Hi,
I am trying to create a sqlite datatype. But whenever I upload the database its corrupted. With the latest galaxy-dist checkout changeset: 8153:5dcbbdfe1087 tag: tip user: Daniel Blankenberg dan@bx.psu.edu date: Tue Nov 06 12:57:23 2012 -0500 summary: Allow rerun to access hidden datasets.
from http://wiki.galaxyproject.org/Admin/Datatypes/Adding%20Datatypes I thought that adding subclass="True" in datatypes_conf.xml would be enough to register my new type, but it seems like I stil have to add an entry in binary.py for it to be recognized. But its still corrupted.
thank you very much, ido
------ Tool: Upload File Name: hg19.sqlite Created: Dec 07, 2012 Filesize: 11.1 MB Dbkey: hg19 Format: sqlite Tool Version: Tool Standard Output: stdout Tool Standard Error: stderr Tool Exit Code: 0 ------ Input Parameter Value File Format sqlite Genome File Format sqlite Inheritance Chain hg19.sqlite ------
I tried combinations of: datatypes_conf.xml <datatype extension="sqlite" type="galaxy.datatypes.binary:SQLite" mimetype="application/octet-stream" display_in_upload="true" subclass="True"/>
with/without: in lib/galaxy/datatypes/binary.py
class SQLite(Binary): """SQLite file""" file_ext = "sqlite"
def set_peek( self, dataset, is_multi_byte=False ): if not dataset.dataset.purged: dataset.peek = "sqlite file" dataset.blurb = data.nice_size( dataset.get_size() ) else: dataset.peek = 'file does not exist' dataset.blurb = 'file purged from disk' def display_peek( self, dataset ): try: return dataset.peek except: return "sqlite file (%s)" % ( data.nice_size( dataset.get_size() ) )
Binary.register_unsniffable_binary_ext("sqlite")