| 7ff56bf | Dave Bouvier | 03 June 2013, 20:12:24 UTC | Cleanup after merge conflict. | 03 June 2013, 20:12:24 UTC |
| b8ed2c1 | Nate Coraor | 03 June 2013, 19:45:31 UTC | Added tag release_2013.06.03 for changeset 58811a78af8a | 03 June 2013, 19:45:31 UTC |
| 0bc8e9f | Nate Coraor | 03 June 2013, 19:44:31 UTC | Merge changes from next-stable to stable. | 03 June 2013, 19:44:31 UTC |
| c04ccc3 | Nate Coraor | 03 June 2013, 19:43:31 UTC | Close the next-stable branch. | 03 June 2013, 19:43:31 UTC |
| f4106af | Greg Von Kuster | 03 June 2013, 19:40:37 UTC | Fix for rendering xml elements that were not loaded using normal parsing methods. | 03 June 2013, 19:40:37 UTC |
| 485add5 | Dave Bouvier | 03 June 2013, 16:33:02 UTC | Fix for installing a tool dependencies when set_environment actions are distributed between multiple action tag groups. | 03 June 2013, 16:33:02 UTC |
| 950c146 | Greg Von Kuster | 03 June 2013, 16:05:24 UTC | Fix for handling tool panel section selection when installting tool shed repositories. | 03 June 2013, 16:05:24 UTC |
| f1e572b | Jeremy Goecks | 03 June 2013, 13:43:42 UTC | Remove documentation for Tophat -F option because it is no longer supported. | 03 June 2013, 13:43:42 UTC |
| 84a2fd3 | Greg Von Kuster | 01 June 2013, 21:22:27 UTC | Fix for resetting all metadata on writable repositories in the tool shed when the user is not an admin. | 01 June 2013, 21:22:27 UTC |
| 12b1cfc | Greg Von Kuster | 01 June 2013, 18:29:31 UTC | Strip traling / from tool shed url when using it's value to search the Galaxy database. | 01 June 2013, 18:29:31 UTC |
| 1d320bd | Dave Bouvier | 31 May 2013, 20:19:21 UTC | Fix for populating environment variables referenced with the $ENV[] syntax when installing repositories with complex repository dependencies. | 31 May 2013, 20:19:21 UTC |
| 232afae | Dave Bouvier | 31 May 2013, 16:53:56 UTC | Fix for redundant environment settings in env.sh when set_environment actions are distributed across multiple action sections. | 31 May 2013, 16:53:56 UTC |
| 97e8dc4 | Jeremy Goecks | 30 May 2013, 21:38:57 UTC | During workflow export, update workflow modules before visiting inputs to avoid errors resulting from parameter changes. | 30 May 2013, 21:38:57 UTC |
| 4ef01c2 | Jeremy Goecks | 30 May 2013, 21:17:23 UTC | Enhance unicodify to correctly handle non-string input. | 30 May 2013, 21:17:23 UTC |
| 758189c | Jeremy Goecks | 30 May 2013, 20:57:03 UTC | Remove manual JSON parsing because it is not needed. | 30 May 2013, 20:57:03 UTC |
| 51f8c4b | Greg Von Kuster | 30 May 2013, 19:32:25 UTC | Add the ability for a user to reset metadata on a selected list of repositories in the tool shed for those repositories for which they are authorized to change. | 30 May 2013, 19:32:25 UTC |
| 80bf94e | Dave Bouvier | 30 May 2013, 17:23:16 UTC | Fix for incorrect changeset revision being selected on the preview page when installing a repository from the tool shed. Fix for exception being raised when resetting metadata on a repository that does not contain tools. | 30 May 2013, 17:23:16 UTC |
| 36fec6c | Dave Bouvier | 30 May 2013, 14:36:40 UTC | Fix error reporting in the tool dependency installation process. | 30 May 2013, 14:36:40 UTC |
| 8eebd20 | Carl Eberhard | 29 May 2013, 20:25:01 UTC | HDA.get_api_value: remove history_id as tuple | 29 May 2013, 20:25:01 UTC |
| 4f7d717 | Greg Von Kuster | 29 May 2013, 20:18:27 UTC | Fix styles for automated tool test results containers in the tool shed. | 29 May 2013, 20:18:27 UTC |
| c1fb32d | Nate Coraor | 29 May 2013, 20:16:11 UTC | Update pgcleanup.py for dialect name change. | 29 May 2013, 20:16:11 UTC |
| 25c9866 | Dave Bouvier | 29 May 2013, 19:24:52 UTC | Make the functional test results RSS feed output properly formatted data. | 29 May 2013, 19:24:52 UTC |
| c9ca524 | Nate Coraor | 29 May 2013, 17:55:08 UTC | Make PBKDF2 password hashing conditional, enable by default. | 29 May 2013, 17:55:08 UTC |
| 795dfde | Dave Bouvier | 29 May 2013, 17:26:38 UTC | Fix for set_environment appearing in multiple action sections. Fix for interpolating multiple environment variables in set_environment actions. | 29 May 2013, 17:26:38 UTC |
| c2afb99 | Dannon Baker | 28 May 2013, 21:23:17 UTC | Bugfix for standard dataset upload | 28 May 2013, 21:23:17 UTC |
| d477295 | Dave Bouvier | 28 May 2013, 18:49:19 UTC | Explicitly filter by tag name actions when building the actions dict for tool dependency installation. | 28 May 2013, 18:49:19 UTC |
| b65685f | John Chilton | 26 May 2013, 20:15:19 UTC | Fix job splitting to rewrite references in config files in addition to command-line. | 26 May 2013, 20:15:19 UTC |
| 8999130 | John Chilton | 26 May 2013, 20:10:43 UTC | Fix API uploads (must have broken with API/Web transaction unification). | 26 May 2013, 20:10:43 UTC |
| 8eb3e7d | Greg Von Kuster | 28 May 2013, 16:24:52 UTC | Eliminate the use of Galaxy's elementree egg within the tool shed. | 28 May 2013, 16:24:52 UTC |
| 5e912d4 | Dave Bouvier | 28 May 2013, 13:53:36 UTC | Fixes for backward compatibility with 2012-12-20 release of Galaxy. | 28 May 2013, 13:53:36 UTC |
| f5432bd | Dave Bouvier | 24 May 2013, 18:02:14 UTC | Fix for missing_test_components always being present, causing misleading test result display on repository pages. | 24 May 2013, 18:02:14 UTC |
| 43863a3 | Daniel Blankenberg | 24 May 2013, 17:59:26 UTC | Unicode fixes for tool parameters | 24 May 2013, 17:59:26 UTC |
| 6a5b539 | Daniel Blankenberg | 24 May 2013, 17:56:42 UTC | Fix for displaying unicode characters in TextField in form_builder. | 24 May 2013, 17:56:42 UTC |
| 9b7cb64 | Daniel Blankenberg | 24 May 2013, 17:43:25 UTC | Fix for displaying unicode characters in select checkboxes in form_builder. | 24 May 2013, 17:43:25 UTC |
| 54298b3 | Daniel Blankenberg | 24 May 2013, 17:36:17 UTC | Fix for displaying unicode characters in select menus in form_builder. | 24 May 2013, 17:36:17 UTC |
| 1a362aa | Daniel Blankenberg | 24 May 2013, 17:04:32 UTC | Fix for MetadataInDataTableColumnValidator becoming stale when a tool data table is updated during Galaxy runtime. | 24 May 2013, 17:04:32 UTC |
| 6bda99e | Dave Bouvier | 23 May 2013, 19:49:46 UTC | Fix of environment variables being set in set_environment_for_install, but not being propagated to set_environment actions. | 23 May 2013, 19:49:46 UTC |
| ba34c92 | Carl Eberhard | 23 May 2013, 19:44:17 UTC | Remove access check from get_hda_dict; Add profiler version of same | 23 May 2013, 19:44:17 UTC |
| 98948dd | Greg Von Kuster | 23 May 2013, 18:57:12 UTC | Fixes for xml handling in the tol shed. | 23 May 2013, 18:57:12 UTC |
| d21bf21 | Carl Eberhard | 23 May 2013, 17:47:03 UTC | Controllers.dataset: add exception string to log msg in _delete | 23 May 2013, 17:47:03 UTC |
| e7945c8 | Greg Von Kuster | 23 May 2013, 15:49:52 UTC | Keep all contents of dependency definition files when re-writing them to include missing toolshed and changeset_revision attributes. | 23 May 2013, 15:49:52 UTC |
| 8a15acb | Daniel Blankenberg | 23 May 2013, 15:11:37 UTC | Fix for TabularToolDataTable.get_column_name_list() when value column is overloaded by e.g. name. | 23 May 2013, 15:11:37 UTC |
| e8c57e2 | Daniel Blankenberg | 23 May 2013, 15:11:37 UTC | Fix for TabularToolDataTable.get_column_name_list() when value column is overloaded by e.g. name. | 23 May 2013, 15:11:37 UTC |
| 6547215 | Dave Bouvier | 23 May 2013, 13:45:24 UTC | Fix for missing tool test results display on manage repository page. | 23 May 2013, 13:45:24 UTC |
| ce76fce | Greg Von Kuster | 22 May 2013, 20:11:55 UTC | Populate the toolshed attribute when it is missing from the repository tag in dependency definitions with the current tool shed url. | 22 May 2013, 20:11:55 UTC |
| 755256a | Jeremy Goecks | 22 May 2013, 19:23:15 UTC | Trackster: for variant track painter, only draw loci in viewing region. | 22 May 2013, 19:23:15 UTC |
| d618359 | Jeremy Goecks | 22 May 2013, 18:47:37 UTC | Trackster: fix for subsetting variant tracks. | 22 May 2013, 18:47:37 UTC |
| c8594b4 | Dave Bouvier | 22 May 2013, 14:40:04 UTC | Fix for filtering by skip_tool_test in the repository revisions tool shed API controller. | 22 May 2013, 14:40:04 UTC |
| fc23abb | Daniel Blankenberg | 22 May 2013, 13:51:47 UTC | Fix for RawObjectWrapper when None values are provided. | 22 May 2013, 13:51:47 UTC |
| 4bb901e | Greg Von Kuster | 21 May 2013, 20:46:16 UTC | Fix for defining set_environment_for_install tags in multiple tag sets instead of multiple repositories per tag set. | 21 May 2013, 20:46:16 UTC |
| 6844205 | Nate Coraor | 21 May 2013, 20:28:44 UTC | Pass a db session in to MetadataParameters' wrap() method so that MetadataFiles can be returned as real mapped objects and passed to the object store. | 21 May 2013, 20:28:44 UTC |
| 52807ff | Daniel Blankenberg | 21 May 2013, 20:21:17 UTC | Fix for detecting Data Manager tool dependencies when installed from a tool shed. | 21 May 2013, 20:21:17 UTC |
| 5b892ef | Dave Bouvier | 21 May 2013, 19:53:42 UTC | Fix for repositories incorrectly being displayed in the list of repositories with failing tool tests. | 21 May 2013, 19:53:42 UTC |
| 017a3c3 | Carl Eberhard | 21 May 2013, 19:19:33 UTC | History: add simple profiling method | 21 May 2013, 19:19:33 UTC |
| 7d7f04a | Jeremy Goecks | 21 May 2013, 18:37:51 UTC | Viz framework fixes: (a) add hda_ldda attribute to API dicts of HDAs and LDDAs; (b) remove summary tree from Circster; (c) make Circster compatible with recent change to get HDAs from API. Pack scripts. | 21 May 2013, 18:37:51 UTC |
| a13d13d | Carl Eberhard | 21 May 2013, 16:54:21 UTC | Scatterplot: use named data provider, fix encoding of ids; pack scripts | 21 May 2013, 16:54:21 UTC |
| 4d781de | Greg Von Kuster | 21 May 2013, 16:26:55 UTC | Fixes for complext repository dependency definitions that do not include a changeset_revision attribute. A fix for indenting the updates XML file is also included. | 21 May 2013, 16:26:55 UTC |
| 730a156 | Carl Eberhard | 21 May 2013, 15:15:10 UTC | Fixes to phyloviz | 21 May 2013, 15:15:10 UTC |
| d98e75d | Carl Eberhard | 21 May 2013, 14:58:08 UTC | Fix to scatterplot to use non-dictionary hda | 21 May 2013, 14:58:08 UTC |
| 7f61cab | Daniel Blankenberg | 21 May 2013, 14:39:47 UTC | Fix for uploading toolshed repository via hg. | 21 May 2013, 14:39:47 UTC |
| 27fbf0a | Dave Bouvier | 20 May 2013, 20:50:32 UTC | Fix for uploading repository_dependencies.xml without a changeset revision specified when the target repository's latest downloadable changeset revision is followed by two or more non-downloadable changeset revisions. | 20 May 2013, 20:50:32 UTC |
| 2140a14 | Jeremy Goecks | 20 May 2013, 20:16:03 UTC | Trackster: transparency and state fixes for variant painter. | 20 May 2013, 20:16:03 UTC |
| 1862ec2 | Nate Coraor | 20 May 2013, 19:55:46 UTC | Merge stable branch to next-stable. | 20 May 2013, 19:55:46 UTC |
| 06f36b5 | Nate Coraor | 20 May 2013, 19:54:08 UTC | Open next-stable branch for upcoming June 3, 2013 release. | 20 May 2013, 19:54:08 UTC |
| 1b8ef07 | Nate Coraor | 20 May 2013, 19:00:11 UTC | Merged in jmchilton/galaxy-central-lwr (pull request #166) LWR fix for setting metadata externally. | 20 May 2013, 19:00:11 UTC |
| 7743dc9 | Nate Coraor | 20 May 2013, 18:56:51 UTC | Merge. | 20 May 2013, 18:56:51 UTC |
| 649a6aa | Nate Coraor | 20 May 2013, 18:56:07 UTC | Merged in jmchilton/galaxy-central-library-refactoring (pull request #167) Implement setting up tool dependency action (setup_virtualenv) to automatically setup python virtual environments. | 20 May 2013, 18:56:07 UTC |
| b696637 | Nate Coraor | 20 May 2013, 18:55:57 UTC | Changes to the setup_virtualenv tool_dependency action: - Download and use a local copy of virtualenv rather than rely on virtualenv being on the $PATH. - Do not use activate (except when installing packages e.g. with pip) since only one virtualenv can be active at a time. This allows for the use of multiple dependencies that use virtualenv. - Support setup_virtualenv with complex dependencies. | 20 May 2013, 18:55:57 UTC |
| 834cbd6 | Jeremy Goecks | 20 May 2013, 17:48:08 UTC | Pack script. | 20 May 2013, 17:48:08 UTC |
| 8ce1e97 | Jeremy Goecks | 20 May 2013, 17:46:46 UTC | Do not abbreviate dataaset name for tool data inputs. | 20 May 2013, 17:46:46 UTC |
| 9768337 | Jeremy Goecks | 20 May 2013, 17:41:58 UTC | Trackster: add base functions for manipulating modes. | 20 May 2013, 17:41:58 UTC |
| 508f4a8 | Nate Coraor | 20 May 2013, 17:16:04 UTC | Do not abort on failures in dependency installation. | 20 May 2013, 17:16:04 UTC |
| b67157f | Dave Bouvier | 20 May 2013, 16:04:05 UTC | Remove backward compatibility code, fix error with incorrect tool test status being reported to the tool shed. | 20 May 2013, 16:04:05 UTC |
| aef326d | John Chilton | 20 May 2013, 13:25:03 UTC | Implement setting up tool dependency action (setup_virtualenv) to automatically setup python virtual environments. Install requirements from file requirements.txt of downloaded bundle: <action type="setup_virtualenv" /> - or - Install requirements from specified file from downloaded bundle: <action type="setup_virtualenv">tools/requirements.txt</action> - or - Manually specify contents of requirements.txt file to create dynamically. <action type="setup_virtualenv">pyyaml==3.2.0 lxml==2.3.0</action> Other small refactorings to support this. Including: - Rework expansion of $INSTALL_DIR in tool_dependency.xml files to use string.Template and allow additional variables. $system_install now expands to the install dir to mimic what what we do with CloudBioLinux Galaxy tool dependency creation. Ultimately, would like to have $tool_version to expand as well, since most downloads differ only based on this version which must be set anyway. - Refactor a more general function, create_or_update_env_shell_file_with_command, out of create_or_update_env_shell_file. Use this more general function to implement Python virtualenv activation in tool dependencies. - Implement shell quoting create_or_update_env_shell_file_with_command to handle special characters in paths. | 20 May 2013, 13:25:03 UTC |
| 97a64db | Jeremy Goecks | 19 May 2013, 15:59:50 UTC | Add library normalization and dispersion options to Cuffdiff wrapper. | 19 May 2013, 15:59:50 UTC |
| edfa0bd | Daniel Blankenberg | 17 May 2013, 21:10:51 UTC | Update job runner code to use start and end slices of long stderr and stdout. | 17 May 2013, 21:10:51 UTC |
| 4f93f0a | Daniel Blankenberg | 17 May 2013, 21:10:50 UTC | Add get_file_size and shrink_stream_by_size to galaxy.util | 17 May 2013, 21:10:50 UTC |
| 3a55b4a | Dave Bouvier | 17 May 2013, 20:42:48 UTC | Functional tests for automatically determining the target changeset revision in repository dependencies. | 17 May 2013, 20:42:48 UTC |
| 483cfb6 | Carl Eberhard | 17 May 2013, 20:30:50 UTC | Bugfix: remove DEFAULT_ORDER_BY in visualizations mixin. | 17 May 2013, 20:30:50 UTC |
| 7559e46 | Carl Eberhard | 17 May 2013, 19:06:51 UTC | Visualizations API: rough draft of index, show, create, and update; Browser tests: tests for visualizations API | 17 May 2013, 19:06:51 UTC |
| 77d6acd | Carl Eberhard | 17 May 2013, 18:50:27 UTC | API/datasets.show: allow _raw_data to assign a DataProvider by name | 17 May 2013, 18:50:27 UTC |
| df19274 | Carl Eberhard | 17 May 2013, 18:45:07 UTC | Visualizations framework: allow users to associate custom visualizations with models, datatypes, etc. via an xml configuration file (visualizations_conf.xml) | 17 May 2013, 18:45:07 UTC |
| 936df8d | Dave Bouvier | 17 May 2013, 16:50:47 UTC | Modify the upload_directory and upload_tar methods to handle complex and simple repository dependencies without changeset revisions specified. | 17 May 2013, 16:50:47 UTC |
| 2ac57c4 | Jeremy Goecks | 17 May 2013, 16:06:14 UTC | Trackster: enable composite feature tracks. When feature/read tracks are composited, coverage data for each track is composited together. | 17 May 2013, 16:06:14 UTC |
| a21a87e | Daniel Blankenberg | 17 May 2013, 15:26:00 UTC | Add ToolShed metadata comparison method for Data Managers. | 17 May 2013, 15:26:00 UTC |
| 535d5e9 | Daniel Blankenberg | 17 May 2013, 15:21:00 UTC | Fix for setting data manager version. | 17 May 2013, 15:21:00 UTC |
| 4796ce6 | Daniel Blankenberg | 17 May 2013, 14:47:30 UTC | Fix for commit_util.UNDESIRABLE_DIRS in lib/galaxy/webapps/tool_shed/controllers/upload.py. | 17 May 2013, 14:47:30 UTC |
| 7dbe4b1 | Greg Von Kuster | 17 May 2013, 11:30:53 UTC | Fixes for committing to a tool shed repository - bug introduced when the tool shed uplaod controller was refactored. | 17 May 2013, 11:30:53 UTC |
| 1d8a1ec | Greg Von Kuster | 17 May 2013, 01:45:54 UTC | Refactor the tool shed upload controller. | 17 May 2013, 01:45:54 UTC |
| 4083dbe | Greg Von Kuster | 16 May 2013, 20:57:10 UTC | Eliminate the requirement for repository dependency tag sets to include a changeset_revision attribute. Here is an example of what used to be required: <repository name="molecule_datatypes" owner="test" changeset_revision="1a070566e9c6" /> Now the following is supported: <repository name="molecule_datatypes" owner="test" /> When the changeset_revision is missing, the tool shed uplad process will automatically determine the latest installable changeset revsion for the repository defined by the name and owner tag attributes and populate the tag with the changeset discovered changeset revision value. Caveat emptor: 0) I wanted to get this changeset committed before the next stable branch is created on Monday, 5/20/13, so that it would be included in the next Galaxy release. By definition, anything I do to this new feature from now on will be a bug fix. ;) This featue should be fully functional within the next week. 1) This currently only works when uplaoding a single file named repository_dependencies.xml or tool_dependencies.xml. It does not yet work when files with this name are include in a tarball or are uploaded using the ftp or hg clone options in the tool shed upload form. 2) This feature is not yet fully tested, but doesn't break anything I've tried (all tool shed functional tests pass). I've tested it with both simple repository dependency definitions and complex repository dependency definitions. I've also tested it with the recently supported <action type="set_environment_for_install"> tag set. | 16 May 2013, 20:57:10 UTC |
| 2d83d0b | Dave Bouvier | 16 May 2013, 19:55:01 UTC | Only display the tool test results folder if a repository has been installed and tested. | 16 May 2013, 19:55:01 UTC |
| d4ec9df | Dave Bouvier | 16 May 2013, 19:50:58 UTC | Add tool shed functional test temporary directory to .hgignore. | 16 May 2013, 19:50:58 UTC |
| 819f827 | Dave Bouvier | 16 May 2013, 19:47:29 UTC | Add tests for the skip_tool_tests option on repository changeset revisions. Remove unused import in test_0000. | 16 May 2013, 19:47:29 UTC |
| db96e65 | Dave Bouvier | 16 May 2013, 19:22:18 UTC | Additional exception handling when testing repositories that fail installation before a row is created in the Galaxy database. | 16 May 2013, 19:22:18 UTC |
| 0847c56 | Dave Bouvier | 16 May 2013, 19:18:39 UTC | Backward compatibility fix for installing repositories with repository dependencies. | 16 May 2013, 19:18:39 UTC |
| 4ab3b3b | Greg Von Kuster | 16 May 2013, 15:55:41 UTC | Fixes for determining if a new metadata revision is required when inspecting tool shed repository dependency definitions. | 16 May 2013, 15:55:41 UTC |
| df236aa | John Chilton | 16 May 2013, 04:50:19 UTC | Fix bug that was preventing LWR jobs from entering the RUNNING state post job "recover" on Galaxy startup. | 16 May 2013, 04:50:19 UTC |
| da992ce | John Chilton | 16 May 2013, 04:37:16 UTC | Implement queued state for LWR jobs - previously all queued and running LWR jobs were marked as running in the Galaxy. | 16 May 2013, 04:37:16 UTC |
| df5e8e5 | Dave Bouvier | 16 May 2013, 03:51:39 UTC | Add exception handling for edge case when a repository record is not created by the install method. | 16 May 2013, 03:51:39 UTC |
| e941e2f | Greg Von Kuster | 16 May 2013, 00:15:11 UTC | Add the ability for a repository owner to check a "Skip automated testing of tools in this revision" checkbox on the Manage repository page. If checked, the tool shed automated test framework will skip testing the tools in that revision. | 16 May 2013, 00:15:11 UTC |
