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PitchInteractiveInc / Phinch

Phinch is an open-source framework for visualizing biological data, funded by a grant from the Alfred P. Sloan foundation. This project represents an interdisciplinary collaboration between Pitch Interactive, a data visualization studio in Oakland, CA, and biological researchers at UC Riverside.
http://phinch.org/
BSD 2-Clause "Simplified" License
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Problem : Phinch recognizing the biom file but not the data #62

Closed Anais-Barray closed 8 years ago

Anais-Barray commented 8 years ago

Hello Phinch team !

First thank you to help us visualize, compare and magnify our metagenomics data.

I have a major issue : I am trying to generate biom files with a homemade python script on a unix system, that I know Phinch could accept (when tried with handmade files); the json output seems correct when opened, contains metadata and so on ( : http://codebeautify.org/htmlviewer/cb114a43 ).

But when I load it into Phinch, the metadata appears, the samples are recognized, but not the data it seems ( : http://imgur.com/a/5LQlo).

When I export data, it is mostly empty ( : http://codebeautify.org/htmlviewer/cb7a542e )

I would be extremely grateful if you had any idea where the formatting could be wrong.

Thank you for your time. Best regards, Anaïs.

hollybik commented 8 years ago

Hi Anaïs, your BIOM file header says it is formatted as a BIOM v2.1 file (this would be HDF5 format) - however Phinch only accepts BIOM v1.0 files (JSON-formatted). However, your homemade file looks like it is in JSON format, so it might be a problem with the file header - Phinch may not be loading the data because it thinks the file is in BIOM v2.1 format.

On phinch.org, I would click "load a test file" and then export the file so you can look at the headers and data format. There may be a minor error in your file formatting or header text that is preventing Phinch from loading your file. Make sure all { } [ ] brackets are in the right places and you have the correct punctuation separating everything.

Hope that helps!

AdrienSeon commented 8 years ago

Hello,

The "date" metadata of the columns is not ISO8601 compliant which is a problem for Phinch since it analyses automatically any metadata named "date" and is expecting an ISO8601 format to work with.

For more information see here

Implementing better error handling as defined in https://github.com/PitchInteractiveInc/Phinch/issues/15 seems really needed to avoid these problems.

Hope it helped

Anais-Barray commented 8 years ago

Hello again, and thank you both for your answer.

Indeed my files are not BIOM1.0 formatted files, but I have reasons why I cannot, hence I am just converting from hdf5 to JSON with BIOM2.1 version.

The reason why my file couldn't be analyzed properly was indeed because my "Date" metadata was not ISO8601 compliant.

Thanks again !

Best regards, Anaïs