May 2018 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 55f728: More password encoding handling fixes.
by GitHub 23 May '18

23 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 55f7280d790fcaf9bc74d543f22541d86521cef0 https://github.com/galaxyproject/galaxy/commit/55f7280d790fcaf9bc74d543f225… Author: John Chilton <jmchilton(a)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: ec5924dd649ccd4936398c9df82000c1f1ce4a24 https://github.com/galaxyproject/galaxy/commit/ec5924dd649ccd4936398c9df820… Author: Martin Cech <marten(a)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. Compare: https://github.com/galaxyproject/galaxy/compare/ab656c7e2d57...ec5924dd649c **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.

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[galaxyproject/galaxy] a301d2: Fix for loading container resolvers config file
by GitHub 23 May '18

23 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: a301d240165f0c14acc7126b36084293bdb59e45 https://github.com/galaxyproject/galaxy/commit/a301d240165f0c14acc7126b3608… Author: Nate Coraor <nate(a)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: ab656c7e2d57cce71006c519e5c737617ac04084 https://github.com/galaxyproject/galaxy/commit/ab656c7e2d57cce71006c519e5c7… Author: Dannon <dannon.baker(a)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 Compare: https://github.com/galaxyproject/galaxy/compare/bd049665d120...ab656c7e2d57 **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.

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[galaxyproject/galaxy] 72d07e: remove mention of 18.09, that is only for dev
by GitHub 23 May '18

23 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 72d07e07d5164519e31bfe5811ce9dbd980ecf1e https://github.com/galaxyproject/galaxy/commit/72d07e07d5164519e31bfe5811ce… Author: Martin Cech <marten(a)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: bd049665d1201a3c35d3bd1e3ff48891cd54fbcd https://github.com/galaxyproject/galaxy/commit/bd049665d1201a3c35d3bd1e3ff4… Author: John Chilton <jmchilton(a)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 Compare: https://github.com/galaxyproject/galaxy/compare/a8e0eda44db8...bd049665d120 **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.

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[galaxyproject/usegalaxy-playbook] 980595: Update Test
by GitHub 23 May '18

23 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 980595026090b885992705a0a5531b009de47054 https://github.com/galaxyproject/usegalaxy-playbook/commit/980595026090b885… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-23 (Wed, 23 May 2018) Changed paths: M env/test/files/galaxy/galaxy_version.yml M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/group_vars/all.yml Log Message: ----------- Update Test **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.

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[galaxyproject/galaxy] 84c599: Allow non-ascii chars in passwords.
by GitHub 23 May '18

23 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 84c59917e6e0c4b90d4f29720d547de816302230 https://github.com/galaxyproject/galaxy/commit/84c59917e6e0c4b90d4f29720d54… Author: Dannon Baker <dannon.baker(a)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: a8e0eda44db84f756004e266865d16d0fb13eb3e https://github.com/galaxyproject/galaxy/commit/a8e0eda44db84f756004e266865d… Author: John Chilton <jmchilton(a)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 Compare: https://github.com/galaxyproject/galaxy/compare/44e57ba8b45d...a8e0eda44db8 **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.

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[galaxyproject/galaxy] 7bf55f: Fix history list bottom border
by GitHub 23 May '18

23 May '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7bf55fc301cb6819b371e25030014cde830c05c9 https://github.com/galaxyproject/galaxy/commit/7bf55fc301cb6819b371e2503001… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M client/galaxy/style/scss/history.scss M static/style/blue/base.css Log Message: ----------- Fix history list bottom border Commit: 029975a9f8abe57b6f4ef9d9a9cc50a07f401113 https://github.com/galaxyproject/galaxy/commit/029975a9f8abe57b6f4ef9d9a9cc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M client/galaxy/style/scss/history.scss Log Message: ----------- A more accurate version of what was set before, with the same outcome (though, it could change if we toggle the grey) Commit: 8d1cff2bba25c70baeebf8fde0878b4e5caa8b2f https://github.com/galaxyproject/galaxy/commit/8d1cff2bba25c70baeebf8fde087… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M client/galaxy/style/scss/list-item.scss M static/style/blue/base.css Log Message: ----------- Fix dataset messagesmall display, was a TODO left from migration Commit: e06639e9456ba022ce6a12e4eba15a696fb37e51 https://github.com/galaxyproject/galaxy/commit/e06639e9456ba022ce6a12e4eba1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M client/galaxy/style/scss/history.scss M static/style/blue/base.css Log Message: ----------- Fix one more busted fade Commit: eadfd406d238b5ef7ad97c964a44e39d6a9d46e9 https://github.com/galaxyproject/galaxy/commit/eadfd406d238b5ef7ad97c964a44… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Fix (ancient, should replace this, but might as well make it work until we do) tool-shed-only grid search button Commit: 74377074ac12fcadb771f5ea212fa1bd7a048df8 https://github.com/galaxyproject/galaxy/commit/74377074ac12fcadb771f5ea212f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css M templates/webapps/tool_shed/common/grid_common.mako Log Message: ----------- Drop submit-image custom styling, use standard fa; left it as inline style to keep it clean and remove all at once when this grid goes. Commit: 162fa3a5bbd52ea75db5ec22c32a7a3d86560029 https://github.com/galaxyproject/galaxy/commit/162fa3a5bbd52ea75db5ec22c32a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-23 (Wed, 23 May 2018) Changed paths: M client/galaxy/style/scss/list-item.scss M static/style/blue/base.css Log Message: ----------- Fix list panel control message margins. Commit: 51b93ebc48b96278342b06583642af14fe48ce3a https://github.com/galaxyproject/galaxy/commit/51b93ebc48b96278342b06583642… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-23 (Wed, 23 May 2018) Changed paths: M client/galaxy/style/scss/upload.scss Log Message: ----------- This is correct now Commit: a57600cadfe4b3f383ce69afaf3dc09c237456f8 https://github.com/galaxyproject/galaxy/commit/a57600cadfe4b3f383ce69afaf3d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-23 (Wed, 23 May 2018) Changed paths: M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/history.scss M client/galaxy/style/scss/list-item.scss M client/galaxy/style/scss/upload.scss M static/style/blue/base.css M templates/webapps/tool_shed/common/grid_common.mako Log Message: ----------- Merge pull request #6197 from dannon/1805stylefixes [18.05] Minor style fixes Compare: https://github.com/galaxyproject/galaxy/compare/2cf1c0013786...a57600cadfe4 **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.

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[galaxyproject/usegalaxy-playbook] 72d228: Put limits on reserved jobs
by GitHub 23 May '18

23 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 72d228f3b217aff385bc408d6eac47aa141181c7 https://github.com/galaxyproject/usegalaxy-playbook/commit/72d228f3b217aff3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-23 (Wed, 23 May 2018) Changed paths: M env/main/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Put limits on reserved jobs **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.

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[galaxyproject/galaxy] 65c1cd: Fix data_source.py for upload changes in 18.05 rel...
by GitHub 23 May '18

23 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 65c1cd761c48ba121a847d4d501eb8a97a911e70 https://github.com/galaxyproject/galaxy/commit/65c1cd761c48ba121a847d4d501e… Author: John Chilton <jmchilton(a)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/ef6f7f62ab679928045c816a3cb7… I believe. Commit: 44e57ba8b45d2ddd624333547ec1adeb62d70b9c https://github.com/galaxyproject/galaxy/commit/44e57ba8b45d2ddd624333547ec1… Author: Nicola Soranzo <nicola.soranzo(a)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. Compare: https://github.com/galaxyproject/galaxy/compare/ebc6734ed787...44e57ba8b45d **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.

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[galaxyproject/galaxy] cfaf71: Support building and publishing pre-release docs
by GitHub 22 May '18

22 May '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cfaf7186bda346445e0c1e0bd706eefe826b9323 https://github.com/galaxyproject/galaxy/commit/cfaf7186bda346445e0c1e0bd706… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M doc/source/conf.versioning.py Log Message: ----------- Support building and publishing pre-release docs Commit: ebc6734ed787fd4b10858d622e3c7e49d33309ac https://github.com/galaxyproject/galaxy/commit/ebc6734ed787fd4b10858d622e3c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M doc/source/conf.versioning.py Log Message: ----------- Merge pull request #6199 from natefoo/docs-pre-release [18.05] Support building and publishing pre-release docs Commit: 2cf1c00137862fd90ce8ccc2fa34751e65e7f960 https://github.com/galaxyproject/galaxy/commit/2cf1c00137862fd90ce8ccc2fa34… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M doc/source/conf.versioning.py Log Message: ----------- Merge branch 'release_18.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/bffeacad0816...2cf1c0013786 **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.

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[galaxyproject/galaxy] cfaf71: Support building and publishing pre-release docs
by GitHub 22 May '18

22 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: cfaf7186bda346445e0c1e0bd706eefe826b9323 https://github.com/galaxyproject/galaxy/commit/cfaf7186bda346445e0c1e0bd706… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M doc/source/conf.versioning.py Log Message: ----------- Support building and publishing pre-release docs Commit: ebc6734ed787fd4b10858d622e3c7e49d33309ac https://github.com/galaxyproject/galaxy/commit/ebc6734ed787fd4b10858d622e3c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M doc/source/conf.versioning.py Log Message: ----------- Merge pull request #6199 from natefoo/docs-pre-release [18.05] Support building and publishing pre-release docs Compare: https://github.com/galaxyproject/galaxy/compare/a5297af19017...ebc6734ed787 **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.

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