Hi Eric,

Documentation for tool output actions is limited but available from 
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Cactions.3E_tag_set
 and the code is located at lib/galaxy/tools/parameters/output.py. The 
LiftOver, Cut, BWA, fimo, tophat, ccat, srma, mosaik, bfast, sam to bam, and 
Bowtie tools also currently use them. 


Thanks for using Galaxy,

Dan


On Oct 3, 2011, at 2:51 PM, Paniagua, Eric wrote:

> Hi Dan,
> 
> Regarding the tool output actions, could you point me to any documentation or 
> additional good examples for handling tool output post-processing?
> 
> Thanks,
> Eric
> 
> ________________________________
> From: Daniel Blankenberg [d...@bx.psu.edu]
> Sent: Monday, October 03, 2011 2:00 PM
> To: Paniagua, Eric
> Cc: Nate Coraor; galaxy-dev@lists.bx.psu.edu
> Subject: Re: [galaxy-dev] (Composite) Dataset Upload not Setting Metadata
> 
> Hi Eric,
> 
> Can you provide an example of the composite datatype that is experiencing the 
> metadata problems?
> 
> The code and tool hooks are deprecated, but there could still be some 
> instances where they may need to be used.  However, dynamic options (see eg 
> "<options from_dataset="input1">"  from 
> tools/filters/extract_GFF_Features.xml) can handle much of the functions 
> where code files are used for population parameters. Additionally, tool 
> output actions (see e.g. tools/filters/cutWrapper.xml) can be used to set 
> metadata ( e.g. column assignments ) on tool outputs without using hooks. 
> Please let us know if we can provide additional information.
> 
> 
> Thanks for using Galaxy,
> 
> Dan
> 
> 
> On Sep 30, 2011, at 1:15 PM, Paniagua, Eric wrote:
> 
> Hi Nate,
> 
> Thanks for your answers.  I will look into setting 
> set_metadata_externally=True.
> 
> I've observed no impact (suggesting someone did error handling properly), but 
> upload is the only tool I've tested it with so far.  I'll be doing more 
> shortly, but going with the exec_after_process solution since I don't then 
> need to modify core code here.
> 
> I'm glad to hear that abstraction layer is in the works.
> 
> Regarding the upload and general handling of compressed files, please refer 
> to my response to Brent a short time ago, subject line "[galaxy-user] upload 
> zip file to custom tool".  In particular, I pointed out that it doesn't work 
> even with a manually set file type and why, at least in terms of code.  I was 
> hoping you might know if it was that way on purpose and, if so, why.
> 
> Regarding deprecation of the <code> tag and of tool hooks (am I correct to 
> understand that these are deprecated too?), there's been an example at the 
> top of my mind (since I'm going to start working on this today).  In the 
> abstract, the scenario is dynamically populating the tool UI based on a 
> computation on the contents of one or more input datasets.  To an extent, the 
> <conditional> and <page> tags are helpful with this, but without the <code> 
> tag I'm not clear on how to call out to code that inspects the datasets and 
> returns, for the sake of simplicity, options for a single parameter.
> 
> My specific example has to do with constructing a microarray expression 
> analysis pipeline, with one of my starting points being Ross Lazarus's 
> Rexpression code.  I may be able to get around the issue by storing the 
> relevant information in metadata (in a custom datatype's set_meta).  Not sure 
> yet.  Of course, that relies on metadata being handled correctly.  If I run 
> into something more specific, I'll start a new thread.
> 
> Thanks,
> Eric
> 
> ________________________________________
> From: Nate Coraor [n...@bx.psu.edu]
> Sent: Friday, September 30, 2011 11:03 AM
> To: Paniagua, Eric
> Cc: galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>
> Subject: Re: [galaxy-dev] (Composite) Dataset Upload not Setting Metadata
> 
> Paniagua, Eric wrote:
> Hi Nate,
> 
> Thank you for your response!  I am glad that it was you in particular who did 
> respond, because I also have some questions about the way the upload tool 
> handles compressed files and saw that you have opened several Issues related 
> to this on the Galaxy bitbucket site.  First though, I'll fill you in on my 
> further progress on the composite file issue.
> 
> As I mentioned in my original email, the trouble is that JobWrapper.finish() 
> calls dataset.set_meta() before it calls collect_associated_files(), 
> resulting dataset.extra_files_path being inaccurate because the files haven't 
> been moved yet from the job working directory.  This is all with 
> set_metadata_externally=False.  (I haven't worked with setting metadata 
> externally yet, but I think it is worth verifying whether everything works 
> correctly for the case I pointed out when set_metadata_externally=True.)
> 
> Since my last email, I poked around a bit more and found that my suggested 
> short patch was not correct but incomplete.  The core problem is that 
> component files are not moved with the primary file, so I changed that (patch 
> attached, relative to { https://bitbucket.org/galaxy/galaxy-dist 
> 5955:949e4f5fa03a }.  Early in JobWrapper.finish() the primary file is moved 
> from the working directory to the appropriate directory under 
> config.file_path.  This patch uses the structure of the path naming 
> convention to build the accurate path to the component files, and then moves 
> them along with the primary file.  It's the least invasive (in terms of 
> modifying Galaxy core code) potential fix I came up with, but since it relies 
> explicitly on path structure and naming conventions I still think it's a bit 
> of a hack.  However, it does seem to work, at least to me.  I don't have the 
> resources or experience yet to attempt to test whether it negatively (or 
> positively!) impacts others' use cases!
> .  I do hope that someone more intimately familiar with the project would be 
> able to vet it and make improvements / provide feedback / incorporate a fix 
> for this issue to the Galaxy mainline.
> 
> However, since the group I'm working for operates downstream of the main 
> Galaxy Development Team (primarily to add tools and maintain a local Galaxy 
> server for our institution), we really try to avoid complications in merges 
> when pulling down updates by avoiding changing Galaxy core code as much as 
> possible.  Consequently, I had to shift focus from finding the best correct 
> fix to simply finding a workaround, and I found a very simple one.  However, 
> it relies on the deprecated <code> tool config tag, so it will only work 
> until support for the <code> tag is removed.  It's self-explanatory and also 
> attached.
> 
> Hi Eric,
> 
> I haven't tried out the patch, but would this have an impact on
> processing that occurs when collect_associated_files() runs since they
> have been moved back already by your code?
> 
> I'd suggest enabling set_metadata_externally = True as I suspect this
> will solve the problems since metadata will be set while the primary
> file is still in the temporary location.  set_metadata_externally = True
> should really be the default setting and we may remove internal metadata
> setting entirely at some point.
> 
> Regarding potential fixes: Is there any reason why component files of a 
> composite dataset should not always follow the primary file?  I don't know of 
> one, but maybe there is some case in running Galaxy over a cluster where 
> there is reason to do otherwise.  If the answer is no, it seems the best 
> approach is to add an abstraction layer between the datasets and the file 
> system to avoid various paths that might be associated to a dataset from 
> falling out of sync.  One (obviously motivational) function of this layer 
> would be to move or copy datasets on the file system atomically.  This seems 
> pretty important especially for enabling even more flexible support of 
> distributed or clustered installations.
> 
> We're going to be working on just such an abstraction layer shortly.
> 
> Regarding the upload tool: I just saw your response to my other email on 
> Leandro's thread.  Thanks for pointing me to the code responsible.  I've 
> already forked a version of the upload tool for our Galaxy instance.  There 
> are a lot of issues with the way the way the default upload tool works, and 
> it sounds like you're aware of that and perhaps it's been a headache for you 
> too.  If it might help make progress more swift in the Galaxy mainline, I'd 
> be glad to send you patches for updates and changes I make in the upload 
> tool.  I do have at least one big question about it though: It currently 
> attempts to sniff and uncompress files regardless of whether "Auto-detect" 
> was selected for "File format"; is that by design or accident?  It seems that 
> (particularly the bits try uncompressing files) causes headaches for a number 
> of developers/users.  I'm likely to remove that behavior from my version of 
> the upload tool, but I'll be less inclined to do so if that will make it 
> diverge si!
> gnificantly from Galaxy's expected design path.
> 
> We definitely need to make it easier to upload compressed files that
> intentionally stay compressed.  This should be the case when setting the
> specific file type, though.
> 
> Finally, I noted that the <code> tag is deprecated.  I learned this from the 
> Tool Config Syntax page on the Wiki 
> (http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Ccode.3E_tag_set).
>   It says there that it and the tool hooks (like exec_after_process) are 
> being replaced, but doesn't give many details.  Is there anything you can 
> tell me about what syntax or mechanism is planned to replace them?  The 
> ability to generate UI parameters, have the tool page itself interact with 
> other data sources and programs, use hooks to control tool execution, and 
> generally interleave arbitrary code with tool/job runs is very useful.  
> Unfortunately, the tools page appears to be out of date or just not remotely 
> comprehensive; I've found many examples of syntax in other tools' 
> configurations that are simply not documented on the Tool Config Syntax page 
> at all.
> 
> It's true that <code> is deprecated, although I can't provide much
> useful information beyond that.  If you post up what you're using hooks
> for one of my colleagues with more familiarity with tool configs can
> probably reply with the best way to accomplish what you're doing without
> hooks.
> 
> --nate
> 
> 
> Please do let me know if you're able to doing anything (with or without my 
> suggestions) about the issue I ran into with the way Galaxy handles composite 
> datasets on the file system.  Or anything more generally about composite 
> dataset design intentions, upload functionality, and known issues.  I'd 
> greatly appreciate it.  Thanks for answering my email!
> 
> 
> Thanks,
> Eric
> 
> 
> PS: I'm also unable to download composite datasets that I successfully 
> uploaded; instead I get an error page saying the URL path doesn't exist.  
> However, I haven't dug into this one enough to think it's not a local 
> configuration problem on my end.  Do you recognize this as (related to) a 
> known issue?
> 
> ________________________________________
> From: Nate Coraor [n...@bx.psu.edu]
> Sent: Wednesday, September 28, 2011 9:24 AM
> To: Paniagua, Eric
> Cc: galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>
> Subject: Re: [galaxy-dev] (Composite) Dataset Upload not Setting Metadata
> 
> Paniagua, Eric wrote:
> Hi all,
> 
> Can anyone tell me why JobWrapper.finish() moves the primary dataset file 
> dataset_path.false_path to dataset_path.real_path (contingent on 
> config.outputs_to_working_directory == True) but does not move the "extra 
> files"?  (lib/galaxy/jobs/__init__.py:540-553)  It seems to me that if you 
> want to move a dataset, you want to move the whole dataset, and that perhaps 
> this should be factored out, perhaps into the galaxy.util module?
> 
> Why does class DatasetPath only account for the path to the primary file and 
> not the path to the "extra files"?  It could be used to account for the 
> "extra files" by path splitting as in my previous suggested bug fix, but only 
> if that fix is correct.  It doesn't seem to be used for that purpose in the 
> Galaxy code.
> 
> I look forward to an informative response.
> 
> Hi Eric,
> 
> Sorry for the delay in responding, and thanks for your very detailed
> digging into this problem.  To answer your above question, DatasetPath
> only deals with the primary dataset because extra files are already
> written to the working directory and moved back by the wrapper with
> collect_associated_files().
> 
> Making it possible to read these extra files from the working directory
> will be necessary when set_metadata_externally = True in the config,
> although I am surprised this has been broken the whole time.  Have you
> made progress past your last email?  I can pick up from wherever you've
> left off.
> 
> 
> Thanks,
> Eric Paniagua
> 
> ________________________________________
> From: 
> galaxy-dev-boun...@lists.bx.psu.edu<mailto:galaxy-dev-boun...@lists.bx.psu.edu>
>  [galaxy-dev-boun...@lists.bx.psu.edu] on behalf of Paniagua, Eric 
> [epani...@cshl.edu]
> Sent: Monday, September 12, 2011 7:37 PM
> To: galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>
> Subject: Re: [galaxy-dev] (Composite) Dataset Upload not Setting Metadata
> 
> Hello again,
> 
> It looks like the config.outputs_to_working_directory variable is intended to 
> do something closely related, but setting it to either of True and False does 
> not in fact fix the problem.
> 
> The output path for files in a composite dataset upload (dataset.files_path) 
> that is used in the tools/data_source/upload.xml tool is set to a path under 
> the job working directory by lib/galaxy/tools/__init__.py:1519.  The 
> preceding code (lines 1507-1516) select the path for the primary file 
> contingent on config.outputs_to_working_directory.
> 
> Why is the path set in line 1519 not contingent on 
> config.outputs_to_working_directory?  Indeed, the following small change 
> fixes the bug I'm observing:
> 
> diff -r 949e4f5fa03a lib/galaxy/tools/__init__.py
> --- a/lib/galaxy/tools/__init__.py      Mon Aug 29 14:42:04 2011 -0400
> +++ b/lib/galaxy/tools/__init__.py      Mon Sep 12 19:32:26 2011 -0400
> @@ -1516,7 +1516,9 @@
>                param_dict[name] = DatasetFilenameWrapper( hda )
>            # Provide access to a path to store additional files
>            # TODO: path munging for cluster/dataset server relocatability
> -            param_dict[name].files_path = os.path.abspath(os.path.join( 
> job_working_directory, "dataset_%s_files" % (hda.dataset.id) ))
> +            #param_dict[name].files_path = os.path.abspath(os.path.join( 
> job_working_directory, "dataset_%s_files" % (hda.dataset.id) ))
> +            # This version should make it always follow the primary file
> +            param_dict[name].files_path = os.path.abspath( os.path.join( 
> os.path.split( param_dict[name].file_name )[0], "dataset_%s_files" % 
> (hda.dataset.id) ))
>            for child in hda.children:
>                param_dict[ "_CHILD___%s___%s" % ( name, child.designation ) ] 
> = DatasetFilenameWrapper( child )
>        for out_name, output in self.outputs.iteritems():
> 
> Would this break anything?
> 
> If that cannot be changed, would the best solution be to modify the upload 
> tool so that it took care of this on its own?  That seems readily doable, but 
> starts to decentralize control of data flow policy.
> 
> Please advise.
> 
> Thanks,
> Eric Paniagua
> ________________________________________
> From: 
> galaxy-dev-boun...@lists.bx.psu.edu<mailto:galaxy-dev-boun...@lists.bx.psu.edu>
>  [galaxy-dev-boun...@lists.bx.psu.edu] on behalf of Paniagua, Eric 
> [epani...@cshl.edu]
> Sent: Monday, September 12, 2011 1:45 PM
> To: galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>
> Subject: [galaxy-dev] (Composite) Dataset Upload not Setting Metadata
> 
> Hi everyone,
> 
> I've been getting my feet wet with Galaxy development working to get some of 
> the rexpression tools online, and I've run into a snag that I've traced back 
> to a set_meta datatype method not being able to find a file from which it 
> wants to extract metadata.  After reading the code, I believe this would also 
> be a problem for non-composite datatypes.
> 
> The specific test case I've been looking at is uploading an affybatch file 
> (and associated pheno file) using Galaxy's built-in upload tool and selecting 
> the File Format manually (ie choosing "affybatch" in the dropdown).  I am 
> using unmodified datatype definitions provided in 
> lib/galaxy/datatypes/genetics.py and unmodified core Galaxy upload code as of 
> 5955:949e4f5fa03a.  (I am also testing with modified versions, but I am able 
> to reproduce and track this bug in the specified clean version).
> 
> The crux of the cause of error is that in JobWrapper.finish(), 
> dataset.set_meta() is called (lib/galaxy/jobs/__init__.py:607) before the 
> composite dataset uploaded files are moved (in a call to a Tool method 
> "self.tool.collect_associated_files(out_data, self.working_directory)" on 
> line 670) from the job working directory to the final destination under 
> config.file_path (which defaults to "database/files").
> 
> In my test case, "database.set_meta( overwrite = False )" eventually calls 
> lib/galaxy/datatypes/genetics.py:Rexp.set_meta(dataset, **kwd).  As far as I 
> can tell, the only ways to construct a path to a file (or the file) in a 
> dataset without using hard-coded paths from external knowledge is to use the 
> Dataset.get_file_name or Dataset.extra_files_path properties.  Unless 
> explicitly told otherwise, both of these methods construct a path based on 
> the Dataset.file_path class data member, whose value is set during Galaxy 
> startup to config.file_path (default "database/files").  However, at the time 
> set_meta is called in this case, the files are not under config.file_path, 
> but rather under the job working directory.  Attempting to open files from 
> the dataset therefore fails when using these paths.  However, unless the job 
> working directory is passed to set_meta or during construction of the 
> underlying Dataset object, there doesn't appear to be a way for a Dataset 
> method to acces!
> s th!
> e currently running job (for instance to get its job ID or working 
> directory).  (The second suggestion is actually not possible; since the 
> standard upload is asynchronous, the Dataset object is created (and 
> persisted) before the Job that will process it is created.)
> 
> Thoughts?  This issue affects Rexp.set_peek also, as well as any other 
> functions that may want to read data from the uploaded files before they are 
> moved to permanent location.  This is why if you have an affybatch file and 
> its associated pheno file and you test this on, say, the public Galaxy server 
> at http://main.g2.bx.psu.edu/ you'll see that the peek info says (for 
> example): "##failed to find 
> /galaxy/main_database/files/002/948/dataset_2948818_files/affybatch_test.pheno"
> 
> It seems that if the current way that Dataset.file_path, Dataset.file_name, 
> and Dataset.extra_files_path is part of the desired design of Galaxy, that 
> methods like set_meta should be run after the files have been moved to 
> config.file_path so they can set metadata based on file contents.  It looks 
> like this is intended to happen at least in some cases, from looking at 
> lib/galaxy/jobs/__init__.py:568-586.  However, in my tests this code is not 
> kicking in because hda_tool_output is None.
> 
> Any clarification on what's happening here, what's supposed to be happening 
> for setting metadata on (potentially composite) uploads, why 
> dataset.set_meta() isn't already being called after the files are moved to 
> config.file_path, or any insights on related Galaxy design decisions I may 
> not know about or design constraints I may have missed would be very greatly 
> appreciated.
> 
> I'd also be glad to provide further detail or test files upon request.
> 
> Thank you,
> Eric Paniagua
> 
> PS: Further notes on passing the job working directory to set_meta or 
> set_peek - I have been successful modifying the code to do this for set_meta 
> since the call chain starting from dataset.set_meta() in JobWrapper.finish() 
> to Rexp.set_meta() accepts and forwards keyword argument dictionaries along 
> the way.  However, set_peek does not accept arbitrary keyword arguments, 
> making it harder to pass along the job working directory when needed without 
> stepping on the toes of any other code.
> 
> ___________________________________________________________
> 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/
> 
> ___________________________________________________________
> 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/
> 
> # This file provides a workaround to the problem of premature set_meta calls 
> in
> # JobWrapper.finish(), which calls set_meta before the component files of a
> # a composite dataset have been moved to their correct paths. This workaround
> # exploits the fact that the exec_after_process hook is called after the 
> component
> # files have been moved.
> #
> # This problem affects tools that produce composite datasets in their output.
> #
> # To use this workaround, add the following to your tool's XML configuration
> # (assuming it's in the same directory as this file):
> #
> #       <code file="composite_metadata_workaround.py"/>
> #
> # Also, composite types should set peek to start with '##failed' to be 
> compatible.
> 
> # Retry set_peek and set_meta after the tool has collected all files
> def exec_after_process( app, inp_data, out_data, param_dict,tool, stdout, 
> stderr):
>   for name, data in out_data.items():
>       if data.peek.find( '##failed' ) == 0:
>           data.set_meta( overwrite=False )
>           data.set_peek( is_multi_byte=data.is_multi_byte() )
>           app.model.context.add( data )
>           app.model.context.flush()
> 
> diff -r -c -x '.hg*' psu_dist/lib/galaxy/jobs/__init__.py 
> glxtemp/lib/galaxy/jobs/__init__.py
> *** psu_dist/lib/galaxy/jobs/__init__.py      Fri Sep 16 11:03:48 2011
> --- glxtemp/lib/galaxy/jobs/__init__.py       Wed Sep 28 13:58:28 2011
> ***************
> *** 551,556 ****
> --- 551,574 ----
>                     else:
>                         self.fail( "Job %s's output dataset(s) could not be 
> read" % job.id )
>                         return
> +                 efp_fake = dataset_path.false_path.replace( '.dat', 
> '_files' )
> +                 efp_real = dataset_path.real_path.replace( '.dat', '_files' 
> )
> +                 try:
> +                     shutil.move( efp_fake, efp_real )
> +                     log.debug( "finish(): Moved %s to %s" % (efp_fake, 
> efp_real) )
> +                 except ( IOError, OSError ) as e:
> +                     # this can happen if Galaxy is restarted during the 
> job's
> +                     # finish method - the false_path file has already moved,
> +                     # and when the job is recovered, it won't be found.
> +                     if os.path.exists( efp_fake ):
> +                         log.warning( "finish(): Path %s does exist, but 
> could not be moved: " % (efp_fake, e.strerror) )
> +                     else:
> +                         log.warning( "finish(): Path %s doesn't exist" )
> +                     if os.path.exists( efp_real ) and os.path.isdir( 
> efp_real ):
> +                         log.warning( "finish(): %s found, so it will be 
> used instead" % ( efp_fake, efp_real ) )
> +                     else:
> +                         self.fail( "Job %s's output dataset(s) could not be 
> read" % job.id )
> +                         return
>         job_context = ExpressionContext( dict( stdout = stdout, stderr = 
> stderr ) )
>         job_tool = self.app.toolbox.tools_by_id.get( job.tool_id, None )
>         def in_directory( file, directory ):
> diff -r -c -x '.hg*' psu_dist/lib/galaxy/tools/__init__.py 
> glxtemp/lib/galaxy/tools/__init__.py
> *** psu_dist/lib/galaxy/tools/__init__.py     Fri Sep 16 11:03:48 2011
> --- glxtemp/lib/galaxy/tools/__init__.py      Wed Sep 28 13:58:44 2011
> ***************
> *** 1516,1522 ****
>                 param_dict[name] = DatasetFilenameWrapper( hda )
>             # Provide access to a path to store additional files
>             # TODO: path munging for cluster/dataset server relocatability
> !             param_dict[name].files_path = os.path.abspath(os.path.join( 
> job_working_directory, "dataset_%s_files" % (hda.dataset.id) ))
>             for child in hda.children:
>                 param_dict[ "_CHILD___%s___%s" % ( name, child.designation ) 
> ] = DatasetFilenameWrapper( child )
>         for out_name, output in self.outputs.iteritems():
> --- 1516,1524 ----
>                 param_dict[name] = DatasetFilenameWrapper( hda )
>             # Provide access to a path to store additional files
>             # TODO: path munging for cluster/dataset server relocatability
> !             #param_dict[name].files_path = os.path.abspath(os.path.join( 
> job_working_directory, "dataset_%s_files" % (hda.dataset.id) ))
> !             # This version should make it always follow the primary file
> !             param_dict[name].files_path = os.path.abspath( os.path.join( 
> os.path.split( param_dict[name].file_name )[0], os.path.split( 
> param_dict[name].file_name )[1].replace( '.dat', '_files' ) ))
>             for child in hda.children:
>                 param_dict[ "_CHILD___%s___%s" % ( name, child.designation ) 
> ] = DatasetFilenameWrapper( child )
>         for out_name, output in self.outputs.iteritems():
> 
> 
> ___________________________________________________________
> 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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