[galaxy-commits] [galaxyproject/galaxy] 71460a: Allowing for configurable priorities.

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 71460a6778bad5ade9712e3d5f133113da2e21b5 https://github.com/galaxyproject/galaxy/commit/71460a6778bad5ade9712e3d5f133... Author: Matthew Spelchak <mspelcha@wtma.corefacility.ca> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- Allowing for configurable priorities. Any priority listed in the global 'default desinations' section in the tool destinations config is considered a valid priority. All other priorities are invalid. This allows for the configuration and usage of an arbitrary number of priorities Commit: 4722c48a645d6ae5c91aeea673139451ca5edd8b https://github.com/galaxyproject/galaxy/commit/4722c48a645d6ae5c91aeea673139... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- checking for valid destinations in tool destination config dynamic_tool_destination.py now checks that any job destination referenced exists in job_conf.xml by matching the name of the destination in tool_destinations.yml to a destination id in job_conf.xml Commit: cdfe2268f4f0a73d74c4d844dc62c38d3908185e https://github.com/galaxyproject/galaxy/commit/cdfe2268f4f0a73d74c4d844dc62c... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- some code cleanup and changing default priority on tools The default priority for tools if not specified in the tool destination config is now whatever the middle priority is in the list of global default destinations Commit: d315dfc2022552e29da25b2edd475ff6f5cd5858 https://github.com/galaxyproject/galaxy/commit/d315dfc2022552e29da25b2edd475... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- Fixing some error messages Commit: 6fc2d4d95c94ca58e8f16760842f28ecc960430c https://github.com/galaxyproject/galaxy/commit/6fc2d4d95c94ca58e8f16760842f2... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- adhering (closer) to pep8 Commit: fd439b3e4309321880ecb64ead8c32e4b02ae011 https://github.com/galaxyproject/galaxy/commit/fd439b3e4309321880ecb64ead8c3... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- fixing bug Commit: 8f3eb41bb808609b4801705a7747320081063598 https://github.com/galaxyproject/galaxy/commit/8f3eb41bb808609b4801705a77473... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- Fix typo in validated config; test all destinations for validity Previously, the validate_config method would return a config with a 'default' section instead of 'destination_default'. This caused some unit tests to error out and raise a JobMappingException. This has been fixed. Previously, only destinations that went through the validate_rules method would be checked to ensure existence. Now, destinations in top-level 'default_destination' and tool-level 'default_destination' are also checked. Commit: 2628e5fdfad90165ad3da087d42fadd74d4e87e1 https://github.com/galaxyproject/galaxy/commit/2628e5fdfad90165ad3da087d42fa... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- Fix error with validated configs Commit: c01bff7b8f6139e30354d37dea82c8bf61f25d7f https://github.com/galaxyproject/galaxy/commit/c01bff7b8f6139e30354d37dea82c... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-02-05 (Mon, 05 Feb 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- Change priority and destination lists to sets By using sets instead of lists for the valid priority and destination, the checks for item uniqueness in these datatypes is now handled inherently, with little detriment. The only drawback to this is that the system that chooses the default priority for each tool now simply chooses the first element from iter(), rather than the one in the middle of the list. This isn't a huge deal, as that was no more than a guess at what a mid-level priority would be, and would even cause errors when the chosen priority wasn't in the tool's default destination section. Using sets insetad still result in the same issue, so this will need to be fixed soon, as it prevents certain tool destination configs from working properly. Commit: d78421cdb9cef32b53939ca1130e95877763a004 https://github.com/galaxyproject/galaxy/commit/d78421cdb9cef32b53939ca1130e9... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-02-05 (Mon, 05 Feb 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- Only call get_valid_destinations_from_config once Commit: e4b07e05a6b7c76f2429d5ba3a876cf9b1a90447 https://github.com/galaxyproject/galaxy/commit/e4b07e05a6b7c76f2429d5ba3a876... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-02-05 (Mon, 05 Feb 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- Implement hack to fix tools not having destinations for default priority Commit: 20c7fc5b3bf8055d7d1c445c94fcf398fe2bcb36 https://github.com/galaxyproject/galaxy/commit/20c7fc5b3bf8055d7d1c445c94fcf... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-02-05 (Mon, 05 Feb 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py Log Message: ----------- Make users adhere to same priorities as tools, better handle tools without default priority destination, stop destination and priority sets from retaining values between test cases, updating tests Previously, user's had their own sets of priorities (low, med, high) that did not match the new system with configurable priorities. As mapping these user priorities onto tool priorities would be impossible without extra config sections, or hardcoding of things that map to one another, the user priorities are now on the same system. IE: all priorities declared in the user sections much match priorities in the "default_destination" section. Dynamic_tool_destination also now uses a less-hacky method of handling tools that don't have a default destination for the default priority (which is still unfortunately arbitrarily chosen; this presents a rather large issue that will need to be addressed in the future.) Essentially, the global default destination for the default priority is used if there isn't one defined in the tool's defaults or its rules. There was also a bug previously that caused dynamic_tool_destination's priority_list and and destination_list (formerly valid_destinations) to retain values in between test cases, causes the test results to differ from the expected results. This bug has been fixed. Finally, the test_dynamic_tool_destination program has been updated to reflect the exptected outcome of test cases with the new program's expected functionality in mind. Note that this does not mean the tests are testing what they should be -- they simply don't fail anymore for expected behaviour. There is test that still fails -- and it deals with the fact that there no longer is a default priority that all tools need to adhere to. Because default priorities are determined now in an arbitrary way (this shouldn't be permanent behaviour), a destination other than the expected one may be chosen for a given tool that does not implement that (arbitrarily chosen) default priority. Commit: 7ed1fa1a69dfcf88f09fa1be2adb0b4f695dbcbe https://github.com/galaxyproject/galaxy/commit/7ed1fa1a69dfcf88f09fa1be2adb0... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-02-05 (Mon, 05 Feb 2018) Changed paths: M .gitignore Log Message: ----------- Ignore backup files I append ".bak" to copies of new files that I'm working on as a quick and dirty backup method. Updated the .gitignore file to ignore these Commit: ad5933f1ce9658cb5275b4a81bc77e052441d9de https://github.com/galaxyproject/galaxy/commit/ad5933f1ce9658cb5275b4a81bc77... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-02-06 (Tue, 06 Feb 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/ymltests.py Log Message: ----------- Fix error messages, add tests, miscellaneous fix A few error messages have been altered to be a bit clearer, and a bug was fixed that stopped an error from being fired. Tests were also added to test some of the new functionality of dynamic_tool_destination. The added tests: - test for an error being thrown when a priority in priority_list does not appear in a tool's default_destination section (this may not be final behaviour) - test to ensure that errors are fired if a destination is referenced that is not in the destinations section of the job_conf.xml Commit: 4f47980e76041101cff0080363af8402ac16beb6 https://github.com/galaxyproject/galaxy/commit/4f47980e76041101cff0080363af8... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-02-06 (Tue, 06 Feb 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/ymltests.py Log Message: ----------- Add more tests, make error messages more specific Three new tests were added to ensure that errors are thrown if a destination is used as a straight string value (without a priority) and that destination does not exist in the job_conf.xml Also updated a few error messages to explicitely mention that the destination is not in job_conf.xml, hopefully ensuring users who get the message know what to do to fix the error. Commit: ec3bb7d7ee47879fa7a8ab3d2d3e24c5d2b3a8cd https://github.com/galaxyproject/galaxy/commit/ec3bb7d7ee47879fa7a8ab3d2d3e2... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-02-06 (Tue, 06 Feb 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/ymltests.py Log Message: ----------- Alter error messages, add new tests A few error messages were altered to start with lowercase letters. Why? Don't ask me, that was yesterday. Expect all the error messages to be altered to start with capitals (as I believe they should) soon. Two new tests were added, ensuring that errors are fired when priorities are referenced that don't appear in the config's global default_destinaion section. Commit: 25e50cfba4711ba073d7388b4623bced3b89c543 https://github.com/galaxyproject/galaxy/commit/25e50cfba4711ba073d7388b4623b... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-02-07 (Wed, 07 Feb 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py Log Message: ----------- Make all error messages start with capitals, and adjust the tests to expect this Commit: ccf21444da0cb2df78bbb7dca2a75cdc1cd76010 https://github.com/galaxyproject/galaxy/commit/ccf21444da0cb2df78bbb7dca2a75... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-02-07 (Wed, 07 Feb 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- Allow job config xml files to be passed as an argument job configuration xml files can now be passed as arguments to the application with the -j or the --job-config options. To facilitate this change, the parse_yaml constructor has been altered to accept a new parameter, job_conf_path, the path to the job configuration. For simplicity, get_destination_list_from_job_config is now called from parse yaml instead of validate_config. This simply reduces the amount of times the job_conf path needs to be passed between functions. Commit: acb0f152208b1be6f7561b35025f08f057954a14 https://github.com/galaxyproject/galaxy/commit/acb0f152208b1be6f7561b35025f0... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-02-07 (Wed, 07 Feb 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py A test/unit/jobs/dynamic_tool_destination/data/job_conf.xml M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py Log Message: ----------- Tests include their own job_conf.xml, fix bug when specifying job_conf.xml paths, code cleanup The built-in dynamic_tool_destination tests now use a job_conf.xml included alongside the testing tool destination yaml files. This means that DTD can finally be tested in an automated fashion -- no more manually putting a job_conf.xml into the config folder to make things work. This means that map_tool_to_destination now has an additional parameter, job_conf_path -- the path to the job_config.xml file. Also fixed is a bug that would add the Galaxy config folder path to custom job_conf.xml paths. Finally, the tests that were not relevant to the new version of DTD that were commented out are now removed altogether. Commit: 385de923bdb730cc28c4687e94a4dcbe54145d7c https://github.com/galaxyproject/galaxy/commit/385de923bdb730cc28c4687e94a4d... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-02-07 (Wed, 07 Feb 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/ymltests.py Log Message: ----------- Clean up comments Commit: 76b771d7bc32aadc2cbcb302ff0114ab2f9fcd97 https://github.com/galaxyproject/galaxy/commit/76b771d7bc32aadc2cbcb302ff011... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-02-07 (Wed, 07 Feb 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py Log Message: ----------- Follow pep8 (mostly) Commit: f61990646996aafff92bc9bf26a0e1e1b3a5e67e https://github.com/galaxyproject/galaxy/commit/f61990646996aafff92bc9bf26a0e... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- Adhering (better) to Galaxy style guidelines Commit: d41df08b38cabfa13ed79820550e9f38da557d51 https://github.com/galaxyproject/galaxy/commit/d41df08b38cabfa13ed79820550e9... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- Adjust doc comments to 79 character max line length Commit: cc98bafdbf1c5517eb2a72072871af74d0fdffa5 https://github.com/galaxyproject/galaxy/commit/cc98bafdbf1c5517eb2a72072871a... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- Shorten logical lines over 79 characters where it makes sense Commit: 330b515bfd741be13d60cc8857f507e8fa53a8b0 https://github.com/galaxyproject/galaxy/commit/330b515bfd741be13d60cc8857f50... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M test/unit/jobs/dynamic_tool_destination/data/job_conf.xml M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/ymltests.py Log Message: ----------- Trim test configs, add new tests The configurations used by the DTD unit tests have been trimmed, stripping out parts that do not contribute to test results. Two new tests were also added, both testing to ensure that a tool is reported to not have any default destinations *or* rules if its only default destination is invalid, and it has no rules. Commit: 966e053b84c791f1b271099122304280b82d1a7f https://github.com/galaxyproject/galaxy/commit/966e053b84c791f1b271099122304... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-02-09 (Fri, 09 Feb 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py Log Message: ----------- Fix tests that didn't run. Previously, two tests would not run because I forgot to name them to something that wasn't a copy/paste from another test. I renamed them so they actually run. Commit: c9867a88c7970e33d1847bdc7acfaf72e786d53c https://github.com/galaxyproject/galaxy/commit/c9867a88c7970e33d1847bdc7acfa... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-02-09 (Fri, 09 Feb 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/ymltests.py Log Message: ----------- Add ability to set default priority, update tests, small fixes This is a relatively large commit -- a new section in tool_destinations.yml is now required: default_priority, which sets which priority to be used as default for all tools, replacing the way 'med' was previously assumed to be default, back when priorities were not configurable. As a fallback to ensure compatibility with the old style of config, if no default_priority is specified in the config, but 'med' exists as a valid priority, the priority will be set to 'med'. Additionally, tests were updated to expect this new behaviour. A collection of small bug fixes were also added, such as: - not adding anything to the list of priorities when the global default_destination is only a string, - Making error messages clearer - fixing some indentation Commit: f4a2c55a1908a93da289e797237c1d4884281551 https://github.com/galaxyproject/galaxy/commit/f4a2c55a1908a93da289e797237c1... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-02-09 (Fri, 09 Feb 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py Log Message: ----------- Ensure default_destination for each rule contains a destination for default_priority Commit: 4c402b3859e85aece4cd81feb95c344cdd8f9abf https://github.com/galaxyproject/galaxy/commit/4c402b3859e85aece4cd81feb95c3... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-02-09 (Fri, 09 Feb 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- Revert previous commit It doesn't make sense to have the config validation fail just because a tool doesn't have a destination for the default priority: the destination should just go to the global default destination, as the user would likely expect to happen. Commit: cdcd07f2bbfe7f667303cf794566bb2d1da44df4 https://github.com/galaxyproject/galaxy/commit/cdcd07f2bbfe7f667303cf794566b... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-02-12 (Mon, 12 Feb 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/ymltests.py Log Message: ----------- Fix error message order, add test Fixed some error message logic. Previously, a tool_destinations.yml config with an empty priority key in global 'default_destination' would throw two errors in a strange order; one about no valid default priority destinations, and another about no default destination. This has been changed so with the same config there is now just a 'No default destinations in config' message. Also added a test that confirms this behaviour Commit: 87d23cfba382ecf03df5a57de3f3fd153336b89c https://github.com/galaxyproject/galaxy/commit/87d23cfba382ecf03df5a57de3f3f... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-02-12 (Mon, 12 Feb 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/ymltests.py Log Message: ----------- Add new tests, add new category to valid keys check Added three new tests, testing cases where all destinations are str, where the default_destination is a str but a tool default_destination is a dict, and where the default_destination is a str but a tool rule destination is a dict. Also fixed a bug that was caught with these new tests -- default_priority was not actually in the list of valid config categories so using the default_priority key would result in errors. Whoops. Commit: 62945e72e3a4a2cd1fbf475df4e34a3b8c200973 https://github.com/galaxyproject/galaxy/commit/62945e72e3a4a2cd1fbf475df4e34... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-02-12 (Mon, 12 Feb 2018) Changed paths: M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/ymltests.py Log Message: ----------- Reorganize test code Commit: 3d1cd3dc0f3a22f0eb105aa01a4e85d1ce17f8bb https://github.com/galaxyproject/galaxy/commit/3d1cd3dc0f3a22f0eb105aa01a4e8... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-02-12 (Mon, 12 Feb 2018) Changed paths: M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/ymltests.py Log Message: ----------- Make new tests actually run Commit: 6943470250124352b10700899697f1b0ca05491d https://github.com/galaxyproject/galaxy/commit/6943470250124352b10700899697f... 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tools/metag_tools/blat_wrapper.py M tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/next_gen_conversion/solid2fastq.py M tools/phenotype_association/senatag.py M tools/plotting/bar_chart.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velvetg_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py M tox.ini Log Message: ----------- Merge branch 'dev' of https://github.com/phac-nml/galaxy into configurable_priorities__default_priorities Commit: cb2860191d2a722e120b026ea34657c919ccd73a https://github.com/galaxyproject/galaxy/commit/cb2860191d2a722e120b026ea3465... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- Fix default priority assignment order Moved where default_priority is actually generated in the map_tool_to_destination function. Now it calculates and assigns default_priority to priority *before* the job/workflow parameter- specified priority is assigned. Commit: a5e8d82b46904a587403636c1211c7d1589bade3 https://github.com/galaxyproject/galaxy/commit/a5e8d82b46904a587403636c1211c... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- Add comments to describe some of the new functionality Commit: 125d126591c55445bacbe29adc8a5992a8d23342 https://github.com/galaxyproject/galaxy/commit/125d126591c55445bacbe29adc8a5... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/ymltests.py Log Message: ----------- Adhere to Galaxy Python standards Commit: d30bccb888f46926cb066725a35ce36dc93e4bcf https://github.com/galaxyproject/galaxy/commit/d30bccb888f46926cb066725a35ce... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/ymltests.py Log Message: ----------- Fix test that didn't run Commit: 5158b13845a4dd3c061ec6df8f8fdd42c8aa18c7 https://github.com/galaxyproject/galaxy/commit/5158b13845a4dd3c061ec6df8f8fd... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- Begin adding system to suggest typo corrections Implemented a function to check for edit distance that I found online, and wrote a function that compares a given string with all entries in a set and returns the one with fewest edits. Added code to validate_destination in RuleValidator to suggest corrections for possibly mispelled priorities, but haven't tested it yet. Commit: 5c9196af0fba85f93969733872401c93ad51f63b https://github.com/galaxyproject/galaxy/commit/5c9196af0fba85f93969733872401... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- Finish implementing typo correction suggestions Code has been added in all locations in the code that check values against the list of valid values, and checks if there are similar valid values in the list if the value in the config is invalid. If there is a similar value (edit distance 3 or closer, currently,) output will be printed pointing out the similar, valid value. Commit: a00a77c604c8cd437729b6c5fce746f75954c2c1 https://github.com/galaxyproject/galaxy/commit/a00a77c604c8cd437729b6c5fce74... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- Fix max_edit_dist not being set or used Commit: a2bf469f211f6bf7a4e0e13fb9f73fddb710882e https://github.com/galaxyproject/galaxy/commit/a2bf469f211f6bf7a4e0e13fb9f73... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- Change max_edit_dist to 2 Commit: cc8a90561b84b406f1265faa8542b38c5312d2e2 https://github.com/galaxyproject/galaxy/commit/cc8a90561b84b406f1265faa8542b... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/ymltests.py Log Message: ----------- Start adding tests Added two tests to check if correct destinations were recommended when 'waffles_low' was mispelled in default destinations sections. Commit: 55452b1638d4abb9ed342cfea423f453739cef00 https://github.com/galaxyproject/galaxy/commit/55452b1638d4abb9ed342cfea423f... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-02-16 (Fri, 16 Feb 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/ymltests.py Log Message: ----------- Add more tests Test that correct suggestions occur in all cases where values that don't match the ones in priority_list or destination_list are used. Commit: 89b8f27ab50a6a2d4d35ba199e23fdc643a83ea3 https://github.com/galaxyproject/galaxy/commit/89b8f27ab50a6a2d4d35ba199e23f... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-02-16 (Fri, 16 Feb 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/ymltests.py Log Message: ----------- Add case insensitive comparison to get_typo_correction, new test to test this. get_typo_correction has been updated to prefer suggesting strings that are identical after .lower() is run on both. A new test has also been added to help confirm this new functionality. Commit: 307ed49436f528026366aeed2a8c8b863333c4fb https://github.com/galaxyproject/galaxy/commit/307ed49436f528026366aeed2a8c8... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- Remove old comment Commit: 6ce1556f96268281dd921db4b8d3e071ca39ed55 https://github.com/galaxyproject/galaxy/commit/6ce1556f96268281dd921db4b8d3e... 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templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako M templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako M templates/galaxy_client_app.mako M templates/js-app.mako M templates/user/register.mako M templates/webapps/galaxy/dataset/security_common.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/history/display_structured.mako M templates/webapps/galaxy/workflow/sharing.mako M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako M templates/webapps/tool_shed/repository/tool_form.mako A test-data/bam_native_from_sam.bam A test-data/new_tags_1.txt M test-data/sam_with_header.sam M test/api/test_tools.py M test/api/test_visualizations.py M test/api/test_webhooks.py M test/api/test_workflows.py M test/base/driver_util.py M test/base/integration_util.py M test/base/interactor.py M test/base/workflows_format_2/converter.py M test/docker/base/run_test_wrapper.sh M test/functional/tools/collection_creates_dynamic_list_of_pairs.xml A test/functional/tools/job_environment_default.xml A test/functional/tools/job_environment_default_legacy.xml A test/functional/tools/job_environment_explicit_shared_home.xml A test/functional/tools/mulled_example_explicit.xml A test/functional/tools/mulled_example_simple.xml A test/functional/tools/sam_to_bam_native.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml M test/functional/twilltestcase.py A test/functional/webhooks/history_test1/config.yml R test/functional/webhooks/history_test1/config/history_test1.yml A test/functional/webhooks/history_test2/config.yml R test/functional/webhooks/history_test2/config/history_test2.yml A test/functional/webhooks/masthead_test/config.yml R test/functional/webhooks/masthead_test/config/masthead_test.yml A test/functional/webhooks/phdcomics/__init__.py A test/functional/webhooks/phdcomics/config.yaml R 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test/integration/simple_job_conf.xml A test/integration/test_dockerized_jobs.py A test/integration/test_job_environments.py M test/manual/launch_and_run.sh M test/selenium_tests/test_tool_describing_tours.py M test/shed_functional/base/twilltestcase.py A test/unit/config/1705_allow_path_paste/config/galaxy.ini A test/unit/config/__init__.py M test/unit/config/test_config_manage.py M test/unit/jobs/test_mapper.py M test/unit/jobs/test_runner_local.py M test/unit/managers/test_HistoryManager.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_tool_validation.py M tox.ini Log Message: ----------- Merge branch 'dev' of https://github.com/phac-nml/galaxy into configurable_priorities__default_priorities__guess_typos Commit: faed1951e8a886764f0cd208a53ae70a683effd0 https://github.com/galaxyproject/galaxy/commit/faed1951e8a886764f0cd208a53ae... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M test/unit/jobs/dynamic_tool_destination/data/job_conf.xml M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/ymltests.py Log Message: ----------- remove references to waffles Commit: c77bb86c726190f4042b5b61cc0e6a93d82464de https://github.com/galaxyproject/galaxy/commit/c77bb86c726190f4042b5b61cc0e6... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-02-19 (Mon, 19 Feb 2018) Log Message: ----------- Merge branch 'configurable_priorities' of https://github.com/phac-nml/galaxy into configurable_priorities Commit: de8c0a18aa211c3eebfcca553fb09abea97a0ec2 https://github.com/galaxyproject/galaxy/commit/de8c0a18aa211c3eebfcca553fb09... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-02-20 (Tue, 20 Feb 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/data/priority_tool_destination.yml M test/unit/jobs/dynamic_tool_destination/data/test_no_verbose.yml M test/unit/jobs/dynamic_tool_destination/data/test_num_input_datasets.yml M test/unit/jobs/dynamic_tool_destination/data/tool_destination.yml Log Message: ----------- Check for sample job_conf files if the standard one doesn't exist, other miscellaneous fixes Updated __main__ code and get_destination_list_from_job_config to check for the sample job config files if the default one doesn't exist, and if in verbose mode, notify the user to which one will be used. Also changed the version number to 1.1 Also removed references to waffles in the test files Commit: ad5100e6926a157751ffbad6ab125df10c473dc9 https://github.com/galaxyproject/galaxy/commit/ad5100e6926a157751ffbad6ab125... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-02-20 (Tue, 20 Feb 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- Better handling of no job configs, fixing indentation Now, if no job config is specified and none can be found in the 'config/' folder, rather than crashing trying to access a file that doesn't exist, the program just keeps the destination_list empty, resulting in a bunch of "destination not found" errors (as expected,) but (hopefully) no crashing. Also fixed weird 2-space indentation that happened in the previous few commits. Commit: 46f8cb3185a147934f8718e2d6afcaf9899a0f1f https://github.com/galaxyproject/galaxy/commit/46f8cb3185a147934f8718e2d6afc... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-02-20 (Tue, 20 Feb 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- Fix nesting error A simple error in indentation that caused job configs to not be read properly has been fixed. Commit: 8f19f4f77220c3fdba2926ff401f541a98144e2e https://github.com/galaxyproject/galaxy/commit/8f19f4f77220c3fdba2926ff401f5... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-02-23 (Fri, 23 Feb 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- Create list of valid categories Upgraded check for valid categories by creaing a valid_category global variable containing all of the valid categories that are accepted. Commit: 5d698a6ac4b99fef29c5a2860a89da36a253b95c https://github.com/galaxyproject/galaxy/commit/5d698a6ac4b99fef29c5a2860a89d... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/mockGalaxy.py Log Message: ----------- When in online mode, use galaxy's get_destination method Commit: f1f8f6989de935e5fefef5a488a9b8628299284d https://github.com/galaxyproject/galaxy/commit/f1f8f6989de935e5fefef5a488a9b... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- Create method for verifying destinations Now, destinations are validated in a function that returns both the validity of destination, as well as a suggestion for typo correction if a typo is suspected. This function is what does the check for if `app` exists now, making validating destinations use much less lines of code now, and also making these sections of code much easier to read. Commit: 2d18f165d7f85121199b3d2c7b1460245c854fdb https://github.com/galaxyproject/galaxy/commit/2d18f165d7f85121199b3d2c7b146... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- pass `app` instead of having it be a global var Commit: ead6dbfa6cffc9eddeea85cb4cf26a8540ec0d37 https://github.com/galaxyproject/galaxy/commit/ead6dbfa6cffc9eddeea85cb4cf26... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-03-02 (Fri, 02 Mar 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- Alter `validate_destination` to also print error messages Now, `validate_destination` is also passed an error message to format, and a tuple of values to be be used in the formatted message. All code that calls validate_destination has been updated to acknowledge this new functionality. Commit: 920be90ccc310b4b79a963241921debff505aedd https://github.com/galaxyproject/galaxy/commit/920be90ccc310b4b79a963241921d... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-03-05 (Mon, 05 Mar 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/ymltests.py Log Message: ----------- Add New Tests, Fix Bug Uncovered From Test Added two new tests to test for `valid_config` not being messed with by previous assignments to it. This proved that the previous design of setting `valid_config` to the value of `validate_destination` in `validate_config` caused errant behaviour when a default destination was invalid but a tool default destination was valid. This case caused the program to still end up returning `valid_config` as True even when an invalid default destination was found. Commit: 25dfcc268267e5e52a53ffc5797170db37ee7d4c https://github.com/galaxyproject/galaxy/commit/25dfcc268267e5e52a53ffc579717... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/extended.js A client/galaxy/scripts/components/DisplayStructured.vue A client/galaxy/scripts/components/HistoryView.vue M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/scripts/mvc/tool/tool-genomespace.js 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test/integration/sets_tmp_dir_expression_job_conf.xml A test/integration/sets_tmp_dir_to_true_job_conf.xml A test/integration/simple_job_conf.xml A test/integration/test_dockerized_jobs.py A test/integration/test_job_environments.py M test/integration/test_upload_configuration_options.py M test/manual/launch_and_run.sh M test/selenium_tests/test_jupyter.py M test/selenium_tests/test_saved_histories.py M test/selenium_tests/test_tool_describing_tours.py M test/shed_functional/base/twilltestcase.py A test/unit/config/1705_allow_path_paste/config/galaxy.ini A test/unit/config/__init__.py M test/unit/config/test_config_manage.py M test/unit/jobs/test_mapper.py M test/unit/jobs/test_runner_local.py M test/unit/managers/test_HistoryManager.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_tool_validation.py M test/unit/tools/test_toolbox.py M tools/data_source/upload.py M tools/data_source/upload.xml M tox.ini Log Message: ----------- Merge branch 'dev' of 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Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-03-06 (Tue, 06 Mar 2018) Log Message: ----------- Merge branch 'dev' into configurable_priorities Commit: 9808033f455a7d77ba3337692ab6799b8fba4675 https://github.com/galaxyproject/galaxy/commit/9808033f455a7d77ba3337692ab67... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/ymltests.py Log Message: ----------- Fix Formatting Commit: 6c9073ed3889e21ca029674914bf816c5d6c19b5 https://github.com/galaxyproject/galaxy/commit/6c9073ed3889e21ca029674914bf8... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-03-07 (Wed, 07 Mar 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- Adhere to Linting Rules Commit: 292516ee0fce023c791f08c9ef8984d7b4dff5c7 https://github.com/galaxyproject/galaxy/commit/292516ee0fce023c791f08c9ef898... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-03-07 (Wed, 07 Mar 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- Try To Pass Linting (Again) Commit: 7bb6b195ecf0d1fc559980932456009a98c9b082 https://github.com/galaxyproject/galaxy/commit/7bb6b195ecf0d1fc5599809324560... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-03-07 (Wed, 07 Mar 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into configurable_priorities Commit: 5120ec668774eb9b0e6e1b1d11a5a1b8ab5051db https://github.com/galaxyproject/galaxy/commit/5120ec668774eb9b0e6e1b1d11a5a... Author: Matthew Spelchak <matthew.spelchak@canada.ca> Date: 2018-03-07 (Wed, 07 Mar 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- Adhere to Linting Rules (Again Again) Commit: 729714f9408a256b950cf7fa0a2e58b5b3cd8024 https://github.com/galaxyproject/galaxy/commit/729714f9408a256b950cf7fa0a2e5... 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Author: Matthew Spelchak <mrs11teen@gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M .gitignore R config/workflow_resource_mapper_conf.yml.sample R config/workflow_resource_params_conf.xml.sample M lib/galaxy/jobs/mapper.py M lib/galaxy/util/__init__.py R lib/galaxy/workflow/resources/__init__.py R lib/galaxy/workflow/resources/example.py.sample Log Message: ----------- Remove Unrelated Files (Again) Commit: 460c40b63c7cb62003fbae5b877d371ff99a79e9 https://github.com/galaxyproject/galaxy/commit/460c40b63c7cb62003fbae5b877d3... Author: Matthew Spelchak <mrs11teen@gmail.com> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M config/galaxy.yml.sample A config/workflow_resource_mapper_conf.yml.sample A config/workflow_resource_params_conf.xml.sample M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/mapper.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/execute.py M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/workflow/modules.py A lib/galaxy/workflow/resources/example.py.sample M lib/galaxy/workflow/run_request.py Log Message: ----------- Reset Unrelated Files to Their State in upstream/dev Commit: c621b8091228d3816d9f3e3bb194affbc9a85382 https://github.com/galaxyproject/galaxy/commit/c621b8091228d3816d9f3e3bb194a... 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Author: Matthew Spelchak <mrs11teen@gmail.com> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: A lib/galaxy/workflow/resources/__init__.py Log Message: ----------- Reset One More File to Their State in upstream/dev Commit: a345b2e2658ebdd5eb92790dd3048a625e9f5cbb https://github.com/galaxyproject/galaxy/commit/a345b2e2658ebdd5eb92790dd3048... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py A test/unit/jobs/dynamic_tool_destination/data/job_conf.xml M test/unit/jobs/dynamic_tool_destination/data/priority_tool_destination.yml M test/unit/jobs/dynamic_tool_destination/data/test_no_verbose.yml M test/unit/jobs/dynamic_tool_destination/data/test_num_input_datasets.yml M test/unit/jobs/dynamic_tool_destination/data/tool_destination.yml M test/unit/jobs/dynamic_tool_destination/mockGalaxy.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/ymltests.py Log Message: ----------- Merge pull request #5645 from phac-nml/configurable_priorities Update Dynamic Tool Destinations With Configurable Priorities and Better Validation Compare: https://github.com/galaxyproject/galaxy/compare/0369a4028d17...a345b2e2658e