commit/galaxy-central: 5 new changesets

9 May 2013

5 new commits in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/35b87dd34a79/
Changeset:   35b87dd34a79
Branch:      stable
User:        Dave Bouvier
Date:        2013-05-09 20:25:51
Summary:     Only look for and process tool help image definitions if the tool XML defines a help block.
Affected #:  1 file

diff -r 7930e04adb535b8bf3c7973efc5cdce0fb384034 -r 35b87dd34a79aa4b94c9c3dd8ff17b4143cd340c lib/galaxy/tools/__init__.py

--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -1357,23 +1357,23 @@
         """
         # TODO: Allow raw HTML or an external link.
         self.help = root.find("help")
-        # Handle tool shelp image display for tools that are contained in repositories that are in the lool shed or installed into Galaxy.
-        # When tool config files use the speical string $PATH_TO_IMAGES, the folloing code will replace that string with the path on disk.
-        if self.repository_id and self.help.text.find( '$PATH_TO_IMAGES' ) >= 0:
-            if self.app.name == 'galaxy':
-                repository = self.sa_session.query( self.app.model.ToolShedRepository ).get( self.app.security.decode_id( self.repository_id ) )
-                if repository:
-                    path_to_images = '/tool_runner/static/images/%s' % self.repository_id
-                    self.help.text = self.help.text.replace( '$PATH_TO_IMAGES', path_to_images )
-            elif self.app.name == 'tool_shed':
-                repository = self.sa_session.query( self.app.model.Repository ).get( self.app.security.decode_id( self.repository_id ) )
-                if repository:
-                    path_to_images = '/repository/static/images/%s' % self.repository_id
-                    self.help.text = self.help.text.replace( '$PATH_TO_IMAGES', path_to_images )
         self.help_by_page = list()
         help_header = ""
         help_footer = ""
         if self.help is not None:
+            # Handle tool help image display for tools that are contained in repositories that are in the tool shed or installed into Galaxy.
+            # When tool config files use the special string $PATH_TO_IMAGES, the following code will replace that string with the path on disk.
+            if self.repository_id and self.help.text.find( '$PATH_TO_IMAGES' ) >= 0:
+                if self.app.name == 'galaxy':
+                    repository = self.sa_session.query( self.app.model.ToolShedRepository ).get( self.app.security.decode_id( self.repository_id ) )
+                    if repository:
+                        path_to_images = '/tool_runner/static/images/%s' % self.repository_id
+                        self.help.text = self.help.text.replace( '$PATH_TO_IMAGES', path_to_images )
+                elif self.app.name == 'tool_shed':
+                    repository = self.sa_session.query( self.app.model.Repository ).get( self.app.security.decode_id( self.repository_id ) )
+                    if repository:
+                        path_to_images = '/repository/static/images/%s' % self.repository_id
+                        self.help.text = self.help.text.replace( '$PATH_TO_IMAGES', path_to_images )
             help_pages = self.help.findall( "page" )
             help_header = self.help.text
             try:


https://bitbucket.org/galaxy/galaxy-central/commits/d914458eb4f3/
Changeset:   d914458eb4f3
User:        Dave Bouvier
Date:        2013-05-09 20:26:35
Summary:     Merge in fixes from stable branch.
Affected #:  4 files

diff -r 6ba6f297b9694e29ff774a33e9b88b9f666ddee7 -r d914458eb4f31b39f175ccdbc31668b13072ea23 lib/galaxy/tools/__init__.py
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -1266,23 +1266,23 @@
         """
         # TODO: Allow raw HTML or an external link.
         self.help = root.find("help")
-        # Handle tool shelp image display for tools that are contained in repositories that are in the lool shed or installed into Galaxy.
-        # When tool config files use the speical string $PATH_TO_IMAGES, the folloing code will replace that string with the path on disk.
-        if self.repository_id and self.help.text.find( '$PATH_TO_IMAGES' ) >= 0:
-            if self.app.name == 'galaxy':
-                repository = self.sa_session.query( self.app.model.ToolShedRepository ).get( self.app.security.decode_id( self.repository_id ) )
-                if repository:
-                    path_to_images = '/tool_runner/static/images/%s' % self.repository_id
-                    self.help.text = self.help.text.replace( '$PATH_TO_IMAGES', path_to_images )
-            elif self.app.name == 'tool_shed':
-                repository = self.sa_session.query( self.app.model.Repository ).get( self.app.security.decode_id( self.repository_id ) )
-                if repository:
-                    path_to_images = '/repository/static/images/%s' % self.repository_id
-                    self.help.text = self.help.text.replace( '$PATH_TO_IMAGES', path_to_images )
         self.help_by_page = list()
         help_header = ""
         help_footer = ""
         if self.help is not None:
+            # Handle tool help image display for tools that are contained in repositories that are in the tool shed or installed into Galaxy.
+            # When tool config files use the special string $PATH_TO_IMAGES, the following code will replace that string with the path on disk.
+            if self.repository_id and self.help.text.find( '$PATH_TO_IMAGES' ) >= 0:
+                if self.app.name == 'galaxy':
+                    repository = self.sa_session.query( self.app.model.ToolShedRepository ).get( self.app.security.decode_id( self.repository_id ) )
+                    if repository:
+                        path_to_images = '/tool_runner/static/images/%s' % self.repository_id
+                        self.help.text = self.help.text.replace( '$PATH_TO_IMAGES', path_to_images )
+                elif self.app.name == 'tool_shed':
+                    repository = self.sa_session.query( self.app.model.Repository ).get( self.app.security.decode_id( self.repository_id ) )
+                    if repository:
+                        path_to_images = '/repository/static/images/%s' % self.repository_id
+                        self.help.text = self.help.text.replace( '$PATH_TO_IMAGES', path_to_images )
             help_pages = self.help.findall( "page" )
             help_header = self.help.text
             try:


https://bitbucket.org/galaxy/galaxy-central/commits/7e72e623a2aa/
Changeset:   7e72e623a2aa
User:        Dave Bouvier
Date:        2013-05-09 20:43:45
Summary:     Merged.
Affected #:  1 file

diff -r d914458eb4f31b39f175ccdbc31668b13072ea23 -r 7e72e623a2aa71a7eaae78b9f7f03e3abff4fce6 templates/webapps/tool_shed/repository/common.mako
--- a/templates/webapps/tool_shed/repository/common.mako
+++ b/templates/webapps/tool_shed/repository/common.mako
@@ -544,6 +544,7 @@
 <%def name="render_repository_dependency( repository_dependency, pad, parent, row_counter, row_is_header=False )"><%
+        from galaxy.util import string_as_bool
         encoded_id = trans.security.encode_id( repository_dependency.id )
         if trans.webapp.name == 'galaxy':
             if repository_dependency.tool_shed_repository_id:
@@ -557,6 +558,7 @@
         repository_name = str( repository_dependency.repository_name )
         repository_owner = str( repository_dependency.repository_owner )
         changeset_revision = str( repository_dependency.changeset_revision )
+        prior_installation_required = string_as_bool( str( repository_dependency.prior_installation_required ) ) 
         if prior_installation_required:
             prior_installation_required_str = " <i>(prior install required)</i>"
         else:
@@ -676,6 +678,7 @@
 
 <%def name="render_tool_dependency( tool_dependency, pad, parent, row_counter, row_is_header )"><%
+        from galaxy.util import string_as_bool
         encoded_id = trans.security.encode_id( tool_dependency.id )
         is_missing = tool_dependency.installation_status not in [ 'Installed' ]
         if row_is_header:
@@ -725,7 +728,17 @@
                     ${tool_dependency.install_dir | h}
                 %endif
             %else:
-                ${tool_dependency.is_orphan | h}
+                %if row_is_header:
+                    ${tool_dependency.is_orphan | h}
+                %else:
+                    <%
+                        if string_as_bool( str( tool_dependency.is_orphan ) ):
+                            is_orpan = 'yes'
+                        else:
+                            is_orphan = 'no'
+                    %>
+                    ${is_orphan | h}
+                %endif
             %endif
         </${cell_type}></tr>


https://bitbucket.org/galaxy/galaxy-central/commits/6905bc773595/
Changeset:   6905bc773595
User:        Dave Bouvier
Date:        2013-05-09 20:56:19
Summary:     Fix Galaxy side user creation in tool shed functional tests.
Affected #:  1 file

diff -r 7e72e623a2aa71a7eaae78b9f7f03e3abff4fce6 -r 6905bc773595db5951247d6057e9c42b9c6e735f test/tool_shed/base/twilltestcase.py
--- a/test/tool_shed/base/twilltestcase.py
+++ b/test/tool_shed/base/twilltestcase.py
@@ -312,12 +312,7 @@
         
     def create_user_in_galaxy( self, cntrller='user', email='test@bx.psu.edu', password='testuser', username='admin-user', redirect='' ):
         self.visit_galaxy_url( "/user/create?cntrller=%s&use_panels=False" % cntrller )
-        tc.fv( '1', 'email', email )
-        tc.fv( '1', 'redirect', redirect )
-        tc.fv( '1', 'password', password )
-        tc.fv( '1', 'confirm', password )
-        tc.fv( '1', 'username', username )
-        tc.submit( 'create_user_button' )
+        self.submit_form( '1', 'create_user_button', email=email, password=password, confirm=password, username=username, redirect=redirect )
         previously_created = False
         username_taken = False
         invalid_username = False
@@ -509,10 +504,7 @@
             self.create_user_in_galaxy( email=email, password=password, username=username, redirect=redirect )
         if previously_created:
             self.visit_galaxy_url( "/user/login?use_panels=False" )
-            tc.fv( '1', 'email', email )
-            tc.fv( '1', 'redirect', redirect )
-            tc.fv( '1', 'password', password )
-            tc.submit( 'login_button' )
+            self.submit_form( '1', 'login_button', email=email, redirect=redirect, password=password )
         
     def galaxy_logout( self ):
         self.home()


https://bitbucket.org/galaxy/galaxy-central/commits/75a49f8d1bd3/
Changeset:   75a49f8d1bd3
User:        Dave Bouvier
Date:        2013-05-09 21:50:27
Summary:     Merged again.
Affected #:  1 file
Diff not available.

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

--

This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.

    

commits-noreply＠bitbucket.org

tags

participants (1)