How to retrieve the current history ID
Hi, I already asked a similar question to the Galaxy mailing list toward this topic, but it didn't quite solve my problem. I was seeking help on a way to create a tool which would be able to retrieve all the details (the information you get when clicking on the "eye" icon in a job in the history) for all jobs from an history. This tool would simply create sort of a log file which would contains all the parameters used for each job in the history. I am not interested by retrieving the actual datasets, but only by the "details" information related to the jobs. As I have access to the database, I could create a tool which would access the right tables and retrieve all this information. Although to achieve that, I think I would need to retrieve the history ID first (to be able to retrieve the information related to that particular history from the database). My question is then: Is it possible, from a tool, to retrieve the history ID of the current history? If not, would it be possible to make some changes in galaxy's files, that would make the history ID appear somewhere on the galaxy page, so the user could manually enter the history ID as a tool parameter? Thank you all for your help. This is greatly appreciated!! Thanks, Jean-François
On Thu, Jun 14, 2012 at 2:08 PM, Jean-Francois Payotte <jean-francois.payotte@dnalandmarks.ca> wrote:
My question is then: Is it possible, from a tool, to retrieve the history ID of the current history?
I think the answer is no - assuming you mean tool as in the script or binary being executed - after all the tool might be running on a cluster node with no direct connection to the Galaxy server. But see below...
If not, would it be possible to make some changes in galaxy's files, that would make the history ID appear somewhere on the galaxy page, so the user could manually enter the history ID as a tool parameter?
That sounds like a horrible UI :( I do have an alternative suggestion: Is it possible for the tool XML file to access the history ID, just like $__user_id__ can be used to get the user's ID etc? See this wiki page for other available information: http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax It is possible this can already be done via $__app__, but as noted on the wiki that is considered a last resort and liable to change. Peter
Hi Peter and thank you for your answer, I think I have misspoken when I said that I would like to retrieve the history ID from a tool. As you suggest, I was indeed speaking about retrieving the history ID from the XML file instead. And I agree with you that showing the history ID on the galaxy page would look terrible from a GUI point of view. :) About your alternative suggestion, I already looked at Galaxy's environment variables (such as $__user_id__), but I don't think the history ID can be access this way. In fact, and I could be wrong, but I've found that the only Galaxy's environment variables are : $GALAXY_HOME , ${GALAXY_DATA_INDEX_DIR}, $__new_file_path__ , $__tool_data_path__, $__root_dir__, $__datatypes_config__ , $__user_id__, $__user_email__ and $__app__. About the $__app__ variable.. I was aware that it might be used to retrieve the history ID (even though I didn't found how to do it), but as you said, this variable is marked as "to be used in last resort and that it could go away in future releases". So I was seeking a way to retrieve the history ID (from the XML file) that would be stable and that would not risks to become non-functional with new Galaxy releases.. Best regards, Jean-François From: Peter Cock <p.j.a.cock@googlemail.com> To: Jean-Francois Payotte <jean-francois.payotte@dnalandmarks.ca> Cc: galaxy-dev@lists.bx.psu.edu Date: 14/06/2012 09:17 AM Subject: Re: [galaxy-dev] How to retrieve the current history ID On Thu, Jun 14, 2012 at 2:08 PM, Jean-Francois Payotte <jean-francois.payotte@dnalandmarks.ca> wrote:
My question is then: Is it possible, from a tool, to retrieve the
history ID
of the current history?
If not, would it be possible to make some changes in galaxy's files,
I think the answer is no - assuming you mean tool as in the script or binary being executed - after all the tool might be running on a cluster node with no direct connection to the Galaxy server. But see below... that
would make the history ID appear somewhere on the galaxy page, so the user could manually enter the history ID as a tool parameter?
That sounds like a horrible UI :( I do have an alternative suggestion: Is it possible for the tool XML file to access the history ID, just like $__user_id__ can be used to get the user's ID etc? See this wiki page for other available information: http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax It is possible this can already be done via $__app__, but as noted on the wiki that is considered a last resort and liable to change. Peter
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Jean-Francois Payotte -
Peter Cock