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merenlab / anvio

An analysis and visualization platform for 'omics data
http://merenlab.org/software/anvio
GNU General Public License v3.0
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Saved state + additional metadata #145

Closed meren closed 9 years ago

meren commented 9 years ago

Hi Özcan,

I just run into a bug that I wanted to write about. I haven't looked into the code, so please feel free to WONTFIX it if it is too complicated.

You can reproduce the bug like this:

$ cd tests/mini_test/test-output
$ anvi-interactive -p 204-MERGED/PROFILE.db -a ANNOTATION.db

save the state from the interface. kill the server, then run this:

$ anvi-interactive -p 204-MERGED/PROFILE.db -a ANNOTATION.db --state 204-MERGED/SAVED_STATE

runs perfectly. kill the server, then run this:

$ anvi-interactive -p 204-MERGED/PROFILE.db -a ANNOTATION.db -A anvio_concoct_clusters.txt

runs perfectly. kill the server, then run this:

$ anvi-interactive -p 204-MERGED/PROFILE.db -a ANNOTATION.db -A anvio_concoct_clusters.txt --state 204-MERGED/SAVED_STATE

treelib.js dies (because it finds the layer, but it is undefined, for obvious reasons).

Of course now there is an extra layer that was not in the state file. The other way around is possible too. I mean, you may run the interface first with a layer of additional metadata, save the state, and now you can't use that state without using the additional metadata again.

I have no suggestions, just wanted to let you know and see where would you like to go with this :) As I said, WONTFIX is an option, too (in that case I would write a small check to show an error message that says "your state file says X layers, you have just given me Y, that state is garbage yo").

Best,

ozcan commented 9 years ago

Hmm this bug is obvious, maybe we should store layer/view settings using layer name instead of layer id ( i mean column order on metadata table ), it's doable, i will look into this.