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