Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d0447fea2bc6dd63f9f13ebbab685d151ecc5db9 https://github.com/galaxyproject/galaxy/commit/d0447fea2bc6dd63f9f13ebbab685... Author: guerler aysam.guerler@gmail.com Date: 2016-04-21 (Thu, 21 Apr 2016)
Changed paths: M lib/galaxy/webapps/galaxy/controllers/tool_runner.py
Log Message: ----------- Add validation check for data_source tools URL parameter
Commit: f7fa63365368cf3aa8ab81b8bd2762233bcd9490 https://github.com/galaxyproject/galaxy/commit/f7fa63365368cf3aa8ab81b8bd276... Author: Bjoern Gruening bjoern.gruening@gmail.com Date: 2016-04-27 (Wed, 27 Apr 2016)
Changed paths: M lib/galaxy/tools/deps/__init__.py
Log Message: ----------- it's called conda_ensure_channels
Commit: 630a004e3797c9e39349af5f62e07326b9fa8f47 https://github.com/galaxyproject/galaxy/commit/630a004e3797c9e39349af5f62e07... Author: Martin Cech cech.marten@gmail.com Date: 2016-04-30 (Sat, 30 Apr 2016)
Changed paths: M lib/galaxy/tools/deps/__init__.py
Log Message: ----------- Merge pull request #2255 from bgruening/release_16.04
[16.04] Update `_condarc` automatically
Commit: 787b351404950ae33a1b601eab059d32c817a6fd https://github.com/galaxyproject/galaxy/commit/787b351404950ae33a1b601eab059... Author: Martin Cech cech.marten@gmail.com Date: 2016-05-01 (Sun, 01 May 2016)
Changed paths: M lib/galaxy/webapps/galaxy/controllers/tool_runner.py
Log Message: ----------- Merge pull request #2208 from guerler/fix_error_message_001
[16.04] Add fixed validation check for data_source tools URL parameter
Commit: cef9270527ba9f56ba4c0fb91a0be5be95095b0d https://github.com/galaxyproject/galaxy/commit/cef9270527ba9f56ba4c0fb91a0be... Author: John Chilton jmchilton@gmail.com Date: 2016-05-02 (Mon, 02 May 2016)
Changed paths: M config/galaxy.ini.sample M lib/galaxy/jobs/command_factory.py
Log Message: ----------- Switch Dockerized commands to use sh instead of bash.
We switched to bash for the conda and that doesn't get sourced in containers - so we should be a bit pragmatic about this and switch back to /bin/sh for containers which is more common than /bin/bash.
xref https://github.com/galaxyproject/galaxy/pull/2278
Update galaxy.ini.sample to mention this as suggested by @bgruening in https://github.com/galaxyproject/galaxy/pull/2282#issuecomment-216232788.
Commit: 9290ddc8a72fba1bf8de7ae5788becef56030223 https://github.com/galaxyproject/galaxy/commit/9290ddc8a72fba1bf8de7ae5788be... Author: Eric Rasche rasche.eric@gmail.com Date: 2016-05-02 (Mon, 02 May 2016)
Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M static/maps/mvc/form/form-input.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-input.js M templates/webapps/galaxy/workflow/display.mako M templates/webapps/galaxy/workflow/run.mako
Log Message: ----------- Fixes #2230
This sanitizes some instances where tool parameters were included directly into the DOM.
workflow/run.mako displayed the parameter as a value in a hidden input. This was base64 encoded as there was no better solution apparent at the time. I'm not sure where this parameter is POSTed to but we should figure that out and b64decode it, or remove the hidden parameter.
client/... added the parameter value into the DOM. This was easily sanitized using a standard method.
workflow/display.mako included the parameter value directly into the HTML. This was cgi.esacped
Conflicts: static/scripts/bundled/libs.bundled.js.map
Commit: 5cf329732307b1fb092825dbfdbad0da464c99c7 https://github.com/galaxyproject/galaxy/commit/5cf329732307b1fb092825dbfdbad... Author: Björn Grüning bjoern@gruenings.eu Date: 2016-05-02 (Mon, 02 May 2016)
Changed paths: M config/galaxy.ini.sample M lib/galaxy/jobs/command_factory.py
Log Message: ----------- Merge pull request #2282 from jmchilton/the_containerz_have_no_bash___doh
[16.04] Switch Dockerized commands to use sh instead of bash.
Commit: b9b79839d0f812c660dcd39a7316af154728e1a2 https://github.com/galaxyproject/galaxy/commit/b9b79839d0f812c660dcd39a7316a... Author: John Chilton jmchilton@gmail.com Date: 2016-05-02 (Mon, 02 May 2016)
Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M static/maps/mvc/form/form-input.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-input.js M templates/webapps/galaxy/workflow/display.mako M templates/webapps/galaxy/workflow/run.mako
Log Message: ----------- Merge pull request #2284 from martenson/backport-2230-04
[16.04] Backport of 2230
Commit: 7166a8736448a6383c3a1d286c17d5b568f75aef https://github.com/galaxyproject/galaxy/commit/7166a8736448a6383c3a1d286c17d... Author: Dannon Baker dannon.baker@gmail.com Date: 2016-05-02 (Mon, 02 May 2016)
Changed paths: M config/galaxy.ini.sample M lib/galaxy/jobs/command_factory.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/webapps/galaxy/controllers/tool_runner.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
Log Message: ----------- Merge branch 'release_16.04' into dev
Compare: https://github.com/galaxyproject/galaxy/compare/c667e52642ef...7166a8736448
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