Pivotal Tracker story 27410303 (Psalm Haseley - Apr 2, 2012)

Pivotal Tracker story 27550029 (Nils Gehlenborg - Apr 4, 2012)

Created with Eclipe Mylyn.

Finish up galaxy workflows and download results to a selected directory
Tasks:

• Download analysis results to directory

Pivotal Tracker story 27458343 (Richard Park - Apr 3, 2012)

Pivotal Tracker story 32709133 (Nils Gehlenborg - Jul 12, 2012)

Data sets (core) will contain one or more instances of a ISA-TAB investigation. Only the most recent one will be "active" (e.g. for indexing and searching.

Pivotal Tracker story 28338013 (Nils Gehlenborg - Apr 19, 2012)

The slugs are not enforced to be unique.

submit a zipped ISA-Tab file via POST, unzip and parse

Pivotal Tracker story 28890601 (Ilya Sytchev - May 1, 2012)

currently git clone url in readme is:

git clone [email protected]:parklab/refinery-platform.git

Running it gives:
Cloning into 'refinery-platform'...
Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.

git clone https://github.com/parklab/refinery-platform.git

worked for me.

Instructions indicated to:
django-admin.py createsuperuser

no createsuperuser command found

using

python manage.py createsuperuser

from /vagrant/refinery dir worked for me

modify ISA-Tab processing to log into a single file

Pivotal Tracker story 32490181 (Nils Gehlenborg - Jul 9, 2012)

I was wondering if you have time to look into logging in Django and how we could use this for Refinery. It looks like Django 1.3 introduced extensive logging facilities but I'm specifically interested in whether there is there is already an extension or project with a UI to centrally monitor the log messages for a Django project (such as Refinery). Maybe this has been implemented or could be implemented in the Django admin interface.

In Refinery we would like to avoid exposing all errors to the end users because there is not much that they can do if a problem occurs so I imagine that we will have (a) a log monitor for the system administrator with all messages and (b) log monitors for project administrators/users that contains only messages that they can address themselves (problems with user uploaded files, approaching disk quotas, etc.).

For now all you'd need to do is to read up on this and get an overview of what is out there that could help us with these tasks. The next step would be to work on (a) and figure out what the best way is to implement filters, search, notifications etc. for log messages. Once we have figured this out (b) should be easy to implement.

Pivotal Tracker story 26823249 (Nils Gehlenborg - Mar 21, 2012)

First test on fisher. 2x2 inputs and experiments totaling about 2 GB creates a final analysis set of about 6.5 gb. The total expansion factor is about 2-3x.

Pivotal Tracker story 27409219 (Psalm Haseley - Apr 2, 2012)

Pivotal Tracker story 33435297 (Psalm Haseley - Jul 26, 2012)

Pivotal Tracker story 29236651 (Nils Gehlenborg - May 8, 2012)

Tasks:

• flag outputs in Galaxy workflow editor
• update get_history_file_list() to (by default) ignore visible=false files

Pivotal Tracker story 27611871 (Nils Gehlenborg - Apr 5, 2012)

Pivotal Tracker story 33081827 (Richard Park - Jul 19, 2012)

create symlinks to files added to the file store from local file system

Pivotal Tracker story 32560893 (Ilya Sytchev - Jul 10, 2012)

The number of steps for an expanded workflow is now stored in the analysis model.

Pivotal Tracker story 27294253 (Nils Gehlenborg - Mar 30, 2012)

Pivotal Tracker story 27409145 (Psalm Haseley - Apr 2, 2012)

Something needs to be fixed.

Once an analysis has completed the results (i.e. specific output files) have to be stored in the repository together with information about how they were created.

Pivotal Tracker story 26784185 (Nils Gehlenborg - Mar 21, 2012)

Pivotal Tracker story 26784421 (Nils Gehlenborg - Mar 21, 2012)

Tasks:

• extend data model
• store files (zipped)

Pivotal Tracker story 26872163 (Nils Gehlenborg - Mar 22, 2012)

Pivotal Tracker story 27478955 (Psalm Haseley - Apr 3, 2012)

Pivotal Tracker story 26823669 (Nils Gehlenborg - Mar 21, 2012)

Use states of the current history to implement this.
Tasks:

• implement monitoring with callbacks
• implemented monitoring via analysis_manager for workflows

Pivotal Tracker story 26811059 (Nils Gehlenborg - Mar 21, 2012)

Pivotal Tracker story 33084467 (Nils Gehlenborg - Jul 19, 2012)

Nothing initializes in Firefox if an analysis is selected. IGV viewing works.

create(), read(), import(), delete() and update()

Pivotal Tracker story 28888117 (Nils Gehlenborg - May 1, 2012)

Following the instructions for importing a workflow from galaxy into refinery.
Step 1 is to create a galaxy instance in refinery.

The instructions say to use the administration interface, which i can't seam to find.
At 1st i thought my refinery user didn't have enough permissions to see the administration interface (perhaps my creation of the django super user failed, though an account was created....)

Then I found the create_galaxy_instance command in manage.py.
Though there was no details on how to use it.

Using my imagination i tried:
python manage.py create_galaxy_instance galaxyAPIURL
But that didn't work either.

Figure out a way for galaxy to zip a collection of files with the proper names via the cluster to prevent the front end from being bogged down by extra processing

Pivotal Tracker story 32495693 (Richard Park - Jul 9, 2012)

takes in a directory of isa-archives or a single isa-archive

Pivotal Tracker story 33121935 (Psalm Haseley - Jul 20, 2012)

Pivotal Tracker story 35637161 (Nils Gehlenborg - Sep 6, 2012)

Reproduce: click the "View in IGV" button multiple times in quick succession after selecting a subset of files.

Possible cause: Multiple requests get send but previous requests do not get aborted or their returns do not get handled correctly.

Pivotal Tracker story 27410481 (Psalm Haseley - Apr 2, 2012)

Pivotal Tracker story 28337969 (Nils Gehlenborg - Apr 19, 2012)

Pivotal Tracker story 27409117 (Psalm Haseley - Apr 2, 2012)

Right now there are two ISA-Tab processing tasks and they should be merged to avoid duplication of code (DRY). See data_set_manager.tasks.py (towards the end of the file).

Pivotal Tracker story 33677665 (Nils Gehlenborg - Jul 31, 2012)

Pivotal Tracker story 33084397 (Nils Gehlenborg - Jul 19, 2012)

What is the difference between Sphinx and PyDocs? What does Read the Docs offer? Can we download the docs from RTD easily?

We want a solution that would also allow us to write brief tutorials and step-by-step descriptions on how to perform certain tasks, see e.g. http://django-haystack.readthedocs.org/en/latest/tutorial.html

Pivotal Tracker story 27557737 (Nils Gehlenborg - Apr 4, 2012)

lines 17 and 123

Pivotal Tracker story 33123325 (Psalm Haseley - Jul 20, 2012)

Pivotal Tracker story 33122351 (Psalm Haseley - Jul 20, 2012)

Pivotal Tracker story 27478911 (Psalm Haseley - Apr 3, 2012)

Pivotal Tracker story 32742007 (Nils Gehlenborg - Jul 13, 2012)

Steps to reproduce:
Open a data set view (/data_sets//). Select a workflow and assign inputs. Add or remove a column, or change a facet filter. Assign inputs.

Observed behavior:
Workflow input assignment is reset after view columns are added/removed or if filters are applied. Inputs are not available for selection until the workflow is deselected then selected again.

Expected behavior:
Input assignments should not be changed by applying filters or selecting/removing view columns. If input assignments are reset, they should be available for selection without having to de-select then re-select the workflow.

A quick overview - mention what "icebox" means.

Pivotal Tracker story 26822389 (Nils Gehlenborg - Mar 21, 2012)

TypeError exception is sometimes raised when trying to run a workflow from Available Samples page.

Steps to reproduce:

1. Import an ISA-Tab file.
2. Proceed to the Available Samples page.
3. Select a workflow and its inputs, and click Run Workflow.

Analysis Results page loads but progress bars are not displayed. Data is not imported in Galaxy. No errors appear in Django server console but the following output appears in Celery console:

[2012-07-13 17:52:40,053: WARNING/PoolWorker-1] analysis_manager.chord_postprocessing called
[2012-07-13 17:52:40,065: WARNING/PoolWorker-1] analysis_manger.download_history_files called
[2012-07-13 17:52:40,122: ERROR/MainProcess] Task analysis_manager.tasks.chord_postprocessing[d5c88166-9d1d-47ac-bacc-375b950cd927] raised exception: TypeError("cannot concatenate 'str' and 'NoneType' objects",)
Traceback (most recent call last):
  File "/Users/isytchev/environments/refinery/lib/python2.7/site-packages/celery/execute/trace.py", line 47, in trace
    return cls(states.SUCCESS, retval=fun(*args, **kwargs))
  File "/Users/isytchev/environments/refinery/lib/python2.7/site-packages/celery/app/task/__init__.py", line 247, in __call__
    return self.run(*args, **kwargs)
  File "/Users/isytchev/environments/refinery/lib/python2.7/site-packages/celery/app/__init__.py", line 175, in run
    return fun(*args, **kwargs)
  File "/Users/isytchev/workspace/Refinery/refinery/analysis_manager/tasks.py", line 74, in chord_postprocessing
    postprocessing_taskset = download_history_files(analysis)
  File "/Users/isytchev/environments/refinery/lib/python2.7/site-packages/celery/app/task/__init__.py", line 247, in __call__
    return self.run(*args, **kwargs)
  File "/Users/isytchev/environments/refinery/lib/python2.7/site-packages/celery/app/__init__.py", line 175, in run
    return fun(*args, **kwargs)
  File "/Users/isytchev/workspace/Refinery/refinery/analysis_manager/tasks.py", line 399, in download_history_files
    download_list = connection.get_history_file_list(analysis.history_id)
  File "/Users/isytchev/workspace/Refinery/refinery/galaxy_connector/connection.py", line 124, in get_history_file_list
    print self.get_history_contents( history_id )
  File "/Users/isytchev/workspace/Refinery/refinery/galaxy_connector/connection.py", line 98, in get_history_contents
    return self.get( "histories" + "/" + history_id + "/" + "contents" )
TypeError: cannot concatenate 'str' and 'NoneType' objects

Traceback (most recent call last):
  File "/Users/isytchev/environments/refinery/lib/python2.7/site-packages/celery/execute/trace.py", line 47, in trace
    return cls(states.SUCCESS, retval=fun(*args, **kwargs))
  File "/Users/isytchev/environments/refinery/lib/python2.7/site-packages/celery/app/task/__init__.py", line 247, in __call__
    return self.run(*args, **kwargs)
  File "/Users/isytchev/environments/refinery/lib/python2.7/site-packages/celery/app/__init__.py", line 175, in run
    return fun(*args, **kwargs)
  File "/Users/isytchev/workspace/Refinery/refinery/analysis_manager/tasks.py", line 74, in chord_postprocessing
    postprocessing_taskset = download_history_files(analysis)
  File "/Users/isytchev/environments/refinery/lib/python2.7/site-packages/celery/app/task/__init__.py", line 247, in __call__
    return self.run(*args, **kwargs)
  File "/Users/isytchev/environments/refinery/lib/python2.7/site-packages/celery/app/__init__.py", line 175, in run
    return fun(*args, **kwargs)
  File "/Users/isytchev/workspace/Refinery/refinery/analysis_manager/tasks.py", line 399, in download_history_files
    download_list = connection.get_history_file_list(analysis.history_id)
  File "/Users/isytchev/workspace/Refinery/refinery/galaxy_connector/connection.py", line 124, in get_history_file_list
    print self.get_history_contents( history_id )
  File "/Users/isytchev/workspace/Refinery/refinery/galaxy_connector/connection.py", line 98, in get_history_contents
    return self.get( "histories" + "/" + history_id + "/" + "contents" )
TypeError: cannot concatenate 'str' and 'NoneType' objects

• interfaces with: Analysis Manager, Data Set Manager (Repository), external repositories, Connectors?
• includes cache, analysis input/output directories, original meta data files, data files for the local repository

Pivotal Tracker story 26871757 (Nils Gehlenborg - Mar 22, 2012)

Pivotal Tracker story 28259971 (Nils Gehlenborg - Apr 18, 2012)