Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: eb15c147504ca4e871afed5f0ff005552b54e85f
https://github.com/galaxyproject/galaxy/commit/eb15c147504ca4e871afed5f0ff0…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-04-19 (Tue, 19 Apr 2016)
Changed paths:
M lib/galaxy/web/framework/middleware/remoteuser.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Prepass on remote user header based on maildomain and normalize config. This resolves an error reported on -dev with maildomain and user being set incorrectly.
Commit: cdea922890683f8db0cd9dae3b6eed5695cfd094
https://github.com/galaxyproject/galaxy/commit/cdea922890683f8db0cd9dae3b6e…
Author: Nitesh Turaga <nitesh.turaga(a)gmail.com>
Date: 2016-05-02 (Mon, 02 May 2016)
Changed paths:
M lib/galaxy/web/framework/middleware/remoteuser.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Merge pull request #2195 from dannon/remoteuser_work
[16.01] Prepass on remote user header based on maildomain and normalize confi…
Commit: d282ed9ce3e80b06cc89e84add4ca9a32489db9a
https://github.com/galaxyproject/galaxy/commit/d282ed9ce3e80b06cc89e84add4c…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-05-02 (Mon, 02 May 2016)
Changed paths:
M lib/galaxy/web/framework/middleware/remoteuser.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Merge branch 'release_16.01' into release_16.04
Commit: 5cd6b47d68902c79631d05ee35d63ccf46e4640d
https://github.com/galaxyproject/galaxy/commit/5cd6b47d68902c79631d05ee35d6…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-05-02 (Mon, 02 May 2016)
Changed paths:
M lib/galaxy/web/framework/middleware/remoteuser.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Merge branch 'release_16.04' into dev
Compare: https://github.com/galaxyproject/galaxy/compare/7166a8736448...5cd6b47d6890
Branch: refs/heads/release_16.04
Home: https://github.com/galaxyproject/galaxy
Commit: eb15c147504ca4e871afed5f0ff005552b54e85f
https://github.com/galaxyproject/galaxy/commit/eb15c147504ca4e871afed5f0ff0…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-04-19 (Tue, 19 Apr 2016)
Changed paths:
M lib/galaxy/web/framework/middleware/remoteuser.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Prepass on remote user header based on maildomain and normalize config. This resolves an error reported on -dev with maildomain and user being set incorrectly.
Commit: cdea922890683f8db0cd9dae3b6eed5695cfd094
https://github.com/galaxyproject/galaxy/commit/cdea922890683f8db0cd9dae3b6e…
Author: Nitesh Turaga <nitesh.turaga(a)gmail.com>
Date: 2016-05-02 (Mon, 02 May 2016)
Changed paths:
M lib/galaxy/web/framework/middleware/remoteuser.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Merge pull request #2195 from dannon/remoteuser_work
[16.01] Prepass on remote user header based on maildomain and normalize confi…
Commit: d282ed9ce3e80b06cc89e84add4ca9a32489db9a
https://github.com/galaxyproject/galaxy/commit/d282ed9ce3e80b06cc89e84add4c…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-05-02 (Mon, 02 May 2016)
Changed paths:
M lib/galaxy/web/framework/middleware/remoteuser.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Merge branch 'release_16.01' into release_16.04
Compare: https://github.com/galaxyproject/galaxy/compare/b9b79839d0f8...d282ed9ce3e8
Branch: refs/heads/release_16.01
Home: https://github.com/galaxyproject/galaxy
Commit: eb15c147504ca4e871afed5f0ff005552b54e85f
https://github.com/galaxyproject/galaxy/commit/eb15c147504ca4e871afed5f0ff0…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-04-19 (Tue, 19 Apr 2016)
Changed paths:
M lib/galaxy/web/framework/middleware/remoteuser.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Prepass on remote user header based on maildomain and normalize config. This resolves an error reported on -dev with maildomain and user being set incorrectly.
Commit: cdea922890683f8db0cd9dae3b6eed5695cfd094
https://github.com/galaxyproject/galaxy/commit/cdea922890683f8db0cd9dae3b6e…
Author: Nitesh Turaga <nitesh.turaga(a)gmail.com>
Date: 2016-05-02 (Mon, 02 May 2016)
Changed paths:
M lib/galaxy/web/framework/middleware/remoteuser.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Merge pull request #2195 from dannon/remoteuser_work
[16.01] Prepass on remote user header based on maildomain and normalize confi…
Compare: https://github.com/galaxyproject/galaxy/compare/9e980862c8b7...cdea92289068
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: d0447fea2bc6dd63f9f13ebbab685d151ecc5db9
https://github.com/galaxyproject/galaxy/commit/d0447fea2bc6dd63f9f13ebbab68…
Author: guerler <aysam.guerler(a)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/f7fa63365368cf3aa8ab81b8bd27…
Author: Bjoern Gruening <bjoern.gruening(a)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/630a004e3797c9e39349af5f62e0…
Author: Martin Cech <cech.marten(a)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/787b351404950ae33a1b601eab05…
Author: Martin Cech <cech.marten(a)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/cef9270527ba9f56ba4c0fb91a0b…
Author: John Chilton <jmchilton(a)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/9290ddc8a72fba1bf8de7ae5788b…
Author: Eric Rasche <rasche.eric(a)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/5cf329732307b1fb092825dbfdba…
Author: Björn Grüning <bjoern(a)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/b9b79839d0f812c660dcd39a7316…
Author: John Chilton <jmchilton(a)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/7166a8736448a6383c3a1d286c17…
Author: Dannon Baker <dannon.baker(a)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
Branch: refs/heads/release_16.04
Home: https://github.com/galaxyproject/galaxy
Commit: 9290ddc8a72fba1bf8de7ae5788becef56030223
https://github.com/galaxyproject/galaxy/commit/9290ddc8a72fba1bf8de7ae5788b…
Author: Eric Rasche <rasche.eric(a)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: b9b79839d0f812c660dcd39a7316af154728e1a2
https://github.com/galaxyproject/galaxy/commit/b9b79839d0f812c660dcd39a7316…
Author: John Chilton <jmchilton(a)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
Compare: https://github.com/galaxyproject/galaxy/compare/5cf329732307...b9b79839d0f8