Greg Von Kuster
ca364f7ed2
Reverting to rev 1459.
2008-10-02 15:51:17 -04:00
Greg Von Kuster
e01b8e5527
Remove a debug statement from root controller...
2008-10-02 13:18:50 -04:00
Greg Von Kuster
91620b3218
Fix all root controller methods so that history_dataset_association.id is not confused with history_dataset_association.dataset_id.
2008-10-02 12:45:03 -04:00
Greg Von Kuster
64c4c808f5
Fix for root/display() - history_dataset_association.dataset_id no longer confused with history_dataset_association.id.
2008-10-01 12:43:59 -04:00
Daniel Blankenberg
61ca17eade
Add a change_format tag to output datasets in tools. This allows for dynamic switching of output datatype based upon input values.
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Several tools have been updated to take advantage of this, eliminating their need for code_files.
2008-09-30 16:17:12 -04:00
Greg Von Kuster
48066e035d
Fix for disk usage report in the webapps system controller.
2008-09-29 10:37:54 -04:00
Daniel Blankenberg
929c68106d
Update to implicit converter discovery. Will now allow the use of converters that create datatypes that are a subclass of what is needed by the tool.
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i.e. If tool input requires 'interval', and a datatype has a BED converter available but no interval converter, the BED converter can now be used.
2008-09-26 14:22:37 -04:00
Daniel Blankenberg
0794f1315f
Fix for interval to bed converter.
2008-09-26 09:10:04 -04:00
Daniel Blankenberg
ba81daedf7
Enhance the way dataset.set_meta() behaves, by adding a flag 'overwrite', which when False will only overwrite metadata values that are not previously set or are not accessable for user modification.
2008-09-25 15:03:05 -04:00
Greg Von Kuster
61ef35c0f3
Eliminate enable_beta_features ( and the concept of 'beta' from the controllers ).
2008-09-24 15:05:38 -04:00
Daniel Blankenberg
6ad31f73bc
Some metadata updates.
2008-09-24 13:52:01 -04:00
Greg Von Kuster
7aace9ccaa
Convert metadata unicode strings to ascii ( previous code doesn't seem to do anything, am I missing something? ). Add no_value metadata attribute to columns and column_types metadata. Fix for column_maker and filter tools.
2008-09-24 11:14:44 -04:00
Greg Von Kuster
b4890c1bbb
Integrate with intermine ( data source ) and epigraph ( data destination ). Receiving data from epigraph coming soon. Data is sent to epigraph using a combination of DATA_URL and REDIRECT_URL tool params. This tool creates jobs, but does not queue them for execution.
2008-09-22 10:36:34 -04:00
Wen-Yu Chung
07118387a1
Fix a bug in shrimp_wrapper and add a tool for splitting paired-end reads.
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Update datatype/fastqsolexa so the number of sequences is correct.
2008-09-19 12:02:13 -04:00
Daniel Blankenberg
25fd3e140f
Add a wrapper for metadata inside of DatasetFilenameWrapper to allow proper string substitution in
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commandline and templates.
2008-09-18 16:48:29 -04:00
Nate Coraor
d8c3162dab
Quick 'n easy solution to the EMBOSS stage in/out problem: read the
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outputs from the "real" galaxy path instead of the temp stage path.
2008-09-17 10:45:20 -04:00
Daniel Blankenberg
90e30a30ae
The MetadataCollection object is now created only once per dataset object instance (and when datatype is changed), instead of each time dataset.metadata is called.
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The 'no_value' attribute for a metadata element's spec is returned when the metadata element's value is None.
2008-09-16 15:23:23 -04:00
Daniel Blankenberg
218a631b81
Strip whitespace from columns in file for dataset_metadata_in_file validator.
2008-09-16 14:10:53 -04:00
Daniel Blankenberg
9eb8caca6f
Small update for maf stats tool.
2008-09-16 13:25:42 -04:00
Daniel Blankenberg
940432f0e8
Update MAF stitcher to be more efficient. Requires bx-pyhon rev>=449.
2008-09-12 15:50:20 -04:00
James Taylor
5293399bcc
Allow complete logging configuration to be specified in the ini file,
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in which case this is used instead of the "log_level" and "log_format"
keys under the app configuration. PasteScript actually handles this, so
we just do nothing related to logging config if the ini file contains a
"[loggers]" section. For example, you could add this to the end of your
universe_wsgi.ini to include SQLAlchemy debugging and include the thread
name with every log message.
# Logger overrides
[loggers]
keys = root, sqlalchemy.engine, sqlalchemy.orm.unitofwork, paste.httpserver.ThreadPool
[logger_root]
level = DEBUG
handlers = console
[logger_sqlalchemy.engine]
level = INFO
handlers = console
qualname = sqlalchemy.engine
[logger_sqlalchemy.orm.unitofwork]
level = DEBUG
handlers = console
qualname = sqlalchemy.orm.unitofwork
[logger_paste.httpserver.ThreadPool]
level = INFO
handlers = console
qualname = paste.httpserver.ThreadPool
[handlers]
keys = console
[handler_console]
class = StreamHandler
args = (sys.stderr,)
level = NOTSET
formatter = generic
[formatters]
keys = generic
[formatter_generic]
format = %(threadName)s %(name)s %(levelname)s %(asctime)s %(message)s
2008-09-10 09:58:29 -04:00
Daniel Blankenberg
2495dc5166
The interval to BED converter will now use the name field specified via metadata, if available.
2008-09-08 11:15:58 -04:00
Daniel Blankenberg
5073bfb57a
Add a metadata parameter to Alignment datatypes which stores chromosome information found in the alignment for each species.
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GMAJ tool no longer needs to have the chromosome specified for annotations.
2008-08-28 15:12:53 -04:00
Daniel Blankenberg
2d65cd378b
Between page reloads, Drill Down parameter type will now keep parent nodes expanded when a descendant is selected.
2008-08-27 16:36:41 -04:00
Daniel Blankenberg
23ac99beca
dbkey must be set after _metadata column is initialized in the init of HDA, or else the dbkey is clobered.
2008-08-25 15:28:57 -04:00
Greg Von Kuster
4f56b82e17
Fix for dataset_metadata_in_file validator: all locally cached data files that are columnar must have columns separated by tabs characters, not white space. I've eliminated the 'split' param from the validator as it was causing problems. Extract genomic DNA tool should now finally work correctly.
2008-08-22 11:22:44 -04:00
Nate Coraor
2c73110e11
Reports: Wrap the stderr and traceback in pre tags so they display nicely.
2008-08-08 13:42:32 -04:00
Daniel Blankenberg
9b263ea4de
Fix for dynamic select lists generated from contents of input file when no valid datasets exist in the history.
2008-08-07 11:41:59 -04:00
Greg Von Kuster
223bb40e74
Better fix for gops command line parser, now properly handles no strand column.
2008-08-04 10:20:23 -04:00
Daniel Blankenberg
ec3176905a
Fix for the creation of workflows from shared histories.
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Added a column 'copied_from_history_dataset_association' to history_dataset_association. This requires a db change.
2008-08-01 15:05:54 -04:00
Greg Von Kuster
693caa34fc
Fix for gops metadata param parser when strand column not included in input dataset, added new test for gops intersect. Fix for datatype converters - now use new approach to metadata params.
2008-08-01 14:34:16 -04:00
Greg Von Kuster
81bb5e4996
Fix for JobWrapper.finish, dataset state no longer flushed prior to other attributes ( e.g., metadata) being flushed.
2008-08-01 14:25:42 -04:00
James Taylor
3221a71df3
Fix for preserving values of parameters after a repeat/conditional in
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Tool.update_state. This should fix the problem reported by Dan with the
subject "Re: [galaxy-bugs] Galaxy tool error report from cathy@bx.psu.edu ".
2008-07-31 17:55:41 -04:00
Nate Coraor
497ff6e05d
Rolling back Dan's most recent commits, we'll be setting up a branch for this.
2008-07-30 17:15:40 -04:00
Daniel Blankenberg
fd6b8b9b9d
Bug fix for Concatenate FASTA alignment by species tool.
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Also added a warning stating that this tool will only work on Galaxy style FASTA headers.
2008-07-29 11:24:28 -04:00
Daniel Blankenberg
633a218fce
Removing newly created history controller, and moving history_set_permissions into the root controller with the rest of the history methods.
2008-07-28 13:01:18 -04:00
Daniel Blankenberg
1554a13287
Allow users to specify the default permissions assigned to new histories.
2008-07-28 12:48:15 -04:00
Daniel Blankenberg
9a010cc626
Allow users to change the default permissions assigned to new datasets (not relying on input) for their current history.
2008-07-28 12:32:09 -04:00
Daniel Blankenberg
404d86d2ea
First pass with adding role based access controls. Added roles and groups. Users can be associated with groups. Roles can be associated with roles, datasets, groups, and users.
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Currently the creator of a dataset can mark the dataset as private, preventing other users from viewing or utilizing this dataset, even if it's containing history is shared. This is done via the edit attributes page for a particular dataset.
This requires enable_beta_features to be set.
2008-07-25 14:16:41 -04:00
Greg Von Kuster
5dd014a91e
Completed an old FIXME in DefaultToolAction.execute() - metadata no longer added to "incoming". Tool config params changed from things like$input_chromCol to ${input.metadata.chromCol}.
2008-07-23 15:27:39 -04:00
Greg Von Kuster
0ca286098f
Add use_remote_user to the reports config.
2008-07-23 09:24:13 -04:00
Greg Von Kuster
872c0d6c94
Make sure dataset peek is set before trying to display it.
2008-07-22 12:27:26 -04:00
James Taylor
958770640d
Fixes to tool parameter error handling in workflows. Workflows are now
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ordered by update_time desc in index pages. The menu frame refreshes
properly on changing the workflow menu.
2008-07-21 21:15:10 -04:00
James Taylor
1033fcf211
Allow result of file upload (and other datasets that don't have job records)
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to be used as "Input Datasets" when constructing a workflow from a history.
Fix problem with dynamic selects in histories (the values are now properly
wrapped with UnvalidatedValue).
2008-07-21 20:04:11 -04:00
James Taylor
d2c5e99b9e
Eager load HDAs. Must be careful with these joins, this was really slowing
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down /history on test. Run with "echo=True" for a while after making
substantial database changes.
2008-07-21 19:59:42 -04:00
James Taylor
e65294e0d5
Fix workflow menu configuration (submitting with not entries works,
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orphaned entry rows are deleted). Also prevent users from sharing a workflow
with themselves.
2008-07-21 18:39:18 -04:00
Greg Von Kuster
f8c00de9bc
Fix for displaying peek columns if a column contains no data.
2008-07-21 10:51:46 -04:00
Daniel Blankenberg
2c38721060
Typo in last commit.
2008-07-18 12:11:58 -04:00
Daniel Blankenberg
a19093d158
Fix bug in JobWrapper.get_input_fnames(), used by pbs runner, when an input dataset was optional and left empty.
2008-07-18 12:10:23 -04:00
James Taylor
70c4b8ee23
Workflows (owned and shared) can now be added to the tool menu.
2008-07-17 22:14:40 -04:00
Greg Von Kuster