1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/af24105e47a9/
changeset: af24105e47a9
user: dan
date: 2011-12-08 22:25:08
summary: UCSC BAM display will now pass the pairEndsByName attribute. Closes #455.
affected #: 1 file
diff -r d93edf2dc43612e38a9e7aafac4d50fba60ae647 -r af24105e47a9966566ad92833f0990805da69ac3 display_applications/ucsc/bam.xml
--- a/display_applications/ucsc/bam.xml
+++ b/display_applications/ucsc/bam.xml
@@ -12,6 +12,6 @@
<url>${ucsc_link}db=${qp($bam_file.dbkey)}&hgt.customText=${qp($track.url)}</url><param type="data" name="bam_file" url="galaxy_${DATASET_HASH}.bam" /><param type="data" name="bai_file" url="galaxy_${DATASET_HASH}.bam.bai" metadata="bam_index" /><!-- UCSC expects index file to exist as bam_file_name.bai -->
- <param type="template" name="track" viewable="True">track type="bam" name="${bam_file.name.replace( '\\', '\\\\' ).replace( '"', '\\"' )}" bigDataUrl="${bam_file.url}" db="${bam_file.dbkey}"</param>
+ <param type="template" name="track" viewable="True">track type="bam" name="${bam_file.name.replace( '\\', '\\\\' ).replace( '"', '\\"' )}" bigDataUrl="${bam_file.url}" db="${bam_file.dbkey}" pairEndsByName="."</param></dynamic_links></display>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/0639c7b53077/
changeset: 0639c7b53077
user: dannon
date: 2011-12-08 18:08:53
summary: Email action on job failure, resolves bb issue #600. Fail/cleanup logic condensation.
affected #: 1 file
diff -r 5e211b535425ba3ea80723153043be21446230d7 -r 0639c7b530774aea53776cc207b39cee22a5499a lib/galaxy/jobs/__init__.py
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -443,7 +443,7 @@
job = self.get_job()
self.sa_session.refresh( job )
# if the job was deleted, don't fail it
- if not job.state == model.Job.states.DELETED:
+ if not job.state == job.states.DELETED:
# Check if the failure is due to an exception
if exception:
# Save the traceback immediately in case we generate another
@@ -474,15 +474,18 @@
dataset.extension = 'data'
self.sa_session.add( dataset )
self.sa_session.flush()
- job.state = model.Job.states.ERROR
+ job.state = job.states.ERROR
job.command_line = self.command_line
job.info = message
self.sa_session.add( job )
self.sa_session.flush()
+ #Perform email action even on failure.
+ for pja in [x for x in job.post_job_actions if x.action_type == "EmailAction"]:
+ ActionBox.execute(self.app, self.sa_session, pja.post_job_action, job)
# If the job was deleted, call tool specific fail actions (used for e.g. external metadata) and clean up
if self.tool:
self.tool.job_failed( self, message, exception )
- if self.app.config.cleanup_job == 'always':
+ if self.app.cleanup_job == 'always' or (self.app.config.cleanup_job == 'onsuccess' and job.state == job.states.DELETED):
self.cleanup()
def change_state( self, state, info = False ):
@@ -525,14 +528,9 @@
self.sa_session.expunge_all()
job = self.get_job()
# if the job was deleted, don't finish it
- if job.state == job.states.DELETED:
- if self.app.config.cleanup_job in ( 'always', 'onsuccess' ):
- self.cleanup()
- return
- elif job.state == job.states.ERROR:
- # Job was deleted by an administrator
- self.fail( job.info )
- return
+ if job.state == job.states.DELETED or job.state == job.states.ERROR:
+ #ERROR at this point means the job was deleted by an administrator.
+ return self.fail( job.info )
if stderr:
job.state = job.states.ERROR
else:
@@ -555,8 +553,7 @@
if os.path.exists( dataset_path.real_path ) and os.stat( dataset_path.real_path ).st_size > 0:
log.warning( "finish(): %s not found, but %s is not empty, so it will be used instead" % ( dataset_path.false_path, dataset_path.real_path ) )
else:
- self.fail( "Job %s's output dataset(s) could not be read" % job.id )
- return
+ return self.fail( "Job %s's output dataset(s) could not be read" % job.id )
job_context = ExpressionContext( dict( stdout = stdout, stderr = stderr ) )
job_tool = self.app.toolbox.tools_by_id.get( job.tool_id, None )
def in_directory( file, directory ):
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/5e211b535425/
changeset: 5e211b535425
user: greg
date: 2011-12-08 17:49:52
summary: Do not allow public user names to be changed within the tool shed if the user has created a tool shed repository.
affected #: 2 files
diff -r 862d562e31670dd22a6bd575b2fa79328acabb4d -r 5e211b535425ba3ea80723153043be21446230d7 templates/user/info.mako
--- a/templates/user/info.mako
+++ b/templates/user/info.mako
@@ -21,12 +21,28 @@
</div><div class="form-row"><label>Public name:</label>
- <input type="text" name="username" size="40" value="${username}"/>
- <div class="toolParamHelp" style="clear: both;">
- Your public name is an optional identifier that will be used to generate addresses for information
- you share publicly. Public names must be at least four characters in length and contain only lower-case
- letters, numbers, and the '-' character.
- </div>
+ %if webapp == 'community':
+ ${username}
+ %if user.active_repositories:
+ <div class="toolParamHelp" style="clear: both;">
+ You cannot change your public name after you have created a repository in this tool shed.
+ </div>
+ %else:
+ <div class="toolParamHelp" style="clear: both;">
+ Your public name provides a means of identifying you publicly within this tool shed. Public
+ names must be at least four characters in length and contain only lower-case letters, numbers,
+ and the '-' character. You cannot change your public name after you have created a repository
+ in this tool shed.
+ </div>
+ %endif
+ %else:
+ <input type="text" name="username" size="40" value="${username}"/>
+ <div class="toolParamHelp" style="clear: both;">
+ Your public name is an optional identifier that will be used to generate addresses for information
+ you share publicly. Public names must be at least four characters in length and contain only lower-case
+ letters, numbers, and the '-' character.
+ </div>
+ %endif
</div><div class="form-row"><input type="submit" name="login_info_button" value="Save"/>
diff -r 862d562e31670dd22a6bd575b2fa79328acabb4d -r 5e211b535425ba3ea80723153043be21446230d7 templates/user/register.mako
--- a/templates/user/register.mako
+++ b/templates/user/register.mako
@@ -50,11 +50,20 @@
<div class="form-row"><label>Public name:</label><input type="text" name="username" size="40" value="${username}"/>
- <div class="toolParamHelp" style="clear: both;">
- Your public name is an identifier that will be used to generate addresses for information
- you share publicly. Public names must be at least four characters in length and contain only lower-case
- letters, numbers, and the '-' character.
- </div>
+ %if webapp == 'galaxy':
+ <div class="toolParamHelp" style="clear: both;">
+ Your public name is an identifier that will be used to generate addresses for information
+ you share publicly. Public names must be at least four characters in length and contain only lower-case
+ letters, numbers, and the '-' character.
+ </div>
+ %else:
+ <div class="toolParamHelp" style="clear: both;">
+ Your public name provides a means of identifying you publicly within this tool shed. Public
+ names must be at least four characters in length and contain only lower-case letters, numbers,
+ and the '-' character. You cannot change your public name after you have created a repository
+ in this tool shed.
+ </div>
+ %endif
</div>
%if trans.app.config.smtp_server:
<div class="form-row">
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/862d562e3167/
changeset: 862d562e3167
user: dan
date: 2011-12-08 17:44:22
summary: Escape backslashes and quotes in name attributes for UCSC external display applications which use bigDataUrls. Remove no longer required strip_https attribute. Resolves #627.
affected #: 3 files
diff -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca -r 862d562e31670dd22a6bd575b2fa79328acabb4d display_applications/ucsc/bam.xml
--- a/display_applications/ucsc/bam.xml
+++ b/display_applications/ucsc/bam.xml
@@ -10,8 +10,8 @@
<filter>${dataset.dbkey in $builds}</filter><!-- We define url and params as normal, but values defined in dynamic_param are available by specified name --><url>${ucsc_link}db=${qp($bam_file.dbkey)}&hgt.customText=${qp($track.url)}</url>
- <param type="data" name="bam_file" url="galaxy_${DATASET_HASH}.bam" strip_https="True" />
- <param type="data" name="bai_file" url="galaxy_${DATASET_HASH}.bam.bai" metadata="bam_index" strip_https="True" /><!-- UCSC expects index file to exist as bam_file_name.bai -->
- <param type="template" name="track" viewable="True" strip_https="True">track type=bam name="${bam_file.name}" bigDataUrl=${bam_file.url} db=${bam_file.dbkey}</param>
+ <param type="data" name="bam_file" url="galaxy_${DATASET_HASH}.bam" />
+ <param type="data" name="bai_file" url="galaxy_${DATASET_HASH}.bam.bai" metadata="bam_index" /><!-- UCSC expects index file to exist as bam_file_name.bai -->
+ <param type="template" name="track" viewable="True">track type="bam" name="${bam_file.name.replace( '\\', '\\\\' ).replace( '"', '\\"' )}" bigDataUrl="${bam_file.url}" db="${bam_file.dbkey}"</param></dynamic_links></display>
diff -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca -r 862d562e31670dd22a6bd575b2fa79328acabb4d display_applications/ucsc/bigbed.xml
--- a/display_applications/ucsc/bigbed.xml
+++ b/display_applications/ucsc/bigbed.xml
@@ -10,7 +10,7 @@
<filter>${dataset.dbkey in $builds}</filter><!-- We define url and params as normal, but values defined in dynamic_param are available by specified name --><url>${ucsc_link}db=${qp($bigbed_file.dbkey)}&hgt.customText=${qp($track.url)}</url>
- <param type="data" name="bigbed_file" url="galaxy_${DATASET_HASH}.bigbed" strip_https="True" />
- <param type="template" name="track" viewable="True" strip_https="True">track type=bigBed name="${bigbed_file.name}" bigDataUrl=${bigbed_file.url} db=${bigbed_file.dbkey}</param>
+ <param type="data" name="bigbed_file" url="galaxy_${DATASET_HASH}.bigbed" />
+ <param type="template" name="track" viewable="True">track type="bigBed" name="${bigbed_file.name.replace( '\\', '\\\\' ).replace( '"', '\\"' )}" bigDataUrl="${bigbed_file.url}" db="${bigbed_file.dbkey}"</param></dynamic_links></display>
diff -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca -r 862d562e31670dd22a6bd575b2fa79328acabb4d display_applications/ucsc/bigwig.xml
--- a/display_applications/ucsc/bigwig.xml
+++ b/display_applications/ucsc/bigwig.xml
@@ -10,7 +10,7 @@
<filter>${dataset.dbkey in $builds}</filter><!-- We define url and params as normal, but values defined in dynamic_param are available by specified name --><url>${ucsc_link}db=${qp($bigwig_file.dbkey)}&hgt.customText=${qp($track.url)}</url>
- <param type="data" name="bigwig_file" url="galaxy_${DATASET_HASH}.bigwig" strip_https="True" />
- <param type="template" name="track" viewable="True" strip_https="True">track type=bigWig name="${bigwig_file.name}" bigDataUrl=${bigwig_file.url} db=${bigwig_file.dbkey}</param>
+ <param type="data" name="bigwig_file" url="galaxy_${DATASET_HASH}.bigwig" />
+ <param type="template" name="track" viewable="True">track type="bigWig" name="${bigwig_file.name.replace( '\\', '\\\\' ).replace( '"', '\\"' )}" bigDataUrl="${bigwig_file.url}" db="${bigwig_file.dbkey}"</param></dynamic_links></display>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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