Hi Nate,
thanks for your reply. My solution will break down in such a case, indeed. So
here is what I need/have:
I have a tool which allows the user to select a specific workflow and
appropriate input data from his/her
history. On execution a script is used to do several preprocessing steps and at
last the selected workflow
will be executed via the API functions (in batch mode if the user selected more
than one input (pair).
As far as I have seen from the documentation one needs to specifiy a history
name or id which will hold
the output data. Logically the output should be submitted to the users current
history which serves as the
input source. That?s why I need the id of the users current history.
Of course, workflows can be executed directly within Galaxy but we need to
perform these preprocessing
steps like copying files and, more important, we have paired end data which
isn?t that good supported for
batch processing yet.
Thanks for your help!
Cheers,
Sascha
Original Message
processed by CONSOLIDATE
Subject:
Re: [galaxy-dev] Some questions about histories
Sent:
Mittwoch, 15. August 2012 17:07
From:
Nate Coraor (n...@bx.psu.edu)
On Aug 15, 2012, at 10:08 AM, Sascha Kastens wrote:
> Hi again!
> I was able to implement a quite dirty solution:
>
> first I edited /lib/galaxy/model/mapping.py and extended
>
> assign_mapper( context, User, User.table,
> properties=dict( histories=relation( History, backref="user",
>
> order_by=desc(History.table.c.update_time) ),
> active_histories=relation( History, primaryjoin=( (
> History.table.c.user_id == User.table.c.id ) & ( not_(
> History.table.c.deleted ) ) ), order_by=desc( History.table.c.update_time ) ),
> galaxy_sessions=relation( GalaxySession, order_by=desc(
> GalaxySession.table.c.update_time ) ),
> stored_workflow_menu_entries=relation(
> StoredWorkflowMenuEntry, backref="user",
> cascade="all,
> delete-orphan",
>
> collection_class=ordering_list( ’order_index’ ) ),
> _preferences=relation( UserPreference, backref="user",
> collection_class=attribute_mapped_collection(’name’)),
> # addresses=relation( UserAddress,
> # primaryjoin=( User.table.c.id ==
> UserAddress.table.c.user_id ) )
> values=relation( FormValues,
> primaryjoin=(
> User.table.c.form_values_id == FormValues.table.c.id ) ),
> api_keys=relation( APIKeys, backref="user",
> order_by=desc( APIKeys.table.c.create_time ) ),
> ) )
>
> by this:
> currentHistory=relation( History, primaryjoin=( ( History.table.c.user_id ==
> User.table.c.id ) & ( not_( History.table.c.deleted ) ) &
> (GalaxySession.table.c.current_history_id == History.table.c.id) ),
> order_by=desc( GalaxySession.table.c.update_time ) )
>
> As far as I am correct, this selects all current histories of all sessions
> per user. These histories get sorted by the latest session change
> which should always lead to the current history as the first entry.
>
> Inside my tool I use this to get the current history id and hash it to an id
> which can be used for API calls:
>
> ${__app__.security.encode_id( ’%s’ %
> $__app__.model.User.get($__user_id__).currentHistory[0].id )}
>
> Until now everything seems to work as it should.
Hi Sascha,
This will break down if you have a user with more than one active sessions (in
two browsers, for example). The most recent session and its current history
will always be used, rather than the one that the job was initiated from.
Jobs are intentionally decoupled from histories since histories are not the
only context in which a job can run. There may be accurate ways of getting to
the parent history at the job context, but it?d help to know what you?re trying
to do.
Thanks,
--nate
>
> Finally I have another question about the histories and API. Referring to
> this thread:
> http://gmod.827538.n3.nabble.com/How-to-use-scripts-api-update-py-td3657803.html#a3700436
>
> Are you working on this? Updating history items via the API would be really
> helpful for my usecase. If not, can you give me some hints where I can have a
> look at to enable it by my own?
No, nothing?s been written for this yet. Have a look at
lib/galaxy/web/api/history_contents.py, and you may find the update() method in
other API controllers to be a useful template. One that is fairly well sorted
is the quota API (quotas.py).
--nate
>
> Thanks a lot!
>
> Cheers,
> Sascha
>
> Original Message
> processed by CONSOLIDATE
> Subject:
> [galaxy-dev] Some questions about histories
> Sent:
> Dienstag, 14. August 2012 12:10
> From:
> Sascha Kastens (s.kast...@gatc-biotech.com)
> Hi all!
>
> I have two questions about histories in Galaxy:
>
> 1. Is it possible to mark/set a history as published via the API?
> 2. How can I get the ID of the current users history via a tool? Something
> like
> ${__app__.model.User.get($__user_id__).histories[0].id} ?!
>
>
> Thanks in advance!
>
> Cheers,
> Sascha
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