diff --git a/gui/src/components/ConfirmDialog.js b/gui/src/components/ConfirmDialog.js
index a54d60b8843c387549864f11db43df6eb884c7ee..1591239c70dfe9f293d0adb74b5448c5e8b028ab 100644
--- a/gui/src/components/ConfirmDialog.js
+++ b/gui/src/components/ConfirmDialog.js
@@ -6,39 +6,49 @@ import DialogActions from '@material-ui/core/DialogActions'
import DialogContent from '@material-ui/core/DialogContent'
import DialogContentText from '@material-ui/core/DialogContentText'
import DialogTitle from '@material-ui/core/DialogTitle'
+import { FormGroup, Checkbox, FormLabel } from '@material-ui/core'
class ConfirmDialog extends React.Component {
static propTypes = {
- onOk: PropTypes.func.isRequired,
+ onPublish: PropTypes.func.isRequired,
onClose: PropTypes.func.isRequired,
- open: PropTypes.bool,
- title: PropTypes.string,
- children: PropTypes.any
+ open: PropTypes.bool.isRequired
}
- render() {
- const { children, title } = this.props
+ state = {
+ withEmbargo: false
+ }
+ render() {
+ const { onPublish, onClose, open } = this.props
+ const { withEmbargo } = this.state
return (
<div>
<Dialog
- open={this.props.open}
- onClose={this.handleClose}
- aria-labelledby="alert-dialog-title"
- aria-describedby="alert-dialog-description"
+ open={open}
+ onClose={onClose}
>
- <DialogTitle id="alert-dialog-title">{title || 'Confirm'}</DialogTitle>
+ <DialogTitle>Publish data</DialogTitle>
<DialogContent>
- <DialogContentText id="alert-dialog-description">
- {children}
+ <DialogContentText>
+ If you agree the selected uploads will move out of your private staging
+ area into the public nomad.
</DialogContentText>
+
+ <FormGroup row style={{alignItems: 'center'}}>
+ <Checkbox
+ checked={!withEmbargo}
+ onChange={() => this.setState({withEmbargo: !withEmbargo})}
+ />
+ <FormLabel>publish without embargo</FormLabel>
+ </FormGroup>
</DialogContent>
<DialogActions>
- <Button onClick={this.props.onClose} color="primary">
- Disagree
+ <Button onClick={onClose} color="primary">
+ Cancel
</Button>
- <Button onClick={this.props.onOk} color="primary" autoFocus>
- Agree
+ <Button onClick={() => onPublish(withEmbargo)} color="primary" autoFocus>
+ {withEmbargo ? 'Publish with embargo' : 'Publish'}
</Button>
</DialogActions>
</Dialog>
diff --git a/gui/src/components/Upload.js b/gui/src/components/Upload.js
index 033ee26c8e81ded5b91be391f7f3583836a1b1ee..fedca6333530c9c5fece43b413c599b8c08c1415 100644
--- a/gui/src/components/Upload.js
+++ b/gui/src/components/Upload.js
@@ -190,7 +190,7 @@ class Upload extends React.Component {
const { calcs, tasks, current_task, tasks_running, tasks_status, process_running, current_process, errors } = upload
// map tasks [ uploading, extracting, parse_all, cleanup ] to steps
- const steps = [ 'upload', 'process', 'commit' ]
+ const steps = [ 'upload', 'process', 'publish' ]
let step = null
const task_index = tasks.indexOf(current_task)
if (task_index === 0) {
@@ -198,7 +198,7 @@ class Upload extends React.Component {
} else if (task_index > 0 && tasks_running) {
step = 'process'
} else {
- step = 'commit'
+ step = 'publish'
}
const stepIndex = steps.indexOf(step)
@@ -278,11 +278,11 @@ class Upload extends React.Component {
)
}
},
- commit: (props) => {
+ publish: (props) => {
props.children = 'inspect'
if (process_running) {
- if (current_process === 'commit_upload') {
+ if (current_process === 'publish_upload') {
props.children = 'approved'
props.optional = <Typography variant="caption">moving data ...</Typography>
} else if (current_process === 'delete_upload') {
@@ -290,7 +290,7 @@ class Upload extends React.Component {
props.optional = <Typography variant="caption">deleting data ...</Typography>
}
} else {
- props.optional = <Typography variant="caption">commit or delete</Typography>
+ props.optional = <Typography variant="caption">publish or delete</Typography>
}
}
}
diff --git a/gui/src/components/Uploads.js b/gui/src/components/Uploads.js
index d36a3697c47af051cd70c615ecde563dd8abe24b..a3ebc24d6727b75f5c234eff01a495d95264b6e3 100644
--- a/gui/src/components/Uploads.js
+++ b/gui/src/components/Uploads.js
@@ -1,9 +1,10 @@
import React from 'react'
-import PropTypes from 'prop-types'
+import PropTypes, { instanceOf } from 'prop-types'
import Markdown from './Markdown'
import { withStyles, Paper, IconButton, FormGroup, Checkbox, FormControlLabel, FormLabel,
LinearProgress,
- Typography} from '@material-ui/core'
+ Typography,
+ Tooltip} from '@material-ui/core'
import UploadIcon from '@material-ui/icons/CloudUpload'
import Dropzone from 'react-dropzone'
import Upload from './Upload'
@@ -12,14 +13,16 @@ import DeleteIcon from '@material-ui/icons/Delete'
import ReloadIcon from '@material-ui/icons/Cached'
import CheckIcon from '@material-ui/icons/Check'
import ConfirmDialog from './ConfirmDialog'
-import { Help } from './help'
+import { Help, Agree } from './help'
import { withApi } from './api'
+import { withCookies, Cookies } from 'react-cookie'
class Uploads extends React.Component {
static propTypes = {
classes: PropTypes.object.isRequired,
api: PropTypes.object.isRequired,
- raiseError: PropTypes.func.isRequired
+ raiseError: PropTypes.func.isRequired,
+ cookies: instanceOf(Cookies).isRequired
}
static styles = theme => ({
@@ -72,7 +75,7 @@ class Uploads extends React.Component {
uploadCommand: 'loading ...',
selectedUploads: [],
loading: true,
- showAccept: false
+ showPublish: false
}
componentDidMount() {
@@ -107,15 +110,16 @@ class Uploads extends React.Component {
})
}
- onAcceptClicked() {
- this.setState({showAccept: true})
+ onPublishClicked() {
+ this.setState({showPublish: true})
}
- handleAccept() {
+ onPublish(withEmbargo) {
this.setState({loading: true})
- Promise.all(this.state.selectedUploads.map(upload => this.props.api.commitUpload(upload.upload_id)))
+ Promise.all(this.state.selectedUploads
+ .map(upload => this.props.api.publishUpload(upload.upload_id, withEmbargo)))
.then(() => {
- this.setState({showAccept: false})
+ this.setState({showPublish: false})
return this.update()
})
.catch(error => {
@@ -163,7 +167,7 @@ class Uploads extends React.Component {
renderUploads() {
const { classes } = this.props
- const { selectedUploads } = this.state
+ const { selectedUploads, showPublish } = this.state
const uploads = this.state.uploads || []
return (<div>
@@ -175,23 +179,36 @@ class Uploads extends React.Component {
onChange={(_, checked) => this.onSelectionAllChanged(checked)}
/>
)} />
- <IconButton onClick={() => this.update()}><ReloadIcon /></IconButton>
+ <Tooltip title="reload uploads" >
+ <IconButton onClick={() => this.update()}><ReloadIcon /></IconButton>
+ </Tooltip>
<FormLabel classes={{root: classes.selectLabel}}>
{`selected uploads ${selectedUploads.length}/${uploads.length}`}
</FormLabel>
- <IconButton
- disabled={selectedUploads.length === 0}
- onClick={this.onDeleteClicked.bind(this)}
- >
- <DeleteIcon />
- </IconButton>
+ <Tooltip title="delete selected uploads" >
+ <div>
+ <IconButton
+ disabled={selectedUploads.length === 0}
+ onClick={this.onDeleteClicked.bind(this)}
+ >
+ <DeleteIcon />
+ </IconButton>
+ </div>
+ </Tooltip>
+
+ <Tooltip title="publish selected uploads" >
+ <div>
+ <IconButton disabled={selectedUploads.length === 0} onClick={() => this.onPublishClicked()}>
+ <CheckIcon />
+ </IconButton>
+ </div>
+ </Tooltip>
- <IconButton disabled={selectedUploads.length === 0} onClick={this.onAcceptClicked.bind(this)}>
- <CheckIcon />
- </IconButton>
- <ConfirmDialog open={this.state.showAccept} onClose={() => this.setState({showAccept: false})} onOk={this.handleAccept.bind(this)}>
- If you agree the selected uploads will move out of your private staging area into the public nomad.
- </ConfirmDialog>
+ <ConfirmDialog
+ open={showPublish}
+ onClose={() => this.setState({showPublish: false})}
+ onPublish={(withEmbargo) => this.onPublish(withEmbargo)}
+ />
</FormGroup>
</div>
@@ -200,11 +217,15 @@ class Uploads extends React.Component {
? (
<div>
<Help cookie="uploadList">{`
- These are all your existing not commiting uploads. You can see how processing
- progresses and review your uploads before commiting them to the *nomad repository*.
+ These are all your uploads in the *staging area*. You can see the
+ progress on data progresses and review your uploads before publishing
+ them to the *nomad repository*.
- Select uploads to delete or commit them. Click on uploads to see individual
+ Select uploads to delete or publish them. Click on uploads to see individual
calculations. Click on calculations to see more details on each calculation.
+
+ When you select and click publish, you will be ask if you want to publish
+ with or without the optional *embargo period*.
`}</Help>
{
this.sortedUploads().map(upload => (
@@ -224,46 +245,69 @@ class Uploads extends React.Component {
const { classes } = this.props
const { uploadCommand } = this.state
+ const agreement = `
+ By uploading and downloading data, you agree to the
+ [terms of use](https://www.nomad-coe.eu/the-project/nomad-repository/nomad-repository-terms).
+
+ Note that uploaded files become downloadable. Uploaded data is licensed under the
+ Creative Commons Attribution license ([CC BY 3.0](https://creativecommons.org/licenses/by/3.0/)).
+ You can put an *embargo* on uploaded data. The *embargo period* lasts up to 36 month.
+ If you do not decide on an *embargo* after upload, data will be made public after 48h
+ automatically.
+ `
+
return (
<div className={classes.root}>
<Typography variant="h4">Upload your own data</Typography>
- <Help cookie="uploadHelp" component={Markdown}>{`
- You can upload your own data. Have your code output ready in a popular archive
- format (e.g. \`*.zip\` or \`*.tar.gz\`). Your upload can
- comprise the output of multiple runs, even of different codes. Don't worry, nomad
- will find it, just drop it below:
- `}</Help>
+ <Agree message={agreement} cookie="agreedToUploadTerms">
+ <Help cookie="uploadHelp" component={Markdown}>{`
+ To upload your own data, please put all relevant files in a
+ \`*.zip\` or \`*.tar.gz\` archive. We encourage you to add all code input and
+ output files, as well as any other auxiliary files that you might have created.
+ You can put data from multiple calculations, using your preferred directory
+ structure, into your archives. Drop your archive file(s) below.
+
+ Uploaded data will not be public immediately. This is called the *staging area*.
+ After uploading and processing, you can decide if you want to make the data public,
+ delete it again, or put an *embargo* on it.
+
+ The *embargo* allows you to shared it with selected users, create a DOI
+ for your data, and later publish the data. The *embargo* might last up to
+ 36 month before it becomes public automatically. During an *embargo*
+ some meta-data will be available.
+ `}</Help>
- <Paper className={classes.dropzoneContainer}>
- <Dropzone
- accept={['application/zip', 'application/gzip', 'application/bz2']}
- className={classes.dropzone}
- activeClassName={classes.dropzoneAccept}
- rejectClassName={classes.dropzoneReject}
- onDrop={this.onDrop.bind(this)}
- >
- <p>drop files here</p>
- <UploadIcon style={{fontSize: 36}}/>
- </Dropzone>
- </Paper>
+ <Paper className={classes.dropzoneContainer}>
+ <Dropzone
+ accept={['application/zip', 'application/gzip', 'application/bz2']}
+ className={classes.dropzone}
+ activeClassName={classes.dropzoneAccept}
+ rejectClassName={classes.dropzoneReject}
+ onDrop={this.onDrop.bind(this)}
+ >
+ <p>drop files here</p>
+ <UploadIcon style={{fontSize: 36}}/>
+ </Dropzone>
+ </Paper>
- <Help cookie="uploadCommandHelp">{`
- Alternatively, you can upload files via the following shell command.
- Replace \`<local_file>\` with your file. After executing the command,
- return here and reload.
- `}</Help>
+ <Help cookie="uploadCommandHelp">{`
+ Alternatively, you can upload files via the following shell command.
+ Replace \`<local_file>\` with your archive file. After executing the command,
+ return here and reload (e.g. press the reload button below).
+ `}</Help>
- <Markdown>{`
- \`\`\`
- ${uploadCommand}
- \`\`\`
- `}</Markdown>
+ <Markdown>{`
+ \`\`\`
+ ${uploadCommand}
+ \`\`\`
+ `}</Markdown>
- {this.renderUploads()}
- {this.state.loading ? <LinearProgress/> : ''}
+ {this.renderUploads()}
+ {this.state.loading ? <LinearProgress/> : ''}
+ </Agree>
</div>
)
}
}
-export default compose(withApi(true), withStyles(Uploads.styles))(Uploads)
+export default compose(withApi(true), withCookies, withStyles(Uploads.styles))(Uploads)
diff --git a/gui/src/components/api.js b/gui/src/components/api.js
index 0b909f064e7bed3bc58c7ac1411d0452ecc3f583..47445af4d9b9e1fc06b54f0dec6ab72760bcb518 100644
--- a/gui/src/components/api.js
+++ b/gui/src/components/api.js
@@ -215,12 +215,15 @@ class Api {
.then(response => response.body)
}
- async commitUpload(uploadId) {
+ async publishUpload(uploadId, withEmbargo) {
const client = await this.swaggerPromise
- return client.apis.uploads.exec_upload_command({
+ return client.apis.uploads.exec_upload_operation({
upload_id: uploadId,
payload: {
- command: 'commit'
+ operation: 'publish',
+ metadata: {
+ with_embargo: withEmbargo
+ }
}
})
.catch(this.handleApiError)
diff --git a/gui/src/components/help.js b/gui/src/components/help.js
index 69220a9d80c79efbe869895c95ae524a3732ad75..0e27f234c7c22d912f8446c84047d17305ea747c 100644
--- a/gui/src/components/help.js
+++ b/gui/src/components/help.js
@@ -1,8 +1,9 @@
import React from 'react'
-import { withStyles, Button } from '@material-ui/core'
+import { withStyles, Button, Collapse, Fade } from '@material-ui/core'
import Markdown from './Markdown'
import PropTypes, { instanceOf } from 'prop-types'
import { Cookies, withCookies } from 'react-cookie'
+import classNames from 'classnames'
export const HelpContext = React.createContext()
@@ -51,17 +52,98 @@ class HelpProviderComponent extends React.Component {
}
}
-class HelpComponent extends React.Component {
+export class Help extends React.Component {
+ static propTypes = {
+ children: PropTypes.any,
+ cookie: PropTypes.string.isRequired
+ }
+
+ render() {
+ const { children, cookie } = this.props
+
+ return (
+ <HelpContext.Consumer>{
+ help => (
+ <Collapse in={help.isOpen(cookie)}>
+ <GotIt onGotIt={() => help.gotIt(cookie)}>
+ {children}
+ </GotIt>
+ </Collapse>
+ )
+ }</HelpContext.Consumer>
+ )
+ }
+}
+
+class AgreeComponent extends React.Component {
+ static propTypes = {
+ children: PropTypes.oneOfType([
+ PropTypes.node, PropTypes.arrayOf(PropTypes.node)
+ ]).isRequired,
+ message: PropTypes.string.isRequired,
+ cookie: PropTypes.string.isRequired,
+ cookies: instanceOf(Cookies).isRequired
+ }
+
+ state = {
+ agreed: this.props.cookies.get(this.props.cookie)
+ }
+
+ onAgreeClicked() {
+ this.props.cookies.set(this.props.cookie, true)
+ this.setState({agreed: true})
+ }
+
+ render() {
+ const { children, message } = this.props
+ const { agreed } = this.state
+
+ return (
+ <div>
+ <Collapse in={!agreed}>
+ <GotIt onGotIt={() => this.onAgreeClicked()} color="error">
+ {message}
+ </GotIt>
+ </Collapse>
+ <Fade in={!!agreed}>
+ <div>
+ {children}
+ </div>
+ </Fade>
+ </div>
+ )
+ }
+}
+
+export const Agree = withCookies(AgreeComponent)
+
+class GotItUnstyled extends React.Component {
+ static propTypes = {
+ classes: PropTypes.object.isRequired,
+ onGotIt: PropTypes.func.isRequired,
+ children: PropTypes.node.isRequired,
+ color: PropTypes.oneOf(['primary', 'error']).isRequired
+ }
+
+ static defaultProps = {
+ color: 'primary'
+ }
+
static styles = theme => ({
root: {
marginTop: theme.spacing.unit * 2,
marginBottom: theme.spacing.unit * 2,
borderRadius: theme.spacing.unit * 0.5,
- border: `1px solid ${theme.palette.primary.main}`,
display: 'flex',
flexDirection: 'row',
alignItems: 'center'
},
+ rootPrimary: {
+ border: `1px solid ${theme.palette.primary.main}`
+ },
+ rootError: {
+ border: `1px solid ${theme.palette.error.main}`
+ },
content: {
paddingLeft: theme.spacing.unit * 2,
flex: '1 1 auto'
@@ -72,34 +154,27 @@ class HelpComponent extends React.Component {
}
})
- static propTypes = {
- classes: PropTypes.object.isRequired,
- children: PropTypes.any,
- cookie: PropTypes.string.isRequired
- }
-
render() {
- const { classes, children, cookie } = this.props
-
+ const { classes, children, onGotIt, color } = this.props
+ const rootClassName = classNames(classes.root, {
+ [classes.rootPrimary]: color === 'primary',
+ [classes.rootError]: color === 'error'
+ })
return (
- <HelpContext.Consumer>{
- help => (
- help.isOpen(cookie)
- ? <div className={classes.root}>
- <div className={classes.content}>
- <Markdown>
- {children}
- </Markdown>
- </div>
- <div className={classes.actions}>
- <Button color="primary" onClick={() => help.gotIt(cookie)}>Got it</Button>
- </div>
- </div> : ''
- )
- }</HelpContext.Consumer>
+ <div className={rootClassName}>
+ <div className={classes.content}>
+ <Markdown>
+ {children}
+ </Markdown>
+ </div>
+ <div className={classes.actions}>
+ <Button color="primary" onClick={onGotIt}>Got it</Button>
+ </div>
+ </div>
)
}
}
+const GotIt = withStyles(GotItUnstyled.styles)(GotItUnstyled)
+
export const HelpProvider = withCookies(HelpProviderComponent)
-export const Help = withStyles(HelpComponent.styles)(HelpComponent)
diff --git a/nomad/api/upload.py b/nomad/api/upload.py
index 17ab525ac4a66c7deb77d57e1fee85d08be55715..241038773bdf5032784f881d550e1a16531a6f0b 100644
--- a/nomad/api/upload.py
+++ b/nomad/api/upload.py
@@ -103,8 +103,8 @@ upload_with_calcs_model = api.inherit('UploadWithPaginatedCalculations', upload_
}))
})
-upload_command_model = api.model('UploadCommand', {
- 'command': fields.String(description='Currently commit is the only command.'),
+upload_operation_model = api.model('UploadOperation', {
+ 'operation': fields.String(description='Currently publish is the only operation.'),
'metadata': fields.Nested(model=upload_metadata_model, description='Additional upload and calculation meta data. Will replace previously given metadata.')
})
@@ -300,20 +300,20 @@ class UploadResource(Resource):
return upload, 200
- @api.doc('exec_upload_command')
+ @api.doc('exec_upload_operation')
@api.response(404, 'Upload does not exist or not in staging')
@api.response(400, 'Operation is not supported or the upload is still/already processed')
- @api.response(401, 'If the command is not allowed for the current user')
- @api.marshal_with(upload_model, skip_none=True, code=200, description='Upload commited successfully')
- @api.expect(upload_command_model)
+ @api.response(401, 'If the operation is not allowed for the current user')
+ @api.marshal_with(upload_model, skip_none=True, code=200, description='Upload published successfully')
+ @api.expect(upload_operation_model)
@login_really_required
def post(self, upload_id):
"""
- Execute an upload command. Available operations: ``commit``
+ Execute an upload operation. Available operations: ``publish``
Unstage accepts further meta data that allows to provide coauthors, comments,
external references, etc. See the model for details. The fields that start with
- ``_underscore`` are only available for users with administrative priviledges.
+ ``_underscore`` are only available for users with administrative privileges.
Unstage changes the visibility of the upload. Clients can specify the visibility
via meta data.
@@ -330,7 +330,7 @@ class UploadResource(Resource):
if json_data is None:
json_data = {}
- command = json_data.get('command')
+ operation = json_data.get('operation')
metadata = json_data.get('metadata', {})
for key in metadata:
@@ -339,20 +339,20 @@ class UploadResource(Resource):
abort(401, message='Only admin users can use _metadata_keys.')
break
- if command == 'commit':
+ if operation == 'publish':
if upload.tasks_running:
abort(400, message='The upload is not processed yet')
if upload.tasks_status == FAILURE:
- abort(400, message='Cannot commit an upload that failed processing')
+ abort(400, message='Cannot publish an upload that failed processing')
try:
upload.metadata = metadata
- upload.commit_upload()
+ upload.publish_upload()
except ProcessAlreadyRunning:
abort(400, message='The upload is still/already processed')
return upload, 200
- abort(400, message='Unsuported command %s.' % command)
+ abort(400, message='Unsuported operation %s.' % operation)
upload_command_model = api.model('UploadCommand', {
diff --git a/nomad/client/upload.py b/nomad/client/upload.py
index 815076e7f6d5b9e649ac03719ba723cb16621951..84d13056def6ddfeab907c673ca6f96277800916 100644
--- a/nomad/client/upload.py
+++ b/nomad/client/upload.py
@@ -23,7 +23,7 @@ from nomad.processing import FAILURE, SUCCESS
from .main import cli, create_client
-def upload_file(file_path: str, name: str = None, offline: bool = False, commit: bool = False, client=None):
+def upload_file(file_path: str, name: str = None, offline: bool = False, publish: bool = False, client=None):
"""
Upload a file to nomad.
@@ -31,7 +31,7 @@ def upload_file(file_path: str, name: str = None, offline: bool = False, commit:
file_path: path to the file, absolute or relative to call directory
name: optional name, default is the file_path's basename
offline: allows to process data without upload, requires client to be run on the server
- commit: automatically commit after successful processing
+ publish: automatically publish after successful processing
Returns: The upload_id
"""
@@ -66,8 +66,8 @@ def upload_file(file_path: str, name: str = None, offline: bool = False, commit:
click.echo('There have been errors:')
for error in upload.errors:
click.echo(' %s' % error)
- elif commit:
- client.uploads.exec_upload_command(upload_id=upload.upload_id, command='commit').reponse()
+ elif publish:
+ client.uploads.exec_upload_operation(upload_id=upload.upload_id, payload=dict(operation='publish')).response()
return upload.upload_id
@@ -84,9 +84,9 @@ def upload_file(file_path: str, name: str = None, offline: bool = False, commit:
help='Upload files "offline": files will not be uploaded, but processed were they are. '
'Only works when run on the nomad host.')
@click.option(
- '--commit', is_flag=True, default=False,
+ '--publish', is_flag=True, default=False,
help='Automatically move upload out of the staging area after successful processing')
-def upload(path, name: str, offline: bool, commit: bool):
+def upload(path, name: str, offline: bool, publish: bool):
utils.configure_logging()
paths = path
click.echo('uploading files from %s paths' % len(paths))
@@ -94,7 +94,7 @@ def upload(path, name: str, offline: bool, commit: bool):
click.echo('uploading %s' % path)
if os.path.isfile(path):
name = name if name is not None else os.path.basename(path)
- upload_file(path, name, offline, commit)
+ upload_file(path, name, offline, publish)
elif os.path.isdir(path):
for (dirpath, _, filenames) in os.walk(path):
@@ -102,7 +102,7 @@ def upload(path, name: str, offline: bool, commit: bool):
if filename.endswith('.zip'):
file_path = os.path.abspath(os.path.join(dirpath, filename))
name = os.path.basename(file_path)
- upload_file(file_path, name, offline, commit)
+ upload_file(file_path, name, offline, publish)
else:
click.echo('Unknown path type %s.' % path)
diff --git a/nomad/coe_repo/upload.py b/nomad/coe_repo/upload.py
index 1d4a03787ac32bee9ff20ea4b832b001843f1f84..5ff22258a2a20aa6e9424ebcd23369ef264af04d 100644
--- a/nomad/coe_repo/upload.py
+++ b/nomad/coe_repo/upload.py
@@ -130,6 +130,8 @@ class Upload(Base, datamodel.Upload): # type: ignore
meta data) that should be added to upload and calculations.
"""
upload_metadata = UploadMetaData(metadata)
+ assert upload.uploader is not None
+
repo_db = infrastructure.repository_db
repo_db.begin()
@@ -222,8 +224,13 @@ class Upload(Base, datamodel.Upload): # type: ignore
coe_calc.set_value(base.topic_basis_set_type, calc.basis_set_type)
# user relations
- owner_user_id = calc_metadata.get('_uploader', int(self.user_id))
- coe_calc.owners.append(repo_db.query(User).get(owner_user_id))
+ owner_user_id = calc_metadata.get('_uploader', None)
+ if owner_user_id is not None:
+ uploader = repo_db.query(User).get(owner_user_id)
+ else:
+ uploader = self.user
+
+ coe_calc.owners.append(uploader)
for coauthor_id in calc_metadata.get('coauthors', []):
coe_calc.coauthors.append(repo_db.query(User).get(coauthor_id))
diff --git a/nomad/infrastructure.py b/nomad/infrastructure.py
index a8498bf2349a247827afc6a47f2e4e3c8e1d0d15..be3ef673158e1dbb5a78ddc7667e59515bcb15c8 100644
--- a/nomad/infrastructure.py
+++ b/nomad/infrastructure.py
@@ -56,7 +56,7 @@ def setup():
setup_logging()
setup_mongo()
setup_elastic()
- setup_repository_db()
+ setup_repository_db(readonly=False)
def setup_logging():
diff --git a/nomad/migration.py b/nomad/migration.py
index 4ef5cc08bd92fca5c7f05302aea810aa4cd83bbc..83c99208286daa3bf89235580acbe493a9ba7b7c 100644
--- a/nomad/migration.py
+++ b/nomad/migration.py
@@ -373,7 +373,7 @@ class NomadCOEMigration:
'no match or processed calc for source calc',
mainfile=source_calc.mainfile)
- # commit upload
+ # publish upload
admin_keys = ['upload_time, uploader, pid']
def transform(calcWithMetadata):
@@ -394,9 +394,9 @@ class NomadCOEMigration:
if calc.__migrated]
if report.total_calcs > report.failed_calcs:
- upload = self.client.uploads.exec_upload_command(
+ upload = self.client.uploads.exec_upload_operation(
upload_id=upload.upload_id,
- payload=dict(command='commit', metadata=upload_metadata)
+ payload=dict(operation='publish', metadata=upload_metadata)
).response().result
while upload.process_running:
@@ -405,7 +405,7 @@ class NomadCOEMigration:
upload_id=upload.upload_id).response().result
time.sleep(0.1)
except HTTPNotFound:
- # the proc upload will be deleted by the commit command
+ # the proc upload will be deleted by the publish operation
break
# report
diff --git a/nomad/processing/data.py b/nomad/processing/data.py
index 9ddd11b05e431c0e3de9f285fb6cf947b366ddd8..ed89f436c49125f4bcd9e850e4df5d5ab28a0e4e 100644
--- a/nomad/processing/data.py
+++ b/nomad/processing/data.py
@@ -358,7 +358,7 @@ class Upload(Chord, datamodel.Upload):
return True # do not save the process status on the delete upload
@process
- def commit_upload(self):
+ def publish_upload(self):
"""
Moves the upload out of staging to add it to the coe repository. It will
pack the staging upload files in to public upload files, add entries to the
@@ -367,19 +367,19 @@ class Upload(Chord, datamodel.Upload):
"""
logger = self.get_logger()
- with utils.lnr(logger, 'commit failed'):
+ with utils.lnr(logger, 'publish failed'):
with utils.timer(
- logger, 'upload added to repository', step='commit',
+ logger, 'upload added to repository', step='publish',
upload_size=self.upload_files.size):
coe_repo.Upload.add(self, self.metadata)
with utils.timer(
- logger, 'staged upload files packed', step='commit',
+ logger, 'staged upload files packed', step='publish',
upload_size=self.upload_files.size):
self.upload_files.pack()
with utils.timer(
- logger, 'staged upload deleted', step='commit',
+ logger, 'staged upload deleted', step='publish',
upload_size=self.upload_files.size):
self.upload_files.delete()
self.delete()
diff --git a/tests/test_api.py b/tests/test_api.py
index fc0a58d9a9a4eba8ef1fb37328542ea8d565ff2d..b593e6797c44063946fbe9e5691659614c77e7e8 100644
--- a/tests/test_api.py
+++ b/tests/test_api.py
@@ -236,18 +236,18 @@ class TestUploads:
rv = client.post(
'/uploads/%s' % upload_id,
headers=test_user_auth,
- data=json.dumps(dict(command='commit', metadata=metadata)),
+ data=json.dumps(dict(operation='publish', metadata=metadata)),
content_type='application/json')
assert rv.status_code == 200
upload = self.assert_upload(rv.data)
- assert upload['current_process'] == 'commit_upload'
+ assert upload['current_process'] == 'publish_upload'
assert upload['process_running']
self.assert_upload_does_not_exist(client, upload_id, test_user_auth)
assert_coe_upload(upload_id, empty=empty_upload, metadata=metadata)
def assert_upload_does_not_exist(self, client, upload_id: str, test_user_auth):
- # poll until commit/delete completed
+ # poll until publish/delete completed
while True:
time.sleep(0.1)
rv = client.get('/uploads/%s' % upload_id, headers=test_user_auth)
@@ -378,7 +378,7 @@ class TestUploads:
rv = client.post(
'/uploads/%s' % upload['upload_id'],
headers=test_user_auth,
- data=json.dumps(dict(command='commit', metadata=dict(_pid=256))),
+ data=json.dumps(dict(operation='publish', metadata=dict(_pid=256))),
content_type='application/json')
assert rv.status_code == 401
@@ -390,7 +390,7 @@ class TestUploads:
# rv = client.post(
# '/uploads/%s' % upload['upload_id'],
# headers=test_user_auth,
- # data=json.dumps(dict(command='commit', metadata=dict(doesnotexist='hi'))),
+ # data=json.dumps(dict(operation='publish', metadata=dict(doesnotexist='hi'))),
# content_type='application/json')
# assert rv.status_code == 400