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
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…
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
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
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...…