clingen-data-model / allele

Documentation for data model of ClinGen
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broken links! #187

Closed bpow closed 6 years ago

bpow commented 6 years ago

Many broken links:

link referenced in
primary-transcript-region-type.html implementation/value_set_list/ancillary_transcript_region_type.html
primary-amino-acid-change-type.html implementation/value_set_list/ancillary_amino_acid_change_type.html
reference_sequence/index.html conceptual/contextual_allele/index.html
../../discussion/coordinate_numbering.html conceptual/contextual_allele/reference_coordinate.html
genomic_reference_sequence.html conceptual/contextual_allele/transcript_reference_coordinate.html
genomic_reference_sequence.html conceptual/contextual_allele/transcript_reference_coordinate.html
genomic_reference_sequence.html conceptual/contextual_allele/transcript_reference_coordinate.html
canonical_allele.html conceptual/contextual_allele/reference_coordinate.html
../reference_coordinate.html conceptual/contextual_allele/position.html
external_position conceptual/contextual_allele/position.html
../../discussion/coordinate_numbering.html conceptual/contextual_allele/position.html
../reference_coordinate.html conceptual/contextual_allele/internal_position.html
../reference_coordinate.html conceptual/contextual_allele/external_position.html
../reference_sequence.html conceptual/contextual_allele/internal_position.html
../reference_sequence.html conceptual/contextual_allele/external_position.html
simple_canonical_allele.html conceptual/contextual_allele/genomic_contextual_allele.html
genomic_reference_sequence.html conceptual/contextual_allele/external_position.html
nucleotide_contextual_allele.html conceptual/canonical_allele/simple_nucleotide_canonical_allele.html
simple_amino_acid_allele.html conceptual/canonical_allele/simple_amino_acid_canonical_allele.html
genomic_allele_reference_coordinate.html conceptual/reference_sequence/genomic_reference_sequence.html
reference_sequence.html conceptual/reference_sequence/genomic_reference_sequence.html

Update:

These have now been fixed:

link referenced in
contextual_allele.html conceptual/contextual_allele/amino_acid_contextual_allele.html
contextual_allele.html conceptual/contextual_allele/transcript_contextual_allele.html
contextual_allele.html conceptual/contextual_allele/genomic_contextual_allele.html
contextual_allele.html conceptual/contextual_allele/nucleotide_contextual_allele.html
contextual_allele.html conceptual/contextual_allele/nucleotide_reference_coordinate.html
contextual_allele.html conceptual/contextual_allele/genomic_reference_coordinate.html
contextual_allele.html conceptual/contextual_allele/amino_acid_reference_coordinate.html
contextual_allele.html conceptual/contextual_allele/transcript_reference_coordinate.html
contextual_allele.html conceptual/contextual_allele/reference_coordinate.html
bpow commented 6 years ago

@larrybabb , @cbizon , @nafisakhandaker : thoughts on how we should address these? Some are just instances were a file is being referenced instead of the directory (or appropriate index.html: like the ones referring to contextual_allele.html). Others are just missing, and may need to be made from info in the schema/model.

larrybabb commented 6 years ago

Can I take ownership of this between now and Jan 3rd? If so, I do have an idea on how to deal with this in a more sane manner. I do think we may still want to move things around and I'd prefer not to have this continue to happen.

@bpow please approve or deny my request. I don't want to spend time on this if you will be doing the same.

sgoehringer commented 6 years ago

@larrybabb I have a few ideas as well based on .htaccess and rewrite rules but I’m not certain it will work in the Github site account.

Let me know if my 2 cents would be helpful.

Scott

Sent from my iPhone

On Dec 20, 2017, at 2:21 PM, Larry Babb notifications@github.com wrote:

Can I take ownership of this between now and Jan 3rd? If so, I do have an idea on how to deal with this in a more sane manner. I do think we may still want to move things around and I'd prefer not to have this continue to happen.

@bpow please approve or deny my request. I don't want to spend time on this if you will be doing the same.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

larrybabb commented 6 years ago

I was thinking of doing something like this (super high level)

Put all the Entity pages in a single directory where there is one named (.md) file for each entity. This structure would not necessarily reflect the menu outline we use to navigate on the right-hand side.

Organize our menus on the right-hand side (however we want) - but as is for now. Use "redirects" in proxy pages (which can be .md or .html) to point to the real page.

This way a single entity can be found by navigating down one of several paths in our outline.

I've found that our outline struggles when it tries to demonstrate a "kind of hierarchy" and a "kind of grouping" approach. What is "Core", Do we really want to show "DomainEntity" (it isn't in our schema or model - really).

Anyway, I think this approach will eliminate or reduce the issues surrounding broken links going forward and decouple our model from our website layout.

Feel free to bash this idea. @sgoehringer I'm all ears on your rewrite rules. Don't know about .htaccess though. Please email me with details or let me know if we need to chat directly.

sgoehringer commented 6 years ago

I quickly looked and Github doesn’t look to support rewrite rules, at least in a traditional way... I can snoop around a little more but I think your plan is where to start.

Scott

Sent from my iPhone

On Dec 20, 2017, at 3:11 PM, Larry Babb notifications@github.com wrote:

I was thinking of doing something like this (super high level)

Put all the Entity pages in a single directory where there is one named (.md) file for each entity. This structure would not necessarily reflect the menu outline we use to navigate on the right-hand side.

Organize our menus on the right-hand side (however we want) - but as is for now. Use "redirects" in proxy pages (which can be .md or .html) to point to the real page.

This way a single entity can be found by navigating down one of several paths in our outline.

I've found that our outline struggles when it tries to demonstrate a "kind of hierarchy" and a "kind of grouping" approach. What is "Core", Do we really want to show "DomainEntity" (it isn't in our schema or model - really).

Anyway, I think this approach will eliminate or reduce the issues surrounding broken links going forward and decouple our model from our website layout.

Feel free to bash this idea. @sgoehringer I'm all ears on your rewrite rules. Don't know about .htaccess though. Please email me with details or let me know if we need to chat directly.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

bpow commented 6 years ago

@larrybabb : I think you may be conflating these broken links with the ones in the interpretation model repo. I fixed the ones in interpretation, and they should be more robust to moving directories around (used erb around the md to allow for the middleman link_to helper..., since it's a static site and rewrite rules don't work).

This issue has to do with the allele model-- I think some were just people being sloppy making the links, and others are pointing to files that don't appear to exist.

bpow commented 6 years ago

Updated original issue to reflect some fixes

larrybabb commented 6 years ago

Got it. Thanks for clarifying. I’ll still clean it up over the holiday.

Sent from my iPhone

On Dec 20, 2017, at 10:01 PM, Bradford Powell notifications@github.com wrote:

@larrybabb : I think you may be conflating these broken links with the ones in the interpretation model repo. I fixed the ones in interpretation, and they should be more robust to moving directories around (used erb around the md to allow for the middleman link_to helper..., since it's a static site and rewrite rules don't work).

This issue has to do with the allele model-- I think some were just people being sloppy making the links, and others are pointing to files that don't appear to exist.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

larrybabb commented 6 years ago

done.