sections*) in the hierarchy.
-By specifing certain sections with specific contents or all contents (via
+By specifying certain sections with specific contents or all contents (via
the directive `"*"`), you can determine what sections and what quantities should
be returned. The default is the whole archive, i.e., `"*"`.
@@ -441,13 +444,20 @@ def _do_exaustive_search(owner: Owner, query: Query, include: List[str], user: U
break
-class _Uploads():
+class _Uploads:
'''
A helper class that caches subsequent access to upload files the same upload.
'''
+
def __init__(self):
self._upload_files = None
+ def __enter__(self):
+ return self
+
+ def __exit__(self, exc_type, exc_val, exc_tb):
+ self.close()
+
def get_upload_files(self, upload_id: str) -> files.UploadFiles:
if self._upload_files is not None and self._upload_files.upload_id != upload_id:
self._upload_files.close()
@@ -492,13 +502,9 @@ def _answer_entries_rawdir_request(
required=MetadataRequired(include=['entry_id', 'upload_id', 'mainfile']),
user_id=user.user_id if user is not None else None)
- uploads = _Uploads()
- try:
- response_data = [
- _create_entry_rawdir(entry_metadata, uploads)
- for entry_metadata in search_response.data]
- finally:
- uploads.close()
+ with _Uploads() as uploads:
+ response_data = [_create_entry_rawdir(
+ entry_metadata, uploads) for entry_metadata in search_response.data]
return EntriesRawDirResponse(
owner=search_response.owner,
@@ -670,68 +676,107 @@ def _read_archive(entry_metadata, uploads, required_reader: RequiredReader):
return {
'entry_id': entry_id,
'parser_name': entry_metadata['parser_name'],
- 'archive': required_reader.read(archive, entry_id)
- }
+ 'archive': required_reader.read(archive, entry_id)}
except ArchiveQueryError as e:
- raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(e))
+ raise HTTPException(status.HTTP_400_BAD_REQUEST, detail=str(e))
def _validate_required(required: ArchiveRequired) -> RequiredReader:
try:
return RequiredReader(required)
except RequiredValidationError as e:
- raise HTTPException(status_code=status.HTTP_422_UNPROCESSABLE_ENTITY, detail=[dict(
- msg=e.msg, loc=['required'] + e.loc)])
+ raise HTTPException(
+ status.HTTP_422_UNPROCESSABLE_ENTITY,
+ detail=[dict(msg=e.msg, loc=['required'] + e.loc)])
+
+
+def _read_entry_from_archive(entry, uploads, required_reader: RequiredReader):
+ entry_id, upload_id = entry['entry_id'], entry['upload_id']
+
+ # all other exceptions are handled by the caller `_read_entries_from_archive`
+ try:
+ upload_files = uploads.get_upload_files(upload_id)
+
+ with upload_files.read_archive(entry_id, True) as archive:
+ return {
+ 'entry_id': entry_id,
+ 'upload_id': upload_id,
+ 'parser_name': entry['parser_name'],
+ 'archive': required_reader.read(archive, entry_id)}
+ except ArchiveQueryError as e:
+ raise HTTPException(status.HTTP_400_BAD_REQUEST, detail=str(e))
+ except KeyError as e:
+ logger.error('missing archive', exc_info=e, entry_id=entry_id)
+
+ return None
+
+
+def _read_entries_from_archive(entries, required):
+ '''
+ Takes pickleable arguments so that it can be offloaded to worker processes.
+
+ It is important to ensure the return values are also pickleable.
+ '''
+ with _Uploads() as uploads:
+ required_reader = _validate_required(required)
+
+ responses = [_read_entry_from_archive(
+ entry, uploads, required_reader) for entry in entries if entry is not None]
+
+ return list(filter(None, responses))
def _answer_entries_archive_request(
owner: Owner, query: Query, pagination: MetadataPagination, required: ArchiveRequired,
user: User):
-
if owner == Owner.all_:
- raise HTTPException(status_code=status.HTTP_401_UNAUTHORIZED, detail=strip('''
- The owner=all is not allowed for this operation as it will search for entries
- that you might now be allowed to access.
- '''))
+ raise HTTPException(
+ status_code=status.HTTP_401_UNAUTHORIZED, detail=strip(
+ '''The owner=all is not allowed for this operation as it will search for entries
+ that you might now be allowed to access.'''))
if required is None:
required = '*'
- required_reader = _validate_required(required)
-
search_response = perform_search(
owner=owner, query=query,
pagination=pagination,
required=MetadataRequired(include=['entry_id', 'upload_id', 'parser_name']),
user_id=user.user_id if user is not None else None)
- uploads = _Uploads()
- response_data = {}
- for entry_metadata in search_response.data:
- entry_id, upload_id = entry_metadata['entry_id'], entry_metadata['upload_id']
+ # fewer than 8 entries per process is not useful
+ # more than config.max_process_number processes is too much for the server
+ number: int = min(
+ len(search_response.data) // config.archive.min_entires_per_process,
+ config.archive.max_process_number)
- archive_data = None
+ if number <= 1:
+ request_data: list = _read_entries_from_archive(search_response.data, required)
+ else:
+ entries_per_process = len(search_response.data) // number + 1
- try:
- archive_data = _read_archive(entry_metadata, uploads, required_reader)['archive']
- except KeyError as e:
- logger.error('missing archive', exc_info=e, entry_id=entry_id)
- continue
-
- response_data[entry_id] = {
- 'entry_id': entry_id,
- 'upload_id': upload_id,
- 'parser_name': entry_metadata['parser_name'],
- 'archive': archive_data}
+ # use process pool
+ pool: multiprocessing.pool.Pool = multiprocessing.pool.Pool(processes=number)
- uploads.close()
+ try:
+ responses = pool.map(
+ functools.partial(_read_entries_from_archive, required=required),
+ zip_longest(*[iter(search_response.data)] * entries_per_process))
+ finally:
+ # gracefully shutdown the pool
+ pool.close()
+ pool.join()
+
+ # collect results from each process
+ # https://stackoverflow.com/a/45323085
+ request_data = functools.reduce(operator.iconcat, responses, [])
return EntriesArchiveResponse(
owner=search_response.owner,
query=search_response.query,
pagination=search_response.pagination,
required=required,
- data=list(response_data.values()))
+ data=request_data)
_entries_archive_docstring = strip('''
@@ -805,7 +850,6 @@ def _answer_entries_archive_download_request(
'The limit of maximum number of entries in a single download (%d) has been '
'exeeded (%d).' % (config.max_entry_download, response.pagination.total)))
- uploads = _Uploads()
manifest = []
search_includes = ['entry_id', 'upload_id', 'parser_name']
@@ -833,12 +877,10 @@ def _answer_entries_archive_download_request(
manifest_content = json.dumps(manifest, indent=2).encode()
yield StreamedFile(path='manifest.json', f=io.BytesIO(manifest_content), size=len(manifest_content))
- try:
+ with _Uploads() as uploads:
# create the streaming response with zip file contents
content = create_zipstream(streamed_files(), compress=files_params.compress)
return StreamingResponse(content, media_type='application/zip')
- finally:
- uploads.close()
_entries_archive_download_docstring = strip('''
@@ -936,11 +978,9 @@ async def get_entry_rawdir(
status_code=status.HTTP_404_NOT_FOUND,
detail='The entry with the given id does not exist or is not visible to you.')
- uploads = _Uploads()
- try:
- return EntryRawDirResponse(entry_id=entry_id, data=_create_entry_rawdir(response.data[0], uploads))
- finally:
- uploads.close()
+ with _Uploads() as uploads:
+ return EntryRawDirResponse(
+ entry_id=entry_id, data=_create_entry_rawdir(response.data[0], uploads))
@router.get(
@@ -1044,13 +1084,12 @@ def answer_entry_archive_request(query: Dict[str, Any], required: ArchiveRequire
entry_metadata = response.data[0]
entry_id = entry_metadata['entry_id']
- uploads = _Uploads()
- try:
+ with _Uploads() as uploads:
try:
archive_data = _read_archive(entry_metadata, uploads, required_reader)['archive']
except KeyError:
raise HTTPException(
- status_code=status.HTTP_404_NOT_FOUND,
+ status.HTTP_404_NOT_FOUND,
detail='The entry does exist, but it has no archive.')
return {
@@ -1060,10 +1099,7 @@ def answer_entry_archive_request(query: Dict[str, Any], required: ArchiveRequire
'entry_id': entry_id,
'upload_id': entry_metadata['upload_id'],
'parser_name': entry_metadata['parser_name'],
- 'archive': archive_data
- }}
- finally:
- uploads.close()
+ 'archive': archive_data}}
@router.get(
diff --git a/nomad/archive/__init__.py b/nomad/archive/__init__.py
index 7b4ef387d72ce84976e25da1b43c91ee1f8d276e..b7cb22460a1b884de38386c697ac56bf4e5a4d08 100644
--- a/nomad/archive/__init__.py
+++ b/nomad/archive/__init__.py
@@ -35,7 +35,7 @@ section annotations/categories.
from .storage import (
write_archive, read_archive, ArchiveError, ArchiveReader, ArchiveWriter,
- ArchiveObject, ArchiveList, ArchiveItem)
+ ArchiveDict, ArchiveList, ArchiveItem)
from .query import query_archive, filter_archive, ArchiveQueryError
from .partial import (
read_partial_archive_from_mongo, read_partial_archives_from_mongo,
diff --git a/nomad/archive/query.py b/nomad/archive/query.py
index 6aae0eda3693205b4d420d5d200bb66dd8bba982..54dbb180a05ef3aca99055b6c4ec47e170808708 100644
--- a/nomad/archive/query.py
+++ b/nomad/archive/query.py
@@ -16,13 +16,70 @@
# limitations under the License.
#
-from typing import Any, Tuple, Dict, Callable, Union, List
-from io import BytesIO
+import functools
import re
+from typing import Any, Dict, Callable, Union, Tuple
+from io import BytesIO
from nomad import utils
-from .storage import ArchiveReader, ArchiveList, ArchiveObject
+from .storage import ArchiveReader, ArchiveList, ArchiveDict, _to_son
+
+_query_archive_key_pattern = re.compile(r'^([\s\w\-]+)(\[([-?0-9]*)(:([-?0-9]*))?])?$')
+
+
+@functools.lru_cache(maxsize=1024)
+def _fix_index(index, length):
+ if index is None:
+ return index
+
+ return max(-length, index) if index < 0 else min(length, index)
+
+
+@functools.lru_cache(maxsize=1024)
+def _extract_key_and_index(match) -> Tuple[str, Union[Tuple[int, int], int]]:
+ key = match.group(1)
+
+ # noinspection PyTypeChecker
+ index: Union[Tuple[int, int], int] = None
+
+ # check if we have indices
+ if match.group(2) is not None:
+ group = match.group(3)
+ first_index = None if group == '' else int(group)
+
+ if match.group(4) is None:
+ index = first_index # one item
+ else:
+ group = match.group(5)
+ last_index = None if group == '' else int(group)
+ index = (0 if first_index is None else first_index, last_index)
+
+ return key, index
+
+
+# @cached(thread_safe=False, max_size=1024)
+def _extract_child(archive_item, prop, index) -> Union[dict, list]:
+ archive_child = archive_item[prop]
+ is_list = isinstance(archive_child, (ArchiveList, list))
+
+ if index is None and is_list:
+ index = (0, None)
+ elif index is not None and not is_list:
+ raise ArchiveQueryError(f'cannot use list key on none list {prop}')
+
+ if index is not None:
+ length = len(archive_child)
+ if isinstance(index, tuple):
+ index = (_fix_index(index[0], length), _fix_index(index[1], length))
+ if index[0] == index[1]:
+ archive_child = [archive_child[index[0]]]
+ else:
+ archive_child = archive_child[index[0]: index[1]]
+ else:
+ archive_child = [archive_child[_fix_index(index, length)]]
+
+ return archive_child
class ArchiveQueryError(Exception):
@@ -33,9 +90,6 @@ class ArchiveQueryError(Exception):
pass
-__query_archive_key_pattern = re.compile(r'^([\s\w\-]+)(\[([-?0-9]*)(:([-?0-9]*))?\])?$')
-
-
def query_archive(
f_or_archive_reader: Union[str, ArchiveReader, BytesIO], query_dict: dict,
**kwargs) -> Dict:
@@ -72,43 +126,25 @@ def query_archive(
* exclude (in combination with wildcard keys), replaces the value with null
'''
- def _to_son(data):
- if isinstance(data, (ArchiveList, List)):
- data = [_to_son(item) for item in data]
-
- elif isinstance(data, ArchiveObject):
- data = data.to_dict()
-
- return data
-
- def _load_data(query_dict: Dict[str, Any], archive_item: ArchiveObject) -> Dict:
- query_dict_with_fixed_ids = {
- utils.adjust_uuid_size(key): value for key, value in query_dict.items()}
- return filter_archive(query_dict_with_fixed_ids, archive_item, transform=_to_son)
-
if isinstance(f_or_archive_reader, ArchiveReader):
return _load_data(query_dict, f_or_archive_reader)
-
elif isinstance(f_or_archive_reader, (BytesIO, str)):
with ArchiveReader(f_or_archive_reader, **kwargs) as archive:
return _load_data(query_dict, archive)
else:
- raise TypeError('%s is neither a file-like nor ArchiveReader' % f_or_archive_reader)
+ raise TypeError(f'{f_or_archive_reader} is neither a file-like nor ArchiveReader')
-def filter_archive(
- required: Union[str, Dict[str, Any]], archive_item: Union[Dict, ArchiveObject, str],
- transform: Callable, result_root: Dict = None, resolve_inplace: bool = False) -> Dict:
+def _load_data(query_dict: Dict[str, Any], archive_item: ArchiveDict) -> Dict:
+ query_dict_with_fixed_ids = {utils.adjust_uuid_size(
+ key): value for key, value in query_dict.items()}
+ return filter_archive(query_dict_with_fixed_ids, archive_item, transform=_to_son)
- def _fix_index(index, length):
- if index is None:
- return index
- if index < 0:
- return max(-(length), index)
- else:
- return min(length, index)
+def filter_archive(
+ required: Union[str, Dict[str, Any]], archive_item: Union[Dict, ArchiveDict, str],
+ transform: Callable, result_root: Dict = None, resolve_inplace: bool = False) -> Dict:
if archive_item is None:
return None
@@ -119,51 +155,31 @@ def filter_archive(
if required == 'resolve':
# TODO this requires to reflect on the definition to determine what are references!
pass
-
elif required in ['*', 'include']:
pass
-
else:
raise ArchiveQueryError(f'unknown directive {required}')
return transform(archive_item)
- elif not isinstance(required, dict):
+ if not isinstance(required, dict):
raise ArchiveQueryError('a value in required is neither dict not string directive')
if isinstance(archive_item, str):
# The archive item is a reference, the required is still a dict, the references
# needs to be resolved
# TODO
- raise ArchiveQueryError(f'resolving references in non partial archives is not yet implemented')
+ raise ArchiveQueryError(
+ f'resolving references in non partial archives is not yet implemented')
result: Dict[str, Any] = {}
for key, val in required.items():
key = key.strip()
# process array indices
- match = __query_archive_key_pattern.match(key)
- index: Union[Tuple[int, int], int] = None
+ match = _query_archive_key_pattern.match(key)
if match:
- key = match.group(1)
-
- # check if we have indices
- if match.group(2) is not None:
- first_index, last_index = None, None
- group = match.group(3)
- first_index = None if group == '' else int(group)
-
- if match.group(4) is not None:
- group = match.group(5)
- last_index = None if group == '' else int(group)
- index = (0 if first_index is None else first_index, last_index)
-
- else:
- index = first_index # one item
-
- else:
- index = None
-
+ key, index = _extract_key_and_index(match)
elif key == '*':
# TODO
raise ArchiveQueryError('key wildcards not yet implemented')
@@ -171,32 +187,11 @@ def filter_archive(
raise ArchiveQueryError('invalid key format: %s' % key)
try:
- archive_child = archive_item[key]
- is_list = isinstance(archive_child, (ArchiveList, list))
-
- if index is None and is_list:
- index = (0, None)
-
- elif index is not None and not is_list:
- raise ArchiveQueryError('cannot use list key on none list %s' % key)
-
- if index is None:
- pass
- else:
- length = len(archive_child)
- if isinstance(index, tuple):
- index = (_fix_index(index[0], length), _fix_index(index[1], length))
- if index[0] == index[1]:
- archive_child = [archive_child[index[0]]]
- else:
- archive_child = archive_child[index[0]: index[1]]
- else:
- archive_child = [archive_child[_fix_index(index, length)]]
+ archive_child = _extract_child(archive_item, key, index)
if isinstance(archive_child, (ArchiveList, list)):
- result[key] = [
- filter_archive(val, item, transform=transform)
- for item in archive_child]
+ result[key] = [filter_archive(
+ val, item, transform=transform) for item in archive_child]
else:
result[key] = filter_archive(val, archive_child, transform=transform)
diff --git a/nomad/archive/required.py b/nomad/archive/required.py
index fe1b2e7d63915c046bcc8c02992c108dc3a4bdba..6d6dbbfac1fce0ddbe27499c7363aeb6673120d1 100644
--- a/nomad/archive/required.py
+++ b/nomad/archive/required.py
@@ -16,14 +16,14 @@
# limitations under the License.
#
-from typing import cast, Union, Dict, Tuple, List, Any, Callable
-import re
+import functools
+from typing import cast, Union, Dict, Tuple, Any
from nomad import utils
from nomad.metainfo import Definition, Section, Quantity, SubSection, Reference, QuantityReference
-
-from .storage import ArchiveReader, ArchiveList, ArchiveObject, ArchiveError
-from .query import ArchiveQueryError # TODO
+from .storage import ArchiveReader, ArchiveList, ArchiveError
+from .query import ArchiveQueryError, _to_son, _query_archive_key_pattern, _extract_key_and_index, \
+ _extract_child
class RequiredValidationError(Exception):
@@ -33,6 +33,29 @@ class RequiredValidationError(Exception):
self.loc = loc
+@functools.lru_cache(maxsize=1024)
+def _parse_required_key(key: str) -> Tuple[str, Union[Tuple[int, int], int]]:
+ key = key.strip()
+ match = _query_archive_key_pattern.match(key)
+
+ if not match:
+ raise Exception(f'invalid key format: {key}')
+
+ return _extract_key_and_index(match)
+
+
+def _setdefault(target: Union[dict, list], key, value_type: type):
+ if isinstance(target, list):
+ if target[key] is None:
+ target[key] = value_type()
+ return target[key]
+
+ if key not in target:
+ target[key] = value_type()
+
+ return target[key]
+
+
class RequiredReader:
'''
Clients can read only the required parts of an archive. They specify the required
@@ -54,7 +77,7 @@ class RequiredReader:
}
}
- The structure has to adheres to metainfo definitions of an archive's sub-sections and
+ The structure has to adhere to metainfo definitions of an archive's subsections and
quantities. At each point in the specification, children can be replaced with certain
directives.
@@ -70,38 +93,23 @@ class RequiredReader:
- required: The requirement specification as a python dictionary or directive string.
'''
- __query_archive_key_pattern = re.compile(r'^([\s\w\-]+)(\[([-?0-9]*)(:([-?0-9]*))?\])?$')
-
- def __init__(self, required: Union[dict, str], root_section_def: Section = None, resolve_inplace: bool = False):
+ def __init__(
+ self, required: Union[dict, str], root_section_def: Section = None,
+ resolve_inplace: bool = False):
if root_section_def is None:
from nomad import datamodel
self.root_section_def = datamodel.EntryArchive.m_def
else:
self.root_section_def = root_section_def
- self.__result_root: dict = None
- self.__archive_root: dict = None # it is actually an ArchvieReader, but we use it as dict
+ # noinspection PyTypeChecker
+ self._result_root: dict = None
+ # noinspection PyTypeChecker
+ self._archive_root: dict = None # it is actually an ArchiveReader, but we use it as dict
self.resolve_inplace = resolve_inplace
self.required = self.validate(required, is_root=True)
- def __to_son(self, data):
- if isinstance(data, (ArchiveList, List)):
- data = [self.__to_son(item) for item in data]
-
- elif isinstance(data, ArchiveObject):
- data = data.to_dict()
-
- return data
-
- def __fix_index(self, index, length):
- if index is None:
- return index
- if index < 0:
- return max(-(length), index)
- else:
- return min(length, index)
-
def validate(
self, required: Union[str, dict], definition: Definition = None,
loc: list = None, is_root=False) -> dict:
@@ -109,11 +117,11 @@ class RequiredReader:
Validates the required specification of this instance. It will replace all
string directives with dicts. Those will have keys `_def` and `_directive`. It
will add a key `_def` to all dicts. The `_def` will be the respective metainfo
- definition. If will also add key `_ref`. It will be None or contain a
+ definition. It will also add key `_ref`. It will be None or contain a
Reference instance, if the definition is a reference target.
This method will raise an exception (:class:`RequiredValidationError`) to denote
- any mismatches between the required specification and the metainfo. Also to denote
+ any mismatches between the required specification and the metainfo, also, to denote
misused directives, bad structure, etc.
raises:
@@ -124,8 +132,7 @@ class RequiredReader:
if isinstance(resolve_inplace, bool):
self.resolve_inplace = resolve_inplace
elif resolve_inplace is not None:
- raise RequiredValidationError(
- 'resolve-inplace is not a bool', ['resolve-inplace'])
+ raise RequiredValidationError('resolve-inplace is not a bool', ['resolve-inplace'])
if definition is None:
definition = self.root_section_def
@@ -164,7 +171,7 @@ class RequiredReader:
loc.append(key)
try:
- prop, index = self.__parse_required_key(key)
+ prop, index = _parse_required_key(key)
except Exception:
raise RequiredValidationError(f'invalid key format {key}', loc)
if prop == '*':
@@ -173,8 +180,7 @@ class RequiredReader:
try:
prop_def = cast(Section, definition).all_properties[prop]
except KeyError:
- raise RequiredValidationError(
- f'{definition.name} has not property {prop}', loc)
+ raise RequiredValidationError(f'{definition.name} has not property {prop}', loc)
result[key] = self.validate(value, prop_def, loc)
result[key].update(_prop=prop, _index=index)
loc.pop()
@@ -186,64 +192,34 @@ class RequiredReader:
Reads the archive of the given entry id from the given archive reader and applies
the instance's requirement specification.
'''
- assert self.__result_root is None and self.__archive_root is None, \
+ assert self._result_root is None and self._archive_root is None, \
'instance cannot be used concurrently for multiple reads at the same time'
- self.__archive_root = archive_reader[utils.adjust_uuid_size(entry_id)]
+ self._archive_root = archive_reader[utils.adjust_uuid_size(entry_id)]
result: dict = {}
- self.__result_root = result
- result.update(**cast(dict, self.__apply_required(self.required, self.__archive_root)))
+ self._result_root = result
+ result.update(**cast(dict, self._apply_required(self.required, self._archive_root)))
- self.__archive_root = None
- self.__result_root = None
+ self._archive_root = None
+ self._result_root = None
return result
- def __parse_required_key(self, key: str) -> Tuple[str, Union[Tuple[int, int], int]]:
- key = key.strip()
- match = RequiredReader.__query_archive_key_pattern.match(key)
- index: Union[Tuple[int, int], int] = None
- if match:
- key = match.group(1)
-
- # check if we have indices
- if match.group(2) is not None:
- first_index, last_index = None, None
- group = match.group(3)
- first_index = None if group == '' else int(group)
-
- if match.group(4) is not None:
- group = match.group(5)
- last_index = None if group == '' else int(group)
- index = (0 if first_index is None else first_index, last_index)
-
- else:
- index = first_index # one item
-
- else:
- index = None
-
- else:
- raise Exception('invalid key format: %s' % key)
-
- return key, index
-
- def __resolve_refs(self, archive: dict, definition: Definition) -> dict:
+ def _resolve_refs(self, archive: dict, definition: Definition) -> dict:
''' Resolves all references in archive. '''
if isinstance(definition, Quantity):
# it's a quantity ref, the archive is already resolved
- return self.__to_son(archive[definition.name])
+ return _to_son(archive[definition.name])
# it's a section ref
section_def = cast(Section, definition)
- archive = self.__to_son(archive)
+ archive = _to_son(archive)
result = {}
- for prop in archive:
- value = archive[prop]
+ for prop, value in archive.items():
prop_def = section_def.all_properties[prop]
- handle_item: Callable[[Any], Any] = None
if isinstance(prop_def, SubSection):
- handle_item = lambda value: self.__resolve_refs(value, prop_def.sub_section.m_resolved())
+ def handle_item(v):
+ return self._resolve_refs(v, prop_def.sub_section.m_resolved())
elif isinstance(prop_def.type, Reference):
if isinstance(prop_def.type, QuantityReference):
target_def = prop_def.type.target_quantity_def.m_resolved()
@@ -252,18 +228,19 @@ class RequiredReader:
required = dict(
_directive='include-resolved', _def=target_def, _ref=prop_def.type)
- handle_item = lambda value: self.__resolve_ref(required, value)
- else:
- handle_item = lambda value: value
- if isinstance(value, (list, ArchiveList)):
- result[prop] = [handle_item(item) for item in value]
+ def handle_item(v):
+ return self._resolve_ref(required, v)
else:
- result[prop] = handle_item(value)
+ result[prop] = value.to_list() if isinstance(value, ArchiveList) else value
+ continue
+
+ result[prop] = [handle_item(item) for item in value] if isinstance(
+ value, (list, ArchiveList)) else handle_item(value)
return result
- def __resolve_ref(self, required: dict, path: str) -> Union[dict, str]:
+ def _resolve_ref(self, required: dict, path: str) -> Union[dict, str]:
# The archive item is a reference, the required is still a dict, the references
# This is a simplified version of the metainfo implementation (m_resolve).
# It implements the same semantics, but does not apply checks.
@@ -274,44 +251,28 @@ class RequiredReader:
# TODO support custom reference resolution, e.g. user_id based
return path
- resolved = self.__archive_root
+ resolved = self._archive_root
path_stack = path.strip('/').split('/')
- path_stack.reverse()
try:
- while len(path_stack) > 0:
- prop = path_stack.pop()
- resolved = resolved[prop]
- if len(path_stack) > 0 and path_stack[-1].isdigit():
- resolved = resolved[int(path_stack.pop())]
-
+ for prop in path_stack:
+ resolved = resolved[int(prop) if prop.isdigit() else prop]
except Exception:
raise ArchiveError('could not resolve reference')
# apply required to resolved archive_item
if isinstance(required['_def'], Quantity):
- resolved_result = self.__to_son(resolved)
+ resolved_result = _to_son(resolved)
else:
- resolved_result = self.__apply_required(required, resolved)
+ resolved_result = self._apply_required(required, resolved)
# return or add to root depending on self.resolve_inplace
if self.resolve_inplace:
return resolved_result
- def _setdefault(target: Union[dict, list], prop, value_type: type):
- if isinstance(target, list):
- if target[prop] is None:
- target[prop] = value_type()
- return target[prop]
-
- if prop not in target:
- target[prop] = value_type()
-
- return target[prop]
-
- path_stack = path.strip('/').split('/')
path_stack.reverse()
- target_container: Union[dict, list] = self.__result_root
+ target_container: Union[dict, list] = self._result_root
+ # noinspection PyTypeChecker
prop_or_index: Union[str, int] = None
while len(path_stack) > 0:
if prop_or_index is not None:
@@ -319,17 +280,16 @@ class RequiredReader:
prop_or_index = path_stack.pop()
if len(path_stack) > 0 and path_stack[-1].isdigit():
- target_list = _setdefault(target_container, prop_or_index, list)
- index = int(path_stack.pop())
- for _ in range(len(target_list), index + 1):
- target_list.append(None)
- target_container = target_list
- prop_or_index = index
+ target_container = _setdefault(target_container, prop_or_index, list)
+ prop_or_index = int(path_stack.pop())
+ size_diff: int = prop_or_index - len(target_container) + 1
+ if size_diff > 0:
+ target_container.extend([None] * size_diff) # type: ignore
target_container[prop_or_index] = resolved_result # type: ignore
return path
- def __apply_required(self, required: dict, archive_item: Union[dict, str]) -> Union[Dict, str]:
+ def _apply_required(self, required: dict, archive_item: Union[dict, str]) -> Union[Dict, str]:
if archive_item is None:
return None
@@ -337,17 +297,17 @@ class RequiredReader:
if directive is not None:
if directive == 'include-resolved':
if isinstance(archive_item, str):
- return self.__resolve_ref(required, archive_item)
- return self.__resolve_refs(archive_item, required['_def'])
+ return self._resolve_ref(required, archive_item)
- elif directive in ['*', 'include']:
- return self.__to_son(archive_item)
+ return self._resolve_refs(archive_item, required['_def'])
- else:
- raise ArchiveQueryError(f'unknown directive {required}')
+ if directive in ['*', 'include']:
+ return _to_son(archive_item)
+
+ raise ArchiveQueryError(f'unknown directive {required}')
if isinstance(archive_item, str):
- return self.__resolve_ref(required, archive_item)
+ return self._resolve_ref(required, archive_item)
result: dict = {}
for key, val in required.items():
@@ -357,35 +317,12 @@ class RequiredReader:
prop, index = val['_prop'], val['_index']
try:
- archive_child = archive_item[prop]
- is_list = isinstance(archive_child, (ArchiveList, list))
-
- if index is None and is_list:
- index = (0, None)
-
- elif index is not None and not is_list:
- raise ArchiveQueryError('cannot use list key on none list %s' % prop)
-
- if index is None:
- pass
- else:
- length = len(archive_child)
- if isinstance(index, tuple):
- index = (self.__fix_index(index[0], length), self.__fix_index(index[1], length))
- if index[0] == index[1]:
- archive_child = [archive_child[index[0]]]
- else:
- archive_child = archive_child[index[0]: index[1]]
- else:
- archive_child = [archive_child[self.__fix_index(index, length)]]
+ archive_child = _extract_child(archive_item, prop, index)
if isinstance(archive_child, (ArchiveList, list)):
- result[prop] = [
- self.__apply_required(val, item)
- for item in archive_child]
+ result[prop] = [self._apply_required(val, item) for item in archive_child]
else:
- result[prop] = self.__apply_required(val, archive_child)
-
+ result[prop] = self._apply_required(val, archive_child)
except (KeyError, IndexError):
continue
diff --git a/nomad/archive/storage.py b/nomad/archive/storage.py
index 4cc6db9a4e227f674ff26cbd02020d7ef45c716c..bf8ed1805f220d4cc59bffb49d0d63dcc1fdbb3b 100644
--- a/nomad/archive/storage.py
+++ b/nomad/archive/storage.py
@@ -19,26 +19,59 @@
from typing import Iterable, Any, Tuple, Dict, BinaryIO, Union, List, cast
from io import BytesIO, BufferedReader
from collections.abc import Mapping, Sequence
+
+from memoization import cached
import msgpack
from msgpack.fallback import Packer, StringIO
import struct
import json
-import math
from nomad import utils
-
+from nomad.config import archive
__packer = msgpack.Packer(autoreset=True, use_bin_type=True)
+_toc_uuid_size = utils.default_hash_len + 1
+_toc_item_size = _toc_uuid_size + 25 # packed(uuid + [10-byte-pos, 10-byte-pos])
+_entries_per_block = archive.block_size // _toc_item_size
+_bytes_per_block = _entries_per_block * _toc_item_size
+
-def packb(o, **kwargs):
+def packb(o):
return __packer.pack(o)
-def unpackb(o, **kwargs):
+def unpackb(o):
return msgpack.unpackb(o, raw=False)
+def _encode(start: int, end: int) -> bytes:
+ return start.to_bytes(5, byteorder='little', signed=False) + end.to_bytes(
+ 5, byteorder='little', signed=False)
+
+
+def _decode(position: bytes) -> Tuple[int, int]:
+ return int.from_bytes(position[:5], byteorder='little', signed=False), int.from_bytes(
+ position[5:], byteorder='little', signed=False)
+
+
+def _unpack_entry(data: bytes) -> Tuple[Any, Tuple[Any, Any]]:
+ entry_uuid = unpackb(data[: _toc_uuid_size])
+ positions_encoded = unpackb(data[_toc_uuid_size:])
+ return entry_uuid, (_decode(positions_encoded[0]), _decode(positions_encoded[1]))
+
+
+def _to_son(data):
+ if isinstance(data, ArchiveList):
+ data = data.to_list()
+
+ elif isinstance(data, ArchiveDict):
+ data = data.to_dict()
+
+ # no need to convert build-in types
+ return data
+
+
class ArchiveError(Exception):
''' An error that indicates a broken archive. '''
pass
@@ -51,77 +84,78 @@ class TOCPacker(Packer):
Uses a combination of the pure python msgpack fallback packer and the "real"
c-based packing.
'''
+
def __init__(self, toc_depth: int, *args, **kwargs):
self.toc_depth = toc_depth
+ # noinspection PyTypeChecker
self.toc: Dict[str, Any] = None
self._depth = 0
# Because we cannot change msgpacks interface of _pack, this _stack is used to
- # tranfer the result of _pack calls in terms of the TOC.
+ # transfer the result of _pack calls in terms of the TOC.
self._stack: List[Any] = []
super().__init__(*args, **kwargs)
- def pack(self, obj, *args, **kwargs):
- assert isinstance(obj, dict), 'TOC packer can only pack dicts, %s' % obj.__class__
- self._depth = 0
- self._buffer = StringIO()
- result = super().pack(obj, *args, **kwargs)
- self.toc = self._stack.pop()
- assert len(self._stack) == 0
- return result
-
def _pos(self):
return self._buffer.getbuffer().nbytes
- def _pack(self, obj, *args, **kwargs):
- if isinstance(obj, dict):
- toc_result = {}
- start = self._pos()
- if self._depth >= self.toc_depth:
- pack_result = self._buffer.write(packb(obj))
- else:
- self._depth += 1
- pack_result = super()._pack(obj, *args, **kwargs)
- self._depth -= 1
-
- toc = {}
- for key, value in reversed(list(obj.items())):
- if isinstance(value, (list, tuple)):
- # this makes some assumptions about the non emptyness and uniformness
- # of array items
- if len(value) > 0 and isinstance(value[0], dict):
- toc[key] = self._stack.pop()
-
- elif isinstance(value, (dict, list, tuple)):
- toc[key] = self._stack.pop()
-
- toc_result['toc'] = {key: value for key, value in reversed(list(toc.items()))}
-
- end = self._pos()
- toc_result['pos'] = [start, end]
-
- self._stack.append(toc_result)
-
- elif isinstance(obj, list):
- toc_result = []
- pack_result = super()._pack(obj, *args, **kwargs)
+ def _pack_list(self, obj, *args, **kwargs):
+ pack_result = super()._pack(obj, *args, **kwargs)
- # same assumption and condition as above
- if len(obj) > 0 and isinstance(obj[0], dict):
- for _ in obj:
- toc_result.append(self._stack.pop())
+ toc_result = []
+ # same assumption and condition as above
+ if len(obj) > 0 and isinstance(obj[0], dict):
+ for _ in obj:
+ toc_result.append(self._stack.pop())
- self._stack.append(list(reversed(toc_result)))
+ self._stack.append(list(reversed(toc_result)))
- else:
+ return pack_result
+
+ def _pack_dict(self, obj, *args, **kwargs):
+ toc_result = {}
+ start = self._pos()
+ if self._depth >= self.toc_depth:
pack_result = self._buffer.write(packb(obj))
+ else:
+ self._depth += 1
+ pack_result = super()._pack(obj, *args, **kwargs)
+ self._depth -= 1
+
+ toc = {}
+ for key, value in reversed(list(obj.items())):
+ if isinstance(value, dict) or (isinstance(value, (list, tuple)) and len(
+ value) > 0 and isinstance(value[0], dict)):
+ # assumes non emptiness and uniformity of array items
+ toc[key] = self._stack.pop()
+
+ toc_result['toc'] = {key: value for key, value in reversed(list(toc.items()))}
+
+ end = self._pos()
+ toc_result['pos'] = [start, end]
+
+ self._stack.append(toc_result)
return pack_result
+ def _pack(self, obj, *args, **kwargs):
+ if isinstance(obj, dict):
+ return self._pack_dict(obj, *args, **kwargs)
+
+ if isinstance(obj, list):
+ return self._pack_list(obj, *args, **kwargs)
-_toc_uuid_size = utils.default_hash_len + 1
-_toc_item_size = _toc_uuid_size + 25 # packed(uuid + [10-byte-pos, 10-byte-pos])
+ return self._buffer.write(packb(obj))
+
+ def pack(self, obj):
+ assert isinstance(obj, dict), f'TOC packer can only pack dicts, {obj.__class__}'
+ self._depth = 0
+ self._buffer = StringIO()
+ result = super().pack(obj)
+ self.toc = self._stack.pop()
+ assert len(self._stack) == 0
+ return result
class ArchiveWriter:
@@ -130,8 +164,10 @@ class ArchiveWriter:
self.n_entries = n_entries
self._pos = 0
+ # noinspection PyTypeChecker
self._toc_position: Tuple[int, int] = None
self._toc: Dict[str, Tuple[Tuple[int, int], Tuple[int, int]]] = {}
+ # noinspection PyTypeChecker
self._f: BinaryIO = None
self._toc_packer = TOCPacker(toc_depth=entry_toc_depth)
@@ -146,24 +182,19 @@ class ArchiveWriter:
# write empty placeholder header
self._write_map_header(3)
- self.write(packb('toc_pos'))
- self.write(packb(ArchiveWriter._encode_position(0, 0)))
+ self._writeb('toc_pos')
+ self._writeb(_encode(0, 0))
- self.write(packb('toc'))
+ self._writeb('toc')
toc_start, _ = self._write_map_header(self.n_entries)
- _, toc_end = self.write(b'0' * _toc_item_size * self.n_entries)
+ _, toc_end = self._write(b'0' * _toc_item_size * self.n_entries)
self._toc_position = toc_start, toc_end
- self.write(packb('data'))
+ self._writeb('data')
self._write_map_header(self.n_entries)
return self
- def write(self, b: bytes) -> Tuple[int, int]:
- start = self._pos
- self._pos += self._f.write(b)
- return start, self._pos
-
def __exit__(self, exc_type, exc_val, exc_tb):
if exc_val is not None:
raise exc_val
@@ -174,28 +205,36 @@ class ArchiveWriter:
assert len(self._toc) == self.n_entries
toc_items = sorted(self._toc.items(), key=lambda item: item[0])
- toc = {
- uuid: [
- ArchiveWriter._encode_position(*positions[0]),
- ArchiveWriter._encode_position(*positions[1])]
- for uuid, positions in toc_items}
+ toc = {uuid: [_encode(*positions[0]), _encode(
+ *positions[1])] for uuid, positions in toc_items}
self._write_map_header(3)
- self.write(packb('toc_pos'))
- self.write(
- packb(ArchiveWriter._encode_position(*self._toc_position), use_bin_type=True))
+ self._writeb('toc_pos')
+ self._writeb(_encode(*self._toc_position))
- self.write(packb('toc'))
- toc_position = self.write(packb(toc, use_bin_type=True))
- assert toc_position == self._toc_position, '%s - %s' % (toc_position, self._toc_position)
+ self._writeb('toc')
+ toc_position = self._writeb(toc)
+ assert toc_position == self._toc_position, f'{toc_position} - {self._toc_position}'
if isinstance(self.file_or_path, str):
self._f.close()
- @staticmethod
- def _encode_position(start: int, end: int) -> bytes:
- return start.to_bytes(5, byteorder='little', signed=False) + \
- end.to_bytes(5, byteorder='little', signed=False)
+ def _write_map_header(self, n):
+ if n <= 0x0f:
+ return self._write(struct.pack('B', 0x80 + n))
+ if n <= 0xffff:
+ return self._write(struct.pack(">BH", 0xde, n))
+ if n <= 0xffffffff:
+ return self._write(struct.pack(">BI", 0xdf, n))
+ raise ValueError("Dict is too large")
+
+ def _write(self, b: bytes) -> Tuple[int, int]:
+ start = self._pos
+ self._pos += self._f.write(b)
+ return start, self._pos
+
+ def _writeb(self, obj):
+ return self._write(packb(obj))
def add(self, uuid: str, data: Any) -> None:
uuid = utils.adjust_uuid_size(uuid)
@@ -204,198 +243,196 @@ class ArchiveWriter:
packed = self._toc_packer.pack(data)
toc = self._toc_packer.toc
- self.write(packb(uuid))
+ self._writeb(uuid)
self._write_map_header(2)
- self.write(packb('toc'))
- toc_pos = self.write(packb(toc, use_bin_type=True))
- self.write(packb('data'))
- data_pos = self.write(packed)
+ self._writeb('toc')
+ toc_pos = self._writeb(toc)
+ self._writeb('data')
+ data_pos = self._write(packed)
self._toc[uuid] = (toc_pos, data_pos)
- def _write_map_header(self, n):
- if n <= 0x0f:
- return self.write(struct.pack('B', 0x80 + n))
- if n <= 0xffff:
- return self.write(struct.pack(">BH", 0xde, n))
- if n <= 0xffffffff:
- return self.write(struct.pack(">BI", 0xdf, n))
- raise ValueError("Dict is too large")
-
class ArchiveItem:
- def __init__(self, toc_entry: list, f: BytesIO, offset: int = 0):
- self.toc_entry = toc_entry
+ def __init__(self, f: BytesIO, offset: int = 0):
self._f = f
self._offset = offset
+ def _direct_read(self, size: int, offset: int):
+ self._f.seek(offset)
+ return self._f.read(size)
+
def _read(self, position: Tuple[int, int]):
start, end = position
- self._f.seek(start + self._offset)
- return unpackb(self._f.read(end - start))
+ raw_data = self._direct_read(end - start, start + self._offset)
+ return unpackb(raw_data)
- def _getchild(self, child_toc_entry):
+ @cached(thread_safe=False, max_size=512)
+ def _child(self, child_toc_entry):
if isinstance(child_toc_entry, dict):
if 'toc' in child_toc_entry:
- return ArchiveObject(child_toc_entry, self._f, self._offset)
- else:
- return self._read(child_toc_entry['pos'])
+ return ArchiveDict(child_toc_entry, self._f, self._offset)
- elif isinstance(child_toc_entry, list):
+ return self._read(child_toc_entry['pos'])
+
+ if isinstance(child_toc_entry, list):
return ArchiveList(child_toc_entry, self._f, self._offset)
- else:
- assert False, 'unreachable'
+ assert False, 'unreachable'
class ArchiveList(ArchiveItem, Sequence):
+ def __init__(self, toc_entry: list, *args, **kwargs):
+ super().__init__(*args, **kwargs)
+ self._toc_entry = toc_entry
+ self._full_list = None
def __getitem__(self, index):
- child_toc_entry = self.toc_entry[index]
- return self._getchild(child_toc_entry)
+ if self._full_list is None:
+ child_entry = self._toc_entry[index]
+ return self._child(child_entry)
+
+ return self._full_list[index]
def __len__(self):
- return self.toc_entry.__len__()
+ return self._toc_entry.__len__()
+
+ def to_list(self):
+ if self._full_list is None:
+ self._full_list = [_to_son(self._child(child_entry)) for child_entry in self._toc_entry]
+ return self._full_list
-class ArchiveObject(ArchiveItem, Mapping):
- def __init__(self, *args, **kwargs):
+class ArchiveDict(ArchiveItem, Mapping):
+ def __init__(self, toc_entry: dict, *args, **kwargs):
super().__init__(*args, **kwargs)
- self._data = None
+ self._toc_entry = toc_entry
def __getitem__(self, key):
- if self._data is None:
- try:
- child_toc_entry = self.toc_entry['toc'][key]
- except KeyError:
- return self.to_dict().__getitem__(key)
- return self._getchild(child_toc_entry)
- else:
- return self._data.__getitem__(key)
+ try:
+ child_toc_entry = self._toc_entry['toc'][key]
+ return self._child(child_toc_entry)
+ except KeyError:
+ return self.to_dict().__getitem__(key)
def __iter__(self):
- if self._data is None:
- return self.toc_entry['toc'].__iter__()
- else:
- return self._data.__iter__()
+ return self._toc_entry['toc'].__iter__()
def __len__(self):
- if self._data is None:
- return self.toc_entry['toc'].__len__()
- else:
- return self._data.__len__()
+ return self._toc_entry['toc'].__len__()
+ @cached(thread_safe=False)
def to_dict(self):
- return self._read(self.toc_entry['pos'])
+ # todo: potential bug here, what if children are ArchiveList or ArchiveDict?
+ return self._read(self._toc_entry['pos'])
-class ArchiveReader(ArchiveObject):
+class ArchiveReader(ArchiveDict):
def __init__(self, file_or_path: Union[str, BytesIO], use_blocked_toc=True):
- self.file_or_path = file_or_path
+ self._file_or_path = file_or_path
- f: BytesIO = None
- if isinstance(self.file_or_path, str):
- f = cast(BytesIO, open(self.file_or_path, 'rb'))
- elif isinstance(self.file_or_path, BytesIO):
- f = self.file_or_path
- elif isinstance(self.file_or_path, BufferedReader):
- f = self.file_or_path
+ if isinstance(self._file_or_path, str):
+ f: BytesIO = cast(
+ BytesIO, open(self._file_or_path, 'rb', buffering=archive.read_buffer_size))
+ elif isinstance(self._file_or_path, (BytesIO, BufferedReader)):
+ f = cast(BytesIO, self._file_or_path)
else:
raise ValueError('not a file or path')
+ # noinspection PyTypeChecker
super().__init__(None, f)
- self._toc_entry = None
-
# this number is determined by the msgpack encoding of the file beginning:
# { 'toc_pos': <...>
# ^11
- self._f.seek(11)
- self.toc_position = ArchiveReader._decode_position(self._f.read(10))
-
- self.use_blocked_toc = use_blocked_toc
- if use_blocked_toc:
- self._f.seek(11)
- self._toc: Dict[str, Any] = {}
- toc_start = self.toc_position[0]
- self._f.seek(toc_start)
- b = self._f.read(1)[0]
- if b & 0b11110000 == 0b10000000:
- self._n_toc = b & 0b00001111
- self._toc_offset = toc_start + 1
- elif b == 0xde:
- self._n_toc, = struct.unpack_from(">H", self._f.read(2))
- self._toc_offset = toc_start + 3
- elif b == 0xdf:
- self._n_toc, = struct.unpack_from(">I", self._f.read(4))
- self._toc_offset = toc_start + 5
- else:
- raise ArchiveError('Archive top-level TOC is not a msgpack map (dictionary).')
-
+ self._toc_position = _decode(self._direct_read(10, 11))
+
+ self._use_blocked_toc = use_blocked_toc
+
+ if not self._use_blocked_toc:
+ self._toc_entry = self._read(self._toc_position)
+ return
+
+ toc_start = self._toc_position[0]
+ b = self._direct_read(1, toc_start)[0]
+ if b & 0b11110000 == 0b10000000:
+ self._toc_number = b & 0b00001111
+ self._toc_offset = toc_start + 1
+ elif b == 0xde:
+ self._toc_number, = struct.unpack_from(">H", self._direct_read(2, toc_start + 1))
+ self._toc_offset = toc_start + 3
+ elif b == 0xdf:
+ self._toc_number, = struct.unpack_from(">I", self._direct_read(4, toc_start + 1))
+ self._toc_offset = toc_start + 5
else:
- self.toc_entry = self._read(self.toc_position)
+ raise ArchiveError('Archive top-level TOC is not a msgpack map (dictionary).')
+
+ self._toc: Dict[str, Any] = {}
+ self._toc_block_info = [None] * (self._toc_number // _entries_per_block + 1)
def __enter__(self):
return self
- fs_block_size = 4096
- toc_block_size_entries = math.ceil(4096 / _toc_item_size)
- toc_block_size_bytes = math.ceil(4096 / 54) * _toc_item_size
+ def __exit__(self, exc_type, exc_val, exc_tb):
+ self.close()
def _load_toc_block(self, i_entry: int):
- i_block = math.floor(i_entry / ArchiveReader.toc_block_size_entries)
+ i_block = i_entry // _entries_per_block
+
+ if self._toc_block_info[i_block]:
+ return self._toc_block_info[i_block]
+
+ i_offset = i_block * _bytes_per_block + self._toc_offset
+ block_data = self._direct_read(_bytes_per_block, i_offset)
- self._f.seek(i_block * ArchiveReader.toc_block_size_bytes + self._toc_offset)
- block_data = self._f.read(ArchiveReader.toc_block_size_bytes)
first, last = None, None
- toc_block_size_entries = min(
- ArchiveReader.toc_block_size_entries,
- self._n_toc - i_block * ArchiveReader.toc_block_size_entries)
-
- for i in range(0, toc_block_size_entries):
- offset = i * _toc_item_size
- entry_uuid = unpackb(block_data[offset:offset + _toc_uuid_size])
- positions_encoded = unpackb(block_data[offset + _toc_uuid_size:offset + _toc_item_size])
- positions = (
- ArchiveReader._decode_position(positions_encoded[0]),
- ArchiveReader._decode_position(positions_encoded[1]))
+
+ entries_current_block = min(
+ _entries_per_block, self._toc_number - i_block * _entries_per_block)
+
+ offset: int = 0
+ for i in range(entries_current_block):
+ entry_uuid, positions = _unpack_entry(block_data[offset:offset + _toc_item_size])
self._toc[entry_uuid] = positions
+ offset += _toc_item_size
if i == 0:
first = entry_uuid
- if i + 1 == toc_block_size_entries:
+ if i + 1 == entries_current_block:
last = entry_uuid
- return first, last
+ self._toc_block_info[i_block] = (first, last)
+
+ return self._toc_block_info[i_block]
def __getitem__(self, key):
key = utils.adjust_uuid_size(key)
- if self.use_blocked_toc and self.toc_entry is None:
- if self._n_toc == 0:
+ if self._use_blocked_toc and self._toc_entry is None:
+ if self._toc_number == 0:
raise KeyError(key)
positions = self._toc.get(key)
# TODO use hash algorithm instead of binary search
if positions is None:
r_start = 0
- r_end = self._n_toc
- i_block = None
+ r_end = self._toc_number
+ i_entry = None
while r_start <= r_end:
- new_i_block = r_start + math.floor((r_end - r_start) / 2)
- if i_block == new_i_block:
+ m_entry = r_start + (r_end - r_start) // 2
+ if i_entry == m_entry:
break
- else:
- i_block = new_i_block
- first, last = self._load_toc_block(i_block)
+ i_entry = m_entry
+
+ first, last = self._load_toc_block(i_entry)
if key < first:
- r_end = i_block - 1
+ r_end = i_entry - 1
elif key > last:
- r_start = i_block + 1
+ r_start = i_entry + 1
else:
break
@@ -404,48 +441,38 @@ class ArchiveReader(ArchiveObject):
raise KeyError(key)
toc_position, data_position = positions
-
else:
- positions_encoded = self.toc_entry[key]
- toc_position = ArchiveReader._decode_position(positions_encoded[0])
- data_position = ArchiveReader._decode_position(positions_encoded[1])
+ positions = self._toc_entry[key]
+ toc_position = _decode(positions[0])
+ data_position = _decode(positions[1])
- toc = self._read(toc_position)
- return ArchiveObject(toc, self._f, data_position[0])
+ return ArchiveDict(self._read(toc_position), self._f, data_position[0])
def __iter__(self):
- if self.toc_entry is None:
+ if self._toc_entry is None:
# is not necessarily read when using blocked toc
- self.toc_entry = self._read(self.toc_position)
+ self._toc_entry = self._read(self._toc_position)
- return self.toc_entry.__iter__()
+ return self._toc_entry.__iter__()
def __len__(self):
- if self.toc_entry is None:
+ if self._toc_entry is None:
# is not necessarily read when using blocked toc
- self.toc_entry = self._read(self.toc_position)
+ self._toc_entry = self._read(self._toc_position)
- return self.toc_entry.__len__()
+ return self._toc_entry.__len__()
def close(self):
- if isinstance(self.file_or_path, str):
+ if isinstance(self._file_or_path, str):
self._f.close()
- def __exit__(self, exc_type, exc_val, exc_tb):
- self.close()
-
- @staticmethod
- def _decode_position(position: bytes) -> Tuple[int, int]:
- return int.from_bytes(position[0:5], byteorder='little', signed=False), \
- int.from_bytes(position[5:], byteorder='little', signed=False)
-
def is_closed(self):
return self._f.closed
def write_archive(
- path_or_file: Union[str, BytesIO], n_entries: int, data: Iterable[Tuple[str, Any]],
- entry_toc_depth: int = 2) -> None:
+ path_or_file: Union[str, BytesIO], n_entries: int,
+ data: Iterable[Tuple[str, Any]], entry_toc_depth: int = 2) -> None:
'''
Writes a msgpack-based archive file. The file contents will be a valid msgpack-object.
The data will contain extra table-of-contents (TOC) objects that map some keys to
@@ -495,7 +522,7 @@ def write_archive(
TOCs are regular msgpack encoded integers.
Arguments:
- file_or_path: A file path or file-like to the archive file that should be written.
+ path_or_file: A file path or file-like to the archive file that should be written.
n_entries: The number of entries that will be added to the file.
data: The file contents as an iterator of entry id, data tuples.
entry_toc_depth: The depth of the table of contents in each entry. Only objects will
@@ -506,7 +533,7 @@ def write_archive(
writer.add(uuid, entry)
-def read_archive(file_or_path: str, **kwargs) -> ArchiveReader:
+def read_archive(file_or_path: Union[str, BytesIO], **kwargs) -> ArchiveReader:
'''
Allows to read a msgpack-based archive.
@@ -525,7 +552,6 @@ def read_archive(file_or_path: str, **kwargs) -> ArchiveReader:
if __name__ == '__main__':
-
def benchmark():
from time import time
import sys
@@ -551,7 +577,9 @@ if __name__ == '__main__':
start = time()
for _ in range(0, 23):
read_archive(buffer, use_blocked_toc=use_blocked_toc)[example_uuid]['run']['system']
- print('archive.py: access single entry system (23), blocked %d: ' % use_blocked_toc, (time() - start) / 23)
+ print(
+ f'archive.py: access single entry system (23), blocked {use_blocked_toc:d}: ',
+ (time() - start) / 23)
# read every n-ed entry from archive
buffer = BytesIO(buffer.getbuffer())
@@ -562,7 +590,9 @@ if __name__ == '__main__':
for i, entry in enumerate(example_archive):
if i % access_every == 0:
data[entry[0]]['run']['system']
- print('archive.py: access every %d-ed entry single entry system (23), blocked %d: ' % (access_every, use_blocked_toc), (time() - start) / 23)
+ print(
+ f'archive.py: access every {access_every:d}-ed entry single entry system (23), '
+ f'blocked {use_blocked_toc:d}: ', (time() - start) / 23)
# just msgpack
start = time()
diff --git a/nomad/config.py b/nomad/config.py
index f11340314debf658b4e06ff6f62fd87c50c5bb0d..a4f4cbb0077ffe1efe8ae77224ce521ce19e5099 100644
--- a/nomad/config.py
+++ b/nomad/config.py
@@ -311,7 +311,7 @@ datacite = NomadConfig(
)
meta = NomadConfig(
- version='1.0.7',
+ version='1.0.8',
commit=gitinfo.commit,
deployment='devel',
label=None,
@@ -381,6 +381,13 @@ bundle_import = NomadConfig(
)
)
+archive = NomadConfig(
+ block_size=256 * 1024,
+ read_buffer_size=256 * 1024, # GPFS needs at least 256K to achieve decent performance
+ max_process_number=20, # maximum number of processes can be assigned to process archive query
+ min_entires_per_process=20 # minimum number of entries per process
+)
+
auxfile_cutoff = 100
parser_matching_size = 150 * 80 # 150 lines of 80 ASCII characters per line
console_log_level = logging.WARNING
diff --git a/nomad/datamodel/metainfo/simulation/calculation.py b/nomad/datamodel/metainfo/simulation/calculation.py
index 0198b734ec5240abe1959467e32b7dfcccbe98a3..bd4219902cca57eb275e4b33c109e1f0c2220a6e 100644
--- a/nomad/datamodel/metainfo/simulation/calculation.py
+++ b/nomad/datamodel/metainfo/simulation/calculation.py
@@ -126,6 +126,7 @@ class AtomicValues(MSection):
m_def = Section(validate=False)
+ # TODO rename this to spin_channel
spin = Quantity(
type=np.dtype(np.int32),
shape=[],
@@ -210,6 +211,7 @@ class EnergyEntry(Atomic):
cell.
''')
+ # TODO rename this to value_atomic
values_per_atom = Quantity(
type=np.dtype(np.float64),
shape=['n_atoms'],
@@ -409,6 +411,38 @@ class Energy(MSection):
''',
repeats=True)
+ enthalpy = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Value of the calculated enthalpy per cell i.e. energy_total + pressure * volume.
+ ''')
+
+ entropy = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule / kelvin',
+ description='''
+ Value of the entropy.
+ ''')
+
+ chemical_potential = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Value of the chemical potential.
+ ''')
+
+ internal = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Value of the internal energy.
+ ''')
+
# TODO remove this should be be entropy.correction
correction_entropy = SubSection(
sub_section=EnergyEntry.m_def,
@@ -529,38 +563,6 @@ class Forces(MSection):
corresponding to the minus gradient of energy_T0.
''')
- enthalpy = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='joule',
- description='''
- Value of the calculated enthalpy per cell i.e. energy_total + pressure * volume.
- ''')
-
- entropy = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='joule / kelvin',
- description='''
- Value of the entropy.
- ''')
-
- chemical_potential = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='joule',
- description='''
- Value of the chemical potential.
- ''')
-
- internal = Quantity(
- type=np.dtype(np.float64),
- shape=[],
- unit='joule',
- description='''
- Value of the internal energy.
- ''')
-
contributions = SubSection(
sub_section=ForcesEntry.m_def,
description='''
@@ -646,6 +648,20 @@ class ChargesValue(AtomicValues):
Value of the charge projected on atom and orbital.
''')
+ n_electrons = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ Value of the number of electrons projected on atom and orbital.
+ ''')
+
+ spin_z = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ Value of the azimuthal spin projected on atom and orbital.
+ ''')
+
class Charges(Atomic):
'''
@@ -670,6 +686,15 @@ class Charges(Atomic):
Value of the atomic charges calculated through analysis_method.
''')
+ n_electrons = Quantity(
+ type=np.dtype(np.float64),
+ shape=['n_atoms'],
+ description='''
+ Value of the number of electrons on the atoms.
+ ''')
+
+ # TODO should this be on a separate section magnetic_moments or charges should be
+ # renamed population
spins = Quantity(
type=np.dtype(np.float64),
shape=['n_atoms'],
@@ -1428,7 +1453,7 @@ class ExcitedStates(MSection):
''')
-class VibrationsValues(MSection):
+class VibrationalFrequenciesValues(MSection):
'''
Section describing a vibrational spectrum.
'''
@@ -1472,7 +1497,7 @@ class VibrationsValues(MSection):
''')
-class Vibrations(MSection):
+class VibrationalFrequencies(MSection):
'''
Section containing results related to vibrational frequencies.
'''
@@ -1491,12 +1516,14 @@ class Vibrations(MSection):
shape=['n_frequencies'],
unit='1 / meter',
description='''
- Values of vibration Frequenices (cm-1)
+ Values of vibrational frequencies (m-1)
''')
- raman = SubSection(sub_section=VibrationsValues.m_def, repeats=False)
+ # TODO add normal modes
+
+ raman = SubSection(sub_section=VibrationalFrequenciesValues.m_def, repeats=False)
- infrared = SubSection(sub_section=VibrationsValues.m_def, repeats=False)
+ infrared = SubSection(sub_section=VibrationalFrequenciesValues.m_def, repeats=False)
class BaseCalculation(MSection):
@@ -1649,7 +1676,7 @@ class BaseCalculation(MSection):
excited_states = SubSection(sub_section=ExcitedStates.m_def, repeats=True)
- vibrational_frequencies = SubSection(sub_section=Vibrations.m_def, repeats=True)
+ vibrational_frequencies = SubSection(sub_section=VibrationalFrequencies.m_def, repeats=True)
potential = SubSection(sub_section=Potential.m_def, repeats=True)
diff --git a/nomad/datamodel/metainfo/simulation/system.py b/nomad/datamodel/metainfo/simulation/system.py
index b42f30d8193309a7f93b28ced703e4ab5e9e03ba..4cae537bde7b95c477824c04c09a6c973e901366 100644
--- a/nomad/datamodel/metainfo/simulation/system.py
+++ b/nomad/datamodel/metainfo/simulation/system.py
@@ -27,6 +27,70 @@ from ..common import FastAccess
m_package = Package()
+class AtomsGroup(MSection):
+ '''
+ Describes a group of atoms which may constitute a sub system as in the case of a
+ molecule.
+ '''
+
+ m_def = Section(validate=False)
+
+ label = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Label of the group.
+ ''')
+
+ type = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Type of the group.
+ ''')
+
+ index = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Index of the group with respect to its parent group.
+ ''')
+
+ composition_formula = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ The overall composition of the group with respect to its subgroups.
+ The syntax for a groups composed of X and Y with x and y components of each,
+ respectively, is X(x)Y(y).
+ ''')
+
+ n_atoms = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ The total number of atoms in the group.
+ ''')
+
+ atom_indices = Quantity(
+ type=np.dtype(np.int32),
+ shape=['n_atoms'],
+ description='''
+ Indices of the atoms in the group with respect to the system.
+ ''')
+
+ is_molecule = Quantity(
+ type=bool,
+ shape=[],
+ description='''
+ Denotes if the atoms in this group represent a molecule. That is, all atoms
+ in the group are connected via bonds, and no other atoms contain bonds
+ with these atoms.
+ ''')
+
+ atoms_group = SubSection(sub_section=SectionProxy('AtomsGroup'), repeats=True)
+
+
class Atoms(MSection):
'''
Describes the atomic structure of the physical system. This includes the atom
@@ -484,6 +548,8 @@ class System(MSection):
atoms = SubSection(sub_section=Atoms.m_def, categories=[FastAccess])
+ atoms_group = SubSection(sub_section=AtomsGroup.m_def, repeats=True)
+
chemical_composition = Quantity(
type=str,
shape=[],
diff --git a/nomad/datamodel/metainfo/workflow.py b/nomad/datamodel/metainfo/workflow.py
index 2a5edb943d6e6a5e620405344097668f4e83d834..308f34c8dcb235ba9550610452b994200b226734 100644
--- a/nomad/datamodel/metainfo/workflow.py
+++ b/nomad/datamodel/metainfo/workflow.py
@@ -1331,6 +1331,230 @@ class MolecularDynamics(MSection):
Indicates if calculation contains thermodynamic data.
''')
+ radial_distribution_functions = SubSection(sub_section=SectionProxy('RadialDistributionFunction'), repeats=True)
+
+ mean_squared_displacements = SubSection(sub_section=SectionProxy('MeanSquaredDisplacement'), repeats=True)
+
+
+class EnsemblePropertyValues(MSection):
+ '''
+ Generic section containing information regarding the values of an ensemble property.
+ '''
+
+ m_def = Section(validate=False)
+
+ label = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Describes the atoms or molecule types involved in determining the property.
+ ''')
+
+
+class EnsembleProperty(MSection):
+ '''
+ Generic section containing information about a calculation of any static observable
+ from a trajectory (i.e., from an ensemble average).
+ '''
+
+ m_def = Section(validate=False)
+
+ type = Quantity(
+ type=MEnum('Molecular', 'Atomic'),
+ shape=[],
+ description='''
+ Describes if the observable is calculated at the molecular or atomic level.
+ ''')
+
+ n_smooth = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Number of bins over which the running average was computed for
+ the observable `values'.
+ ''')
+
+ error_type = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Describes the type of error reported for this observable.
+ ''')
+
+ n_variables = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Number of variables along which the property is determined.
+ ''')
+
+ variables_name = Quantity(
+ type=np.dtype(str),
+ shape=['n_variables'],
+ description='''
+ Name/description of the independent variables along which the observable is defined.
+ ''')
+
+
+class RadialDistributionFunctionValues(EnsemblePropertyValues):
+ '''
+ Section containing information regarding the values of
+ radial distribution functions (rdfs).
+ '''
+
+ m_def = Section(validate=False)
+
+ n_bins = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Number of bins.
+ ''')
+
+ bins = Quantity(
+ type=np.dtype(np.float64),
+ shape=['n_bins'],
+ unit='m',
+ description='''
+ Distances along which the rdf was calculated.
+ ''')
+
+ value = Quantity(
+ type=np.dtype(np.float64),
+ shape=['n_bins'],
+ description='''
+ Values of the property.
+ ''')
+
+
+class RadialDistributionFunction(EnsembleProperty):
+ '''
+ Section containing information about the calculation of
+ radial distribution functions (rdfs).
+ '''
+
+ m_def = Section(validate=False)
+
+ radial_distribution_function_values = SubSection(sub_section=RadialDistributionFunctionValues.m_def, repeats=True)
+
+
+class CorrelationFunctionValues(MSection):
+ '''
+ Generic section containing information regarding the values of a correlation function.
+ '''
+
+ m_def = Section(validate=False)
+
+ label = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Describes the atoms or molecule types involved in determining the property.
+ ''')
+
+ n_times = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Number of times windows for the calculation of the correlation function.
+ ''')
+
+
+class CorrelationFunction(MSection):
+ '''
+ Generic section containing information about a calculation of any time correlation
+ function from a trajectory.
+ '''
+
+ m_def = Section(validate=False)
+
+ type = Quantity(
+ type=MEnum('Molecular', 'Atomic'),
+ shape=[],
+ description='''
+ Describes if the correlation function is calculated at the molecular or atomic level.
+ ''')
+
+ direction = Quantity(
+ type=MEnum('x', 'y', 'z', 'xy', 'yz', 'xz', 'xyz'),
+ shape=[],
+ description='''
+ Describes the direction in which the correlation function was calculated.
+ ''')
+
+ error_type = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Describes the type of error reported for this correlation function.
+ ''')
+
+
+class DiffusionConstantValues(MSection):
+ '''
+ Section containing information regarding the diffusion constants.
+ '''
+
+ m_def = Section(validate=False)
+
+ value = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='m^2/s',
+ description='''
+ Values of the diffusion constants.
+ ''')
+
+ error_type = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Describes the type of error reported for this observable.
+ ''')
+
+ errors = Quantity(
+ type=np.dtype(np.float64),
+ shape=['*'],
+ description='''
+ Error associated with the determination of the diffusion constant.
+ ''')
+
+
+class MeanSquaredDisplacementValues(CorrelationFunctionValues):
+ '''
+ Section containing information regarding the values of a mean squared displacements (msds).
+ '''
+
+ m_def = Section(validate=False)
+
+ times = Quantity(
+ type=np.dtype(np.float64),
+ shape=['n_times'],
+ unit='s',
+ description='''
+ Time windows used for the calculation of the msds.
+ ''')
+
+ value = Quantity(
+ type=np.dtype(np.float64),
+ shape=['n_times'],
+ unit='m^2',
+ description='''
+ Msd values.
+ ''')
+
+ diffusion_constant = SubSection(sub_section=DiffusionConstantValues.m_def, repeats=False)
+
+
+class MeanSquaredDisplacement(CorrelationFunction):
+ '''
+ Section containing information about a calculation of any mean squared displacements (msds).
+ '''
+
+ m_def = Section(validate=False)
+
+ mean_squared_displacement_values = SubSection(sub_section=MeanSquaredDisplacementValues.m_def, repeats=True)
+
class SinglePoint(MSection):
'''
diff --git a/nomad/files.py b/nomad/files.py
index a0084b06bef503901c53e67147dbd23c32aa4e2d..5d82a9cb9c42b4d553f44b7c810f3a9f20722e92 100644
--- a/nomad/files.py
+++ b/nomad/files.py
@@ -618,7 +618,7 @@ class UploadFiles(DirectoryObject, metaclass=ABCMeta):
mime_type = 'application/octet-stream'
return mime_type
- def read_archive(self, entry_id: str) -> ArchiveReader:
+ def read_archive(self, entry_id: str, use_blocked_toc: bool = True) -> ArchiveReader:
'''
Returns an :class:`nomad.archive.ArchiveReader` that contains the
given entry_id.
@@ -763,9 +763,9 @@ class StagingUploadFiles(UploadFiles):
return self.archive_file_object(entry_id).size
- def read_archive(self, entry_id: str) -> ArchiveReader:
+ def read_archive(self, entry_id: str, use_blocked_toc: bool = True) -> ArchiveReader:
try:
- return read_archive(self.archive_file_object(entry_id).os_path)
+ return read_archive(self.archive_file_object(entry_id).os_path, use_blocked_toc=use_blocked_toc)
except FileNotFoundError:
raise KeyError(entry_id)
@@ -1201,7 +1201,7 @@ class PublicUploadFiles(UploadFiles):
self.access # Invoke to initialize
return self._archive_msg_file_object
- def _open_msg_file(self) -> ArchiveReader:
+ def _open_msg_file(self, use_blocked_toc: bool = True) -> ArchiveReader:
if self._archive_msg_file is not None:
if not self._archive_msg_file.is_closed():
return self._archive_msg_file
@@ -1211,7 +1211,7 @@ class PublicUploadFiles(UploadFiles):
if not msg_file_object.exists():
raise FileNotFoundError()
- archive = read_archive(msg_file_object.os_path)
+ archive = read_archive(msg_file_object.os_path, use_blocked_toc=use_blocked_toc)
assert archive is not None
self._archive_msg_file = archive
@@ -1374,9 +1374,9 @@ class PublicUploadFiles(UploadFiles):
raise KeyError(file_path)
- def read_archive(self, entry_id: str) -> Any:
+ def read_archive(self, entry_id: str, use_blocked_toc: bool = True) -> Any:
try:
- archive = self._open_msg_file()
+ archive = self._open_msg_file(use_blocked_toc)
if entry_id in archive:
return archive
except FileNotFoundError:
diff --git a/nomad/normalizing/workflow.py b/nomad/normalizing/workflow.py
index 7caa048e483c7b72443288a04ba6ac25db9da56d..8054310342af98bfcb9e90a1621ac5a07d1af6ef 100644
--- a/nomad/normalizing/workflow.py
+++ b/nomad/normalizing/workflow.py
@@ -247,6 +247,8 @@ class GeometryOptimizationNormalizer(TaskNormalizer):
except (IndexError, AttributeError):
invalid = True
break
+ if energy is None:
+ continue
energies.append(energy.magnitude)
if invalid:
self.logger.warning("energy not reported for an scc that is part of a geometry optimization")
diff --git a/nomad/parsing/parsers.py b/nomad/parsing/parsers.py
index b9a8076b1f3ec0607270b21f6e72086aec4ae836..0405151642593aa40f6f3312aea07e7ad201ba1f 100644
--- a/nomad/parsing/parsers.py
+++ b/nomad/parsing/parsers.py
@@ -265,6 +265,12 @@ parsers = [
name='parsers/molcas', code_name='MOLCAS', code_homepage='http://www.molcas.org/',
domain='dft', mainfile_contents_re=r'M O L C A 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(
'electronicparsers.NWChemParser',
name='parsers/nwchem', code_name='NWChem', code_homepage='http://www.nwchem-sw.org/',
@@ -281,6 +287,13 @@ parsers = [
name='parsers/onetep', code_name='ONETEP', code_homepage='https://www.onetep.org/',
domain='dft', mainfile_contents_re=r'####### # # ####### ####### ####### ######'
),
+ MatchingParserInterface(
+ 'electronicparsers.OpenmxParser',
+ name='parsers/openmx', code_name='OpenMX', code_homepage='http://www.openmx-square.org/',
+ 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/',
@@ -364,6 +377,11 @@ parsers = [
name='parsers/asap', code_name='ASAP', domain='dft',
mainfile_name_re=r'.*.traj$', mainfile_mime_re=r'application/octet-stream'
),
+ MatchingParserInterface(
+ 'atomisticparsers.BOPfoxParser',
+ name='parsers/bopfox', code_name='BOPfox',
+ mainfile_contents_re=r'\s+\-+\s+BOPfox'
+ ),
MatchingParserInterface(
'atomisticparsers.DFTBPlusParser',
name='parsers/dftbplus', code_name='DFTB+', domain='dft',
@@ -404,12 +422,6 @@ parsers = [
name='parsers/lib-atoms', code_name='libAtoms', code_homepage='https://libatoms.github.io/',
mainfile_contents_re=(r'\s*<GAP_params\s'),
),
- MatchingParserInterface(
- 'atomisticparsers.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',
@@ -427,6 +439,17 @@ parsers = [
name='parsers/tinker', code_name='TINKER', domain='dft',
mainfile_contents_re=r'TINKER --- Software Tools for Molecular Design'
),
+ MatchingParserInterface(
+ 'atomisticparsers.XTBParser',
+ name='parsers/xtb', code_name='XTB',
+ code_homepage='https://www.chemie.uni-bonn.de/pctc/mulliken-center/software/xtb/xtb',
+ mainfile_contents_re=(
+ r'\s*-----------------------------------------------------------\s*'
+ r'\s*\| ===================== \|\s*'
+ r'\s*\| x T B \|\s*'
+ r'\s*\| ===================== \|\s*'
+ )
+ ),
MatchingParserInterface(
'workflowparsers.AFLOWParser',
name='parsers/aflow', code_name='AFlow', code_homepage='http://www.aflowlib.org/',
@@ -474,9 +497,9 @@ parsers = [
mainfile_contents_re=(r'^LOBSTER\s*v[\d\.]+.*'),
),
MatchingParserInterface(
- 'workflowparsers.MPParser',
- name='parsers/mp', code_name='MaterialsProject',
- code_homepage='https://materialsproject.org',
+ 'workflowparsers.AtomateParser',
+ name='parsers/atomate', code_name='Atomate',
+ code_homepage='https://atomate.org',
mainfile_mime_re=r'(application/json)|(text/.*)',
mainfile_name_re=r'.*mp.+materials\.json',
mainfile_contents_re=(r'"pymatgen_version":')
diff --git a/ops/helm/nomad/Chart.yaml b/ops/helm/nomad/Chart.yaml
index d9cc2e12e65b51b43e0f77e06b9429e713e4a448..8e5795431ff8a33b425fd6a9e972e519862c2da8 100644
--- a/ops/helm/nomad/Chart.yaml
+++ b/ops/helm/nomad/Chart.yaml
@@ -1,5 +1,5 @@
apiVersion: v1
-appVersion: "1.0.7"
+appVersion: "1.0.8"
description: A Helm chart for Kubernetes that only runs nomad services and uses externally hosted databases.
name: nomad
-version: "1.0.7"
+version: "1.0.8"
diff --git a/ops/helm/nomad/deployments/prod-staging-values.yaml b/ops/helm/nomad/deployments/prod-staging-values.yaml
index 4831d21a33da004177ba2fa31fd71321b9eda346..8d3371673543d1e02bce889020abbfffcf8ac2dd 100644
--- a/ops/helm/nomad/deployments/prod-staging-values.yaml
+++ b/ops/helm/nomad/deployments/prod-staging-values.yaml
@@ -1,8 +1,8 @@
version:
- label: "1.0.7"
+ label: "1.0.8"
isBeta: true
usesBetaData: false
- officialUrl: "https://nomad-lab.eu/prod/rae/gui"
+ officialUrl: "https://nomad-lab.eu/prod/v1/gui"
image:
tag: "latest"
diff --git a/ops/helm/nomad/deployments/prod-test-values.yaml b/ops/helm/nomad/deployments/prod-test-values.yaml
index c82fe644a7430f770daf1df34dcba27b3970ddd1..dca786303d3c23b47847eaeb2ca6fbd3b9ce455b 100644
--- a/ops/helm/nomad/deployments/prod-test-values.yaml
+++ b/ops/helm/nomad/deployments/prod-test-values.yaml
@@ -1,8 +1,8 @@
version:
- label: "1.0.7"
- isBeta: true
+ label: "1.0.8"
+ isBeta: false
usesBetaData: true
- officialUrl: "https://nomad-lab.eu/prod/rae/gui"
+ officialUrl: "https://nomad-lab.eu/prod/v1/gui"
image:
tag: "latest"
diff --git a/ops/helm/nomad/deployments/prod-util-values.yaml b/ops/helm/nomad/deployments/prod-util-values.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..b1e60a8d2d65d74e3ae45ba800e6bc8caf290808
--- /dev/null
+++ b/ops/helm/nomad/deployments/prod-util-values.yaml
@@ -0,0 +1,79 @@
+version:
+ label: "1.0.8"
+ isBeta: false
+ usesBetaData: false
+ officialUrl: "https://nomad-lab.eu/prod/v1/gui"
+
+image:
+ tag: "latest"
+ pullPolicy: "Always"
+
+proxy:
+ nodePort: 30016
+ nodeIP: '130.183.207.81'
+ external:
+ host: "nomad-lab.eu"
+ path: "/prod/v1/util"
+
+gui:
+ debug: true
+ matomoEnabled: false
+ matomoSiteId: 2
+ encyclopediaBase: 'https://nomad-lab.eu/prod/rae/encyclopedia/#'
+ aitoolkitEnabled: false
+
+app:
+ replicas: 1
+ worker: 1
+ threads: 4
+ workerClass: "gthread"
+ nomadNodeType: "public"
+
+worker:
+ replicas: 1
+ routing: "worker"
+ processes: 12
+ nomadNodeType: "prod-worker"
+
+elastic:
+ host: elasticsearch.elasticsearch-7.svc.cluster.local
+ port: 9200
+
+mongo:
+ host: rs0/mongodb-0.mongo.mongodb.svc.cluster.local,mongodb-1.mongo.mongodb.svc.cluster.local,mongodb-2.mongo.mongodb.svc.cluster.local
+
+logstash:
+ host: logstash.elk.svc.cluster.local
+
+dbname: nomad_prod_v1
+
+uploadurl: 'https://nomad-lab.eu/prod/v1/util/api/uploads'
+
+client:
+ passwordSecret: 'nomad-keycloak-password'
+
+keycloak:
+ serverUrl: "https://nomad-lab.eu/fairdi/keycloak/auth/"
+ serverExternalUrl: "https://nomad-lab.eu/fairdi/keycloak/auth/"
+ passwordSecret: 'nomad-keycloak-password'
+ realmName: 'fairdi_nomad_prod'
+ clientId: 'nomad_public'
+ admin_user_id: '82efac55-6187-408c-8027-b98580c0e1c5'
+
+volumes:
+ prefixSize: 1
+ public: /nomad/fairdi/prod/fs/public
+ staging: /scratch/fairdi/prod/fs/staging
+ tmp: /nomad/fairdi/prod/fs/tmp
+ nomad: /nomad
+ archiveVersionSuffix: v1
+
+mail:
+ enabled: false
+ host: 'mailrelay.mpcdf.mpg.de'
+ port: 25
+ from: 'support@nomad-lab.eu'
+
+datacite:
+ secret: 'nomad-datacite'
+ enabled: false
diff --git a/ops/helm/nomad/deployments/prod-v1-values.yaml b/ops/helm/nomad/deployments/prod-v1-values.yaml
index 6ec2c50eca88496d658c3158adac95124da7431f..5317b88834a6df008f56f89c22c8c0e64447989e 100644
--- a/ops/helm/nomad/deployments/prod-v1-values.yaml
+++ b/ops/helm/nomad/deployments/prod-v1-values.yaml
@@ -1,8 +1,8 @@
version:
- label: "1.0.7"
- isBeta: true
+ label: "1.0.8"
+ isBeta: false
usesBetaData: false
- officialUrl: "https://nomad-lab.eu/prod/rae/gui"
+ officialUrl: "https://nomad-lab.eu/prod/v1/gui"
image:
tag: "latest"
diff --git a/ops/helm/nomad/values.yaml b/ops/helm/nomad/values.yaml
index fdf9e90383c96706b3dc5497c7d98d758f344172..82af036bace82d8076c628ebd4180705afae460e 100644
--- a/ops/helm/nomad/values.yaml
+++ b/ops/helm/nomad/values.yaml
@@ -1,6 +1,6 @@
## Default values for nomad@FAIRDI
version:
- label: "1.0.7"
+ label: "1.0.8"
isTest: false
isBeta: false
usesBetaData: false
diff --git a/requirements.txt b/requirements.txt
index ad6f31a120cd5eb9892bb1694b43c72edf75a43f..460e80e7b9c725e299ad093209320c6928b8643a 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -23,6 +23,7 @@ elasticsearch-dsl==7.4.0
pydantic==1.8.2
jmespath==0.10.0
httpx==0.22.0
+memoization==0.4.0
# [parsing]
netCDF4==1.5.4
diff --git a/run.sh b/run.sh
index 97b5580678acd147f6c72d31a118e4b21cad24b8..cd34360f15d4eb1875ab5d78b30b993691e2776f 100644
--- a/run.sh
+++ b/run.sh
@@ -3,4 +3,4 @@ python -m nomad.cli admin ops gui-config
params=()
[ -e gunicorn.conf ] && params+=(--config gunicorn.conf)
[ -e gunicorn.log.conf ] && params+=(--log-config gunicorn.log.conf)
-python -m gunicorn.app.wsgiapp "${params[@]}" --timeout 120 --worker-class=uvicorn.workers.UvicornWorker -b 0.0.0.0:8000 nomad.app.main:app
+python -m gunicorn.app.wsgiapp "${params[@]}" --timeout 120 --keep-alive 5 --worker-class=uvicorn.workers.UvicornWorker -b 0.0.0.0:8000 nomad.app.main:app
diff --git a/tests/data/parsers/mp/mp-1/elasticity.json b/tests/data/parsers/atomate/mp-1/elasticity.json
similarity index 100%
rename from tests/data/parsers/mp/mp-1/elasticity.json
rename to tests/data/parsers/atomate/mp-1/elasticity.json
diff --git a/tests/data/parsers/mp/mp-1/eos.json b/tests/data/parsers/atomate/mp-1/eos.json
similarity index 100%
rename from tests/data/parsers/mp/mp-1/eos.json
rename to tests/data/parsers/atomate/mp-1/eos.json
diff --git a/tests/data/parsers/mp/mp-1/magnetism.json b/tests/data/parsers/atomate/mp-1/magnetism.json
similarity index 100%
rename from tests/data/parsers/mp/mp-1/magnetism.json
rename to tests/data/parsers/atomate/mp-1/magnetism.json
diff --git a/tests/data/parsers/mp/mp-1/materials.json b/tests/data/parsers/atomate/mp-1/materials.json
similarity index 100%
rename from tests/data/parsers/mp/mp-1/materials.json
rename to tests/data/parsers/atomate/mp-1/materials.json
diff --git a/tests/data/parsers/mp/mp-1/surface_properties.json b/tests/data/parsers/atomate/mp-1/surface_properties.json
similarity index 100%
rename from tests/data/parsers/mp/mp-1/surface_properties.json
rename to tests/data/parsers/atomate/mp-1/surface_properties.json
diff --git a/tests/data/parsers/mp/mp-1/tasks.json b/tests/data/parsers/atomate/mp-1/tasks.json
similarity index 100%
rename from tests/data/parsers/mp/mp-1/tasks.json
rename to tests/data/parsers/atomate/mp-1/tasks.json
diff --git a/tests/data/parsers/mp/mp-1/thermo.json b/tests/data/parsers/atomate/mp-1/thermo.json
similarity index 100%
rename from tests/data/parsers/mp/mp-1/thermo.json
rename to tests/data/parsers/atomate/mp-1/thermo.json
diff --git a/tests/parsing/test_parsing.py b/tests/parsing/test_parsing.py
index 0b6e64b08125f746e3604fe8afafa414d213d995..13e3e6d341c8b3d871d04fa3fc9491a8f112a44b 100644
--- a/tests/parsing/test_parsing.py
+++ b/tests/parsing/test_parsing.py
@@ -72,7 +72,7 @@ parser_examples = [
('parsers/eels', 'tests/data/parsers/eels.json'),
('parsers/lobster', 'tests/data/parsers/lobster/NaCl/lobsterout'),
('parsers/aflow', 'tests/data/parsers/aflow/Ag1Co1O2_ICSD_246157/aflowlib.json'),
- ('parsers/mp', 'tests/data/parsers/mp/mp-1/materials.json'),
+ ('parsers/atomate', 'tests/data/parsers/atomate/mp-1/materials.json'),
('parsers/asr', 'tests/data/parsers/asr/archive_ccdc26c4f32546c5a00ad03a093b73dc.json'),
('parsers/psi4', 'tests/data/parsers/psi4/adc1/output.ref'),
('parsers/yambo', 'tests/data/parsers/yambo/hBN/r-10b_1Ry_HF_and_locXC_gw0_em1d_ppa'),
diff --git a/tests/test_archive.py b/tests/test_archive.py
index 77acecc9bd796edc5237951982bcdb61626606fb..4088457ec96c267f91c6368fd7c32bc03671b2cc 100644
--- a/tests/test_archive.py
+++ b/tests/test_archive.py
@@ -26,7 +26,7 @@ import json
from nomad import utils, config
from nomad.metainfo import MSection, Quantity, Reference, SubSection, QuantityReference
from nomad.datamodel import EntryArchive
-from nomad.archive.storage import TOCPacker
+from nomad.archive.storage import TOCPacker, _decode, _entries_per_block
from nomad.archive import (
write_archive, read_archive, ArchiveReader, ArchiveQueryError, query_archive,
write_partial_archive_to_mongo, read_partial_archive_from_mongo, read_partial_archives_from_mongo,
@@ -147,12 +147,10 @@ def test_write_archive_single(example_uuid, example_entry):
toc_packer.pack(example_entry)
assert archive['data'][example_uuid]['toc'] == toc_packer.toc
- toc = _unpack(packed_archive, ArchiveReader._decode_position(archive['toc_pos']))
+ toc = _unpack(packed_archive, _decode(archive['toc_pos']))
assert example_uuid in toc
- assert _unpack(
- packed_archive, ArchiveReader._decode_position(toc[example_uuid][0])) == toc_packer.toc
- assert _unpack(
- packed_archive, ArchiveReader._decode_position(toc[example_uuid][1])) == example_entry
+ assert _unpack(packed_archive, _decode(toc[example_uuid][0])) == toc_packer.toc
+ assert _unpack(packed_archive, _decode(toc[example_uuid][1])) == example_entry
def test_write_archive_multi(example_uuid, example_entry):
@@ -203,7 +201,7 @@ def test_read_archive_single(example_uuid, example_entry, use_blocked_toc):
@pytest.mark.parametrize('use_blocked_toc', [False, True])
def test_read_archive_multi(example_uuid, example_entry, use_blocked_toc):
- archive_size = ArchiveReader.toc_block_size_entries * 2 + 23
+ archive_size = _entries_per_block * 2 + 23
f = BytesIO()
write_archive(
f, archive_size,
@@ -215,10 +213,10 @@ def test_read_archive_multi(example_uuid, example_entry, use_blocked_toc):
if use_blocked_toc:
reader._load_toc_block(0)
assert reader._toc.get(create_example_uuid(0)) is not None
- assert len(reader._toc) == ArchiveReader.toc_block_size_entries
+ assert len(reader._toc) == _entries_per_block
reader._load_toc_block(archive_size - 1)
assert reader._toc.get(create_example_uuid(archive_size - 1)) is not None
- assert len(reader._toc) > ArchiveReader.toc_block_size_entries
+ assert len(reader._toc) > _entries_per_block
for i in range(0, archive_size):
reader.get(create_example_uuid(i)) is not None
diff --git a/tests/test_client.py b/tests/test_client.py
index 684c0090a510a6b92090ec4b8a737363f3e7c440..fe4cae8ab0824feb984497e32235622153a05300 100644
--- a/tests/test_client.py
+++ b/tests/test_client.py
@@ -94,32 +94,6 @@ def async_api_v1(monkeysession):
return test_client
-def test_async_query():
- required = {
- 'workflow': {
- 'calculation_result_ref': {
- 'energy': '*',
- 'system_ref': {
- 'chemical_composition_reduced': '*'
- }
- }
- }
- }
-
- query = {
- 'results.method.simulation.program_name': 'VASP',
- 'results.material.elements': ['Ti', 'O']
- }
-
- async_query = ArchiveQuery(query=query, required=required, page_size=100, results_max=10000)
-
- num_entry = async_query.fetch(1000)
- num_entry -= len(async_query.download(100))
- num_entry -= len(async_query.download(100))
-
- assert num_entry == sum([count for _, count in async_query.upload_list()])
-
-
def test_async_query_basic(async_api_v1, published_wo_user_metadata):
async_query = ArchiveQuery()