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improve validator page
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@Remi-Gau
Remi-Gau committed May 10, 2024
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2 changes: 1 addition & 1 deletion docs/starter_kit
Submodule starter_kit updated 1 files
+1 −186 src/validator.md
108 changes: 54 additions & 54 deletions docs/tools/validator.md
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Expand Up @@ -96,83 +96,83 @@ user@host:~/bids-examples$ bids-validator sub001

### Types of Feedback

#### Error
!!! failure "Error"

As is the case w/ the browser or any version of the validator follow
the `[ERR]` messages and correct until bids-validator returns 0 errors after running.
As is the case w/ the browser or any version of the validator follow
the `[ERR]` messages and correct until bids-validator returns 0 errors after running.

```bash
user@host:~/bids-examples$ bids-validator sub001
```bash
user@host:~/bids-examples$ bids-validator sub001

bids-validator@1.7.1
bids-validator@1.7.1

1: [ERR] Invalid JSON file. The file is not formatted according the schema. (code: 55 - JSON_SCHEMA_VALIDATION_ERROR)
./sub-01/ses-baseline/pet/sub-01_ses-baseline_pet.json
Evidence: should have property InjectedRadioactivityUnits when property InjectedRadioactivity is present
./sub-01/ses-baseline/pet/sub-01_ses-baseline_pet.json
Evidence: should have required property 'InjectedMassUnits'
...
...
... and 3 more files having this issue (Use --verbose to see them all).
1: [ERR] Invalid JSON file. The file is not formatted according the schema. (code: 55 - JSON_SCHEMA_VALIDATION_ERROR)
./sub-01/ses-baseline/pet/sub-01_ses-baseline_pet.json
Evidence: should have property InjectedRadioactivityUnits when property InjectedRadioactivity is present
./sub-01/ses-baseline/pet/sub-01_ses-baseline_pet.json
Evidence: should have required property 'InjectedMassUnits'
...
...
... and 3 more files having this issue (Use --verbose to see them all).

Please visit https://neurostars.org/search?q=JSON_SCHEMA_VALIDATION_ERROR for existing conversations about this issue.
Please visit https://neurostars.org/search?q=JSON_SCHEMA_VALIDATION_ERROR for existing conversations about this issue.


Summary: Available Tasks: Available Modalities:
14 Files, 5.72MB T1w
1 - Subject pet
2 - Sessions events
Summary: Available Tasks: Available Modalities:
14 Files, 5.72MB T1w
1 - Subject pet
2 - Sessions events


If you have any questions, please post on https://neurostars.org/tags/bids.
```
If you have any questions, please post on https://neurostars.org/tags/bids.
```

#### Warning
!!! warning

As stated with the browser version above, one may elect to ignore warnings,
but the information provided via the validator should help to pinpoint
where and how to resolve some of these warnings.
When in doubt consult the [BIDS Spec](https://bids-specification.readthedocs.io/en/latest/)
As stated with the browser version above, one may elect to ignore warnings,
but the information provided via the validator should help to pinpoint
where and how to resolve some of these warnings.
When in doubt consult the [BIDS Spec](https://bids-specification.readthedocs.io/en/latest/)

```bash
user@host:~/bids-examples$ bids-validator sub001/
```bash
user@host:~/bids-examples$ bids-validator sub001/

bids-validator@1.7.1
bids-validator@1.7.1

1: [WARN] Tabular file contains custom columns not described in a data dictionary (code: 82 - CUSTOM_COLUMN_WITHOUT_DESCRIPTION)
./sub-01/func/sub-01_task-balloonanalogrisktask_run-01_events.tsv
...
...
... and 38 more files having this issue (Use --verbose to see them all).
1: [WARN] Tabular file contains custom columns not described in a data dictionary (code: 82 - CUSTOM_COLUMN_WITHOUT_DESCRIPTION)
./sub-01/func/sub-01_task-balloonanalogrisktask_run-01_events.tsv
...
...
... and 38 more files having this issue (Use --verbose to see them all).

Please visit https://neurostars.org/search?q=CUSTOM_COLUMN_WITHOUT_DESCRIPTION for existing conversations about this issue.
Please visit https://neurostars.org/search?q=CUSTOM_COLUMN_WITHOUT_DESCRIPTION for existing conversations about this issue.


Summary: Available Tasks: Available Modalities:
134 Files, 411.53KB balloon analog risk task T1w
16 - Subjects inplaneT2
1 - Session bold
events
Summary: Available Tasks: Available Modalities:
134 Files, 411.53KB balloon analog risk task T1w
16 - Subjects inplaneT2
1 - Session bold
events


If you have any questions, please post on https://neurostars.org/tags/bids.
```
If you have any questions, please post on https://neurostars.org/tags/bids.
```

#### Success
!!! success "Success :rocket:"

Pass go and collect 200 dollars, the data set in question passes validation.
Pass go and collect 200 dollars, the data set in question passes validation.

```bash
user@host:~/bids-examples$ bids-validator sub001
bids-validator@1.7.1
```bash
user@host:~/bids-examples$ bids-validator sub001
bids-validator@1.7.1

This dataset appears to be BIDS compatible.
This dataset appears to be BIDS compatible.

Summary: Available Tasks: Available Modalities:
12 Files, 218.75KB T1w
1 - Subject pet
1 - Session blood
Summary: Available Tasks: Available Modalities:
12 Files, 218.75KB T1w
1 - Subject pet
1 - Session blood


If you have any questions, please post on https://neurostars.org/tags/bids
```
If you have any questions, please post on https://neurostars.org/tags/bids
```

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