Participant_id_column

I’m using

openneuro upload

I get this error:

bids-validator@1.9.3
bids-specification@undefined
1: [ERR] Participants and phenotype .tsv files must have a ‘participant_id’ column. (code: 48 - PARTICIPANT_ID_COLUMN)
./participants.tsv
@ line: 1
Evidence: Column headers: “participant_id”, “age”, “sex”, “first_condition”, “Donor-id”

participants.txt (1.2 KB)

Looks like there are quotes around all of the values in the TSV. If you remove those, it should work.

Thank you Chris,
The quotes is only because I save it as .txt to upload it here
I don’t have it in my original .tsv file (btw I’m using ubuntu)

If you open participants.tsv in a text editor, what do you see?

You were write…
Now I don’t have Err (only warnings)

But now:

Blockquote
bids-validator@1.9.3
bids-specification@undefined
Summary: Available Tasks: Available Modalities:
531 Files, 24.58GB PSAP MRI
33 - Subjects TODO: full task name for PSAP
2 - Sessions

Blockquote
(node:561587) ExperimentalWarning: The Fetch API is an experimental feature. This feature could change at any time
(Use node --trace-warnings ... to show where the warning was created)
“ds004273” created
=======================================================================
863 files to be uploaded with a total size of 24.6 GB
? Begin upload? Yes
=======================================================================
Starting a new upload (288086bc) to dataset: ‘ds004273’
ds004273 [----------------------------------------] 1% | ETA: 48s | 9/863Error [ERR_STREAM_PREMATURE_CLOSE]: Premature close
at new NodeError (node:internal/errors:393:5)
at ClientHttp2Stream.onclose (node:internal/streams/end-of-stream:147:30)
at ClientHttp2Stream.elasticAPMCallbackWrapper (/usr/local/lib/node_modules/@openneuro/cli/node_modules/elastic-apm-node/lib/instrumentation/index.js:328:27)
at ClientHttp2Stream.emit (node:events:525:35)
at ClientHttp2Stream.emit (node:domain:489:12)
at closeStream (node:internal/http2/core:1919:14)
at Http2Stream.onStreamClose (node:internal/http2/core:544:5)
at Http2Stream.callbackTrampoline (node:internal/async_hooks:130:17) {
code: ‘ERR_STREAM_PREMATURE_CLOSE’
}
Warning: “.heudiconv/10/ses-001/info/heuristic.py” read zero bytes - check that this file is readable and try again
Error [ERR_STREAM_PREMATURE_CLOSE]: Premature close
at new NodeError (node:internal/errors:393:5)
at ClientHttp2Stream.onclose (node:internal/streams/end-of-stream:147:30)
at ClientHttp2Stream.elasticAPMCallbackWrapper (/usr/local/lib/node_modules/@openneuro/cli/node_modules/elastic-apm-node/lib/instrumentation/index.js:328:27)
at ClientHttp2Stream.emit (node:events:525:35)
at ClientHttp2Stream.emit (node:domain:489:12)
at closeStream (node:internal/http2/core:1919:14)
at Http2Stream.onStreamClose (node:internal/http2/core:544:5)
at Http2Stream.callbackTrampoline (node:internal/async_hooks:130:17) {
code: ‘ERR_STREAM_PREMATURE_CLOSE’
}
Warning: “.heudiconv/10/ses-001/info/10_ses-001.edit.txt” read zero bytes - check that this file is readable and try again
Error [ERR_STREAM_PREMATURE_CLOSE]: Premature close
at new NodeError (node:internal/errors:393:5)
at ClientHttp2Stream.onclose (node:internal/streams/end-of-stream:147:30)
at ClientHttp2Stream.elasticAPMCallbackWrapper (/usr/local/lib/node_modules/@openneuro/cli/node_modules/elastic-apm-node/lib/instrumentation/index.js:328:27)
at ClientHttp2Stream.emit (node:events:525:35)
at ClientHttp2Stream.emit (node:domain:489:12)
at closeStream (node:internal/http2/core:1919:14)
at Http2Stream.onStreamClose (node:internal/http2/core:544:5)
at Http2Stream.callbackTrampoline (node:internal/async_hooks:130:17) {
code: ‘ERR_STREAM_PREMATURE_CLOSE’
}
Warning: “.heudiconv/10/ses-001/info/dicominfo_ses-001.tsv” read zero bytes - check that this file is readable and try again
Error [ERR_STREAM_PREMATURE_CLOSE]: Premature close
at new NodeError (node:internal/errors:393:5)
at ClientHttp2Stream.onclose (node:internal/streams/end-of-stream:147:30)
at ClientHttp2Stream.elasticAPMCallbackWrapper (/usr/local/lib/node_modules/@openneuro/cli/node_modules/elastic-apm-node/lib/instrumentation/index.js:328:27)
at ClientHttp2Stream.emit (node:events:525:35)
at ClientHttp2Stream.emit (node:domain:489:12)
at closeStream (node:internal/http2/core:1919:14)
at Http2Stream.onStreamClose (node:internal/http2/core:544:5)
at Http2Stream.callbackTrampoline (node:internal/async_hooks:130:17) {
code: ‘ERR_STREAM_PREMATURE_CLOSE’
}
Warning: “.heudiconv/1/ses-002/info/filegroup_ses-002.json” read zero bytes - check that this file is readable and try again
Error [ERR_STREAM_PREMATURE_CLOSE]: Premature close
at new NodeError (node:internal/errors:393:5)
at ClientHttp2Stream.onclose (node:internal/streams/end-of-stream:147:30)
at ClientHttp2Stream.elasticAPMCallbackWrapper (/usr/local/lib/node_modules/@openneuro/cli/node_modules/elastic-apm-node/lib/instrumentation/index.js:328:27)
at ClientHttp2Stream.emit (node:events:525:35)
at ClientHttp2Stream.emit (node:domain:489:12)
at closeStream (node:internal/http2/core:1919:14)
at Http2Stream.onStreamClose (node:internal/http2/core:544:5)
at Http2Stream.callbackTrampoline (node:internal/async_hooks:130:17) {
code: ‘ERR_STREAM_PREMATURE_CLOSE’
}
Warning: “.heudiconv/1/ses-002/info/1_ses-002.edit.txt” read zero bytes - check that this file is readable and try again
Error [ERR_STREAM_PREMATURE_CLOSE]: Premature close
at new NodeError (node:internal/errors:393:5)
at ClientHttp2Stream.onclose (node:internal/streams/end-of-stream:147:30)
at ClientHttp2Stream.elasticAPMCallbackWrapper (/usr/local/lib/node_modules/@openneuro/cli/node_modules/elastic-apm-node/lib/instrumentation/index.js:328:27)
at ClientHttp2Stream.emit (node:events:525:35)
at ClientHttp2Stream.emit (node:domain:489:12)
at closeStream (node:internal/http2/core:1919:14)
at Http2Stream.onStreamClose (node:internal/http2/core:544:5)
at Http2Stream.callbackTrampoline (node:internal/async_hooks:130:17) {
code: ‘ERR_STREAM_PREMATURE_CLOSE’
}
Warning: “.heudiconv/1/ses-001/info/heuristic.py” read zero bytes - check that this file is readable and try again
Error [ERR_STREAM_PREMATURE_CLOSE]: Premature close
at new NodeError (node:internal/errors:393:5)
at ClientHttp2Stream.onclose (node:internal/streams/end-of-stream:147:30)
at ClientHttp2Stream.elasticAPMCallbackWrapper (/usr/local/lib/node_modules/@openneuro/cli/node_modules/elastic-apm-node/lib/instrumentation/index.js:328:27)
at ClientHttp2Stream.emit (node:events:525:35)
at ClientHttp2Stream.emit (node:domain:489:12)
at closeStream (node:internal/http2/core:1919:14)
at Http2Stream.onStreamClose (node:internal/http2/core:544:5)
at Http2Stream.callbackTrampoline (node:internal/async_hooks:130:17) {
code: ‘ERR_STREAM_PREMATURE_CLOSE’
}
Warning: “.heudiconv/1/ses-001/info/filegroup_ses-001.json” read zero bytes - check that this file is readable and try again
Error [ERR_STREAM_PREMATURE_CLOSE]: Premature close
at new NodeError (node:internal/errors:393:5)
at ClientHttp2Stream.onclose (node:internal/streams/end-of-stream:147:30)
at ClientHttp2Stream.elasticAPMCallbackWrapper (/usr/local/lib/node_modules/@openneuro/cli/node_modules/elastic-apm-node/lib/instrumentation/index.js:328:27)
at ClientHttp2Stream.emit (node:events:525:35)
at ClientHttp2Stream.emit (node:domain:489:12)
at closeStream (node:internal/http2/core:1919:14)
at Http2Stream.onStreamClose (node:internal/http2/core:544:5)
at Http2Stream.callbackTrampoline (node:internal/async_hooks:130:17) {
code: ‘ERR_STREAM_PREMATURE_CLOSE’
}
Warning: “.heudiconv/1/ses-001/info/dicominfo_ses-001.tsv” read zero bytes - check that this file is readable and try again
Error [ERR_STREAM_PREMATURE_CLOSE]: Premature close
at new NodeError (node:internal/errors:393:5)
at ClientHttp2Stream.onclose (node:internal/streams/end-of-stream:147:30)
at ClientHttp2Stream.elasticAPMCallbackWrapper (/usr/local/lib/node_modules/@openneuro/cli/node_modules/elastic-apm-node/lib/instrumentation/index.js:328:27)
at ClientHttp2Stream.emit (node:events:525:35)
at ClientHttp2Stream.emit (node:domain:489:12)
at closeStream (node:internal/http2/core:1919:14)
at Http2Stream.onStreamClose (node:internal/http2/core:544:5)
at Http2Stream.callbackTrampoline (node:internal/async_hooks:130:17) {
code: ‘ERR_STREAM_PREMATURE_CLOSE’
}
Warning: “.heudiconv/1/ses-001/info/1_ses-001.auto.txt” read zero bytes - check that this file is readable and try again