galaxy-commits February 2016

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[galaxyproject/galaxy] ca123a: Add a safe_relpath util function for ensuring a pa...
by GitHub 24 Feb '16

24 Feb '16

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: ca123a4f2674351e01235bab545559b299b99ff9 https://github.com/galaxyproject/galaxy/commit/ca123a4f2674351e01235bab5455… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Add a safe_relpath util function for ensuring a path does not reference an absolute or parent directory Commit: 3b963226a110b8de8aa11d3c4e053a220bbcba53 https://github.com/galaxyproject/galaxy/commit/3b963226a110b8de8aa11d3c4e05… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py Log Message: ----------- Security fixes for history imports Commit: 5ab53c3fda3a43236b444a31aa408c9f5cb5c4c4 https://github.com/galaxyproject/galaxy/commit/5ab53c3fda3a43236b444a31aa40… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Add a safe_relpath util function for ensuring a path does not reference an absolute or parent directory Commit: 88277c9723c558e2b2003f1b81c7f2d16143fcc6 https://github.com/galaxyproject/galaxy/commit/88277c9723c558e2b2003f1b81c7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py Log Message: ----------- Security fixes for history imports Commit: d650055ca824d5cf8ab1ede389e9b3060c1f4094 https://github.com/galaxyproject/galaxy/commit/d650055ca824d5cf8ab1ede389e9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py Log Message: ----------- Security fixes for object store paths Commit: 32c910ac4021b0e65112d557a7f12d24e158171d https://github.com/galaxyproject/galaxy/commit/32c910ac4021b0e65112d557a7f1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py Log Message: ----------- Security fixes for object store paths Commit: 37548ef8edb95d59fddd73283561e8b1a6588c10 https://github.com/galaxyproject/galaxy/commit/37548ef8edb95d59fddd73283561… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py R templates/admin/requests/select_datasets_to_transfer.mako M templates/webapps/galaxy/requests/common/common.mako M templates/webapps/galaxy/requests/common/view_request_history.mako M templates/webapps/galaxy/requests/common/view_sample_datasets.mako Log Message: ----------- Remove sample tracking manual external service transfer due to security concerns Commit: 78f441b9c7bfd68f7b3ee030f4ffe4a95b5fdc58 https://github.com/galaxyproject/galaxy/commit/78f441b9c7bfd68f7b3ee030f4ff… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py R templates/admin/requests/select_datasets_to_transfer.mako M templates/webapps/galaxy/requests/common/common.mako M templates/webapps/galaxy/requests/common/view_request_history.mako M templates/webapps/galaxy/requests/common/view_sample_datasets.mako Log Message: ----------- Remove sample tracking manual external service transfer due to security concerns Commit: 4f3397fa0ab187a4b5c32e1268265925fc1a8753 https://github.com/galaxyproject/galaxy/commit/4f3397fa0ab187a4b5c32e126826… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/util/shed_util_common.py M templates/admin/tool_shed_repository/common.mako M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Security fixes for tool shed repository browsing Commit: 8468871ee481598a84888b5329139590ec75e98d https://github.com/galaxyproject/galaxy/commit/8468871ee481598a84888b532913… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Add a safe_relpath util function for ensuring a path does not reference an absolute or parent directory Commit: cee85bae67377d3fad42bec5b4ebb022aaf7b2c7 https://github.com/galaxyproject/galaxy/commit/cee85bae67377d3fad42bec5b4eb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/util/shed_util_common.py M templates/admin/tool_shed_repository/common.mako M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Security fixes for tool shed repository browsing Commit: 4845a39071ab4e2652e564efdf7647a942563603 https://github.com/galaxyproject/galaxy/commit/4845a39071ab4e2652e564efdf76… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/repository_content_util.py Log Message: ----------- Security fixes for tool shed hg push and capsule/tarball uploads Commit: ef4a9f6e2114e69f6ea3167e99a857f2ea4d28af https://github.com/galaxyproject/galaxy/commit/ef4a9f6e2114e69f6ea3167e99a8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py Log Message: ----------- Security fixes for history imports Commit: 61cd045ffa947a69abacddea459f725ba569584a https://github.com/galaxyproject/galaxy/commit/61cd045ffa947a69abacddea459f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Log Message: ----------- Merge branch 'release_14.10' into release_15.01 Commit: 2a8089749caab12c087064c840708fb05b0104cd https://github.com/galaxyproject/galaxy/commit/2a8089749caab12c087064c84070… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Add a safe_relpath util function for ensuring a path does not reference an absolute or parent directory Commit: 6e3b74869a54558fe48d6e1633c5af7197051447 https://github.com/galaxyproject/galaxy/commit/6e3b74869a54558fe48d6e1633c5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py Log Message: ----------- Security fixes for history imports Commit: c8963786d53efd2cf3b359b2f9a000e00688285f https://github.com/galaxyproject/galaxy/commit/c8963786d53efd2cf3b359b2f9a0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py Log Message: ----------- Security fixes for object store paths Commit: ce88f2f81caff6af7dc730ef9c1fbc2a40922dab https://github.com/galaxyproject/galaxy/commit/ce88f2f81caff6af7dc730ef9c1f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py Log Message: ----------- Security fixes for object store paths Commit: d4b94722f992c9309aa2ec5bfa5bce2dacd9b218 https://github.com/galaxyproject/galaxy/commit/d4b94722f992c9309aa2ec5bfa5b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py R templates/admin/requests/select_datasets_to_transfer.mako M templates/webapps/galaxy/requests/common/common.mako M templates/webapps/galaxy/requests/common/view_request_history.mako M templates/webapps/galaxy/requests/common/view_sample_datasets.mako Log Message: ----------- Remove sample tracking manual external service transfer due to security concerns Commit: fcd8f50448cd1db7b50a58321c8fa391506bf997 https://github.com/galaxyproject/galaxy/commit/fcd8f50448cd1db7b50a58321c8f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py R templates/admin/requests/select_datasets_to_transfer.mako M templates/webapps/galaxy/requests/common/common.mako M templates/webapps/galaxy/requests/common/view_request_history.mako M templates/webapps/galaxy/requests/common/view_sample_datasets.mako Log Message: ----------- Remove sample tracking manual external service transfer due to security concerns Commit: 626cade512894e54c5b3e5257543f267a1826a71 https://github.com/galaxyproject/galaxy/commit/626cade512894e54c5b3e5257543… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/util/shed_util_common.py M templates/admin/tool_shed_repository/common.mako M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Security fixes for tool shed repository browsing Commit: 91f5fa81fe3c1c4d45b3987b27c187c4cb53f8e8 https://github.com/galaxyproject/galaxy/commit/91f5fa81fe3c1c4d45b3987b27c1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/util/shed_util_common.py M templates/admin/tool_shed_repository/common.mako M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Security fixes for tool shed repository browsing Commit: 581808aa98a6058a4bdbe13c21271ca4b0d3ef77 https://github.com/galaxyproject/galaxy/commit/581808aa98a6058a4bdbe13c2127… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/repository_content_util.py Log Message: ----------- Security fixes for tool shed hg push and capsule/tarball uploads Commit: 2bda436473b116c7d98c36a8435056745bf832f2 https://github.com/galaxyproject/galaxy/commit/2bda436473b116c7d98c36a84350… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/repository_content_util.py Log Message: ----------- Security fixes for tool shed hg push and capsule/tarball uploads Commit: f8a1aef76c022612a8a28938e1d57412348884ab https://github.com/galaxyproject/galaxy/commit/f8a1aef76c022612a8a28938e1d5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Log Message: ----------- Merge branch 'release_15.01' into release_15.03 Commit: 47a8b6e86733472ad3c0dbe2d5774d69ecba44eb https://github.com/galaxyproject/galaxy/commit/47a8b6e86733472ad3c0dbe2d577… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Add a safe_relpath util function for ensuring a path does not reference an absolute or parent directory Commit: 6190f6fa6db26ada3380c9a54b5481d12b3ac9ae https://github.com/galaxyproject/galaxy/commit/6190f6fa6db26ada3380c9a54b54… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py Log Message: ----------- Security fixes for history imports Commit: 27d7298ec4788a2e59a5988007fde05e5fc004ce https://github.com/galaxyproject/galaxy/commit/27d7298ec4788a2e59a5988007fd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py Log Message: ----------- Security fixes for object store paths Commit: c465489ea1676905ddb4cfb88605c1e869a7019c https://github.com/galaxyproject/galaxy/commit/c465489ea1676905ddb4cfb88605… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py R templates/admin/requests/select_datasets_to_transfer.mako M templates/webapps/galaxy/requests/common/common.mako M templates/webapps/galaxy/requests/common/view_request_history.mako M templates/webapps/galaxy/requests/common/view_sample_datasets.mako Log Message: ----------- Remove sample tracking manual external service transfer due to security concerns Commit: 18b3126a15ec7fe3873253be0c1344e9f067f0ca https://github.com/galaxyproject/galaxy/commit/18b3126a15ec7fe3873253be0c13… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/util/shed_util_common.py M templates/admin/tool_shed_repository/common.mako M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Security fixes for tool shed repository browsing Commit: 40a90831ed28b762e90cf2b50abec7e8bef738d6 https://github.com/galaxyproject/galaxy/commit/40a90831ed28b762e90cf2b50abe… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/repository_content_util.py Log Message: ----------- Security fixes for tool shed hg push and capsule/tarball uploads Commit: f65bcb3383ba142d514b38ab5ed03d5f9ecd5f1d https://github.com/galaxyproject/galaxy/commit/f65bcb3383ba142d514b38ab5ed0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Log Message: ----------- Merge branch 'release_15.03' into release_15.05 Commit: ab1a135dd4a422897c74ea87e5210ec5baa27ff7 https://github.com/galaxyproject/galaxy/commit/ab1a135dd4a422897c74ea87e521… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Log Message: ----------- Merge branch 'release_15.05' into release_15.07 Commit: b3e0315e1e40912366c8103412e64a645e0a93a9 https://github.com/galaxyproject/galaxy/commit/b3e0315e1e40912366c8103412e6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Add a safe_relpath util function for ensuring a path does not reference an absolute or parent directory Commit: 8736c7bd77bd3c5cd38225538085c0eb2a40e8f4 https://github.com/galaxyproject/galaxy/commit/8736c7bd77bd3c5cd38225538085… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py Log Message: ----------- Security fixes for history imports Commit: 23e203c48180b6ab1e4886be81447e33afb853e5 https://github.com/galaxyproject/galaxy/commit/23e203c48180b6ab1e4886be8144… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py Log Message: ----------- Security fixes for object store paths Commit: 64cd02ae385fb509378c78e6e4832768ff4f1e00 https://github.com/galaxyproject/galaxy/commit/64cd02ae385fb509378c78e6e483… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py R templates/admin/requests/select_datasets_to_transfer.mako M templates/webapps/galaxy/requests/common/common.mako M templates/webapps/galaxy/requests/common/view_request_history.mako M templates/webapps/galaxy/requests/common/view_sample_datasets.mako Log Message: ----------- Remove sample tracking manual external service transfer due to security concerns Commit: 2dcbda93b29e4dd975453af8eeb4f171f7db2918 https://github.com/galaxyproject/galaxy/commit/2dcbda93b29e4dd975453af8eeb4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/util/shed_util_common.py M templates/admin/tool_shed_repository/common.mako M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Security fixes for tool shed repository browsing Commit: b11b8e68500a3d074bf20b08958671d958d42eca https://github.com/galaxyproject/galaxy/commit/b11b8e68500a3d074bf20b089586… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/repository_content_util.py Log Message: ----------- Security fixes for tool shed hg push and capsule/tarball uploads Commit: 8c4542b136ef1eab3231ba0df4aab53b91f504af https://github.com/galaxyproject/galaxy/commit/8c4542b136ef1eab3231ba0df4aa… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Log Message: ----------- Merge branch 'release_15.07' into release_15.10 Commit: 0122040fad865487e2377cee35360af49e37d0e8 https://github.com/galaxyproject/galaxy/commit/0122040fad865487e2377cee3536… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 15.03.4 Commit: 3516e94e5cb0e971d8e10de018b72cf22296766e https://github.com/galaxyproject/galaxy/commit/3516e94e5cb0e971d8e10de018b7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Log Message: ----------- Merge branch 'release_15.03' into release_15.05 Commit: c8e9845c5c57714042a75053d954b1c7f0962672 https://github.com/galaxyproject/galaxy/commit/c8e9845c5c57714042a75053d954… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 15.05.2 Commit: 3d832aff0abe5a4ca48bfc80c84032f388bf7024 https://github.com/galaxyproject/galaxy/commit/3d832aff0abe5a4ca48bfc80c840… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Log Message: ----------- Merge branch 'release_15.05' into release_15.07 Commit: 30608c177c625f4ce66f1376a66621687fe7711e https://github.com/galaxyproject/galaxy/commit/30608c177c625f4ce66f1376a666… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 15.07.1 Commit: 21cc5b2da540eba18445603146407c1779257bba https://github.com/galaxyproject/galaxy/commit/21cc5b2da540eba1844560314640… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Log Message: ----------- Merge branch 'release_15.07' into release_15.10 Commit: b5949bcbbfbc613b0ec72ce23e4da448c9316c49 https://github.com/galaxyproject/galaxy/commit/b5949bcbbfbc613b0ec72ce23e4d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 15.10.2 Compare: https://github.com/galaxyproject/galaxy/compare/6c83fbe24dd0...b5949bcbbfbc

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[galaxyproject/galaxy] ca123a: Add a safe_relpath util function for ensuring a pa...
by GitHub 24 Feb '16

24 Feb '16

Branch: refs/heads/release_15.07 Home: https://github.com/galaxyproject/galaxy Commit: ca123a4f2674351e01235bab545559b299b99ff9 https://github.com/galaxyproject/galaxy/commit/ca123a4f2674351e01235bab5455… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Add a safe_relpath util function for ensuring a path does not reference an absolute or parent directory Commit: 3b963226a110b8de8aa11d3c4e053a220bbcba53 https://github.com/galaxyproject/galaxy/commit/3b963226a110b8de8aa11d3c4e05… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py Log Message: ----------- Security fixes for history imports Commit: 5ab53c3fda3a43236b444a31aa408c9f5cb5c4c4 https://github.com/galaxyproject/galaxy/commit/5ab53c3fda3a43236b444a31aa40… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Add a safe_relpath util function for ensuring a path does not reference an absolute or parent directory Commit: 88277c9723c558e2b2003f1b81c7f2d16143fcc6 https://github.com/galaxyproject/galaxy/commit/88277c9723c558e2b2003f1b81c7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py Log Message: ----------- Security fixes for history imports Commit: d650055ca824d5cf8ab1ede389e9b3060c1f4094 https://github.com/galaxyproject/galaxy/commit/d650055ca824d5cf8ab1ede389e9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py Log Message: ----------- Security fixes for object store paths Commit: 32c910ac4021b0e65112d557a7f12d24e158171d https://github.com/galaxyproject/galaxy/commit/32c910ac4021b0e65112d557a7f1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py Log Message: ----------- Security fixes for object store paths Commit: 37548ef8edb95d59fddd73283561e8b1a6588c10 https://github.com/galaxyproject/galaxy/commit/37548ef8edb95d59fddd73283561… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py R templates/admin/requests/select_datasets_to_transfer.mako M templates/webapps/galaxy/requests/common/common.mako M templates/webapps/galaxy/requests/common/view_request_history.mako M templates/webapps/galaxy/requests/common/view_sample_datasets.mako Log Message: ----------- Remove sample tracking manual external service transfer due to security concerns Commit: 78f441b9c7bfd68f7b3ee030f4ffe4a95b5fdc58 https://github.com/galaxyproject/galaxy/commit/78f441b9c7bfd68f7b3ee030f4ff… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py R templates/admin/requests/select_datasets_to_transfer.mako M templates/webapps/galaxy/requests/common/common.mako M templates/webapps/galaxy/requests/common/view_request_history.mako M templates/webapps/galaxy/requests/common/view_sample_datasets.mako Log Message: ----------- Remove sample tracking manual external service transfer due to security concerns Commit: 4f3397fa0ab187a4b5c32e1268265925fc1a8753 https://github.com/galaxyproject/galaxy/commit/4f3397fa0ab187a4b5c32e126826… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/util/shed_util_common.py M templates/admin/tool_shed_repository/common.mako M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Security fixes for tool shed repository browsing Commit: 8468871ee481598a84888b5329139590ec75e98d https://github.com/galaxyproject/galaxy/commit/8468871ee481598a84888b532913… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Add a safe_relpath util function for ensuring a path does not reference an absolute or parent directory Commit: cee85bae67377d3fad42bec5b4ebb022aaf7b2c7 https://github.com/galaxyproject/galaxy/commit/cee85bae67377d3fad42bec5b4eb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/util/shed_util_common.py M templates/admin/tool_shed_repository/common.mako M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Security fixes for tool shed repository browsing Commit: 4845a39071ab4e2652e564efdf7647a942563603 https://github.com/galaxyproject/galaxy/commit/4845a39071ab4e2652e564efdf76… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/repository_content_util.py Log Message: ----------- Security fixes for tool shed hg push and capsule/tarball uploads Commit: ef4a9f6e2114e69f6ea3167e99a857f2ea4d28af https://github.com/galaxyproject/galaxy/commit/ef4a9f6e2114e69f6ea3167e99a8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py Log Message: ----------- Security fixes for history imports Commit: 61cd045ffa947a69abacddea459f725ba569584a https://github.com/galaxyproject/galaxy/commit/61cd045ffa947a69abacddea459f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Log Message: ----------- Merge branch 'release_14.10' into release_15.01 Commit: 2a8089749caab12c087064c840708fb05b0104cd https://github.com/galaxyproject/galaxy/commit/2a8089749caab12c087064c84070… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Add a safe_relpath util function for ensuring a path does not reference an absolute or parent directory Commit: 6e3b74869a54558fe48d6e1633c5af7197051447 https://github.com/galaxyproject/galaxy/commit/6e3b74869a54558fe48d6e1633c5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py Log Message: ----------- Security fixes for history imports Commit: c8963786d53efd2cf3b359b2f9a000e00688285f https://github.com/galaxyproject/galaxy/commit/c8963786d53efd2cf3b359b2f9a0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py Log Message: ----------- Security fixes for object store paths Commit: ce88f2f81caff6af7dc730ef9c1fbc2a40922dab https://github.com/galaxyproject/galaxy/commit/ce88f2f81caff6af7dc730ef9c1f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py Log Message: ----------- Security fixes for object store paths Commit: d4b94722f992c9309aa2ec5bfa5bce2dacd9b218 https://github.com/galaxyproject/galaxy/commit/d4b94722f992c9309aa2ec5bfa5b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py R templates/admin/requests/select_datasets_to_transfer.mako M templates/webapps/galaxy/requests/common/common.mako M templates/webapps/galaxy/requests/common/view_request_history.mako M templates/webapps/galaxy/requests/common/view_sample_datasets.mako Log Message: ----------- Remove sample tracking manual external service transfer due to security concerns Commit: fcd8f50448cd1db7b50a58321c8fa391506bf997 https://github.com/galaxyproject/galaxy/commit/fcd8f50448cd1db7b50a58321c8f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py R templates/admin/requests/select_datasets_to_transfer.mako M templates/webapps/galaxy/requests/common/common.mako M templates/webapps/galaxy/requests/common/view_request_history.mako M templates/webapps/galaxy/requests/common/view_sample_datasets.mako Log Message: ----------- Remove sample tracking manual external service transfer due to security concerns Commit: 626cade512894e54c5b3e5257543f267a1826a71 https://github.com/galaxyproject/galaxy/commit/626cade512894e54c5b3e5257543… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/util/shed_util_common.py M templates/admin/tool_shed_repository/common.mako M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Security fixes for tool shed repository browsing Commit: 91f5fa81fe3c1c4d45b3987b27c187c4cb53f8e8 https://github.com/galaxyproject/galaxy/commit/91f5fa81fe3c1c4d45b3987b27c1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/util/shed_util_common.py M templates/admin/tool_shed_repository/common.mako M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Security fixes for tool shed repository browsing Commit: 581808aa98a6058a4bdbe13c21271ca4b0d3ef77 https://github.com/galaxyproject/galaxy/commit/581808aa98a6058a4bdbe13c2127… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/repository_content_util.py Log Message: ----------- Security fixes for tool shed hg push and capsule/tarball uploads Commit: 2bda436473b116c7d98c36a8435056745bf832f2 https://github.com/galaxyproject/galaxy/commit/2bda436473b116c7d98c36a84350… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/repository_content_util.py Log Message: ----------- Security fixes for tool shed hg push and capsule/tarball uploads Commit: f8a1aef76c022612a8a28938e1d57412348884ab https://github.com/galaxyproject/galaxy/commit/f8a1aef76c022612a8a28938e1d5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Log Message: ----------- Merge branch 'release_15.01' into release_15.03 Commit: 47a8b6e86733472ad3c0dbe2d5774d69ecba44eb https://github.com/galaxyproject/galaxy/commit/47a8b6e86733472ad3c0dbe2d577… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Add a safe_relpath util function for ensuring a path does not reference an absolute or parent directory Commit: 6190f6fa6db26ada3380c9a54b5481d12b3ac9ae https://github.com/galaxyproject/galaxy/commit/6190f6fa6db26ada3380c9a54b54… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py Log Message: ----------- Security fixes for history imports Commit: 27d7298ec4788a2e59a5988007fde05e5fc004ce https://github.com/galaxyproject/galaxy/commit/27d7298ec4788a2e59a5988007fd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py Log Message: ----------- Security fixes for object store paths Commit: c465489ea1676905ddb4cfb88605c1e869a7019c https://github.com/galaxyproject/galaxy/commit/c465489ea1676905ddb4cfb88605… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py R templates/admin/requests/select_datasets_to_transfer.mako M templates/webapps/galaxy/requests/common/common.mako M templates/webapps/galaxy/requests/common/view_request_history.mako M templates/webapps/galaxy/requests/common/view_sample_datasets.mako Log Message: ----------- Remove sample tracking manual external service transfer due to security concerns Commit: 18b3126a15ec7fe3873253be0c1344e9f067f0ca https://github.com/galaxyproject/galaxy/commit/18b3126a15ec7fe3873253be0c13… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/util/shed_util_common.py M templates/admin/tool_shed_repository/common.mako M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Security fixes for tool shed repository browsing Commit: 40a90831ed28b762e90cf2b50abec7e8bef738d6 https://github.com/galaxyproject/galaxy/commit/40a90831ed28b762e90cf2b50abe… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/repository_content_util.py Log Message: ----------- Security fixes for tool shed hg push and capsule/tarball uploads Commit: f65bcb3383ba142d514b38ab5ed03d5f9ecd5f1d https://github.com/galaxyproject/galaxy/commit/f65bcb3383ba142d514b38ab5ed0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Log Message: ----------- Merge branch 'release_15.03' into release_15.05 Commit: ab1a135dd4a422897c74ea87e5210ec5baa27ff7 https://github.com/galaxyproject/galaxy/commit/ab1a135dd4a422897c74ea87e521… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Log Message: ----------- Merge branch 'release_15.05' into release_15.07 Commit: 0122040fad865487e2377cee35360af49e37d0e8 https://github.com/galaxyproject/galaxy/commit/0122040fad865487e2377cee3536… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 15.03.4 Commit: 3516e94e5cb0e971d8e10de018b72cf22296766e https://github.com/galaxyproject/galaxy/commit/3516e94e5cb0e971d8e10de018b7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Log Message: ----------- Merge branch 'release_15.03' into release_15.05 Commit: c8e9845c5c57714042a75053d954b1c7f0962672 https://github.com/galaxyproject/galaxy/commit/c8e9845c5c57714042a75053d954… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 15.05.2 Commit: 3d832aff0abe5a4ca48bfc80c84032f388bf7024 https://github.com/galaxyproject/galaxy/commit/3d832aff0abe5a4ca48bfc80c840… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Log Message: ----------- Merge branch 'release_15.05' into release_15.07 Commit: 30608c177c625f4ce66f1376a66621687fe7711e https://github.com/galaxyproject/galaxy/commit/30608c177c625f4ce66f1376a666… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 15.07.1 Compare: https://github.com/galaxyproject/galaxy/compare/ed992b3b28c7...30608c177c62

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[galaxyproject/galaxy] ca123a: Add a safe_relpath util function for ensuring a pa...
by GitHub 24 Feb '16

24 Feb '16

Branch: refs/heads/release_15.05 Home: https://github.com/galaxyproject/galaxy Commit: ca123a4f2674351e01235bab545559b299b99ff9 https://github.com/galaxyproject/galaxy/commit/ca123a4f2674351e01235bab5455… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Add a safe_relpath util function for ensuring a path does not reference an absolute or parent directory Commit: 3b963226a110b8de8aa11d3c4e053a220bbcba53 https://github.com/galaxyproject/galaxy/commit/3b963226a110b8de8aa11d3c4e05… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py Log Message: ----------- Security fixes for history imports Commit: 5ab53c3fda3a43236b444a31aa408c9f5cb5c4c4 https://github.com/galaxyproject/galaxy/commit/5ab53c3fda3a43236b444a31aa40… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Add a safe_relpath util function for ensuring a path does not reference an absolute or parent directory Commit: 88277c9723c558e2b2003f1b81c7f2d16143fcc6 https://github.com/galaxyproject/galaxy/commit/88277c9723c558e2b2003f1b81c7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py Log Message: ----------- Security fixes for history imports Commit: d650055ca824d5cf8ab1ede389e9b3060c1f4094 https://github.com/galaxyproject/galaxy/commit/d650055ca824d5cf8ab1ede389e9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py Log Message: ----------- Security fixes for object store paths Commit: 32c910ac4021b0e65112d557a7f12d24e158171d https://github.com/galaxyproject/galaxy/commit/32c910ac4021b0e65112d557a7f1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py Log Message: ----------- Security fixes for object store paths Commit: 37548ef8edb95d59fddd73283561e8b1a6588c10 https://github.com/galaxyproject/galaxy/commit/37548ef8edb95d59fddd73283561… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py R templates/admin/requests/select_datasets_to_transfer.mako M templates/webapps/galaxy/requests/common/common.mako M templates/webapps/galaxy/requests/common/view_request_history.mako M templates/webapps/galaxy/requests/common/view_sample_datasets.mako Log Message: ----------- Remove sample tracking manual external service transfer due to security concerns Commit: 78f441b9c7bfd68f7b3ee030f4ffe4a95b5fdc58 https://github.com/galaxyproject/galaxy/commit/78f441b9c7bfd68f7b3ee030f4ff… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py R templates/admin/requests/select_datasets_to_transfer.mako M templates/webapps/galaxy/requests/common/common.mako M templates/webapps/galaxy/requests/common/view_request_history.mako M templates/webapps/galaxy/requests/common/view_sample_datasets.mako Log Message: ----------- Remove sample tracking manual external service transfer due to security concerns Commit: 4f3397fa0ab187a4b5c32e1268265925fc1a8753 https://github.com/galaxyproject/galaxy/commit/4f3397fa0ab187a4b5c32e126826… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/util/shed_util_common.py M templates/admin/tool_shed_repository/common.mako M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Security fixes for tool shed repository browsing Commit: 8468871ee481598a84888b5329139590ec75e98d https://github.com/galaxyproject/galaxy/commit/8468871ee481598a84888b532913… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Add a safe_relpath util function for ensuring a path does not reference an absolute or parent directory Commit: cee85bae67377d3fad42bec5b4ebb022aaf7b2c7 https://github.com/galaxyproject/galaxy/commit/cee85bae67377d3fad42bec5b4eb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/util/shed_util_common.py M templates/admin/tool_shed_repository/common.mako M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Security fixes for tool shed repository browsing Commit: 4845a39071ab4e2652e564efdf7647a942563603 https://github.com/galaxyproject/galaxy/commit/4845a39071ab4e2652e564efdf76… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/repository_content_util.py Log Message: ----------- Security fixes for tool shed hg push and capsule/tarball uploads Commit: ef4a9f6e2114e69f6ea3167e99a857f2ea4d28af https://github.com/galaxyproject/galaxy/commit/ef4a9f6e2114e69f6ea3167e99a8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py Log Message: ----------- Security fixes for history imports Commit: 61cd045ffa947a69abacddea459f725ba569584a https://github.com/galaxyproject/galaxy/commit/61cd045ffa947a69abacddea459f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Log Message: ----------- Merge branch 'release_14.10' into release_15.01 Commit: 2a8089749caab12c087064c840708fb05b0104cd https://github.com/galaxyproject/galaxy/commit/2a8089749caab12c087064c84070… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Add a safe_relpath util function for ensuring a path does not reference an absolute or parent directory Commit: 6e3b74869a54558fe48d6e1633c5af7197051447 https://github.com/galaxyproject/galaxy/commit/6e3b74869a54558fe48d6e1633c5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py Log Message: ----------- Security fixes for history imports Commit: c8963786d53efd2cf3b359b2f9a000e00688285f https://github.com/galaxyproject/galaxy/commit/c8963786d53efd2cf3b359b2f9a0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py Log Message: ----------- Security fixes for object store paths Commit: ce88f2f81caff6af7dc730ef9c1fbc2a40922dab https://github.com/galaxyproject/galaxy/commit/ce88f2f81caff6af7dc730ef9c1f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py Log Message: ----------- Security fixes for object store paths Commit: d4b94722f992c9309aa2ec5bfa5bce2dacd9b218 https://github.com/galaxyproject/galaxy/commit/d4b94722f992c9309aa2ec5bfa5b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py R templates/admin/requests/select_datasets_to_transfer.mako M templates/webapps/galaxy/requests/common/common.mako M templates/webapps/galaxy/requests/common/view_request_history.mako M templates/webapps/galaxy/requests/common/view_sample_datasets.mako Log Message: ----------- Remove sample tracking manual external service transfer due to security concerns Commit: fcd8f50448cd1db7b50a58321c8fa391506bf997 https://github.com/galaxyproject/galaxy/commit/fcd8f50448cd1db7b50a58321c8f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py R templates/admin/requests/select_datasets_to_transfer.mako M templates/webapps/galaxy/requests/common/common.mako M templates/webapps/galaxy/requests/common/view_request_history.mako M templates/webapps/galaxy/requests/common/view_sample_datasets.mako Log Message: ----------- Remove sample tracking manual external service transfer due to security concerns Commit: 626cade512894e54c5b3e5257543f267a1826a71 https://github.com/galaxyproject/galaxy/commit/626cade512894e54c5b3e5257543… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/util/shed_util_common.py M templates/admin/tool_shed_repository/common.mako M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Security fixes for tool shed repository browsing Commit: 91f5fa81fe3c1c4d45b3987b27c187c4cb53f8e8 https://github.com/galaxyproject/galaxy/commit/91f5fa81fe3c1c4d45b3987b27c1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/util/shed_util_common.py M templates/admin/tool_shed_repository/common.mako M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Security fixes for tool shed repository browsing Commit: 581808aa98a6058a4bdbe13c21271ca4b0d3ef77 https://github.com/galaxyproject/galaxy/commit/581808aa98a6058a4bdbe13c2127… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/repository_content_util.py Log Message: ----------- Security fixes for tool shed hg push and capsule/tarball uploads Commit: 2bda436473b116c7d98c36a8435056745bf832f2 https://github.com/galaxyproject/galaxy/commit/2bda436473b116c7d98c36a84350… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/repository_content_util.py Log Message: ----------- Security fixes for tool shed hg push and capsule/tarball uploads Commit: f8a1aef76c022612a8a28938e1d57412348884ab https://github.com/galaxyproject/galaxy/commit/f8a1aef76c022612a8a28938e1d5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Log Message: ----------- Merge branch 'release_15.01' into release_15.03 Commit: f65bcb3383ba142d514b38ab5ed03d5f9ecd5f1d https://github.com/galaxyproject/galaxy/commit/f65bcb3383ba142d514b38ab5ed0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Log Message: ----------- Merge branch 'release_15.03' into release_15.05 Commit: 0122040fad865487e2377cee35360af49e37d0e8 https://github.com/galaxyproject/galaxy/commit/0122040fad865487e2377cee3536… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 15.03.4 Commit: 3516e94e5cb0e971d8e10de018b72cf22296766e https://github.com/galaxyproject/galaxy/commit/3516e94e5cb0e971d8e10de018b7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Log Message: ----------- Merge branch 'release_15.03' into release_15.05 Commit: c8e9845c5c57714042a75053d954b1c7f0962672 https://github.com/galaxyproject/galaxy/commit/c8e9845c5c57714042a75053d954… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 15.05.2 Compare: https://github.com/galaxyproject/galaxy/compare/0bf60a520594...c8e9845c5c57

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[galaxyproject/galaxy] ca123a: Add a safe_relpath util function for ensuring a pa...
by GitHub 24 Feb '16

24 Feb '16

Branch: refs/heads/release_15.03 Home: https://github.com/galaxyproject/galaxy Commit: ca123a4f2674351e01235bab545559b299b99ff9 https://github.com/galaxyproject/galaxy/commit/ca123a4f2674351e01235bab5455… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Add a safe_relpath util function for ensuring a path does not reference an absolute or parent directory Commit: 3b963226a110b8de8aa11d3c4e053a220bbcba53 https://github.com/galaxyproject/galaxy/commit/3b963226a110b8de8aa11d3c4e05… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py Log Message: ----------- Security fixes for history imports Commit: 5ab53c3fda3a43236b444a31aa408c9f5cb5c4c4 https://github.com/galaxyproject/galaxy/commit/5ab53c3fda3a43236b444a31aa40… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Add a safe_relpath util function for ensuring a path does not reference an absolute or parent directory Commit: 88277c9723c558e2b2003f1b81c7f2d16143fcc6 https://github.com/galaxyproject/galaxy/commit/88277c9723c558e2b2003f1b81c7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py Log Message: ----------- Security fixes for history imports Commit: d650055ca824d5cf8ab1ede389e9b3060c1f4094 https://github.com/galaxyproject/galaxy/commit/d650055ca824d5cf8ab1ede389e9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py Log Message: ----------- Security fixes for object store paths Commit: 32c910ac4021b0e65112d557a7f12d24e158171d https://github.com/galaxyproject/galaxy/commit/32c910ac4021b0e65112d557a7f1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py Log Message: ----------- Security fixes for object store paths Commit: 37548ef8edb95d59fddd73283561e8b1a6588c10 https://github.com/galaxyproject/galaxy/commit/37548ef8edb95d59fddd73283561… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py R templates/admin/requests/select_datasets_to_transfer.mako M templates/webapps/galaxy/requests/common/common.mako M templates/webapps/galaxy/requests/common/view_request_history.mako M templates/webapps/galaxy/requests/common/view_sample_datasets.mako Log Message: ----------- Remove sample tracking manual external service transfer due to security concerns Commit: 78f441b9c7bfd68f7b3ee030f4ffe4a95b5fdc58 https://github.com/galaxyproject/galaxy/commit/78f441b9c7bfd68f7b3ee030f4ff… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py R templates/admin/requests/select_datasets_to_transfer.mako M templates/webapps/galaxy/requests/common/common.mako M templates/webapps/galaxy/requests/common/view_request_history.mako M templates/webapps/galaxy/requests/common/view_sample_datasets.mako Log Message: ----------- Remove sample tracking manual external service transfer due to security concerns Commit: 4f3397fa0ab187a4b5c32e1268265925fc1a8753 https://github.com/galaxyproject/galaxy/commit/4f3397fa0ab187a4b5c32e126826… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/util/shed_util_common.py M templates/admin/tool_shed_repository/common.mako M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Security fixes for tool shed repository browsing Commit: 8468871ee481598a84888b5329139590ec75e98d https://github.com/galaxyproject/galaxy/commit/8468871ee481598a84888b532913… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Add a safe_relpath util function for ensuring a path does not reference an absolute or parent directory Commit: cee85bae67377d3fad42bec5b4ebb022aaf7b2c7 https://github.com/galaxyproject/galaxy/commit/cee85bae67377d3fad42bec5b4eb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/util/shed_util_common.py M templates/admin/tool_shed_repository/common.mako M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Security fixes for tool shed repository browsing Commit: 4845a39071ab4e2652e564efdf7647a942563603 https://github.com/galaxyproject/galaxy/commit/4845a39071ab4e2652e564efdf76… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/repository_content_util.py Log Message: ----------- Security fixes for tool shed hg push and capsule/tarball uploads Commit: ef4a9f6e2114e69f6ea3167e99a857f2ea4d28af https://github.com/galaxyproject/galaxy/commit/ef4a9f6e2114e69f6ea3167e99a8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py Log Message: ----------- Security fixes for history imports Commit: 61cd045ffa947a69abacddea459f725ba569584a https://github.com/galaxyproject/galaxy/commit/61cd045ffa947a69abacddea459f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Log Message: ----------- Merge branch 'release_14.10' into release_15.01 Commit: c8963786d53efd2cf3b359b2f9a000e00688285f https://github.com/galaxyproject/galaxy/commit/c8963786d53efd2cf3b359b2f9a0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py Log Message: ----------- Security fixes for object store paths Commit: d4b94722f992c9309aa2ec5bfa5bce2dacd9b218 https://github.com/galaxyproject/galaxy/commit/d4b94722f992c9309aa2ec5bfa5b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py R templates/admin/requests/select_datasets_to_transfer.mako M templates/webapps/galaxy/requests/common/common.mako M templates/webapps/galaxy/requests/common/view_request_history.mako M templates/webapps/galaxy/requests/common/view_sample_datasets.mako Log Message: ----------- Remove sample tracking manual external service transfer due to security concerns Commit: 626cade512894e54c5b3e5257543f267a1826a71 https://github.com/galaxyproject/galaxy/commit/626cade512894e54c5b3e5257543… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/util/shed_util_common.py M templates/admin/tool_shed_repository/common.mako M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Security fixes for tool shed repository browsing Commit: 581808aa98a6058a4bdbe13c21271ca4b0d3ef77 https://github.com/galaxyproject/galaxy/commit/581808aa98a6058a4bdbe13c2127… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/repository_content_util.py Log Message: ----------- Security fixes for tool shed hg push and capsule/tarball uploads Commit: f8a1aef76c022612a8a28938e1d57412348884ab https://github.com/galaxyproject/galaxy/commit/f8a1aef76c022612a8a28938e1d5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Log Message: ----------- Merge branch 'release_15.01' into release_15.03 Commit: 0122040fad865487e2377cee35360af49e37d0e8 https://github.com/galaxyproject/galaxy/commit/0122040fad865487e2377cee3536… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 15.03.4 Compare: https://github.com/galaxyproject/galaxy/compare/b23acda7d865...0122040fad86

1 0

[galaxyproject/galaxy] ca123a: Add a safe_relpath util function for ensuring a pa...
by GitHub 24 Feb '16

24 Feb '16

Branch: refs/heads/release_15.01 Home: https://github.com/galaxyproject/galaxy Commit: ca123a4f2674351e01235bab545559b299b99ff9 https://github.com/galaxyproject/galaxy/commit/ca123a4f2674351e01235bab5455… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Add a safe_relpath util function for ensuring a path does not reference an absolute or parent directory Commit: 3b963226a110b8de8aa11d3c4e053a220bbcba53 https://github.com/galaxyproject/galaxy/commit/3b963226a110b8de8aa11d3c4e05… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py Log Message: ----------- Security fixes for history imports Commit: 5ab53c3fda3a43236b444a31aa408c9f5cb5c4c4 https://github.com/galaxyproject/galaxy/commit/5ab53c3fda3a43236b444a31aa40… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Add a safe_relpath util function for ensuring a path does not reference an absolute or parent directory Commit: 88277c9723c558e2b2003f1b81c7f2d16143fcc6 https://github.com/galaxyproject/galaxy/commit/88277c9723c558e2b2003f1b81c7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py Log Message: ----------- Security fixes for history imports Commit: d650055ca824d5cf8ab1ede389e9b3060c1f4094 https://github.com/galaxyproject/galaxy/commit/d650055ca824d5cf8ab1ede389e9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py Log Message: ----------- Security fixes for object store paths Commit: 32c910ac4021b0e65112d557a7f12d24e158171d https://github.com/galaxyproject/galaxy/commit/32c910ac4021b0e65112d557a7f1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py Log Message: ----------- Security fixes for object store paths Commit: 37548ef8edb95d59fddd73283561e8b1a6588c10 https://github.com/galaxyproject/galaxy/commit/37548ef8edb95d59fddd73283561… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py R templates/admin/requests/select_datasets_to_transfer.mako M templates/webapps/galaxy/requests/common/common.mako M templates/webapps/galaxy/requests/common/view_request_history.mako M templates/webapps/galaxy/requests/common/view_sample_datasets.mako Log Message: ----------- Remove sample tracking manual external service transfer due to security concerns Commit: 78f441b9c7bfd68f7b3ee030f4ffe4a95b5fdc58 https://github.com/galaxyproject/galaxy/commit/78f441b9c7bfd68f7b3ee030f4ff… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py R templates/admin/requests/select_datasets_to_transfer.mako M templates/webapps/galaxy/requests/common/common.mako M templates/webapps/galaxy/requests/common/view_request_history.mako M templates/webapps/galaxy/requests/common/view_sample_datasets.mako Log Message: ----------- Remove sample tracking manual external service transfer due to security concerns Commit: 4f3397fa0ab187a4b5c32e1268265925fc1a8753 https://github.com/galaxyproject/galaxy/commit/4f3397fa0ab187a4b5c32e126826… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/util/shed_util_common.py M templates/admin/tool_shed_repository/common.mako M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Security fixes for tool shed repository browsing Commit: cee85bae67377d3fad42bec5b4ebb022aaf7b2c7 https://github.com/galaxyproject/galaxy/commit/cee85bae67377d3fad42bec5b4eb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/util/shed_util_common.py M templates/admin/tool_shed_repository/common.mako M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Security fixes for tool shed repository browsing Commit: 4845a39071ab4e2652e564efdf7647a942563603 https://github.com/galaxyproject/galaxy/commit/4845a39071ab4e2652e564efdf76… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/repository_content_util.py Log Message: ----------- Security fixes for tool shed hg push and capsule/tarball uploads Commit: 61cd045ffa947a69abacddea459f725ba569584a https://github.com/galaxyproject/galaxy/commit/61cd045ffa947a69abacddea459f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Log Message: ----------- Merge branch 'release_14.10' into release_15.01 Compare: https://github.com/galaxyproject/galaxy/compare/46e67b5bfa04...61cd045ffa94

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[galaxyproject/galaxy] ca123a: Add a safe_relpath util function for ensuring a pa...
by GitHub 24 Feb '16

24 Feb '16

Branch: refs/heads/release_14.10 Home: https://github.com/galaxyproject/galaxy Commit: ca123a4f2674351e01235bab545559b299b99ff9 https://github.com/galaxyproject/galaxy/commit/ca123a4f2674351e01235bab5455… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Add a safe_relpath util function for ensuring a path does not reference an absolute or parent directory Commit: 3b963226a110b8de8aa11d3c4e053a220bbcba53 https://github.com/galaxyproject/galaxy/commit/3b963226a110b8de8aa11d3c4e05… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py Log Message: ----------- Security fixes for history imports Commit: 32c910ac4021b0e65112d557a7f12d24e158171d https://github.com/galaxyproject/galaxy/commit/32c910ac4021b0e65112d557a7f1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py Log Message: ----------- Security fixes for object store paths Commit: 78f441b9c7bfd68f7b3ee030f4ffe4a95b5fdc58 https://github.com/galaxyproject/galaxy/commit/78f441b9c7bfd68f7b3ee030f4ff… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py R templates/admin/requests/select_datasets_to_transfer.mako M templates/webapps/galaxy/requests/common/common.mako M templates/webapps/galaxy/requests/common/view_request_history.mako M templates/webapps/galaxy/requests/common/view_sample_datasets.mako Log Message: ----------- Remove sample tracking manual external service transfer due to security concerns Commit: cee85bae67377d3fad42bec5b4ebb022aaf7b2c7 https://github.com/galaxyproject/galaxy/commit/cee85bae67377d3fad42bec5b4eb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/util/shed_util_common.py M templates/admin/tool_shed_repository/common.mako M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Security fixes for tool shed repository browsing Compare: https://github.com/galaxyproject/galaxy/compare/360a6ad76d43...cee85bae6737

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[galaxyproject/galaxy] a47a4f: Remove len(stderr), breaks on recent docker versio...
by GitHub 24 Feb '16

24 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a47a4f40b47302c43dea33f8b040f41570b0587c https://github.com/galaxyproject/galaxy/commit/a47a4f40b47302c43dea33f8b040… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Remove len(stderr), breaks on recent docker versions Commit: f2a27acff8fd5d199eda841fd575305c3644c439 https://github.com/galaxyproject/galaxy/commit/f2a27acff8fd5d199eda841fd575… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M doc/source/releases/16.01_announce.rst Log Message: ----------- Drop Python 2.6 with 16.04. xref #1596 Commit: b4020934793829f3735fa696de1fa3237391d945 https://github.com/galaxyproject/galaxy/commit/b4020934793829f3735fa696de1f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M lib/galaxy/workflow/modules.py M test/functional/tools/output_format.xml Log Message: ----------- format_source in workflow editor is too restrictive. Case made well by @erasche on #1746, fixes #1746. To resolve this more correctly (and many other potential type problems) - the workflow editor should be significantly reworked to track the datatype (or a range of datatypes) on each terminal (the way it does for collection mapping information). The change would be a weeks worth of development effort and inappropriate to apply to a release branch. Commit: 9acbfdf3c3444ca0cb0cf87f80c57d00765673d9 https://github.com/galaxyproject/galaxy/commit/9acbfdf3c3444ca0cb0cf87f80c5… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M client/galaxy/style/less/base.less M client/galaxy/style/less/ui/icon-btn.less M static/style/blue/base.css Log Message: ----------- Fix chrome-only intermittent rendering error of font awesome icons that have their sizes changed by overriding 4.2 font-size inheritance rule from core.less Commit: 3621d6f2212566b8a172424177b8eafc92af7fca https://github.com/galaxyproject/galaxy/commit/3621d6f2212566b8a172424177b8… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M client/galaxy/style/less/base.less M client/galaxy/style/less/ui/icon-btn.less M static/style/blue/base.css Log Message: ----------- Merge pull request #1784 from carlfeberhard/fix.fa [16.01] Fix chrome-only intermittent rendering error of font awesome icons th… Commit: 805b5906b2f43947af36814fe67b5914acc35a08 https://github.com/galaxyproject/galaxy/commit/805b5906b2f43947af36814fe67b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M doc/source/releases/16.01_announce.rst Log Message: ----------- Merge pull request #1772 from jmchilton/python26_drop [16.01] Deprecation notice - Python 2.6. Commit: a5c30c563e878c3b0171bdc992eaea248e2371cf https://github.com/galaxyproject/galaxy/commit/a5c30c563e878c3b0171bdc992ea… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #1771 from mvdbeek/16.01_fix_ies [16.01] Remove len(stderr), breaks on recent docker versions Commit: 6bb43aa4aff83f832997d01fc5663b9d501bc866 https://github.com/galaxyproject/galaxy/commit/6bb43aa4aff83f832997d01fc566… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M lib/galaxy/workflow/modules.py M test/functional/tools/output_format.xml Log Message: ----------- Merge pull request #1786 from jmchilton/format_source_restrictive [16.01] format_source in workflow editor is too restrictive. Commit: 1f530b45b3d6815a4ff876fda98ca57bf7a2ef89 https://github.com/galaxyproject/galaxy/commit/1f530b45b3d6815a4ff876fda98c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M client/galaxy/style/less/base.less M client/galaxy/style/less/ui/icon-btn.less M doc/source/releases/16.01_announce.rst M lib/galaxy/workflow/modules.py M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/style/blue/base.css M test/functional/tools/output_format.xml Log Message: ----------- Merge branch 'release_16.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/2a64fac0c7bf...1f530b45b3d6

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[galaxyproject/galaxy] b40209: format_source in workflow editor is too restrictiv...
by GitHub 23 Feb '16

23 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: b4020934793829f3735fa696de1fa3237391d945 https://github.com/galaxyproject/galaxy/commit/b4020934793829f3735fa696de1f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M lib/galaxy/workflow/modules.py M test/functional/tools/output_format.xml Log Message: ----------- format_source in workflow editor is too restrictive. Case made well by @erasche on #1746, fixes #1746. To resolve this more correctly (and many other potential type problems) - the workflow editor should be significantly reworked to track the datatype (or a range of datatypes) on each terminal (the way it does for collection mapping information). The change would be a weeks worth of development effort and inappropriate to apply to a release branch. Commit: 6bb43aa4aff83f832997d01fc5663b9d501bc866 https://github.com/galaxyproject/galaxy/commit/6bb43aa4aff83f832997d01fc566… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M lib/galaxy/workflow/modules.py M test/functional/tools/output_format.xml Log Message: ----------- Merge pull request #1786 from jmchilton/format_source_restrictive [16.01] format_source in workflow editor is too restrictive. Compare: https://github.com/galaxyproject/galaxy/compare/a5c30c563e87...6bb43aa4aff8

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[galaxyproject/galaxy] c8469b: Refactor the Html Datatype Class into text.py inst...
by GitHub 23 Feb '16

23 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c8469b7d0e788eb0a1b4e80b686eebfd5a3e6d11 https://github.com/galaxyproject/galaxy/commit/c8469b7d0e788eb0a1b4e80b686e… Author: Remi Marenco <remi.marenco(a)gmail.com> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/text.py M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Refactor the Html Datatype Class into text.py instead of images.py Commit: 2a64fac0c7bf098b1c459055b6d145f07b4d178a https://github.com/galaxyproject/galaxy/commit/2a64fac0c7bf098b1c459055b6d1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/text.py M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Merge pull request #1760 from remimarenco/html_refactoring Refactor the Html Datatype Class into text.py instead of images.py Compare: https://github.com/galaxyproject/galaxy/compare/a41f4750179c...2a64fac0c7bf

1 0

[galaxyproject/galaxy] a47a4f: Remove len(stderr), breaks on recent docker versio...
by GitHub 23 Feb '16

23 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: a47a4f40b47302c43dea33f8b040f41570b0587c https://github.com/galaxyproject/galaxy/commit/a47a4f40b47302c43dea33f8b040… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Remove len(stderr), breaks on recent docker versions Commit: a5c30c563e878c3b0171bdc992eaea248e2371cf https://github.com/galaxyproject/galaxy/commit/a5c30c563e878c3b0171bdc992ea… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #1771 from mvdbeek/16.01_fix_ies [16.01] Remove len(stderr), breaks on recent docker versions Compare: https://github.com/galaxyproject/galaxy/compare/805b5906b2f4...a5c30c563e87

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