Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: bd921368413002f6b57e0c6ee229b2ff06e7482d
https://github.com/galaxyproject/galaxy/commit/bd921368413002f6b57e0c6ee229…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-10 (Fri, 10 Aug 2018)
Changed paths:
M lib/galaxy/dependencies/pipfiles/develop/Pipfile
M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt
A pytest.ini
M run_tests.sh
M scripts/plugin_staging.py
M test/docker/base/Dockerfile
M test/docker/base/run_test_wrapper.sh
Log Message:
-----------
Setup pytest python3 API testing
Commit: 1b3f5550548741370e70ff2b25bc404e84d2594e
https://github.com/galaxyproject/galaxy/commit/1b3f5550548741370e70ff2b25bc…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-10 (Fri, 10 Aug 2018)
Changed paths:
M run_tests.sh
Log Message:
-----------
Bump docker image version
Commit: 7342a7ebbc404c275fb0635c1628eecb92b56ff5
https://github.com/galaxyproject/galaxy/commit/7342a7ebbc404c275fb0635c1628…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-10 (Fri, 10 Aug 2018)
Changed paths:
M test/docker/base/Dockerfile
Log Message:
-----------
Avoid prepopulating database twice
Commit: 4e3a981003f9bd0c99a604327e17f37e16f07f33
https://github.com/galaxyproject/galaxy/commit/4e3a981003f9bd0c99a604327e17…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-10 (Fri, 10 Aug 2018)
Changed paths:
M run_tests.sh
Log Message:
-----------
Temporarily run tests with image published in my channel
Commit: 661b3101c635fc376d9c16878fd8b23122ab4950
https://github.com/galaxyproject/galaxy/commit/661b3101c635fc376d9c16878fd8…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-10 (Fri, 10 Aug 2018)
Changed paths:
A .ci/jenkins/api-py3/run_tests.sh
Log Message:
-----------
Add py3 build script for jenkins
Commit: 39e1877ccedd36242bc93696d897f62d5c8f0126
https://github.com/galaxyproject/galaxy/commit/39e1877ccedd36242bc93696d897…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-10 (Fri, 10 Aug 2018)
Changed paths:
M test/docker/base/Dockerfile
Log Message:
-----------
Explicitly create a python 3 virtualenv
Commit: 5b02f5ccedd87a9d529d19a49950df57cc29a8cf
https://github.com/galaxyproject/galaxy/commit/5b02f5ccedd87a9d529d19a49950…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-10 (Fri, 10 Aug 2018)
Changed paths:
M run_tests.sh
Log Message:
-----------
Bump docker image version
Commit: eb1cb57f424d7ab286658699d2313621ed9e1d4e
https://github.com/galaxyproject/galaxy/commit/eb1cb57f424d7ab286658699d231…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-10 (Fri, 10 Aug 2018)
Changed paths:
M test/docker/base/Dockerfile
Log Message:
-----------
Fix up Dockerfile for bdbag installation
Commit: 091ba0f32c75b6046938c95b0521b3271d9c3a72
https://github.com/galaxyproject/galaxy/commit/091ba0f32c75b6046938c95b0521…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-10 (Fri, 10 Aug 2018)
Changed paths:
M run_tests.sh
Log Message:
-----------
Use 18.09.0 tag
Commit: 327ec3d4e9e9d0ab15ae07c2cd0596d6a8abbe90
https://github.com/galaxyproject/galaxy/commit/327ec3d4e9e9d0ab15ae07c2cd05…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-10 (Fri, 10 Aug 2018)
Changed paths:
M .ci/jenkins/api-py3/run_tests.sh
Log Message:
-----------
Do use python 3
Commit: a6b78e7a614aaf3e8254fdea32723f6f06678b5e
https://github.com/galaxyproject/galaxy/commit/a6b78e7a614aaf3e8254fdea3272…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-10 (Fri, 10 Aug 2018)
Changed paths:
M test/base/populators.py
Log Message:
-----------
Decode bytestring returned by source_string
Commit: d659d91d331eb434221940a1cddbd5458d75d8b3
https://github.com/galaxyproject/galaxy/commit/d659d91d331eb434221940a1cddb…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-10 (Fri, 10 Aug 2018)
Changed paths:
M lib/galaxy/web/framework/middleware/batch.py
Log Message:
-----------
Decode body when using json.loads in batch middleware
Commit: 61fa9711dc406dc15b434630aff3c3497f18fd52
https://github.com/galaxyproject/galaxy/commit/61fa9711dc406dc15b434630aff3…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-10 (Fri, 10 Aug 2018)
Changed paths:
M test/base/populators.py
M test/base/rules_test_data.py
Log Message:
-----------
More resource_string fixes
Commit: 03f80f8aef781908f4290f613de9ee78f58b632c
https://github.com/galaxyproject/galaxy/commit/03f80f8aef781908f4290f613de9…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-10 (Fri, 10 Aug 2018)
Changed paths:
M lib/galaxy/model/custom_types.py
Log Message:
-----------
Patch LargeBinary to cast strings to bytestring
I don't fully understand the issue, and we might be accumulating
technical debt here. What I'm seeing without this commit is this
when I run for instance the VisualizationsApiTestCase.test_create
API test.
```
Traceback (most recent call last):
File "/galaxy/lib/galaxy/web/framework/decorators.py", line 283, in decorator
rval = func(self, trans, *args, **kwargs)
File "/galaxy/lib/galaxy/webapps/galaxy/api/visualizations.py", line 55, in index
visualizations = self.get_visualizations_by_user(trans, user)
File "/galaxy/lib/galaxy/web/base/controller.py", line 664, in get_visualizations_by_user
return query.all()
File "/galaxy_venv3/lib/python3.5/site-packages/sqlalchemy/orm/query.py", line 2737, in all
return list(self)
File "/galaxy_venv3/lib/python3.5/site-packages/sqlalchemy/orm/loading.py", line 98, in instances
util.raise_from_cause(err)
File "/galaxy_venv3/lib/python3.5/site-packages/sqlalchemy/util/compat.py", line 203, in raise_from_cause
reraise(type(exception), exception, tb=exc_tb, cause=cause)
File "/galaxy_venv3/lib/python3.5/site-packages/sqlalchemy/util/compat.py", line 187, in reraise
raise value
File "/galaxy_venv3/lib/python3.5/site-packages/sqlalchemy/orm/loading.py", line 79, in instances
rows = [proc(row) for row in fetch]
File "/galaxy_venv3/lib/python3.5/site-packages/sqlalchemy/orm/loading.py", line 79, in <listcomp>
rows = [proc(row) for row in fetch]
File "/galaxy_venv3/lib/python3.5/site-packages/sqlalchemy/orm/loading.py", line 493, in _instance
loaded_instance, populate_existing, populators)
File "/galaxy_venv3/lib/python3.5/site-packages/sqlalchemy/orm/loading.py", line 604, in _populate_full
populator(state, dict_, row)
File "/galaxy_venv3/lib/python3.5/site-packages/sqlalchemy/orm/strategies.py", line 1782, in load_scalar_from_joined_new_row
dict_[key] = _instance(row)
File "/galaxy_venv3/lib/python3.5/site-packages/sqlalchemy/orm/loading.py", line 493, in _instance
loaded_instance, populate_existing, populators)
File "/galaxy_venv3/lib/python3.5/site-packages/sqlalchemy/orm/loading.py", line 593, in _populate_full
dict_[key] = getter(row)
File "/galaxy_venv3/lib/python3.5/site-packages/sqlalchemy/sql/type_api.py", line 1204, in process
return process_value(impl_processor(value), dialect)
File "/galaxy_venv3/lib/python3.5/site-packages/sqlalchemy/sql/sqltypes.py", line 902, in process
value = bytes(value)
TypeError: string argument without an encoding
```
I think LargeBinary isn't meant to store strings the way we do this (we
dump JSON as bytestring), and somehow on python 3 we get unicode strings
back from the database, which blows up here. I suspect this might be
configured on the connection level (see
http://docs.sqlalchemy.org/en/latest/dialects/postgresql.html#unicode),
but not blowing up here seems like a good default.
Commit: 2527038ffce1f7f1b987f9318671bc4fec567ec0
https://github.com/galaxyproject/galaxy/commit/2527038ffce1f7f1b987f9318671…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-10 (Fri, 10 Aug 2018)
Changed paths:
M run_tests.sh
M test/docker/base/run_test_wrapper.sh
Log Message:
-----------
Mount in run_tests script at container runtime
This allows changing variables in the script without rebuilding the
container
Commit: 3d9c0b154ab744345808d36c8af38972524ab2c3
https://github.com/galaxyproject/galaxy/commit/3d9c0b154ab744345808d36c8af3…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-10 (Fri, 10 Aug 2018)
Changed paths:
M test/api/test_workflows.py
M test/base/data/test_workflow_with_runtime_input.ga
M tools/filters/random_lines_two_pass.py
M tools/filters/randomlines.xml
Log Message:
-----------
Make random_lines1 consistent on py2 and py3 (again)
Turns out integers are used as is in `random.seed()`, but strings are
hashed (in the version 1 protocol), and the hashing isn't stable. So
instead we hack around this by using `ord()` on each character and
concatenating the digits. Yucky, but probably better than using numpy
and putting this tool on the list of tools that inherit galaxy's
environment (or adding a requirement tag and resolving with conda ...).
Commit: b2fed75059767aece3c0a75c630c9f30e31f0078
https://github.com/galaxyproject/galaxy/commit/b2fed75059767aece3c0a75c630c…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-11 (Sat, 11 Aug 2018)
Changed paths:
M run_tests.sh
Log Message:
-----------
Flip testing image back to galaxy namespace
Commit: ae3d41924ac844d22c454fbd01d49a9ac3ee3b74
https://github.com/galaxyproject/galaxy/commit/ae3d41924ac844d22c454fbd01d4…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-14 (Tue, 14 Aug 2018)
Changed paths:
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
M lib/tool_shed/util/encoding_util.py
Log Message:
-----------
py3: Fix repository installation
I'm very surprised this actually worked. I suppose we called my system's
`hg` ?!
Commit: 4d5ea3d724cf1a7fac1c6a2f9eeac133c47c2a06
https://github.com/galaxyproject/galaxy/commit/4d5ea3d724cf1a7fac1c6a2f9eea…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-14 (Tue, 14 Aug 2018)
Changed paths:
A .ci/jenkins/integration-py3/run_tests.sh
M run_tests.sh
Log Message:
-----------
Start testing integration tests on python 3
Commit: b47c246e0c688be2f9474c36e1d12b786deb2ac0
https://github.com/galaxyproject/galaxy/commit/b47c246e0c688be2f9474c36e1d1…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-14 (Tue, 14 Aug 2018)
Changed paths:
M lib/galaxy/datatypes/data.py
Log Message:
-----------
Fix showing, creating and downloading HTML files
Commit: 37b5120197d8a8bf39b52585408998252e601d82
https://github.com/galaxyproject/galaxy/commit/37b5120197d8a8bf39b525854089…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-14 (Tue, 14 Aug 2018)
Changed paths:
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/util/renamed_temporary_file.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/galaxy_install/tools/data_manager.py
M test/integration/test_data_manager_table_reload.py
M test/integration/tool_sheds_conf.xml
M test/integration/uses_shed.py
Log Message:
-----------
py3: fix installing and running data managers
Commit: 167e0e912907821943bd93eab2c0986a3d31136c
https://github.com/galaxyproject/galaxy/commit/167e0e912907821943bd93eab2c0…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-14 (Tue, 14 Aug 2018)
Changed paths:
M lib/galaxy/tools/verify/interactor.py
Log Message:
-----------
Fix dictify_outputs
The hack of setting `.__len` doesn't work on python 3.
Subclassing OrderedDict and providing list-like access
using integers should have the same effect.
Commit: 14b1e1acd4eedce4a86b96094a496cbb76dd4239
https://github.com/galaxyproject/galaxy/commit/14b1e1acd4eedce4a86b96094a49…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-14 (Tue, 14 Aug 2018)
Changed paths:
M lib/galaxy/util/none_like.py
Log Message:
-----------
py3: Fix optional dataset bool value
This fixes cheetah like `#if $input.dataset: ... #end if`.
Which is a little weird, but fastqc uses this pattern.
Commit: 344f68ea6d9c48a2a6f9dd56dd434633167d8f8e
https://github.com/galaxyproject/galaxy/commit/344f68ea6d9c48a2a6f9dd56dd43…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-14 (Tue, 14 Aug 2018)
Changed paths:
M lib/galaxy/web/stack/__init__.py
M lib/galaxy/web/stack/transport.py
M scripts/galaxy-main
Log Message:
-----------
py3: Fix uwsgi mule startup
Commit: 0b30a94bbe34fb40eaf6fc97c816fcbe0586d078
https://github.com/galaxyproject/galaxy/commit/0b30a94bbe34fb40eaf6fc97c816…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-14 (Tue, 14 Aug 2018)
Changed paths:
M lib/galaxy/webapps/galaxy/api/uploads.py
Log Message:
-----------
py3: Fix new direct API-backed uploads
Commit: dc4a4b0eb5c9a07d9048e893b9fa48b43eb58c09
https://github.com/galaxyproject/galaxy/commit/dc4a4b0eb5c9a07d9048e893b9fa…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-14 (Tue, 14 Aug 2018)
Changed paths:
M scripts/secret_decoder_ring.py
Log Message:
-----------
py3: fix secret decoder script
Commit: 293ce5a4720c7fc2ec26d44985750188e3762e6b
https://github.com/galaxyproject/galaxy/commit/293ce5a4720c7fc2ec26d4498575…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-14 (Tue, 14 Aug 2018)
Changed paths:
M test/base/driver_util.py
M test/integration/test_mules_as_job_handlers.py
Log Message:
-----------
py3: Fix mules test cases
We're now just copying the current python path. Also the handler names
have actually changed, I think this hasn't been updated after a late
change (it is now as it should be, based on the documentation).
Commit: cfce2468451e52c72bf7f0544c1bc7e209cc9224
https://github.com/galaxyproject/galaxy/commit/cfce2468451e52c72bf7f0544c1b…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-14 (Tue, 14 Aug 2018)
Changed paths:
M test/integration/test_scripts.py
Log Message:
-----------
Fix GRT export test
Commit: 620375c9d045e0085e2b260a97b3fdd5912fb45a
https://github.com/galaxyproject/galaxy/commit/620375c9d045e0085e2b260a97b3…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-14 (Tue, 14 Aug 2018)
Changed paths:
M test/integration/test_mules_as_job_handlers.py
Log Message:
-----------
Do test mules on Jenkins, I don't see why this shouldn't work
Commit: 6e7a66cdc0b9f467341af77d4d2fd5eadc9f409d
https://github.com/galaxyproject/galaxy/commit/6e7a66cdc0b9f467341af77d4d2f…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-14 (Tue, 14 Aug 2018)
Changed paths:
M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
Log Message:
-----------
Fix repository dependency manager
Commit: dd7e4c601a3f31ce9c4fa06afc8234a39f0a5804
https://github.com/galaxyproject/galaxy/commit/dd7e4c601a3f31ce9c4fa06afc82…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-14 (Tue, 14 Aug 2018)
Changed paths:
M test/base/driver_util.py
Log Message:
-----------
Deal with docker localhost quirks
Commit: fc06e78743086d3078d18e3928512cf62915bfb9
https://github.com/galaxyproject/galaxy/commit/fc06e78743086d3078d18e392851…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-14 (Tue, 14 Aug 2018)
Changed paths:
M lib/galaxy/datatypes/sequence.py
Log Message:
-----------
py3: Fix Maf datatype
Commit: dfba132d11b0f6f6d15cb9fc8c79e0645640489e
https://github.com/galaxyproject/galaxy/commit/dfba132d11b0f6f6d15cb9fc8c79…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-14 (Tue, 14 Aug 2018)
Changed paths:
M lib/galaxy/jobs/output_checker.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/local.py
M lib/galaxy/util/__init__.py
Log Message:
-----------
Fix stdout/stderr exception handling
Commit: 853b2d03abcfe563b12c817db84d871fbc291725
https://github.com/galaxyproject/galaxy/commit/853b2d03abcfe563b12c817db84d…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-08-14 (Tue, 14 Aug 2018)
Changed paths:
A .ci/jenkins/api-py3/run_tests.sh
A .ci/jenkins/integration-py3/run_tests.sh
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/dependencies/pipfiles/develop/Pipfile
M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt
M lib/galaxy/jobs/output_checker.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/local.py
M lib/galaxy/model/custom_types.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/verify/interactor.py
M lib/galaxy/util/__init__.py
M lib/galaxy/util/none_like.py
M lib/galaxy/util/renamed_temporary_file.py
M lib/galaxy/web/framework/middleware/batch.py
M lib/galaxy/web/stack/__init__.py
M lib/galaxy/web/stack/transport.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/api/uploads.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
M lib/tool_shed/galaxy_install/tools/data_manager.py
M lib/tool_shed/util/encoding_util.py
A pytest.ini
M run_tests.sh
M scripts/galaxy-main
M scripts/plugin_staging.py
M scripts/secret_decoder_ring.py
M test/api/test_workflows.py
M test/base/data/test_workflow_with_runtime_input.ga
M test/base/driver_util.py
M test/base/populators.py
M test/base/rules_test_data.py
M test/docker/base/Dockerfile
M test/docker/base/run_test_wrapper.sh
M test/integration/test_data_manager_table_reload.py
M test/integration/test_mules_as_job_handlers.py
M test/integration/test_scripts.py
M test/integration/tool_sheds_conf.xml
M test/integration/uses_shed.py
M tools/filters/random_lines_two_pass.py
M tools/filters/randomlines.xml
Log Message:
-----------
Merge pull request #6565 from mvdbeek/setup_py3_test_job
Setup py3 test job
Compare: https://github.com/galaxyproject/galaxy/compare/164a7d7f04be...853b2d03abcf
**NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 00e8d4ee76c65652e6a0b208f44d957c79db40b1
https://github.com/galaxyproject/galaxy/commit/00e8d4ee76c65652e6a0b208f44d…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-13 (Mon, 13 Aug 2018)
Changed paths:
M tools/stats/filtering.xml
Log Message:
-----------
Quote Filter1 input and output
Commit: 819ee07af36d10734b32474fa832ce9e09e1b376
https://github.com/galaxyproject/galaxy/commit/819ee07af36d10734b32474fa832…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-13 (Mon, 13 Aug 2018)
Changed paths:
M lib/galaxy/model/__init__.py
Log Message:
-----------
Respect unavilable peek when serializing HDA
Also call display_peek() just once.
That fixes the following exception that occurs when running the Filter1
tool through the API:
```
galaxy.datatypes.tabular ERROR 2018-08-12 22:53:42,939 make_html_peek_rows failed on HDA 64
Traceback (most recent call last):
File "/Users/mvandenb/src/galaxy/lib/galaxy/datatypes/tabular.py", line 186, in make_html_peek_rows
dataset.set_peek()
File "/Users/mvandenb/src/galaxy/lib/galaxy/model/__init__.py", line 2264, in set_peek
return self.datatype.set_peek(self)
File "/Users/mvandenb/src/galaxy/lib/galaxy/datatypes/tabular.py", line 57, in set_peek
super(TabularData, self).set_peek(dataset, line_count=line_count, WIDTH=WIDTH, skipchars=skipchars, line_wrap=False)
File "/Users/mvandenb/src/galaxy/lib/galaxy/datatypes/data.py", line 813, in set_peek
dataset.peek = get_file_peek(dataset.file_name, WIDTH=WIDTH, skipchars=skipchars, line_wrap=line_wrap)
File "/Users/mvandenb/src/galaxy/lib/galaxy/datatypes/data.py", line 1029, in get_file_peek
with compression_utils.get_fileobj(file_name, "U") as temp:
File "/Users/mvandenb/src/galaxy/lib/galaxy/util/compression_utils.py", line 29, in get_fileobj
return get_fileobj_raw(filename, mode, compressed_formats)[1]
File "/Users/mvandenb/src/galaxy/lib/galaxy/util/compression_utils.py", line 58, in get_fileobj_raw
return compressed_format, io.open(filename, mode, encoding='utf-8')
FileNotFoundError: [Errno 2] No such file or directory: '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpan_4qaow/tmpfzus9jhv/tmplqjtbp5c/database/files/000/dataset_40.dat'
```
This is because we serialize the HDA just after the job has been
created, meaning the file may not exist yet.
Commit: f4343d876f13e55e92ca228582b4430dcd01e4aa
https://github.com/galaxyproject/galaxy/commit/f4343d876f13e55e92ca228582b4…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-13 (Mon, 13 Aug 2018)
Changed paths:
M lib/galaxy/jobs/__init__.py
Log Message:
-----------
Clarify set_peek setting when finishing job
Commit: 3d0763f71c795549e6c133f2734cf7ae5337c296
https://github.com/galaxyproject/galaxy/commit/3d0763f71c795549e6c133f2734c…
Author: Dannon <dannon.baker(a)gmail.com>
Date: 2018-08-13 (Mon, 13 Aug 2018)
Changed paths:
M lib/galaxy/jobs/__init__.py
M lib/galaxy/model/__init__.py
M tools/stats/filtering.xml
Log Message:
-----------
Merge pull request #6594 from mvdbeek/respect_unavailable_display_peek
Respect unavailable display peek
Compare: https://github.com/galaxyproject/galaxy/compare/e853762fdbb2...3d0763f71c79
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