Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 84c59917e6e0c4b90d4f29720d547de816302230 https://github.com/galaxyproject/galaxy/commit/84c59917e6e0c4b90d4f29720d547... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M lib/galaxy/security/passwords.py Log Message: ----------- Allow non-ascii chars in passwords. Commit: 65c1cd761c48ba121a847d4d501eb8a97a911e70 https://github.com/galaxyproject/galaxy/commit/65c1cd761c48ba121a847d4d501eb... Author: John Chilton <jmchilton@gmail.com> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/upload_util.py M lib/galaxy/jobs/__init__.py M lib/galaxy_ext/metadata/set_metadata.py Log Message: ----------- Fix data_source.py for upload changes in 18.05 release cycle. handle_uploaded_dataset_file was used by tools external to ``lib/`` include data_source.py and potentially tools in the tool shed. This restores the interface as a wrapper around a new method handle_uploaded_dataset_file_internal. Broken in https://github.com/galaxyproject/galaxy/commit/ef6f7f62ab679928045c816a3cb71... I believe. Commit: 44e57ba8b45d2ddd624333547ec1adeb62d70b9c https://github.com/galaxyproject/galaxy/commit/44e57ba8b45d2ddd624333547ec1a... Author: Nicola Soranzo <nicola.soranzo@gmail.com> Date: 2018-05-23 (Wed, 23 May 2018) Changed paths: M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/upload_util.py M lib/galaxy/jobs/__init__.py M lib/galaxy_ext/metadata/set_metadata.py Log Message: ----------- Merge pull request #6196 from jmchilton/fix_metadata [18.05] Fix data_source.py for upload changes in 18.05 release cycle. Commit: 72d07e07d5164519e31bfe5811ce9dbd980ecf1e https://github.com/galaxyproject/galaxy/commit/72d07e07d5164519e31bfe5811ce9... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-23 (Wed, 23 May 2018) Changed paths: R doc/source/releases/18.09_announce.rst M doc/source/releases/index.rst Log Message: ----------- remove mention of 18.09, that is only for dev Commit: a8e0eda44db84f756004e266865d16d0fb13eb3e https://github.com/galaxyproject/galaxy/commit/a8e0eda44db84f756004e266865d1... Author: John Chilton <jmchilton@gmail.com> Date: 2018-05-23 (Wed, 23 May 2018) Changed paths: M lib/galaxy/security/passwords.py Log Message: ----------- Merge pull request #6175 from dannon/password_fixes [18.05] Allow non-ascii chars in pbkdf2 passwords Commit: 55f7280d790fcaf9bc74d543f22541d86521cef0 https://github.com/galaxyproject/galaxy/commit/55f7280d790fcaf9bc74d543f2254... Author: John Chilton <jmchilton@gmail.com> Date: 2018-05-23 (Wed, 23 May 2018) Changed paths: M lib/galaxy/security/passwords.py A test/unit/test_security_passwords.py Log Message: ----------- More password encoding handling fixes. Fix handling comparison of older hashes in Python 2 and fix the hanlding of both for Python 3. The previous iteration gave me some errors in Python 3, I brought in and adapted @mvdbeek's Python 3 fixes to fix these: ``` ====================================================================== ERROR: test_security_passwords.test_hash_and_check ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/john/workspace/galaxy-lib/.tox/py34/lib/python3.4/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) File "/Users/john/workspace/galaxy-lib/tests/test_security_passwords.py", line 12, in test_hash_and_check simple_pass_hash = passwords.hash_password(simple_pass) File "/Users/john/workspace/galaxy-lib/galaxy/security/passwords.py", line 21, in hash_password return hash_password_PBKDF2(password) File "/Users/john/workspace/galaxy-lib/galaxy/security/passwords.py", line 44, in hash_password_PBKDF2 hashed = pbkdf2_bin(smart_str(password), salt, COST_FACTOR, KEY_LENGTH, getattr(hashlib, HASH_FUNCTION)) File "/Users/john/workspace/galaxy-lib/galaxy/security/passwords.py", line 78, in pbkdf2_bin rv = u = _pseudorandom(salt + _pack_int(block)) File "/Users/john/workspace/galaxy-lib/galaxy/security/passwords.py", line 75, in _pseudorandom return [ord(_) for _ in h.digest()] File "/Users/john/workspace/galaxy-lib/galaxy/security/passwords.py", line 75, in <listcomp> return [ord(_) for _ in h.digest()] TypeError: ord() expected string of length 1, but int found ====================================================================== ERROR: test_security_passwords.test_hash_consistent ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/john/workspace/galaxy-lib/.tox/py34/lib/python3.4/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) File "/Users/john/workspace/galaxy-lib/tests/test_security_passwords.py", line 38, in test_hash_consistent assert passwords.check_password(simple_pass, simple_pass_hash) File "/Users/john/workspace/galaxy-lib/galaxy/security/passwords.py", line 30, in check_password if check_password_PBKDF2(guess, hashed): File "/Users/john/workspace/galaxy-lib/galaxy/security/passwords.py", line 53, in check_password_PBKDF2 hashed_guess = pbkdf2_bin(smart_str(guess), salt, int(cost_factor), KEY_LENGTH, getattr(hashlib, hash_function)) File "/Users/john/workspace/galaxy-lib/galaxy/security/passwords.py", line 78, in pbkdf2_bin rv = u = _pseudorandom(salt + _pack_int(block)) TypeError: Can't convert 'bytes' object to str implicitly ``` Added tests that all now pass in Python 3 - including generating some passwords in Python 3 and verifying they pass when checked in Python 2 and vice versa. Commit: a301d240165f0c14acc7126b36084293bdb59e45 https://github.com/galaxyproject/galaxy/commit/a301d240165f0c14acc7126b36084... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-05-23 (Wed, 23 May 2018) Changed paths: M lib/galaxy/tools/deps/containers.py Log Message: ----------- Fix for loading container resolvers config file Commit: bd049665d1201a3c35d3bd1e3ff48891cd54fbcd https://github.com/galaxyproject/galaxy/commit/bd049665d1201a3c35d3bd1e3ff48... Author: John Chilton <jmchilton@gmail.com> Date: 2018-05-23 (Wed, 23 May 2018) Changed paths: R doc/source/releases/18.09_announce.rst M doc/source/releases/index.rst Log Message: ----------- Merge pull request #6203 from martenson/remove-1809 [18.05] remove mention of 18.09, that is only for dev Commit: ab656c7e2d57cce71006c519e5c737617ac04084 https://github.com/galaxyproject/galaxy/commit/ab656c7e2d57cce71006c519e5c73... Author: Dannon <dannon.baker@gmail.com> Date: 2018-05-23 (Wed, 23 May 2018) Changed paths: M lib/galaxy/tools/deps/containers.py Log Message: ----------- Merge pull request #6205 from natefoo/container-resolvers-conf-fix [18.05] Container resolvers conf fix Commit: ec5924dd649ccd4936398c9df82000c1f1ce4a24 https://github.com/galaxyproject/galaxy/commit/ec5924dd649ccd4936398c9df8200... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-23 (Wed, 23 May 2018) Changed paths: M lib/galaxy/security/passwords.py A test/unit/test_security_passwords.py Log Message: ----------- Merge pull request #6204 from jmchilton/password_fixes [18.05] More password encoding handling fixes. Commit: 2ab75d861bd74ae718893ca6a97015960f9036de https://github.com/galaxyproject/galaxy/commit/2ab75d861bd74ae718893ca6a9701... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-05-23 (Wed, 23 May 2018) Changed paths: R doc/source/releases/18.09_announce.rst M doc/source/releases/index.rst M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/upload_util.py M lib/galaxy/jobs/__init__.py M lib/galaxy/security/passwords.py M lib/galaxy/tools/deps/containers.py M lib/galaxy_ext/metadata/set_metadata.py A test/unit/test_security_passwords.py Log Message: ----------- Merge remote-tracking branch 'origin/release_18.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/a57600cadfe4...2ab75d861bd7 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.