Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: aea04a98715d921eacf86d58ebf5fd754ecfcad1 https://github.com/galaxyproject/galaxy/commit/aea04a98715d921eacf86d58ebf5f... Author: Jesse c j van Dam <jesse.vandam@wur.nl> Date: 2015-06-24 (Wed, 24 Jun 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/graph.py A lib/galaxy/datatypes/triples.py Log Message: ----------- Added better support for formats that store triples, these formats include 'N-Triples', 'N3','Turtle','RDF/XML' and 'JSON-LD' Commit: e097de3570cb525687ee1800c1582375c6e22b94 https://github.com/galaxyproject/galaxy/commit/e097de3570cb525687ee1800c1582... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-24 (Wed, 24 Jun 2015) Changed paths: M .ci/pep8_sources.txt M lib/galaxy/datatypes/triples.py Log Message: ----------- PEP-8 fixes for triples.py and to flake checks. Commit: e714759d409a3099ba04284de8167f66af32424e https://github.com/galaxyproject/galaxy/commit/e714759d409a3099ba04284de8167... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-24 (Wed, 24 Jun 2015) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/graph.py Log Message: ----------- Add restore as deprecated old path to RDF. It will be in many old datatype_conf.xml files so perhaps it should be deprecated before removing it completely. Using this new infrastructure - people will be warned if the they load it from the old location and told to update datatypes_conf.xml to reference the new location. Commit: c9e27c9425932573d7c7503dedb655ef62a92914 https://github.com/galaxyproject/galaxy/commit/c9e27c9425932573d7c7503dedb65... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-24 (Wed, 24 Jun 2015) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/triples.py Log Message: ----------- File reading infrastructure for datatypes. Use to ensure triple-related datatypes properly close file handles and restrict the amount of memory they consume when reading lines from files. Commit: 82f62bc14768e66fc1fb127058acd1c17e4ce3e1 https://github.com/galaxyproject/galaxy/commit/82f62bc14768e66fc1fb127058acd... Author: Jesse <jesse.vandam@wur.nl> Date: 2015-06-24 (Wed, 24 Jun 2015) Changed paths: M .ci/pep8_sources.txt M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/graph.py M lib/galaxy/datatypes/triples.py Log Message: ----------- Merge pull request #1 from jmchilton/triples Various fixes for triples.py. Commit: 6c3cedcfd517ac6af3c109a6eec2c555a8313d84 https://github.com/galaxyproject/galaxy/commit/6c3cedcfd517ac6af3c109a6eec2c... Author: Jesse c j van Dam <jesse.vandam@wur.nl> Date: 2015-06-24 (Wed, 24 Jun 2015) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- fix sniffers of the triple format Commit: e5d1b4ee26a16d6f9859de0d1f5ee5b5113430c4 https://github.com/galaxyproject/galaxy/commit/e5d1b4ee26a16d6f9859de0d1f5ee... Author: Jesse c j van Dam <jesse.vandam@wur.nl> Date: 2015-06-24 (Wed, 24 Jun 2015) Changed paths: M lib/galaxy/datatypes/triples.py Log Message: ----------- fix comment in triples.py (example for regexp) Commit: c03f84b1d76285f75d3b5f84c06e31fc5bf54f96 https://github.com/galaxyproject/galaxy/commit/c03f84b1d76285f75d3b5f84c06e3... Author: Jesse c j van Dam <jesse.vandam@wur.nl> Date: 2015-06-25 (Thu, 25 Jun 2015) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/triples.py Log Message: ----------- use sizehint from python readline(s) function for sniffers in triples.py Commit: 94c00b0238d50d9703609000d25f6b1bc56a9281 https://github.com/galaxyproject/galaxy/commit/94c00b0238d50d9703609000d25f6... Author: Jesse c j van Dam <jesse.vandam@wur.nl> Date: 2015-06-25 (Thu, 25 Jun 2015) Changed paths: M lib/galaxy/datatypes/triples.py Log Message: ----------- PEP-8 fixes to triples.py Commit: ae1a56e26d1931add633970a206b97aff3f45dae https://github.com/galaxyproject/galaxy/commit/ae1a56e26d1931add633970a206b9... Author: Jesse c j van Dam <jesse.vandam@wur.nl> Date: 2015-06-26 (Fri, 26 Jun 2015) Changed paths: M lib/galaxy/datatypes/triples.py Log Message: ----------- Make the RDF sniffer in triples.py a bit more specific Commit: fb2784003d39e7ae8ce144ff7ab793f65d4771d8 https://github.com/galaxyproject/galaxy/commit/fb2784003d39e7ae8ce144ff7ab79... Author: Jesse c j van Dam <jesse.vandam@wur.nl> Date: 2015-08-24 (Mon, 24 Aug 2015) Changed paths: A .ci/flake8_blacklist.txt M .ci/flake8_wrapper.sh R .ci/pep8_sources.txt M CONTRIBUTING.md M client/GruntFile.js M client/README.md M client/bower.json M client/galaxy/scripts/galaxy.menu.js R client/galaxy/scripts/galaxy.workflow_editor.canvas.js R client/galaxy/scripts/galaxy.workflows.js M client/galaxy/scripts/libs/d3.js M client/galaxy/scripts/libs/farbtastic.js M client/galaxy/scripts/libs/handlebars.runtime.js A client/galaxy/scripts/libs/jquery.sparklines.js M client/galaxy/scripts/libs/jquery/jqtouch.js M client/galaxy/scripts/libs/raven.js M client/galaxy/scripts/libs/require.js M client/galaxy/scripts/libs/tracekit.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/form/form-view.js M 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test/unit/tools/test_tool_loader.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/workflows/test_extract_summary.py M tool-data/all_fasta.loc.sample M tool-data/faseq.loc.sample R tool-data/fastx_clipper_sequences.txt M tool-data/liftOver.loc.sample M tool-data/mosaik_index.loc.sample M tool-data/ngs_sim_fasta.loc.sample M tool-data/perm_base_index.loc.sample M tool-data/perm_color_index.loc.sample M tool-data/picard_index.loc.sample M tool-data/regions.loc.sample M tool-data/srma_index.loc.sample M tool_list.py M tools/data_source/data_source.py M tools/extract/extract_genomic_dna.py M tools/extract/extract_genomic_dna.xml M tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/stats/grouping.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev Conflicts: .ci/pep8_sources.txt lib/galaxy/datatypes/graph.py Commit: c873d565834b8aa9f5d39901e025bbcec5fa2631 https://github.com/galaxyproject/galaxy/commit/c873d565834b8aa9f5d39901e025b... Author: Jesse c j van Dam <jesse.vandam@wur.nl> Date: 2015-08-24 (Mon, 24 Aug 2015) Changed paths: M lib/galaxy/datatypes/graph.py Log Message: ----------- graph.RDF got defined twice after merge Commit: ba054a189ef8efe922154c34462bf49d104d1abe https://github.com/galaxyproject/galaxy/commit/ba054a189ef8efe922154c34462bf... Author: Jesse c j van Dam <jesse.vandam@wur.nl> Date: 2015-08-24 (Mon, 24 Aug 2015) Changed paths: M lib/galaxy/datatypes/graph.py Log Message: ----------- pip8 problem Commit: 37f3bbf26772f78af132527a1aa19a8da60fb540 https://github.com/galaxyproject/galaxy/commit/37f3bbf26772f78af132527a1aa19... Author: Jesse c j van Dam <jesse.vandam@wur.nl> Date: 2015-08-25 (Tue, 25 Aug 2015) Changed paths: M lib/galaxy/datatypes/triples.py Log Message: ----------- improved the specificity for the xml/rdf sniffer Commit: 1444c101aaee74d5e6512a475295970973be68df https://github.com/galaxyproject/galaxy/commit/1444c101aaee74d5e6512a4752959... Author: Jesse c j van Dam <jesse.vandam@wur.nl> Date: 2015-08-25 (Tue, 25 Aug 2015) Changed paths: M lib/galaxy/datatypes/triples.py Log Message: ----------- pip8 fix Commit: 4203ab5b1f032d6f0bcda11295c2856171b738ce https://github.com/galaxyproject/galaxy/commit/4203ab5b1f032d6f0bcda11295c28... Author: Jesse c j van Dam <jesse.vandam@wur.nl> Date: 2015-08-25 (Tue, 25 Aug 2015) Changed paths: M lib/galaxy/datatypes/triples.py Log Message: ----------- fix Commit: 00e58e21f93b0a13caacc23081e02ea4b140bf66 https://github.com/galaxyproject/galaxy/commit/00e58e21f93b0a13caacc23081e02... Author: Jesse c j van Dam <jesse.vandam@wur.nl> Date: 2015-10-19 (Mon, 19 Oct 2015) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- changed log.warn to print because log.warn will stop a job Commit: a443d99fddc14b58698618860076032cb9540dca https://github.com/galaxyproject/galaxy/commit/a443d99fddc14b586986188600760... Author: John Chilton <jmchilton@gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/graph.py Log Message: ----------- Undo deprecated datatypes stuff, doesn't work with Galaxy well. Commit: 4c13c92540c7ed4f8305dcb0216c2a448f33c24d https://github.com/galaxyproject/galaxy/commit/4c13c92540c7ed4f8305dcb0216c2... Author: Jesse <jesse.vandam@wur.nl> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/graph.py Log Message: ----------- Merge pull request #2 from jmchilton/triples_2 Remove deprecated datatype stuff Commit: a57095661246fab1d9045e0cabb1845f662edb5d https://github.com/galaxyproject/galaxy/commit/a57095661246fab1d9045e0cabb18... Author: John Chilton <jmchilton@gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/graph.py A lib/galaxy/datatypes/triples.py Log Message: ----------- Merge pull request #396 from jessevdam/dev Added better support for formats that store triples. Compare: https://github.com/galaxyproject/galaxy/compare/65e6a1c3b6ca...a57095661246