Greg Von Kuster
94f3489952
Add support for all Galaxy form widget types to data library templates ( library templates now support SelectField, AddressField, CheckboxField, WorkflowField in addition to previously supported TextArea and TextField ).
...
Create a new UsesFormDefinitionWidgets base controller class for use with all inheriting controllers that use Galaxy forms. Clean up some of the existing code by re-using mehtods in this new controller.
Fix bugs related to new user address creation and editing existing user addresses: (1) form contents are now actually checked and if required, error messages are displayed (2) since there is only 1 "address" row in the UserAddress table, eliminate the address1 / address2 form field combination that was appened together for storage in the table ( ther eis now only 1 address line on all forms ).
Fix functional tests to reflect above changes.
2010-08-26 10:55:47 -04:00
Greg Von Kuster
a7e30c4441
Apply patch from Brad Chapman providing support for detecting, uploading and displaying UCSC bigWig and bigBed. Add new functional tests for uploading and detecting bigbed and bigwig formats, and correct and clean up the test_get_data.py functional test script.
2010-08-19 13:58:10 -04:00
Nate Coraor
6e7427e8e2
Removed binseq.zip test and replace it with a zip test.
2010-07-01 08:59:26 -04:00
Ramkrishna Chakrabarty
45cb09579f
lims: requests/request_admin controller refactor
...
A new controller called requests_common now handles all common tasks like create/edit/delete requests & samples. The requests controller has only the grid definition and requests_admin controller has the request_type code and the sequencer data transfer code.
Also fixed a form importer bug in forms.py
2010-06-30 10:46:50 -04:00
Nate Coraor
b7119df159
Security fixes for the library_common controller.
2010-06-21 11:15:13 -04:00
Daniel Blankenberg
183c2d3d13
Bug fix for handling 'spaces to tab' for non-binary composite datatype files.
...
Add upload tests for testing 'space to tab' when uploading composite and non-composite datatypes.
2010-06-07 15:34:20 -04:00
Greg Von Kuster
3135ffa5fc
Fix for LibraryDatasetDatasetAssociation objects when created by importing a history item iinto a library, the copied_from_history_dataset_association_id will now be kept.
...
Add a get_display_name() method to the LibraryDatasetDatasetAssociation class.
Fix for the test_forms_and_requests.py functional test script, purge all created libraries created during the tests so following test runs will test correctly.
2010-06-02 14:24:48 -04:00
Greg Von Kuster
e96b597b26
Fix the test_forms_and_requests.py functional test script to purge the group named "Group One" from the database in the reset data method so that later tests that create a group with the same name will pass. All library functional tests should now pass.
2010-06-01 10:02:34 -04:00
Greg Von Kuster
033bcecd0d
Send the web freamework ( trans ) to the grid's build_initial_query() method rather than the web framework's db session so that the method can take advantage of all of the web freamwork's attributes. Change the library controller to use grids for the data libraries display.
2010-05-24 11:22:12 -04:00
Ross Lazarus
d4ebd35d3a
More tweaks to some snp/wga composite output test comparisons - all png/pdf should be sim_size rather than lines_diff
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Updated test outputs for snp/wga tools
Testing a new hgignore so welcome.html should not be overwritten
2010-05-20 12:38:35 -04:00
Ross Lazarus
aaca176ed7
Add mimetypes to snp/wga datatypes in genetics.py
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Fix edit_attributes to snp/wga composite files in tests
2010-05-11 11:51:49 -04:00
Jeremy Goecks
06f1110d2a
Bug fixes for history import: (a) import can now be used by users who have access via sharing and (b) import changes the current history to the imported history. Functional tests updated to reflect new functionality and error messages.
2010-05-02 15:34:41 -04:00
Ramkrishna Chakrabarty
aa381ae70d
lims:
...
- ui cleanup
- fixed a functional test bug
2010-04-23 15:31:52 -04:00
Ramkrishna Chakrabarty
d38a1128bc
lims: add tests for request_type permissions
2010-04-23 13:16:40 -04:00
Greg Von Kuster
a08759edc2
Allow non-admin users that have the LIBRARY_MODIFY permission to delete / undelete library items as well as display / hide deleted library items.
2010-04-14 15:16:03 -04:00
Greg Von Kuster
5295965931
Decouple the TagHandler from the model by allowing sub-classes to point to a specified model. Add a baseline functional tests script to provide coverage for tagging histories and history items ( more coverage is needed, of course, and can easily be added to this script ).
2010-04-13 15:35:32 -04:00
Ramkrishna Chakrabarty
5fb95b2d8b
fixed forms and user_info functional tests
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removed a debugging print stmt
2010-04-13 10:16:46 -04:00
Greg Von Kuster
dc728ca16f
Handle user registration and login in the galaxy_main frame to ensure masthead. After registration or login, use javascript to redirect to the page the user was viewing when they attempted login. If javascript is disabled, a page will be displayed with links to the page they were visiting or the home page. Revamp functional tests to cover new behavior. Fix bugs where the username was not validated when a user registered, and add functional tests to cover. Fix a bug where the user's new session may have set it's history to the user's previous history, even if the history was deleted. Now a new history will be created for the current session instead. Add a new logout.mako template, and remove a create.mako template that was no longer used.
2010-04-02 15:00:53 -04:00
Greg Von Kuster
453ddcb06e
De-couple the user controller from the model, adding a webapp param to some method signatures to allow for different webapps to use the controller. Clean up the methods in the controller, eliminating all that are no longer used. Fix the verification mehtod for resetting user names to use rules for setting user names. Add new mako templates for the login and reset password methods instead of the inline form building. Fix a bug where the user's private roles was not correctly updated when the user's email address was changed. Overhaul the test_user_info functional test script, cleaning up the mehtod code and to provide coverage for all of the above fixed bugs.
2010-03-31 09:42:50 -04:00
Kelly Vincent
710e9cfd07
Added new tabular/pileup join tool and associated test files. Also added pileup datatype.
2010-03-26 12:00:55 -04:00
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
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- 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:
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- 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:
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- 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
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- 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