commit/galaxy-central: 3 new changesets
3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/375e0c252f6c/ Changeset: 375e0c252f6c Branch: next-stable User: dan Date: 2014-04-10 19:38:44 Summary: Include tool version information in bug reports. Affected #: 1 file diff -r 376ffdb91bd1c1a7881e72c5cb6da8dea0e0534f -r 375e0c252f6c3448e1d7c743f1ffe408be9752ec lib/galaxy/tools/errors.py --- a/lib/galaxy/tools/errors.py +++ b/lib/galaxy/tools/errors.py @@ -28,7 +28,9 @@ ----------------------------------------------------------------------------- job id: ${job_id} tool id: ${job_tool_id} +tool version: ${tool_version} job pid or drm id: ${job_runner_external_id} +job tool version: ${job_tool_version} ----------------------------------------------------------------------------- job command line: ${job_command_line} @@ -86,7 +88,9 @@ history_item_name=hda.get_display_name(), history_view_link=history_view_link, job_id=job.id, + tool_version=job.tool_version, job_tool_id=job.tool_id, + job_tool_version=hda.tool_version, job_runner_external_id=job.job_runner_external_id, job_command_line=job.command_line, job_stderr=util.unicodify( job.stderr ), https://bitbucket.org/galaxy/galaxy-central/commits/7e9a2ea753bd/ Changeset: 7e9a2ea753bd Branch: next-stable User: dan Date: 2014-04-10 19:39:41 Summary: When posting to BioStar include a ToolShed url, as applicable. Affected #: 2 files diff -r 375e0c252f6c3448e1d7c743f1ffe408be9752ec -r 7e9a2ea753bde82120de4543618f196e86bf7b04 lib/galaxy/model/tool_shed_install/__init__.py --- a/lib/galaxy/model/tool_shed_install/__init__.py +++ b/lib/galaxy/model/tool_shed_install/__init__.py @@ -4,6 +4,8 @@ from galaxy.util.bunch import Bunch from galaxy.util import asbool from tool_shed.util import common_util +from tool_shed.util.shed_util_common import get_url_from_tool_shed +from urlparse import urljoin log = logging.getLogger( __name__ ) @@ -73,6 +75,12 @@ def can_reinstall_or_activate( self ): return self.deleted + def get_sharable_url( self, app ): + tool_shed_url = get_url_from_tool_shed( app, self.tool_shed ) + if tool_shed_url: + return urljoin( tool_shed_url, 'view/%s/%s' % ( self.owner, self.name ) ) + return tool_shed_url + def get_shed_config_filename( self ): shed_config_filename = None if self.metadata: diff -r 375e0c252f6c3448e1d7c743f1ffe408be9752ec -r 7e9a2ea753bde82120de4543618f196e86bf7b04 lib/galaxy/util/biostar.py --- a/lib/galaxy/util/biostar.py +++ b/lib/galaxy/util/biostar.py @@ -86,7 +86,14 @@ def populate_tool_payload( payload=None, tool=None ): payload = populate_tag_payload( payload=payload, tool=tool ) payload[ 'title' ] = 'Need help with "%s" tool' % ( tool.name ) - payload[ 'content' ] = '<br /><hr /><p>Tool name: %s</br>Tool version: %s</br>Tool ID: %s</p>' % ( tool.name, tool.version, tool.id ) + tool_url = None + if tool.tool_shed_repository: + tool_url = tool.tool_shed_repository.get_sharable_url( tool.app ) + if tool_url: + tool_url = '</br>ToolShed URL: <a href="%s">%s</a>' % ( tool_url, tool_url ) + if not tool_url: + tool_url = '' + payload[ 'content' ] = '<br /><hr /><p>Tool name: %s</br>Tool version: %s</br>Tool ID: %s%s</p></br>' % ( tool.name, tool.version, tool.id, tool_url ) return payload def determine_cookie_domain( galaxy_hostname, biostar_hostname ): https://bitbucket.org/galaxy/galaxy-central/commits/44ad9370003c/ Changeset: 44ad9370003c User: dan Date: 2014-04-10 19:40:00 Summary: merge next-stable Affected #: 3 files diff -r 165927888055c164e493a948e05d10c00d018458 -r 44ad9370003cfa3217f15d1ee8a2d6a114cb50bb lib/galaxy/model/tool_shed_install/__init__.py --- a/lib/galaxy/model/tool_shed_install/__init__.py +++ b/lib/galaxy/model/tool_shed_install/__init__.py @@ -4,6 +4,8 @@ from galaxy.util.bunch import Bunch from galaxy.util import asbool from tool_shed.util import common_util +from tool_shed.util.shed_util_common import get_url_from_tool_shed +from urlparse import urljoin log = logging.getLogger( __name__ ) @@ -73,6 +75,12 @@ def can_reinstall_or_activate( self ): return self.deleted + def get_sharable_url( self, app ): + tool_shed_url = get_url_from_tool_shed( app, self.tool_shed ) + if tool_shed_url: + return urljoin( tool_shed_url, 'view/%s/%s' % ( self.owner, self.name ) ) + return tool_shed_url + def get_shed_config_filename( self ): shed_config_filename = None if self.metadata: diff -r 165927888055c164e493a948e05d10c00d018458 -r 44ad9370003cfa3217f15d1ee8a2d6a114cb50bb lib/galaxy/tools/errors.py --- a/lib/galaxy/tools/errors.py +++ b/lib/galaxy/tools/errors.py @@ -28,7 +28,9 @@ ----------------------------------------------------------------------------- job id: ${job_id} tool id: ${job_tool_id} +tool version: ${tool_version} job pid or drm id: ${job_runner_external_id} +job tool version: ${job_tool_version} ----------------------------------------------------------------------------- job command line: ${job_command_line} @@ -86,7 +88,9 @@ history_item_name=hda.get_display_name(), history_view_link=history_view_link, job_id=job.id, + tool_version=job.tool_version, job_tool_id=job.tool_id, + job_tool_version=hda.tool_version, job_runner_external_id=job.job_runner_external_id, job_command_line=job.command_line, job_stderr=util.unicodify( job.stderr ), diff -r 165927888055c164e493a948e05d10c00d018458 -r 44ad9370003cfa3217f15d1ee8a2d6a114cb50bb lib/galaxy/util/biostar.py --- a/lib/galaxy/util/biostar.py +++ b/lib/galaxy/util/biostar.py @@ -86,7 +86,14 @@ def populate_tool_payload( payload=None, tool=None ): payload = populate_tag_payload( payload=payload, tool=tool ) payload[ 'title' ] = 'Need help with "%s" tool' % ( tool.name ) - payload[ 'content' ] = '<br /><hr /><p>Tool name: %s</br>Tool version: %s</br>Tool ID: %s</p>' % ( tool.name, tool.version, tool.id ) + tool_url = None + if tool.tool_shed_repository: + tool_url = tool.tool_shed_repository.get_sharable_url( tool.app ) + if tool_url: + tool_url = '</br>ToolShed URL: <a href="%s">%s</a>' % ( tool_url, tool_url ) + if not tool_url: + tool_url = '' + payload[ 'content' ] = '<br /><hr /><p>Tool name: %s</br>Tool version: %s</br>Tool ID: %s%s</p></br>' % ( tool.name, tool.version, tool.id, tool_url ) return payload def determine_cookie_domain( galaxy_hostname, biostar_hostname ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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