October 2016 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 6d27a3: Fix initial conda version at 4.0.5
by GitHub 05 Oct '16

05 Oct '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 6d27a3c4b6184b393e535afd32f87e55e7a07b70 https://github.com/galaxyproject/galaxy/commit/6d27a3c4b6184b393e535afd32f8… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Fix initial conda version at 4.0.5 This should prevent missing `activate` in <conda_prefix>/bin when downgrading to 3.19.3. This is what the conda people use in their CI environment ( [see](https://github.com/conda/conda/blob/master/utils/travis-run-install.sh… and perhaps why that bug made it into the release in the first place). Commit: f7c3e25e5db1a1d99c81380f552719bee07c1790 https://github.com/galaxyproject/galaxy/commit/f7c3e25e5db1a1d99c81380f5527… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge pull request #3009 from mvdbeek/conda_downgrade [16.01] Backport #2869 Fix initial conda version at 4.0.5 Commit: 224c2126c73617ec906abc1e08d5f5a7548633b1 https://github.com/galaxyproject/galaxy/commit/224c2126c73617ec906abc1e08d5… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Compare: https://github.com/galaxyproject/galaxy/compare/45e6949eeae8...224c2126c736

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[galaxyproject/galaxy] 6d27a3: Fix initial conda version at 4.0.5
by GitHub 05 Oct '16

05 Oct '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 6d27a3c4b6184b393e535afd32f87e55e7a07b70 https://github.com/galaxyproject/galaxy/commit/6d27a3c4b6184b393e535afd32f8… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Fix initial conda version at 4.0.5 This should prevent missing `activate` in <conda_prefix>/bin when downgrading to 3.19.3. This is what the conda people use in their CI environment ( [see](https://github.com/conda/conda/blob/master/utils/travis-run-install.sh… and perhaps why that bug made it into the release in the first place). Commit: f7c3e25e5db1a1d99c81380f552719bee07c1790 https://github.com/galaxyproject/galaxy/commit/f7c3e25e5db1a1d99c81380f5527… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge pull request #3009 from mvdbeek/conda_downgrade [16.01] Backport #2869 Fix initial conda version at 4.0.5 Compare: https://github.com/galaxyproject/galaxy/compare/8bf7256ca8ec...f7c3e25e5db1

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[galaxyproject/galaxy] 975325: API access to genome fasta index and sequence
by GitHub 05 Oct '16

05 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 97532515ea24325ba26877696991b24401733ee6 https://github.com/galaxyproject/galaxy/commit/97532515ea24325ba26877696991… Author: Jim Johnson <jj(a)umn.edu> Date: 2016-09-20 (Tue, 20 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/genomes.py Log Message: ----------- API access to genome fasta index and sequence Allows visualization components, e.g. IGV.js, to incrementally retrieve sequence as needed. Commit: efbc06eb0178f495d1581aec7a8c1467af93f2d7 https://github.com/galaxyproject/galaxy/commit/efbc06eb0178f495d1581aec7a8c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-28 (Wed, 28 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/genomes.py Log Message: ----------- Cleanup 97532515ea24325ba26877696991b24401733ee6. Commit: 16c2227b93151c31caefa369e17e36cdfb75e381 https://github.com/galaxyproject/galaxy/commit/16c2227b93151c31caefa369e17e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/genomes.py Log Message: ----------- Merge pull request #2939 from jj-umn/patch-4 API access to genome fasta index and sequence Compare: https://github.com/galaxyproject/galaxy/compare/f0f26e0654b2...16c2227b9315

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[galaxyproject/galaxy] 5095fc: Remove internal api endpoint, merge into invocatio...
by GitHub 05 Oct '16

05 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5095fc02c4cfb830748179c29ea9e1b1aaf0b455 https://github.com/galaxyproject/galaxy/commit/5095fc02c4cfb830748179c29ea9… Author: guerler <aysam.guerler(a)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/9d9e5f026dff5523e7e6aef1a944… Author: guerler <aysam.guerler(a)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/c840730101823107396104dcc736… Author: guerler <aysam.guerler(a)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/9a9726e9a174a230b3a71bdb40bc… Author: guerler <aysam.guerler(a)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/838fad39a14674986680edfccfbd… Author: guerler <aysam.guerler(a)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/0a767d4d5343d7eaf3697373922d… Author: guerler <aysam.guerler(a)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/477d3f9ae94acf2b9c57eba641c2… Author: guerler <aysam.guerler(a)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/991d81cdbeeca43891b2ed5464c7… Author: guerler <aysam.guerler(a)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/3d7bfeb6dd08b0241d8fa75f37c5… Author: guerler <aysam.guerler(a)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/1cb67308771edf40716ef5f30f43… Author: guerler <aysam.guerler(a)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/e34019e52806fde224781cfe3bc4… Author: guerler <aysam.guerler(a)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/3545a0ef1f8a2fbde86558fcaf5d… Author: guerler <aysam.guerler(a)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/6f7e9cd5df6eb444974e3d45f1df… Author: guerler <aysam.guerler(a)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/b1eaf85480fbfef5166925294257… Author: guerler <aysam.guerler(a)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/1cc8e04c819487c898c09471132b… Author: guerler <aysam.guerler(a)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/e14fe506434e55d999995b3da115… Author: guerler <aysam.guerler(a)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/67eb2c6530bd62f4b6542937f38f… Author: guerler <aysam.guerler(a)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/70df25e74b306337e18ce0c2d829… Author: guerler <aysam.guerler(a)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/ed7bba5e2027bf239bf86359b68a… Author: John Chilton <jmchilton(a)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/8166276679cb1d1bf90d9cf47310… Author: guerler <aysam.guerler(a)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/8fab4f141b93e298487e1a5ed58f… Author: John Chilton <jmchilton(a)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/f4ca27d50dbac3d89ad758262633… Author: guerler <aysam.guerler(a)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/5b70453e5ea2d98052635c509ee5… Author: John Chilton <jmchilton(a)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/ab2a5198afeb0b651643b84c0dd3… Author: John Chilton <jmchilton(a)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/92034e67766c0e608b8cec6c63e2… Author: John Chilton <jmchilton(a)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/72980bc967a8fb7b988b4c33a79a… Author: John Chilton <jmchilton(a)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/3d4e02f1314cdeeae6fc6285e7b0… Author: John Chilton <jmchilton(a)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/4fea03acc917089498cb2a897e93… Author: guerler <aysam.guerler(a)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/c67e4ac1a391348fdac942ebe291… Author: guerler <aysam.guerler(a)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/9df99d2bb0f5c34c66f1d0730c01… Author: John Chilton <jmchilton(a)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/0263c3259ebcf7d604bfc9da8ba1… Author: John Chilton <jmchilton(a)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/eb288cd4e122b0c5ff11a75fbac3… Author: John Chilton <jmchilton(a)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/a2e265e8b148da7e4a6ba50eb9b6… Author: John Chilton <jmchilton(a)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/e60fd0490526e76f58210151d9ea… Author: John Chilton <jmchilton(a)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/b106c48b68f87b2c9008e6f03b5c… Author: John Chilton <jmchilton(a)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/aaf5cc4075fcf3951850b979b4b4… Author: Aysam Guerler <aysam.guerler(a)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/dc209c7a003bbc63d590cbbc45fb… Author: guerler <aysam.guerler(a)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/76201eba45c39e9b5b62be865bc5… Author: guerler <aysam.guerler(a)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/5e6af483d799137c2a956d98aad7… Author: guerler <aysam.guerler(a)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/0f6ad3f41469816cbb31b6c5a2a6… Author: guerler <aysam.guerler(a)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/ce7cf6cc230827c1ad485579a7ef… Author: guerler <aysam.guerler(a)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/d5c54907dad35d5ba8578f4d563c… Author: guerler <aysam.guerler(a)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/0b03a800abdab4540152adea44ed… Author: guerler <aysam.guerler(a)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/f3ce9a927caf193ee7f681553c62… Author: guerler <aysam.guerler(a)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/ea1879d4410eda95506e9645adad… Author: guerler <aysam.guerler(a)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/00f471156574cb1a5bba3cf62ee2… Author: guerler <aysam.guerler(a)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/c2f1b635cc65aafd32309b788d80… Author: guerler <aysam.guerler(a)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/4d871fa734e0982e685fb1bf356f… Author: guerler <aysam.guerler(a)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/329ee052510c0c720ae5d44bac23… Author: guerler <aysam.guerler(a)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/922d9ee53a9d9400cda622c12d6f… Author: John Chilton <jmchilton(a)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/5a5d770455f5a41f0630cf6b7fad… Author: Aysam Guerler <aysam.guerler(a)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/b595cd3f4775c1435a28ee80159f… Author: guerler <aysam.guerler(a)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/2ca1af225f8fe1715ef058fd0f51… Author: guerler <aysam.guerler(a)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/f0f26e0654b2f9f3bdd3a159ea28… Author: John Chilton <jmchilton(a)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

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[galaxyproject/galaxy] 240781: Remove unnecessary line from test cases
by GitHub 05 Oct '16

05 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 240781811e3f6f6b05dc53bee69850745f71d5c2 https://github.com/galaxyproject/galaxy/commit/240781811e3f6f6b05dc53bee698… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-10-04 (Tue, 04 Oct 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Remove unnecessary line from test cases Commit: 5595bf2e40687f6e67e34748867f57eedbd7ceab https://github.com/galaxyproject/galaxy/commit/5595bf2e40687f6e67e34748867f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #3005 from guerler/simplify_basic_py Remove unnecessary line from parameter unit test cases Compare: https://github.com/galaxyproject/galaxy/compare/d9af95b401eb...5595bf2e4068

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[galaxyproject/galaxy] 17c4af: Docstring fixes for galaxy.exceptions and galaxy.j...
by GitHub 04 Oct '16

04 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 17c4af285d75e4a271880b37f4727df59987655a https://github.com/galaxyproject/galaxy/commit/17c4af285d75e4a271880b37f472… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-04 (Tue, 04 Oct 2016) Changed paths: M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.py M lib/galaxy/jobs/metrics/__init__.py M lib/galaxy/jobs/metrics/collectl/__init__.py M lib/galaxy/jobs/metrics/collectl/cli.py M lib/galaxy/jobs/metrics/collectl/subsystems.py M lib/galaxy/jobs/metrics/formatting.py M lib/galaxy/jobs/metrics/instrumenters/__init__.py M lib/galaxy/jobs/metrics/instrumenters/collectl.py M lib/galaxy/jobs/metrics/instrumenters/core.py M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py M lib/galaxy/jobs/metrics/instrumenters/env.py M lib/galaxy/jobs/metrics/instrumenters/meminfo.py M lib/galaxy/jobs/metrics/instrumenters/uname.py Log Message: ----------- Docstring fixes for galaxy.exceptions and galaxy.jobs.metrics. xref https://github.com/galaxyproject/galaxy-lib/pull/21. Rebase with spelling fixes thanks to @nsoranzo. Commit: d9af95b401ebec1db5cd6653f5ebbb9a7fd5c3f5 https://github.com/galaxyproject/galaxy/commit/d9af95b401ebec1db5cd6653f5eb… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-10-04 (Tue, 04 Oct 2016) Changed paths: M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.py M lib/galaxy/jobs/metrics/__init__.py M lib/galaxy/jobs/metrics/collectl/__init__.py M lib/galaxy/jobs/metrics/collectl/cli.py M lib/galaxy/jobs/metrics/collectl/subsystems.py M lib/galaxy/jobs/metrics/formatting.py M lib/galaxy/jobs/metrics/instrumenters/__init__.py M lib/galaxy/jobs/metrics/instrumenters/collectl.py M lib/galaxy/jobs/metrics/instrumenters/core.py M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py M lib/galaxy/jobs/metrics/instrumenters/env.py M lib/galaxy/jobs/metrics/instrumenters/meminfo.py M lib/galaxy/jobs/metrics/instrumenters/uname.py Log Message: ----------- Merge pull request #3003 from jmchilton/docstrings1 Docstring fixes for galaxy.exceptions and galaxy.jobs.metrics. Compare: https://github.com/galaxyproject/galaxy/compare/824f556ea7d0...d9af95b401eb

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[galaxyproject/galaxy] 375ed8: polish resolvers section in conda faq docs
by GitHub 03 Oct '16

03 Oct '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 375ed8cc81590a18a52b61e32307562488fd551e https://github.com/galaxyproject/galaxy/commit/375ed8cc81590a18a52b61e32307… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-03 (Mon, 03 Oct 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- polish resolvers section in conda faq docs Commit: ba274e37f2f0e8c9973b19c46fe99c5565c5118c https://github.com/galaxyproject/galaxy/commit/ba274e37f2f0e8c9973b19c46fe9… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-03 (Mon, 03 Oct 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- describe the conda installation behavior a bit better Commit: 2899372791fdbba4f8db7c414a5447cf049987f3 https://github.com/galaxyproject/galaxy/commit/2899372791fdbba4f8db7c414a54… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-10-03 (Mon, 03 Oct 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- Update conda_faq.rst Commit: fdfe9d8c20a63e6e6e6951d5fe5cbd7d74446d0a https://github.com/galaxyproject/galaxy/commit/fdfe9d8c20a63e6e6e6951d5fe5c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-03 (Mon, 03 Oct 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- Merge pull request #19 from martenson/nsoranzo-patch-1-1 Small fixes to conda_faq.rst changes Commit: d9fab3345856770a16a98f18cf9e6185a4eae91a https://github.com/galaxyproject/galaxy/commit/d9fab3345856770a16a98f18cf9e… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-10-03 (Mon, 03 Oct 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- Merge pull request #2998 from martenson/conda-faq-polish [16.07] Conda FAQ polish Compare: https://github.com/galaxyproject/galaxy/compare/04d62e242412...d9fab3345856

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[galaxyproject/galaxy] 55cce8: Reload metadata and lib tools on toolbox reload
by GitHub 03 Oct '16

03 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 55cce84189510e14b55a042168e5f63c71be7fe3 https://github.com/galaxyproject/galaxy/commit/55cce84189510e14b55a042168e5… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-09-30 (Fri, 30 Sep 2016) Changed paths: M lib/galaxy/queue_worker.py Log Message: ----------- Reload metadata and lib tools on toolbox reload Should close #2988. Commit: 824f556ea7d04b5141307ede3258850fcc17ed77 https://github.com/galaxyproject/galaxy/commit/824f556ea7d04b5141307ede3258… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-03 (Mon, 03 Oct 2016) Changed paths: M lib/galaxy/queue_worker.py Log Message: ----------- Merge pull request #2992 from mvdbeek/reload_special_tools Reload metadata and lib tools on toolbox reload Compare: https://github.com/galaxyproject/galaxy/compare/66a5bd45bd3c...824f556ea7d0

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