Hi Steve, Galaxy try to sniff the data to guess the appropriate datatype. For Binaries, if any datatype (sniffer) is found from https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/binary... <https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/binary.py> , you get this message "The binary uploaded file contains inappropriate content." For your wave file, you will have to add a class (https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/binary... <https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/binary.py#L1334>) for the wave format and implement a sniffer (https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/binary... <https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/binary.py#L1354>) with a test if/else https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/binary... <https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/binary.py#L1358> Typically for Binary, you can get the first n bytes which used to be a text and check it’s equal to, i hope, "wave". There are bunch of example in the file. And finally, a Pull Request on https://github.com/galaxyproject/galaxy <https://github.com/galaxyproject/galaxy> :) Good luck Gildas ----------------------------------------------------------------- Gildas Le Corguillé - Bioinformatician/Bioanalyste Plateform ABiMS (Analyses and Bioinformatics for Marine Science) http://abims.sb-roscoff.fr <http://abims.sb-roscoff.fr/> Member of the Workflow4Metabolomics project http://workflow4metabolomics.org <http://workflow4metabolomics.org/> Station Biologique de Roscoff - UPMC/CNRS - FR2424 Place Georges Teissier 29680 Roscoff FRANCE tel: +33 2 98 29 23 81 ------------------------------------------------------------------
Le 22 oct. 2016 à 12:36, Peter Cock <p.j.a.cock@googlemail.com> a écrit :
Hi Steve,
You are on the right track, but something in the WAV file has triggered one of Galaxy's security protections to try to block uploading of potentially dangerous files. There may be some settings here you can relax - I've not had to deal with this myself.
Peter
On Fri, Oct 21, 2016 at 8:55 PM, Steve Cassidy <steve.cassidy@mq.edu.au> wrote:
Thanks all, it seems that my real problem is that the audio file (.wav) is not being identified as a valid datatype and ending up as a zero length text file. So, I need to start to explore the world of datatypes.
Following the docs (https://wiki.galaxyproject.org/Admin/Datatypes/Adding%20Datatypes) I can modify datatypes_conf.xml in my Galaxy sources and add a new datatype for wav files:
<datatype extension="wav" type="galaxy.datatypes.binary:Binary" display_in_upload="true" mimetype="audio/wav" subclass="True”/>
but, I get a message "The uploaded binary file contains inappropriate content” and a zero length file just as I did before adding this - although the datatype is now set to ‘wav’.
I didn’t add a sniffer for this and set the datatype explicitly on upload.
Also, this doesn’t seem like a modular way to add datatypes - how do I include datatypes in my tool definition? I can see from some other tools that I include a datatypes_conf.xml in my tool folder. When I try that and test with planemo the new type isn’t found.
Pointers welcome.
Thanks,
Steve
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