[galaxy-commits] [galaxyproject/galaxy] 051627: Added CloudBridge to the requirements list.

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0516279b7c5a5b6c11118017517ec06e4e3745d6 https://github.com/galaxyproject/galaxy/commit/0516279b7c5a5b6c11118017517ec... Author: vahid <jalili.vahid@gmail.com> Date: 2017-07-20 (Thu, 20 Jul 2017) Changed paths: M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Added CloudBridge to the requirements list. Commit: aaad00162f3ea84798031de798fe99fb0fafe05b https://github.com/galaxyproject/galaxy/commit/aaad00162f3ea84798031de798fe9... Author: vahid <jalili.vahid@gmail.com> Date: 2017-07-20 (Thu, 20 Jul 2017) Changed paths: M lib/galaxy/dependencies/__init__.py Log Message: ----------- Added CloudBridge to the dependencies check. Commit: 55c976cb85237bb0906379d692e212f05a327c2b https://github.com/galaxyproject/galaxy/commit/55c976cb85237bb0906379d692e21... Author: vahid <jalili.vahid@gmail.com> Date: 2017-07-21 (Fri, 21 Jul 2017) Changed paths: M lib/galaxy/dependencies/__init__.py A lib/galaxy/objectstore/cloud.py Log Message: ----------- (1) Added Cloud to ObjectStore; (2) updated CloudBridge dependencies. Commit: e4c00dd695bf23a506ffeec15f98a6f6d1a05312 https://github.com/galaxyproject/galaxy/commit/e4c00dd695bf23a506ffeec15f98a... Author: vahid <jalili.vahid@gmail.com> Date: 2017-07-25 (Tue, 25 Jul 2017) Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/cloud.py Log Message: ----------- - Updated `Cloud` to account for changes in `CloudBridge` interface. - Added `Cloud` to objectstore import. Commit: ab34fc9bd92041065dd8f140194c56e0f7b2954f https://github.com/galaxyproject/galaxy/commit/ab34fc9bd92041065dd8f140194c5... Author: vahid <jalili.vahid@gmail.com> Date: 2017-07-26 (Wed, 26 Jul 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Updated `Babel` and `requests` packages version to meet the minimum requirements of `cloudbridge` package. Commit: e8541a71a4fdd7f975b3e8d0c6b054bdc33480ab https://github.com/galaxyproject/galaxy/commit/e8541a71a4fdd7f975b3e8d0c6b05... Author: vahid <jalili.vahid@gmail.com> Date: 2017-07-26 (Wed, 26 Jul 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Reverted the changes on package versions, as these changes are requests via a different PR. Commit: cde2ff82b02233721af81936d588b6558ab3ffa5 https://github.com/galaxyproject/galaxy/commit/cde2ff82b02233721af81936d588b... Author: vahid <jalili.vahid@gmail.com> Date: 2017-07-27 (Thu, 27 Jul 2017) Log Message: ----------- Merge remote-tracking branch 'upstream/master' Commit: 7ad7d881046ddd20276998d6e1fca495d1ac9f50 https://github.com/galaxyproject/galaxy/commit/7ad7d881046ddd20276998d6e1fca... Author: vahid <jalili.vahid@gmail.com> Date: 2017-07-28 (Fri, 28 Jul 2017) Changed paths: M lib/galaxy/objectstore/cloud.py Log Message: ----------- Changed boto import style. Commit: 9c57adb90481b871cc6f98f58227caca4e414467 https://github.com/galaxyproject/galaxy/commit/9c57adb90481b871cc6f98f58227c... Author: vahid <jalili.vahid@gmail.com> Date: 2017-08-02 (Wed, 02 Aug 2017) Changed paths: M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Updated CloudBridge to its current latest version. Commit: 2589c745ae7f88ada7a08265f1238ae00274425e https://github.com/galaxyproject/galaxy/commit/2589c745ae7f88ada7a08265f1238... Author: vahid <jalili.vahid@gmail.com> Date: 2017-08-02 (Wed, 02 Aug 2017) Changed paths: M lib/galaxy/objectstore/cloud.py Log Message: ----------- Commented on boto import, and removed a `use_reduced_redundancy` config. Commit: 89be432770d3cf9442f9c003ead8c6ea6a16f395 https://github.com/galaxyproject/galaxy/commit/89be432770d3cf9442f9c003ead8c... Author: vahid <jalili.vahid@gmail.com> Date: 2017-08-02 (Wed, 02 Aug 2017) Changed paths: M lib/galaxy/objectstore/cloud.py Log Message: ----------- Removed boto import, and replaced all S3-specific exception catches with a generic exception--a temporary solution till CloudBridge wraps the exceptions properly. Commit: fafb019f4be3b33ad9cab4bfd2ded6788b419592 https://github.com/galaxyproject/galaxy/commit/fafb019f4be3b33ad9cab4bfd2ded... Author: vahid <jalili.vahid@gmail.com> Date: 2017-08-02 (Wed, 02 Aug 2017) Changed paths: M lib/galaxy/objectstore/cloud.py Log Message: ----------- Consolidated two upload methods, i.e., upload from file and string, because CloudBridge internally maps to appropriate functions depending on the input type. Commit: fb25495d191c2172ce22496900db2310d6fc9b69 https://github.com/galaxyproject/galaxy/commit/fb25495d191c2172ce22496900db2... Author: vahid <jalili.vahid@gmail.com> Date: 2017-08-02 (Wed, 02 Aug 2017) Changed paths: M lib/galaxy/objectstore/cloud.py Log Message: ----------- Removed a S3-related comment, and swapped an if/else condition. Commit: 7727c0bf627af5905c6e029417602389238f120e https://github.com/galaxyproject/galaxy/commit/7727c0bf627af5905c6e029417602... Author: vahid <jalili.vahid@gmail.com> Date: 2017-08-02 (Wed, 02 Aug 2017) Changed paths: M lib/galaxy/objectstore/cloud.py Log Message: ----------- Removed a comment section. Commit: 37efbd03ce4215086d29e8f4e9fd977b8e1299e0 https://github.com/galaxyproject/galaxy/commit/37efbd03ce4215086d29e8f4e9fd9... Author: vahid <jalili.vahid@gmail.com> Date: 2017-08-06 (Sun, 06 Aug 2017) Changed paths: M lib/galaxy/objectstore/cloud.py Log Message: ----------- Changed indentation of two lines. Commit: 9a5016fdcf4f36d5c20991f44d4b02fe7904ef66 https://github.com/galaxyproject/galaxy/commit/9a5016fdcf4f36d5c20991f44d4b0... Author: Vahid <VJalili@users.noreply.github.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Update CloudBridge to its current latest Should use the wheel created at [this PR](https://github.com/galaxyproject/starforge/pull/139). Commit: 4e17c8e3b790d2d21bcf12c3d4a855b1226d810d https://github.com/galaxyproject/galaxy/commit/4e17c8e3b790d2d21bcf12c3d4a85... Author: vahid <jalili.vahid@gmail.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M config/object_store_conf.xml.sample Log Message: ----------- Add Cloud configuration to object_store_conf.xml.sample Commit: 0ec02b5528e64f62b50567e79d2519a9e84e20d1 https://github.com/galaxyproject/galaxy/commit/0ec02b5528e64f62b50567e79d251... 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tools/ngs_simulation/ngs_simulation.py M tools/plotting/bar_chart.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velvetg_wrapper.py M tools/sr_assembly/velveth_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/sr_mapping/srma_wrapper.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py M tools/visualization/LAJ.py M tools/visualization/LAJ_code.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'remotes/upstream/dev' into CloudObjectStore Commit: a8784369e4b243856b9582f9417039bf0c6bc83a https://github.com/galaxyproject/galaxy/commit/a8784369e4b243856b9582f941703... Author: vahid <jalili.vahid@gmail.com> Date: 2017-08-23 (Wed, 23 Aug 2017) Changed paths: M lib/galaxy/objectstore/cloud.py Log Message: ----------- Removed white spaces. Commit: eaa5931d195d4710d939e6f8d53bfe2fed38ba2f https://github.com/galaxyproject/galaxy/commit/eaa5931d195d4710d939e6f8d53bf... Author: vahid <jalili.vahid@gmail.com> Date: 2017-08-23 (Wed, 23 Aug 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Updated requirements: sqlalchemy-migrate and pbr. Commit: 90c444d9a136400af608cb7fd7f8e8d59de3ba90 https://github.com/galaxyproject/galaxy/commit/90c444d9a136400af608cb7fd7f8e... Author: vahid <jalili.vahid@gmail.com> Date: 2017-08-23 (Wed, 23 Aug 2017) Changed paths: M lib/galaxy/dependencies/__init__.py Log Message: ----------- Removed a white space between parenthesis and arguments Commit: f6586a8e6d861c8c6803f96340641abf6470c2fc https://github.com/galaxyproject/galaxy/commit/f6586a8e6d861c8c6803f96340641... Author: vahid <jalili.vahid@gmail.com> Date: 2017-08-24 (Thu, 24 Aug 2017) Changed paths: M lib/galaxy/objectstore/cloud.py Log Message: ----------- Surrounded CloudBridge import in a try-catch block. Commit: 26cbf04ed0f30f72c994af0ffab54eab7dd8ac0b https://github.com/galaxyproject/galaxy/commit/26cbf04ed0f30f72c994af0ffab54... Author: John Chilton <jmchilton@gmail.com> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M lib/galaxy/objectstore/cloud.py Log Message: ----------- Rework conditional dependency handling in galaxy.objectstore.cloud. This file may be loaded (e.g. for testing) but not used, so we shouldn't log a generic error about cloudbridge being unavailable, if someone attempts to actually use the object store and it isn't available then raise an informative exception. Commit: cf56d1d37b77b5ca18037da8a392d68199fcb4d6 https://github.com/galaxyproject/galaxy/commit/cf56d1d37b77b5ca18037da8a392d... Author: Vahid <VJalili@users.noreply.github.com> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M lib/galaxy/objectstore/cloud.py Log Message: ----------- Merge pull request #3 from jmchilton/CloudObjectStore Rework conditional dependency handling in galaxy.objectstore.cloud. Commit: 6d65e902b12b4fca9af613085b5bc828c8a6d2fc https://github.com/galaxyproject/galaxy/commit/6d65e902b12b4fca9af613085b5bc... Author: vahid <jalili.vahid@gmail.com> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M lib/galaxy/objectstore/cloud.py Log Message: ----------- Updated an error message. Commit: cfce6c221c3f453e75542d53262f53c7e3411f86 https://github.com/galaxyproject/galaxy/commit/cfce6c221c3f453e75542d53262f5... Author: vahid <jalili.vahid@gmail.com> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M lib/galaxy/objectstore/cloud.py Log Message: ----------- Removed `boto` logging level set. Commit: b55583701cbf33f52db88f147dda6b04499243d7 https://github.com/galaxyproject/galaxy/commit/b55583701cbf33f52db88f147dda6... Author: vahid <jalili.vahid@gmail.com> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M lib/galaxy/objectstore/cloud.py Log Message: ----------- Removed retries for getting a bucket. Commit: 5977056715a5d2e12b638012b6fc99d885ea034a https://github.com/galaxyproject/galaxy/commit/5977056715a5d2e12b638012b6fc9... Author: vahid <jalili.vahid@gmail.com> Date: 2017-09-11 (Mon, 11 Sep 2017) Changed paths: M lib/galaxy/objectstore/cloud.py Log Message: ----------- Resolved a bug with uploading a dataset using Cloud (not differentiating between uploading from a file vs. string). Commit: 45ac767a4eb6ab9e15a1e46a1e9e4ae70591e188 https://github.com/galaxyproject/galaxy/commit/45ac767a4eb6ab9e15a1e46a1e9e4... Author: vahid <jalili.vahid@gmail.com> Date: 2017-09-11 (Mon, 11 Sep 2017) Changed paths: M lib/galaxy/objectstore/cloud.py Log Message: ----------- Removed an unused variable (i.e., mb_size) from Cloud Commit: 9f0676d7d4984fa2540c1be001f705b02d33cd8d https://github.com/galaxyproject/galaxy/commit/9f0676d7d4984fa2540c1be001f70... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-12-11 (Mon, 11 Dec 2017) Changed paths: M config/object_store_conf.xml.sample M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/objectstore/__init__.py A lib/galaxy/objectstore/cloud.py Log Message: ----------- Merge remote-tracking branch 'VJalili/CloudObjectStore' into dev Compare: https://github.com/galaxyproject/galaxy/compare/7f30028d32b5...9f0676d7d498