Re: [galaxy-dev] Unable to set metadata in API call
Silly me - 'misc_info' shows up in the show() output, but I didn't bother to
verify that it was metadata and not some other member.
Thanks!
John Duddy
Sr. Staff Software Engineer
Illumina, Inc.
9885 Towne Centre Drive
San Diego, CA 92121
Tel: 858-736-3584
E-mail: jdu...@illumina.com
-Original Message-
From: Nate Coraor [mailto:n...@bx.psu.edu]
Sent: Monday, May 09, 2011 8:27 AM
To: Duddy, John
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Unable to set metadata in API call
Duddy, John wrote:
> I need to be able to set some metadata in some custom data types. For now,
> I'm just trying to set the value of the 'misc_info' field. The client script
> is this:
> put( sys.argv[1], sys.argv[2], { 'update_type' : 'metadata', 'misc_info' :
> 'meta data msg' } )
> and my API method is as follows. It executes fine, but the values do not show
> on the next show() call.
Hi John,
Your method below works fine for existing metadata items like
'data_lines', so I suspect the problem is not with the update method,
but with the datatype definition. Does your class have a 'misc_info'
MetadataElement?
--nate
> Disclaimer: Python is still quite new to me, and it's very likely I do not
> understand the metadata model and the way library dataset associates work.
>
> Any clues will be greatly appreaciated!
> @web.expose_api
> def update( self, trans, id, library_id, payload, **kwd ):
> """
> PUT
> /api/libraries/{encoded_library_id}/contents/{encoded_content_type_and_id}
> Sets attributes (metadata) on a library item.
> """
> update_type = None
> if 'update_type' not in payload:
> trans.response.status = 400
> return "Missing required 'update_type' parameter. Please consult
> the API documentation for help."
> else:
> update_type = payload.pop( 'update_type' )
> if update_type not in ( 'metadata' ):
> trans.response.status = 400
> return "Invalid value for 'update_type' parameter ( %s )
> specified. Please consult the API documentation for help." % update_type
> content_id = id
> decoded_type_and_id = trans.security.decode_string_id( content_id )
> content_type, decoded_content_id = decoded_type_and_id.split( '.' )
> if content_type not in ( 'file' ):
> trans.response.status = 400
> return "Updates allowed only on files, not directories"
> try:
> content = trans.sa_session.query(
> trans.app.model.LibraryDatasetDatasetAssociation ).get( decoded_content_id )
> except:
> content = None
> if not content or ( not trans.user_is_admin() and not
> trans.app.security_agent.can_modify_library_item(
> trans.get_current_user_roles(), content, trans.user ) ):
> trans.response.status = 400
> return "Invalid %s id ( %s ) specified." % ( content_type, str(
> content_id ) )
>
> metadata = content.get_metadata()
> content.datatype.before_setting_metadata(content)
>
> if not metadata:
>metadata = {}
>
> for name in payload:
> if name not in [ 'name', 'info', 'dbkey' ]:
> setattr( metadata, name, payload[name])
>
> content.set_metadata(metadata)
> content.datatype.after_setting_metadata( content )
> trans.sa_session.flush()
>
> return "OK"
>
>
> John Duddy
> Sr. Staff Software Engineer
> Illumina, Inc.
> 9885 Towne Centre Drive
> San Diego, CA 92121
> Tel: 858-736-3584
> E-mail: jdu...@illumina.com<mailto:jdu...@illumina.com>
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client. To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
> http://lists.bx.psu.edu/
___
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Re: [galaxy-dev] Unable to set metadata in API call
Duddy, John wrote:
> I need to be able to set some metadata in some custom data types. For now,
> I'm just trying to set the value of the 'misc_info' field. The client script
> is this:
> put( sys.argv[1], sys.argv[2], { 'update_type' : 'metadata', 'misc_info' :
> 'meta data msg' } )
> and my API method is as follows. It executes fine, but the values do not show
> on the next show() call.
Hi John,
Your method below works fine for existing metadata items like
'data_lines', so I suspect the problem is not with the update method,
but with the datatype definition. Does your class have a 'misc_info'
MetadataElement?
--nate
> Disclaimer: Python is still quite new to me, and it's very likely I do not
> understand the metadata model and the way library dataset associates work.
>
> Any clues will be greatly appreaciated!
> @web.expose_api
> def update( self, trans, id, library_id, payload, **kwd ):
> """
> PUT
> /api/libraries/{encoded_library_id}/contents/{encoded_content_type_and_id}
> Sets attributes (metadata) on a library item.
> """
> update_type = None
> if 'update_type' not in payload:
> trans.response.status = 400
> return "Missing required 'update_type' parameter. Please consult
> the API documentation for help."
> else:
> update_type = payload.pop( 'update_type' )
> if update_type not in ( 'metadata' ):
> trans.response.status = 400
> return "Invalid value for 'update_type' parameter ( %s )
> specified. Please consult the API documentation for help." % update_type
> content_id = id
> decoded_type_and_id = trans.security.decode_string_id( content_id )
> content_type, decoded_content_id = decoded_type_and_id.split( '.' )
> if content_type not in ( 'file' ):
> trans.response.status = 400
> return "Updates allowed only on files, not directories"
> try:
> content = trans.sa_session.query(
> trans.app.model.LibraryDatasetDatasetAssociation ).get( decoded_content_id )
> except:
> content = None
> if not content or ( not trans.user_is_admin() and not
> trans.app.security_agent.can_modify_library_item(
> trans.get_current_user_roles(), content, trans.user ) ):
> trans.response.status = 400
> return "Invalid %s id ( %s ) specified." % ( content_type, str(
> content_id ) )
>
> metadata = content.get_metadata()
> content.datatype.before_setting_metadata(content)
>
> if not metadata:
>metadata = {}
>
> for name in payload:
> if name not in [ 'name', 'info', 'dbkey' ]:
> setattr( metadata, name, payload[name])
>
> content.set_metadata(metadata)
> content.datatype.after_setting_metadata( content )
> trans.sa_session.flush()
>
> return "OK"
>
>
> John Duddy
> Sr. Staff Software Engineer
> Illumina, Inc.
> 9885 Towne Centre Drive
> San Diego, CA 92121
> Tel: 858-736-3584
> E-mail: jdu...@illumina.com
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client. To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
> http://lists.bx.psu.edu/
___
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
[galaxy-dev] Unable to set metadata in API call
I need to be able to set some metadata in some custom data types. For now, I'm
just trying to set the value of the 'misc_info' field. The client script is
this:
put( sys.argv[1], sys.argv[2], { 'update_type' : 'metadata', 'misc_info' :
'meta data msg' } )
and my API method is as follows. It executes fine, but the values do not show
on the next show() call.
Disclaimer: Python is still quite new to me, and it's very likely I do not
understand the metadata model and the way library dataset associates work.
Any clues will be greatly appreaciated!
@web.expose_api
def update( self, trans, id, library_id, payload, **kwd ):
"""
PUT
/api/libraries/{encoded_library_id}/contents/{encoded_content_type_and_id}
Sets attributes (metadata) on a library item.
"""
update_type = None
if 'update_type' not in payload:
trans.response.status = 400
return "Missing required 'update_type' parameter. Please consult
the API documentation for help."
else:
update_type = payload.pop( 'update_type' )
if update_type not in ( 'metadata' ):
trans.response.status = 400
return "Invalid value for 'update_type' parameter ( %s ) specified.
Please consult the API documentation for help." % update_type
content_id = id
decoded_type_and_id = trans.security.decode_string_id( content_id )
content_type, decoded_content_id = decoded_type_and_id.split( '.' )
if content_type not in ( 'file' ):
trans.response.status = 400
return "Updates allowed only on files, not directories"
try:
content = trans.sa_session.query(
trans.app.model.LibraryDatasetDatasetAssociation ).get( decoded_content_id )
except:
content = None
if not content or ( not trans.user_is_admin() and not
trans.app.security_agent.can_modify_library_item(
trans.get_current_user_roles(), content, trans.user ) ):
trans.response.status = 400
return "Invalid %s id ( %s ) specified." % ( content_type, str(
content_id ) )
metadata = content.get_metadata()
content.datatype.before_setting_metadata(content)
if not metadata:
metadata = {}
for name in payload:
if name not in [ 'name', 'info', 'dbkey' ]:
setattr( metadata, name, payload[name])
content.set_metadata(metadata)
content.datatype.after_setting_metadata( content )
trans.sa_session.flush()
return "OK"
John Duddy
Sr. Staff Software Engineer
Illumina, Inc.
9885 Towne Centre Drive
San Diego, CA 92121
Tel: 858-736-3584
E-mail: jdu...@illumina.com
___
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
