From ef45ae3752a4ea4da73719e2917a064c8e239ab3 Mon Sep 17 00:00:00 2001 From: pvanheus Date: Mon, 19 Mar 2018 16:31:51 +0200 Subject: [PATCH 1/4] Upgrade clone failure logging to error When a failed clone logs as log.debug() this is invisible to a production Galaxy admin. This change upgrades the logging to 'log.error()'. --- lib/tool_shed/util/hg_util.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/tool_shed/util/hg_util.py b/lib/tool_shed/util/hg_util.py index 30b3e5e4d02..d2518227f9d 100644 --- a/lib/tool_shed/util/hg_util.py +++ b/lib/tool_shed/util/hg_util.py @@ -62,7 +62,7 @@ def clone_repository(repository_clone_url, repository_file_dir, ctx_rev): error_message = 'Error cloning repository: %s' % e if isinstance(e, subprocess.CalledProcessError): error_message += "\nOutput was:\n%s" % stdouterr - log.debug(error_message) + log.error(error_message) return False, error_message From 50035b184e0ceba61f21f223e5f701710dd86d19 Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Mon, 19 Mar 2018 13:36:36 -0400 Subject: [PATCH 2/4] improve update commands in RN, clarify uwsgi config changes --- doc/source/releases/18.01_announce.rst | 16 +++++++--------- 1 file changed, 7 insertions(+), 9 deletions(-) diff --git a/doc/source/releases/18.01_announce.rst b/doc/source/releases/18.01_announce.rst index c6b00ecff6d..5e75e7a1d47 100644 --- a/doc/source/releases/18.01_announce.rst +++ b/doc/source/releases/18.01_announce.rst @@ -14,9 +14,7 @@ Highlights **Web Server and Configuration** The default web server used by Galaxy has changed from Paste to `uWSGI `__ and the default configuration file for Galaxy is now ``config/galaxy.yml`` instead of ``config/galaxy.ini``. - uWSGI is more production ready and allows Galaxy to scale better in its default - configuration. In the future uWSGI will allow Galaxy to setup GIE proxies without additional - configuration and use modern web technologies such as web sockets. + To minimize the impact of this change on existing Galaxy instances, if a Galaxy has a ``galaxy.ini`` file configured, it will continue to use Paste by default unless additional steps are taken by the administrator Read more about the server, configuration, and documentation changes in the `uWSGI details`_ section of this document. **Dataset Collection Usability** @@ -78,7 +76,7 @@ To get a new Galaxy repository run: To update an existing Galaxy repository run: .. code-block:: shell - $ git checkout release_18.01 && git pull --ff-only origin release_18.01 + $ git fetch origin && git checkout release_18.01 && git pull --ff-only origin release_18.01 See the `community hub `__ for additional details regarding the source code locations. @@ -128,17 +126,17 @@ In addition to that, the PlantTribes datatypes have been commented out in the so uWSGI details ============= - -To minimize the impact of this change on existing Galaxy instances, if a Galaxy has a ``galaxy.ini`` -file configured, it will continue to use Paste by default unless additional steps are -taken by the administrator (Galaxy can be forced to start under uWSGI even with an older configuration file -by setting ``APP_WEBSERVER=uwsgi`` in the environment). As part of the transition to YAML-based +Galaxy can be forced to start under uWSGI even with an older configuration file +by setting ``APP_WEBSERVER=uwsgi`` in the environment. As part of the transition to YAML-based configuration files, we have implemented a schema to validate Galaxy configuration files. Run ``make config-validate`` from Galaxy's root directory to validate a schema and ``make config-lint`` to check for best practices. While there is no need to convert your configuration file (``galaxy.ini`` hasn't been deprecated), you can run ``make config-convert-dry-run`` and ``make config-convert`` to respectively test and perform the conversion of an ``ini`` configuration file to a YAML one. +uWSGI is more production ready and allows Galaxy to scale better in its default configuration. +In the future uWSGI will allow Galaxy to setup GIE proxies without additional configuration and use modern web technologies such as web sockets. + These are big changes that affect many parts of Galaxy's administration documentation and makes this documentation very dependent on which Galaxy version they are targeting. To address this, we have moved a significant amount of administration documentation into Galaxy's code From 924eecc67a3155578aea6a484d9bfd86d0cc5aba Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Mon, 19 Mar 2018 17:56:58 +0000 Subject: [PATCH 3/4] Add missing `.` --- doc/source/releases/18.01_announce.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/releases/18.01_announce.rst b/doc/source/releases/18.01_announce.rst index 5e75e7a1d47..7a439e6c09f 100644 --- a/doc/source/releases/18.01_announce.rst +++ b/doc/source/releases/18.01_announce.rst @@ -14,7 +14,7 @@ Highlights **Web Server and Configuration** The default web server used by Galaxy has changed from Paste to `uWSGI `__ and the default configuration file for Galaxy is now ``config/galaxy.yml`` instead of ``config/galaxy.ini``. - To minimize the impact of this change on existing Galaxy instances, if a Galaxy has a ``galaxy.ini`` file configured, it will continue to use Paste by default unless additional steps are taken by the administrator + To minimize the impact of this change on existing Galaxy instances, if a Galaxy has a ``galaxy.ini`` file configured, it will continue to use Paste by default unless additional steps are taken by the administrator. Read more about the server, configuration, and documentation changes in the `uWSGI details`_ section of this document. **Dataset Collection Usability** From 3699e9e4919dcb727af3ff0e7457794642973dfa Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Mon, 19 Mar 2018 14:01:22 -0400 Subject: [PATCH 4/4] re-add the motivation for uwsgi switch --- doc/source/releases/18.01_announce.rst | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/doc/source/releases/18.01_announce.rst b/doc/source/releases/18.01_announce.rst index 7a439e6c09f..e2032f067bb 100644 --- a/doc/source/releases/18.01_announce.rst +++ b/doc/source/releases/18.01_announce.rst @@ -15,7 +15,7 @@ Highlights **Web Server and Configuration** The default web server used by Galaxy has changed from Paste to `uWSGI `__ and the default configuration file for Galaxy is now ``config/galaxy.yml`` instead of ``config/galaxy.ini``. To minimize the impact of this change on existing Galaxy instances, if a Galaxy has a ``galaxy.ini`` file configured, it will continue to use Paste by default unless additional steps are taken by the administrator. - Read more about the server, configuration, and documentation changes in the `uWSGI details`_ section of this document. + uWSGI is more production ready and allows Galaxy to scale better in its default configuration. Read more about the server, configuration, and documentation changes in the `uWSGI details`_ section of this document. **Dataset Collection Usability** This release has significantly improved the usability of Galaxy dataset collections. Dozens of improvements @@ -134,7 +134,6 @@ check for best practices. While there is no need to convert your configuration f been deprecated), you can run ``make config-convert-dry-run`` and ``make config-convert`` to respectively test and perform the conversion of an ``ini`` configuration file to a YAML one. -uWSGI is more production ready and allows Galaxy to scale better in its default configuration. In the future uWSGI will allow Galaxy to setup GIE proxies without additional configuration and use modern web technologies such as web sockets. These are big changes that affect many parts of Galaxy's administration documentation and makes