It looks like the problem may have to do with the file I am using ???

It is a *.nii.gz file.

Does galaxy try to uncompress ? do something to *.gz files when using the api 
(as it tries to do in ~/galaxy-dist/tools/data_source/upload.py

Does anyone know of where in the code I can edit so my mile can be uploaded?

Thanks
Neil

From: Burdett, Neil (ICT Centre, Herston - RBWH)
Sent: Wednesday, 8 May 2013 3:15 PM
To: galaxy-dev@lists.bx.psu.edu
Subject: RE: Getting example_watch_folder.py to work...

Further, it seems that it doesn't manage to get hold of the file specified in 
the input directory as I can see from the output:

http://barium-rbh/csiro/api/histories/964b37715ec9bd22/contents/2faba7054d92b2df

{

    "data_type": "html",

    "deleted": false,

    "download_url": "/csiro/datasets/2faba7054d92b2df/display?to_ext=html",

    "file_name": "/home/galaxy/galaxy-dist/database/files/000/dataset_137.dat",

    "file_size": 194,

    "genome_build": "?",

    "id": "2faba7054d92b2df",

    "metadata_data_lines": null,

    "metadata_dbkey": "?",

    "misc_blurb": "error",

    "misc_info": "Wed May  8 15:07:27 2013\nbashScript is: 
/home/galaxy/galaxy-dist/tools/visualization/extractSlice-wrapper.sh\ninput_image
 is: None\ncat: None: No such file or directory\nFailed reading file 
/tmp/tmp.9LWrz6SaLy.nii.gz\nitk::ERROR: PNGImageIO(0x1abdcf0): PNGIma",

    "model_class": "HistoryDatasetAssociation",

    "name": "Extract 2D slice on None",

    "state": "error",

    "visible": true

}


input_image is: None

Does anybody know why the file may not be getting read? It is being copied from 
the specified input directory to the output directory.

I have set :
allow_library_path_paste = True

and added my user to:
admin_users

Thanks for any help

Neil


________________________________
From: Burdett, Neil (ICT Centre, Herston - RBWH)
Sent: Wednesday, May 08, 2013 2:46 PM
To: galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>
Subject: Getting example_watch_folder.py to work...
Hi,
     I'm trying to get the example_watch_folder.py to run but it seems to fail, 
and I'm not sure why?

I run:

 ./example_watch_folder.py 64f3209856a3cf4f2d034a1ad5bf851c 
http://barium-rbh/csiro/api/ /home/galaxy/galaxy-drop/input 
/home/galaxy/galaxy-drop/output "My API Import" f597429621d6eb2b

I got the workflow Id from :

http://barium-rbh/csiro/api/workflows

which gave me:

[

    {

        "id": "f597429621d6eb2b",

        "name": "extract",

        "url": "/csiro/api/workflows/f597429621d6eb2b"

    },

    {

        "id": "f2db41e1fa331b3e",

        "name": "FULL CTE",

        "url": "/csiro/api/workflows/f2db41e1fa331b3e"

    }

]

The output I get from the command line is:
{'outputs': ['ba0fa2aed4052bce'], 'history': 'ba03619785539f8c'}

The files I put into /home/galaxy/galaxy-drop/input get copied to 
/home/galaxy/galaxy-drop/output

But nothing else happens.

If I go to http://barium-rbh/csiro/api/histories

I can see:
{

        "id": "ba03619785539f8c",

        "name": "colin.nii.gz - extract",

        "url": "/csiro/api/histories/ba03619785539f8c"

    },

However when I go to:
http://barium-rbh/csiro/api/histories/ba03619785539f8c

I get:
{

    "contents_url": "/csiro/api/histories/ba03619785539f8c/contents",

    "id": "ba03619785539f8c",

    "name": "colin.nii.gz - extract",

    "state": "error",

    "state_details": {

        "discarded": 0,

        "empty": 0,

        "error": 1,

        "failed_metadata": 0,

        "new": 0,

        "ok": 0,

        "queued": 0,

        "running": 0,

        "setting_metadata": 0,

        "upload": 0

    }

}

Any ideas much appreciated

Thanks
Neil

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