- galaxy-commits - lists.galaxyproject.org

[galaxyproject/infrastructure-playbook] 4a07bb: Update nginx role for SmartOS fixes
by GitHub 28 Nov '17

28 Nov '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 4a07bbd01fbac0e0ea18a02c02749a352b8c8cd5 https://github.com/galaxyproject/infrastructure-playbook/commit/4a07bbd01fb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M roles/galaxyproject.nginx/defaults/main.yml M roles/galaxyproject.nginx/meta/.galaxy_install_info M roles/galaxyproject.nginx/tasks/pkgin.yml M roles/galaxyproject.nginx/tasks/ssl.yml M roles/galaxyproject.nginx/vars/pkgin.yml Log Message: ----------- Update nginx role for SmartOS fixes

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[galaxyproject/infrastructure-playbook] 3f7ee4: Upgrade nginx role
by GitHub 28 Nov '17

28 Nov '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 3f7ee441636f9277fa56381f9d146df438f0728f https://github.com/galaxyproject/infrastructure-playbook/commit/3f7ee441636… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M galaxyenv/playbook.yml A roles/galaxyproject.nginx/README.md A roles/galaxyproject.nginx/defaults/main.yml A roles/galaxyproject.nginx/handlers/main.yml A roles/galaxyproject.nginx/meta/.galaxy_install_info A roles/galaxyproject.nginx/meta/main.yml A roles/galaxyproject.nginx/tasks/apt.yml A roles/galaxyproject.nginx/tasks/main.yml A roles/galaxyproject.nginx/tasks/pkgin.yml A roles/galaxyproject.nginx/tasks/ssl.yml A roles/galaxyproject.nginx/tasks/yum.yml A roles/galaxyproject.nginx/templates/epel-nginx.conf.j2 A roles/galaxyproject.nginx/templates/http_options.conf.j2 A roles/galaxyproject.nginx/templates/pkgin-nginx.conf.j2 A roles/galaxyproject.nginx/templates/ssl.conf.j2 A roles/galaxyproject.nginx/templates/supervisord.conf.j2 A roles/galaxyproject.nginx/vars/pkgin.yml R roles/galaxyprojectdotorg.nginx/README.md R roles/galaxyprojectdotorg.nginx/defaults/main.yml R roles/galaxyprojectdotorg.nginx/handlers/main.yml R roles/galaxyprojectdotorg.nginx/meta/.galaxy_install_info R roles/galaxyprojectdotorg.nginx/meta/main.yml R roles/galaxyprojectdotorg.nginx/tasks/apt.yml R roles/galaxyprojectdotorg.nginx/tasks/main.yml R roles/galaxyprojectdotorg.nginx/tasks/pkgin.yml R roles/galaxyprojectdotorg.nginx/tasks/yum.yml R roles/galaxyprojectdotorg.nginx/templates/epel-nginx.conf.j2 R roles/galaxyprojectdotorg.nginx/templates/http_options.conf.j2 R roles/galaxyprojectdotorg.nginx/templates/pkgin-nginx.conf.j2 R roles/galaxyprojectdotorg.nginx/templates/ssl.conf.j2 R roles/galaxyprojectdotorg.nginx/templates/supervisord.conf.j2 R roles/galaxyprojectdotorg.nginx/vars/pkgin.yml M taccenv/playbook.yml Log Message: ----------- Upgrade nginx role Commit: 651d0ef79fd9f784d86c3cea7e8293a558824d91 https://github.com/galaxyproject/infrastructure-playbook/commit/651d0ef79fd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: A common_env/files/ssl/incommon_chain.pem A galaxyenv/files/ssl/incommon_chain.pem M galaxyenv/host_vars/athena.galaxyproject.org.yml M galaxyenv/host_vars/chouffe.galaxyproject.org.yml M galaxyenv/host_vars/delirium.galaxyproject.org.yml M galaxyenv/host_vars/duvel.galaxyproject.org.yml M galaxyenv/host_vars/orval.galaxyproject.org.yml Log Message: ----------- Update galaxy env for updated nginx role Commit: 9b3e42b3400bddf1521d9f824b52fe25a099604f https://github.com/galaxyproject/infrastructure-playbook/commit/9b3e42b3400… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M taccenv/host_vars/galaxy04.tacc.utexas.edu.yml M taccenv/host_vars/galaxy06.tacc.utexas.edu.yml Log Message: ----------- Update tacc env for nginx role update Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/c15b07641f…

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[galaxyproject/galaxy] c4a2d8: Fix html sniffer to not return True in case of exc...
by GitHub 28 Nov '17

28 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c4a2d8c2189423e45124d847928431a726587eec https://github.com/galaxyproject/galaxy/commit/c4a2d8c2189423e45124d8479284… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Fix html sniffer to not return True in case of exception Commit: 1ba863d4d6af388aaf5911b1f57a1ce59eb20f09 https://github.com/galaxyproject/galaxy/commit/1ba863d4d6af388aaf5911b1f57a… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M lib/tool_shed/util/tool_util.py Log Message: ----------- Remove duplicated functions Added in commits 777d6a155c369e49127084b63dee5701da7589f1 and 917d5a72e83741594912578ee14d1df19f5974c9 Commit: 0df99d89d7d749df8d3432a3506d76b2461e8bfe https://github.com/galaxyproject/galaxy/commit/0df99d89d7d749df8d3432a3506d… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/454Score.pdf Log Message: ----------- Improve and test the PDF sniffer Read just the first 4 bytes in binary mode. Commit: 4a19bf62e35d52236a1fe5572a19e24ac20c3efe https://github.com/galaxyproject/galaxy/commit/4a19bf62e35d52236a1fe5572a19… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M test-data/1.fastqsanger M test-data/1.fastqsolexa M test-data/simple_line_alternative.txt M test-data/simple_lines_interleaved.txt Log Message: ----------- Add missing newline at end of some test files It gets added anyway when the file is uploaded to Galaxy due to the default "Use POSIX standard" (to_posix_lines) option. Many tests which simply copy them with cat and compare them would fail a strict diff test. Commit: 5a2cb8546948c2f57d780201c1252d55269fcfe3 https://github.com/galaxyproject/galaxy/commit/5a2cb8546948c2f57d780201c125… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Fix `SnpSiftDbNSFP.generate_primary_file()` to return a string Also use a `with` statement to open/close a file in `SnpSiftDbNSFP.regenerate_primary_file()` . Commit: 6b730ae961c12375bd37e870cc52e0f77e4c0e17 https://github.com/galaxyproject/galaxy/commit/6b730ae961c12375bd37e870cc52… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- Add a datatype to sniff_order only if it has a sniff() method This reduces the number of default sniffers from 412 to 246. Commit: 59f44cf2be48abd4bed0f7c6ddf7cc0aee5ad1f5 https://github.com/galaxyproject/galaxy/commit/59f44cf2be48abd4bed0f7c6ddf7… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M lib/galaxy/datatypes/annotation.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/blast.py M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/graph.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/plant_tribes.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/triples.py M lib/galaxy/datatypes/xml.py M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/tools/verify/__init__.py M lib/galaxy/util/compression_utils.py M tools/data_source/data_source.py M tools/data_source/upload.py Log Message: ----------- Update `get_fileobj()` to use utf-8 encoding in text mode Also, merge its 3 parameters `gzip_only`, `bz2_only`, `zip_only` into `compressed_formats` (a list of allowed formats). As a consequence of the changes in `get_fileobj()`, update: - `files_diff()` - `get_file_peek()`, which now determines that a file is binary when a `UnicodeDecodeError` exception is raised and doesn't need `is_multi_byte` any more - `iter_headers()` and `get_headers()`, which now return Unicode and don't need `is_multi_byte` parameter any more As a consequence of the changes in `get_file_peek()`, update: - `set_peek()`, which now doesn't need `is_multi_byte` any more As a consequence of the changes in `get_headers()`, update: - `guess_ext` and `is_column_based()`, which now determine that a file is binary when a `UnicodeDecodeError` exception is raised and don't need `is_multi_byte` any more As a consequence of the changes to `guess_ext`, update: - `handle_uploaded_dataset_file() doesn't need `is_multi_byte` any more Also, remove duplicated calls to `get_file_peek()` in lib/galaxy/datatypes/molecules.py and lib/galaxy/datatypes/msa.py The `is_multi_byte` was not removed from the signature of `get_file_peek()` and `set_peek()` in order to preserve compatibility for ToolShed datatypes, thanks @jmchilton for the review. Commit: 8d7f344140d77a6c50d945fa9b48f842e00e837f https://github.com/galaxyproject/galaxy/commit/8d7f344140d77a6c50d945fa9b48… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M lib/galaxy/datatypes/annotation.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/blast.py M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/graph.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/plant_tribes.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/datatypes/test/454Score.pdf M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/triples.py M lib/galaxy/datatypes/xml.py M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/tools/verify/__init__.py M lib/galaxy/util/compression_utils.py M lib/tool_shed/util/tool_util.py M test-data/1.fastqsanger M test-data/1.fastqsolexa M test-data/simple_line_alternative.txt M test-data/simple_lines_interleaved.txt M tools/data_source/data_source.py M tools/data_source/upload.py Log Message: ----------- Merge pull request #5062 from nsoranzo/remove_wchartype_dep Remove wchartype dependency and is_multi_byte [1/2] Compare: https://github.com/galaxyproject/galaxy/compare/68795e415c16...8d7f344140d7

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[galaxyproject/galaxy] 385aaf: Fix exception in admin panel
by GitHub 28 Nov '17

28 Nov '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 385aaf2bd7e2b1c79f4b21f0449aed98fc9d6446 https://github.com/galaxyproject/galaxy/commit/385aaf2bd7e2b1c79f4b21f0449a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-27 (Mon, 27 Nov 2017) Changed paths: M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py Log Message: ----------- Fix exception in admin panel TypeError: Non-hexadecimal digit found File "galaxy/web/framework/middleware/sentry.py", line 40, in __call__ iterable = self.application(environ, start_response) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/paste/recursive.py", line 85, in __call__ return self.application(environ, start_response) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/paste/httpexceptions.py", line 640, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/base.py", line 136, in __call__ return self.handle_request(environ, start_response) File "galaxy/web/framework/base.py", line 215, in handle_request body = method(trans, **kwargs) File "galaxy/web/framework/decorators.py", line 98, in decorator return func(self, trans, *args, **kwargs) File "galaxy/webapps/galaxy/controllers/admin_toolshed.py", line 660, in manage_repositories return self.repository_installation_grid(trans, **kwd) File "galaxy/web/framework/helpers/grids.py", line 85, in __call__ query = self.build_initial_query(trans, **kwargs) File "tool_shed/galaxy_install/grids/admin_toolshed_grids.py", line 334, in build_initial_query clause_list.append(self.model_class.table.c.id == trans.security.decode_id(tool_shed_repository_id)) File "galaxy/web/security/__init__.py", line 107, in decode_id return int(id_cipher.decrypt(obj_id.decode('hex')).lstrip("!")) File "encodings/hex_codec.py", line 42, in hex_decode output = binascii.a2b_hex(input) This is due to `tool_shed_repository_ids` being a json dump of a list in certain consitions (noticed this after installing a new repository). Commit: a82d325d18375797ce8ab53366320f3c9a772ab7 https://github.com/galaxyproject/galaxy/commit/a82d325d18375797ce8ab5336632… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py Log Message: ----------- Merge pull request #5079 from mvdbeek/admin_panel_exception_fix [17.09] Fix exception in admin panel Compare: https://github.com/galaxyproject/galaxy/compare/e903cb708e2f...a82d325d1837

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[galaxyproject/usegalaxy-playbook] ab736b: Upgrade nginx role for Debian fix
by GitHub 28 Nov '17

28 Nov '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ab736b6186ab3f6ccf65913d1b04d4734ecc759c https://github.com/galaxyproject/usegalaxy-playbook/commit/ab736b6186ab3f6c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M roles/galaxyproject.nginx/meta/.galaxy_install_info M roles/galaxyproject.nginx/tasks/ssl.yml Log Message: ----------- Upgrade nginx role for Debian fix

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[galaxyproject/usegalaxy-playbook] fd5886: Upgrade ciphers on the Tool Shed
by GitHub 28 Nov '17

28 Nov '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: fd5886ab2f831e7a5f3ea6898f35b289c2473be8 https://github.com/galaxyproject/usegalaxy-playbook/commit/fd5886ab2f831e7a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M env/common/group_vars/toolshedwebservers.yml Log Message: ----------- Upgrade ciphers on the Tool Shed

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[galaxyproject/usegalaxy-playbook] d5f3d3: Disable TLS 1.0, enable OCSP stapling, and upgrad...
by GitHub 28 Nov '17

28 Nov '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: d5f3d38334120c1c2653e537df14bf67b12c1dcf https://github.com/galaxyproject/usegalaxy-playbook/commit/d5f3d38334120c1c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M env/test/group_vars/webservers/vars.yml M roles/galaxyproject.nginx/README.md M roles/galaxyproject.nginx/defaults/main.yml M roles/galaxyproject.nginx/meta/.galaxy_install_info M roles/galaxyproject.nginx/tasks/main.yml A roles/galaxyproject.nginx/tasks/ssl.yml M roles/galaxyproject.nginx/templates/ssl.conf.j2 Log Message: ----------- Disable TLS 1.0, enable OCSP stapling, and upgrade to more secure ciphers on Test, Commit: e23193fe56dfeabdc38211f4669869567cac4274 https://github.com/galaxyproject/usegalaxy-playbook/commit/e23193fe56dfeabd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M env/main/group_vars/galaxystagingservers.yml M env/main/group_vars/galaxywebservers.yml Log Message: ----------- Upgrade SSL ciphers on Main Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/3d86f6d831a1...…

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[galaxyproject/usegalaxy-playbook] 3d86f6: Correct db user for stats
by GitHub 28 Nov '17

28 Nov '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 3d86f6d831a1ae7d9e5f27ea627cce4984ce9275 https://github.com/galaxyproject/usegalaxy-playbook/commit/3d86f6d831a1ae7d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M env/main/group_vars/dbservers/vault.yml Log Message: ----------- Correct db user for stats

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[galaxyproject/galaxy] 827ac9: Do not attempt to visit parameters of invalid cond...
by GitHub 28 Nov '17

28 Nov '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 827ac9c0433f581166b5bd06b70a14a39f22ded2 https://github.com/galaxyproject/galaxy/commit/827ac9c0433f581166b5bd06b70a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Do not attempt to visit parameters of invalid conditionals Commit: 1457fa7f937522d4825bb814a927a87b2e363cc8 https://github.com/galaxyproject/galaxy/commit/1457fa7f937522d4825bb814a927… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Check for key/value errors only when testing conditional cases Commit: 75f84bfc476ea94c22a38097d20f694265fcded6 https://github.com/galaxyproject/galaxy/commit/75f84bfc476ea94c22a38097d20f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Add test cases to cover version changes Commit: 9e9edb7e338bcf6a3d4174fc0d8e420a5184ad6b https://github.com/galaxyproject/galaxy/commit/9e9edb7e338bcf6a3d4174fc0d8e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Remove unnecessary name setting for non-group parameters Commit: 64eced315887f19b7efd6334d4a28f91e8fd6116 https://github.com/galaxyproject/galaxy/commit/64eced315887f19b7efd6334d4a2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Fix comments Commit: e903cb708e2f33bccebf5a0dd89b3bfe13667e03 https://github.com/galaxyproject/galaxy/commit/e903cb708e2f33bccebf5a0dd89b… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Merge pull request #5010 from guerler/fix_pages_workflows [17.09] Do not visit child inputs of invalid conditionals Compare: https://github.com/galaxyproject/galaxy/compare/802c943fff71...e903cb708e2f

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[galaxyproject/galaxy] 8f5437: Fix caller names which do not return html anymore
by GitHub 28 Nov '17

28 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8f543788702561284d6bcbda3697cbc79355defe https://github.com/galaxyproject/galaxy/commit/8f543788702561284d6bcbda3697… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-16 (Thu, 16 Nov 2017) Changed paths: M lib/galaxy/model/metadata.py Log Message: ----------- Fix caller names which do not return html anymore Commit: 3e0b565e7e644b45190dd0ca4adfff39cd6889c6 https://github.com/galaxyproject/galaxy/commit/3e0b565e7e644b45190dd0ca4adf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-16 (Thu, 16 Nov 2017) Changed paths: M lib/galaxy/model/metadata.py Log Message: ----------- Fix name in metadata parameter factory Commit: 86f03fbb11dc7d20fed12499028d7b664e1ba3c8 https://github.com/galaxyproject/galaxy/commit/86f03fbb11dc7d20fed12499028d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-16 (Thu, 16 Nov 2017) Changed paths: M lib/galaxy/model/metadata.py Log Message: ----------- Remove unused function Commit: 5777c7d589a0e38618e6deeea33c734ef2d6319f https://github.com/galaxyproject/galaxy/commit/5777c7d589a0e38618e6deeea33c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-16 (Thu, 16 Nov 2017) Changed paths: M lib/galaxy/web/form_builder.py Log Message: ----------- Fix optional attribute identification Commit: 48701490957f6e26bb7661d9fcebb7af6c99ac56 https://github.com/galaxyproject/galaxy/commit/48701490957f6e26bb7661d9fceb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-16 (Thu, 16 Nov 2017) Changed paths: M lib/galaxy/web/form_builder.py Log Message: ----------- Prioritize optional flag over required attribute Commit: ae07744c3445238569f57ac8de262f5309dfe5d4 https://github.com/galaxyproject/galaxy/commit/ae07744c3445238569f57ac8de26… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-16 (Thu, 16 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Fix optional specification for metadata parameters Commit: edbe7ec4c09749fe296e0d694c5845d75d020f03 https://github.com/galaxyproject/galaxy/commit/edbe7ec4c09749fe296e0d694c58… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-16 (Thu, 16 Nov 2017) Changed paths: M lib/galaxy/web/form_builder.py Log Message: ----------- Fix import style Commit: 68795e415c16dc814f5116ae6555ab5762871a10 https://github.com/galaxyproject/galaxy/commit/68795e415c16dc814f5116ae6555… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M lib/galaxy/model/metadata.py M lib/galaxy/web/form_builder.py M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Merge pull request #5027 from guerler/edit_info Metadata parameters rely on their own optional setting not on the field attribute Compare: https://github.com/galaxyproject/galaxy/compare/fac65894d3ef...68795e415c16

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[galaxyproject/galaxy] a58586: Cleanup SA objects between workflow invocation sch...
by GitHub 28 Nov '17

28 Nov '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: a58586f0e4973aa6855142222ed8be124add9ad5 https://github.com/galaxyproject/galaxy/commit/a58586f0e4973aa6855142222ed8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-24 (Fri, 24 Nov 2017) Changed paths: M lib/galaxy/workflow/scheduling_manager.py Log Message: ----------- Cleanup SA objects between workflow invocation scheduling attempts. This would seem to be a fairly serious memory leak in the abstract but I don't have data that it fixes anything. None the less if it gets into dev and the tests seem to pass I'll open a PR to backport it to at least 17.05 and maybe back even more. Commit: 802c943fff711dbeb6105b8b3ece68bf29cdee9e https://github.com/galaxyproject/galaxy/commit/802c943fff711dbeb6105b8b3ece… Author: Eric Rasche <hxr(a)hx42.org> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M lib/galaxy/workflow/scheduling_manager.py Log Message: ----------- Merge pull request #5073 from jmchilton/backport_5045 [17.09] Backport #5045 Compare: https://github.com/galaxyproject/galaxy/compare/ff3a6b084931...802c943fff71

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[galaxyproject/galaxy] b476cc: Fail job if job output collection fails
by GitHub 28 Nov '17

28 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b476cc4c57ad86c507eba22c88221584a62954a5 https://github.com/galaxyproject/galaxy/commit/b476cc4c57ad86c507eba22c8822… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-23 (Thu, 23 Nov 2017) Changed paths: M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Fail job if job output collection fails We now set a non-zero exit code to actually set a job to failed. I belive this is a reasonable action, and it avoids green, empty datasets with log messages like: ``` galaxy.jobs.runners ERROR 2017-11-14 13:32:06,469 (19020/860246.torque6.curie.fr) Job output not returned from cluster: [Errno 2] No such file or directory: '/data/users/mvandenb/gx 124/tmp_nfs/jwd/019/19020/galaxy_19020.o' galaxy.jobs.runners DEBUG 2017-11-14 13:32:06,491 (19020/860246.torque6.curie.fr) Unable to cleanup /data/users/mvandenb/gx124/tmp_nfs/jwd/019/19020/galaxy_19020.o: [Errno 2] No suc h file or directory: '/data/users/mvandenb/gx124/tmp_nfs/jwd/019/19020/galaxy_19020.o' galaxy.jobs.runners DEBUG 2017-11-14 13:32:06,503 (19020/860246.torque6.curie.fr) Unable to cleanup /data/users/mvandenb/gx124/tmp_nfs/jwd/019/19020/galaxy_19020.e: [Errno 2] No suc h file or directory: '/data/users/mvandenb/gx124/tmp_nfs/jwd/019/19020/galaxy_19020.e' galaxy.jobs.runners DEBUG 2017-11-14 13:32:06,513 (19020/860246.torque6.curie.fr) Unable to cleanup /data/users/mvandenb/gx124/tmp_nfs/jwd/019/19020/galaxy_19020.ec: [Errno 2] No su ch file or directory: '/data/users/mvandenb/gx124/tmp_nfs/jwd/019/19020/galaxy_19020.ec' ``` Commit: 73454e12df8b8fe05aefc8ae120286e976985db8 https://github.com/galaxyproject/galaxy/commit/73454e12df8b8fe05aefc8ae1202… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-27 (Mon, 27 Nov 2017) Changed paths: M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Fix undefined exit_code_str problem (thx @nsoranzo) Commit: cacd6eadc5b95686173c9394f635d5a25527f503 https://github.com/galaxyproject/galaxy/commit/cacd6eadc5b95686173c9394f635… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Mark job wrapper as failed in a more direct way Commit: 13f6eeecf099316acc586282773316f3858c0549 https://github.com/galaxyproject/galaxy/commit/13f6eeecf099316acc5862827733… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/state_handlers/resubmit.py Log Message: ----------- Add new runner state for 'Job output not returned from cluster' This would allow adimns to write resubmit conditions for this specific failure. Commit: fac65894d3efd339ae0449300fba162d177efaed https://github.com/galaxyproject/galaxy/commit/fac65894d3efd339ae0449300fba… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/state_handlers/resubmit.py Log Message: ----------- Merge pull request #5078 from mvdbeek/fail_if_job_output_collection_fails Fail job if job output collection fails Compare: https://github.com/galaxyproject/galaxy/compare/c6c55e1046a7...fac65894d3ef

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[galaxyproject/galaxy] 049376: Always fill `message` to avoid KeyError for sentry...
by GitHub 28 Nov '17

28 Nov '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 0493763938ab6146dc383b735a7b3523914c2342 https://github.com/galaxyproject/galaxy/commit/0493763938ab6146dc383b735a7b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M lib/galaxy/tools/error_reports/plugins/sentry.py Log Message: ----------- Always fill `message` to avoid KeyError for sentry ERROR_TEMPLATE Commit: ff3a6b084931f532dbce9a6d82059cda0137e3e3 https://github.com/galaxyproject/galaxy/commit/ff3a6b084931f532dbce9a6d8205… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M lib/galaxy/tools/error_reports/plugins/sentry.py Log Message: ----------- Merge pull request #5086 from mvdbeek/sentry_report_fix [17.09] Always fill `message` to avoid KeyError for sentry ERROR_TEMPLATE Compare: https://github.com/galaxyproject/galaxy/compare/f6aedb0d2094...ff3a6b084931

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[galaxyproject/galaxy] 36e0e0: Run job handlers as uWSGI mules
by GitHub 28 Nov '17

28 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 36e0e01b6b9da78ae6f37f556385befba513bc14 https://github.com/galaxyproject/galaxy/commit/36e0e01b6b9da78ae6f37f556385… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-21 (Mon, 21 Aug 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/model/__init__.py M lib/galaxy/util/handlers.py Log Message: ----------- Run job handlers as uWSGI mules Commit: 85ea2d272803e174915680be8419e3053c8f947c https://github.com/galaxyproject/galaxy/commit/85ea2d272803e174915680be8419… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-21 (Mon, 21 Aug 2017) Changed paths: A lib/galaxy/script/__init__.py M run.sh A scripts/get_uwsgi_args.py M scripts/manage_tool_dependencies.py Log Message: ----------- Script reusage and generate uWSGI mule args Commit: e2e3e5f7d12a2f862595b380bf9da12b3b201333 https://github.com/galaxyproject/galaxy/commit/e2e3e5f7d12a2f862595b380bf9d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-21 (Mon, 21 Aug 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/manager.py M lib/galaxy/model/__init__.py M lib/galaxy/util/handlers.py M lib/galaxy/web/stack/__init__.py A lib/galaxy/web/stack/uwsgi_mule/handler.py M scripts/get_uwsgi_args.py Log Message: ----------- WIP job handlers as uWSGI mules from GCC 2017 Hackathon. Commit: 092a6b49230c65bc93070d9a388105ac568058dd https://github.com/galaxyproject/galaxy/commit/092a6b49230c65bc93070d9a3881… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-21 (Mon, 21 Aug 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/manager.py M lib/galaxy/script/__init__.py M lib/galaxy/util/handlers.py M lib/galaxy/web/stack/__init__.py R lib/galaxy/web/stack/uwsgi_mule/handler.py M run.sh M scripts/galaxy-main M scripts/get_uwsgi_args.py Log Message: ----------- WIP uWSGI mule job handlers - it works! Commit: c7663a4e2e24536f1f3257186de86144399142d2 https://github.com/galaxyproject/galaxy/commit/c7663a4e2e24536f1f3257186de8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-21 (Mon, 21 Aug 2017) Changed paths: M lib/galaxy/app.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/manager.py M lib/galaxy/web/stack/__init__.py A lib/galaxy/web/stack/message.py A lib/galaxy/web/stack/transport.py Log Message: ----------- WIP job handlers as uWSGI mules refactor Commit: a06d6cf6167f1ce9aee9a34a28aa50473d19cb35 https://github.com/galaxyproject/galaxy/commit/a06d6cf6167f1ce9aee9a34a28aa… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-21 (Mon, 21 Aug 2017) Changed paths: M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/jobs/manager.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/history_imp_exp.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/util/handlers.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/web/stack/message.py M lib/galaxy/web/stack/transport.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- WIP: Job handlers as UWSGI mules, attempt at unprogrammed mules. Commit: ece3f242fb857a1363a0d143fd62033de4ce9e63 https://github.com/galaxyproject/galaxy/commit/ece3f242fb857a1363a0d143fd62… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-21 (Mon, 21 Aug 2017) Changed paths: M lib/galaxy/app.py M lib/galaxy/jobs/manager.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/web/stack/transport.py M scripts/galaxy-main M scripts/get_uwsgi_args.py Log Message: ----------- Abandoning unprogrammed mules (for now), fixes for programmed mules Commit: 27a0b1ba40dfdf44b3e92ec09b4733df9563103e https://github.com/galaxyproject/galaxy/commit/27a0b1ba40dfdf44b3e92ec09b47… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-21 (Mon, 21 Aug 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/manager.py A lib/galaxy/util/configdict.py M lib/galaxy/util/handlers.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/web/stack/transport.py M scripts/galaxy-main M scripts/get_uwsgi_args.py Log Message: ----------- WIP: attempted to support workers shared between pools, but locking won't allow for this, since you can't wait on messages from a specific farm. Commit: d7dd9b2b6590a3ecddb2bbacec9130a3dbf9e4e2 https://github.com/galaxyproject/galaxy/commit/d7dd9b2b6590a3ecddb2bbacec91… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-21 (Mon, 21 Aug 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/app.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/manager.py R lib/galaxy/util/configdict.py M lib/galaxy/util/handlers.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/web/stack/message.py M lib/galaxy/web/stack/transport.py M scripts/get_uwsgi_args.py Log Message: ----------- WIP: drop stack configurability, this will come later. Cleanup for WIP PR Commit: 68542b615c70c7d85885827f42ecfc8521155bbf https://github.com/galaxyproject/galaxy/commit/68542b615c70c7d85885827f42ec… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-21 (Mon, 21 Aug 2017) Changed paths: M scripts/galaxy-main Log Message: ----------- Remove unneeded server_name manipulation from galaxy-main script Commit: c5bd3d4729b04d30dc94a798659ecc6d34683a06 https://github.com/galaxyproject/galaxy/commit/c5bd3d4729b04d30dc94a798659e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-22 (Tue, 22 Aug 2017) Changed paths: M config/workflow_schedulers_conf.xml.sample M lib/galaxy/jobs/handler.py M lib/galaxy/web/stack/message.py M lib/galaxy/workflow/scheduling_manager.py Log Message: ----------- Support workflow scheduling via stack messaging. Commit: 03368ef549c37f5f4e4f95f2734246930914a368 https://github.com/galaxyproject/galaxy/commit/03368ef549c37f5f4e4f95f27342… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-24 (Thu, 24 Aug 2017) Changed paths: M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Start job runner worker threads post fork. Commit: bb7795bcfd18c64244634418040d0b89605a8c92 https://github.com/galaxyproject/galaxy/commit/bb7795bcfd18c64244634418040d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-24 (Thu, 24 Aug 2017) Changed paths: A lib/galaxy/util/facts.py M lib/galaxy/web/stack/__init__.py Log Message: ----------- Generalize the collection of system/application "facts" usable for string templating. Commit: 14e9dddadec856a1a8aa916b4a4459f5fb487a06 https://github.com/galaxyproject/galaxy/commit/14e9dddadec856a1a8aa916b4a44… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/webapps/galaxy/buildapp.py M scripts/galaxy-main Log Message: ----------- WIP: support log configuration from yaml/json app config with logging.config.dictConfig. Still working on yaml/json config loading in the webless app. Commit: aff0a7460e69b59cba67769040d761ac768032c3 https://github.com/galaxyproject/galaxy/commit/aff0a7460e69b59cba67769040d7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/util/facts.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/stack/__init__.py M scripts/galaxy-main Log Message: ----------- Finish dictConfig logging feature Commit: ea70bafa0cf5b4b68a09ea62aeabb24b9ef62878 https://github.com/galaxyproject/galaxy/commit/ea70bafa0cf5b4b68a09ea62aeab… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M lib/galaxy/web/stack/__init__.py Log Message: ----------- Fix mule starting under uWSGI with --ini-paste Commit: 17ea3d671facb06ec9a1101f80505c5c64758fe7 https://github.com/galaxyproject/galaxy/commit/17ea3d671facb06ec9a1101f8050… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M run.sh M scripts/get_uwsgi_args.py Log Message: ----------- Improve automatic uWSGI startup options interaction with [uwsgi] section in config file Commit: 1326a4d67107206babd4acd457734511f24a8996 https://github.com/galaxyproject/galaxy/commit/1326a4d67107206babd4acd45773… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/util/facts.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/web/stack/transport.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/workflow/scheduling_manager.py M scripts/galaxy-main M scripts/get_uwsgi_args.py M test/unit/jobs/test_job_configuration.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Cleaning, lint and test fixes. Commit: 4d962d4ad29bfdad7c6f108d0300c79354d01a01 https://github.com/galaxyproject/galaxy/commit/4d962d4ad29bfdad7c6f108d0300… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M scripts/get_uwsgi_args.py Log Message: ----------- Only include --paste-logger in uWSGI args if logging is configured in the PasteDeploy config Commit: bcfa874158bb82b7c45f8ff51d0701cb7b734f06 https://github.com/galaxyproject/galaxy/commit/bcfa874158bb82b7c45f8ff51d07… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M scripts/get_uwsgi_args.py Log Message: ----------- Fix for job_handler_count = 0 Commit: 9da850289f0d403ccba565ab88123c942db5b491 https://github.com/galaxyproject/galaxy/commit/9da850289f0d403ccba565ab8812… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M test/base/driver_util.py Log Message: ----------- Allow test framework to run uwsgi tests. Commit: 5c01c1cc3b71dbc069e03639c4804f084bdb37dc https://github.com/galaxyproject/galaxy/commit/5c01c1cc3b71dbc069e03639c480… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M test/base/driver_util.py M test/base/integration_util.py A test/integration/test_mules_as_job_handlers.py Log Message: ----------- Add mules integration test and integration test framework updates to support uwsgi. Commit: ac4d8477177e94b858519d7873beba352aec0431 https://github.com/galaxyproject/galaxy/commit/ac4d8477177e94b858519d7873be… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M test/base/driver_util.py Log Message: ----------- Fix connection rejected errors for linux when waiting for uwsgi servers in test framework. Commit: 27e34d5ad93aa1f62ae5d55d3ceed98d2da3dd7b https://github.com/galaxyproject/galaxy/commit/27e34d5ad93aa1f62ae5d55d3cee… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M test/base/driver_util.py Log Message: ----------- Do a better job cleaning up uwsgi processes for tests. Commit: 8fb47a0a2c211b83e31e64557ec04a05dea17f2b https://github.com/galaxyproject/galaxy/commit/8fb47a0a2c211b83e31e64557ec0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M test/integration/test_mules_as_job_handlers.py Log Message: ----------- Fix mules test to not require ``app`` in test's memory. Just run a simple upload using a DatasetPopulator instead of running a tool test that requires the tool be in memory. Commit: 1fe9883774f53f0a03418021eebd78c86978e8b6 https://github.com/galaxyproject/galaxy/commit/1fe9883774f53f0a03418021eebd… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-31 (Thu, 31 Aug 2017) Changed paths: M test/base/driver_util.py Log Message: ----------- Be a more forceful about cleaning uwsgi during tests. Commit: 00b8574404dd79e112b22f13ec72043a7b09ab09 https://github.com/galaxyproject/galaxy/commit/00b8574404dd79e112b22f13ec72… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-31 (Thu, 31 Aug 2017) Changed paths: M lib/galaxy/web/stack/__init__.py Log Message: ----------- Fix a segfault in uWSGI mules caused by trying to access invalid memory post-fork. There may be more cases like this that we'll have to handle in the mule fixup function. Context ======= uWSGI mules don't fork()/exec(), they fork() and then (as documented) run supplied code[1]. In order to read the URL parameter for IGV builds in the default tool_data_table_conf.xml, Galaxy imports urlopen() from six.moves.urllib.request. In Python 2.7, this imports the same function from urllib2. urllib2 uses (and reuses) a module global "opener" object[2]. This is initialized during the prefork application startup when used for the IGV data table, and then the same object is used postfork for the mule to load the same data table. It was discovered when attempting to run the mule job handler test under macOS, it does not occur in testing on Linux, nor does it occur on macOS with the default tool_conf.xml.sample and datatypes_conf.xml.sample. Whether or not the segfault was encountered seemed to depend on which tools or datatypes were loaded, but not in any clear pattern. The cause is presumably due to differences in memory allocation schemes between macOS and Linux, and perhaps garbage collection differences depending on different config file sizes? Regardless, it seems to be a classical case of holding on to references to memory that has been deallocated elsewhere. The segfault is specifically on the socket_getaddrinfo function in the _socket C module that provides functionality for the socket module in the standard Python lib. socket.getaddrinfo() is called by urlopen() by way of httplib. uWSGI mule debugging -------------------- I ultimately figured out the cause of the segfault with lldb. To make that experience better, I used a debug build of both Python and uWSGI (uWSGI was probably less important to do but that process is explained here anyway). Python with debugging is not ABI compatible with non-debug Python, so building all of Galaxy's C Extension wheels was necessary. In many cases, pip will do this for you (using the standard pip invocation in scripts/common_startup.sh), but not all will be successful. To build debug Python and debug uWSGI and run Galaxy under them, I used the following steps: 1. You will need a newer version OpenSSL than the one that ships with Sierra, I used the one from Brew: CFLAGS=-I/usr/local/opt/openssl/include \ LDFLAGS=-L/usr/local/opt/openssl/lib \ MACOSX_DEPLOYMENT_TARGET=10.12 \ ./configure --prefix=$HOME/pydebug --with-pydebug Be sure to set $MACOSX_DEPLOYMENT_TARGET. If you do not, the `getaddrinfo` function will utilize locking around `getaddrinfo` that should not be used[3]. 2. After intsalling Python, `virtualenv -p ~/pydebug .venv` in the Galaxy root. 3. In the uWSGI source, copy buildconf/default.ini to buildconf/debug.ini, set `debug = true` in debug.ini and then (with .venv activated) run: UWSGI_PROFILE=buildconf/debug.ini python setup.py install 4. Manually install a few problematic dependencies: - Use the Starforge recipe for building pysam[4], which mainly means grabbing a tarball of @dannon's fork, fixing the version number, and running `python setup.py install`. The ssdist tarball for this verison on wheels.galaxyproject.org is broken (files are missing from its manifest) and I need to fix that. Dannon is also currently working on upstreaming his changes and updating Galaxy for the latest version of pysam so this shouldn't be a problem in the future. - The mercurial sdist tarball on wheels.galaxyproject.org is also broken, download the correct version tarball directly from the mercurial release distribution site and `python setup.py install` it. I need to fix this as well. - Install numpy before bx-python (if it's not installed before bx is, bx will be missing needed features): pip install -i https://wheels.galaxyproject.org --no-binary :all: \ $(grep -i numpy= requirements.txt) 5. Install remaining requirements, iirc the rest should be ok: pip install -i https://wheels.galaxyproject.org --no-binary :all: \ -r requirements.txt --no-binary :all: is necessary because there are numerous macOS wheels in PyPI with a `none` SOABI tag, meaning these wheels will install but will not work for the debug Python ABI. When you run Galaxy under the debugger, you won't be able to directly control the fork()ed mules. Instead, you'll need to fire up a second debugger to catch the mule[5]: 1. Start up Galaxy under lldb, set a breakpoint on fork Be sure that your virtualenv is *NOT* activated before starting lldb, or it will fail miserably at loading its own python module. % lldb .venv/bin/uwsgi (lldb) b fork 2. Run Galaxy, e.g.: (lldb) r --virtualenv /Users/nate/galaxy/.venv --module galaxy.webapps.galaxy.buildapp:uwsgi_app_factory() --yaml config/galaxy.yml --processes 1 --threads 4 --http localhost:8080 --pythonpath lib --master --static-map /static/style=/Users/nate/galaxy/static/style/blue --static-map /static=/Users/nate/galaxy/static --die-on-term --enable-threads --py-call-osafterfork --mule=lib/galaxy/main.py --farm=job-handlers:1 3. The first fork() is for the workers, so you'll want to skip this: (lldb) n 4. The second fork is for the mule. At this point, start a second lldb in another terminal, set a breakpoint on something interesting, and attach it to the process that is about to start: % lldb (lldb) b socket_getaddrinfo (lldb) pro at -n uwsgi -w 5. Continue the fork in the original lldb: (lldb) n 6. Continue debugging in the second lldb, which is now attached to the mule. [1]: https://github.com/unbit/uwsgi/blob/5039a4b679735348422638baa7cff7a8116762e… [2]: https://github.com/python/cpython/blob/20958e6d91d11a80d6c664ce6346791259b1… [3]: https://emptysqua.re/blog/getaddrinfo-deadlock/ [4]: https://github.com/galaxyproject/starforge/blob/f1013ddf6119381ffba6df06e8d… [5]: https://stackoverflow.com/questions/14746315/how-to-attach-to-child-process… Commit: e91db56f0e377f94574f80c833182e79a43156fb https://github.com/galaxyproject/galaxy/commit/e91db56f0e377f94574f80c83318… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-31 (Thu, 31 Aug 2017) Changed paths: M test/base/driver_util.py Log Message: ----------- Use fancy uWSGI log messages when running tests under uWSGI, or you can set whatever log format string you want with `$GALAXY_TEST_LOG_FORMAT`. If unset, and not running under uWSGI, galaxy.config.logging (the logging.config.dictConfig dict) will not be set and the default logging config will be used. Commit: 3477906dc556ce17223bafbc470f1d809f6196cb https://github.com/galaxyproject/galaxy/commit/3477906dc556ce17223bafbc470f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-31 (Thu, 31 Aug 2017) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Provide failure reason when tool configs fail to load due to system errors (ENOENT, EPERM, etc.). Commit: 3f0082515af630bd095ee5fc57bac044369c8f0e https://github.com/galaxyproject/galaxy/commit/3f0082515af630bd095ee5fc57ba… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-31 (Thu, 31 Aug 2017) Changed paths: M test/base/driver_util.py A test/functional/tools/config_vars.xml M test/functional/tools/samples_tool_conf.xml M test/integration/test_mules_as_job_handlers.py Log Message: ----------- Improvements for mule job handler testing. Ensure that the server running the job is a mule. Added a test tool that will write Galaxy app.config attributes to the output dataset. Commit: 09feaf6f4d46509c7401970013b5a8097a5d4c4e https://github.com/galaxyproject/galaxy/commit/09feaf6f4d46509c7401970013b5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/azure_blob.py M lib/galaxy/objectstore/pithos.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py M lib/galaxy/script/__init__.py M lib/galaxy/util/__init__.py A lib/galaxy/util/path.py M lib/galaxy/util/properties.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/stack/__init__.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/util/commit_util.py M run.sh M run_reports.sh M run_tool_shed.sh M scripts/common_startup_functions.sh M scripts/galaxy-main M scripts/get_uwsgi_args.py M test/base/driver_util.py Log Message: ----------- - Do all logging configuration other than paste fileConfig logging from dictConfig. Default log message format varies by stack. - Refactor a lot of file extension handling in to galaxy.util.path. - Simplify and improve config file finding. - Simplify and improve native app creation. - Integrate uWSGI argument generation with @jmchilton's improvements to the startup scripts. - Fix starting without a config file under uWSGI Commit: 11857db011f4814a4aa0feb151a8a838f91b8c88 https://github.com/galaxyproject/galaxy/commit/11857db011f4814a4aa0feb151a8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M test/base/driver_util.py Log Message: ----------- Attempt uWSGI restarts when running for testing. It's not able to detect if it failed due to port binding, but it'll retry if uwsgi exits non-zero. Commit: 318bf0bd01ffe6a2bd08fbbfffd8be88e95ae8f7 https://github.com/galaxyproject/galaxy/commit/318bf0bd01ffe6a2bd08fbbfffd8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M test/base/driver_util.py Log Message: ----------- Rework cleanup of uwsgi in tests... This looks cleaner and was closer to what I originally wanted - undoes some stuff @natefoo did hopefully he isn't mad. Commit: 37738b94fbcad6e5aefe410f0c01af4dbac17281 https://github.com/galaxyproject/galaxy/commit/37738b94fbcad6e5aefe410f0c01… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M test/integration/test_mules_as_job_handlers.py Log Message: ----------- More mule testing. Commit: 1e6080e1bf6d410a617079af93e85a29cad21243 https://github.com/galaxyproject/galaxy/commit/1e6080e1bf6d410a617079af93e8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-02 (Sat, 02 Sep 2017) Changed paths: M test/base/driver_util.py Log Message: ----------- Don't require integration tests to use the same port for every Galaxy instance. The previous logic would pick a port at random if one wasn't explicitly defined and then set an environment variable requiring each instance to re-use that. This new logic doesn't reuse randomly assigned ports that way by tracking if a port was randomly assigned or not. Commit: 32a280bf3100f359e1d046206d47a36e0d92db62 https://github.com/galaxyproject/galaxy/commit/32a280bf3100f359e1d046206d47… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-03 (Sun, 03 Sep 2017) Changed paths: M test/base/integration_util.py M test/integration/test_mules_as_job_handlers.py Log Message: ----------- Just skip the mule tests on Jenkins. They work locally alone or ran together, they work locally in the same Docker container as Jenkins, I don't understand. Commit: d7aec7e04dc064fd9e133d9a592e1cb5ef486037 https://github.com/galaxyproject/galaxy/commit/d7aec7e04dc064fd9e133d9a592e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-09 (Thu, 09 Nov 2017) Changed paths: M test/base/integration_util.py M test/integration/test_mules_as_job_handlers.py Log Message: ----------- Revert "Just skip the mule tests on Jenkins." This reverts commit 32a280bf3100f359e1d046206d47a36e0d92db62. Commit: 30266c522127d4b9b13fd0a7433473747cec023c https://github.com/galaxyproject/galaxy/commit/30266c522127d4b9b13fd0a74334… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-09 (Thu, 09 Nov 2017) Changed paths: M .ci/flake8_lint_include_list.txt R .ci/flake8_py3_wrapper.sh A .ci/jenkins/selenium-compose/Dockerfile A .ci/jenkins/selenium-compose/docker-compose.yml A .ci/jenkins/selenium-compose/galaxy.ini A .ci/jenkins/selenium-compose/run_galaxy.bash A .ci/jenkins/selenium-compose/run_tests.sh R .ci/jenkins/selenium/Dockerfile R .ci/jenkins/selenium/docker-compose.yml R .ci/jenkins/selenium/galaxy.ini R .ci/jenkins/selenium/run_galaxy.bash M .ci/jenkins/selenium/run_tests.sh M .ci/py3_sources.txt M .gitignore M .travis.yml M CITATION M Makefile M README.rst A client/.babelrc M client/GruntFile.js M client/README.md M client/bower.json M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M 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tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/next_gen_conversion/solid2fastq.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.xml 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 remote-tracking branch 'origin/dev' into job-handler-mules Commit: 4eface7e722ff46276225457da0dcacc537fb10e https://github.com/galaxyproject/galaxy/commit/4eface7e722ff46276225457da0d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-09 (Thu, 09 Nov 2017) Changed paths: R lib/galaxy/util/path.py M lib/galaxy/util/path/__init__.py Log Message: ----------- Fix path module divergence Commit: b75583ea26269101f12cb29df76a23eeecf68ab5 https://github.com/galaxyproject/galaxy/commit/b75583ea26269101f12cb29df76a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-09 (Thu, 09 Nov 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/util/properties.py M lib/galaxy/web/stack/transport.py M lib/galaxy/webapps/galaxy/buildapp.py M scripts/galaxy-main M scripts/get_uwsgi_args.py M scripts/manage_tool_dependencies.py Log Message: ----------- Fix post-merge lint issues Commit: bf9e2b6a9696a7b3ecc0b369424c9b805ac64a11 https://github.com/galaxyproject/galaxy/commit/bf9e2b6a9696a7b3ecc0b369424c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-09 (Thu, 09 Nov 2017) Changed paths: M lib/galaxy/util/path/__init__.py Log Message: ----------- Fix call to __listify. Commit: e97de138e32d350d4fc7593498130ca9cd3c9d06 https://github.com/galaxyproject/galaxy/commit/e97de138e32d350d4fc759349813… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-10 (Fri, 10 Nov 2017) Changed paths: M test/base/integration_util.py M test/integration/test_mules_as_job_handlers.py Log Message: ----------- Revert "Revert "Just skip the mule tests on Jenkins."" This reverts commit d7aec7e04dc064fd9e133d9a592e1cb5ef486037. Commit: b96a8476899aef2dfe1e1b6cde5048afae8e3428 https://github.com/galaxyproject/galaxy/commit/b96a8476899aef2dfe1e1b6cde50… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-10 (Fri, 10 Nov 2017) Changed paths: M lib/galaxy/util/properties.py Log Message: ----------- Fix an iterator bug with find_config_file() when using include_samples and write a doctest for it. Commit: df6a1dedc0c68c8b743b63a6fddaaac71c2b56bc https://github.com/galaxyproject/galaxy/commit/df6a1dedc0c68c8b743b63a6fdda… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-10 (Fri, 10 Nov 2017) Changed paths: M lib/galaxy/model/orm/scripts.py Log Message: ----------- Fix config file finding in the orm scripts utility and make its doctest clean up after itself Commit: b8df770bfd3d0e3bd2d5cb26db3cf159ed4e8d3a https://github.com/galaxyproject/galaxy/commit/b8df770bfd3d0e3bd2d5cb26db3c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-10 (Fri, 10 Nov 2017) Changed paths: M lib/galaxy/util/properties.py M lib/galaxy/web/stack/__init__.py M lib/tool_shed/capsule/capsule_manager.py Log Message: ----------- Fix import linting errors Commit: cf9ba1e0cc88f695a27d74c96895b3d6b093e583 https://github.com/galaxyproject/galaxy/commit/cf9ba1e0cc88f695a27d74c96895… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/app.py M lib/galaxy/util/properties.py Log Message: ----------- Clarifications/fixes from @nsoranzo's comments Commit: b805fa5945e1f6799e6cf28097155e7b1d434b4e https://github.com/galaxyproject/galaxy/commit/b805fa5945e1f6799e6cf2809715… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/azure_blob.py M lib/galaxy/objectstore/pithos.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/__init__.py M lib/tool_shed/capsule/capsule_manager.py Log Message: ----------- Undo changes unrelated to uWSGI mule work Commit: 806438edc9b3b407b9cb259f7cdaa8a85fe97f64 https://github.com/galaxyproject/galaxy/commit/806438edc9b3b407b9cb259f7cda… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: R lib/galaxy/script/__init__.py A lib/galaxy/util/script.py M scripts/get_uwsgi_args.py M scripts/manage_tool_dependencies.py Log Message: ----------- Revert script changes unrelated to uWSGI mule work. Includes galaxy.util.script so that get_uwsgi_args.py still works, but that will be PR'd separately and merged later. Commit: 1062c705a2a7a8e4cb1b8c6899941474a620885d https://github.com/galaxyproject/galaxy/commit/1062c705a2a7a8e4cb1b8c689994… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/util/facts.py Log Message: ----------- Fix typo in facts module Commit: c340d4ebecd56583d7b524e380dedf460e5a7175 https://github.com/galaxyproject/galaxy/commit/c340d4ebecd56583d7b524e380de… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M lib/galaxy/model/orm/scripts.py M lib/tool_shed/galaxy_install/migrate/check.py R manage_tools.sh R scripts/manage_tools.py Log Message: ----------- Fix tool migrations with config file changes, do everything from manage_db.sh. Commit: 418fd53739800b639924455722618b7172e23168 https://github.com/galaxyproject/galaxy/commit/418fd53739800b63992445572261… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: R .ci/flake8_lint_include_list.txt R .ci/flake8_wrapper_imports.sh M .ci/jenkins/selenium/run_tests.sh M .travis.yml M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-contents.js A client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/utils/ajax-queue.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample A config/plugins/interactive_environments/askomics/config/allowed_images.yml.sample A config/plugins/interactive_environments/askomics/config/askomics.ini.sample A config/plugins/interactive_environments/askomics/config/askomics.xml A config/plugins/interactive_environments/askomics/static/js/askomics.js A config/plugins/interactive_environments/askomics/templates/askomics.mako M config/plugins/webhooks/demo/tour_generator/static/script.js M doc/source/releases/17.09_announce.rst A lib/galaxy/actions/library.py M lib/galaxy/app.py M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/auth/providers/pam_auth.py M lib/galaxy/config.py M lib/galaxy/dataset_collections/matching.py M lib/galaxy/dataset_collections/registry.py M lib/galaxy/dataset_collections/types/list.py M lib/galaxy/dataset_collections/types/paired.py M lib/galaxy/datatypes/converters/bgzip.py A lib/galaxy/datatypes/converters/cram_to_bam.py A lib/galaxy/datatypes/converters/cram_to_bam_converter.xml M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/display_applications/application.py M lib/galaxy/datatypes/graph.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/tracks.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/Pipfile M lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock M 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test/base/driver_util.py M test/base/populators.py M test/base/testcase.py M test/functional/test_toolbox.py A test/functional/tools/cat_data_and_sleep.xml M test/functional/tools/samples_tool_conf.xml A test/functional/webhooks/tour_generator M test/galaxy_selenium/components.py M test/galaxy_selenium/data.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml A test/integration/test_local_job_cancellation.py M test/manual/workflows_scaling.py M test/selenium_tests/framework.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_history_dataset_state.py M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_jupyter.py M test/selenium_tests/test_library_contents.py M test/selenium_tests/test_library_landing.py M test/selenium_tests/test_published_histories_grid.py M test/selenium_tests/test_saved_histories.py M test/selenium_tests/test_stock_tours.py A test/selenium_tests/test_tool_describing_tours.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_management.py M test/selenium_tests/test_workflow_run.py M test/shed_functional/base/twilltestcase.py M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/datatypes/dataproviders/test_line_dataproviders.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_mapper.py M test/unit/jobs/test_runner_local.py M test/unit/managers/base.py M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HDCAManager.py M test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/shed_unit/test_installed_repository_manager.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/test_objectstore.py M test/unit/tools/test_actions.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_column_parameters.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_parsing.py M test/unit/tools/test_select_parameters.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_tool_loader.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_watcher.py M test/unit/tools_support.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_run_parameters.py M test/unit/workflows/test_workflow_progress.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/phenotype_association/senatag.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'origin/dev' into job-handler-mules Commit: e68b8a312e3051b9378e59340ef42dd91302c1c0 https://github.com/galaxyproject/galaxy/commit/e68b8a312e3051b9378e59340ef4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/util/facts.py Log Message: ----------- Fix use of configure_logging() by scripts that pass the config as a dict rather than a galaxy configuration object Commit: c270614fac007c35eefe473a9023964d7feafe89 https://github.com/galaxyproject/galaxy/commit/c270614fac007c35eefe473a9023… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-16 (Thu, 16 Nov 2017) Changed paths: M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/webapps/galaxy/api/history_contents.py M templates/user/register.mako M test/api/test_history_contents.py M test/api/test_libraries.py M test/api/test_workflows.py M test/base/populators.py M test/functional/tools/create_2.xml M test/integration/test_data_manager_table_reload.py M tools/data_source/microbial_import.xml Log Message: ----------- Merge remote-tracking branch 'origin/dev' into job-handler-mules Commit: 43138be11f8194dabc4645d20d58bb156f9bdb3c https://github.com/galaxyproject/galaxy/commit/43138be11f8194dabc4645d20d58… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-16 (Thu, 16 Nov 2017) Changed paths: M lib/galaxy/config.py Log Message: ----------- Reenable automatic silencing of chatty loggers by default. This is needed when Paste is used but PasteDeploy is not, e.g. with tests. Commit: f78436bba0209d5d886387f81020d3383e08c327 https://github.com/galaxyproject/galaxy/commit/f78436bba0209d5d886387f81020… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-17 (Fri, 17 Nov 2017) Changed paths: M lib/galaxy/util/facts.py Log Message: ----------- Fix None server_name when using the default under uWSGI Commit: c18521d7f774febb75a715e4de7926ff957daab9 https://github.com/galaxyproject/galaxy/commit/c18521d7f774febb75a715e4de79… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-17 (Fri, 17 Nov 2017) Changed paths: M lib/galaxy/app.py M lib/galaxy/web/stack/__init__.py M scripts/galaxy-main Log Message: ----------- Move signal handling from uWSGI stack to main Commit: 1ec960bcf66769c682135901cbd4623b6719fdf8 https://github.com/galaxyproject/galaxy/commit/1ec960bcf66769c682135901cbd4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-17 (Fri, 17 Nov 2017) Changed paths: M lib/galaxy/web/stack/__init__.py M lib/galaxy/web/stack/message.py M lib/galaxy/web/stack/transport.py M lib/galaxy/webapps/galaxy/buildapp.py M scripts/galaxy-main M scripts/get_uwsgi_args.py Log Message: ----------- Improve shutdown cleanliness under uWSGI. Commit: b4863b2df8214972b5e14b0b318591e1ded613f6 https://github.com/galaxyproject/galaxy/commit/b4863b2df8214972b5e14b0b3185… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-17 (Fri, 17 Nov 2017) Changed paths: M lib/galaxy/app.py M scripts/galaxy-main Log Message: ----------- Fix lint errors Commit: eda29c81c16c4422167c7d22f7a79980f7799baa https://github.com/galaxyproject/galaxy/commit/eda29c81c16c4422167c7d22f7a7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-17 (Fri, 17 Nov 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/webapps/tool_shed/config.py M test/base/driver_util.py M test/shed_functional/functional_tests.py Log Message: ----------- Remove deprecated job runner URL config options Commit: e858ceb84a340c658c682d33e350eb7c19649978 https://github.com/galaxyproject/galaxy/commit/e858ceb84a340c658c682d33e350… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-17 (Fri, 17 Nov 2017) Changed paths: M config/galaxy.ini.sample M scripts/get_uwsgi_args.py Log Message: ----------- Do not autostart uWSGI mules Commit: 47473cb85d38a4c7c4ccc9c03186787693f28efb https://github.com/galaxyproject/galaxy/commit/47473cb85d38a4c7c4ccc9c03186… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-17 (Fri, 17 Nov 2017) Changed paths: M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/manager.py M lib/galaxy/workflow/scheduling_manager.py Log Message: ----------- Postfork thread start fixes Commit: e8a22447fd6b9d5f077e2d6b8a0d1144b2cb20db https://github.com/galaxyproject/galaxy/commit/e8a22447fd6b9d5f077e2d6b8a0d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-17 (Fri, 17 Nov 2017) Changed paths: M lib/galaxy/util/handlers.py Log Message: ----------- Run jobs in web workers if no job-handlers farm is configured and using a default job conf (no job_conf.xml) Commit: 49158ba38ba7204a078f2da22ddd6bad75c25f23 https://github.com/galaxyproject/galaxy/commit/49158ba38ba7204a078f2da22ddd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-17 (Fri, 17 Nov 2017) Changed paths: M lib/galaxy/web/stack/__init__.py M scripts/galaxy-main Log Message: ----------- Add multi-farm support to the main script Commit: 2764fe0b5cb73087f76c701a6faf1e71b3c96394 https://github.com/galaxyproject/galaxy/commit/2764fe0b5cb73087f76c701a6faf… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-20 (Mon, 20 Nov 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/util/facts.py M lib/galaxy/web/stack/__init__.py Log Message: ----------- Fix/improve server name manipulation Commit: 4b2c177ae504af7d290d1a6ed436ce0ed4207400 https://github.com/galaxyproject/galaxy/commit/4b2c177ae504af7d290d1a6ed436… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-20 (Mon, 20 Nov 2017) Changed paths: M lib/galaxy/app.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/manager.py M lib/galaxy/util/handlers.py M lib/galaxy/workflow/scheduling_manager.py Log Message: ----------- Attempt to deal with job_conf.xml handlers in a backwards-compatible way. Commit: a3346e2fb7c8cc4d800684f36bb3ca5ae82ced72 https://github.com/galaxyproject/galaxy/commit/a3346e2fb7c8cc4d800684f36bb3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-20 (Mon, 20 Nov 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Fix unit tests Commit: c6c55e1046a74686d58f5de8010b6654b70e2421 https://github.com/galaxyproject/galaxy/commit/c6c55e1046a74686d58f5de8010b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M config/workflow_schedulers_conf.xml.sample M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/manager.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/history_imp_exp.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/actions/upload_common.py A lib/galaxy/util/facts.py M lib/galaxy/util/handlers.py M lib/galaxy/util/path/__init__.py M lib/galaxy/util/properties.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/stack/__init__.py A lib/galaxy/web/stack/message.py A lib/galaxy/web/stack/transport.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/workflow/scheduling_manager.py M lib/tool_shed/galaxy_install/migrate/check.py M lib/tool_shed/util/commit_util.py R manage_tools.sh M run.sh M run_reports.sh M run_tool_shed.sh M scripts/common_startup_functions.sh M scripts/galaxy-main A scripts/get_uwsgi_args.py R scripts/manage_tools.py M test/base/driver_util.py M test/base/integration_util.py A test/functional/tools/config_vars.xml M test/functional/tools/samples_tool_conf.xml A test/integration/test_mules_as_job_handlers.py M test/shed_functional/functional_tests.py M test/unit/jobs/test_job_configuration.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Merge pull request #4475 from natefoo/job-handler-mules Run Galaxy fully under uWSGI, including job handlers Compare: https://github.com/galaxyproject/galaxy/compare/d82933d410f6...c6c55e1046a7

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[galaxyproject/galaxy] 1cfdf8: add ICM datatype for glimmer
by GitHub 28 Nov '17

28 Nov '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 1cfdf85879213018affc3ec19142e3ebccdb8c40 https://github.com/galaxyproject/galaxy/commit/1cfdf85879213018affc3ec19142… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2017-11-20 (Mon, 20 Nov 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- add ICM datatype for glimmer Commit: f44175b03c1671e6db11f1b072c3cd704a95fd58 https://github.com/galaxyproject/galaxy/commit/f44175b03c1671e6db11f1b072c3… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2017-11-20 (Mon, 20 Nov 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- copy paste mistake... Commit: 0bb7612977a44422acdf9c7d559d555ece1d17da https://github.com/galaxyproject/galaxy/commit/0bb7612977a44422acdf9c7d559d… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2017-11-21 (Tue, 21 Nov 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- don't read too much Commit: f6aedb0d2094256eb7f45ce7fc75f327db5b560c https://github.com/galaxyproject/galaxy/commit/f6aedb0d2094256eb7f45ce7fc75… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #5042 from abretaud/icm_dt [17.09] Add ICM datatype for glimmer Compare: https://github.com/galaxyproject/galaxy/compare/ed162d5a69a3...f6aedb0d2094

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[galaxyproject/galaxy] adfb62: Fix metadata setting for Otu datatypes
by GitHub 27 Nov '17

27 Nov '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: adfb623224810a0f383dc4ddf88be4ce51d3aa71 https://github.com/galaxyproject/galaxy/commit/adfb623224810a0f383dc4ddf88b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-24 (Fri, 24 Nov 2017) Changed paths: M lib/galaxy/datatypes/mothur.py Log Message: ----------- Fix metadata setting for Otu datatypes I broke this in https://github.com/galaxyproject/galaxy/pull/4388. I went through the other changes in that PR, and I believe this should be the only error. Figured out through the great detective work of @abernard. Commit: ed162d5a69a3fac061f6becf592e737eed678411 https://github.com/galaxyproject/galaxy/commit/ed162d5a69a3fac061f6becf592e… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-11-27 (Mon, 27 Nov 2017) Changed paths: M lib/galaxy/datatypes/mothur.py Log Message: ----------- Merge pull request #5072 from mvdbeek/metadata_investigation [BUG][17.09] Fix metadata setting for Otu datatypes Compare: https://github.com/galaxyproject/galaxy/compare/f16491cd6506...ed162d5a69a3

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[galaxyproject/galaxy] d868ff: Improved qunit testing options.
by GitHub 27 Nov '17

27 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d868ffd08b8a5b539ba7977172e7c5a5c7be49a3 https://github.com/galaxyproject/galaxy/commit/d868ffd08b8a5b539ba7977172e7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-24 (Fri, 24 Nov 2017) Changed paths: M Makefile A client/galaxy/scripts/qunit/test.js M client/karma.config.js M client/package.json Log Message: ----------- Improved qunit testing options. - Speed up qunit testing but not re-building production bundles that aren't used anyway. - Add a watch option for qunit. - Add option to speed up running all tests by building tests as single bundle instead of many bundles. (May be future default for ``make client-test``.) This is as close as I think we are going to get to closing #4843. Commit: d82933d410f61fc703b5191d235f13f6b370a936 https://github.com/galaxyproject/galaxy/commit/d82933d410f61fc703b5191d235f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-26 (Sun, 26 Nov 2017) Changed paths: M Makefile A client/galaxy/scripts/qunit/test.js M client/karma.config.js M client/package.json Log Message: ----------- Merge pull request #5066 from jmchilton/qunit_improvements Improved Karma configuration and options. Compare: https://github.com/galaxyproject/galaxy/compare/52eb970d1804...d82933d410f6

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[galaxyproject/galaxy] c28b36: Re-enable qunit tests.
by GitHub 25 Nov '17

25 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c28b3681abe0f15b40b709471a625f816df1923a https://github.com/galaxyproject/galaxy/commit/c28b3681abe0f15b40b709471a62… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-23 (Thu, 23 Nov 2017) Changed paths: M .travis.yml Log Message: ----------- Re-enable qunit tests. Commit: 4b20acbed1d082c24e766da33588c049622ff7f9 https://github.com/galaxyproject/galaxy/commit/4b20acbed1d082c24e766da33588… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-23 (Thu, 23 Nov 2017) Changed paths: M Makefile Log Message: ----------- Fix client-test Makefile target. Commit: f2b6af6ef9167cd859dd4790d56d13eb38bf5e26 https://github.com/galaxyproject/galaxy/commit/f2b6af6ef9167cd859dd4790d56d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-24 (Fri, 24 Nov 2017) Changed paths: M Makefile Log Message: ----------- Guess we need to build full client before webpack for qunit? Commit: 52eb970d180424654d380b9997ab345de8e49417 https://github.com/galaxyproject/galaxy/commit/52eb970d180424654d380b9997ab… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-25 (Sat, 25 Nov 2017) Changed paths: M .travis.yml M Makefile Log Message: ----------- Merge pull request #5063 from jmchilton/reenable_qunit Re-enable qunit testing. Compare: https://github.com/galaxyproject/galaxy/compare/3303fab75b90...52eb970d1804

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[galaxyproject/galaxy] 8db428: Fixes galaxy startup when LC_TYPE=UTF-8 on os-x
by GitHub 24 Nov '17

24 Nov '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 8db4288ab5dcf379a669a5ae6ececc217b3c9da0 https://github.com/galaxyproject/galaxy/commit/8db4288ab5dcf379a669a5ae6ece… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-24 (Fri, 24 Nov 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Fixes galaxy startup when LC_TYPE=UTF-8 on os-x Closes https://github.com/galaxyproject/galaxy/issues/2645. Commit: f16491cd6506eb0734c415be1e0456faf9c1dd04 https://github.com/galaxyproject/galaxy/commit/f16491cd6506eb0734c415be1e04… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-24 (Fri, 24 Nov 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Merge pull request #5070 from mvdbeek/docutils_upgrade [BUG][[17.09] Fixes galaxy startup when LC_TYPE=UTF-8 on os-x Compare: https://github.com/galaxyproject/galaxy/compare/a71d5aa2db41...f16491cd6506

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[galaxyproject/galaxy] cbc74f: Ignore OSError when chmod'ing integrated_tool_pane...
by GitHub 24 Nov '17

24 Nov '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: cbc74f99e462ac3c71dc9bcb2a4c8c735e80170f https://github.com/galaxyproject/galaxy/commit/cbc74f99e462ac3c71dc9bcb2a4c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-24 (Fri, 24 Nov 2017) Changed paths: M lib/galaxy/tools/toolbox/integrated_panel.py Log Message: ----------- Ignore OSError when chmod'ing integrated_tool_panel_conf.xml This fixes the first error in https://github.com/galaxyproject/galaxy/issues/5031: ``` Exception in thread ToolConfWatcher.thread: Traceback (most recent call last): File "/usr/lib/python2.7/threading.py", line 810, in __bootstrap_inner self.run() File "/usr/lib/python2.7/threading.py", line 763, in run self.__target(*self.__args, **self.__kwargs) File "lib/galaxy/tools/toolbox/watcher.py", line 138, in check self.reload_callback() File "lib/galaxy/webapps/galaxy/config_watchers.py", line 24, in <lambda> self.tool_config_watcher = get_tool_conf_watcher(reload_callback=lambda: reload_toolbox(self.app), tool_cache=self.app.tool_cache) File "lib/galaxy/queue_worker.py", line 92, in reload_toolbox _get_new_toolbox(app) File "lib/galaxy/queue_worker.py", line 111, in _get_new_toolbox new_toolbox = tools.ToolBox(tool_configs, app.config.tool_path, app) File "lib/galaxy/tools/__init__.py", line 226, in __init__ app=app, File "lib/galaxy/tools/toolbox/base.py", line 1061, in __init__ super(BaseGalaxyToolBox, self).__init__(config_filenames, tool_root_dir, app) File "lib/galaxy/tools/toolbox/base.py", line 87, in __init__ self._save_integrated_tool_panel() File "lib/galaxy/tools/toolbox/integrated_panel.py", line 46, in _save_integrated_tool_panel self._write_integrated_tool_panel_config_file() File "lib/galaxy/tools/toolbox/integrated_panel.py", line 106, in _write_integrated_tool_panel_config_file os.chmod(self._integrated_tool_panel_config, 0o644) OSError: [Errno 2] No such file or directory: '/data/users/mvandenb/gx/config/integrated_tool_panel.xml' ``` Commit: a71d5aa2db41a289b9410b129e6e70652f456593 https://github.com/galaxyproject/galaxy/commit/a71d5aa2db41a289b9410b129e6e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-24 (Fri, 24 Nov 2017) Changed paths: M lib/galaxy/tools/toolbox/integrated_panel.py Log Message: ----------- Merge pull request #5071 from mvdbeek/installation_fixes [BUG][17.09] Ignore OSError when chmod'ing integrated_tool_panel_conf.xml Compare: https://github.com/galaxyproject/galaxy/compare/a7c8edbaa448...a71d5aa2db41

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[galaxyproject/galaxy] 3303fa: Restore admin form routes (#5065)
by GitHub 24 Nov '17

24 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3303fab75b90a4b146776dcd109636043b866577 https://github.com/galaxyproject/galaxy/commit/3303fab75b90a4b146776dcd1096… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-11-24 (Fri, 24 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Restore admin form routes (#5065)

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[galaxyproject/galaxy] b7482a: Remove unused workflow rename controller endpoint
by GitHub 24 Nov '17

24 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b7482aa1ff88d4339578205f398e209c48934d97 https://github.com/galaxyproject/galaxy/commit/b7482aa1ff88d4339578205f398e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Remove unused workflow rename controller endpoint Commit: 32e00137be73485d3bc5a17121edec23366641eb https://github.com/galaxyproject/galaxy/commit/32e00137be73485d3bc5a17121ed… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Revise workflow create endpoint Commit: 63c61d2ce7148e5201686e3e7fde9aefe90d65bd https://github.com/galaxyproject/galaxy/commit/63c61d2ce7148e5201686e3e7fde… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/workflow/workflow.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M static/maps/layout/menu.js.map M static/maps/mvc/workflow/workflow.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/layout/menu.js M static/scripts/mvc/workflow/workflow.js Log Message: ----------- Resolve inconsistent routings names Commit: d6d577029ecb6c882d65586779de937eac64c6ae https://github.com/galaxyproject/galaxy/commit/d6d577029ecb6c882d65586779de… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/tag.js M client/galaxy/scripts/mvc/workflow/workflow.js M static/maps/mvc/tag.js.map M static/maps/mvc/workflow/workflow.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/tag.js M static/scripts/mvc/workflow/workflow.js Log Message: ----------- Fix more routes for consistency and resilience Commit: bd254de59b833c04208b5de3aa23571c935de33d https://github.com/galaxyproject/galaxy/commit/bd254de59b833c04208b5de3aa23… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Fix route for imported workflows success message Commit: 4692de3fafa55dc4566971f4b5d2c0fee4dc1868 https://github.com/galaxyproject/galaxy/commit/4692de3fafa55dc4566971f4b5d2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Fix error message Commit: ab16991ef4ee1073e8a4287f2c6511aea17e4290 https://github.com/galaxyproject/galaxy/commit/ab16991ef4ee1073e8a4287f2c65… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Fix lint Commit: ef0e2530584671b5735d210d20603881224b9d5e https://github.com/galaxyproject/galaxy/commit/ef0e2530584671b5735d210d2060… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-16 (Thu, 16 Nov 2017) Changed paths: M test/selenium_tests/test_workflow_editor.py Log Message: ----------- Fix selenium test attempt Fix Commit: 6e2285d3f2bc687c68b38c5689b3524283c86fc6 https://github.com/galaxyproject/galaxy/commit/6e2285d3f2bc687c68b38c5689b3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-16 (Thu, 16 Nov 2017) Changed paths: R .ci/flake8_lint_include_list.txt R .ci/flake8_wrapper_imports.sh M .travis.yml M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-contents.js A client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample A config/plugins/interactive_environments/askomics/config/allowed_images.yml.sample A config/plugins/interactive_environments/askomics/config/askomics.ini.sample A config/plugins/interactive_environments/askomics/config/askomics.xml A config/plugins/interactive_environments/askomics/static/js/askomics.js A config/plugins/interactive_environments/askomics/templates/askomics.mako M config/plugins/webhooks/demo/tour_generator/static/script.js M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/dataset_collections/matching.py M lib/galaxy/dataset_collections/registry.py M lib/galaxy/dataset_collections/types/list.py M lib/galaxy/dataset_collections/types/paired.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/display_applications/application.py M lib/galaxy/datatypes/graph.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M 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lib/tool_shed/repository_types/registry.py M lib/tool_shed/tools/data_table_manager.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/tools/tool_version_manager.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M lib/tool_shed/utility_containers/__init__.py M scripts/common_startup.sh M scripts/functional_tests.py M scripts/manage_tool_dependencies.py M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/history/hdca-li-edit.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/history/hdca-model.js.map M static/maps/mvc/history/history-content-model.js.map M static/maps/mvc/history/history-contents.js.map A static/maps/mvc/history/history-item-li.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/admin.bundled.js 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test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_mapper.py M test/unit/jobs/test_runner_local.py M test/unit/managers/base.py M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HDCAManager.py M test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/shed_unit/test_installed_repository_manager.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/test_objectstore.py M test/unit/tools/test_actions.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_column_parameters.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_parsing.py M test/unit/tools/test_select_parameters.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_tool_loader.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_watcher.py M test/unit/tools_support.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_run_parameters.py M test/unit/workflows/test_workflow_progress.py M tools/data_source/microbial_import.xml M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/phenotype_association/senatag.py M tox.ini Log Message: ----------- Merge branch 'dev' into remove_unused_workflow_endpoint Commit: 33eb15b63c8ffd1ffb23db299356b682d5e45042 https://github.com/galaxyproject/galaxy/commit/33eb15b63c8ffd1ffb23db299356… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-18 (Sat, 18 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py M test/selenium_tests/test_workflow_editor.py Log Message: ----------- Fix import order and style Commit: 739dab0d80f9bb1cd5814884f464d114908eed9b https://github.com/galaxyproject/galaxy/commit/739dab0d80f9bb1cd5814884f464… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-20 (Mon, 20 Nov 2017) Changed paths: M test/shed_functional/base/twilltestcase.py Log Message: ----------- Fix toolshed tests Commit: 3b8d5981c7540f911575d8b48990044dc3598ff3 https://github.com/galaxyproject/galaxy/commit/3b8d5981c7540f911575d8b48990… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-20 (Mon, 20 Nov 2017) Changed paths: M test/selenium_tests/test_workflow_editor.py Log Message: ----------- Fix selector Fix Fix Commit: 59e4d401a06dd5e835165d228ede3ea399b877c3 https://github.com/galaxyproject/galaxy/commit/59e4d401a06dd5e835165d228ede… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-20 (Mon, 20 Nov 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/form/form-wrapper.js M lib/galaxy/webapps/galaxy/controllers/workflow.py M static/maps/mvc/form/form-wrapper.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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/form/form-wrapper.js Log Message: ----------- Augment form wrapper redirect, load workflow editor after creation Commit: da2e38c723c4253914b0698a1daa4a30b7da6a3e https://github.com/galaxyproject/galaxy/commit/da2e38c723c4253914b0698a1daa… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-21 (Tue, 21 Nov 2017) Changed paths: M test/selenium_tests/test_workflow_editor.py Log Message: ----------- Allow transitioning to workflow editor before clicking inputs menu. Commit: 343c39f31680588489156b35ca27d295779ec082 https://github.com/galaxyproject/galaxy/commit/343c39f31680588489156b35ca27… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-21 (Tue, 21 Nov 2017) Changed paths: M test/selenium_tests/test_workflow_editor.py Log Message: ----------- Use better identifiers in test Commit: 01e0ca602d5fc62bbe249d297b8b064d5a310fa0 https://github.com/galaxyproject/galaxy/commit/01e0ca602d5fc62bbe249d297b8b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-21 (Tue, 21 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Fix link Commit: 4a3dca504e5d500bb507e8ec937fa371b66bef5e https://github.com/galaxyproject/galaxy/commit/4a3dca504e5d500bb507e8ec937f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-22 (Wed, 22 Nov 2017) Changed paths: M .travis.yml M Makefile A client/galaxy/scripts/apps/admin-toolshed.js M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/apps/library.js A client/galaxy/scripts/apps/masthead.js M client/galaxy/scripts/apps/panels/admin-panel.js A client/galaxy/scripts/apps/viz.js A client/galaxy/scripts/apps/workflow.js A client/galaxy/scripts/components/citations.vue A client/galaxy/scripts/components/user_api_keys.vue M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/layout/panel.js R client/galaxy/scripts/mvc/citation/citation-model.js R client/galaxy/scripts/mvc/citation/citation-view.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-node.js A client/galaxy/scripts/qunit/assets/base.css A client/galaxy/scripts/qunit/test-app.js A client/galaxy/scripts/qunit/test-data/bootstrapped.js A client/galaxy/scripts/qunit/test-data/fakeserver.js A client/galaxy/scripts/qunit/test-data/job-dag-1.js A client/galaxy/scripts/qunit/test-data/paired-collection-creator.data.js A client/galaxy/scripts/qunit/tests/form_tests.js A client/galaxy/scripts/qunit/tests/galaxy-app-base.js A client/galaxy/scripts/qunit/tests/graph.js A client/galaxy/scripts/qunit/tests/hda-base.js A client/galaxy/scripts/qunit/tests/history_contents_model_tests.js A client/galaxy/scripts/qunit/tests/job-dag.js A client/galaxy/scripts/qunit/tests/list-of-pairs-collection-creator.js A client/galaxy/scripts/qunit/tests/masthead_tests.js A client/galaxy/scripts/qunit/tests/metrics-logger.js A client/galaxy/scripts/qunit/tests/modal_tests.js A client/galaxy/scripts/qunit/tests/page_tests.js A client/galaxy/scripts/qunit/tests/popover_tests.js A client/galaxy/scripts/qunit/tests/ui_tests.js A client/galaxy/scripts/qunit/tests/upload_dialog_tests.js A client/galaxy/scripts/qunit/tests/utils_test.js A client/galaxy/scripts/qunit/tests/workflow_editor_tests.js M client/galaxy/style/less/base.less M client/gulpfile.js A client/karma.config.js M client/package.json M client/webpack.config.js M client/yarn.lock M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/matrix.cool M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/metrics/instrumenters/core.py M lib/galaxy/managers/collections.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/userskeys.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/workflow/scheduling_manager.py M run_tests.sh M static/maps/galaxy.library.js.map M static/maps/layout/panel.js.map M static/maps/mvc/citation/citation-model.js.map M static/maps/mvc/citation/citation-view.js.map A static/maps/mvc/citations.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-libraryrow-view.js.map M static/maps/mvc/tool/tool-form-base.js.map A static/maps/mvc/user/user_api_keys.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map A static/scripts/bundled/adminToolshed.bundled.js A static/scripts/bundled/adminToolshed.bundled.js.map M static/scripts/bundled/analysis.bundled.js M 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static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-libraryrow-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-node.js M static/style/blue/base.css M templates/webapps/galaxy/base_panels.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/galaxy.panels.mako R templates/webapps/galaxy/history/citations.mako R templates/webapps/galaxy/user/list_users.mako M templates/webapps/galaxy/workflow/editor.mako M test/api/test_configuration.py M test/api/test_history_contents.py M test/api/test_workflows.py M test/functional/tools/create_2.xml M test/integration/test_data_manager_table_reload.py R test/qunit/Gruntfile.js R test/qunit/README.txt R test/qunit/package.json R test/qunit/scripts R test/qunit/test-app.js R test/qunit/test-common.js R test/qunit/test-data/bootstrapped.js R test/qunit/test-data/fakeserver.js R test/qunit/test-data/job-dag-1.js R test/qunit/test-data/paired-collection-creator.data.js R test/qunit/tests/form_tests.html R test/qunit/tests/form_tests.js R test/qunit/tests/galaxy-app-base.html R test/qunit/tests/galaxy-app-base.js R test/qunit/tests/graph.html R test/qunit/tests/graph.js R test/qunit/tests/hda-base.html R test/qunit/tests/hda-base.js R test/qunit/tests/history_contents_model_tests.html R test/qunit/tests/history_contents_model_tests.js R test/qunit/tests/job-dag.html R test/qunit/tests/job-dag.js R test/qunit/tests/list-of-pairs-collection-creator.html R test/qunit/tests/list-of-pairs-collection-creator.js R test/qunit/tests/masthead_tests.html R test/qunit/tests/masthead_tests.js R test/qunit/tests/metrics-logger.html R test/qunit/tests/metrics-logger.js R test/qunit/tests/modal_tests.html R test/qunit/tests/modal_tests.js R test/qunit/tests/page_tests.html R test/qunit/tests/page_tests.js R test/qunit/tests/popover_tests.html R test/qunit/tests/popover_tests.js R test/qunit/tests/ui_tests.html R test/qunit/tests/ui_tests.js R test/qunit/tests/upload_dialog_tests.html R test/qunit/tests/upload_dialog_tests.js R test/qunit/tests/utils_test.html R test/qunit/tests/utils_test.js R test/qunit/tests/workflow_editor_tests.html R test/qunit/tests/workflow_editor_tests.js M tools/stats/gsummary.py M tox.ini Log Message: ----------- Merge branch 'dev' into remove_unused_workflow_endpoint Commit: 476579648ac15e4c3e1da8761bee9fba1b47c20e https://github.com/galaxyproject/galaxy/commit/476579648ac15e4c3e1da8761bee… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-22 (Wed, 22 Nov 2017) Changed paths: M .gitignore M client/gulpfile.js M client/webpack.config.js R static/maps/admin.toolshed.js.map R static/maps/analysis.js.map R static/maps/app.js.map R static/maps/app/analysis.js.map R static/maps/galaxy-app-base.js.map R static/maps/galaxy.interactive_environments.js.map R static/maps/galaxy.js.map R static/maps/galaxy.library.js.map R 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static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/user/user-quotameter.js M static/scripts/mvc/visualization/visualization-model.js M static/scripts/mvc/webhooks.js M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/mvc/workflow/workflow-connector.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-icons.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-model.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view-data.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view-terminals.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/mvc/workflow/workflow.js M static/scripts/nls/de/locale.js M static/scripts/nls/es/locale.js M static/scripts/nls/fr/locale.js M static/scripts/nls/ja/locale.js M static/scripts/nls/locale.js M static/scripts/nls/zh/locale.js M static/scripts/onload.js M static/scripts/polyfills.js M static/scripts/reports_webapp/run_stats.js M static/scripts/ui/autocom_tagging.js M static/scripts/ui/editable-text.js M static/scripts/ui/fa-icon-button.js M static/scripts/ui/filter-control.js M static/scripts/ui/hoverhighlight.js M static/scripts/ui/loading-indicator.js M static/scripts/ui/mode-button.js M static/scripts/ui/pagination.js M static/scripts/ui/peek-column-selector.js M static/scripts/ui/popupmenu.js M static/scripts/ui/scroll-panel.js M static/scripts/ui/search-input.js M static/scripts/utils/add-logging.js M static/scripts/utils/ajax-queue.js M static/scripts/utils/async-save-text.js M static/scripts/utils/config.js M static/scripts/utils/deferred.js M static/scripts/utils/graph.js M static/scripts/utils/levenshtein.js M static/scripts/utils/localization.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/natural-sort.js M static/scripts/utils/query-string-parsing.js M static/scripts/utils/uploadbox.js M static/scripts/utils/utils.js M static/scripts/viz/bbi-data-manager.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/sweepster.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/slotting.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/trackster/util.js M static/scripts/viz/visualization.js M static/scripts/viz/viz_views.js Log Message: ----------- Merge branch 'dev' into remove_unused_workflow_endpoint Commit: e03ea6d7819700446d1f19fef8d1982366c60faf https://github.com/galaxyproject/galaxy/commit/e03ea6d7819700446d1f19fef8d1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-24 (Fri, 24 Nov 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/tag.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/workflow.py R static/maps/galaxy.library.js.map R static/maps/layout/panel.js.map R static/maps/mvc/citation/citation-model.js.map R static/maps/mvc/citation/citation-view.js.map R static/maps/mvc/citations.js.map R static/maps/mvc/history/options-menu.js.map R static/maps/mvc/library/library-folderlist-view.js.map R static/maps/mvc/library/library-foldertoolbar-view.js.map R static/maps/mvc/library/library-libraryrow-view.js.map R static/maps/mvc/tool/tool-form-base.js.map R static/maps/mvc/user/user_api_keys.js.map M static/scripts/bundled/admin.bundled.js R static/scripts/bundled/admin.bundled.js.map R static/scripts/bundled/adminToolshed.bundled.js.map M static/scripts/bundled/analysis.bundled.js R static/scripts/bundled/analysis.bundled.js.map R static/scripts/bundled/library.bundled.js.map R static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js R static/scripts/bundled/login.bundled.js.map M static/scripts/bundled/masthead.bundled.js R static/scripts/bundled/masthead.bundled.js.map R static/scripts/bundled/viz.bundled.js.map M static/scripts/bundled/workflow.bundled.js R static/scripts/bundled/workflow.bundled.js.map M static/scripts/layout/menu.js M static/scripts/mvc/form/form-wrapper.js M static/scripts/mvc/tag.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/mvc/workflow/workflow.js M test/selenium_tests/test_workflow_editor.py M test/shed_functional/base/twilltestcase.py Log Message: ----------- Merge pull request #4996 from guerler/remove_unused_workflow_endpoint Revise workflow create form, remove unused rename endpoint Compare: https://github.com/galaxyproject/galaxy/compare/5c6e4a5c77c0...e03ea6d78197

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[galaxyproject/galaxy] 07ab21: (squashed)
by GitHub 24 Nov '17

24 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 07ab21494ad16ff3dd9f9fc04c1da6696fb460b3 https://github.com/galaxyproject/galaxy/commit/07ab21494ad16ff3dd9f9fc04c1d… Author: mtekman <m.tekman(a)ucl.ac.uk> Date: 2017-11-06 (Mon, 06 Nov 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/genetics.py A lib/galaxy/datatypes/test/linkstudies.allegro_fparam A lib/galaxy/datatypes/test/linkstudies.allegro_ihaplo A lib/galaxy/datatypes/test/linkstudies.alohomora_gts A lib/galaxy/datatypes/test/linkstudies.alohomora_maf A lib/galaxy/datatypes/test/linkstudies.alohomora_map A lib/galaxy/datatypes/test/linkstudies.alohomora_ped A lib/galaxy/datatypes/test/linkstudies.linkage_datain A lib/galaxy/datatypes/test/linkstudies.linkage_map A lib/galaxy/datatypes/test/linkstudies.linkage_pedin Log Message: ----------- (squashed) Added common linkage file formats and sniffers Commit: 148b5841ef8d66dab9b67e70a01afe52f35f6599 https://github.com/galaxyproject/galaxy/commit/148b5841ef8d66dab9b67e70a01a… Author: Mehmet Tekman <m.tekman(a)ucl.ac.uk> Date: 2017-11-11 (Sat, 11 Nov 2017) Changed paths: M lib/galaxy/datatypes/genetics.py Log Message: ----------- tokenizer now non-static, eval in doc-test remove Commit: bca3fdec4447663b371309bde70c0f021eef4c5f https://github.com/galaxyproject/galaxy/commit/bca3fdec4447663b371309bde70c… Author: Mehmet Tekman <m.tekman(a)ucl.ac.uk> Date: 2017-11-11 (Sat, 11 Nov 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- whitespace removal Commit: d44f9a0b71951b3375444ede69cede223cf4c419 https://github.com/galaxyproject/galaxy/commit/d44f9a0b71951b3375444ede69ce… Author: Mehmet Tekman <m.tekman(a)ucl.ac.uk> Date: 2017-11-11 (Sat, 11 Nov 2017) Changed paths: M lib/galaxy/datatypes/genetics.py Log Message: ----------- fix to classnames in doc-test Commit: e545ed4848db61b702b261d7602655eadb8aebb9 https://github.com/galaxyproject/galaxy/commit/e545ed4848db61b702b261d76026… Author: Mehmet Tekman <m.tekman(a)ucl.ac.uk> Date: 2017-11-11 (Sat, 11 Nov 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/genetics.py R lib/galaxy/datatypes/test/linkstudies.alohomora_maf R lib/galaxy/datatypes/test/linkstudies.alohomora_map R lib/galaxy/datatypes/test/linkstudies.alohomora_ped Log Message: ----------- retired alohomora pedigree, map, and maf datatypes/sniffers/test files (tabular) Commit: 6115ae8d2dd2be3b41fb7a9dbe86ebd22050505f https://github.com/galaxyproject/galaxy/commit/6115ae8d2dd2be3b41fb7a9dbe86… Author: Mehmet Tekman <m.tekman(a)ucl.ac.uk> Date: 2017-11-11 (Sat, 11 Nov 2017) Changed paths: M lib/galaxy/datatypes/genetics.py Log Message: ----------- list comparison in header check Commit: 1e28e6231b8c61b6a4b9cd9aff80b4dd535af94b https://github.com/galaxyproject/galaxy/commit/1e28e6231b8c61b6a4b9cd9aff80… Author: Mehmet Tekman <m.tekman(a)ucl.ac.uk> Date: 2017-11-11 (Sat, 11 Nov 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/genetics.py R lib/galaxy/datatypes/test/linkstudies.linkage_pedin Log Message: ----------- changed PreMakePed to Tabular, and removed sniffer/datatype -> migrated line_op into AllegroHaplo Commit: a5b2929f9e02e96b6fdaa02ebb1a55917d63329e https://github.com/galaxyproject/galaxy/commit/a5b2929f9e02e96b6fdaa02ebb1a… Author: Mehmet Tekman <m.tekman(a)ucl.ac.uk> Date: 2017-11-11 (Sat, 11 Nov 2017) Changed paths: M lib/galaxy/datatypes/genetics.py Log Message: ----------- removed tokenizer + extra fluff Commit: e6bab259faf5da34cd39eebfb8c44855f3051cf1 https://github.com/galaxyproject/galaxy/commit/e6bab259faf5da34cd39eebfb8c4… Author: Mehmet Tekman <m.tekman(a)ucl.ac.uk> Date: 2017-11-11 (Sat, 11 Nov 2017) Changed paths: M lib/galaxy/datatypes/test/linkstudies.allegro_fparam R lib/galaxy/datatypes/test/linkstudies.allegro_ihaplo M lib/galaxy/datatypes/test/linkstudies.alohomora_gts M lib/galaxy/datatypes/test/linkstudies.linkage_map Log Message: ----------- smaller test files Commit: 38601e69b1a59ef50c885c153eaa3fb8569fb322 https://github.com/galaxyproject/galaxy/commit/38601e69b1a59ef50c885c153eaa… Author: Mehmet Tekman <m.tekman(a)ucl.ac.uk> Date: 2017-11-11 (Sat, 11 Nov 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/genetics.py Log Message: ----------- removed AllegroHaplo and AllegroDescent classes (tabular) Commit: 2703b52558236f2faf5401b86cb0a16f90069904 https://github.com/galaxyproject/galaxy/commit/2703b52558236f2faf5401b86cb0… Author: Mehmet Tekman <m.tekman(a)ucl.ac.uk> Date: 2017-11-20 (Mon, 20 Nov 2017) Changed paths: M lib/galaxy/datatypes/genetics.py Log Message: ----------- removed per-line-op from superclass and into subclasses Commit: c9f44398b1ad48a9510feb2fd361943e96046d3d https://github.com/galaxyproject/galaxy/commit/c9f44398b1ad48a9510feb2fd361… Author: Mehmet Tekman <m.tekman(a)ucl.ac.uk> Date: 2017-11-20 (Mon, 20 Nov 2017) Changed paths: M lib/galaxy/datatypes/genetics.py Log Message: ----------- reverted back to super in init, line test in header_check Commit: 0ce67da13c311016c80b33d8c36b766895037389 https://github.com/galaxyproject/galaxy/commit/0ce67da13c311016c80b33d8c36b… Author: Mehmet Tekman <m.tekman(a)ucl.ac.uk> Date: 2017-11-24 (Fri, 24 Nov 2017) Changed paths: M lib/galaxy/datatypes/genetics.py Log Message: ----------- enumerated lines, removed eof_res, header_check Commit: 5c6e4a5c77c07c165918faa2ce635e5b27dd9a77 https://github.com/galaxyproject/galaxy/commit/5c6e4a5c77c07c165918faa2ce63… Author: Eric Rasche <hxr(a)hx42.org> Date: 2017-11-24 (Fri, 24 Nov 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/genetics.py A lib/galaxy/datatypes/test/linkstudies.allegro_fparam A lib/galaxy/datatypes/test/linkstudies.alohomora_gts A lib/galaxy/datatypes/test/linkstudies.linkage_datain A lib/galaxy/datatypes/test/linkstudies.linkage_map Log Message: ----------- Merge pull request #4894 from mtekman/linkage Add Classical linkage and haplotype datatypes Compare: https://github.com/galaxyproject/galaxy/compare/7ee9215c0779...5c6e4a5c77c0

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[galaxyproject/galaxy] 8dee6e: Removes map building along with sourcemaps from th...
by GitHub 22 Nov '17

22 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8dee6e14f9a2abd090451fd31abcaa7737d03040 https://github.com/galaxyproject/galaxy/commit/8dee6e14f9a2abd090451fd31abc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-22 (Wed, 22 Nov 2017) Changed paths: M client/gulpfile.js M client/webpack.config.js R static/maps/admin.toolshed.js.map R static/maps/analysis.js.map R static/maps/app.js.map R static/maps/app/analysis.js.map R static/maps/galaxy-app-base.js.map R static/maps/galaxy.interactive_environments.js.map R static/maps/galaxy.js.map R static/maps/galaxy.menu.js.map R static/maps/galaxy.pages.js.map R static/maps/i18n.js.map R static/maps/layout/generic-nav-view.js.map R static/maps/layout/masthead.js.map R static/maps/layout/menu.js.map R static/maps/layout/modal.js.map R static/maps/layout/page.js.map R static/maps/layout/router.js.map R static/maps/layout/scratchbook.js.map R static/maps/libs/backbone.js.map R static/maps/libs/bbi/bigwig.js.map R static/maps/libs/bbi/jquery-ajax-native.js.map R static/maps/libs/bbi/jszlib.js.map R static/maps/libs/bbi/spans.js.map R static/maps/libs/bibtex.js.map R static/maps/libs/bootstrap-tour.js.map R static/maps/libs/bootstrap.js.map R static/maps/libs/common-libs.js.map R static/maps/libs/d3.js.map R static/maps/libs/farbtastic.js.map R static/maps/libs/jquery.complexify.js.map R static/maps/libs/jquery.sparklines.js.map R static/maps/libs/jquery/jquery-ui.js.map R static/maps/libs/jquery/jquery.autocomplete.js.map R static/maps/libs/jquery/jquery.complexify.js.map R static/maps/libs/jquery/jquery.cookie.js.map R static/maps/libs/jquery/jquery.dynatree.js.map R static/maps/libs/jquery/jquery.event.drag.js.map R static/maps/libs/jquery/jquery.event.drop.js.map R static/maps/libs/jquery/jquery.event.hover.js.map R static/maps/libs/jquery/jquery.form.js.map R static/maps/libs/jquery/jquery.js.map R static/maps/libs/jquery/jquery.migrate.js.map R 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static/maps/mvc/collection/list-of-pairs-collection-creator.js.map R static/maps/mvc/collection/pair-collection-creator.js.map R static/maps/mvc/collection/paired-collection-creator.js.map R static/maps/mvc/dataset/data.js.map R static/maps/mvc/dataset/dataset-choice.js.map R static/maps/mvc/dataset/dataset-edit-attributes.js.map R static/maps/mvc/dataset/dataset-error.js.map R static/maps/mvc/dataset/dataset-li-edit.js.map R static/maps/mvc/dataset/dataset-li.js.map R static/maps/mvc/dataset/dataset-list.js.map R static/maps/mvc/dataset/dataset-model.js.map R static/maps/mvc/dataset/states.js.map R static/maps/mvc/form/form-data.js.map R static/maps/mvc/form/form-input.js.map R static/maps/mvc/form/form-parameters.js.map R static/maps/mvc/form/form-repeat.js.map R static/maps/mvc/form/form-section.js.map R static/maps/mvc/form/form-view.js.map R static/maps/mvc/form/form-wrapper.js.map R static/maps/mvc/grid/grid-model.js.map R static/maps/mvc/grid/grid-shared.js.map R static/maps/mvc/grid/grid-template.js.map R static/maps/mvc/grid/grid-view.js.map R static/maps/mvc/groups/group-detail-view.js.map R static/maps/mvc/groups/group-groupdetail-view.js.map R static/maps/mvc/groups/group-grouprow-view.js.map R static/maps/mvc/groups/group-list-view.js.map R static/maps/mvc/groups/group-listrow-view.js.map R static/maps/mvc/groups/group-model.js.map R static/maps/mvc/groups/group.model.js.map R static/maps/mvc/history/copy-dialog.js.map R static/maps/mvc/history/hda-li-edit.js.map R static/maps/mvc/history/hda-li.js.map R static/maps/mvc/history/hda-model.js.map R static/maps/mvc/history/hdca-li-edit.js.map R static/maps/mvc/history/hdca-li.js.map R static/maps/mvc/history/hdca-model.js.map R static/maps/mvc/history/history-content-model.js.map R static/maps/mvc/history/history-contents.js.map R static/maps/mvc/history/history-item-li.js.map R static/maps/mvc/history/history-list.js.map R static/maps/mvc/history/history-model.js.map R static/maps/mvc/history/history-preferences.js.map R static/maps/mvc/history/history-structure-view.js.map R static/maps/mvc/history/history-view-annotated.js.map R static/maps/mvc/history/history-view-edit-current.js.map R static/maps/mvc/history/history-view-edit.js.map R static/maps/mvc/history/history-view.js.map R static/maps/mvc/history/job-dag.js.map R static/maps/mvc/history/multi-panel.js.map R static/maps/mvc/job/job-li.js.map R static/maps/mvc/job/job-model.js.map R static/maps/mvc/job/job-params.js.map R static/maps/mvc/lazy/lazy-limited.js.map R static/maps/mvc/library/library-dataset-view.js.map R static/maps/mvc/library/library-folder-view.js.map R static/maps/mvc/library/library-folderrow-view.js.map R static/maps/mvc/library/library-library-view.js.map R static/maps/mvc/library/library-librarylist-view.js.map R static/maps/mvc/library/library-librarytoolbar-view.js.map R static/maps/mvc/library/library-model.js.map R static/maps/mvc/library/library-util.js.map R static/maps/mvc/list/list-item.js.map R static/maps/mvc/list/list-panel.js.map R static/maps/mvc/list/list-view.js.map R static/maps/mvc/page/page-list.js.map R static/maps/mvc/tag.js.map R static/maps/mvc/tool/tool-form-composite.js.map R static/maps/mvc/tool/tool-form.js.map R static/maps/mvc/tool/tool-genomespace.js.map R static/maps/mvc/tool/tool-template.js.map R static/maps/mvc/tool/tool-webhooks.js.map R static/maps/mvc/tool/tools.js.map R static/maps/mvc/toolshed/categories-view.js.map R static/maps/mvc/toolshed/repo-queue-view.js.map R static/maps/mvc/toolshed/repo-status-view.js.map R static/maps/mvc/toolshed/repositories-view.js.map R static/maps/mvc/toolshed/repository-queue-view.js.map R static/maps/mvc/toolshed/repository-view.js.map R static/maps/mvc/toolshed/shed-category-view.js.map R static/maps/mvc/toolshed/shed-list-view.js.map R static/maps/mvc/toolshed/shed-repo-details-view.js.map R static/maps/mvc/toolshed/shed-repo-list-view.js.map R 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static/maps/mvc/ui/ui-slider.js.map R static/maps/mvc/ui/ui-table.js.map R static/maps/mvc/ui/ui-tabs.js.map R static/maps/mvc/ui/ui-thumbnails.js.map R static/maps/mvc/upload/collection/collection-row.js.map R static/maps/mvc/upload/collection/collection-view.js.map R static/maps/mvc/upload/composite/composite-row.js.map R static/maps/mvc/upload/composite/composite-view.js.map R static/maps/mvc/upload/default/default-row.js.map R static/maps/mvc/upload/default/default-view.js.map R static/maps/mvc/upload/upload-button.js.map R static/maps/mvc/upload/upload-extension.js.map R static/maps/mvc/upload/upload-ftp.js.map R static/maps/mvc/upload/upload-model.js.map R static/maps/mvc/upload/upload-row.js.map R static/maps/mvc/upload/upload-settings.js.map R static/maps/mvc/upload/upload-view.js.map R static/maps/mvc/user/change-password.js.map R static/maps/mvc/user/extra-information.js.map R static/maps/mvc/user/manage-user-information.js.map R static/maps/mvc/user/user-custom-builds.js.map R static/maps/mvc/user/user-model.js.map R static/maps/mvc/user/user-preferences.js.map R static/maps/mvc/user/user-quotameter.js.map R static/maps/mvc/visualization/visualization-model.js.map R static/maps/mvc/webhooks.js.map R static/maps/mvc/workflow/workflow-canvas.js.map R static/maps/mvc/workflow/workflow-configure-menu.js.map R static/maps/mvc/workflow/workflow-connector.js.map R static/maps/mvc/workflow/workflow-forms.js.map R static/maps/mvc/workflow/workflow-icons.js.map R static/maps/mvc/workflow/workflow-manager.js.map R static/maps/mvc/workflow/workflow-model.js.map R static/maps/mvc/workflow/workflow-node.js.map R static/maps/mvc/workflow/workflow-terminals.js.map R static/maps/mvc/workflow/workflow-view-data.js.map R static/maps/mvc/workflow/workflow-view-node.js.map R static/maps/mvc/workflow/workflow-view-terminals.js.map R static/maps/mvc/workflow/workflow-view.js.map R static/maps/mvc/workflow/workflow.js.map R static/maps/nls/de/locale.js.map R static/maps/nls/es/locale.js.map R static/maps/nls/fr/locale.js.map R static/maps/nls/ja/locale.js.map R static/maps/nls/locale.js.map R static/maps/nls/zh/locale.js.map R static/maps/onload.js.map R static/maps/polyfills.js.map R static/maps/reports_webapp/run_stats.js.map R static/maps/templates/compiled/panel_section.js.map R static/maps/templates/compiled/tool_form.js.map R static/maps/templates/compiled/tool_link.js.map R static/maps/templates/compiled/tool_search.js.map R static/maps/toolshed.groups.js.map R static/maps/ui/autocom_tagging.js.map R static/maps/ui/editable-text.js.map R static/maps/ui/fa-icon-button.js.map R static/maps/ui/filter-control.js.map R static/maps/ui/hoverhighlight.js.map R static/maps/ui/loading-indicator.js.map R static/maps/ui/mode-button.js.map R static/maps/ui/pagination.js.map R static/maps/ui/peek-column-selector.js.map R static/maps/ui/popupmenu.js.map R static/maps/ui/scroll-panel.js.map R static/maps/ui/search-input.js.map R static/maps/utils/add-logging.js.map R static/maps/utils/ajax-queue.js.map R static/maps/utils/async-save-text.js.map R static/maps/utils/config.js.map R static/maps/utils/deferred.js.map R static/maps/utils/graph.js.map R static/maps/utils/levenshtein.js.map R static/maps/utils/localization.js.map R static/maps/utils/metrics-logger.js.map R static/maps/utils/natural-sort.js.map R static/maps/utils/query-string-parsing.js.map R static/maps/utils/uploadbox.js.map R static/maps/utils/utils.js.map R static/maps/viz/bbi-data-manager.js.map R static/maps/viz/circster.js.map R static/maps/viz/phyloviz.js.map R static/maps/viz/sweepster.js.map R static/maps/viz/trackster.js.map R static/maps/viz/trackster/filters.js.map R static/maps/viz/trackster/painters.js.map R static/maps/viz/trackster/slotting.js.map R static/maps/viz/trackster/tracks.js.map R static/maps/viz/trackster/util.js.map R static/maps/viz/visualization.js.map R static/maps/viz/viz_views.js.map M static/scripts/admin.toolshed.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/adminToolshed.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/library.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/login.bundled.js M static/scripts/bundled/masthead.bundled.js M static/scripts/bundled/viz.bundled.js M static/scripts/bundled/workflow.bundled.js M static/scripts/galaxy.interactive_environments.js M static/scripts/galaxy.js M static/scripts/galaxy.library.js M static/scripts/galaxy.pages.js M static/scripts/i18n.js M static/scripts/layout/generic-nav-view.js M static/scripts/layout/masthead.js M static/scripts/layout/menu.js M static/scripts/layout/modal.js M static/scripts/layout/page.js M static/scripts/layout/panel.js M static/scripts/layout/router.js M static/scripts/layout/scratchbook.js M static/scripts/mvc/annotation.js M static/scripts/mvc/base-mvc.js M static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/collection/base-creator.js M static/scripts/mvc/collection/collection-li-edit.js M static/scripts/mvc/collection/collection-li.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view-edit.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/dataset/data.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/dataset/dataset-edit-attributes.js M static/scripts/mvc/dataset/dataset-error.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/dataset/dataset-list.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/dataset/states.js M static/scripts/mvc/form/form-data.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/form/form-wrapper.js M static/scripts/mvc/grid/grid-model.js M static/scripts/mvc/grid/grid-shared.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/copy-dialog.js M static/scripts/mvc/history/hda-li-edit.js M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/history/hda-model.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/hdca-model.js M static/scripts/mvc/history/history-content-model.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-item-li.js M static/scripts/mvc/history/history-list.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-preferences.js M static/scripts/mvc/history/history-structure-view.js M static/scripts/mvc/history/history-view-annotated.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/job-dag.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/job/job-li.js M static/scripts/mvc/job/job-model.js M static/scripts/mvc/job/job-params.js M static/scripts/mvc/lazy/lazy-limited.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-library-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-libraryrow-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/library/library-model.js M static/scripts/mvc/library/library-util.js M static/scripts/mvc/list/list-item.js M static/scripts/mvc/list/list-view.js M static/scripts/mvc/tag.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/tool/tool-genomespace.js M static/scripts/mvc/tool/tools.js M static/scripts/mvc/toolshed/categories-view.js M static/scripts/mvc/toolshed/repo-queue-view.js M static/scripts/mvc/toolshed/repo-status-view.js M static/scripts/mvc/toolshed/repositories-view.js M static/scripts/mvc/toolshed/repository-queue-view.js M static/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/toolshed/shed-list-view.js M static/scripts/mvc/toolshed/toolshed-model.js M static/scripts/mvc/toolshed/util.js M static/scripts/mvc/toolshed/workflows-view.js M static/scripts/mvc/tours.js M static/scripts/mvc/ui/error-modal.js M static/scripts/mvc/ui/icon-button.js M static/scripts/mvc/ui/popup-menu.js M static/scripts/mvc/ui/ui-buttons.js M static/scripts/mvc/ui/ui-color-picker.js M static/scripts/mvc/ui/ui-drilldown.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/mvc/ui/ui-list.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-modal.js M static/scripts/mvc/ui/ui-options.js M static/scripts/mvc/ui/ui-popover.js M static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/ui/ui-select-ftp.js M static/scripts/mvc/ui/ui-select-genomespace.js M static/scripts/mvc/ui/ui-select-library.js M static/scripts/mvc/ui/ui-select.js M static/scripts/mvc/ui/ui-slider.js M static/scripts/mvc/ui/ui-table.js M static/scripts/mvc/ui/ui-tabs.js M static/scripts/mvc/ui/ui-thumbnails.js M static/scripts/mvc/upload/collection/collection-row.js M static/scripts/mvc/upload/collection/collection-view.js M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-button.js M static/scripts/mvc/upload/upload-extension.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-model.js M static/scripts/mvc/upload/upload-settings.js M static/scripts/mvc/upload/upload-view.js M static/scripts/mvc/user/user-custom-builds.js M static/scripts/mvc/user/user-model.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/user/user-quotameter.js M static/scripts/mvc/visualization/visualization-model.js M static/scripts/mvc/webhooks.js M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/mvc/workflow/workflow-connector.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-icons.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-model.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view-data.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view-terminals.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/mvc/workflow/workflow.js M static/scripts/nls/de/locale.js M static/scripts/nls/es/locale.js M static/scripts/nls/fr/locale.js M static/scripts/nls/ja/locale.js M static/scripts/nls/locale.js M static/scripts/nls/zh/locale.js M static/scripts/onload.js M static/scripts/polyfills.js M static/scripts/reports_webapp/run_stats.js M static/scripts/ui/autocom_tagging.js M static/scripts/ui/editable-text.js M static/scripts/ui/fa-icon-button.js M static/scripts/ui/filter-control.js M static/scripts/ui/hoverhighlight.js M static/scripts/ui/loading-indicator.js M static/scripts/ui/mode-button.js M static/scripts/ui/pagination.js M static/scripts/ui/peek-column-selector.js M static/scripts/ui/popupmenu.js M static/scripts/ui/scroll-panel.js M static/scripts/ui/search-input.js M static/scripts/utils/add-logging.js M static/scripts/utils/ajax-queue.js M static/scripts/utils/async-save-text.js M static/scripts/utils/config.js M static/scripts/utils/deferred.js M static/scripts/utils/graph.js M static/scripts/utils/levenshtein.js M static/scripts/utils/localization.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/natural-sort.js M static/scripts/utils/query-string-parsing.js M static/scripts/utils/uploadbox.js M static/scripts/utils/utils.js M static/scripts/viz/bbi-data-manager.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/sweepster.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/slotting.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/trackster/util.js M static/scripts/viz/visualization.js M static/scripts/viz/viz_views.js Log Message: ----------- Removes map building along with sourcemaps from the repo. Commit: 60c1136ca9e41eba82e8037214f15f23dc33b564 https://github.com/galaxyproject/galaxy/commit/60c1136ca9e41eba82e8037214f1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-22 (Wed, 22 Nov 2017) Changed paths: M .gitignore Log Message: ----------- Update gitignore. Commit: 7ee9215c0779a517b781f220448b2e39ae10119d https://github.com/galaxyproject/galaxy/commit/7ee9215c0779a517b781f220448b… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-11-22 (Wed, 22 Nov 2017) Changed paths: M .gitignore M client/gulpfile.js M client/webpack.config.js R static/maps/admin.toolshed.js.map R static/maps/analysis.js.map R static/maps/app.js.map R static/maps/app/analysis.js.map R static/maps/galaxy-app-base.js.map R static/maps/galaxy.interactive_environments.js.map R static/maps/galaxy.js.map R static/maps/galaxy.menu.js.map R static/maps/galaxy.pages.js.map R static/maps/i18n.js.map R static/maps/layout/generic-nav-view.js.map R static/maps/layout/masthead.js.map R static/maps/layout/menu.js.map R static/maps/layout/modal.js.map R static/maps/layout/page.js.map R static/maps/layout/router.js.map R static/maps/layout/scratchbook.js.map R static/maps/libs/backbone.js.map R static/maps/libs/bbi/bigwig.js.map R 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static/scripts/ui/loading-indicator.js M static/scripts/ui/mode-button.js M static/scripts/ui/pagination.js M static/scripts/ui/peek-column-selector.js M static/scripts/ui/popupmenu.js M static/scripts/ui/scroll-panel.js M static/scripts/ui/search-input.js M static/scripts/utils/add-logging.js M static/scripts/utils/ajax-queue.js M static/scripts/utils/async-save-text.js M static/scripts/utils/config.js M static/scripts/utils/deferred.js M static/scripts/utils/graph.js M static/scripts/utils/levenshtein.js M static/scripts/utils/localization.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/natural-sort.js M static/scripts/utils/query-string-parsing.js M static/scripts/utils/uploadbox.js M static/scripts/utils/utils.js M static/scripts/viz/bbi-data-manager.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/sweepster.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/slotting.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/trackster/util.js M static/scripts/viz/visualization.js M static/scripts/viz/viz_views.js Log Message: ----------- Merge pull request #5054 from dannon/maps_for_developer_only Sourcemap removal Compare: https://github.com/galaxyproject/galaxy/compare/4d416dcb21cd...7ee9215c0779

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[galaxyproject/galaxy] e59128: Swap to a more flexible bibtex library.
by GitHub 22 Nov '17

22 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e591288cadf5af3acb0700f01cbac1188f07abb1 https://github.com/galaxyproject/galaxy/commit/e591288cadf5af3acb0700f01cba… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-01 (Wed, 01 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M client/gulpfile.js M client/package.json M client/yarn.lock M static/maps/mvc/citation/citation-model.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 R static/scripts/libs/bibtex.js A static/scripts/libs/bibtexParse.js M static/scripts/mvc/citation/citation-model.js Log Message: ----------- Swap to a more flexible bibtex library. Commit: b9ff347e9b2330d2ed87be5f1ada15834535b1cb https://github.com/galaxyproject/galaxy/commit/b9ff347e9b2330d2ed87be5f1ada… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-06 (Mon, 06 Nov 2017) Changed paths: A .ci/jenkins/selenium-compose/Dockerfile A .ci/jenkins/selenium-compose/docker-compose.yml A .ci/jenkins/selenium-compose/galaxy.ini A .ci/jenkins/selenium-compose/run_galaxy.bash A .ci/jenkins/selenium-compose/run_tests.sh R .ci/jenkins/selenium/Dockerfile R .ci/jenkins/selenium/docker-compose.yml R .ci/jenkins/selenium/galaxy.ini R .ci/jenkins/selenium/run_galaxy.bash M .ci/jenkins/selenium/run_tests.sh M Makefile M client/.babelrc M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/login.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/apps/panels/history-panel.js M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/i18n.js M client/galaxy/scripts/layout/generic-nav-view.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/modal.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/layout/router.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/annotation.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/citation/citation-model.js M client/galaxy/scripts/mvc/citation/citation-view.js M client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/dataset/dataset-list.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/dataset/states.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-model.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/copy-dialog.js M client/galaxy/scripts/mvc/history/hda-li-edit.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hda-model.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-content-model.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-model.js M client/galaxy/scripts/mvc/history/history-preferences.js M client/galaxy/scripts/mvc/history/history-structure-view.js M client/galaxy/scripts/mvc/history/history-view-annotated.js M client/galaxy/scripts/mvc/history/history-view-edit-current.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/job-dag.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/job/job-li.js M client/galaxy/scripts/mvc/job/job-model.js M client/galaxy/scripts/mvc/job/job-params.js M client/galaxy/scripts/mvc/lazy/lazy-limited.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/library/library-model.js M client/galaxy/scripts/mvc/library/library-util.js M client/galaxy/scripts/mvc/list/list-item.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/scripts/mvc/tag.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/tool/tool-genomespace.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/toolshed/categories-view.js M client/galaxy/scripts/mvc/toolshed/repo-queue-view.js M client/galaxy/scripts/mvc/toolshed/repo-status-view.js M client/galaxy/scripts/mvc/toolshed/repositories-view.js M 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M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/ui/ui-select-ftp.js M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/mvc/ui/ui-select.js M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/mvc/ui/ui-table.js M client/galaxy/scripts/mvc/ui/ui-tabs.js M client/galaxy/scripts/mvc/ui/ui-thumbnails.js M client/galaxy/scripts/mvc/upload/collection/collection-row.js M client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/mvc/upload/upload-extension.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-model.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-model.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/scripts/mvc/visualization/visualization-model.js M client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-icons.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-model.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view-data.js M 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static/maps/mvc/workflow/workflow-canvas.js.map M static/maps/mvc/workflow/workflow-connector.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-icons.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-model.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-terminals.js.map M static/maps/mvc/workflow/workflow-view-data.js.map M static/maps/mvc/workflow/workflow-view-node.js.map M static/maps/mvc/workflow/workflow-view-terminals.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/mvc/workflow/workflow.js.map M static/maps/nls/de/locale.js.map M static/maps/nls/es/locale.js.map M static/maps/nls/fr/locale.js.map M static/maps/nls/ja/locale.js.map M static/maps/nls/locale.js.map M static/maps/nls/zh/locale.js.map M static/maps/onload.js.map M static/maps/polyfills.js.map M static/maps/reports_webapp/run_stats.js.map M static/maps/ui/autocom_tagging.js.map M static/maps/ui/editable-text.js.map M static/maps/ui/fa-icon-button.js.map M static/maps/ui/filter-control.js.map M static/maps/ui/hoverhighlight.js.map M static/maps/ui/loading-indicator.js.map M static/maps/ui/mode-button.js.map M static/maps/ui/pagination.js.map M static/maps/ui/peek-column-selector.js.map M static/maps/ui/popupmenu.js.map M static/maps/ui/scroll-panel.js.map M static/maps/ui/search-input.js.map M static/maps/utils/add-logging.js.map M static/maps/utils/ajax-queue.js.map M static/maps/utils/async-save-text.js.map M static/maps/utils/config.js.map M static/maps/utils/deferred.js.map M static/maps/utils/graph.js.map M static/maps/utils/levenshtein.js.map M static/maps/utils/localization.js.map M static/maps/utils/metrics-logger.js.map M static/maps/utils/natural-sort.js.map M static/maps/utils/query-string-parsing.js.map M static/maps/utils/uploadbox.js.map M static/maps/utils/utils.js.map M static/maps/viz/bbi-data-manager.js.map M static/maps/viz/circster.js.map M static/maps/viz/phyloviz.js.map M static/maps/viz/sweepster.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/filters.js.map M static/maps/viz/trackster/painters.js.map M static/maps/viz/trackster/slotting.js.map M static/maps/viz/trackster/tracks.js.map M static/maps/viz/trackster/util.js.map M static/maps/viz/visualization.js.map M static/maps/viz/viz_views.js.map M static/scripts/admin.toolshed.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/galaxy.interactive_environments.js M static/scripts/galaxy.js M static/scripts/galaxy.library.js M static/scripts/galaxy.pages.js M static/scripts/i18n.js M static/scripts/layout/generic-nav-view.js M static/scripts/layout/masthead.js M static/scripts/layout/menu.js M static/scripts/layout/modal.js M static/scripts/layout/page.js M static/scripts/layout/panel.js M static/scripts/layout/router.js M static/scripts/layout/scratchbook.js M static/scripts/mvc/annotation.js M static/scripts/mvc/base-mvc.js M static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/citation/citation-model.js M static/scripts/mvc/citation/citation-view.js M static/scripts/mvc/collection/base-creator.js M static/scripts/mvc/collection/collection-li-edit.js M static/scripts/mvc/collection/collection-li.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view-edit.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M 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static/scripts/mvc/history/hda-li-edit.js M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/history/hda-model.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/hdca-model.js M static/scripts/mvc/history/history-content-model.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-list.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-preferences.js M static/scripts/mvc/history/history-structure-view.js M static/scripts/mvc/history/history-view-annotated.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/job-dag.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/job/job-li.js M static/scripts/mvc/job/job-model.js M static/scripts/mvc/job/job-params.js M static/scripts/mvc/lazy/lazy-limited.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-library-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-libraryrow-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/library/library-model.js M static/scripts/mvc/library/library-util.js M static/scripts/mvc/list/list-item.js M static/scripts/mvc/list/list-view.js M static/scripts/mvc/tag.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/tool/tool-genomespace.js M static/scripts/mvc/tool/tools.js M static/scripts/mvc/toolshed/categories-view.js M static/scripts/mvc/toolshed/repo-queue-view.js M static/scripts/mvc/toolshed/repo-status-view.js M static/scripts/mvc/toolshed/repositories-view.js M static/scripts/mvc/toolshed/repository-queue-view.js M static/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/toolshed/shed-list-view.js M static/scripts/mvc/toolshed/toolshed-model.js M static/scripts/mvc/toolshed/util.js M static/scripts/mvc/toolshed/workflows-view.js M static/scripts/mvc/tours.js M static/scripts/mvc/ui/error-modal.js M static/scripts/mvc/ui/icon-button.js M static/scripts/mvc/ui/popup-menu.js M static/scripts/mvc/ui/ui-buttons.js M static/scripts/mvc/ui/ui-color-picker.js M static/scripts/mvc/ui/ui-drilldown.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/mvc/ui/ui-list.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-modal.js M static/scripts/mvc/ui/ui-options.js M static/scripts/mvc/ui/ui-popover.js M 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static/scripts/mvc/upload/upload-settings.js M static/scripts/mvc/upload/upload-view.js M static/scripts/mvc/user/user-custom-builds.js M static/scripts/mvc/user/user-model.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/user/user-quotameter.js M static/scripts/mvc/visualization/visualization-model.js M static/scripts/mvc/webhooks.js M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/mvc/workflow/workflow-connector.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-icons.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-model.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view-data.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view-terminals.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/mvc/workflow/workflow.js M static/scripts/nls/de/locale.js M static/scripts/nls/es/locale.js M static/scripts/nls/fr/locale.js M static/scripts/nls/ja/locale.js M static/scripts/nls/locale.js M static/scripts/nls/zh/locale.js M static/scripts/onload.js M static/scripts/polyfills.js M static/scripts/reports_webapp/run_stats.js M static/scripts/ui/autocom_tagging.js M static/scripts/ui/editable-text.js M static/scripts/ui/fa-icon-button.js M static/scripts/ui/filter-control.js M static/scripts/ui/hoverhighlight.js M static/scripts/ui/loading-indicator.js M static/scripts/ui/mode-button.js M static/scripts/ui/pagination.js M static/scripts/ui/peek-column-selector.js M static/scripts/ui/popupmenu.js M static/scripts/ui/scroll-panel.js M static/scripts/ui/search-input.js M static/scripts/utils/add-logging.js M static/scripts/utils/ajax-queue.js M static/scripts/utils/async-save-text.js M static/scripts/utils/config.js M static/scripts/utils/deferred.js M static/scripts/utils/graph.js M static/scripts/utils/levenshtein.js M static/scripts/utils/localization.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/natural-sort.js M static/scripts/utils/query-string-parsing.js M static/scripts/utils/uploadbox.js M static/scripts/utils/utils.js M static/scripts/viz/bbi-data-manager.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/sweepster.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/slotting.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/trackster/util.js M static/scripts/viz/visualization.js M static/scripts/viz/viz_views.js M static/style/blue/base.css R templates/admin/package_tool.mako R templates/admin/reload_tool.mako M templates/galaxy_client_app.mako M templates/grid_base.mako M templates/webapps/galaxy/admin/center.mako M templates/webapps/galaxy/dataset/display.mako M templates/webapps/galaxy/dataset/tabular_chunked.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/history/citations.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/display_structured.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/structure.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/history/view_multiple.mako M templates/webapps/galaxy/page/editor.mako M templates/webapps/galaxy/visualization/display.mako M templates/webapps/galaxy/visualization/phyloviz.mako M templates/webapps/galaxy/visualization/sweepster.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/tool_shed/group/index.mako M test/api/test_dataset_collections.py M test/api/test_tools_upload.py M test/base/driver_util.py M test/base/integration_util.py M test/base/populators.py M test/docker/base/Dockerfile M test/docker/base/run_test_wrapper.sh A test/docker/base/selenium/LICENSE A test/docker/base/selenium/README A test/docker/base/selenium/entry_point.sh A test/docker/base/selenium/functions.sh A test/docker/base/selenium/generate_config A test/docker/base/selenium/wrap_chrome_binary M test/galaxy_selenium/driver_factory.py M test/qunit/test-app.js M test/qunit/tests/form_tests.js M test/qunit/tests/galaxy-app-base.js M test/qunit/tests/graph.js M test/qunit/tests/hda-base.js M test/qunit/tests/history_contents_model_tests.js M test/qunit/tests/job-dag.js M test/qunit/tests/list-of-pairs-collection-creator.js M test/qunit/tests/masthead_tests.js M test/qunit/tests/metrics-logger.js M test/qunit/tests/modal_tests.js M test/qunit/tests/page_tests.js M test/qunit/tests/popover_tests.js M test/qunit/tests/ui_tests.js M test/qunit/tests/upload_dialog_tests.js M test/qunit/tests/utils_test.js M test/qunit/tests/workflow_editor_tests.js M test/selenium_tests/framework.py M test/selenium_tests/test_published_histories_grid.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into bibtex-replacement-lib Commit: f7fc785eeb711f6ac86cc96fe124178009fe5b9d https://github.com/galaxyproject/galaxy/commit/f7fc785eeb711f6ac86cc96fe124… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-07 (Tue, 07 Nov 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/citation/citation-model.js M client/galaxy/scripts/mvc/citation/citation-view.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/package.json M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/citation/citation-model.js.map M static/maps/mvc/citation/citation-view.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/citation/citation-model.js M static/scripts/mvc/citation/citation-view.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/tool/tool-form-base.js R templates/webapps/galaxy/history/citations.mako Log Message: ----------- Citations work; add client route, remove mako and make it all js-driven. Commit: 3e69d275433da474e68d5bd8b10ed327416c99e6 https://github.com/galaxyproject/galaxy/commit/3e69d275433da474e68d5bd8b10e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-07 (Tue, 07 Nov 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- arrow functions and formatting in analysis.js Commit: b52051e35d3e9d76b99f1ec5bd1f2480073eb3ad https://github.com/galaxyproject/galaxy/commit/b52051e35d3e9d76b99f1ec5bd1f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-07 (Tue, 07 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M static/maps/mvc/citation/citation-model.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/citation/citation-model.js Log Message: ----------- Cleanup in citation-model.js Commit: 1f0f731a4f1b1df455cff49c1d59813d9315cad3 https://github.com/galaxyproject/galaxy/commit/1f0f731a4f1b1df455cff49c1d59… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-07 (Tue, 07 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M static/maps/mvc/citation/citation-model.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/citation/citation-model.js Log Message: ----------- parseBibtex->bibtexParse, remove cruft. Commit: 3b7b294acf7d8967125b69c9e9c5db45bd7cbdc1 https://github.com/galaxyproject/galaxy/commit/3b7b294acf7d8967125b69c9e9c5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-07 (Tue, 07 Nov 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js R client/galaxy/scripts/mvc/citation/citation-model.js R client/galaxy/scripts/mvc/citation/citation-view.js A client/galaxy/scripts/mvc/citations.js M client/galaxy/scripts/mvc/tool/tool-form-base.js A static/maps/mvc/citations.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map R static/scripts/mvc/citation/citation-model.js R static/scripts/mvc/citation/citation-view.js A static/scripts/mvc/citations.js M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Convert to a single citations module; this is much easier to manage. We're shifting *more* towards encapsulated components and having all this stuff split up makes it more difficult to wrangle. Commit: 83e142170b1cf921c911f5d1595ad9a7da535ec0 https://github.com/galaxyproject/galaxy/commit/83e142170b1cf921c911f5d1595a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-07 (Tue, 07 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-view.js M static/maps/mvc/collection/collection-view.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/collection/collection-view.js Log Message: ----------- Remove super chatty collection view creation console.log (if we really need this, it should be using our scoped logger, but I don't thinkwe do) Commit: 4454d50909ea5dca041b52c96c36b5d06e4c1f25 https://github.com/galaxyproject/galaxy/commit/4454d50909ea5dca041b52c96c36… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-07 (Tue, 07 Nov 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Fetch isn't built into the citations model, requires a manual fetch here. Commit: 4071c81a9295f0555653c46861930a899301cc9b https://github.com/galaxyproject/galaxy/commit/4071c81a9295f0555653c4686193… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-07 (Tue, 07 Nov 2017) Changed paths: M client/gulpfile.js M client/package.json M client/webpack.config.js M client/yarn.lock A static/scripts/libs/vue.js Log Message: ----------- Vue lib+build; fixes setimmediate polyfill injection. Commit: 3091994a02d919d486432f917646f76fe35be149 https://github.com/galaxyproject/galaxy/commit/3091994a02d919d486432f917646… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-08 (Wed, 08 Nov 2017) Changed paths: M client/package.json M client/webpack.config.js M client/yarn.lock M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Segmented out single file component build infra for vue Commit: 886cd6c62e08177cb2458bd4ea6f82e93b1484f4 https://github.com/galaxyproject/galaxy/commit/886cd6c62e08177cb2458bd4ea6f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-09 (Thu, 09 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/citations.js M client/package.json M client/webpack.config.js M client/yarn.lock M static/maps/mvc/citations.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/citations.js Log Message: ----------- Better, more robust latex conversion. Commit: c903e9fe1acbe3b90b3cd60c8ffc1d6880f74742 https://github.com/galaxyproject/galaxy/commit/c903e9fe1acbe3b90b3cd60c8ffc… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-11-09 (Thu, 09 Nov 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js A client/galaxy/scripts/mvc/user/user_api_keys.js M client/galaxy/style/less/base.less M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/userskeys.py A static/maps/mvc/user/user_api_keys.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map A static/scripts/mvc/user/user_api_keys.js M static/style/blue/base.css R templates/webapps/galaxy/user/list_users.mako Log Message: ----------- Showcase Vue JS by transforming a mako file to javascript Commit: 8e5f62673d3b6a48df6214d91e00b75f86826a62 https://github.com/galaxyproject/galaxy/commit/8e5f62673d3b6a48df6214d91e00… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-09 (Thu, 09 Nov 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/mvc/user/user_api_keys.js M static/maps/mvc/user/user_api_keys.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user_api_keys.js Log Message: ----------- Fix up admin apikey imports, formatting. Commit: c046565fbfc33a2ded14d41d42272c1cd5aa2d61 https://github.com/galaxyproject/galaxy/commit/c046565fbfc33a2ded14d41d4227… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-09 (Thu, 09 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/citations.js M static/maps/mvc/citations.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Citations formatting. Commit: 0ca4aa7e933de4e9c5471ba110b23d0299ee01bb https://github.com/galaxyproject/galaxy/commit/0ca4aa7e933de4e9c5471ba110b2… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-11-09 (Thu, 09 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/userskeys.py Log Message: ----------- Fixing build fail issues Commit: 3a931e744831a0216d5c1c99db25ec486eced972 https://github.com/galaxyproject/galaxy/commit/3a931e744831a0216d5c1c99db25… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-09 (Thu, 09 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/userskeys.py Log Message: ----------- Remove unused import from userkeys.py Commit: 8810bd0f7c08d9216b85d52a147da44187c4c355 https://github.com/galaxyproject/galaxy/commit/8810bd0f7c08d9216b85d52a147d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-10 (Fri, 10 Nov 2017) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- Add axios Commit: a41c9af3a17853e17f127ebc9a79df1e813d3ec9 https://github.com/galaxyproject/galaxy/commit/a41c9af3a17853e17f127ebc9a79… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-10 (Fri, 10 Nov 2017) Changed paths: M client/galaxy/scripts/layout/panel.js M static/maps/layout/panel.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/panel.js Log Message: ----------- Allow views *or* elements for panel display method. Commit: 1013f6b005bf882acc9dce98c23bb4c1edaffc7f https://github.com/galaxyproject/galaxy/commit/1013f6b005bf882acc9dce98c23b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-10 (Fri, 10 Nov 2017) Changed paths: M client/galaxy/scripts/apps/admin.js A client/galaxy/scripts/components/user_api_keys.vue R client/galaxy/scripts/mvc/user/user_api_keys.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map R static/scripts/mvc/user/user_api_keys.js Log Message: ----------- Vue SFC for admin/user_api_keys. Commit: 1beda0eb7a966cfee408728b0cc0a0dfd8899ac4 https://github.com/galaxyproject/galaxy/commit/1beda0eb7a966cfee408728b0cc0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-10 (Fri, 10 Nov 2017) Changed paths: M client/galaxy/scripts/components/user_api_keys.vue M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Bit of cleanup in user_api_keys SFC Commit: ad26832461bb27aced41f0530ba5f528412b576a https://github.com/galaxyproject/galaxy/commit/ad26832461bb27aced41f0530ba5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-10 (Fri, 10 Nov 2017) Changed paths: M client/galaxy/scripts/components/user_api_keys.vue M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- More cleanup. Commit: f79ae1d1a1a04d72731206fad06b6d0fcc3c6547 https://github.com/galaxyproject/galaxy/commit/f79ae1d1a1a04d72731206fad06b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-10 (Fri, 10 Nov 2017) Changed paths: M .ci/jenkins/selenium/run_tests.sh M README.rst M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/i18n.js M client/galaxy/scripts/layout/modal.js M client/galaxy/scripts/mvc/annotation.js M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/dataset/dataset-list.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.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/hda-li-edit.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view-edit-current.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/job/job-model.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/library/library-model.js M client/galaxy/scripts/mvc/library/library-util.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/scripts/mvc/tag.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/toolshed/util.js M client/galaxy/scripts/mvc/toolshed/workflows-view.js M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/ui/ui-select.js M client/galaxy/scripts/mvc/ui/ui-table.js M client/galaxy/scripts/mvc/ui/ui-thumbnails.js M client/galaxy/scripts/mvc/upload/collection/collection-row.js M client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/user/user-model.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/scripts/mvc/visualization/visualization-model.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/nls/ja/locale.js M client/galaxy/scripts/reports_webapp/run_stats.js M client/galaxy/scripts/ui/autocom_tagging.js M client/galaxy/scripts/ui/fa-icon-button.js M client/galaxy/scripts/ui/filter-control.js M client/galaxy/scripts/ui/mode-button.js M client/galaxy/scripts/ui/pagination.js M client/galaxy/scripts/ui/peek-column-selector.js M client/galaxy/scripts/ui/search-input.js M client/galaxy/scripts/utils/config.js M client/galaxy/scripts/utils/deferred.js M client/galaxy/scripts/utils/localization.js M client/galaxy/scripts/utils/utils.js M client/galaxy/scripts/viz/bbi-data-manager.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/phyloviz.js M client/galaxy/scripts/viz/sweepster.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/filters.js M client/galaxy/scripts/viz/visualization.js M client/galaxy/style/less/trackster.less M config/datatypes_conf.xml.sample M config/galaxy.ini.sample A lib/galaxy/datatypes/converters/cram_to_bam.py A lib/galaxy/datatypes/converters/cram_to_bam_converter.xml A lib/galaxy/datatypes/test/example.iqtree M lib/galaxy/datatypes/text.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/lmod.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M run_tests.sh M static/maps/admin.toolshed.js.map M static/maps/galaxy.interactive_environments.js.map M static/maps/galaxy.library.js.map M static/maps/galaxy.pages.js.map M static/maps/i18n.js.map M static/maps/layout/modal.js.map M static/maps/mvc/annotation.js.map M static/maps/mvc/collection/collection-li-edit.js.map M static/maps/mvc/collection/collection-li.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-view-edit.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/dataset/dataset-list.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/grid/grid-shared.js.map M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/mvc/history/hda-li-edit.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/job/job-model.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-library-view.js.map M static/maps/mvc/library/library-libraryrow-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/maps/mvc/library/library-model.js.map M static/maps/mvc/library/library-util.js.map M static/maps/mvc/list/list-view.js.map M static/maps/mvc/tag.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/toolshed/util.js.map M static/maps/mvc/toolshed/workflows-view.js.map M static/maps/mvc/ui/ui-list.js.map M static/maps/mvc/ui/ui-modal.js.map M static/maps/mvc/ui/ui-popover.js.map M static/maps/mvc/ui/ui-select.js.map M static/maps/mvc/ui/ui-table.js.map M static/maps/mvc/ui/ui-thumbnails.js.map M static/maps/mvc/upload/collection/collection-row.js.map M static/maps/mvc/upload/collection/collection-view.js.map M static/maps/mvc/upload/default/default-row.js.map M static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/maps/mvc/upload/upload-view.js.map M static/maps/mvc/user/user-model.js.map M static/maps/mvc/user/user-preferences.js.map M static/maps/mvc/user/user-quotameter.js.map M static/maps/mvc/visualization/visualization-model.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/mvc/workflow/workflow.js.map M static/maps/nls/ja/locale.js.map M static/maps/reports_webapp/run_stats.js.map M static/maps/ui/autocom_tagging.js.map M static/maps/ui/fa-icon-button.js.map M static/maps/ui/filter-control.js.map M static/maps/ui/mode-button.js.map M static/maps/ui/pagination.js.map M static/maps/ui/peek-column-selector.js.map M static/maps/ui/search-input.js.map M static/maps/utils/config.js.map M static/maps/utils/deferred.js.map M static/maps/utils/localization.js.map M static/maps/utils/utils.js.map M static/maps/viz/bbi-data-manager.js.map M static/maps/viz/circster.js.map M static/maps/viz/phyloviz.js.map M static/maps/viz/sweepster.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/filters.js.map M static/maps/viz/visualization.js.map 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/grid/grid-view.js M static/scripts/reports_webapp/run_stats.js M static/scripts/viz/circster.js M static/scripts/viz/trackster.js M static/style/blue/trackster.css M templates/webapps/reports/run_stats.mako M test/api/test_history_contents.py M test/base/populators.py M test/selenium_tests/framework.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_history_dataset_state.py M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_jupyter.py M test/selenium_tests/test_library_contents.py M test/selenium_tests/test_library_landing.py M test/selenium_tests/test_published_histories_grid.py M test/selenium_tests/test_saved_histories.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_management.py M test/selenium_tests/test_workflow_run.py M test/unit/config/1607_root_filters/config/galaxy.ini M test/unit/config/1607_root_samples/config/galaxy.ini M test/unit/tools/test_conda_resolution.py M test/unit/tools/test_tool_deps.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into bibtex-replacement-lib Commit: c03d011914b7246a587ecaa3e46fa1646570bdd5 https://github.com/galaxyproject/galaxy/commit/c03d011914b7246a587ecaa3e46f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-10 (Fri, 10 Nov 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Simplify Vue creation from SFC, no need to specify template/component separately here. Commit: fc58c45a7e79455c5b51d6d442241c312cae9cb5 https://github.com/galaxyproject/galaxy/commit/fc58c45a7e79455c5b51d6d44224… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/components/citations.vue M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- WIP Citations/Vue Commit: 740234534509cebeadbaf927c97e5031ab955640 https://github.com/galaxyproject/galaxy/commit/740234534509cebeadbaf927c97e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/utils/ajax-queue.js M config/galaxy.ini.sample M doc/source/releases/17.09_announce.rst A lib/galaxy/actions/library.py M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/auth/providers/pam_auth.py M lib/galaxy/config.py M lib/galaxy/datatypes/converters/bgzip.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh A lib/galaxy/jobs/runners/util/job_script/MEMORY_STATEMENT.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/managers/collections.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/cache.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/hash_util.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/library.py R lib/galaxy/webapps/galaxy/controllers/library_admin.py R lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/tools/tool_version_manager.py M lib/tool_shed/util/hg_util.py M static/maps/utils/ajax-queue.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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/utils/ajax-queue.js R templates/admin/library/grid.mako R templates/admin/library/new_library.mako M templates/admin/tool_shed_repository/repository_actions_menu.mako M templates/admin/tool_shed_repository/view_tool_metadata.mako M templates/webapps/galaxy/admin/center.mako R templates/webapps/galaxy/library/common/browse_library.mako R templates/webapps/galaxy/library/common/browse_library_opt.mako R templates/webapps/galaxy/library/common/common.mako R templates/webapps/galaxy/library/common/folder_info.mako R templates/webapps/galaxy/library/common/folder_permissions.mako R templates/webapps/galaxy/library/common/import_datasets_to_histories.mako R templates/webapps/galaxy/library/common/ldda_edit_info.mako R templates/webapps/galaxy/library/common/ldda_info.mako R templates/webapps/galaxy/library/common/ldda_permissions.mako R templates/webapps/galaxy/library/common/library_dataset_info.mako R templates/webapps/galaxy/library/common/library_dataset_permissions.mako R templates/webapps/galaxy/library/common/library_dataset_search_results.mako R templates/webapps/galaxy/library/common/library_info.mako R templates/webapps/galaxy/library/common/library_item_info.mako R templates/webapps/galaxy/library/common/library_permissions.mako R templates/webapps/galaxy/library/common/move_library_item.mako R templates/webapps/galaxy/library/common/new_folder.mako R templates/webapps/galaxy/library/common/upload.mako R templates/webapps/galaxy/library/grid.mako R templates/webapps/galaxy/library/index.mako M test/unit/jobs/test_runner_local.py M test/unit/shed_unit/test_tool_panel_manager.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into bibtex-replacement-lib Commit: a853d54b39b68439374df043f17cf049a06b33e3 https://github.com/galaxyproject/galaxy/commit/a853d54b39b68439374df043f17c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/yarn.lock M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Formatting Commit: 2718f93ab0751042a191941371567a97319ae9bb https://github.com/galaxyproject/galaxy/commit/2718f93ab0751042a19194137156… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M client/galaxy/scripts/components/citations.vue M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Stray console.debug removed. Commit: af2fe1805dd653880eaa8045f238fa326de27bb4 https://github.com/galaxyproject/galaxy/commit/af2fe1805dd653880eaa8045f238… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: R client/galaxy/scripts/mvc/citations.js R static/scripts/mvc/citations.js Log Message: ----------- Remove unused citations.js; this was all pushed into the component. (we may want to pull some of the storage logic back out, elsewhere, but this is an incremental step forward) Commit: 3b2e21373917516c1b192cc27e6274c5adff4804 https://github.com/galaxyproject/galaxy/commit/3b2e21373917516c1b192cc27e62… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M client/galaxy/scripts/components/citations.vue M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Remove some unused styles, push others into component. Commit: 951d8ab4bbef5ed4e459dd624af46f70bfc31ba1 https://github.com/galaxyproject/galaxy/commit/951d8ab4bbef5ed4e459dd624af4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M client/galaxy/scripts/components/citations.vue M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Fix citations display differentiation w/ histories vs specific tool. Commit: e385b7f79570a078b9198d37c458559d0fa70e92 https://github.com/galaxyproject/galaxy/commit/e385b7f79570a078b9198d37c458… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-16 (Thu, 16 Nov 2017) Changed paths: A client/galaxy/scripts/apps/workflow.js M client/webpack.config.js M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Add basic workflow editor app, bundle, entry. Doesn't work yet, need to disentangle all the other bits. Commit: d9897567f93d3005fd1ff186f3ba391a10ae2d10 https://github.com/galaxyproject/galaxy/commit/d9897567f93d3005fd1ff186f3ba… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-16 (Thu, 16 Nov 2017) Changed paths: M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Repack. Commit: c2b6d7b7dc63add49d17667cc887b059538d6b2d https://github.com/galaxyproject/galaxy/commit/c2b6d7b7dc63add49d17667cc887… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-16 (Thu, 16 Nov 2017) Changed paths: M client/galaxy/scripts/apps/workflow.js M client/webpack.config.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M templates/webapps/galaxy/base_panels.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Bundle masthead into application, dramatically cutting down on load time on older pages like workflow editor, etc, in addition to allowing newer features. Commit: d166e41204074d60beec15c305cb8c0eb395996b https://github.com/galaxyproject/galaxy/commit/d166e41204074d60beec15c305cb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-16 (Thu, 16 Nov 2017) Changed paths: A client/galaxy/scripts/apps/masthead.js A static/scripts/bundled/masthead.bundled.js A static/scripts/bundled/masthead.bundled.js.map A static/scripts/bundled/workflow.bundled.js A static/scripts/bundled/workflow.bundled.js.map Log Message: ----------- Actually add masthead and workflow bundles. Commit: a9db144e62c8614c477a3338afa2be90f524997f https://github.com/galaxyproject/galaxy/commit/a9db144e62c8614c477a3338afa2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-16 (Thu, 16 Nov 2017) Changed paths: R .ci/flake8_lint_include_list.txt R .ci/flake8_wrapper_imports.sh M .travis.yml M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-contents.js A client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample A config/plugins/interactive_environments/askomics/config/allowed_images.yml.sample A config/plugins/interactive_environments/askomics/config/askomics.ini.sample A config/plugins/interactive_environments/askomics/config/askomics.xml A config/plugins/interactive_environments/askomics/static/js/askomics.js A config/plugins/interactive_environments/askomics/templates/askomics.mako M config/plugins/webhooks/demo/tour_generator/static/script.js M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/dataset_collections/matching.py M lib/galaxy/dataset_collections/registry.py M lib/galaxy/dataset_collections/types/list.py M lib/galaxy/dataset_collections/types/paired.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/display_applications/application.py M lib/galaxy/datatypes/graph.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/tracks.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/Pipfile M lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock M lib/galaxy/dependencies/pipfiles/flake8/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt R lib/galaxy/dependencies/pipfiles/flake8_imports/Pipfile R lib/galaxy/dependencies/pipfiles/flake8_imports/Pipfile.lock R lib/galaxy/dependencies/pipfiles/flake8_imports/pinned-hashed-requirements.txt R lib/galaxy/dependencies/pipfiles/flake8_imports/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh M lib/galaxy/dependencies/requirements.txt M lib/galaxy/external_services/actions.py M lib/galaxy/external_services/service.py M lib/galaxy/forms/forms.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/mapper.py M lib/galaxy/jobs/metrics/__init__.py M lib/galaxy/jobs/metrics/collectl/processes.py M lib/galaxy/jobs/metrics/instrumenters/collectl.py M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py M lib/galaxy/jobs/metrics/instrumenters/meminfo.py M lib/galaxy/jobs/rule_helper.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/chronos.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/state_handlers/resubmit.py M lib/galaxy/jobs/runners/util/__init__.py M lib/galaxy/jobs/splitters/multi.py M lib/galaxy/managers/citations.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/containers.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/folders.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/hdcas.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/history_contents.py M lib/galaxy/managers/library_datasets.py M lib/galaxy/managers/pages.py M lib/galaxy/managers/ratable.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/managers/roles.py M lib/galaxy/managers/sharable.py M lib/galaxy/managers/tags.py M lib/galaxy/managers/users.py M lib/galaxy/managers/visualizations.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/migrate/check.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/azure_blob.py M lib/galaxy/objectstore/pithos.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py M lib/galaxy/objectstore/s3_multipart_upload.py M lib/galaxy/openid/providers.py M lib/galaxy/queue_worker.py M lib/galaxy/queues.py M lib/galaxy/sample_tracking/request_types.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_tool.py M lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/error_reports/plugins/biostars.py M lib/galaxy/tools/error_reports/plugins/email.py M lib/galaxy/tools/error_reports/plugins/github.py M lib/galaxy/tools/error_reports/plugins/influxdb.py M lib/galaxy/tools/error_reports/plugins/json.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/lint.py M lib/galaxy/tools/linters/inputs.py M lib/galaxy/tools/locations/__init__.py M lib/galaxy/tools/locations/dockstore.py M lib/galaxy/tools/locations/http.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/toolbox/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/tools/toolbox/lineages/interface.py M lib/galaxy/tools/toolbox/panel.py M lib/galaxy/tools/verify/__init__.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/tours/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/util/biostar.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/util/properties.py A lib/galaxy/util/script.py M lib/galaxy/util/submodules.py M lib/galaxy/util/xml_macros.py M lib/galaxy/visualization/data_providers/phyloviz/__init__.py M lib/galaxy/visualization/data_providers/phyloviz/newickparser.py M lib/galaxy/visualization/data_providers/phyloviz/nexusparser.py M lib/galaxy/visualization/data_providers/phyloviz/phyloxmlparser.py M lib/galaxy/visualization/data_providers/registry.py M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/visualization/plugins/resource_parser.py M lib/galaxy/web/form_builder.py M lib/galaxy/web/framework/formbuilder.py M lib/galaxy/web/framework/helpers/__init__.py M lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/web/framework/middleware/graphite.py M lib/galaxy/web/framework/middleware/profile.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/openid_manager.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/web/security/__init__.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/annotations.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/dataset_collections.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/datatypes.py M lib/galaxy/webapps/galaxy/api/extended_metadata.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/folders.py M lib/galaxy/webapps/galaxy/api/forms.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/item_tags.py M lib/galaxy/webapps/galaxy/api/job_files.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/libraries.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/metrics.py M lib/galaxy/webapps/galaxy/api/page_revisions.py M lib/galaxy/webapps/galaxy/api/pages.py M lib/galaxy/webapps/galaxy/api/provenance.py M lib/galaxy/webapps/galaxy/api/quotas.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/api/search.py M lib/galaxy/webapps/galaxy/api/tool_dependencies.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/toolshed.py M lib/galaxy/webapps/galaxy/api/visualizations.py M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/api/workflows.py M 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lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M lib/tool_shed/utility_containers/__init__.py M scripts/common_startup.sh M scripts/functional_tests.py M scripts/manage_tool_dependencies.py M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/history/hdca-li-edit.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/history/hdca-model.js.map M static/maps/mvc/history/history-content-model.js.map M static/maps/mvc/history/history-contents.js.map A static/maps/mvc/history/history-item-li.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/bundled/masthead.bundled.js M static/scripts/bundled/masthead.bundled.js.map M static/scripts/bundled/workflow.bundled.js M static/scripts/bundled/workflow.bundled.js.map M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/hdca-model.js M static/scripts/mvc/history/history-content-model.js M static/scripts/mvc/history/history-contents.js A static/scripts/mvc/history/history-item-li.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/tool/tool-form-base.js R templates/search/index.mako M templates/show_params.mako M templates/user/register.mako M test/api/test_history_contents.py M test/api/test_jobs.py M test/api/test_libraries.py M test/api/test_page_revisions.py M test/api/test_workflows.py M test/base/driver_util.py M test/base/populators.py M test/base/testcase.py M test/functional/test_toolbox.py A test/functional/tools/cat_data_and_sleep.xml M test/functional/tools/create_2.xml M test/functional/tools/samples_tool_conf.xml A test/functional/webhooks/tour_generator M test/galaxy_selenium/components.py M test/galaxy_selenium/data.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/integration/test_data_manager_table_reload.py A test/integration/test_local_job_cancellation.py M test/manual/workflows_scaling.py M test/selenium_tests/test_stock_tours.py A test/selenium_tests/test_tool_describing_tours.py M test/selenium_tests/test_tool_form.py M test/shed_functional/base/twilltestcase.py M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/datatypes/dataproviders/test_line_dataproviders.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_mapper.py M test/unit/jobs/test_runner_local.py M test/unit/managers/base.py M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HDCAManager.py M test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/shed_unit/test_installed_repository_manager.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/test_objectstore.py M test/unit/tools/test_actions.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_column_parameters.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_parsing.py M test/unit/tools/test_select_parameters.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_tool_loader.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_watcher.py M test/unit/tools_support.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_run_parameters.py M test/unit/workflows/test_workflow_progress.py M tools/data_source/microbial_import.xml M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/phenotype_association/senatag.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into bibtex-replacement-lib Commit: a11cffd67886a44ea0df5b96e9bb7795ddb61ef2 https://github.com/galaxyproject/galaxy/commit/a11cffd67886a44ea0df5b96e9bb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-16 (Thu, 16 Nov 2017) Changed paths: M .travis.yml Log Message: ----------- Allow qunit travis failures. *TEMPORARY* Commit: 6637c52864292c7c97e46c71c09faf7dc569b13b https://github.com/galaxyproject/galaxy/commit/6637c52864292c7c97e46c71c09f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-16 (Thu, 16 Nov 2017) Changed paths: M .travis.yml Log Message: ----------- Try again to allow travis failures. Commit: 4c595798b8a68863976d5715d607784150e0e028 https://github.com/galaxyproject/galaxy/commit/4c595798b8a68863976d5715d607… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-16 (Thu, 16 Nov 2017) Changed paths: M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M static/maps/galaxy.library.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-libraryrow-view.js.map M static/scripts/galaxy.library.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-libraryrow-view.js M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Clean up some library imports to slim down require'd components. Kick off masthead correctly w/ galaxy.root settings. Commit: 00147bafc7cc4738ff70ec7a4156363613c54559 https://github.com/galaxyproject/galaxy/commit/00147bafc7cc4738ff70ec7a4156… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-16 (Thu, 16 Nov 2017) Changed paths: M Makefile A client/galaxy/scripts/qunit/assets/base.css A client/galaxy/scripts/qunit/test-app.js A client/galaxy/scripts/qunit/test-data/bootstrapped.js A client/galaxy/scripts/qunit/test-data/fakeserver.js A client/galaxy/scripts/qunit/test-data/job-dag-1.js A client/galaxy/scripts/qunit/test-data/paired-collection-creator.data.js A client/galaxy/scripts/qunit/tests/form_tests.js A client/galaxy/scripts/qunit/tests/galaxy-app-base.js A client/galaxy/scripts/qunit/tests/graph.js A client/galaxy/scripts/qunit/tests/hda-base.js A client/galaxy/scripts/qunit/tests/history_contents_model_tests.js A client/galaxy/scripts/qunit/tests/job-dag.js A client/galaxy/scripts/qunit/tests/list-of-pairs-collection-creator.js A client/galaxy/scripts/qunit/tests/masthead_tests.js A client/galaxy/scripts/qunit/tests/metrics-logger.js A client/galaxy/scripts/qunit/tests/modal_tests.js A client/galaxy/scripts/qunit/tests/page_tests.js A client/galaxy/scripts/qunit/tests/popover_tests.js A client/galaxy/scripts/qunit/tests/ui_tests.js A client/galaxy/scripts/qunit/tests/upload_dialog_tests.js A client/galaxy/scripts/qunit/tests/utils_test.js A client/galaxy/scripts/qunit/tests/workflow_editor_tests.js A client/karma.config.js M client/package.json M run_tests.sh R test/qunit/Gruntfile.js R test/qunit/README.txt R test/qunit/package.json R test/qunit/scripts R test/qunit/test-app.js R test/qunit/test-common.js R test/qunit/test-data/bootstrapped.js R test/qunit/test-data/fakeserver.js R test/qunit/test-data/job-dag-1.js R test/qunit/test-data/paired-collection-creator.data.js R test/qunit/tests/form_tests.html R test/qunit/tests/form_tests.js R test/qunit/tests/galaxy-app-base.html R test/qunit/tests/galaxy-app-base.js R test/qunit/tests/graph.html R test/qunit/tests/graph.js R test/qunit/tests/hda-base.html R test/qunit/tests/hda-base.js R test/qunit/tests/history_contents_model_tests.html R test/qunit/tests/history_contents_model_tests.js R test/qunit/tests/job-dag.html R test/qunit/tests/job-dag.js R test/qunit/tests/list-of-pairs-collection-creator.html R test/qunit/tests/list-of-pairs-collection-creator.js R test/qunit/tests/masthead_tests.html R test/qunit/tests/masthead_tests.js R test/qunit/tests/metrics-logger.html R test/qunit/tests/metrics-logger.js R test/qunit/tests/modal_tests.html R test/qunit/tests/modal_tests.js R test/qunit/tests/page_tests.html R test/qunit/tests/page_tests.js R test/qunit/tests/popover_tests.html R test/qunit/tests/popover_tests.js R test/qunit/tests/ui_tests.html R test/qunit/tests/ui_tests.js R test/qunit/tests/upload_dialog_tests.html R test/qunit/tests/upload_dialog_tests.js R test/qunit/tests/utils_test.html R test/qunit/tests/utils_test.js R test/qunit/tests/workflow_editor_tests.html R test/qunit/tests/workflow_editor_tests.js M tox.ini Log Message: ----------- Run qunit tests under Karma. Commit: 699e10bdecf542c994460282d399e5c20ef97b3f https://github.com/galaxyproject/galaxy/commit/699e10bdecf542c994460282d399… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-17 (Fri, 17 Nov 2017) Changed paths: M Makefile A client/galaxy/scripts/qunit/assets/base.css A client/galaxy/scripts/qunit/test-app.js A client/galaxy/scripts/qunit/test-data/bootstrapped.js A client/galaxy/scripts/qunit/test-data/fakeserver.js A client/galaxy/scripts/qunit/test-data/job-dag-1.js A client/galaxy/scripts/qunit/test-data/paired-collection-creator.data.js A client/galaxy/scripts/qunit/tests/form_tests.js A client/galaxy/scripts/qunit/tests/galaxy-app-base.js A client/galaxy/scripts/qunit/tests/graph.js A client/galaxy/scripts/qunit/tests/hda-base.js A client/galaxy/scripts/qunit/tests/history_contents_model_tests.js A client/galaxy/scripts/qunit/tests/job-dag.js A client/galaxy/scripts/qunit/tests/list-of-pairs-collection-creator.js A client/galaxy/scripts/qunit/tests/masthead_tests.js A client/galaxy/scripts/qunit/tests/metrics-logger.js A client/galaxy/scripts/qunit/tests/modal_tests.js A client/galaxy/scripts/qunit/tests/page_tests.js A client/galaxy/scripts/qunit/tests/popover_tests.js A client/galaxy/scripts/qunit/tests/ui_tests.js A client/galaxy/scripts/qunit/tests/upload_dialog_tests.js A client/galaxy/scripts/qunit/tests/utils_test.js A client/galaxy/scripts/qunit/tests/workflow_editor_tests.js A client/karma.config.js M client/package.json M run_tests.sh R test/qunit/Gruntfile.js R test/qunit/README.txt R test/qunit/package.json R test/qunit/scripts R test/qunit/test-app.js R test/qunit/test-common.js R test/qunit/test-data/bootstrapped.js R test/qunit/test-data/fakeserver.js R test/qunit/test-data/job-dag-1.js R test/qunit/test-data/paired-collection-creator.data.js R test/qunit/tests/form_tests.html R test/qunit/tests/form_tests.js R test/qunit/tests/galaxy-app-base.html R test/qunit/tests/galaxy-app-base.js R test/qunit/tests/graph.html R test/qunit/tests/graph.js R test/qunit/tests/hda-base.html R test/qunit/tests/hda-base.js R test/qunit/tests/history_contents_model_tests.html R test/qunit/tests/history_contents_model_tests.js R test/qunit/tests/job-dag.html R test/qunit/tests/job-dag.js R test/qunit/tests/list-of-pairs-collection-creator.html R test/qunit/tests/list-of-pairs-collection-creator.js R test/qunit/tests/masthead_tests.html R test/qunit/tests/masthead_tests.js R test/qunit/tests/metrics-logger.html R test/qunit/tests/metrics-logger.js R test/qunit/tests/modal_tests.html R test/qunit/tests/modal_tests.js R test/qunit/tests/page_tests.html R test/qunit/tests/page_tests.js R test/qunit/tests/popover_tests.html R test/qunit/tests/popover_tests.js R test/qunit/tests/ui_tests.html R test/qunit/tests/ui_tests.js R test/qunit/tests/upload_dialog_tests.html R test/qunit/tests/upload_dialog_tests.js R test/qunit/tests/utils_test.html R test/qunit/tests/utils_test.js R test/qunit/tests/workflow_editor_tests.html R test/qunit/tests/workflow_editor_tests.js M tox.ini Log Message: ----------- Merge pull request #22 from jmchilton/bibtex-replacement-lib Run qunit tests under Karma. Commit: 01f3cc1c1adacb5c688d17832235f77ae7d7e3a1 https://github.com/galaxyproject/galaxy/commit/01f3cc1c1adacb5c688d17832235… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-17 (Fri, 17 Nov 2017) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- Move testing dependencies to devDependencies, use yarn. Commit: baec91349f521103593a0658285f758421b789b2 https://github.com/galaxyproject/galaxy/commit/baec91349f521103593a0658285f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-17 (Fri, 17 Nov 2017) Changed paths: M client/package.json Log Message: ----------- Remove bin path from package.json for karma. Commit: c871ba605a53ef88a317196ba620eaae315afb95 https://github.com/galaxyproject/galaxy/commit/c871ba605a53ef88a317196ba620… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-17 (Fri, 17 Nov 2017) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- Work around https://github.com/karma-runner/karma-qunit/issues/98 for now, use qunitjs dep Commit: 4bdbe28e79ce6a4889ad6e504b49b10fe32e1c70 https://github.com/galaxyproject/galaxy/commit/4bdbe28e79ce6a4889ad6e504b49… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-17 (Fri, 17 Nov 2017) Changed paths: M client/karma.config.js M client/package.json Log Message: ----------- Fix two more of the qunit tests for webpack setup. Using karma-polyfill. Commit: 0f266997f222ff7d0deb0ba3da540f80432ae61c https://github.com/galaxyproject/galaxy/commit/0f266997f222ff7d0deb0ba3da54… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-17 (Fri, 17 Nov 2017) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- Swap karma-polyfill to devDependencies Commit: 6d9b21776e502dc0225bac6a7677bbbe4f143231 https://github.com/galaxyproject/galaxy/commit/6d9b21776e502dc0225bac6a7677… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-17 (Fri, 17 Nov 2017) Changed paths: M client/gulpfile.js Log Message: ----------- Gulp should ignore the qunit directory here. Commit: e81d89f74faa2678413ecb4b6b89689ba8cc4f11 https://github.com/galaxyproject/galaxy/commit/e81d89f74faa2678413ecb4b6b89… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-17 (Fri, 17 Nov 2017) Changed paths: A client/galaxy/scripts/apps/trackster.js M client/webpack.config.js Log Message: ----------- WIP Trackster entrypoint; more entangled than expected so it needs help. Commit: 8d9998c50f9beb47eb23a67ad040b8721310dee9 https://github.com/galaxyproject/galaxy/commit/8d9998c50f9beb47eb23a67ad040… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-20 (Mon, 20 Nov 2017) Changed paths: M client/galaxy/scripts/apps/trackster.js M lib/galaxy/webapps/galaxy/controllers/visualization.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/bundled/masthead.bundled.js M static/scripts/bundled/masthead.bundled.js.map A static/scripts/bundled/trackster.bundled.js A static/scripts/bundled/trackster.bundled.js.map M static/scripts/bundled/workflow.bundled.js M static/scripts/bundled/workflow.bundled.js.map M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Trackster app entrypoint fix. Commit: 07ea8029a2b85876e064f4e4ba336e0397ee4e0c https://github.com/galaxyproject/galaxy/commit/07ea8029a2b85876e064f4e4ba33… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-20 (Mon, 20 Nov 2017) Changed paths: M client/galaxy/scripts/qunit/test-app.js M client/galaxy/scripts/qunit/test-data/bootstrapped.js M client/galaxy/scripts/qunit/test-data/fakeserver.js M client/galaxy/scripts/qunit/test-data/job-dag-1.js M client/galaxy/scripts/qunit/test-data/paired-collection-creator.data.js M client/galaxy/scripts/qunit/tests/form_tests.js M client/galaxy/scripts/qunit/tests/galaxy-app-base.js M client/galaxy/scripts/qunit/tests/graph.js M client/galaxy/scripts/qunit/tests/hda-base.js M client/galaxy/scripts/qunit/tests/history_contents_model_tests.js M client/galaxy/scripts/qunit/tests/job-dag.js M client/galaxy/scripts/qunit/tests/list-of-pairs-collection-creator.js M client/galaxy/scripts/qunit/tests/masthead_tests.js M client/galaxy/scripts/qunit/tests/metrics-logger.js M client/galaxy/scripts/qunit/tests/modal_tests.js M client/galaxy/scripts/qunit/tests/page_tests.js M client/galaxy/scripts/qunit/tests/popover_tests.js M client/galaxy/scripts/qunit/tests/ui_tests.js M client/galaxy/scripts/qunit/tests/upload_dialog_tests.js M client/galaxy/scripts/qunit/tests/utils_test.js M client/galaxy/scripts/qunit/tests/workflow_editor_tests.js Log Message: ----------- Client-format for tests. Commit: 380e82c5dc9aadec15eccb07c9c778fc7b9c0f29 https://github.com/galaxyproject/galaxy/commit/380e82c5dc9aadec15eccb07c9c7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-20 (Mon, 20 Nov 2017) Changed paths: R client/galaxy/scripts/apps/trackster.js A client/galaxy/scripts/apps/viz.js M client/webpack.config.js M lib/galaxy/webapps/galaxy/controllers/visualization.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/bundled/masthead.bundled.js M static/scripts/bundled/masthead.bundled.js.map R static/scripts/bundled/trackster.bundled.js R static/scripts/bundled/trackster.bundled.js.map A static/scripts/bundled/viz.bundled.js A static/scripts/bundled/viz.bundled.js.map M static/scripts/bundled/workflow.bundled.js M static/scripts/bundled/workflow.bundled.js.map Log Message: ----------- Bundle trackster/circster together as 'viz'. Commit: c92d958c0a3c11b8a6f442abe9a59c127a5b1572 https://github.com/galaxyproject/galaxy/commit/c92d958c0a3c11b8a6f442abe9a5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-20 (Mon, 20 Nov 2017) Changed paths: A client/galaxy/scripts/apps/library.js M client/webpack.config.js M lib/galaxy/webapps/galaxy/controllers/library.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map A static/scripts/bundled/library.bundled.js A static/scripts/bundled/library.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/bundled/masthead.bundled.js M static/scripts/bundled/masthead.bundled.js.map M static/scripts/bundled/viz.bundled.js M static/scripts/bundled/viz.bundled.js.map M static/scripts/bundled/workflow.bundled.js M static/scripts/bundled/workflow.bundled.js.map Log Message: ----------- Bundle libraries. Commit: 76f0eb41726424829f2e93efa08d8336266b7c50 https://github.com/galaxyproject/galaxy/commit/76f0eb41726424829f2e93efa08d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-20 (Mon, 20 Nov 2017) Changed paths: A client/galaxy/scripts/apps/admin-toolshed.js M client/galaxy/scripts/apps/library.js M client/webpack.config.js M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map A static/scripts/bundled/adminToolshed.bundled.js A static/scripts/bundled/adminToolshed.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/library.bundled.js M static/scripts/bundled/library.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/bundled/masthead.bundled.js M static/scripts/bundled/masthead.bundled.js.map M static/scripts/bundled/viz.bundled.js M static/scripts/bundled/viz.bundled.js.map M static/scripts/bundled/workflow.bundled.js M static/scripts/bundled/workflow.bundled.js.map Log Message: ----------- Bundle admin toolshed beta interface. Commit: 953d4859750874b2cedf1351c344cba2da7b5c7f https://github.com/galaxyproject/galaxy/commit/953d4859750874b2cedf1351c344… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-21 (Tue, 21 Nov 2017) Changed paths: M client/galaxy/scripts/components/citations.vue M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/bundled/masthead.bundled.js M static/scripts/bundled/masthead.bundled.js.map M static/scripts/bundled/viz.bundled.js M static/scripts/bundled/viz.bundled.js.map M static/scripts/bundled/workflow.bundled.js M static/scripts/bundled/workflow.bundled.js.map Log Message: ----------- Slight rewording of citation reminder/prompt, change to an infomessage. Commit: d4f33c4bf8a0e488536099e0fe3d155b4ec15f39 https://github.com/galaxyproject/galaxy/commit/d4f33c4bf8a0e488536099e0fe3d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-21 (Tue, 21 Nov 2017) Changed paths: M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Fix workflow onclicks. Commit: 283afd984bca6f36d604e4e48e028ee17fc67719 https://github.com/galaxyproject/galaxy/commit/283afd984bca6f36d604e4e48e02… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-21 (Tue, 21 Nov 2017) Changed paths: M client/galaxy/scripts/components/citations.vue Log Message: ----------- Add a tag to formatted references in citations.vue. No style associated with it yet but it makes it easier to identify for tours and tests. Commit: 7594ae7febf653aa3f08548d4157f73012e15e95 https://github.com/galaxyproject/galaxy/commit/7594ae7febf653aa3f08548d4157… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-21 (Tue, 21 Nov 2017) Changed paths: M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/bundled/masthead.bundled.js M static/scripts/bundled/masthead.bundled.js.map M static/scripts/bundled/viz.bundled.js M static/scripts/bundled/viz.bundled.js.map M static/scripts/bundled/workflow.bundled.js M static/scripts/bundled/workflow.bundled.js.map Log Message: ----------- Rebuild after merges. Commit: 2950bf992446da7d05d2210576f9bcfa86ae977b https://github.com/galaxyproject/galaxy/commit/2950bf992446da7d05d2210576f9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-21 (Tue, 21 Nov 2017) Changed paths: M client/galaxy/scripts/components/citations.vue M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/bundled/masthead.bundled.js M static/scripts/bundled/masthead.bundled.js.map M static/scripts/bundled/viz.bundled.js M static/scripts/bundled/viz.bundled.js.map M static/scripts/bundled/workflow.bundled.js M static/scripts/bundled/workflow.bundled.js.map Log Message: ----------- Only show citations infomessage blurb for the full history view. Commit: 5b531472f7319c07a3847879e427a2a752b5b13e https://github.com/galaxyproject/galaxy/commit/5b531472f7319c07a3847879e427… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-21 (Tue, 21 Nov 2017) Changed paths: M client/galaxy/scripts/components/citations.vue M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/bundled/masthead.bundled.js M static/scripts/bundled/masthead.bundled.js.map M static/scripts/bundled/viz.bundled.js M static/scripts/bundled/viz.bundled.js.map M static/scripts/bundled/workflow.bundled.js M static/scripts/bundled/workflow.bundled.js.map Log Message: ----------- Slight reformatting in message display for history-level citations. Commit: 8426158499d4b1a8fa0c960b964b3ac220c6bac6 https://github.com/galaxyproject/galaxy/commit/8426158499d4b1a8fa0c960b964b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-21 (Tue, 21 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/matrix.cool M lib/galaxy/jobs/metrics/instrumenters/core.py M lib/galaxy/managers/collections.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/workflow/scheduling_manager.py M run_tests.sh M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-node.js M test/api/test_configuration.py M test/api/test_history_contents.py M tools/stats/gsummary.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into bibtex-replacement-lib Commit: 6c47f17857d27ba5c10f54ac520a1adadb493da3 https://github.com/galaxyproject/galaxy/commit/6c47f17857d27ba5c10f54ac520a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-21 (Tue, 21 Nov 2017) Changed paths: M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/workflow.bundled.js M static/scripts/bundled/workflow.bundled.js.map Log Message: ----------- rebundle Commit: 4d416dcb21cdaac9396cf4c8a76ae7bf251d3a79 https://github.com/galaxyproject/galaxy/commit/4d416dcb21cdaac9396cf4c8a76a… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-11-22 (Wed, 22 Nov 2017) Changed paths: M .travis.yml M Makefile A client/galaxy/scripts/apps/admin-toolshed.js M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/apps/library.js A client/galaxy/scripts/apps/masthead.js M client/galaxy/scripts/apps/panels/admin-panel.js A client/galaxy/scripts/apps/viz.js A client/galaxy/scripts/apps/workflow.js A client/galaxy/scripts/components/citations.vue A client/galaxy/scripts/components/user_api_keys.vue M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/layout/panel.js R client/galaxy/scripts/mvc/citation/citation-model.js R client/galaxy/scripts/mvc/citation/citation-view.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js A client/galaxy/scripts/qunit/assets/base.css A client/galaxy/scripts/qunit/test-app.js A client/galaxy/scripts/qunit/test-data/bootstrapped.js A client/galaxy/scripts/qunit/test-data/fakeserver.js A client/galaxy/scripts/qunit/test-data/job-dag-1.js A 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client/karma.config.js M client/package.json M client/webpack.config.js M client/yarn.lock M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/userskeys.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M run_tests.sh M static/maps/galaxy.library.js.map M static/maps/layout/panel.js.map M static/maps/mvc/citation/citation-model.js.map M static/maps/mvc/citation/citation-view.js.map A static/maps/mvc/citations.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-libraryrow-view.js.map M static/maps/mvc/tool/tool-form-base.js.map A static/maps/mvc/user/user_api_keys.js.map M static/scripts/bundled/admin.bundled.js M 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static/scripts/mvc/citation/citation-view.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-libraryrow-view.js M static/scripts/mvc/tool/tool-form-base.js M static/style/blue/base.css M templates/webapps/galaxy/base_panels.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/galaxy.panels.mako R templates/webapps/galaxy/history/citations.mako R templates/webapps/galaxy/user/list_users.mako M templates/webapps/galaxy/workflow/editor.mako R test/qunit/Gruntfile.js R test/qunit/README.txt R test/qunit/package.json R test/qunit/scripts R test/qunit/test-app.js R test/qunit/test-common.js R test/qunit/test-data/bootstrapped.js R test/qunit/test-data/fakeserver.js R test/qunit/test-data/job-dag-1.js R test/qunit/test-data/paired-collection-creator.data.js R test/qunit/tests/form_tests.html R test/qunit/tests/form_tests.js R test/qunit/tests/galaxy-app-base.html R test/qunit/tests/galaxy-app-base.js R test/qunit/tests/graph.html R test/qunit/tests/graph.js R test/qunit/tests/hda-base.html R test/qunit/tests/hda-base.js R test/qunit/tests/history_contents_model_tests.html R test/qunit/tests/history_contents_model_tests.js R test/qunit/tests/job-dag.html R test/qunit/tests/job-dag.js R test/qunit/tests/list-of-pairs-collection-creator.html R test/qunit/tests/list-of-pairs-collection-creator.js R test/qunit/tests/masthead_tests.html R test/qunit/tests/masthead_tests.js R test/qunit/tests/metrics-logger.html R test/qunit/tests/metrics-logger.js R test/qunit/tests/modal_tests.html R test/qunit/tests/modal_tests.js R test/qunit/tests/page_tests.html R test/qunit/tests/page_tests.js R test/qunit/tests/popover_tests.html R test/qunit/tests/popover_tests.js R test/qunit/tests/ui_tests.html R test/qunit/tests/ui_tests.js R test/qunit/tests/upload_dialog_tests.html R test/qunit/tests/upload_dialog_tests.js R test/qunit/tests/utils_test.html R test/qunit/tests/utils_test.js R test/qunit/tests/workflow_editor_tests.html R test/qunit/tests/workflow_editor_tests.js M tox.ini Log Message: ----------- Merge pull request #4978 from dannon/bibtex-replacement-lib Vue integration, bibtex replacement Compare: https://github.com/galaxyproject/galaxy/compare/ce4584956b72...4d416dcb21cd

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