Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 3fa608f54850d9a93e910cdc55fa1f87c4c87c7c
https://github.com/galaxyproject/galaxy/commit/3fa608f54850d9a93e910cdc55fa…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-08 (Fri, 08 Dec 2017)
Changed paths:
M lib/galaxy/datatypes/binary.py
Log Message:
-----------
Use pysam.merge instead of samtools merge
Commit: 16d0d3ecafb47ca8f112e8fa339f492446f9e80c
https://github.com/galaxyproject/galaxy/commit/16d0d3ecafb47ca8f112e8fa339f…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-08 (Fri, 08 Dec 2017)
Changed paths:
A lib/galaxy/datatypes/test/1.unsorted.bam
Log Message:
-----------
Add unsorted test bam
Commit: 3c9999d89acfdd7aa1f56969ca7e03da3d83e655
https://github.com/galaxyproject/galaxy/commit/3c9999d89acfdd7aa1f56969ca7e…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-08 (Fri, 08 Dec 2017)
Changed paths:
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/test/1.bam
M lib/galaxy/datatypes/test/1.unsorted.bam
Log Message:
-----------
Use pysam for metadata setting and grooming
There are also some noteworthy changes here:
- We do always respect the sort-order specified in the header
- If the sort order is not mentioned in the header or no header
exists we coordinate-sort the file.
- We do not use indexing to determine if a file is coordinate sorted,
because this does not work reliably with samtools/pysam > 1.X,
since arbitrarily sorted files can be indexed now.
This also fixes advanced metadata setting (sort_order, bam_version and more),
which appears to have been broken. This probably went by unnoticed because of the catch-all
try-except-pass.
The downside to fixing this is that I had to (temporarilly, hopefully)
comment out the reference_names, reference_lengths, bam_header and readgroups attributes,
because they led to the following error:
```
galaxy.model.metadata DEBUG 2017-11-19 14:47:30,540 loading metadata from file for: HistoryDatasetAssociation 582
galaxy.jobs.runners.local ERROR 2017-11-19 14:47:30,636 Job wrapper finish method failed
Traceback (most recent call last):
File "/Users/mvandenb/src/galaxy/lib/galaxy/jobs/runners/local.py", line 130, in queue_job
job_wrapper.finish(stdout, stderr, exit_code)
File "/Users/mvandenb/src/galaxy/lib/galaxy/jobs/__init__.py", line 1357, in finish
self.sa_session.flush()
File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/orm/scoping.py", line 157, in do
return getattr(self.registry(), name)(*args, **kwargs)
File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 2019, in flush
self._flush(objects)
File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 2137, in _flush
transaction.rollback(_capture_exception=True)
File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/util/langhelpers.py", line 60, in __exit__
compat.reraise(exc_type, exc_value, exc_tb)
File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 2101, in _flush
flush_context.execute()
File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/orm/unitofwork.py", line 373, in execute
rec.execute(self)
File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/orm/unitofwork.py", line 532, in execute
uow
File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/orm/persistence.py", line 170, in save_obj
mapper, table, update)
File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/orm/persistence.py", line 706, in _emit_update_statements
execute(statement, multiparams)
File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 914, in execute
return meth(self, multiparams, params)
File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/elements.py", line 323, in _execute_on_connection
return connection._execute_clauseelement(self, multiparams, params)
File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1010, in _execute_clauseelement
compiled_sql, distilled_params
File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1146, in _execute_context
context)
File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1341, in _handle_dbapi_exception
exc_info
File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 202, in raise_from_cause
reraise(type(exception), exception, tb=exc_tb, cause=cause)
File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1139, in _execute_context
context)
File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 450, in do_execute
cursor.execute(statement, parameters)
OperationalError: (psycopg2.OperationalError) index row size 7208 exceeds maximum 2712 for index "ix_history_dataset_association_metadata"
HINT: Values larger than 1/3 of a buffer page cannot be indexed.
Consider a function index of an MD5 hash of the value, or use full text indexing.
[SQL: 'UPDATE history_dataset_association SET update_time=%(update_time)s, blurb=%(blurb)s, peek=%(peek)s, metadata=%(_metadata)s WHERE history_dataset_association.id = %(history_dataset_association_id)s'] [parameters: {'_metadata': <psycopg2.extensions.Binary object at 0x119ed8990>, 'update_time': datetime.datetime(2017, 11, 19, 13, 47, 30, 598058), 'history_dataset_association_id': 582, 'blurb': '3.5 KB', 'peek': 'Binary bam alignments file'}]
```
Commit: 369485a43ad50a877dc68324c1a2b6ab876030ea
https://github.com/galaxyproject/galaxy/commit/369485a43ad50a877dc68324c1a2…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-08 (Fri, 08 Dec 2017)
Changed paths:
M lib/galaxy/datatypes/binary.py
A test/unit/datatypes/test_bam.py
Log Message:
-----------
Move Bam doctests to unittests
Commit: ae72e5668364f6f72861c21a62a641f9f65636e1
https://github.com/galaxyproject/galaxy/commit/ae72e5668364f6f72861c21a62a6…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-08 (Fri, 08 Dec 2017)
Changed paths:
M lib/galaxy/datatypes/binary.py
M test/unit/datatypes/test_bam.py
Log Message:
-----------
Use subprocess to check if pysam.index succeeds
Checking if pysam.index succeeds tests whether a file is coordinate sorted.
If pysam.index fails to index htslib writes to stderr and this fails set meta
tool. To prevent this we run this in a subprocess and discard stderr.
Commit: 836aea072e84411fb4a24e37fb306b5ec72044c6
https://github.com/galaxyproject/galaxy/commit/836aea072e84411fb4a24e37fb30…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-08 (Fri, 08 Dec 2017)
Changed paths:
A lib/galaxy/datatypes/test/2.shuffled.bam
Log Message:
-----------
Add test file with random order
Commit: bac56d6b27068d3744e84eb9756bc28bf392f718
https://github.com/galaxyproject/galaxy/commit/bac56d6b27068d3744e84eb9756b…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-08 (Fri, 08 Dec 2017)
Changed paths:
M lib/galaxy/datatypes/set_metadata_tool.xml
M tools/data_source/upload.xml
Log Message:
-----------
Drop samtools from metadata and upload tools
We only need samtools for the dataproviders, which shouldn't
be used by these tools.
Commit: df35d089e3ea8c15330afaeedfa24e9c2f0fa7b2
https://github.com/galaxyproject/galaxy/commit/df35d089e3ea8c15330afaeedfa2…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-08 (Fri, 08 Dec 2017)
Changed paths:
A lib/galaxy/datatypes/test/1.vcf
A lib/galaxy/datatypes/test/1.vcf.gz
A lib/galaxy/datatypes/test/2.cram
M test/unit/datatypes/test_bam.py
A test/unit/datatypes/test_bcf.py
A test/unit/datatypes/test_cram.py
A test/unit/datatypes/test_vcf.py
A test/unit/datatypes/util.py
Log Message:
-----------
Add more unittests for CRAM, bcf and vcf
Commit: 3f6a59e85ff8acf2fb0b39670f450a523ea11f38
https://github.com/galaxyproject/galaxy/commit/3f6a59e85ff8acf2fb0b39670f45…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-08 (Fri, 08 Dec 2017)
Changed paths:
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/tabular.py
Log Message:
-----------
Replace bcftools index with pysam.bcftools.index or pysam.tabix_index
Commit: 8e580ec7ac599993ae082732b5c80f2b9bcce493
https://github.com/galaxyproject/galaxy/commit/8e580ec7ac599993ae082732b5c8…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-08 (Fri, 08 Dec 2017)
Changed paths:
M lib/galaxy/datatypes/tabular.py
Log Message:
-----------
Metadata fixes for VcfGz
Commit: 0ac77ad7fd5c6d6660521d69f6010cb61d4947ac
https://github.com/galaxyproject/galaxy/commit/0ac77ad7fd5c6d6660521d69f601…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-08 (Fri, 08 Dec 2017)
Changed paths:
M lib/galaxy/datatypes/tabular.py
M test/unit/datatypes/test_vcf.py
M test/unit/datatypes/util.py
Log Message:
-----------
Fix Vcf index generation and test
Commit: 6ca896ff9b199ac097f408e35e37a3365ff2ec46
https://github.com/galaxyproject/galaxy/commit/6ca896ff9b199ac097f408e35e37…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-08 (Fri, 08 Dec 2017)
Changed paths:
M lib/galaxy/datatypes/tabular.py
M test/unit/datatypes/test_bcf.py
M test/unit/datatypes/test_cram.py
M test/unit/datatypes/test_vcf.py
M test/unit/datatypes/util.py
Log Message:
-----------
Fix index file syntax and fix linting problems
Commit: 9c4a2f70ea6a62f35b3c736730fcc71bddf6dce9
https://github.com/galaxyproject/galaxy/commit/9c4a2f70ea6a62f35b3c736730fc…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-12-08 (Fri, 08 Dec 2017)
Changed paths:
M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py
Log Message:
-----------
Tabix indexing fixes. Upstream used 'index' instead of 'index_filename', and 'force' is now required since we precreate the destination location.
Commit: 2a6e00dd001ea4f27cd7d9a12cddfcf9649da7ef
https://github.com/galaxyproject/galaxy/commit/2a6e00dd001ea4f27cd7d9a12cdd…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-08 (Fri, 08 Dec 2017)
Changed paths:
M test/unit/datatypes/test_cram.py
Log Message:
-----------
one more linting fix
Commit: 07158e03308e026ee013bd6a50708167918c2d27
https://github.com/galaxyproject/galaxy/commit/07158e03308e026ee013bd6a5070…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-08 (Fri, 08 Dec 2017)
Changed paths:
M lib/galaxy/datatypes/tabular.py
Log Message:
-----------
Need force=True in pysam.tabix_index because the index file path exists in the object store
Commit: 64deb4f935ac7969a0e81024297d84d9831a8cfd
https://github.com/galaxyproject/galaxy/commit/64deb4f935ac7969a0e81024297d…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-08 (Fri, 08 Dec 2017)
Changed paths:
M lib/galaxy/datatypes/converters/cram_to_bam.py
Log Message:
-----------
We can use multiple threads when converting cram to bam files
Commit: 90a56aea3f19df6943dfc648474d161e5c8f6d66
https://github.com/galaxyproject/galaxy/commit/90a56aea3f19df6943dfc648474d…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-08 (Fri, 08 Dec 2017)
Changed paths:
M lib/galaxy/datatypes/binary.py
Log Message:
-----------
Use more threads when sorting BAM files and GALAXY_SLOTS is set
Commit: eb636c11361ef8f6cf85c8750f0a37608dcbee1a
https://github.com/galaxyproject/galaxy/commit/eb636c11361ef8f6cf85c8750f0a…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-08 (Fri, 08 Dec 2017)
Changed paths:
A test/unit/datatypes/converters/__init__.py
A test/unit/datatypes/converters/test_interval_to_tabix.py
M test/unit/datatypes/test_bam.py
M test/unit/datatypes/util.py
Log Message:
-----------
Make sure files don't change in-place
Commit: 1195183ea63c3916e1b8e163b2cc0839bd18d8c4
https://github.com/galaxyproject/galaxy/commit/1195183ea63c3916e1b8e163b2cc…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-08 (Fri, 08 Dec 2017)
Changed paths:
M lib/galaxy/visualization/data_providers/genome.py
Log Message:
-----------
Symlink tbi index to work around pysam limitation
Before https://github.com/pysam-developers/pysam/pull/586 is merged and a new release is out
we create a symlink to the tbi file, which is required for creating TabixFile
instances. Since we want to cleanup the symlinks I turned `get_data_file` into a contextmanager.
Along the way I also changed many open()/close() calls to `with` statements.
Commit: 4795e490636e9a9234cb2d61c0a14508472a297d
https://github.com/galaxyproject/galaxy/commit/4795e490636e9a9234cb2d61c0a1…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-08 (Fri, 08 Dec 2017)
Changed paths:
M lib/galaxy/visualization/data_providers/genome.py
Log Message:
-----------
Detect if index symlink hack is necessary
Commit: 46371d1251ed80b740956dc7111708aa93041092
https://github.com/galaxyproject/galaxy/commit/46371d1251ed80b740956dc71117…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-08 (Fri, 08 Dec 2017)
Changed paths:
M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py
M test/unit/datatypes/converters/test_interval_to_tabix.py
M test/unit/datatypes/util.py
Log Message:
-----------
Decompose interval_to_tabix converter script
This renames some variables to make it clearer what files they reflect.
Also adds a very basic test that this works as intended.
Commit: 309b71720e3b5615fac6abd028aa66735fa94eef
https://github.com/galaxyproject/galaxy/commit/309b71720e3b5615fac6abd028aa…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-10 (Sun, 10 Dec 2017)
Changed paths:
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/tabular.py
R lib/galaxy/datatypes/test/1.unsorted.bam
M lib/galaxy/visualization/data_providers/genome.py
M test/unit/datatypes/util.py
Log Message:
-----------
Improvements to datatypes suggested by @nsoranzo
Commit: e198dd75782ce5b2a9619a5283e77a026393e149
https://github.com/galaxyproject/galaxy/commit/e198dd75782ce5b2a9619a5283e7…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2017-12-10 (Sun, 10 Dec 2017)
Changed paths:
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/converters/cram_to_bam.py
M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py
M lib/galaxy/datatypes/set_metadata_tool.xml
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/datatypes/test/1.bam
A lib/galaxy/datatypes/test/1.vcf
A lib/galaxy/datatypes/test/1.vcf.gz
A lib/galaxy/datatypes/test/2.cram
A lib/galaxy/datatypes/test/2.shuffled.bam
M lib/galaxy/visualization/data_providers/genome.py
A test/unit/datatypes/converters/__init__.py
A test/unit/datatypes/converters/test_interval_to_tabix.py
A test/unit/datatypes/test_bam.py
A test/unit/datatypes/test_bcf.py
A test/unit/datatypes/test_cram.py
A test/unit/datatypes/test_vcf.py
A test/unit/datatypes/util.py
M tools/data_source/upload.xml
Log Message:
-----------
Merge pull request #5037 from mvdbeek/samtools_to_pysam
Samtools to pysam
Compare: https://github.com/galaxyproject/galaxy/compare/5ad4f57a63b0...e198dd75782c
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 3dcf9549f6bb4a3d0a5420185c2e7dedb78cc4d5
https://github.com/galaxyproject/galaxy/commit/3dcf9549f6bb4a3d0a5420185c2e…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-12-06 (Wed, 06 Dec 2017)
Changed paths:
A test/integration/resubmission_dynamic_job_conf.xml
M test/integration/resubmission_rules/rules.py
M test/integration/test_job_resubmission.py
Log Message:
-----------
Test resubmit for completely dynamic JobDestination structures.
Commit: 044dcfbb216ad1b2fb46933c6b21597828e42a91
https://github.com/galaxyproject/galaxy/commit/044dcfbb216ad1b2fb46933c6b21…
Author: Eric Rasche <hxr(a)hx42.org>
Date: 2017-12-08 (Fri, 08 Dec 2017)
Changed paths:
A test/integration/resubmission_dynamic_job_conf.xml
M test/integration/resubmission_rules/rules.py
M test/integration/test_job_resubmission.py
Log Message:
-----------
Merge pull request #5139 from jmchilton/resubmit_dynamic
Test resubmit for dynamic JobDestination structures.
Compare: https://github.com/galaxyproject/galaxy/compare/fe0fdeb4ce35...044dcfbb216a
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 3dfbbc7e081cae0c8b95b727e3791915afcc47ec
https://github.com/galaxyproject/galaxy/commit/3dfbbc7e081cae0c8b95b727e379…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-12-07 (Thu, 07 Dec 2017)
Changed paths:
M client/galaxy/scripts/onload.js
M lib/galaxy/webapps/galaxy/controllers/root.py
Log Message:
-----------
Provide Galaxy.config var to indicate whether onload webhooks should kick off; use it. Fixes shed/reports use of them.
Commit: 6f80bed294e99abbc5f880ea7ee0b781e60f7e2a
https://github.com/galaxyproject/galaxy/commit/6f80bed294e99abbc5f880ea7ee0…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-12-07 (Thu, 07 Dec 2017)
Changed paths:
M client/galaxy/scripts/onload.js
Log Message:
-----------
Minor onload.js cleanup.
Commit: 7f1b77ff16c2678327130f3d7282cd900130def8
https://github.com/galaxyproject/galaxy/commit/7f1b77ff16c2678327130f3d7282…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-12-07 (Thu, 07 Dec 2017)
Changed paths:
M client/galaxy/scripts/mvc/tours.js
M client/galaxy/scripts/onload.js
Log Message:
-----------
Move tours kicker out of onload.js; just use the import.
Commit: 8858b5511cdaf282eb5a1e75eda42ce7dde25b42
https://github.com/galaxyproject/galaxy/commit/8858b5511cdaf282eb5a1e75eda4…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-12-07 (Thu, 07 Dec 2017)
Changed paths:
M client/galaxy/scripts/onload.js
Log Message:
-----------
Standardize import naming a little.
Commit: d87e5755c73c59c3dfc4291b76da059fe8a81675
https://github.com/galaxyproject/galaxy/commit/d87e5755c73c59c3dfc4291b76da…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-12-07 (Thu, 07 Dec 2017)
Changed paths:
M client/galaxy/scripts/mvc/tours.js
Log Message:
-----------
Tours import/export cleanup. tour_opts is internal only.
Commit: 3f5aabbf150bd126b8bfa209214874a42399c666
https://github.com/galaxyproject/galaxy/commit/3f5aabbf150bd126b8bfa2092148…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-12-07 (Thu, 07 Dec 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/mvc/tours.js
Log Message:
-----------
Tour launching refactoring.
Commit: a2cf121e34dc4cdb556ffb47337199d1e8a15f1b
https://github.com/galaxyproject/galaxy/commit/a2cf121e34dc4cdb556ffb473371…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-12-07 (Thu, 07 Dec 2017)
Changed paths:
M client/galaxy/scripts/mvc/tours.js
M config/plugins/webhooks/demo/tour_generator/static/script.js
Log Message:
-----------
Reduce tour launch duplication, refine module interface.
Commit: d68dd305d86ae5767b00a0dbd7b2736101500e0a
https://github.com/galaxyproject/galaxy/commit/d68dd305d86ae5767b00a0dbd7b2…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-12-07 (Thu, 07 Dec 2017)
Changed paths:
M client/galaxy/scripts/mvc/tours.js
Log Message:
-----------
Run client-format.
Commit: 03062992cfe037ea6d190c8587de39e66070fc55
https://github.com/galaxyproject/galaxy/commit/03062992cfe037ea6d190c8587de…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-12-07 (Thu, 07 Dec 2017)
Changed paths:
M config/plugins/webhooks/demo/tour_generator/static/script.js
Log Message:
-----------
Actually add /config to the commit...
Commit: afae7c5dbd05bd4e69f4278902b8a0d1e3fde900
https://github.com/galaxyproject/galaxy/commit/afae7c5dbd05bd4e69f4278902b8…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-12-07 (Thu, 07 Dec 2017)
Changed paths:
M client/galaxy/scripts/mvc/tours.js
Log Message:
-----------
Slight reorg in tours.js; internal stuff first, exports at the end.
Commit: 2a7daaaefb605e7567cdafb71d49903e3db3389d
https://github.com/galaxyproject/galaxy/commit/2a7daaaefb605e7567cdafb71d49…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-12-07 (Thu, 07 Dec 2017)
Changed paths:
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/masthead.bundled.js
M static/scripts/bundled/viz.bundled.js
M static/scripts/bundled/workflow.bundled.js
M static/scripts/mvc/tours.js
M static/scripts/onload.js
Log Message:
-----------
Rebuild client.
Commit: fe0fdeb4ce35dc1de9fa2ce26ffffab6276552e0
https://github.com/galaxyproject/galaxy/commit/fe0fdeb4ce35dc1de9fa2ce26fff…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-12-07 (Thu, 07 Dec 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/mvc/tours.js
M client/galaxy/scripts/onload.js
M config/plugins/webhooks/demo/tour_generator/static/script.js
M lib/galaxy/webapps/galaxy/controllers/root.py
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/masthead.bundled.js
M static/scripts/bundled/viz.bundled.js
M static/scripts/bundled/workflow.bundled.js
M static/scripts/mvc/tours.js
M static/scripts/onload.js
Log Message:
-----------
Merge pull request #5116 from dannon/onload_webhook_segmentation
Onload webhook toggles.
Compare: https://github.com/galaxyproject/galaxy/compare/30196f5941df...fe0fdeb4ce35
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 688128feed6147e359969f19775630d11a5281c1
https://github.com/galaxyproject/galaxy/commit/688128feed6147e359969f197756…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-12-06 (Wed, 06 Dec 2017)
Changed paths:
M client/galaxy/scripts/mvc/history/history-list.js
Log Message:
-----------
Minor tweak; use dot notation in history-list.js
Commit: 12da37bb9ab1fbf35b13a36ba808d23f054a738c
https://github.com/galaxyproject/galaxy/commit/12da37bb9ab1fbf35b13a36ba808…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-12-06 (Wed, 06 Dec 2017)
Changed paths:
M client/galaxy/scripts/mvc/grid/grid-view.js
Log Message:
-----------
Grid-view cleanup.
Commit: 35d854b8c13d951692e9f0bc9564031d1dc790e0
https://github.com/galaxyproject/galaxy/commit/35d854b8c13d951692e9f0bc9564…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-12-06 (Wed, 06 Dec 2017)
Changed paths:
M client/galaxy/scripts/mvc/grid/grid-template.js
Log Message:
-----------
Fixes in grid-template. A couple redefined vars, one used out of scope, and some general cleanup.
Commit: f296d1f3334098481f56ac82ea861554cb48ab38
https://github.com/galaxyproject/galaxy/commit/f296d1f3334098481f56ac82ea86…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-12-06 (Wed, 06 Dec 2017)
Changed paths:
M client/galaxy/scripts/mvc/grid/grid-template.js
M client/galaxy/scripts/mvc/grid/grid-view.js
Log Message:
-----------
Minor formatting.
Commit: 53bcd063bce83257546a46918d73074491693324
https://github.com/galaxyproject/galaxy/commit/53bcd063bce83257546a46918d73…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-12-06 (Wed, 06 Dec 2017)
Changed paths:
M client/galaxy/scripts/mvc/history/history-list.js
Log Message:
-----------
Started refactoring more dramatically, but I think we probably want to do a bigger rewrite of this stuff with Vue grid components, Vuex, etc., so this simple subclassing should fix the problems we're seeing for now.
Commit: cb6bbe3a0fbf5fb12507ddc391366b24177724c0
https://github.com/galaxyproject/galaxy/commit/cb6bbe3a0fbf5fb12507ddc39136…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-12-06 (Wed, 06 Dec 2017)
Changed paths:
M client/galaxy/scripts/mvc/history/history-list.js
Log Message:
-----------
Client format.
Commit: 556c17d154e2efe496484b917f25acacaaba7c87
https://github.com/galaxyproject/galaxy/commit/556c17d154e2efe496484b917f25…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-12-06 (Wed, 06 Dec 2017)
Changed paths:
M client/galaxy/scripts/mvc/grid/grid-template.js
Log Message:
-----------
Convert a bunch of iterables to use 'of' syntax instead of 'in'.
Commit: eca993539a2e00895e32316e939e09fdfb79b84d
https://github.com/galaxyproject/galaxy/commit/eca993539a2e00895e32316e939e…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-12-07 (Thu, 07 Dec 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/apps/panels/admin-panel.js
M client/galaxy/scripts/apps/panels/history-panel.js
M client/galaxy/scripts/galaxy.pages.js
M client/galaxy/scripts/layout/generic-nav-view.js
M client/galaxy/scripts/layout/scratchbook.js
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
M client/galaxy/scripts/mvc/dataset/data.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/form/form-repeat.js
M client/galaxy/scripts/mvc/history/history-list.js
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.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/toolshed/repo-status-view.js
M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js
M client/galaxy/scripts/mvc/toolshed/repository-view.js
M client/galaxy/scripts/mvc/toolshed/shed-list-view.js
M client/galaxy/scripts/mvc/toolshed/workflows-view.js
M client/galaxy/scripts/mvc/tours.js
M client/galaxy/scripts/mvc/ui/ui-frames.js
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/mvc/ui/ui-select-genomespace.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-view.js
M client/galaxy/scripts/mvc/user/user-custom-builds.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M client/galaxy/scripts/mvc/workflow/workflow-forms.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M client/galaxy/scripts/mvc/workflow/workflow.js
M client/galaxy/scripts/nls/fr/locale.js
M client/galaxy/scripts/nls/ja/locale.js
M client/galaxy/scripts/nls/locale.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/trackster/tracks.js
M client/galaxy/scripts/viz/visualization.js
A doc/source/admin/cluster.md
M doc/source/admin/index.rst
A doc/source/admin/jobs.md
A doc/source/admin/production.md
A doc/source/admin/scaling.md
A doc/source/admin/special_topics/apache.md
A doc/source/admin/special_topics/ftp.md
M doc/source/admin/special_topics/index.rst
A doc/source/admin/special_topics/job_metrics.md
A doc/source/admin/special_topics/nginx.md
M doc/source/conf.py
M lib/galaxy/model/tool_shed_install/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/parameters/basic.py
A lib/galaxy/tools/repositories.py
A lib/galaxy/util/renamed_temporary_file.py
M lib/galaxy/webapps/galaxy/api/toolshed.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/tool_shed/api/tools.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/webapps/tool_shed/controllers/upload.py
M lib/galaxy/workflow/run.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/metadata/repository_metadata_manager.py
M lib/tool_shed/tools/data_table_manager.py
M lib/tool_shed/tools/tool_validator.py
M lib/tool_shed/util/commit_util.py
M lib/tool_shed/util/tool_util.py
M lib/tool_shed/util/workflow_util.py
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/extended.bundled.js
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/login.bundled.js
M static/scripts/galaxy.pages.js
M static/scripts/layout/generic-nav-view.js
M static/scripts/layout/scratchbook.js
M static/scripts/mvc/collection/list-of-pairs-collection-creator.js
M static/scripts/mvc/dataset/data.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/form/form-repeat.js
M static/scripts/mvc/history/history-list.js
M static/scripts/mvc/library/library-dataset-view.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
M static/scripts/mvc/library/library-librarytoolbar-view.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/toolshed/repo-status-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/workflows-view.js
M static/scripts/mvc/tours.js
M static/scripts/mvc/ui/ui-frames.js
M static/scripts/mvc/ui/ui-select-content.js
M static/scripts/mvc/ui/ui-select-genomespace.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-view.js
M static/scripts/mvc/user/user-custom-builds.js
M static/scripts/mvc/user/user-preferences.js
M static/scripts/mvc/workflow/workflow-forms.js
M static/scripts/mvc/workflow/workflow-view.js
M static/scripts/mvc/workflow/workflow.js
M static/scripts/nls/fr/locale.js
M static/scripts/nls/ja/locale.js
M static/scripts/nls/locale.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/tracks.js
M static/scripts/viz/visualization.js
M test/api/test_workflows.py
A test/shed_functional/test_data/bowtie2_loc_sample/bowtie2_indices.loc.sample
A test/unit/tools/test_tool_validation.py
Log Message:
-----------
Merge remote-tracking branch 'upstream/dev' into fix-history-copy
Commit: a92da1c109c3e5cbc530d17cd148a5877098a676
https://github.com/galaxyproject/galaxy/commit/a92da1c109c3e5cbc530d17cd148…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-12-07 (Thu, 07 Dec 2017)
Changed paths:
M client/galaxy/scripts/mvc/grid/grid-template.js
M client/galaxy/scripts/mvc/grid/grid-view.js
Log Message:
-----------
use encoded ids for popup anchor identifiers instead of sequence; this is more robust
Commit: e08a3d0ffd01a7d58ad7445ef19050e6fbbefae3
https://github.com/galaxyproject/galaxy/commit/e08a3d0ffd01a7d58ad7445ef190…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-12-07 (Thu, 07 Dec 2017)
Changed paths:
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/libs.bundled.js
M static/scripts/mvc/grid/grid-template.js
M static/scripts/mvc/grid/grid-view.js
M static/scripts/mvc/history/history-list.js
Log Message:
-----------
Make client
Commit: 30196f5941df704f6bb0a2a215315db08ffc92bf
https://github.com/galaxyproject/galaxy/commit/30196f5941df704f6bb0a2a21531…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-12-07 (Thu, 07 Dec 2017)
Changed paths:
M client/galaxy/scripts/mvc/grid/grid-template.js
M client/galaxy/scripts/mvc/grid/grid-view.js
M client/galaxy/scripts/mvc/history/history-list.js
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/libs.bundled.js
M static/scripts/mvc/grid/grid-template.js
M static/scripts/mvc/grid/grid-view.js
M static/scripts/mvc/history/history-list.js
Log Message:
-----------
Merge pull request #5144 from dannon/fix-history-copy
Fix history copy
Compare: https://github.com/galaxyproject/galaxy/compare/ef13e2857851...30196f5941df