BUG: users can create incomplete SingleLanePerSamplePairedEndFastqDirFmt about q2-types HOT 5 CLOSED

This block in the framework looks promising:

https://github.com/qiime2/qiime2/blob/3e053cba101ace49ba52e16cba0bd6966973b0b3/qiime2/plugin/model/directory_format.py#L102-L105

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@thermokarst the drive link isn't loading for me.

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Thanks @Oddant1 --- looks like the user stopped sharing their data. No worries.

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I took another look at this and it looks like right here in the framework is where the issue is. https://github.com/qiime2/qiime2/blob/81f9bc1e735a1d9c1c852d144b8302ab4c24a3cc/qiime2/plugin/model/directory_format.py#L89-L105

Specifically on line 93 we regex the pathspec against the actual path which allows any path that is a superset of the pathspec to get through. This explains how "MANIFEST.txt" and "metadata.yml.txt" got through. The path we regex against is the path to the file relative to the root directory of the artifact.

It seems like we might be able to just use re.fullmatch instead of re.match? Provided the pathspec is the full file path from the artifact's root (so if the file is nested within another directory inside the artifact's data directory that directory is part of its pathspec) I think this should work.

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Awesome! Can you write up a unittest that recreates the case presented here in this issue? It will fail, until we get the fix merged into the framework. Thanks!

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