November 2017 - 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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