Re: [galaxy-dev] (Composite) Dataset Upload not Setting Metadata
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.
It's not really that way on purpose, you should be able to define a
filetype and bypass the unarchiving, but as you've discovered, this
can't be done without modifying the code. This is essentially a bug.
There are two issues to track related to fixing this:
https://bitbucket.org/galaxy/galaxy-central/issue/280/allow-zip-file-uploads
https://bitbucket.org/galaxy/galaxy-central/issue/304/make-binary-datatype-uploads-pluggable
Thanks
--nate
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
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 cas!
es. 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
Re: [galaxy-dev] (Composite) Dataset Upload not Setting Metadata
Hi Dan, Sure, here's the example where I discovered the bug (data files are not attached because of a 5MB limit on my email client; see http://main.g2.bx.psu.edu/u/paniag/h/metadata-bug-example for a history with the example dataset). The datatype is AffyBatch (or probably anything derived from RexpBase) in lib/galaxy/datatypes/genetics.py. 1. On Galaxy main (http://main.g2.bx.psu.edu/) go to Get Data - Upload File 2. Select affybatch under file format. 3. Choose the attached files for upload in their corresponding fields. 4. Select genome mm9 5. Hit Execute 6. Wait for job completion, which occurs successfully (ie end up green) 7. Click to expand new history item 8. Note that the peek box displays an error message I further tested by trying to use the newly uploaded dataset with the reQC tool from the Rexpression library (I don't see it on the main site). By looking into that code I realized metadata wasn't getting set, and (as detailed below) I tracked the problem through the upload tool, (local) tool runner, job wrapper, etc and discovered the metadata problem. Best, 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.edumailto: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
Re: [galaxy-dev] (Composite) Dataset Upload not Setting Metadata
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.edumailto: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
Re: [galaxy-dev] (Composite) Dataset Upload not Setting Metadata
Hi Eric, I was able to reproduce the error. We'll work on a fix for this, but, for now, you can fix the metadata after uploading by clicking on the pencil icon and clicking Auto-detect. Thanks for reporting this error. Thanks for using Galaxy, Dan On Oct 3, 2011, at 2:34 PM, Paniagua, Eric wrote: Hi Dan, Sure, here's the example where I discovered the bug (data files are not attached because of a 5MB limit on my email client; see http://main.g2.bx.psu.edu/u/paniag/h/metadata-bug-example for a history with the example dataset). The datatype is AffyBatch (or probably anything derived from RexpBase) in lib/galaxy/datatypes/genetics.py. 1. On Galaxy main (http://main.g2.bx.psu.edu/) go to Get Data - Upload File 2. Select affybatch under file format. 3. Choose the attached files for upload in their corresponding fields. 4. Select genome mm9 5. Hit Execute 6. Wait for job completion, which occurs successfully (ie end up green) 7. Click to expand new history item 8. Note that the peek box displays an error message I further tested by trying to use the newly uploaded dataset with the reQC tool from the Rexpression library (I don't see it on the main site). By looking into that code I realized metadata wasn't getting set, and (as detailed below) I tracked the problem through the upload tool, (local) tool runner, job wrapper, etc and discovered the metadata problem. Best, 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.edumailto: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
Re: [galaxy-dev] (Composite) Dataset Upload not Setting Metadata
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.edumailto: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
Re: [galaxy-dev] (Composite) Dataset Upload not Setting Metadata
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 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 [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 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
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 [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 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 [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 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
Re: [galaxy-dev] (Composite) Dataset Upload not Setting Metadata
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. Thanks, Eric Paniagua From: 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 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 [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 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
[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 access 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/
