Greg Von Kuster
8a7091591b
Fix for editing library templates, add a new functional test to cover the scenario, and some code cleanup.
2010-03-16 16:03:28 -04:00
Greg Von Kuster
85d008846b
New separate functional test scripts for testing admin features, library features, library security and data security. These use a new test_db_util module for all db interaction ( other functional test scripts can be enhanced to use this ). A lot of code cleanup in the functional tests. In twilltestcase, cleaned up library and security related methods to mirror names in recently merged library code.
2010-03-12 16:11:26 -05:00
Ross Lazarus
a6989261b7
Revert the twilltestcase upload_composite code needed for lped/pbed upload testing
2010-03-10 17:10:43 -05:00
Daniel Blankenberg
becb50feaa
Allow renaming of uploaded files in toolbox tests by including a <edit_attributes type="name" value="new dataset name" /> child tag. A rename directive is automatically assigned (no xml changes required) to uploaded composite datasets, so that they can be identified uniquely.
2010-03-10 11:28:50 -05:00
Greg Von Kuster
02565373ec
Fix for deleting a list of library datasets - resolves ticket # 102.
2010-03-10 11:24:49 -05:00
Daniel Blankenberg
80184b52f5
Allow better testing of tool outputs with an unknown number of dynamically created outputs.
2010-03-09 14:28:33 -05:00
Daniel Blankenberg
994f2acdea
Allow uploading and use of composite files in toolbox tests. Along with setting each component of a composite datatype, metadata attributes (e.g. basename in Rgenetics datatypes) can be set.
...
Example Tool:
<tool id='temp' name='temp test'>
<description>test</description>
<command>cat ${i.extra_files_path}/${i.metadata.base_name}.fam > $out_file1</command>
<inputs>
<param name="i" type="data" label="RGenetics genotype data from your current history" format="pbed" />
</inputs>
<outputs>
<data format="text" name="out_file1" />
</outputs>
<tests>
<test>
<param name='i' ftype='pbed'>
<metadata name='base_name' value='rgenetics_CHANGED' />
<composite_data value='temp/somefile1' />
<composite_data value='temp/somefile2' />
<composite_data value='temp/somefile3' />
</param>
<output name='out_file1' file='temp/somefile3' />
</test>
</tests>
</tool>
2010-03-09 13:54:30 -05:00
Daniel Blankenberg
e31e8b8fd9
Add the ability for tests to have a lines_diff attribute set for standard output datasets that will allow the specified number of lines to vary between test-data and tool run results; a 'change' to a line equates to a difference of 2 lines between files (i.e. 1 line added, 1 line removed). Add the ability for test comparisons to use single or multiline regular expressions, this is accessed by adding the attribute compare= "match_re" or "match_re_multiline" (respectively); the standard diff method can be explicitly declared as "diff", or is used at the default when not specified.
2010-03-05 17:21:16 -05:00
Ramkrishna Chakrabarty
9f28113081
Fixed broken functional tests
2010-03-03 13:51:29 -05:00
Greg Von Kuster
3aa2fc3601
Passwords are no longer changed ( sanitized ) as part of processing the request. Enhanced functional tests to cover the scenario where passwords include chars that break in sanitization.
2010-03-01 16:07:54 -05:00
Greg Von Kuster
9ebc5cfdba
Re-fix new functional test support for setting check boxes and boolean tool params to false, and fix a broken functional test in the security and libraries suite.
2010-02-19 10:01:33 -05:00
Greg Von Kuster
c85b48de7f
Sort the datasets by name when browsing a library from the Data Libraries view. Add a cleanup method to the functional test script for forms and requests - functional tests for libraries should now pass.
2010-02-15 16:56:02 -05:00
Greg Von Kuster
572dff9f8f
Add a synopsis column to the library table, fix displaying the mast head when accessing a data library from an external url, and eliminate the display of all non-private roles on permissions forms.
2010-02-15 12:30:49 -05:00
Greg Von Kuster
1a239e9c67
Add the ability to edit library templates and make library template inheritance optional.  Fix another bug in the form builder's CheckboxField.is_checked() method, and clean up some library code. With regard to template inheritance, a LibraryFolder is a special case because if it inherited the template from it's parent, we want to set inheritable to True for it's info_association.  This allows for the default inheritance to be False for each level in the Library hierarchy unless we're creating a new level in the hierarchy, in which case we'll inherit the "inheritable" setting from the parent level.
2010-02-11 14:26:25 -05:00
Greg Von Kuster
f643999432
Data library UI cleanup and improvements. Widgets are now displayed for the currently selected tempalte when adding one to a library item.
2010-02-05 15:51:01 -05:00
Ramkrishna Chakrabarty
cea3324bbb
Sequencer data acquisition for LIMS
...
- Add a data transfer script which fetches datasets from the sequencer
- transfer_datasets.ini for setting up the separate user to login to Galaxy programmatically to add datasets to the data libraries.
- Added a dataset transfer page which includes remote file browser to select files for transfer
Removed library & folder foreign keys from the request table and added them to the sample table. Also the sample table now has a dataset_files column to store the datatsets and the their transfer status.
Add an egg for pexpect which is used in the remote file browser.
The request_type table has a new column datatx_info which stores all the login info for the sequencer machine
2010-02-04 11:01:45 -05:00
Greg Von Kuster
8c91a01e5f
A few improvements to library templates. Behavior is still not optimal, but at least now functional. Functional tests still needed, and coming shortly.
2010-02-01 15:43:07 -05:00
Greg Von Kuster
21c7762269
Fixes for library templates: add the ability to add a template to a librry dataset in addition to a library and a folder, add the ability to delete templates from library items. Fixes for displaying and hiding deleted library folders and datasets.
2010-01-30 07:48:39 -05:00
Greg Von Kuster
c47680c1eb
If a dataset is not public, populate the permissions forms for it with legitimate roles only.
2010-01-26 16:16:03 -05:00
Greg Von Kuster
d345a3c5cd
Fix some problems related to setting the 'manage permissions' permissin on library datasets.
2010-01-26 13:26:42 -05:00
Greg Von Kuster
a8caacc20d
Fix for the general functional test tool failures.
2010-01-22 13:51:56 -05:00
Greg Von Kuster
027d048592
If a library is not public, ensure that the roles displayed on the upload form or any permission form for a contained folder or dataset are derived from the set of users that have access to the library.  Add error checks to the upload tool to display appropriate error messages if ill-legitimate roles were selected ( shouldn't happen since they are filtered out ) or if roles are selected such that the dataset would be in-accessible to everyone.
2010-01-22 11:24:28 -05:00
Jeremy Goecks
f3b08e6e01
Unified sharing model for histories, workflows, and pages; these items can now be private, shared with a set of users, accessible via link for viewing and importing, or published. Specific features added are: (1) added published flag to histories and workflows, added importable flag to pages; (2) added unified sharing interface for setting sharing options; (3) updated grid framework to use new sharing model; (4) updated functional tests to reflect new sharing model; (5) added legacy support for making pretty URLs for items already made importable. Also, new sharing model does not yet allow sharing of multiple items at once, so functional test for this feature has been commented out. Fixes #229 ; Fixes #182 .
2010-01-20 12:26:13 -05:00
Greg Von Kuster
2986e5f01a
Bug fixes: fix importing a history item to a library, fix checking security on libraries from requests, send hid every time to functional test's verify_dataset_correctness() since we can now test multiple output datasets., and fix displaying info for library datasets in some scenarios.
2010-01-13 18:02:37 -05:00
Greg Von Kuster
093a9700ed
Enhance test framework to handle testing multiple outputs from tools.
2010-01-11 16:35:16 -05:00
Greg Von Kuster
98f8c9df29
Enhance lastz tool, enhance functional test framework, and fix a bug in editing permissions on a folder:
...
- until now, lastz will (mostly) ignore alignments in masked regions since soft-masking has been enabled.  Now the default has changed to disable soft masking, and an option has been added to the tool to enable it if desired.
- the functional test framework now allows for a new "sort" attribute in the output tag for functional tests.  For example:  <output name="output1" file="lastz_wrapper_out4.tabular" sort="True" />
If set to True, the output dataset will be sorted prior to comparing.  This is needed for the lastz tool since multiple threads generate output randomly if the input file has more than 1 sequence.  The default is False.
- Decode the id of a folder prior when retrieving from the database - fixes the bug reported by Guru.
2010-01-11 13:26:00 -05:00
Greg Von Kuster
088b9cd030
Bug fixes and code cleanup for managing users, groups and roles.
2010-01-05 14:47:55 -05:00
Greg Von Kuster
d4302ae6b9
UI cleanup and fixes:
...
- only display check boxes on a grid if there are operations to perform
- asynchronous uploads will now properly handle associated library templates
- miscellaneous fixes for issues introduced in the library code merge in change set 3194:4743015d9a57
2010-01-05 10:31:32 -05:00
Greg Von Kuster
14940be7cc
Data library cleanup
...
- move / merge all duplicate methods from the library_and library_admin controllers into the library_common controller
- move / merge all duplicate mako templates into the ~/library/common directory
- make the admin view library browser a grid
- all library item ids are now encoded
2009-12-23 20:26:01 -05:00
Greg Von Kuster
bcd6751cdf
Fix for uploading a Bam file that has not yet been sorted, the call to samtools sort has been moved from the sam_to_bam tool to the Bam()set_meta() method to ensure all Bam datasets are sorted prior to indexing. Added new functional tests to cover uploaing unsorted Bam files. Also cleaned up code in the upload tool for uploaing various binary data formats.
2009-12-07 16:04:33 -05:00
Greg Von Kuster
0e807f13f5
Add support for uploading BAM files.
2009-12-02 20:02:05 -05:00
Ramkrishna Chakrabarty
d2eb5a388b
Request events & request rejection (resolves issue #221 )
...
- added request_events table
- removed 'state' field in the request table
- added 'new' & 'rejected' request states
- color coded request states in the request grid
Grids framework
- added a confirm flag in grid operations which require confirmation before going through with operation
2009-11-25 14:06:28 -05:00
Greg Von Kuster
a722a2aa0a
Move line count processing from set_peek() methods to set_meta() methods for data types since set_meta can run externally and it does line by line processing in some cases. Added new MetadataElements to the Data, Text, Sequence and Maf classes to handle setting dataset.blurb from stored metadata. Cleaned up a lot of code in the process.
2009-11-20 11:03:41 -05:00
Ramkrishna Chakrabarty
c73610de9d
Adding grids to forms, requests & request types pages. Resolves issue #231 .
2009-11-17 14:28:34 -05:00
Greg Von Kuster
8b29c18868
Enhance history item error reports that are emailed
...
- report form now defaults to include the users email address if they are logged in
- email now includes the id of both the dataset and the history, the hid and hda.display_name(), and a link to the history
- admin users now have "view" access to any history and dataset ( this uses the new ~/history/view?id=... feature )
2009-11-16 16:27:48 -05:00
Greg Von Kuster
e38e78f5e4
Fixes, cleanup and new functional tests for data types and upload:
...
- moved all supported binary data types to the new binary.py
- changed GeneTrack data type to subclass from Text rather than Binary
- added Sff data type to datatypes_conf.xml.sample
- merged test_sniffinad_and_metadata_settings.py test scritp into test_get_data.py
- added several additional functional test for data types to test_get_data.py
- fixed some bugs in upload.py when uploading binary data types
2009-11-13 14:13:03 -05:00
Nate Coraor
d2102123d9
Add a "maxseconds" attribute to the "test" tag in tool configs. Allows the tool writer to decide how long Galaxy should wait for tool execution to complete. Resolves issue #219 .
2009-11-12 11:07:05 -05:00
Ramkrishna Chakrabarty
702bad5d25
Added sff datatype
...
Also, made changes to upload.py to sniff sff binary files
2009-11-11 17:55:08 -05:00
Greg Von Kuster
8f6e8213a0
Fix most of the db flushes to be compatibel with sqlalchemy 05. Add the _monkeypatch_query_method() back into assignmapper due to a single object.get() method in the MetadataCollection class since Metadata has no current hook into mapping.context ( the sqlalchemy session ). There a 4 flushes in metadata,py and 20 flushes in model.__init__.py that still use the _monkeypatch_session_method in assignmapper due to the same issue, but all other flushes are fixed.
2009-11-11 15:59:41 -05:00
Nate Coraor
baea4439d1
Add test for library tarball downloads
2009-11-10 15:10:43 -05:00
Ramkrishna Chakrabarty
c3878e925f
Fixed a bug in the view requesttype page.
...
Now barcodes are visible in the request details page itself.
2009-11-10 12:35:00 -05:00
Greg Von Kuster
00c3f84f40
Incorporate latest grid features into managing users, groups and roles from the admin view.
2009-11-09 23:00:55 -05:00
Ramkrishna Chakrabarty
6dce23d603
Fixed some functional tests related to the previous commit
2009-11-09 16:40:59 -05:00
Ramkrishna Chakrabarty
a5c0f9305f
Fixed a checkbox bug in request & user_info
...
Resolved bitbucket issue 221: now there is a reject option for an admin to move a request to an unsubmitted state
2009-11-09 16:15:52 -05:00
James Taylor
905a6e503b
Fix closure in creation of generated test methods, otherwise the last testdef is used for every test
2009-11-06 00:25:02 -05:00
James Taylor
6fdcd4ba08
Fix for tools with multiple tests
2009-11-05 17:55:14 -05:00
Ramkrishna Chakrabarty
7a441130bb
Refactored the new address functional test
2009-11-05 14:19:45 -05:00
James Taylor
1bc08c9546
Fix tool test specification by id
2009-11-04 11:35:50 -05:00
Nate Coraor
87aa7e2287
merge heads
2009-11-03 13:04:35 -05:00
Jeremy Goecks
ec3674f5f0
Improved search functionality for history grid: (a) generic free text search box and (b) advanced search using name, tag, deleted status, and shared status.
2009-11-03 12:58:13 -05:00
Greg Von Kuster