ENH: Added extension to the bids.json to get the 'extension' entity

[yarikoptic]

ATM just a proof of concept to fix #404

TODOs:

• finish up changes to bids.json
• fix tests
• deprecate custom extensions arg where applicable (e.g. get)

[effigies]

Problem is now you have to provide the extension. What if you did:

Suggested change

	"sub-{subject}[/ses-{session}]/anat/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{contrast}][_rec-{reconstruction}]_{suffix<T1w|T2w|T1rho|T1map|T2map|T2star|FLAIR|FLASH|PDmap|PD|PDT2|inplaneT[12]|angio>}.{extension<nii.gz>}",
	"sub-{subject}[/ses-{session}]/anat/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{contrast}][_rec-{reconstruction}]_{suffix<T1w|T2w|T1rho|T1map|T2map|T2star|FLAIR|FLASH|PDmap|PD|PDT2|inplaneT[12]|angio>}.nii.gz",
	"sub-{subject}[/ses-{session}]/anat/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{contrast}][_rec-{reconstruction}]_{suffix<T1w|T2w|T1rho|T1map|T2map|T2star|FLAIR|FLASH|PDmap|PD|PDT2|inplaneT[12]|angio>}.{extension<nii|nii.gz>}",

[effigies]

I think the only "second" extension we permit is .gz, and all extensions are alphabetical, at least for now. I'm not sure if things like surf.gii will be considered extensions, or just gii

Suggested change

	"pattern": "\\.((?:[^_/\\\\]+)+\\.?)$"
	"pattern": "\\.((?:[:Alpha:]+)(?:\\.gz)?)$"

Haven't tested this regex thoroughly...

[tyarkoni]

Probably best to hold off on this—I've got a branch going rewriting everything to use a DB. I'll probably rework the extension handling as I go through with that, but let's leave this open in case I forget.

[yarikoptic]

up to you @tyarkoni . If you decide otherwise (so that db etc could be checked with this change in mind) - let me know and I will try to get back to it to address valuable suggestions from @effigies

[tyarkoni]

@yarikoptic the 0.9 branch drops extensions and treats extension like any other entity. I haven't addressed the default_path_patterns yet though, or Chris's other comments above. So feel free to patch the sqlalchemy branch if you like, or you can wait till it's merged (or I can do it if you prefer).

[yarikoptic]

Thank you Tal!

[effigies]

@yarikoptic I'm not sure if this has been made redundant by 0.9.x, or if there are still changes in here that you'd like to see merged. Needs a merge/rebase if so.

[tyarkoni]

I think everything proposed here was added via 0.9 or other PRs, so I think we're good to close. But @yarikoptic can confirm.

[yarikoptic]

I can no longer tell ;) let's just close it and the issue will raise from the ashes if I sense that smth like this is still needed ;-)