Branch: refs/heads/dev
Home:
https://github.com/galaxyproject/galaxy
Commit: 0d68d4cf389f5864c6fc5676012c9301fe850daa
https://github.com/galaxyproject/galaxy/commit/0d68d4cf389f5864c6fc567601...
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-31 (Sun, 31 Dec 2017)
Changed paths:
M lib/galaxy/jobs/handler.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/mapping.py
A lib/galaxy/model/migrate/versions/0136_add_copied_from_job_id_column.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/execute.py
M lib/galaxy/workflow/modules.py
Log Message:
-----------
WIP: skip job execution if equivalent job exists
Commit: 34b99bd8aaa0a04df5d6b81a2a9abb92d8244abb
https://github.com/galaxyproject/galaxy/commit/34b99bd8aaa0a04df5d6b81a2a...
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-31 (Sun, 31 Dec 2017)
Changed paths:
M lib/galaxy/managers/jobs.py
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Improve detection of equivalent jobs in workflows and collection-context
Commit: cd32afe21e870898b7c8191628a2edcbee819527
https://github.com/galaxyproject/galaxy/commit/cd32afe21e870898b7c8191628...
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-31 (Sun, 31 Dec 2017)
Changed paths:
M lib/galaxy/jobs/handler.py
Log Message:
-----------
Skip creation of JobWrapper for copied jobs, copy metrics and dependencies
Commit: 7defcddd19dfcc259ef6c0d83a7375f2363dc3f3
https://github.com/galaxyproject/galaxy/commit/7defcddd19dfcc259ef6c0d83a...
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-31 (Sun, 31 Dec 2017)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Work around Exception("FileToolParameter cannot be persisted"
Commit: e9a9b2a5c12921c4d9a80b02730f5bbe0f206598
https://github.com/galaxyproject/galaxy/commit/e9a9b2a5c12921c4d9a80b0273...
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-31 (Sun, 31 Dec 2017)
Changed paths:
M lib/galaxy/managers/jobs.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/webapps/galaxy/api/jobs.py
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Also search jobs explicitly by version
Commit: d3a93af1221b4bb747f7c6e1bf54b894ac8a389e
https://github.com/galaxyproject/galaxy/commit/d3a93af1221b4bb747f7c6e1bf...
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-31 (Sun, 31 Dec 2017)
Changed paths:
M lib/galaxy/managers/jobs.py
Log Message:
-----------
Cast tool_version to string and pre-filter jobs with wildcards
Commit: fc92adc1cc7db1fd6d94cb09d5c30be0e892a6ee
https://github.com/galaxyproject/galaxy/commit/fc92adc1cc7db1fd6d94cb09d5...
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-31 (Sun, 31 Dec 2017)
Changed paths:
M lib/galaxy/managers/jobs.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/webapps/galaxy/api/jobs.py
M lib/galaxy/workflow/modules.py
M test/api/test_jobs.py
M test/base/api.py
M test/base/interactor.py
Log Message:
-----------
Take into account HDA name, metadata, element_identifier and datatype
Commit: 009daeff81d60202ac6695304e40599dd1d4085c
https://github.com/galaxyproject/galaxy/commit/009daeff81d60202ac6695304e...
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-31 (Sun, 31 Dec 2017)
Changed paths:
M lib/galaxy/managers/jobs.py
M test/api/test_jobs.py
Log Message:
-----------
Fix the wildcard search
Commit: e75daa1ddd6a5662bf9d837ecc867655c485a8cb
https://github.com/galaxyproject/galaxy/commit/e75daa1ddd6a5662bf9d837ecc...
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-31 (Sun, 31 Dec 2017)
Changed paths:
M lib/galaxy/managers/jobs.py
M test/api/test_jobs.py
Log Message:
-----------
Skip test that deletes the jobs input dataset
This does not work at the moment, since we need to verify a jobs' input name,
dataset and metadata, for which we don't have an explicit trail. The only trace
is via the update_time (i.e if a input dataset hasn't been updated since the
job was created we know these were the actual parameters in use during the
execution of this job).
Commit: 0df2e18058ecf66322f3a15d42d8735ace37a17b
https://github.com/galaxyproject/galaxy/commit/0df2e18058ecf66322f3a15d42...
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-31 (Sun, 31 Dec 2017)
Changed paths:
M lib/galaxy/model/base.py
Log Message:
-----------
Add mechanism for versioning database objects
Commit: 409fa016b9651485d7648437b1f0b8766b4b0c90
https://github.com/galaxyproject/galaxy/commit/409fa016b9651485d7648437b1...
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-31 (Sun, 31 Dec 2017)
Changed paths:
M lib/galaxy/managers/jobs.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/base.py
M lib/galaxy/model/mapping.py
Log Message:
-----------
Add HistoryDatasetAssociationHistory to track mutations of HDAs
Commit: c88d8826d0960af5067830f121d3a54622386aba
https://github.com/galaxyproject/galaxy/commit/c88d8826d0960af5067830f121...
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-31 (Sun, 31 Dec 2017)
Changed paths:
M lib/galaxy/managers/jobs.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/mapping.py
Log Message:
-----------
Compare metadata through _metadata for HDAH objects
HistoryDatasetsAssoicationHistory objects don't have the full blown metadata
objects, instead we compare the raw JSON dumped into the database.
Commit: be09b35ff2da39c97836fe5e61fc0fbefd45cb06
https://github.com/galaxyproject/galaxy/commit/be09b35ff2da39c97836fe5e61...
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-31 (Sun, 31 Dec 2017)
Changed paths:
M lib/galaxy/model/__init__.py
Log Message:
-----------
Avoid storing dbkey as list in metadata
Commit: 91696783b185ca119499b836623a8954ce3a5d46
https://github.com/galaxyproject/galaxy/commit/91696783b185ca119499b83662...
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-31 (Sun, 31 Dec 2017)
Changed paths:
M test/api/test_jobs.py
Log Message:
-----------
Uncomment test that relies on HDAHistory
Commit: 255e3989b57dd90774d5219a97083cca92ed8678
https://github.com/galaxyproject/galaxy/commit/255e3989b57dd90774d5219a97...
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-31 (Sun, 31 Dec 2017)
Changed paths:
A lib/galaxy/model/migrate/versions/0137_add_hda_version.py
A
lib/galaxy/model/migrate/versions/0138_add_history_dataset_association_history_table.py
A
lib/galaxy/model/migrate/versions/0139_add_dataset_version_to_job_to_input_dataset_association_table.py
Log Message:
-----------
Add migration scripts
Commit: 71da068e260ac6584ca9f4a77557a438e0c0f6fb
https://github.com/galaxyproject/galaxy/commit/71da068e260ac6584ca9f4a775...
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-31 (Sun, 31 Dec 2017)
Changed paths:
M lib/galaxy/model/__init__.py
Log Message:
-----------
Require state to be OK in order to track version in database
Commit: e6c374a05a9114c4004de0c54a0f70b6f0b27405
https://github.com/galaxyproject/galaxy/commit/e6c374a05a9114c4004de0c54a...
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-31 (Sun, 31 Dec 2017)
Changed paths:
M lib/galaxy/model/__init__.py
Log Message:
-----------
Fix JobToInputDatasetAssociation recording for tasks (dataset is None)
Commit: 6c79785f6f87632d07aafa275e2d3877ddc5895c
https://github.com/galaxyproject/galaxy/commit/6c79785f6f87632d07aafa275e...
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-31 (Sun, 31 Dec 2017)
Changed paths:
M lib/galaxy/managers/jobs.py
Log Message:
-----------
Avoid recursion in chained sqlalchemy filter statements
See
https://stackoverflow.com/questions/41625847/maximum-recursion-depth-exce...
for details.
Commit: 40884fb94f41e6934483a4deee7d05b1e65c049c
https://github.com/galaxyproject/galaxy/commit/40884fb94f41e6934483a4deee...
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-31 (Sun, 31 Dec 2017)
Changed paths:
M lib/galaxy/managers/jobs.py
Log Message:
-----------
Reduce to single, non-chained query statement
Commit: fac13deb6b979327664647f0e0f10828ae4adc15
https://github.com/galaxyproject/galaxy/commit/fac13deb6b979327664647f0e0...
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-31 (Sun, 31 Dec 2017)
Changed paths:
M lib/galaxy/managers/jobs.py
Log Message:
-----------
Join for used data input ids
This allows us to fetch all used job inputs with a single query as opposed to
one query per input dataset.
Commit: 70f0ec7930e256f0e93f91db07e03cea5e64f03c
https://github.com/galaxyproject/galaxy/commit/70f0ec7930e256f0e93f91db07...
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-31 (Sun, 31 Dec 2017)
Changed paths:
M lib/galaxy/managers/jobs.py
Log Message:
-----------
Fix search for tools without data inputs
Commit: de75540182833732ddcd7e3a8981eb2c6beb80bb
https://github.com/galaxyproject/galaxy/commit/de75540182833732ddcd7e3a89...
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-31 (Sun, 31 Dec 2017)
Changed paths:
M lib/galaxy/managers/jobs.py
Log Message:
-----------
Skip second JobParameter filter if no input datasets have been used
Commit: 732543ea3bbf49ef0a904d63b7fa61ae4efad0ea
https://github.com/galaxyproject/galaxy/commit/732543ea3bbf49ef0a904d63b7...
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-31 (Sun, 31 Dec 2017)
Changed paths:
M lib/galaxy/managers/jobs.py
M lib/galaxy/model/mapping.py
Log Message:
-----------
Move check for deleted output datasets to Job relationship properties
Commit: 0e02cf3aac9636d97f6ce0086da048b909215617
https://github.com/galaxyproject/galaxy/commit/0e02cf3aac9636d97f6ce0086d...
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-31 (Sun, 31 Dec 2017)
Changed paths:
M lib/galaxy/managers/jobs.py
Log Message:
-----------
Remove unused current_jobs_data_ids
Commit: d53918eb2d6aad1865416432710b157d967badad
https://github.com/galaxyproject/galaxy/commit/d53918eb2d6aad186541643271...
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-31 (Sun, 31 Dec 2017)
Changed paths:
M lib/galaxy/managers/jobs.py
Log Message:
-----------
Use joinedload for job parameters which we iterate over
Commit: 75ddb8ef62ca857f3a7f0707a6d7cd749ec32fa7
https://github.com/galaxyproject/galaxy/commit/75ddb8ef62ca857f3a7f0707a6...
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-31 (Sun, 31 Dec 2017)
Changed paths:
M lib/galaxy/managers/jobs.py
Log Message:
-----------
Revert "Use joinedload for job parameters which we iterate over"
This reverts commit a72dcca6ca3d27bf5ada4d98fde784408314e331.
Commit: 528a05e00218ecba0c8180268f7f551cf09768e5
https://github.com/galaxyproject/galaxy/commit/528a05e00218ecba0c8180268f...
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-31 (Sun, 31 Dec 2017)
Changed paths:
A lib/galaxy/dependencies/dev-requirements.txt
R lib/galaxy/dependencies/dev-requirements.txt
M lib/galaxy/managers/jobs.py
Log Message:
-----------
Debug: add profiling to figure out why search is slow sometimes
Commit: b5a4822edbf67eb02213a4f2a5ab762feef1a391
https://github.com/galaxyproject/galaxy/commit/b5a4822edbf67eb02213a4f2a5...
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-31 (Sun, 31 Dec 2017)
Changed paths:
M lib/galaxy/managers/jobs.py
Log Message:
-----------
Optimize query
Commit: 77b9610b59eaa294cfc0a5521e0db50b69caf07e
https://github.com/galaxyproject/galaxy/commit/77b9610b59eaa294cfc0a5521e...
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-31 (Sun, 31 Dec 2017)
Changed paths:
M lib/galaxy/tools/execute.py
Log Message:
-----------
Fix passing correct completed job during threaded job submission
Commit: c8a5ea2996a6af85d61e2db054c16a3826efa89b
https://github.com/galaxyproject/galaxy/commit/c8a5ea2996a6af85d61e2db054...
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-31 (Sun, 31 Dec 2017)
Changed paths:
A lib/galaxy/dependencies/dev-requirements.txt
R lib/galaxy/dependencies/dev-requirements.txt
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Fix bad rebase
Commit: 3178cf13a1789ac18c238d7f180110dc9fabb0f3
https://github.com/galaxyproject/galaxy/commit/3178cf13a1789ac18c238d7f18...
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-31 (Sun, 31 Dec 2017)
Changed paths:
M lib/galaxy/model/mapping.py
Log Message:
-----------
Fix import order
Commit: fd0728abb9276c6e89b9e097cd10ce2d621ce8fa
https://github.com/galaxyproject/galaxy/commit/fd0728abb9276c6e89b9e097cd...
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-31 (Sun, 31 Dec 2017)
Changed paths:
R lib/galaxy/model/migrate/versions/0136_add_copied_from_job_id_column.py
A lib/galaxy/model/migrate/versions/0137_add_copied_from_job_id_column.py
R lib/galaxy/model/migrate/versions/0137_add_hda_version.py
A lib/galaxy/model/migrate/versions/0138_add_hda_version.py
R
lib/galaxy/model/migrate/versions/0138_add_history_dataset_association_history_table.py
R
lib/galaxy/model/migrate/versions/0139_add_dataset_version_to_job_to_input_dataset_association_table.py
A
lib/galaxy/model/migrate/versions/0139_add_history_dataset_association_history_table.py
A
lib/galaxy/model/migrate/versions/0140_add_dataset_version_to_job_to_input_dataset_association_table.py
Log Message:
-----------
Fix migrations
Commit: f6413bfaa5e3d2d1a48355f79380cde0dec1be42
https://github.com/galaxyproject/galaxy/commit/f6413bfaa5e3d2d1a48355f793...
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-31 (Sun, 31 Dec 2017)
Changed paths:
M
lib/galaxy/model/migrate/versions/0139_add_history_dataset_association_history_table.py
Log Message:
-----------
Linting fix (I201)
Commit: 74dd664712909adf5857f34fc6c0b1fe8c866059
https://github.com/galaxyproject/galaxy/commit/74dd664712909adf5857f34fc6...
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-31 (Sun, 31 Dec 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/run.py
M lib/galaxy/workflow/run_request.py
Log Message:
-----------
Make skipping job configurable
Commit: 4b6e403622f1a50a7b31d5d1821c5e61032b111b
https://github.com/galaxyproject/galaxy/commit/4b6e403622f1a50a7b31d5d182...
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-31 (Sun, 31 Dec 2017)
Changed paths:
M lib/galaxy/managers/jobs.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/workflow/modules.py
M test/api/test_tools.py
Log Message:
-----------
Add use_cached_job param to tools and workflow API
Also includes a simple test that runs cat1 three times,
the second time with `use_cached_job=False` (the default),
and the third time with `use_cached_job=True` and verifies
that the second output is different from the third, and that the
first and third output are identical.
Commit: 0dcf9d7fd6504e449b7b222ab78f3b9e8a143043
https://github.com/galaxyproject/galaxy/commit/0dcf9d7fd6504e449b7b222ab7...
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-31 (Sun, 31 Dec 2017)
Changed paths:
M test/api/test_tools.py
Log Message:
-----------
Refine cached job tool test to make less asumptions
Commit: 1c4476a6af6f6042ef8daf7ca3c193bd58f8c96c
https://github.com/galaxyproject/galaxy/commit/1c4476a6af6f6042ef8daf7ca3...
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-31 (Sun, 31 Dec 2017)
Changed paths:
M lib/galaxy/managers/jobs.py
M lib/galaxy/workflow/run.py
M lib/galaxy/workflow/run_request.py
M test/api/test_tools.py
M test/api/test_workflows.py
M test/base/data/test_workflow_1.ga
Log Message:
-----------
Add a test for skipping jobs in workflow context
This is using the simplest of workflows. I had to
remove the chromInfo part from the workflow, because the
path referenced would be changed dynamically and so the
job search wouldn't recognize this as being equivalent.
Commit: c6468f0677002dad4875b2b7cbeb67f018ef5be3
https://github.com/galaxyproject/galaxy/commit/c6468f0677002dad4875b2b7cb...
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-31 (Sun, 31 Dec 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M lib/galaxy/workflow/run_request.py
Log Message:
-----------
Add conditional for use_cached_job to workflow run form
Surprisingly the API endpoint that is used by the UI is a little different from
the `create` endpoint the tests are testing, so this also adds a change in how
the `use_cached_job` is passed along.
Commit: 509b0ca7a1e6a5f53b76b2995551d7705d1376d1
https://github.com/galaxyproject/galaxy/commit/509b0ca7a1e6a5f53b76b29955...
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-31 (Sun, 31 Dec 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form.js
M lib/galaxy/webapps/galaxy/api/tools.py
Log Message:
-----------
Add the possibility to send reuse jobs via the tool form
Commit: 9d38219d6531a4d956145a02d657c6c0ce22412e
https://github.com/galaxyproject/galaxy/commit/9d38219d6531a4d956145a02d6...
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-31 (Sun, 31 Dec 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/run.py
M test/api/test_workflows.py
Log Message:
-----------
Pass use_cached_jobs on to subworkflow invoker
Commit: 81c733d940eb716d48057446faf21c5f99065019
https://github.com/galaxyproject/galaxy/commit/81c733d940eb716d48057446fa...
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-31 (Sun, 31 Dec 2017)
Changed paths:
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/actions/__init__.py
Log Message:
-----------
Revert the dbkey metadata hack; the real fix is to copy the metadata correctly
Commit: 78c37d32d9c0cdbb65b75960c820412185bd129f
https://github.com/galaxyproject/galaxy/commit/78c37d32d9c0cdbb65b75960c8...
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-31 (Sun, 31 Dec 2017)
Changed paths:
M test/api/test_workflows.py
Log Message:
-----------
Assert that histories contains same dataset ids
Commit: 43224af880f2a825d5fd2f655a3f9af11f04f689
https://github.com/galaxyproject/galaxy/commit/43224af880f2a825d5fd2f655a...
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-31 (Sun, 31 Dec 2017)
Changed paths:
M lib/galaxy/model/migrate/versions/0137_add_copied_from_job_id_column.py
M lib/galaxy/model/migrate/versions/0138_add_hda_version.py
M
lib/galaxy/model/migrate/versions/0139_add_history_dataset_association_history_table.py
Log Message:
-----------
Fix migration comments
Commit: c327594ed76fab4d235e547053ebc3ed5572b28a
https://github.com/galaxyproject/galaxy/commit/c327594ed76fab4d235e547053...
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-31 (Sun, 31 Dec 2017)
Changed paths:
M test/api/test_workflows.py
Log Message:
-----------
Simplify use_cached_jobs workflow tests
Commit: 81c3b8cc4d6439aa7d44b1d4cece284c0bb6b813
https://github.com/galaxyproject/galaxy/commit/81c3b8cc4d6439aa7d44b1d4ce...
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-31 (Sun, 31 Dec 2017)
Changed paths:
M test/api/test_workflows.py
Log Message:
-----------
Include more information in assertion
Commit: e973403ae58154de1c65f24dc822eff401e9febb
https://github.com/galaxyproject/galaxy/commit/e973403ae58154de1c65f24dc8...
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-31 (Sun, 31 Dec 2017)
Changed paths:
M lib/galaxy/model/__init__.py
M lib/galaxy/webapps/galaxy/api/users.py
Log Message:
-----------
Simplify retrieval of extra_user_preferences
Commit: 3f3476495815e6fceaa555c5ca0bbb997515447d
https://github.com/galaxyproject/galaxy/commit/3f3476495815e6fceaa555c5ca...
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-31 (Sun, 31 Dec 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/tool/tool-form.js
Log Message:
-----------
Only show use_cached_job options if user has activated this feature in the user
preferences
Commit: 58b8aa986bf3af32de71d6cf17f1f2c60adff17f
https://github.com/galaxyproject/galaxy/commit/58b8aa986bf3af32de71d6cf17...
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-31 (Sun, 31 Dec 2017)
Changed paths:
M config/user_preferences_extra_conf.yml.sample
Log Message:
-----------
Add template to user_preferences_extra_conf.yml.sample for activating job reuse feature
Commit: 47c2f3c0d4e42c27c46ae7f7016900f60ea5c8eb
https://github.com/galaxyproject/galaxy/commit/47c2f3c0d4e42c27c46ae7f701...
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-31 (Sun, 31 Dec 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/tool/tool-form.js
Log Message:
-----------
Don't assume extra_preferences exists
Commit: 3d45cce423de3e4b323b54fb3fd22e354a52dad7
https://github.com/galaxyproject/galaxy/commit/3d45cce423de3e4b323b54fb3f...
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-31 (Sun, 31 Dec 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
Log Message:
-----------
Fix undefined variable
Commit: 655af3026b154e02fb6b25f320b9828b64451deb
https://github.com/galaxyproject/galaxy/commit/655af3026b154e02fb6b25f320...
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-31 (Sun, 31 Dec 2017)
Changed paths:
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/libs.bundled.js
A static/scripts/libs/vue.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/tool/tool-form.js
Log Message:
-----------
Build client
Commit: 32624dfeeeeffcc09b1afea55a4b537d9a15e00d
https://github.com/galaxyproject/galaxy/commit/32624dfeeeeffcc09b1afea55a...
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-01-02 (Tue, 02 Jan 2018)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M config/user_preferences_extra_conf.yml.sample
M lib/galaxy/jobs/handler.py
M lib/galaxy/managers/jobs.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/base.py
M lib/galaxy/model/mapping.py
A lib/galaxy/model/migrate/versions/0137_add_copied_from_job_id_column.py
A lib/galaxy/model/migrate/versions/0138_add_hda_version.py
A
lib/galaxy/model/migrate/versions/0139_add_history_dataset_association_history_table.py
A
lib/galaxy/model/migrate/versions/0140_add_dataset_version_to_job_to_input_dataset_association_table.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/webapps/galaxy/api/jobs.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/run.py
M lib/galaxy/workflow/run_request.py
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/libs.bundled.js
A static/scripts/libs/vue.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/tool/tool-form.js
M test/api/test_jobs.py
M test/api/test_tools.py
M test/api/test_workflows.py
M test/base/api.py
M test/base/data/test_workflow_1.ga
M test/base/interactor.py
Log Message:
-----------
Merge pull request #4690 from mvdbeek/skip_job_execution
Skip job execution if equivalent job exists
Compare:
https://github.com/galaxyproject/galaxy/compare/8e93c2e070af...32624dfeeeef