Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ca123a4f2674351e01235bab545559b299b99ff9 https://github.com/galaxyproject/galaxy/commit/ca123a4f2674351e01235bab54555... Author: Nate Coraor <nate@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/3b963226a110b8de8aa11d3c4e053... Author: Nate Coraor <nate@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/5ab53c3fda3a43236b444a31aa408... Author: Nate Coraor <nate@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/88277c9723c558e2b2003f1b81c7f... Author: Nate Coraor <nate@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/d650055ca824d5cf8ab1ede389e9b... Author: Nate Coraor <nate@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/32c910ac4021b0e65112d557a7f12... Author: Nate Coraor <nate@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/37548ef8edb95d59fddd73283561e... Author: Nate Coraor <nate@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/78f441b9c7bfd68f7b3ee030f4ffe... Author: Nate Coraor <nate@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/4f3397fa0ab187a4b5c32e1268265... Author: Nate Coraor <nate@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/8468871ee481598a84888b5329139... Author: Nate Coraor <nate@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/cee85bae67377d3fad42bec5b4ebb... Author: Nate Coraor <nate@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/4845a39071ab4e2652e564efdf764... Author: Nate Coraor <nate@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/ef4a9f6e2114e69f6ea3167e99a85... Author: Nate Coraor <nate@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/61cd045ffa947a69abacddea459f7... Author: Nate Coraor <nate@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/2a8089749caab12c087064c840708... Author: Nate Coraor <nate@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/6e3b74869a54558fe48d6e1633c5a... Author: Nate Coraor <nate@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/c8963786d53efd2cf3b359b2f9a00... Author: Nate Coraor <nate@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/ce88f2f81caff6af7dc730ef9c1fb... Author: Nate Coraor <nate@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/d4b94722f992c9309aa2ec5bfa5bc... Author: Nate Coraor <nate@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/fcd8f50448cd1db7b50a58321c8fa... Author: Nate Coraor <nate@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/626cade512894e54c5b3e5257543f... Author: Nate Coraor <nate@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/91f5fa81fe3c1c4d45b3987b27c18... Author: Nate Coraor <nate@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/581808aa98a6058a4bdbe13c21271... Author: Nate Coraor <nate@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/2bda436473b116c7d98c36a843505... Author: Nate Coraor <nate@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/f8a1aef76c022612a8a28938e1d57... Author: Nate Coraor <nate@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/47a8b6e86733472ad3c0dbe2d5774... Author: Nate Coraor <nate@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/6190f6fa6db26ada3380c9a54b548... Author: Nate Coraor <nate@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/27d7298ec4788a2e59a5988007fde... Author: Nate Coraor <nate@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/c465489ea1676905ddb4cfb88605c... Author: Nate Coraor <nate@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/18b3126a15ec7fe3873253be0c134... Author: Nate Coraor <nate@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/40a90831ed28b762e90cf2b50abec... Author: Nate Coraor <nate@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/f65bcb3383ba142d514b38ab5ed03... Author: Nate Coraor <nate@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/ab1a135dd4a422897c74ea87e5210... Author: Nate Coraor <nate@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/b3e0315e1e40912366c8103412e64... Author: Nate Coraor <nate@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/8736c7bd77bd3c5cd38225538085c... Author: Nate Coraor <nate@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/23e203c48180b6ab1e4886be81447... Author: Nate Coraor <nate@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/64cd02ae385fb509378c78e6e4832... Author: Nate Coraor <nate@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/2dcbda93b29e4dd975453af8eeb4f... Author: Nate Coraor <nate@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/b11b8e68500a3d074bf20b0895867... Author: Nate Coraor <nate@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: f540a16768307995ea49c5d241948537ebbfa540 https://github.com/galaxyproject/galaxy/commit/f540a16768307995ea49c5d241948... Author: Nate Coraor <nate@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: bf1c77d171f079f42d481ad465dbaef3bac8b4d4 https://github.com/galaxyproject/galaxy/commit/bf1c77d171f079f42d481ad465dba... Author: Nate Coraor <nate@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: 5da91bddcda3ad3a4942e752d9b4bb3e7872046c https://github.com/galaxyproject/galaxy/commit/5da91bddcda3ad3a4942e752d9b4b... Author: Nate Coraor <nate@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: cd8b96553f673145ee64a86d32960ba42643baed https://github.com/galaxyproject/galaxy/commit/cd8b96553f673145ee64a86d32960... Author: Nate Coraor <nate@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: e4a1d5727805168a9fd15aca1cdd21630ada2bbc https://github.com/galaxyproject/galaxy/commit/e4a1d5727805168a9fd15aca1cdd2... Author: Nate Coraor <nate@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: e845d649c672c51cc2336da0d880c9ff74ea6b5f https://github.com/galaxyproject/galaxy/commit/e845d649c672c51cc2336da0d880c... Author: Nate Coraor <nate@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/8c4542b136ef1eab3231ba0df4aab... Author: Nate Coraor <nate@bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Log Message: ----------- Merge branch 'release_15.07' into release_15.10 Commit: 61b59b2082c021feec8ac0ffb17302bb8068633b https://github.com/galaxyproject/galaxy/commit/61b59b2082c021feec8ac0ffb1730... Author: Nate Coraor <nate@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: 7c4b8ff7475735ee14231780545fd99fff5d2b12 https://github.com/galaxyproject/galaxy/commit/7c4b8ff7475735ee14231780545fd... Author: Nate Coraor <nate@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: ffcd4fe1925368eae6cb3aac30eb6bbc5e7976e5 https://github.com/galaxyproject/galaxy/commit/ffcd4fe1925368eae6cb3aac30eb6... Author: Nate Coraor <nate@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: 9e6afea498831f1e4fb1b86a6ff7bf4833ef7be1 https://github.com/galaxyproject/galaxy/commit/9e6afea498831f1e4fb1b86a6ff7b... Author: Nate Coraor <nate@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: 3a006766d3d8ff6f7d745e9f2d25798b6d030a8d https://github.com/galaxyproject/galaxy/commit/3a006766d3d8ff6f7d745e9f2d257... Author: Nate Coraor <nate@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: 624e3837bd3d2dffdee7737f4e55d2e66316896a https://github.com/galaxyproject/galaxy/commit/624e3837bd3d2dffdee7737f4e55d... Author: Nate Coraor <nate@bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Log Message: ----------- Merge branch 'release_15.10' into release_16.01 Commit: ed82982f9b15652628f89a3f203fb5e725a491f9 https://github.com/galaxyproject/galaxy/commit/ed82982f9b15652628f89a3f203fb... Author: Nate Coraor <nate@bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Log Message: ----------- Merge branch 'release_16.01' into dev Commit: c6b010af346d0fed5bba7e5610ea59210be5ceb7 https://github.com/galaxyproject/galaxy/commit/c6b010af346d0fed5bba7e5610ea5... Author: Nate Coraor <nate@bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M doc/source/releases/16.01.rst M doc/source/releases/16.01_announce.rst Log Message: ----------- Add security announcement to v16.01 release notes. Commit: 63d7b7a212f7ac9890b00fd560e8b531a2eb1de0 https://github.com/galaxyproject/galaxy/commit/63d7b7a212f7ac9890b00fd560e8b... Author: Nate Coraor <nate@bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M doc/source/releases/16.01.rst M doc/source/releases/16.01_announce.rst Log Message: ----------- Merge branch 'release_16.01' into dev Commit: 0122040fad865487e2377cee35360af49e37d0e8 https://github.com/galaxyproject/galaxy/commit/0122040fad865487e2377cee35360... Author: Nate Coraor <nate@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/3516e94e5cb0e971d8e10de018b72... Author: Nate Coraor <nate@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/c8e9845c5c57714042a75053d954b... Author: Nate Coraor <nate@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/3d832aff0abe5a4ca48bfc80c8403... Author: Nate Coraor <nate@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/30608c177c625f4ce66f1376a6662... Author: Nate Coraor <nate@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/21cc5b2da540eba18445603146407... Author: Nate Coraor <nate@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/b5949bcbbfbc613b0ec72ce23e4da... Author: Nate Coraor <nate@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 Commit: 70329f64ab8b6dcf9e9a6b6762783543b49c36eb https://github.com/galaxyproject/galaxy/commit/70329f64ab8b6dcf9e9a6b6762783... Author: Nate Coraor <nate@bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Log Message: ----------- Merge branch 'release_15.10' into release_16.01 Commit: 0771e4731cfdfc352aeb0a682edd52753ea50fca https://github.com/galaxyproject/galaxy/commit/0771e4731cfdfc352aeb0a682edd5... Author: Nate Coraor <nate@bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Log Message: ----------- Merge branch 'release_16.01' into dev Commit: 5677c2ee4fce70c9898ea5e6cae125b6147ae36a https://github.com/galaxyproject/galaxy/commit/5677c2ee4fce70c9898ea5e6cae12... Author: Nate Coraor <nate@bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 16.01 Commit: 2656f11b513adf05a2bb76daf54dd5ecab4d2f9c https://github.com/galaxyproject/galaxy/commit/2656f11b513adf05a2bb76daf54dd... Author: Nate Coraor <nate@bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Log Message: ----------- Merge branch 'version-16.01' into version-16.04.dev Compare: https://github.com/galaxyproject/galaxy/compare/1f530b45b3d6...2656f11b513a