Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: eeb6722fe7f7f96ee3e459a2a66ae052c1d3517c
https://github.com/galaxyproject/galaxy/commit/eeb6722fe7f7f96ee3e459a2a66a…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-07-20 (Fri, 20 Jul 2018)
Changed paths:
M lib/galaxy/model/mapping.py
Log Message:
-----------
More optimized HID generation - in one commit instead of two.
Before HID optimization:
galaxy.tools.actions INFO 2018-07-18 11:10:20,164 Added output datasets to history (14.193 ms)
galaxy.tools.actions INFO 2018-07-18 11:10:20,416 Added output datasets to history (17.583 ms)
galaxy.tools.actions INFO 2018-07-18 11:10:20,675 Added output datasets to history (19.875 ms)
galaxy.model.orm.engine_factory INFO 2018-07-18 11:10:21,734 Executed [445] SQL requests in for web request [/api/tools] (1036.418676ms)
After HID optimization:
galaxy.tools.actions INFO 2018-07-18 11:13:41,855 Added output datasets to history (6.049 ms)
galaxy.tools.actions INFO 2018-07-18 11:13:42,018 Added output datasets to history (7.192 ms)
galaxy.tools.actions INFO 2018-07-18 11:13:42,184 Added output datasets to history (10.277 ms)
galaxy.tools.actions INFO 2018-07-18 11:13:42,344 Added output datasets to history (5.800 ms)
galaxy.model.orm.engine_factory INFO 2018-07-18 11:13:43,179 Executed [434] SQL requests in for web request [/api/tools] (818.706274ms)
Commit: 3b629f02933cc20ee3af779f1dd90219f73cda5f
https://github.com/galaxyproject/galaxy/commit/3b629f02933cc20ee3af779f1dd9…
Author: Dannon <dannon.baker(a)gmail.com>
Date: 2018-07-20 (Fri, 20 Jul 2018)
Changed paths:
M lib/galaxy/model/mapping.py
Log Message:
-----------
Merge pull request #6516 from jmchilton/hid_opt
More optimized HID generation - in one commit instead of two.
Compare: https://github.com/galaxyproject/galaxy/compare/5a72bfdf8617...3b629f02933c
**NOTE:** This service 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: 8d687bc3b7e2e4496b464e28c0961ba9fe2ad691
https://github.com/galaxyproject/galaxy/commit/8d687bc3b7e2e4496b464e28c096…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-07-18 (Wed, 18 Jul 2018)
Changed paths:
M lib/galaxy/tools/actions/__init__.py
Log Message:
-----------
Cache chrom_info generation when mapping over collections.
Eliminates several SQL queries per job and 20ms off the time it takes to create a job (about 10% for simple jobs). Timings below based on a branch with other optimizations so this will probably represent a smaller percent of runtime in dev until it catches up but the idea is pretty self contained unlike some other work in local my branch.
Before chrom_info cache:
```
galaxy.tools.actions INFO 2018-07-18 14:59:35,041 Collected inputs for tool execute (14.586 ms)
galaxy.tools.actions INFO 2018-07-18 14:59:35,069 setup execute (28.450 ms)
galaxy.tools.actions INFO 2018-07-18 14:59:35,071 Handled output named out_file1 for tool cat_data_and_sleep (1.082 ms)
galaxy.tools.actions INFO 2018-07-18 14:59:35,077 Added output datasets to history (5.986 ms)
galaxy.tools.actions INFO 2018-07-18 14:59:35,104 Flushed output datasets (27.165 ms)
...
galaxy.tools.actions INFO 2018-07-18 14:59:35,183 Collected inputs for tool execute (9.299 ms)
galaxy.tools.actions INFO 2018-07-18 14:59:35,210 setup execute (26.842 ms)
galaxy.tools.actions INFO 2018-07-18 14:59:35,211 Handled output named out_file1 for tool cat_data_and_sleep (1.375 ms)
galaxy.tools.actions INFO 2018-07-18 14:59:35,217 Added output datasets to history (5.168 ms)
galaxy.tools.actions INFO 2018-07-18 14:59:35,244 Flushed output datasets (27.395 ms)
...
galaxy.model.orm.engine_factory INFO 2018-07-18 14:59:36,033 Executed [417] SQL requests in for web request [/api/tools] (807.188749(s)ms)
```
```
galaxy.tools.actions INFO 2018-07-18 14:58:20,505 Collected inputs for tool execute (8.643 ms)
galaxy.tools.actions INFO 2018-07-18 14:58:20,533 setup execute (27.325 ms)
galaxy.tools.actions INFO 2018-07-18 14:58:20,534 Handled output named out_file1 for tool cat_data_and_sleep (1.201 ms)
galaxy.tools.actions INFO 2018-07-18 14:58:20,539 Added output datasets to history (4.913 ms)
galaxy.tools.actions INFO 2018-07-18 14:58:20,565 Flushed output datasets (25.520 ms)
...
galaxy.tools.actions INFO 2018-07-18 14:58:20,641 Collected inputs for tool execute (7.044 ms)
galaxy.tools.actions INFO 2018-07-18 14:58:20,669 setup execute (27.744 ms)
galaxy.tools.actions INFO 2018-07-18 14:58:20,670 Handled output named out_file1 for tool cat_data_and_sleep (0.990 ms)
galaxy.tools.actions INFO 2018-07-18 14:58:20,674 Added output datasets to history (4.727 ms)
galaxy.tools.actions INFO 2018-07-18 14:58:20,701 Flushed output datasets (26.265 ms)
...
galaxy.model.orm.engine_factory INFO 2018-07-18 14:58:21,480 Executed [417] SQL requests in for web request [/api/tools] (796.465635(s)ms)
```
After chrom_info cache:
```
...
galaxy.tools.actions INFO 2018-07-18 14:56:21,486 Collected inputs for tool execute (9.792 ms)
galaxy.tools.actions INFO 2018-07-18 14:56:21,487 setup execute (0.399 ms)
galaxy.tools.actions INFO 2018-07-18 14:56:21,488 Handled output named out_file1 for tool cat_data_and_sleep (1.068 ms)
galaxy.tools.actions INFO 2018-07-18 14:56:21,497 Added output datasets to history (9.218 ms)
galaxy.tools.actions INFO 2018-07-18 14:56:21,522 Flushed output datasets (24.905 ms)
...
galaxy.model.orm.engine_factory INFO 2018-07-18 14:56:22,352 Executed [381] SQL requests in for web request [/api/tools] (684.080839(s)ms)
```
```
galaxy.tools.actions INFO 2018-07-18 14:55:27,979 Collected inputs for tool execute (8.400 ms)
galaxy.tools.actions INFO 2018-07-18 14:55:27,979 setup execute (0.462 ms)
galaxy.tools.actions INFO 2018-07-18 14:55:27,980 Handled output named out_file1 for tool cat_data_and_sleep (1.208 ms)
galaxy.tools.actions INFO 2018-07-18 14:55:27,991 Added output datasets to history (10.558 ms)
galaxy.tools.actions INFO 2018-07-18 14:55:28,016 Flushed output datasets (24.182 ms)
...
galaxy.model.orm.engine_factory INFO 2018-07-18 14:55:28,838 Executed [381] SQL requests in for web request [/api/tools] (714.353323(s)ms)
```
Commit: b39bebb6a694af2cd50cee8c416443e7dcb501cf
https://github.com/galaxyproject/galaxy/commit/b39bebb6a694af2cd50cee8c4164…
Author: Nicola Soranzo <nicola.soranzo(a)gmail.com>
Date: 2018-07-20 (Fri, 20 Jul 2018)
Changed paths:
M lib/galaxy/tools/actions/__init__.py
Log Message:
-----------
Merge pull request #6515 from jmchilton/chrom_info_cache
Cache chrom_info generation when mapping over collections.
Compare: https://github.com/galaxyproject/galaxy/compare/20f10fe6db8c...b39bebb6a694
**NOTE:** This service 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: 8d3f1b7fbbe1d9acc7d93bc70a27e3f52c8cf9ae
https://github.com/galaxyproject/galaxy/commit/8d3f1b7fbbe1d9acc7d93bc70a27…
Author: Qiang Gu <guqiang01(a)gmail.com>
Date: 2018-06-22 (Fri, 22 Jun 2018)
Changed paths:
A client/galaxy/scripts/components/DataDialog.vue
A client/galaxy/scripts/layout/data.js
M client/galaxy/scripts/layout/modal.js
M client/galaxy/scripts/layout/page.js
M config/datatypes_conf.xml.sample
M config/plugins/visualizations/msa/config/msa.xml
M lib/galaxy/datatypes/binary.py
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/parameters/output_collect.py
M lib/galaxy/tools/relabel_from_file.xml
M lib/galaxy/webapps/galaxy/api/jobs.py
M lib/galaxy/webapps/galaxy/buildapp.py
M scripts/grt/export.py
M test/api/test_jobs.py
Log Message:
-----------
Merge branch 'dev' into data_column_1
Commit: df17fad74a160ed8e8c71097d027b418af9c67e7
https://github.com/galaxyproject/galaxy/commit/df17fad74a160ed8e8c71097d027…
Author: Qiang Gu <guqiang01(a)gmail.com>
Date: 2018-06-22 (Fri, 22 Jun 2018)
Changed paths:
M lib/galaxy/model/__init__.py
M lib/galaxy/model/metadata.py
M lib/galaxy/tools/__init__.py
M test/api/test_tools.py
Log Message:
-----------
Merge branch 'dev' into data_column_1
Commit: ca57b770901c0204e63dec836856cf75dae09acb
https://github.com/galaxyproject/galaxy/commit/ca57b770901c0204e63dec836856…
Author: Qiang Gu <guqiang01(a)gmail.com>
Date: 2018-06-24 (Sun, 24 Jun 2018)
Changed paths:
M lib/galaxy/tools/parameters/wrapped_json.py
Log Message:
-----------
fix data_column cast error when multiple is false
Commit: 88132f9d1609f2e6bf804d9e148e397cd0c2aeee
https://github.com/galaxyproject/galaxy/commit/88132f9d1609f2e6bf804d9e148e…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-06-30 (Sat, 30 Jun 2018)
Changed paths:
A test-data/11.tabular
A test-data/configfile.json
A test/functional/tools/column_param_configfile.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Test dumping multiple="false" data_column param as json
Tests https://github.com/galaxyproject/galaxy/pull/6389
Commit: 2da83ae3fef08703016fb9567807e04d0baeb084
https://github.com/galaxyproject/galaxy/commit/2da83ae3fef08703016fb9567807…
Author: Qiang Gu <36086881+qiagu(a)users.noreply.github.com>
Date: 2018-06-30 (Sat, 30 Jun 2018)
Changed paths:
A test-data/11.tabular
A test-data/configfile.json
A test/functional/tools/column_param_configfile.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Merge pull request #1 from mvdbeek/qiagu-data_column_1
Test dumping multiple="false" data_column param as json
Commit: c9df2ef9be73cf12644cb436cf7d4d23c7308174
https://github.com/galaxyproject/galaxy/commit/c9df2ef9be73cf12644cb436cf7d…
Author: Qiang Gu <36086881+qiagu(a)users.noreply.github.com>
Date: 2018-07-10 (Tue, 10 Jul 2018)
Changed paths:
M test-data/configfile.json
Log Message:
-----------
Update configfile.json
Commit: 53709df8cfb8fd384d60d221786c4167d7aa9658
https://github.com/galaxyproject/galaxy/commit/53709df8cfb8fd384d60d221786c…
Author: Qiang Gu <guqiang01(a)gmail.com>
Date: 2018-07-11 (Wed, 11 Jul 2018)
Changed paths:
M test-data/configfile.json
Log Message:
-----------
Revert "Update configfile.json"
This reverts commit c9df2ef9be73cf12644cb436cf7d4d23c7308174.
Commit: 20f10fe6db8ceb73c843c2a5609ab5fa5cf2f4ba
https://github.com/galaxyproject/galaxy/commit/20f10fe6db8ceb73c843c2a5609a…
Author: Dannon <dannon.baker(a)gmail.com>
Date: 2018-07-18 (Wed, 18 Jul 2018)
Changed paths:
M lib/galaxy/tools/parameters/wrapped_json.py
A test-data/11.tabular
A test-data/configfile.json
A test/functional/tools/column_param_configfile.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Merge pull request #6389 from qiagu/data_column_1
fix data_column cast error when multiple is false
Compare: https://github.com/galaxyproject/galaxy/compare/adb082a805d2...20f10fe6db8c
**NOTE:** This service 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: 267c2320769ad68fc2df0b10b92cf94641c24e15
https://github.com/galaxyproject/galaxy/commit/267c2320769ad68fc2df0b10b92c…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-06-21 (Thu, 21 Jun 2018)
Changed paths:
M lib/galaxy/tools/actions/upload.py
M lib/galaxy/tools/data_fetch.xml
M lib/galaxy/webapps/galaxy/api/tools.py
Log Message:
-----------
Fix for supplying multiple actual uploads to the upload 2.0 tool.
Commit: 8d5a4c3625e96bb7e5c879cadcf1980217801481
https://github.com/galaxyproject/galaxy/commit/8d5a4c3625e96bb7e5c879cadcf1…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-06-21 (Thu, 21 Jun 2018)
Changed paths:
M test/api/test_dataset_collections.py
M test/api/test_jobs.py
M test/api/test_libraries.py
M test/api/test_tools.py
M test/api/test_workflow_extraction.py
M test/api/test_workflows.py
M test/base/populators.py
Log Message:
-----------
Transition API tests from upload datasets and assembling collecitons to uploading collections.
Should be a lot more efficient.
Commit: 9f73bc89854420a4f28188fbcefad7999689ca6b
https://github.com/galaxyproject/galaxy/commit/9f73bc89854420a4f28188fbcefa…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-07-18 (Wed, 18 Jul 2018)
Changed paths:
M test/api/test_dataset_collections.py
Log Message:
-----------
Repsonse->response
Commit: 5171b9bd497cb07c3e7ab940230c97916ab29f6a
https://github.com/galaxyproject/galaxy/commit/5171b9bd497cb07c3e7ab940230c…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-07-18 (Wed, 18 Jul 2018)
Changed paths:
M test/base/populators.py
M test/integration/test_scripts.py
Log Message:
-----------
A couple more typos.
Commit: e794443f488649c8bb1d1d0825e4a113dacee26c
https://github.com/galaxyproject/galaxy/commit/e794443f488649c8bb1d1d0825e4…
Author: Dannon <dannon.baker(a)gmail.com>
Date: 2018-07-18 (Wed, 18 Jul 2018)
Changed paths:
M lib/galaxy/tools/actions/upload.py
M lib/galaxy/tools/data_fetch.xml
M lib/galaxy/webapps/galaxy/api/tools.py
M test/api/test_dataset_collections.py
M test/api/test_jobs.py
M test/api/test_libraries.py
M test/api/test_tools.py
M test/api/test_workflow_extraction.py
M test/api/test_workflows.py
M test/base/populators.py
M test/integration/test_scripts.py
Log Message:
-----------
Merge pull request #6294 from jmchilton/better_tool_tests
Upload collections directly for tests.
Compare: https://github.com/galaxyproject/galaxy/compare/6c668774f7ca...e794443f4886
**NOTE:** This service 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: 489839cb638df8648041cc6197a61faf9cfc7a6a
https://github.com/galaxyproject/galaxy/commit/489839cb638df8648041cc6197a6…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-07-16 (Mon, 16 Jul 2018)
Changed paths:
M client/galaxy/scripts/components/RuleCollectionBuilder.vue
M client/galaxy/scripts/mvc/rules/rule-definitions.js
Log Message:
-----------
Integrate tagging into the rule builder.
- Allow specifying name tags, group tags, and "general" tags on stand-alone datasets and collection content datasets.
- Allow reusing the collection name as a name tag during upload for the whole collection. In this context I think the name tag is especially useful and will typically be the same name as the collection so the UI is kept simple by making it a checkbox.
Commit: 26b5891908757648eed5ce9be3cccbe7104ad7d3
https://github.com/galaxyproject/galaxy/commit/26b5891908757648eed5ce9be3cc…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-07-17 (Tue, 17 Jul 2018)
Changed paths:
M client/galaxy/scripts/components/RuleCollectionBuilder.vue
M client/galaxy/scripts/mvc/rules/rule-definitions.js
Log Message:
-----------
Client-format
Commit: e8b437dfd8e07f88f48a5872ce18693343f33573
https://github.com/galaxyproject/galaxy/commit/e8b437dfd8e07f88f48a5872ce18…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-07-17 (Tue, 17 Jul 2018)
Changed paths:
M client/galaxy/scripts/components/RuleCollectionBuilder.vue
M client/galaxy/scripts/mvc/rules/rule-definitions.js
Log Message:
-----------
Merge branch 'rule_builder_tags' into dev
Compare: https://github.com/galaxyproject/galaxy/compare/4719c4a3f129...e8b437dfd8e0
**NOTE:** This service 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.