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molbiodiv / biom-conversion-server

Conversion tool for the biom format via php webservice
https://biomcs.iimog.org
MIT License
1 stars 0 forks source link

Fix conversion from 1.x to 2.x #4

Open iimog opened 8 years ago

iimog commented 8 years ago

As Holly notes in her referee report for our f1000 article:

The biom-conversion-server does not appear to be backwards compatible (I could not upload and convert a BIOM 1.x file to 2.x format) - this one-way conversion functionality is should be clearly indicated in the first paragraph of the “Application” section. In addition, if users try to upload a BIOM 1.0 file they should be presented with an appropriate error message (I didn’t see one - the tool just froze when I attempted to upload a BIOM 1.0 file).

Bik H. Referee Report For: biojs-io-biom, a BioJS component for handling data in Biological Observation Matrix (BIOM) format [version 1; referees: 2 approved with reservations]. F1000Research 2016, 5:2348 (doi: 10.5256/f1000research.10362.r16436)

Related to https://github.com/molbiodiv/biojs-io-biom/issues/26

iimog commented 8 years ago

In general the biom-conversion-server is not limited to one way conversion. In fact I was able to convert the phinch example biom file which is in BIOM 1.0 format to BIOM 2.1 using the web interface. However it took ~10s before the success message for the upload appeared and after clicking on download for version 2 it took nearly 1min before the download was ready. During this time there was no indication on the page that something is happening so it might lead to the conclusion that the server hangs. Also an error message should already appear if there is an error with the provided file.

@hollybik would you mind trying again and waiting a little while? If the problem persists it would help if you could provide your browser and version as well as the biom file that produced the error. Thanks in advance for your help.

In any case the web interface should indicate the background activity in a way that communicates the status to the user (e.g. a spinner). Also error messages can definitely be improved.