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[BUG] broken internal links #2003

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Remi-Gau opened this issue Dec 12, 2024 · 8 comments · Fixed by #2004
Closed

[BUG] broken internal links #2003

Remi-Gau opened this issue Dec 12, 2024 · 8 comments · Fixed by #2004

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@Remi-Gau
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https://bids-specification.readthedocs.io/en/latest/glossary.html#run-entities

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I believe [ses-<label>][./appendices/entities.md#ses) should actually be a link
@Remi-Gau
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possibly related but we seem to have bunch of "dead" internal links:

from a build on the latest PR

https://app.readthedocs.org/projects/bids-specification/builds/26548792/?utm_source=bids-specification&utm_content=notification

INFO    -  Doc file 'modality-agnostic-files.md' contains a link './glossary.md#objects.subobject.Name', but the doc 'glossary.md' does not contain an anchor '#objects.subobject.Name'.
INFO    -  Doc file 'modality-agnostic-files.md' contains a link './glossary.md#objects.subobject.Version', but the doc 'glossary.md' does not contain an anchor '#objects.subobject.Version'.
INFO    -  Doc file 'modality-agnostic-files.md' contains a link './glossary.md#objects.subobject.Description', but the doc 'glossary.md' does not contain an anchor '#objects.subobject.Description'.
INFO    -  Doc file 'modality-agnostic-files.md' contains a link './glossary.md#objects.subobject.CodeURL', but the doc 'glossary.md' does not contain an anchor '#objects.subobject.CodeURL'.
INFO    -  Doc file 'modality-agnostic-files.md' contains a link './glossary.md#objects.subobject.Container', but the doc 'glossary.md' does not contain an anchor '#objects.subobject.Container'.
INFO    -  Doc file 'appendices/entity-table.md' contains a link '../glossary.md#objects.suffixes.PLI', but the doc 'glossary.md' does not contain an anchor '#objects.suffixes.PLI'.
INFO    -  Doc file 'appendices/entity-table.md' contains a link '../glossary.md#objects.suffixes.2PE', but the doc 'glossary.md' does not contain an anchor '#objects.suffixes.2PE'.
INFO    -  Doc file 'derivatives/imaging.md' contains a link '../appendices/entities.md#segmentation', but the doc 'appendices/entities.md' does not contain an anchor '#segmentation'.
INFO    -  Doc file 'modality-specific-files/behavioral-experiments.md' contains a link '../common-principles.md#tabular-data', but the doc 'common-principles.md' does not contain an anchor '#tabular-data'.
INFO    -  Doc file 'modality-specific-files/electroencephalography.md' contains a link '#example-electrodestsv', but there is no such anchor on this page.
INFO    -  Doc file 'modality-specific-files/electroencephalography.md' contains a link '#example-channelstsv', but there is no such anchor on this page.
INFO    -  Doc file 'modality-specific-files/genetic-descriptor.md' contains a link '../glossary.md#objects.subobject.Dataset', but the doc 'glossary.md' does not contain an anchor '#objects.subobject.Dataset'.
INFO    -  Doc file 'modality-specific-files/genetic-descriptor.md' contains a link '../glossary.md#objects.subobject.Database', but the doc 'glossary.md' does not contain an anchor '#objects.subobject.Database'.
INFO    -  Doc file 'modality-specific-files/genetic-descriptor.md' contains a link '../glossary.md#objects.subobject.Descriptors', but the doc 'glossary.md' does not contain an anchor '#objects.subobject.Descriptors'.
INFO    -  Doc file 'modality-specific-files/magnetic-resonance-imaging-data.md' contains a link '#in-plane-spatial-encoding', but there is no such anchor on this page.
INFO    -  Doc file 'modality-specific-files/magnetic-resonance-imaging-data.md' contains a link '../common-principles.md#keyvalue-files-dictionaries', but the doc 'common-principles.md' does not contain an anchor '#keyvalue-files-dictionaries'.
INFO    -  Doc file 'modality-specific-files/magnetic-resonance-imaging-data.md' contains a link '../glossary.md#objects.subobject.CodeValue', but the doc 'glossary.md' does not contain an anchor '#objects.subobject.CodeValue'.
INFO    -  Doc file 'modality-specific-files/magnetic-resonance-imaging-data.md' contains a link '../glossary.md#objects.subobject.CodeMeaning', but the doc 'glossary.md' does not contain an anchor '#objects.subobject.CodeMeaning'.
INFO    -  Doc file 'modality-specific-files/magnetic-resonance-imaging-data.md' contains a link '../glossary.md#objects.subobject.CodingSchemeDesignator', but the doc 'glossary.md' does not contain an anchor '#objects.subobject.CodingSchemeDesignator'.
INFO    -  Doc file 'modality-specific-files/magnetic-resonance-imaging-data.md' contains a link '../glossary.md#objects.subobject.CodingSchemeVersion', but the doc 'glossary.md' does not contain an anchor '#objects.subobject.CodingSchemeVersion'.
INFO    -  Doc file 'modality-specific-files/magnetoencephalography.md' contains a link '#recording-eeg-simultaneously-with-meg', but there is no such anchor on this page.
INFO    -  Doc file 'modality-specific-files/microscopy.md' contains a link '../glossary.md#objects.suffixes.PLI', but the doc 'glossary.md' does not contain an anchor '#objects.suffixes.PLI'.
INFO    -  Doc file 'modality-specific-files/positron-emission-tomography.md' contains a link '../glossary.md#objects.subobject.CodeValue', but the doc 'glossary.md' does not contain an anchor '#objects.subobject.CodeValue'.
INFO    -  Doc file 'modality-specific-files/positron-emission-tomography.md' contains a link '../glossary.md#objects.subobject.CodeMeaning', but the doc 'glossary.md' does not contain an anchor '#objects.subobject.CodeMeaning'.
INFO    -  Doc file 'modality-specific-files/positron-emission-tomography.md' contains a link '../glossary.md#objects.subobject.CodingSchemeDesignator', but the doc 'glossary.md' does not contain an anchor '#objects.subobject.CodingSchemeDesignator'.
INFO    -  Doc file 'modality-specific-files/positron-emission-tomography.md' contains a link '../glossary.md#objects.subobject.CodingSchemeVersion', but the doc 'glossary.md' does not contain an anchor '#objects.subobject.CodingSchemeVersion'.
INFO    -  Doc file 'modality-specific-files/task-events.md' contains a link '../glossary.md#objects.subobject.OperatingSystem', but the doc 'glossary.md' does not contain an anchor '#objects.subobject.OperatingSystem'.
INFO    -  Doc file 'modality-specific-files/task-events.md' contains a link '../glossary.md#objects.subobject.ScreenDistance', but the doc 'glossary.md' does not contain an anchor '#objects.subobject.ScreenDistance'.
INFO    -  Doc file 'modality-specific-files/task-events.md' contains a link '../glossary.md#objects.subobject.ScreenRefreshRate', but the doc 'glossary.md' does not contain an anchor '#objects.subobject.ScreenRefreshRate'.
INFO    -  Doc file 'modality-specific-files/task-events.md' contains a link '../glossary.md#objects.subobject.ScreenResolution', but the doc 'glossary.md' does not contain an anchor '#objects.subobject.ScreenResolution'.
INFO    -  Doc file 'modality-specific-files/task-events.md' contains a link '../glossary.md#objects.subobject.ScreenSize', but the doc 'glossary.md' does not contain an anchor '#objects.subobject.ScreenSize'.
INFO    -  Doc file 'modality-specific-files/task-events.md' contains a link '../glossary.md#objects.subobject.SoftwareName', but the doc 'glossary.md' does not contain an anchor '#objects.subobject.SoftwareName'.
INFO    -  Doc file 'modality-specific-files/task-events.md' contains a link '../glossary.md#objects.subobject.SoftwareRRID', but the doc 'glossary.md' does not contain an anchor '#objects.subobject.SoftwareRRID'.
INFO    -  Doc file 'modality-specific-files/task-events.md' contains a link '../glossary.md#objects.subobject.SoftwareVersion', but the doc 'glossary.md' does not contain an anchor '#objects.subobject.SoftwareVersion'.
INFO    -  Doc file 'modality-specific-files/task-events.md' contains a link '../glossary.md#objects.subobject.Code', but the doc 'glossary.md' does not contain an anchor '#objects.subobject.Code'.

@Remi-Gau Remi-Gau changed the title [BUG] unrendered link in run entity definition [BUG] broken internal links Dec 12, 2024
@Remi-Gau
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renaming to more general title

@effigies
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@Remi-Gau I'm assuming since you didn't assign yourself that you're not actively working on this, but please correct me if I'm wrong.

For the first, it looks like a typo, using a square bracket instead of a paren.

For the objects.subobject, the subfields of nested objects are not rendered in the glossary. They could be, but they would almost certainly become objects.GeneratedBy.container

INFO - Doc file 'modality-specific-files/behavioral-experiments.md' contains a link '../common-principles.md#tabular-data', but the doc 'common-principles.md' does not contain an anchor '#tabular-data'.

Should be tabular-files

INFO - Doc file 'appendices/entity-table.md' contains a link '../glossary.md#objects.suffixes.PLI', but the doc 'glossary.md' does not contain an anchor '#objects.suffixes.PLI'.
INFO - Doc file 'appendices/entity-table.md' contains a link '../glossary.md#objects.suffixes.2PE', but the doc 'glossary.md' does not contain an anchor '#objects.suffixes.2PE'.

Should be #pli-suffix and #twope-suffix.

Will add some more notes as I investigate.

@Remi-Gau Remi-Gau mentioned this issue Dec 12, 2024
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@effigies
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INFO - Doc file 'derivatives/imaging.md' contains a link '../appendices/entities.md#segmentation', but the doc 'appendices/entities.md' does not contain an anchor '#segmentation'.

Should be #seg.

INFO - Doc file 'modality-specific-files/electroencephalography.md' contains a link '#example-electrodestsv', but there is no such anchor on this page.
INFO - Doc file 'modality-specific-files/electroencephalography.md' contains a link '#example-channelstsv', but there is no such an

Missing underscores. Should be example-_...

INFO - Doc file 'modality-specific-files/magnetic-resonance-imaging-data.md' contains a link '#in-plane-spatial-encoding', but there is no such anchor on this page.

Should be #in-and-out-of-plane-spatial-encoding.

INFO - Doc file 'modality-specific-files/magnetic-resonance-imaging-data.md' contains a link '../common-principles.md#keyvalue-files-dictionaries', but the doc 'common-principles.md' does not contain an anchor '#keyvalue-files-dictionaries'.

Should be #key-value-files-dictionaries

@Remi-Gau
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ah sorry yes I am working on it and we came to the same conclusion in terms of fixes

@Remi-Gau
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INFO - Doc file 'appendices/entity-table.md' contains a link '../glossary.md#objects.suffixes.PLI', but the doc 'glossary.md' does not contain an anchor '#objects.suffixes.PLI'.
INFO - Doc file 'appendices/entity-table.md' contains a link '../glossary.md#objects.suffixes.2PE', but the doc 'glossary.md' does not contain an anchor '#objects.suffixes.2PE'.

Should be #pli-suffix and #twope-suffix.

Looking at the table here the links in microscopy:

microscopy.md' contains a link '../glossary.md#objects.suffixes.PLI', but the doc 'glossary.md' does not contain an anchor '#objects.suffixes.PLI'.

https://bids-specification.readthedocs.io/en/v1.10.0/modality-specific-files/microscopy.html#modality-suffixes

The link for PLI seems to work...

https://bids-specification.readthedocs.io/en/v1.10.0/glossary.html#objects.suffixes.PLI

@Remi-Gau
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For the objects.subobject, the subfields of nested objects are not rendered in the glossary. They could be, but they would almost certainly become objects.GeneratedBy.container

not an 'easy' fix so probably to be done in another PR (I think we may even have an issue for this)

@effigies
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Yeah, I guess those microscopy links actually work. I guess the tool isn't happy with a macro-generated glossary.

@Remi-Gau Remi-Gau mentioned this issue Dec 13, 2024
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[FIX] update some internal links Remi-Gau/bids-specification
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@effigies @Remi-Gau