Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5095fc02c4cfb830748179c29ea9e1b1aaf0b455 https://github.com/galaxyproject/galaxy/commit/5095fc02c4cfb830748179c29ea9e... Author: guerler aysam.guerler@gmail.com Date: 2016-09-25 (Sun, 25 Sep 2016)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js M test/unit/workflows/test_run_parameters.py

Log Message: ----------- Remove internal api endpoint, merge into invocations endpoint

Commit: 9d9e5f026dff5523e7e6aef1a9442c872f5fb77c https://github.com/galaxyproject/galaxy/commit/9d9e5f026dff5523e7e6aef1a9442... Author: guerler aysam.guerler@gmail.com Date: 2016-09-26 (Mon, 26 Sep 2016)

Changed paths: M .gitignore M Makefile A doc/parse_gx_xsd.py A doc/schema_template.md M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/tool_shed/util/metadata_util.py M scripts/bootstrap_history.py M scripts/tool_shed/build_ts_whoosh_index.py M templates/webapps/galaxy/dataset/copy_view.mako M test/shed_functional/functional/test_1400_review_migration_stages.py

Log Message: ----------- Merge branch 'dev' into unite_api

Commit: c840730101823107396104dcc7364534577a2dd4 https://github.com/galaxyproject/galaxy/commit/c840730101823107396104dcc7364... Author: guerler aysam.guerler@gmail.com Date: 2016-09-26 (Mon, 26 Sep 2016)

Changed paths: M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run_request.py

Log Message: ----------- Convert dict keys to integers

Commit: 9a9726e9a174a230b3a71bdb40bceb9e5b0d28c7 https://github.com/galaxyproject/galaxy/commit/9a9726e9a174a230b3a71bdb40bce... Author: guerler aysam.guerler@gmail.com Date: 2016-09-26 (Mon, 26 Sep 2016)

Changed paths: M lib/galaxy/workflow/run_request.py

Log Message: ----------- Fix name generation

Commit: 838fad39a14674986680edfccfbd24232308c07d https://github.com/galaxyproject/galaxy/commit/838fad39a14674986680edfccfbd2... Author: guerler aysam.guerler@gmail.com Date: 2016-09-26 (Mon, 26 Sep 2016)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js M static/maps/mvc/tool/tool-form.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form.js

Log Message: ----------- Add details to error modal

Commit: 0a767d4d5343d7eaf3697373922d056251c5b802 https://github.com/galaxyproject/galaxy/commit/0a767d4d5343d7eaf3697373922d0... Author: guerler aysam.guerler@gmail.com Date: 2016-09-26 (Mon, 26 Sep 2016)

Changed paths: M lib/galaxy/tools/__init__.py

Log Message: ----------- Fix error handling

Commit: 477d3f9ae94acf2b9c57eba641c2dcdd66d5af27 https://github.com/galaxyproject/galaxy/commit/477d3f9ae94acf2b9c57eba641c2d... Author: guerler aysam.guerler@gmail.com Date: 2016-09-27 (Tue, 27 Sep 2016)

Changed paths: M lib/galaxy/workflow/run_request.py A test/api/test_workflow_input_params.ga M test/api/test_workflows.py

Log Message: ----------- Add batch mode test case for invocations api

Commit: 991d81cdbeeca43891b2ed5464c73052fbe20ef3 https://github.com/galaxyproject/galaxy/commit/991d81cdbeeca43891b2ed5464c73... Author: guerler aysam.guerler@gmail.com Date: 2016-09-29 (Thu, 29 Sep 2016)

Changed paths: M lib/galaxy/tools/parameters/basic.py

Log Message: ----------- Fix phrasing of error message

Commit: 3d7bfeb6dd08b0241d8fa75f37c5010762146eeb https://github.com/galaxyproject/galaxy/commit/3d7bfeb6dd08b0241d8fa75f37c50... Author: guerler aysam.guerler@gmail.com Date: 2016-09-29 (Thu, 29 Sep 2016)

Changed paths: M test/api/test_workflows.py

Log Message: ----------- Revise target url

Commit: 1cb67308771edf40716ef5f30f4321051debc4bb https://github.com/galaxyproject/galaxy/commit/1cb67308771edf40716ef5f30f432... Author: guerler aysam.guerler@gmail.com Date: 2016-09-29 (Thu, 29 Sep 2016)

Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py

Log Message: ----------- Always return a list for formats with batch mode option

Commit: e34019e52806fde224781cfe3bc408b633f86179 https://github.com/galaxyproject/galaxy/commit/e34019e52806fde224781cfe3bc40... Author: guerler aysam.guerler@gmail.com Date: 2016-09-29 (Thu, 29 Sep 2016)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js

Log Message: ----------- Improve invocations success message

Commit: 3545a0ef1f8a2fbde86558fcaf5da43e9563710b https://github.com/galaxyproject/galaxy/commit/3545a0ef1f8a2fbde86558fcaf5da... Author: guerler aysam.guerler@gmail.com Date: 2016-09-29 (Thu, 29 Sep 2016)

Changed paths: M test/api/test_workflows.py

Log Message: ----------- Remove unused history wait

Commit: 6f7e9cd5df6eb444974e3d45f1df11f1e3f77281 https://github.com/galaxyproject/galaxy/commit/6f7e9cd5df6eb444974e3d45f1df1... Author: guerler aysam.guerler@gmail.com Date: 2016-09-29 (Thu, 29 Sep 2016)

Changed paths: M test/api/test_workflows.py

Log Message: ----------- Use hid from hda

Commit: b1eaf85480fbfef5166925294257e2b2cc954b4d https://github.com/galaxyproject/galaxy/commit/b1eaf85480fbfef5166925294257e... Author: guerler aysam.guerler@gmail.com Date: 2016-09-29 (Thu, 29 Sep 2016)

Changed paths: M lib/galaxy/tools/parameters/meta.py

Log Message: ----------- Fix indent

Commit: 1cc8e04c819487c898c09471132b385642dd7b8e https://github.com/galaxyproject/galaxy/commit/1cc8e04c819487c898c09471132b3... Author: guerler aysam.guerler@gmail.com Date: 2016-09-29 (Thu, 29 Sep 2016)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js M lib/galaxy/tools/__init__.py M static/maps/mvc/tool/tool-form.js.map

Log Message: ----------- Merge all errors from batch mode run for regular tool executions

Commit: e14fe506434e55d999995b3da115c7a36f7376be https://github.com/galaxyproject/galaxy/commit/e14fe506434e55d999995b3da115c... Author: guerler aysam.guerler@gmail.com Date: 2016-09-30 (Fri, 30 Sep 2016)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/workflow/run_request.py M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js M test/api/test_workflows.py

Log Message: ----------- Use order_index instead of step_id

Commit: 67eb2c6530bd62f4b6542937f38f373e6022c000 https://github.com/galaxyproject/galaxy/commit/67eb2c6530bd62f4b6542937f38f3... Author: guerler aysam.guerler@gmail.com Date: 2016-09-30 (Fri, 30 Sep 2016)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/run_request.py M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js M test/api/test_workflows.py

Log Message: ----------- Use parameters/batch instead of input_params

Commit: 70df25e74b306337e18ce0c2d8291a998da23024 https://github.com/galaxyproject/galaxy/commit/70df25e74b306337e18ce0c2d8291... Author: guerler aysam.guerler@gmail.com Date: 2016-09-30 (Fri, 30 Sep 2016)

Changed paths: A test/api/test_workflow_batch.ga R test/api/test_workflow_input_params.ga M test/api/test_workflows.py

Log Message: ----------- Rename test associated workflow export

Commit: ed7bba5e2027bf239bf86359b68a360149c027dd https://github.com/galaxyproject/galaxy/commit/ed7bba5e2027bf239bf86359b68a3... Author: John Chilton jmchilton@gmail.com Date: 2016-09-30 (Fri, 30 Sep 2016)

Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/run_request.py

Log Message: ----------- Increased consistency in backend workflow run code.

Rename build_workflow_run_config to build_workflow_run_configs since it sometimes returned a list, make it always return a list, one path out of run_request.py:build_workflow_run_configs, ensure batch parameter is respected and throw an exception if it is not and build_workflow_run_configs returns multiple invocations.

Commit: 8166276679cb1d1bf90d9cf473102b3e2eda3b99 https://github.com/galaxyproject/galaxy/commit/8166276679cb1d1bf90d9cf473102... Author: guerler aysam.guerler@gmail.com Date: 2016-09-30 (Fri, 30 Sep 2016)

Changed paths: M lib/galaxy/workflow/run_request.py

Log Message: ----------- Do not copy tags from source history

Commit: 8fab4f141b93e298487e1a5ed58fda24289be7ef https://github.com/galaxyproject/galaxy/commit/8fab4f141b93e298487e1a5ed58fd... Author: John Chilton jmchilton@gmail.com Date: 2016-09-30 (Fri, 30 Sep 2016)

Changed paths: M lib/galaxy/workflow/run_request.py

Log Message: ----------- Unify workflow API history options across approaches.

The old variant of specifying a history attribute should work with new batch parameter mode and the new variant of specifing new_history_name or history_id should work with the existing invocation API stuff.

Commit: f4ca27d50dbac3d89ad758262633777545ee32f4 https://github.com/galaxyproject/galaxy/commit/f4ca27d50dbac3d89ad7582626337... Author: guerler aysam.guerler@gmail.com Date: 2016-09-30 (Fri, 30 Sep 2016)

Changed paths: M lib/galaxy/workflow/run_request.py

Log Message: ----------- Add error response to validate expansion result

Commit: 5b70453e5ea2d98052635c509ee5502574144c06 https://github.com/galaxyproject/galaxy/commit/5b70453e5ea2d98052635c509ee55... Author: John Chilton jmchilton@gmail.com Date: 2016-09-30 (Fri, 30 Sep 2016)

Log Message: ----------- Merge remote-tracking branch 'guerler/unite_api' into unite_api_history

Conflicts: lib/galaxy/workflow/run_request.py

Commit: ab2a5198afeb0b651643b84c0dd3eb6a0e611bb6 https://github.com/galaxyproject/galaxy/commit/ab2a5198afeb0b651643b84c0dd3e... Author: John Chilton jmchilton@gmail.com Date: 2016-09-30 (Fri, 30 Sep 2016)

Changed paths: M lib/galaxy/workflow/run_request.py

Log Message: ----------- Resolve this comment/discussion (https://github.com/galaxyproject/galaxy/pull/2969#issuecomment-250830186).

Commit: 92034e67766c0e608b8cec6c63e29e3405e80333 https://github.com/galaxyproject/galaxy/commit/92034e67766c0e608b8cec6c63e29... Author: John Chilton jmchilton@gmail.com Date: 2016-09-30 (Fri, 30 Sep 2016)

Changed paths: M lib/galaxy/workflow/run_request.py

Log Message: ----------- Revert to an exception instead of an assertion.

I'm close to winning @guerler over - but not quite there yet.

Commit: 72980bc967a8fb7b988b4c33a79af9c3af94bcc2 https://github.com/galaxyproject/galaxy/commit/72980bc967a8fb7b988b4c33a79af... Author: John Chilton jmchilton@gmail.com Date: 2016-09-30 (Fri, 30 Sep 2016)

Log Message: ----------- Merge remote-tracking branch 'guerler/unite_api' into unite_api_history

Conflicts: lib/galaxy/workflow/run_request.py

Commit: 3d4e02f1314cdeeae6fc6285e7b0c35fb2b6f136 https://github.com/galaxyproject/galaxy/commit/3d4e02f1314cdeeae6fc6285e7b0c... Author: John Chilton jmchilton@gmail.com Date: 2016-09-30 (Fri, 30 Sep 2016)

Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/run_request.py

Log Message: ----------- Fixup previous commits bugs.

Commit: 4fea03acc917089498cb2a897e931a5d1cec8a7b https://github.com/galaxyproject/galaxy/commit/4fea03acc917089498cb2a897e931... Author: guerler aysam.guerler@gmail.com Date: 2016-09-30 (Fri, 30 Sep 2016)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/managers/workflows.py M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js

Log Message: ----------- Use explicit order_index when assigning workflow steps

Commit: c67e4ac1a391348fdac942ebe2918cb7e0e08235 https://github.com/galaxyproject/galaxy/commit/c67e4ac1a391348fdac942ebe2918... Author: guerler aysam.guerler@gmail.com Date: 2016-09-30 (Fri, 30 Sep 2016)

Changed paths: M test/api/test_workflows.py

Log Message: ----------- Test case

Commit: 9df99d2bb0f5c34c66f1d0730c012b5cd268899b https://github.com/galaxyproject/galaxy/commit/9df99d2bb0f5c34c66f1d0730c012... Author: John Chilton jmchilton@gmail.com Date: 2016-09-30 (Fri, 30 Sep 2016)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/managers/workflows.py M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js M test/api/test_workflows.py

Log Message: ----------- Merge remote-tracking branch 'guerler/unite_api' into unite_api_history

Commit: 0263c3259ebcf7d604bfc9da8ba1bb69800a27aa https://github.com/galaxyproject/galaxy/commit/0263c3259ebcf7d604bfc9da8ba1b... Author: John Chilton jmchilton@gmail.com Date: 2016-09-30 (Fri, 30 Sep 2016)

Changed paths: M lib/galaxy/workflow/run_request.py

Log Message: ----------- Refactor run_request to reuse step parameter normalization.

Lessens the difference between GUI and API approaches.

Commit: eb288cd4e122b0c5ff11a75fbac34374b080bc3a https://github.com/galaxyproject/galaxy/commit/eb288cd4e122b0c5ff11a75fbac34... Author: John Chilton jmchilton@gmail.com Date: 2016-09-30 (Fri, 30 Sep 2016)

Changed paths: M lib/galaxy/workflow/run_request.py

Log Message: ----------- Refactor build_workflow_run_configs toward unification of API and UI approaches.

Commit: a2e265e8b148da7e4a6ba50eb9b64cdaf6765a93 https://github.com/galaxyproject/galaxy/commit/a2e265e8b148da7e4a6ba50eb9b64... Author: John Chilton jmchilton@gmail.com Date: 2016-09-30 (Fri, 30 Sep 2016)

Changed paths: M lib/galaxy/workflow/run_request.py

Log Message: ----------- Refactor build_workflow_run_configs toward unification of API and UI approaches.

Swap expansion of raw parameters and normalization of parmeters so that we can move the loop outside of the conditional ... and thus elimiante the conditional that distinguishes between API and UI approaches.

Commit: e60fd0490526e76f58210151d9ea6090d9277317 https://github.com/galaxyproject/galaxy/commit/e60fd0490526e76f58210151d9ea6... Author: John Chilton jmchilton@gmail.com Date: 2016-09-30 (Fri, 30 Sep 2016)

Changed paths: M lib/galaxy/workflow/run_request.py

Log Message: ----------- Refine workflow target history handling with bug fix and improved error message.

Commit: b106c48b68f87b2c9008e6f03b5cdb51b951051a https://github.com/galaxyproject/galaxy/commit/b106c48b68f87b2c9008e6f03b5cd... Author: John Chilton jmchilton@gmail.com Date: 2016-09-30 (Fri, 30 Sep 2016)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/workflow/run_request.py M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js M test/api/test_workflows.py

Log Message: ----------- Unify build_workflow_run_configs for API and UI approaches to running workflows.

No more branches - the method runs top to bottom for each approach. One loop for batching regardless and completely available to all API options. Only call WorkflowRunConfig in one place. Remove duplicate fetching of replacement_params. One call to _normalize_step_parameters.

Commit: aaf5cc4075fcf3951850b979b4b4eec288fd5393 https://github.com/galaxyproject/galaxy/commit/aaf5cc4075fcf3951850b979b4b4e... Author: Aysam Guerler aysam.guerler@gmail.com Date: 2016-09-30 (Fri, 30 Sep 2016)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/run_request.py M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js M test/api/test_workflows.py

Log Message: ----------- Merge pull request #13 from jmchilton/unite_api_history

Unify workflow API history options across approaches.

Commit: dc209c7a003bbc63d590cbbc45fbdf48340bbe8c https://github.com/galaxyproject/galaxy/commit/dc209c7a003bbc63d590cbbc45fbd... Author: guerler aysam.guerler@gmail.com Date: 2016-09-30 (Fri, 30 Sep 2016)

Changed paths: M lib/galaxy/managers/workflows.py

Log Message: ----------- Encode unencoded step id when exposing workflow dictionary for execution

Commit: 76201eba45c39e9b5b62be865bc56331bb775d57 https://github.com/galaxyproject/galaxy/commit/76201eba45c39e9b5b62be865bc56... Author: guerler aysam.guerler@gmail.com Date: 2016-09-30 (Fri, 30 Sep 2016)

Changed paths: M lib/galaxy/workflow/run_request.py

Log Message: ----------- Move get target history out of build_workflow_run_configs

Commit: 5e6af483d799137c2a956d98aad79ee30f636101 https://github.com/galaxyproject/galaxy/commit/5e6af483d799137c2a956d98aad79... Author: guerler aysam.guerler@gmail.com Date: 2016-10-01 (Sat, 01 Oct 2016)

Changed paths: M lib/galaxy/workflow/run_request.py

Log Message: ----------- Refactor target history mode validation, remove spaces

Commit: 0f6ad3f41469816cbb31b6c5a2a663cf30f0ecf1 https://github.com/galaxyproject/galaxy/commit/0f6ad3f41469816cbb31b6c5a2a66... Author: guerler aysam.guerler@gmail.com Date: 2016-10-03 (Mon, 03 Oct 2016)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/managers/workflows.py M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js

Log Message: ----------- Use order index to link connected datasets

Commit: ce7cf6cc230827c1ad485579a7efd4a2fa807381 https://github.com/galaxyproject/galaxy/commit/ce7cf6cc230827c1ad485579a7efd... Author: guerler aysam.guerler@gmail.com Date: 2016-10-03 (Mon, 03 Oct 2016)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/managers/workflows.py M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js

Log Message: ----------- Rename step_id to step_index to avoid confusion

Commit: d5c54907dad35d5ba8578f4d563c36c8b06fa43d https://github.com/galaxyproject/galaxy/commit/d5c54907dad35d5ba8578f4d563c3... Author: guerler aysam.guerler@gmail.com Date: 2016-10-03 (Mon, 03 Oct 2016)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js

Log Message: ----------- Rename step_id to step_index to avoid confusion, fix error message response handling

Commit: 0b03a800abdab4540152adea44ed820cbc2782e0 https://github.com/galaxyproject/galaxy/commit/0b03a800abdab4540152adea44ed8... Author: guerler aysam.guerler@gmail.com Date: 2016-10-03 (Mon, 03 Oct 2016)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js

Log Message: ----------- Improve error display robustness for run workflow form

Commit: f3ce9a927caf193ee7f681553c6209dfa3fd05ff https://github.com/galaxyproject/galaxy/commit/f3ce9a927caf193ee7f681553c620... Author: guerler aysam.guerler@gmail.com Date: 2016-10-03 (Mon, 03 Oct 2016)

Changed paths: M lib/galaxy/tools/parameters/meta.py

Log Message: ----------- Remove sorting from workflow expansion test cases

Commit: ea1879d4410eda95506e9645adada1bc8a2247dc https://github.com/galaxyproject/galaxy/commit/ea1879d4410eda95506e9645adada... Author: guerler aysam.guerler@gmail.com Date: 2016-10-03 (Mon, 03 Oct 2016)

Changed paths: M lib/galaxy/tools/parameters/meta.py

Log Message: ----------- Remove sorting from last expansion test case

Commit: 00f471156574cb1a5bba3cf62ee26c8dc4a6e41e https://github.com/galaxyproject/galaxy/commit/00f471156574cb1a5bba3cf62ee26... Author: guerler aysam.guerler@gmail.com Date: 2016-10-03 (Mon, 03 Oct 2016)

Changed paths: M lib/galaxy/tools/parameters/meta.py

Log Message: ----------- Fix order in workflow expansion

Commit: c2f1b635cc65aafd32309b788d809c5d6cf53615 https://github.com/galaxyproject/galaxy/commit/c2f1b635cc65aafd32309b788d809... Author: guerler aysam.guerler@gmail.com Date: 2016-10-03 (Mon, 03 Oct 2016)

Changed paths: M lib/galaxy/tools/parameters/meta.py M test/api/test_workflows.py

Log Message: ----------- Rely on deterministic invocations order in batch mode test case

Commit: 4d871fa734e0982e685fb1bf356f4147ff1ae143 https://github.com/galaxyproject/galaxy/commit/4d871fa734e0982e685fb1bf356f4... Author: guerler aysam.guerler@gmail.com Date: 2016-10-04 (Tue, 04 Oct 2016)

Changed paths: M test/api/test_workflows.py

Log Message: ----------- Check both invocation orders when using the new batch mode feature

Commit: 329ee052510c0c720ae5d44bac23becf639f6506 https://github.com/galaxyproject/galaxy/commit/329ee052510c0c720ae5d44bac23b... Author: guerler aysam.guerler@gmail.com Date: 2016-10-04 (Tue, 04 Oct 2016)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js

Log Message: ----------- Hide children elements instead of destroying them upon successful workflow submission

Commit: 922d9ee53a9d9400cda622c12d6f79fc190673f6 https://github.com/galaxyproject/galaxy/commit/922d9ee53a9d9400cda622c12d6f7... Author: John Chilton jmchilton@gmail.com Date: 2016-10-04 (Tue, 04 Oct 2016)

Changed paths: M lib/galaxy/workflow/run_request.py

Log Message: ----------- Fix for unite_api branch for API key specification without explicit history target.

It is good to not depend on trans.history being set I think and this is required to fix bioblend tests.

Commit: 5a5d770455f5a41f0630cf6b7fad40a2e0e939e0 https://github.com/galaxyproject/galaxy/commit/5a5d770455f5a41f0630cf6b7fad4... Author: Aysam Guerler aysam.guerler@gmail.com Date: 2016-10-04 (Tue, 04 Oct 2016)

Changed paths: M lib/galaxy/workflow/run_request.py

Log Message: ----------- Merge pull request #14 from jmchilton/unite_api_apikey_fix

Fix for unite_api branch for API key specification without explicit history target.

Commit: b595cd3f4775c1435a28ee80159fe16a2b4581b6 https://github.com/galaxyproject/galaxy/commit/b595cd3f4775c1435a28ee80159fe... Author: guerler aysam.guerler@gmail.com Date: 2016-10-04 (Tue, 04 Oct 2016)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/managers/workflows.py M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js

Log Message: ----------- Always submit either history_id or new history name through run form

Commit: 2ca1af225f8fe1715ef058fd0f516a48d32fa325 https://github.com/galaxyproject/galaxy/commit/2ca1af225f8fe1715ef058fd0f516... Author: guerler aysam.guerler@gmail.com Date: 2016-10-04 (Tue, 04 Oct 2016)

Changed paths: M lib/galaxy/workflow/run_request.py

Log Message: ----------- Remove trans.history from target history identification

Commit: f0f26e0654b2f9f3bdd3a159ea2800745980abd2 https://github.com/galaxyproject/galaxy/commit/f0f26e0654b2f9f3bdd3a159ea280... Author: John Chilton jmchilton@gmail.com Date: 2016-10-05 (Wed, 05 Oct 2016)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M lib/galaxy/managers/workflows.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-form.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form.js A test/api/test_workflow_batch.ga M test/api/test_workflows.py M test/unit/workflows/test_run_parameters.py

Log Message: ----------- Merge pull request #2969 from guerler/unite_api

Unite workflow execution api endpoints

Compare: https://github.com/galaxyproject/galaxy/compare/5595bf2e4068...f0f26e0654b2