diff --git a/docs/.DS_Store b/docs/.DS_Store
index 560ae6fbf457a39fcfc8c2f24862414f0648c4c3..efcf6d48ca6cbe1f32bb3708f624e8a39f3a1ada 100644
Binary files a/docs/.DS_Store and b/docs/.DS_Store differ
diff --git a/gui/package.json b/gui/package.json
index a13d638e39d008ccea91741f198347b6e2b0c2ac..b59efaf9ba76643868ac3ada3c895ad2bfa4237a 100644
--- a/gui/package.json
+++ b/gui/package.json
@@ -35,6 +35,7 @@
"eslint": "^4.19.1",
"eslint-config-standard": "^11.0.0",
"eslint-plugin-import": "^2.14.0",
+ "eslint-plugin-node": "^8.0.1",
"eslint-plugin-promise": "^3.7.0",
"eslint-plugin-react": "^7.11.1",
"eslint-plugin-standard": "^3.1.0",
diff --git a/gui/src/api.js b/gui/src/api.js
index 9b33b4474e11d4ad0fa013d8b566376befa4093b..45cdab8ca3b2c8dd50a7e90f36e210bd7731d8c8 100644
--- a/gui/src/api.js
+++ b/gui/src/api.js
@@ -18,31 +18,47 @@ const swaggerPromise = Swagger(`${apiBase}/swagger.json`, {
}
})
-const networkError = (e) => {
- console.log(e)
- throw Error('Network related error, cannot reach API: ' + e)
-}
-
-const handleJsonErrors = (e) => {
- console.log(e)
- throw Error('API return unexpected data format.')
+export class DoesNotExist extends Error {
+ constructor(msg) {
+ super(msg)
+ this.name = 'DoesNotExist'
+ }
}
-const handleResponseErrors = (response) => {
- if (!response.ok) {
- return response.json()
- .catch(() => {
- throw Error(`API error (${response.status}): ${response.statusText}`)
- }).then(data => {
- throw Error(`API error (${response.status}): ${data.message}`)
- })
+const handleApiError = (e) => {
+ if (e.response) {
+ const body = e.response.body
+ const message = (body && body.message) ? body.message : e.response.statusText
+ if (e.response.status === 404) {
+ throw new DoesNotExist(message)
+ } else {
+ throw Error(`API error (${e.response.status}): ${message}`)
+ }
+ } else {
+ throw Error('Network related error, cannot reach API: ' + e)
}
- return response
}
+const upload_to_gui_ids = {}
+let gui_upload_id_counter = 0
+
class Upload {
constructor(json) {
- this.uploading = 0
+ // Cannot use upload_id as key in GUI, because uploads don't have an upload_id
+ // before upload is completed
+ if (json.upload_id) {
+ // instance from the API
+ this.gui_upload_id = upload_to_gui_ids[json.upload_id]
+ if (this.gui_upload_id === undefined) {
+ // never seen in the GUI, needs a GUI id
+ this.gui_upload_id = gui_upload_id_counter++
+ upload_to_gui_ids[json.upload_id] = this.gui_upload_id
+ console.log('new gui ui')
+ }
+ } else {
+ // new instance, not from the API
+ this.gui_upload_id = gui_upload_id_counter++
+ }
Object.assign(this, json)
}
@@ -65,13 +81,14 @@ class Upload {
}
)
if (uploadRequest.error) {
- networkError(uploadRequest.error)
+ handleApiError(uploadRequest.error)
}
if (uploadRequest.aborted) {
throw Error('User abort')
}
this.uploading = 100
this.upload_id = uploadRequest.response.upload_id
+ upload_to_gui_ids[this.upload_id] = this.gui_upload_id
}
return uploadFileWithProgress()
@@ -84,14 +101,13 @@ class Upload {
} else {
if (this.upload_id) {
return swaggerPromise.then(client => client.apis.uploads.get_upload({
- upload_id: this.upload_id,
- page: page || 1,
- per_page: perPage || 5,
- order_by: orderBy || 'mainfile',
- order: order || -1
- }))
- .catch(networkError)
- .then(handleResponseErrors)
+ upload_id: this.upload_id,
+ page: page || 1,
+ per_page: perPage || 5,
+ order_by: orderBy || 'mainfile',
+ order: order || -1
+ }))
+ .catch(handleApiError)
.then(response => response.body)
.then(uploadJson => {
Object.assign(this, uploadJson)
@@ -107,7 +123,7 @@ class Upload {
function createUpload(name) {
return new Upload({
name: name,
- tasks: ['uploading'],
+ tasks: ['uploading', 'extract', 'parse_all', 'cleanup'],
current_task: 'uploading',
uploading: 0,
create_time: new Date()
@@ -117,8 +133,7 @@ function createUpload(name) {
async function getUploads() {
const client = await swaggerPromise
return client.apis.uploads.get_uploads()
- .catch(networkError)
- .then(handleResponseErrors)
+ .catch(handleApiError)
.then(response => response.body.map(uploadJson => {
const upload = new Upload(uploadJson)
upload.uploading = 100
@@ -129,11 +144,10 @@ async function getUploads() {
async function archive(uploadId, calcId) {
const client = await swaggerPromise
return client.apis.archive.get_archive_calc({
- upload_id: uploadId,
- calc_id: calcId
- })
- .catch(networkError)
- .then(handleResponseErrors)
+ upload_id: uploadId,
+ calc_id: calcId
+ })
+ .catch(handleApiError)
.then(response => response.body)
}
@@ -143,61 +157,47 @@ async function calcProcLog(uploadId, calcId) {
upload_id: uploadId,
calc_id: calcId
})
- .catch(networkError)
- .then(response => {
- if (!response.ok) {
- if (response.status === 404) {
- return ''
- } else {
- return handleResponseErrors(response)
- }
- } else {
- return response.text
- }
- })
+ .catch(handleApiError)
+ .then(response => response.text)
}
async function repo(uploadId, calcId) {
const client = await swaggerPromise
return client.apis.repo.get_repo_calc({
- upload_id: uploadId,
- calc_id: calcId
- })
- .catch(networkError)
- .then(handleResponseErrors)
+ upload_id: uploadId,
+ calc_id: calcId
+ })
+ .catch(handleApiError)
.then(response => response.body)
}
async function repoAll(page, perPage, owner) {
const client = await swaggerPromise
return client.apis.repo.get_calcs({
- page: page,
- per_page: perPage,
- ower: owner || 'all'
- })
- .catch(networkError)
- .then(handleResponseErrors)
+ page: page,
+ per_page: perPage,
+ ower: owner || 'all'
+ })
+ .catch(handleApiError)
.then(response => response.body)
}
async function deleteUpload(uploadId) {
const client = await swaggerPromise
return client.apis.uploads.delete_upload({upload_id: uploadId})
- .catch(networkError)
- .then(handleResponseErrors)
+ .catch(handleApiError)
.then(response => response.body)
}
async function commitUpload(uploadId) {
const client = await swaggerPromise
return client.apis.uploads.exec_upload_command({
- upload_id: uploadId,
- payload: {
- operation: 'commit'
- }
- })
- .catch(networkError)
- .then(handleResponseErrors)
+ upload_id: uploadId,
+ payload: {
+ operation: 'commit'
+ }
+ })
+ .catch(handleApiError)
.then(response => response.body)
}
@@ -208,11 +208,11 @@ async function getMetaInfo() {
return cachedMetaInfo
} else {
const loadMetaInfo = async(path) => {
- return fetch(`${apiBase}/archive/metainfo/${path}`)
- .catch(networkError)
- .then(handleResponseErrors)
- .then(response => response.json())
- .catch(handleJsonErrors)
+ const client = await swaggerPromise
+ console.log(path)
+ return client.apis.archive.get_metainfo({metainfo_path: path})
+ .catch(handleApiError)
+ .then(response => response.body)
.then(data => {
if (!cachedMetaInfo) {
cachedMetaInfo = {
@@ -243,8 +243,7 @@ async function getMetaInfo() {
async function getUploadCommand() {
const client = await swaggerPromise
return client.apis.uploads.get_upload_command()
- .catch(networkError)
- .then(handleResponseErrors)
+ .catch(handleApiError)
.then(response => response.body.upload_command)
}
diff --git a/gui/src/components/Upload.js b/gui/src/components/Upload.js
index cb8b261961bf52e4d557bbfb2100fc9020d39079..c9462d57c8cd7fb8b70348287f679931cf53b0df 100644
--- a/gui/src/components/Upload.js
+++ b/gui/src/components/Upload.js
@@ -20,7 +20,8 @@ class Upload extends React.Component {
raiseError: PropTypes.func.isRequired,
upload: PropTypes.object.isRequired,
checked: PropTypes.bool,
- onCheckboxChanged: PropTypes.func
+ onCheckboxChanged: PropTypes.func,
+ onDoesNotExist: PropTypes.func
}
static styles = theme => ({
@@ -77,7 +78,7 @@ class Upload extends React.Component {
params: {
page: 1,
perPage: 5,
- orderBy: 'status',
+ orderBy: 'tasks_status',
order: 'asc'
},
archiveLogs: null, // { uploadId, calcId } ids of archive to show logs for
@@ -96,8 +97,9 @@ class Upload extends React.Component {
this.setState({loading: true})
this.state.upload.get(page, perPage, orderBy, order === 'asc' ? 1 : -1)
.then(upload => {
+ const {tasks_running, process_running, current_task} = upload
if (!this._unmounted) {
- const continueUpdating = upload.status !== 'SUCCESS' && upload.status !== 'FAILURE' && !upload.is_stale
+ const continueUpdating = tasks_running || process_running || current_task === 'uploading'
this.setState({upload: upload, loading: false, params: params, updating: continueUpdating})
if (continueUpdating) {
window.setTimeout(() => {
@@ -111,7 +113,11 @@ class Upload extends React.Component {
.catch(error => {
if (!this._unmounted) {
this.setState({loading: false, ...params})
- this.props.raiseError(error)
+ if (error.name === 'DoesNotExist') {
+ this.props.onDoesNotExist()
+ } else {
+ this.props.raiseError(error)
+ }
}
})
}
@@ -120,6 +126,12 @@ class Upload extends React.Component {
this.update(this.state.params)
}
+ componentDidUpdate(prevProps) {
+ if (!prevProps.upload.process_running && this.props.upload.process_running) {
+ this.update(this.state.params)
+ }
+ }
+
componentWillUnmount() {
this._unmounted = true
}
@@ -169,73 +181,119 @@ class Upload extends React.Component {
renderStepper() {
const { classes } = this.props
const { upload } = this.state
- const { calcs, tasks, current_task, status, errors } = upload
-
- let activeStep = tasks.indexOf(current_task)
- activeStep += (status === 'SUCCESS') ? 1 : 0
+ 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' ]
+ let step = null
+ const task_index = tasks.indexOf(current_task)
+ if (task_index === 0) {
+ step = 'upload'
+ } else if (task_index > 0 && tasks_running) {
+ step = 'process'
+ } else {
+ step = 'commit'
+ }
+ const stepIndex = steps.indexOf(step)
const labelPropsFactories = {
- uploading: (props) => {
- props.children = 'uploading'
- const { uploading } = upload
- if (upload.status !== 'FAILURE') {
- props.optional = (
- <Typography variant="caption">
- {uploading === 100 && current_task === tasks[0] ? 'waiting for processing ...' : `${uploading || 0}%`}
- </Typography>
- )
+ upload: (props) => {
+ if (step === 'upload') {
+ props.children = 'uploading'
+ const { uploading } = upload
+ if (upload.tasks_status !== 'FAILURE') {
+ props.optional = (
+ <Typography variant="caption">
+ {`${uploading || 0}%`}
+ </Typography>
+ )
+ }
+ } else {
+ props.children = 'uploaded'
}
},
- extracting: (props) => {
- props.children = 'extracting'
+ process: (props) => {
+ props.error = tasks_status === 'FAILURE'
+
+ const processIndex = steps.indexOf('process')
+ if (stepIndex <= processIndex) {
+ props.children = 'processing'
+ } else {
+ props.children = 'processed'
+ }
+
if (current_task === 'extracting') {
+ props.children = 'extracting'
props.optional = (
<Typography variant="caption">
be patient
</Typography>
)
+ } else if (current_task === 'parse_all') {
+ props.children = 'parsing'
}
- },
- parse_all: (props) => {
- props.children = 'parse'
- if (!calcs) {
- props.optional = (
- <Typography variant="caption" >
- loading...
- </Typography>
- )
- } else if (calcs.pagination.total > 0) {
- const { total, successes, failures } = calcs.pagination
- if (failures) {
- props.error = true
+ if (stepIndex >= processIndex) {
+ if (!calcs) {
props.optional = (
- <Typography variant="caption" color="error">
- {successes + failures}/{total}, {failures} failed
+ <Typography variant="caption" >
+ matching...
</Typography>
)
- } else {
+ } else if (calcs.pagination.total > 0) {
+ const { total, successes, failures } = calcs.pagination
+ if (failures) {
+ props.error = true
+ props.optional = (
+ <Typography variant="caption" color="error">
+ {successes + failures}/{total}, {failures} failed
+ </Typography>
+ )
+ } else {
+ props.optional = (
+ <Typography variant="caption">
+ {successes + failures}/{total}
+ </Typography>
+ )
+ }
+ } else if (tasks_status === 'SUCCESS') {
+ props.error = true
props.optional = (
- <Typography variant="caption">
- {successes + failures}/{total}
- </Typography>
+ <Typography variant="caption" color="error">No calculations found.</Typography>
)
}
- } else if (status === 'SUCCESS') {
- props.error = true
+ }
+
+ if (tasks_status === 'FAILURE') {
props.optional = (
- <Typography variant="caption" color="error">No calculations found.</Typography>
+ <Typography variant="caption" color="error">
+ {errors.join(' ')}
+ </Typography>
)
}
+ },
+ commit: (props) => {
+ props.children = 'inspect'
+
+ if (process_running) {
+ if (current_process === 'commit_upload') {
+ props.children = 'approved'
+ props.optional = <Typography variant="caption">moving data ...</Typography>
+ } else if (current_process === 'delete_upload') {
+ props.children = 'declined'
+ props.optional = <Typography variant="caption">deleting data ...</Typography>
+ }
+ } else {
+ props.optional = <Typography variant="caption">commit or delete</Typography>
+ }
}
}
return (
- <Stepper activeStep={activeStep} classes={{root: classes.stepper}}>
- {tasks.map((label, index) => {
+ <Stepper activeStep={steps.indexOf(step)} classes={{root: classes.stepper}}>
+ {steps.map((label, index) => {
const labelProps = {
- children: label,
- error: activeStep === index && status === 'FAILURE'
+ children: label
}
const labelPropsFactory = labelPropsFactories[label]
@@ -243,14 +301,6 @@ class Upload extends React.Component {
labelPropsFactory(labelProps)
}
- if (labelProps.error && status === 'FAILURE') {
- labelProps.optional = (
- <Typography variant="caption" color="error">
- {errors.join(' ')}
- </Typography>
- )
- }
-
return (
<Step key={label}>
<StepLabel {...labelProps} />
@@ -264,14 +314,14 @@ class Upload extends React.Component {
renderCalcTable() {
const { classes } = this.props
const { page, perPage, orderBy, order } = this.state.params
- const { calcs, status, waiting } = this.state.upload
+ const { calcs, tasks_status, waiting } = this.state.upload
const { pagination, results } = calcs
if (pagination.total === 0) {
- if (this.state.upload.completed) {
+ if (!this.state.upload.tasks_running) {
return (
<Typography className={classes.detailsContent}>
- {status === 'SUCCESS' ? 'No calculcations found.' : 'No calculations to show.'}
+ {tasks_status === 'SUCCESS' ? 'No calculcations found.' : 'No calculations to show.'}
</Typography>
)
} else {
@@ -292,8 +342,8 @@ class Upload extends React.Component {
}
const renderRow = (calc, index) => {
- const { mainfile, calc_id, upload_id, parser, tasks, current_task, status, errors } = calc
- const color = status === 'FAILURE' ? 'error' : 'default'
+ const { mainfile, calc_id, upload_id, parser, tasks, current_task, tasks_status, errors } = calc
+ const color = tasks_status === 'FAILURE' ? 'error' : 'default'
const row = (
<TableRow key={index}>
<TableCell>
@@ -322,22 +372,20 @@ class Upload extends React.Component {
</TableCell>
<TableCell>
<Typography color={color}>
- {(status === 'SUCCESS' || status === 'FAILURE')
- ?
- <a className={classes.logLink} href="#logs" onClick={() => this.setState({archiveLogs: { uploadId: upload_id, calcId: calc_id }})}>
- {status.toLowerCase()}
- </a>
- : status.toLowerCase()
+ {(tasks_status === 'SUCCESS' || tasks_status === 'FAILURE')
+ ? <a className={classes.logLink} href="#logs" onClick={() => this.setState({archiveLogs: { uploadId: upload_id, calcId: calc_id }})}>
+ {tasks_status.toLowerCase()}
+ </a> : tasks_status.toLowerCase()
}
</Typography>
</TableCell>
<TableCell>
- <CalcLinks uploadId={upload_id} calcId={calc_id} disabled={status !== 'SUCCESS'} />
+ <CalcLinks uploadId={upload_id} calcId={calc_id} disabled={tasks_status !== 'SUCCESS'} />
</TableCell>
</TableRow>
)
- if (status === 'FAILURE') {
+ if (tasks_status === 'FAILURE') {
return (
<Tooltip key={calc_id} title={errors.map((error, index) => (<p key={`${calc_id}-${index}`}>{error}</p>))}>
{row}
@@ -355,7 +403,7 @@ class Upload extends React.Component {
{ id: 'mainfile', sort: true, label: 'mainfile' },
{ id: 'parser', sort: true, label: 'code' },
{ id: 'task', sort: false, label: 'task' },
- { id: 'status', sort: true, label: 'status' },
+ { id: 'tasks_status', sort: true, label: 'status' },
{ id: 'links', sort: false, label: 'links' }
]
@@ -434,7 +482,7 @@ class Upload extends React.Component {
<ExpansionPanel>
<ExpansionPanelSummary
expandIcon={<ExpandMoreIcon/>} classes={{root: classes.summary}}>
- {!(upload.completed || upload.waiting)
+ {(upload.tasks_running || upload.process_running)
? <div className={classes.progress}>
<CircularProgress size={32}/>
</div>
diff --git a/gui/src/components/Uploads.js b/gui/src/components/Uploads.js
index bc44b2733ff5f89be6cfbc70283c64ea412f9448..b87cbdebfc8f3e5037326dcac9aa17b38194a5fd 100644
--- a/gui/src/components/Uploads.js
+++ b/gui/src/components/Uploads.js
@@ -119,6 +119,17 @@ class Uploads extends React.Component {
})
}
+ sortedUploads() {
+ return this.state.uploads.concat()
+ .sort((a, b) => (a.gui_upload_id === b.gui_upload_id) ? 0 : ((a.gui_upload_id < b.gui_upload_id) ? -1 : 1))
+ }
+
+ handleDoesNotExist(nonExistingUupload) {
+ this.setState({
+ uploads: this.state.uploads.filter(upload => upload !== nonExistingUupload)
+ })
+ }
+
onDrop(files) {
files.forEach(file => {
const upload = api.createUpload(file.name)
@@ -139,7 +150,7 @@ class Uploads extends React.Component {
onSelectionAllChanged(checked) {
if (checked) {
- this.setState({selectedUploads: [...this.state.uploads.filter(upload => upload.completed)]})
+ this.setState({selectedUploads: [...this.state.uploads.filter(upload => !upload.tasks_running)]})
} else {
this.setState({selectedUploads: []})
}
@@ -181,9 +192,10 @@ class Uploads extends React.Component {
</FormGroup>
</div>
<div className={classes.uploads}>
- {this.state.uploads.map((upload) => (
- <Upload key={upload.upload_id} upload={upload}
+ {this.sortedUploads().map(upload => (
+ <Upload key={upload.gui_upload_id} upload={upload}
checked={selectedUploads.indexOf(upload) !== -1}
+ onDoesNotExist={() => this.handleDoesNotExist(upload)}
onCheckboxChanged={checked => this.onSelectionChanged(upload, checked)}/>
))}
</div>
diff --git a/gui/yarn.lock b/gui/yarn.lock
index a9a7488e76af6fafc8ed785b2993ba874e196770..093f3836afa8d753f3821f1fa95db8f00f60a296 100644
--- a/gui/yarn.lock
+++ b/gui/yarn.lock
@@ -2660,6 +2660,13 @@ eslint-module-utils@^2.1.1, eslint-module-utils@^2.2.0:
debug "^2.6.8"
pkg-dir "^1.0.0"
+eslint-plugin-es@^1.3.1:
+ version "1.4.0"
+ resolved "https://registry.yarnpkg.com/eslint-plugin-es/-/eslint-plugin-es-1.4.0.tgz#475f65bb20c993fc10e8c8fe77d1d60068072da6"
+ dependencies:
+ eslint-utils "^1.3.0"
+ regexpp "^2.0.1"
+
eslint-plugin-flowtype@2.39.1:
version "2.39.1"
resolved "https://registry.yarnpkg.com/eslint-plugin-flowtype/-/eslint-plugin-flowtype-2.39.1.tgz#b5624622a0388bcd969f4351131232dcb9649cd5"
@@ -2708,6 +2715,17 @@ eslint-plugin-jsx-a11y@5.1.1:
emoji-regex "^6.1.0"
jsx-ast-utils "^1.4.0"
+eslint-plugin-node@^8.0.1:
+ version "8.0.1"
+ resolved "https://registry.yarnpkg.com/eslint-plugin-node/-/eslint-plugin-node-8.0.1.tgz#55ae3560022863d141fa7a11799532340a685964"
+ dependencies:
+ eslint-plugin-es "^1.3.1"
+ eslint-utils "^1.3.1"
+ ignore "^5.0.2"
+ minimatch "^3.0.4"
+ resolve "^1.8.1"
+ semver "^5.5.0"
+
eslint-plugin-promise@^3.7.0:
version "3.8.0"
resolved "https://registry.yarnpkg.com/eslint-plugin-promise/-/eslint-plugin-promise-3.8.0.tgz#65ebf27a845e3c1e9d6f6a5622ddd3801694b621"
@@ -2749,6 +2767,10 @@ eslint-scope@^3.7.1:
esrecurse "^4.1.0"
estraverse "^4.1.1"
+eslint-utils@^1.3.0, eslint-utils@^1.3.1:
+ version "1.3.1"
+ resolved "https://registry.yarnpkg.com/eslint-utils/-/eslint-utils-1.3.1.tgz#9a851ba89ee7c460346f97cf8939c7298827e512"
+
eslint-visitor-keys@^1.0.0:
version "1.0.0"
resolved "https://registry.yarnpkg.com/eslint-visitor-keys/-/eslint-visitor-keys-1.0.0.tgz#3f3180fb2e291017716acb4c9d6d5b5c34a6a81d"
@@ -3823,6 +3845,10 @@ ignore@^3.3.3:
version "3.3.10"
resolved "https://registry.yarnpkg.com/ignore/-/ignore-3.3.10.tgz#0a97fb876986e8081c631160f8f9f389157f0043"
+ignore@^5.0.2:
+ version "5.0.4"
+ resolved "https://registry.yarnpkg.com/ignore/-/ignore-5.0.4.tgz#33168af4a21e99b00c5d41cbadb6a6cb49903a45"
+
import-lazy@^2.1.0:
version "2.1.0"
resolved "https://registry.yarnpkg.com/import-lazy/-/import-lazy-2.1.0.tgz#05698e3d45c88e8d7e9d92cb0584e77f096f3e43"
@@ -5654,7 +5680,7 @@ path-key@^2.0.0:
version "2.0.1"
resolved "https://registry.yarnpkg.com/path-key/-/path-key-2.0.1.tgz#411cadb574c5a140d3a4b1910d40d80cc9f40b40"
-path-parse@^1.0.5:
+path-parse@^1.0.5, path-parse@^1.0.6:
version "1.0.6"
resolved "https://registry.yarnpkg.com/path-parse/-/path-parse-1.0.6.tgz#d62dbb5679405d72c4737ec58600e9ddcf06d24c"
@@ -6570,6 +6596,10 @@ regexpp@^1.0.1:
version "1.1.0"
resolved "https://registry.yarnpkg.com/regexpp/-/regexpp-1.1.0.tgz#0e3516dd0b7904f413d2d4193dce4618c3a689ab"
+regexpp@^2.0.1:
+ version "2.0.1"
+ resolved "https://registry.yarnpkg.com/regexpp/-/regexpp-2.0.1.tgz#8d19d31cf632482b589049f8281f93dbcba4d07f"
+
regexpu-core@^1.0.0:
version "1.0.0"
resolved "https://registry.yarnpkg.com/regexpu-core/-/regexpu-core-1.0.0.tgz#86a763f58ee4d7c2f6b102e4764050de7ed90c6b"
@@ -6734,6 +6764,12 @@ resolve@^1.3.2, resolve@^1.5.0, resolve@^1.6.0:
dependencies:
path-parse "^1.0.5"
+resolve@^1.8.1:
+ version "1.9.0"
+ resolved "https://registry.yarnpkg.com/resolve/-/resolve-1.9.0.tgz#a14c6fdfa8f92a7df1d996cb7105fa744658ea06"
+ dependencies:
+ path-parse "^1.0.6"
+
restore-cursor@^2.0.0:
version "2.0.0"
resolved "https://registry.yarnpkg.com/restore-cursor/-/restore-cursor-2.0.0.tgz#9f7ee287f82fd326d4fd162923d62129eee0dfaf"
@@ -6848,6 +6884,10 @@ semver-diff@^2.0.0:
version "5.5.1"
resolved "https://registry.yarnpkg.com/semver/-/semver-5.5.1.tgz#7dfdd8814bdb7cabc7be0fb1d734cfb66c940477"
+semver@^5.5.0:
+ version "5.6.0"
+ resolved "https://registry.yarnpkg.com/semver/-/semver-5.6.0.tgz#7e74256fbaa49c75aa7c7a205cc22799cac80004"
+
send@0.16.2:
version "0.16.2"
resolved "https://registry.yarnpkg.com/send/-/send-0.16.2.tgz#6ecca1e0f8c156d141597559848df64730a6bbc1"
diff --git a/nomad/api/archive.py b/nomad/api/archive.py
index d8ed55af863e9d5e2fd5d80979d4d092ccaa86ef..75af737f66c41da3fe1e0a306d7b6c4b09614503 100644
--- a/nomad/api/archive.py
+++ b/nomad/api/archive.py
@@ -102,7 +102,7 @@ class ArchiveCalcResource(Resource):
@ns.route('/metainfo/<string:metainfo_path>')
-@api.doc(params=dict(metainfo_path='A path or metainfo definition file name.'))
+@api.doc(params=dict(nomad_metainfo_path='A path or metainfo definition file name.'))
class MetainfoResource(Resource):
@api.doc('get_metainfo')
@api.response(404, 'The metainfo does not exist')
@@ -113,13 +113,13 @@ class MetainfoResource(Resource):
"""
try:
file_dir = os.path.dirname(os.path.abspath(nomad_meta_info.__file__))
- meta_info_path = os.path.normpath(os.path.join(file_dir, metainfo_path.strip()))
+ metainfo_file = os.path.normpath(os.path.join(file_dir, metainfo_path.strip()))
rv = send_file(
- meta_info_path,
+ metainfo_file,
mimetype='application/json',
as_attachment=True,
- attachment_filename=os.path.basename(metainfo_path))
+ attachment_filename=os.path.basename(metainfo_file))
return rv
except FileNotFoundError:
diff --git a/nomad/api/upload.py b/nomad/api/upload.py
index 15861751f7e6efa83c214a9d076345bad6d8f0b1..3ae085d06dceb16659c0c70daf78da8d8aa44d54 100644
--- a/nomad/api/upload.py
+++ b/nomad/api/upload.py
@@ -41,7 +41,7 @@ ns = api.namespace(
proc_model = api.model('Processing', {
'tasks': fields.List(fields.String),
'current_task': fields.String,
- 'tasks_completed': fields.Boolean,
+ 'tasks_running': fields.Boolean,
'tasks_status': fields.String,
'errors': fields.List(fields.String),
'warnings': fields.List(fields.String),
@@ -297,7 +297,7 @@ class UploadResource(Resource):
if upload.user_id != str(g.user.user_id) and not g.user.is_admin:
abort(401, message='Upload with id %s does not belong to you.' % upload_id)
- if not upload.tasks_completed:
+ if upload.tasks_running:
abort(400, message='The upload is not processed yet')
try:
@@ -350,7 +350,7 @@ class UploadResource(Resource):
break
if operation == 'commit':
- if not upload.tasks_completed:
+ if upload.tasks_running:
abort(400, message='The upload is not processed yet')
try:
upload.metadata = metadata
diff --git a/nomad/client.py b/nomad/client.py
index 5dce848741ca6188e0be4cde045beb1c62f6dee7..f8c29d0c6f423b98f1d434a4dc36d04771066f2a 100644
--- a/nomad/client.py
+++ b/nomad/client.py
@@ -327,12 +327,13 @@ def worker():
@run.command(help='Run the nomad development api.')
-def api():
+@click.option('--debug', help='Does run flask in debug.', is_flag=True)
+def api(debug: bool):
config.service = 'nomad_api'
from nomad import infrastructure
from nomad.api.__main__ import run_dev_server
infrastructure.setup()
- run_dev_server(debug=True, port=8000)
+ run_dev_server(debug=debug, port=8000)
@cli.command(help='Runs tests and linting. Useful before commit code.')
diff --git a/nomad/processing/base.py b/nomad/processing/base.py
index 311a695adca0974dce4eed4e11e0acc5ab79c511..21b4f109755e832f0796564e0c5ad5761fb3725f 100644
--- a/nomad/processing/base.py
+++ b/nomad/processing/base.py
@@ -53,7 +53,7 @@ RUNNING = 'RUNNING'
FAILURE = 'FAILURE'
SUCCESS = 'SUCCESS'
-PROCESS_CALLED = 'CALLD'
+PROCESS_CALLED = 'CALLED'
PROCESS_RUNNING = 'RUNNING'
PROCESS_COMPLETED = 'COMPLETED'
@@ -130,9 +130,9 @@ class Proc(Document, metaclass=ProcMetaclass):
process_status = StringField(default=None)
@property
- def tasks_completed(self) -> bool:
+ def tasks_running(self) -> bool:
""" Returns True of the process has failed or succeeded. """
- return self.tasks_status in [SUCCESS, FAILURE]
+ return self.tasks_status not in [SUCCESS, FAILURE]
@property
def process_running(self) -> bool:
@@ -194,7 +194,7 @@ class Proc(Document, metaclass=ProcMetaclass):
def fail(self, *errors, log_level=logging.ERROR, **kwargs):
""" Allows to fail the process. Takes strings or exceptions as args. """
- assert not self.tasks_completed, 'Cannot fail a completed process.'
+ assert self.tasks_running, 'Cannot fail a completed process.'
failed_with_exception = False
@@ -219,7 +219,7 @@ class Proc(Document, metaclass=ProcMetaclass):
def warning(self, *warnings, log_level=logging.WARNING, **kwargs):
""" Allows to save warnings. Takes strings or exceptions as args. """
- assert not self.tasks_completed
+ assert self.tasks_running
logger = self.get_logger(**kwargs)
@@ -266,7 +266,7 @@ class Proc(Document, metaclass=ProcMetaclass):
Reloads the process constantly until it sees a completed process. Should be
used with care as it can block indefinitely. Just intended for testing purposes.
"""
- while not self.tasks_completed:
+ while self.tasks_running:
time.sleep(interval)
self.reload()
@@ -397,7 +397,7 @@ def task(func):
except Exception as e:
self.fail(e)
- if self.__class__.tasks[-1] == self.current_task and not self.tasks_completed:
+ if self.__class__.tasks[-1] == self.current_task and self.tasks_running:
self._complete()
setattr(wrapper, '__task_name', func.__name__)
diff --git a/nomad/processing/data.py b/nomad/processing/data.py
index 98f7b651944df094e38bbabffad8ba40f82d0218..a3c2998fce58fcfa61fcebc8e7e992ac24ec7b0d 100644
--- a/nomad/processing/data.py
+++ b/nomad/processing/data.py
@@ -346,6 +346,8 @@ class Upload(Chord, datamodel.Upload):
with utils.timer(
logger, 'staged upload deleted', step='delete',
upload_size=self.upload_files.size):
+ import time
+ time.sleep(10)
self.upload_files.delete()
self.delete()
diff --git a/tests/processing/test_data.py b/tests/processing/test_data.py
index 224b3363241ebf515762a24927d752e62b06637b..85c4fcecdc5461b56cd40593f0043a1b7b474f2f 100644
--- a/tests/processing/test_data.py
+++ b/tests/processing/test_data.py
@@ -82,7 +82,7 @@ def processed_upload(uploaded_id, test_user, worker, no_warn) -> Upload:
def assert_processing(upload: Upload):
- assert upload.tasks_completed
+ assert not upload.tasks_running
assert upload.current_task == 'cleanup'
assert upload.upload_id is not None
assert len(upload.errors) == 0
@@ -127,7 +127,7 @@ def test_processing_with_warning(uploaded_id_with_warning, worker, test_user):
def test_process_non_existing(worker, test_user, with_error):
upload = run_processing('__does_not_exist', test_user)
- assert upload.tasks_completed
+ assert not upload.tasks_running
assert upload.current_task == 'extracting'
assert upload.tasks_status == 'FAILURE'
assert len(upload.errors) > 0
@@ -154,7 +154,7 @@ def test_task_failure(monkeypatch, uploaded_id, worker, task, test_user, with_er
# run the test
upload = run_processing(uploaded_id, test_user)
- assert upload.tasks_completed
+ assert not upload.tasks_running
if task != 'parsing':
assert upload.tasks_status == 'FAILURE'
diff --git a/tests/test_api.py b/tests/test_api.py
index 80ccb0508bac58ca90c70ab700e1908a52470f59..e81fde6de2fefce2bc86efc7b5d2cc62f43d8e83 100644
--- a/tests/test_api.py
+++ b/tests/test_api.py
@@ -188,7 +188,7 @@ class TestUploads:
assert rv.status_code == 200
upload = self.assert_upload(rv.data)
assert 'upload_time' in upload
- if upload['tasks_completed']:
+ if not upload['tasks_running']:
break
assert len(upload['tasks']) == 4