commit/galaxy-central: dan: Show rerun and info buttons in dataset previews for additional states.
by Bitbucket
1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/4ab5044b3196/
changeset: r5489:4ab5044b3196
user: dan
date: 2011-04-29 23:23:06
summary: Show rerun and info buttons in dataset previews for additional states.
affected #: 1 file (1.7 KB)
--- a/templates/root/history_common.mako Fri Apr 29 16:51:51 2011 -0400
+++ b/templates/root/history_common.mako Fri Apr 29 17:23:06 2011 -0400
@@ -83,15 +83,30 @@
<div>Dataset is uploading</div>
%elif data_state == "queued":
<div>${_('Job is waiting to run')}</div>
+ <div>
+ <a href="${h.url_for( controller='dataset', action='show_params', dataset_id=dataset_id )}" target="galaxy_main" title="View Details" class="icon-button information tooltip"></a>
+ %if for_editing:
+ <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title="Run this job again" class="icon-button arrow-circle tooltip"></a>
+ %endif
+ </div>
%elif data_state == "running":
<div>${_('Job is currently running')}</div>
+ <div>
+ <a href="${h.url_for( controller='dataset', action='show_params', dataset_id=dataset_id )}" target="galaxy_main" title="View Details" class="icon-button information tooltip"></a>
+ %if for_editing:
+ <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title="Run this job again" class="icon-button arrow-circle tooltip"></a>
+ %endif
+ </div>
%elif data_state == "error":
<div>
An error occurred running this job: <i>${data.display_info().strip()}</i></div><div><a href="${h.url_for( controller='dataset', action='errors', id=data.id )}" target="galaxy_main" title="View or report this error" class="icon-button bug tooltip"></a>
- <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title="Run this job again" class="icon-button arrow-circle tooltip"></a>
+ <a href="${h.url_for( controller='dataset', action='show_params', dataset_id=dataset_id )}" target="galaxy_main" title="View Details" class="icon-button information tooltip"></a>
+ %if for_editing:
+ <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title="Run this job again" class="icon-button arrow-circle tooltip"></a>
+ %endif
</div>
%elif data_state == "discarded":
<div>
@@ -101,6 +116,12 @@
<div>${_('Metadata is being Auto-Detected.')}</div>
%elif data_state == "empty":
<div>${_('No data: ')}<i>${data.display_info()}</i></div>
+ <div>
+ <a href="${h.url_for( controller='dataset', action='show_params', dataset_id=dataset_id )}" target="galaxy_main" title="View Details" class="icon-button information tooltip"></a>
+ %if for_editing:
+ <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title="Run this job again" class="icon-button arrow-circle tooltip"></a>
+ %endif
+ </div>
%elif data_state in [ "ok", "failed_metadata" ]:
%if data_state == "failed_metadata":
<div class="warningmessagesmall" style="margin: 4px 0 4px 0">
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: dan: Only allow a user to rerun if they have access permissions on the dataset.
by Bitbucket
1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/7ae63fde7f78/
changeset: r5488:7ae63fde7f78
user: dan
date: 2011-04-29 22:51:51
summary: Only allow a user to rerun if they have access permissions on the dataset.
affected #: 1 file (246 bytes)
--- a/lib/galaxy/web/controllers/tool_runner.py Fri Apr 29 15:32:04 2011 -0400
+++ b/lib/galaxy/web/controllers/tool_runner.py Fri Apr 29 16:51:51 2011 -0400
@@ -90,6 +90,9 @@
error( "Invalid value for 'id' parameter" )
# Get the dataset object
data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( id )
+ #only allow rerunning if user is allowed access to the dataset.
+ if not trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), data.dataset ):
+ error( "You are not allowed to access this dataset" )
# Get the associated job, if any. If this hda was copied from another,
# we need to find the job that created the origial hda
job_hda = data
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: fubar: gcbias still failing on test - works fine here using same data - clean up of fasta munging
by Bitbucket
1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/62a5d6d82151/
changeset: r5485:62a5d6d82151
user: fubar
date: 2011-04-29 18:29:13
summary: gcbias still failing on test - works fine here using same data - clean up of fasta munging
affected #: 2 files (166 bytes)
--- a/tools/picard/picard_wrapper.py Fri Apr 29 10:37:59 2011 -0400
+++ b/tools/picard/picard_wrapper.py Fri Apr 29 12:29:13 2011 -0400
@@ -361,19 +361,19 @@
tmp_dir = opts.outdir
# set ref and dict files to use (create if necessary)
- if opts.ref_file:
+ ref_file_name = opts.ref
+ if opts.ref_file <> None:
csd = 'CreateSequenceDictionary'
realjarpath = os.path.split(opts.jar)[0]
jarpath = os.path.join(realjarpath,'%s.jar' % csd) # for refseq
tmp_ref_fd, tmp_ref_name = tempfile.mkstemp( dir=opts.tmpdir , prefix = pic.picname)
- ref_file_name = '%s.fa' % tmp_ref_name
+ ref_file_name = '%s.fasta' % tmp_ref_name
# build dict
- ## need to change name of fasta to have fasta ext
- dict_file_name = ref_file_name.replace( '.fa', '.dict' )
+ dict_file_name = '%s.dict' % tmp_ref_name
os.symlink( opts.ref_file, ref_file_name )
cl = ['REFERENCE=%s' % ref_file_name]
cl.append('OUTPUT=%s' % dict_file_name)
- cl.append('URI=%s' % os.path.basename( ref_file_name ))
+ cl.append('URI=%s' % os.path.basename( ref_file ))
cl.append('TRUNCATE_NAMES_AT_WHITESPACE=%s' % opts.trunc_names)
if opts.species_name:
cl.append('SPECIES=%s' % opts.species_name)
@@ -381,11 +381,9 @@
cl.append('GENOME_ASSEMBLY=%s' % opts.build_name)
pic.delme.append(dict_file_name)
pic.delme.append(ref_file_name)
+ pic.delme.append(tmp_ref_name)
s = pic.runPic(jarpath, cl)
- elif opts.ref:
- ref_file_name = opts.ref
-
- # run relevant command(s)
+ # run relevant command(s)
cl = ['VALIDATION_STRINGENCY=LENIENT',]
@@ -446,13 +444,15 @@
elif pic.picname == 'CollectAlignmentSummaryMetrics':
+ # Why do we do this fakefasta thing? Because we need NO fai to be available or picard barfs unless it has the same length as the input data.
+ # why? Dunno
fakefasta = os.path.join(opts.outdir,'%s_fake.fasta' % os.path.basename(ref_file_name))
try:
os.symlink(ref_file_name,fakefasta)
except:
s = '## unable to symlink %s to %s - different devices? May need to replace with shutil.copy'
info = s
- shutil.copy(ref_file_name,fakefasta)
+ shutil.copy(ref_file_name,fakefasta)
pic.delme.append(fakefasta)
cl.append('ASSUME_SORTED=%s' % opts.assumesorted)
adaptorseqs = ''.join([' ADAPTER_SEQUENCE=%s' % x for x in opts.adaptors])
@@ -478,13 +478,13 @@
# sigh. Why do we do this fakefasta thing? Because we need NO fai to be available or picard barfs unless it has the same length as the input data.
# why? Dunno
fakefasta = os.path.join(opts.outdir,'%s_fake.fasta' % os.path.basename(ref_file_name))
- pic.delme.append(fakefasta)
try:
os.symlink(ref_file_name,fakefasta)
except:
s = '## unable to symlink %s to %s - different devices? May need to replace with shutil.copy'
info = s
- shutil.copy(ref_file_name,fakefasta)
+ shutil.copy(ref_file_name,fakefasta)
+ pic.delme.append(fakefasta)
x = 'rgPicardGCBiasMetrics'
pdfname = '%s.pdf' % x
jpgname = '%s.jpg' % x
--- a/tools/picard/rgPicardGCBiasMetrics.xml Fri Apr 29 10:37:59 2011 -0400
+++ b/tools/picard/rgPicardGCBiasMetrics.xml Fri Apr 29 12:29:13 2011 -0400
@@ -40,7 +40,7 @@
<param name="mingenomefrac" value="0.00001" type="float" label="Minimum Genome Fraction"
help="For summary metrics, exclude GC windows that include less than this fraction of the genome. Default value: 1.0E-5." /><param name="maxheap" type="select" help="If in doubt, choose 8G and read Picard documentation please"
- label="Java heap size. Java is a pig, the art is long but memory is short">
+ label="Java heap size"><option value="1G">1GB: very small data</option><option value="2G" selected="true">2GB</option><option value="4G">4GB for larger datasets </option>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: natefoo: When using a logout href, load that link at _top, not in the galaxy_main panel.
by Bitbucket
1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/337605f6b630/
changeset: r5484:337605f6b630
user: natefoo
date: 2011-04-29 16:37:59
summary: When using a logout href, load that link at _top, not in the galaxy_main panel.
affected #: 1 file (7 bytes)
--- a/templates/webapps/galaxy/base_panels.mako Fri Apr 29 10:35:42 2011 -0400
+++ b/templates/webapps/galaxy/base_panels.mako Fri Apr 29 10:37:59 2011 -0400
@@ -132,7 +132,7 @@
menu_options = [ [ '<li>Logged in as <span id="user-email">%s</span></li>' % email ] ]
if app.config.use_remote_user:
if app.config.remote_user_logout_href:
- menu_options.append( [ 'Logout', app.config.remote_user_logout_href, "galaxy_main" ] )
+ menu_options.append( [ 'Logout', app.config.remote_user_logout_href, "_top" ] )
else:
menu_options.append( [ 'Preferences', h.url_for( controller='/user', action='index', cntrller='user' ), "galaxy_main" ] )
if app.config.get_bool( 'enable_tracks', False ):
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: natefoo: Minor fix for setting the username during user creation under use_remote_user = True. Converts the user portion of the user's email to lowercase and replaces invalid characters with '-' as per the public name format requirements.
by Bitbucket
1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/4933de88cdb0/
changeset: r5483:4933de88cdb0
user: natefoo
date: 2011-04-29 16:35:42
summary: Minor fix for setting the username during user creation under use_remote_user = True. Converts the user portion of the user's email to lowercase and replaces invalid characters with '-' as per the public name format requirements.
affected #: 1 file (231 bytes)
--- a/lib/galaxy/web/framework/__init__.py Thu Apr 28 22:07:58 2011 -0400
+++ b/lib/galaxy/web/framework/__init__.py Fri Apr 29 10:35:42 2011 -0400
@@ -437,14 +437,17 @@
if not user.default_permissions:
self.app.security_agent.user_set_default_permissions( user, history=True, dataset=True )
elif user is None:
- username = remote_user_email.split( '@', 1 )[0]
+ username = remote_user_email.split( '@', 1 )[0].lower()
random.seed()
user = self.app.model.User( email=remote_user_email )
user.set_password_cleartext( ''.join( random.sample( string.letters + string.digits, 12 ) ) )
user.external = True
+ # Replace invalid characters in the username
+ for char in filter( lambda x: x not in string.ascii_lowercase + string.digits + '-', username ):
+ username = username.replace( char, '-' )
# Find a unique username - user can change it later
if ( self.sa_session.query( self.app.model.User ).filter_by( username=username ).first() ):
- i = 0
+ i = 1
while ( self.sa_session.query( self.app.model.User ).filter_by( username=(username + '-' + str(i) ) ).first() ):
i += 1
username += '-' + str(i)
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: fubar: ok. back to all_fasta.loc - they must be somewhere
by Bitbucket
1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/bb39eef087d4/
changeset: r5482:bb39eef087d4
user: fubar
date: 2011-04-29 04:07:58
summary: ok. back to all_fasta.loc - they must be somewhere
affected #: 2 files (8 bytes)
--- a/tools/picard/rgPicardASMetrics.xml Thu Apr 28 21:44:35 2011 -0400
+++ b/tools/picard/rgPicardASMetrics.xml Thu Apr 28 22:07:58 2011 -0400
@@ -8,7 +8,7 @@
--ref "$genomeSource.ownFile"
#end if
#if $genomeSource.refGenomeSource == "indexed":
- --ref "${ filter( lambda x: str( x[0] ) == str( $genomeSource.index ), $__app__.tool_data_tables[ 'bwa_indexes' ].get_fields() )[0][-1] }"
+ --ref "${ filter( lambda x: str( x[0] ) == str( $genomeSource.index ), $__app__.tool_data_tables[ 'all_fasta' ].get_fields() )[0][-1] }"
#end if
</command><requirements><requirement type="package">picard</requirement></requirements>
@@ -25,7 +25,7 @@
</param><when value="indexed"><param name="index" type="select" label="Select a reference genome">
- <options from_data_table="bwa_indexes">
+ <options from_data_table="all_fasta"><filter type="data_meta" ref="input_file" key="dbkey" column="dbkey" multiple="True" separator=","/><validator type="no_options" message="No reference sequences are available for the build associated with the selected input data"/></options>
--- a/tools/picard/rgPicardGCBiasMetrics.xml Thu Apr 28 21:44:35 2011 -0400
+++ b/tools/picard/rgPicardGCBiasMetrics.xml Thu Apr 28 22:07:58 2011 -0400
@@ -7,7 +7,7 @@
#if $genomeSource.refGenomeSource == "history":
--own_ref "$genomeSource.ownFile"
#else:
- --ref "${ filter( lambda x: str( x[0] ) == str( $genomeSource.index ), $__app__.tool_data_tables[ 'bwa_indexes' ].get_fields() )[0][-1] }"
+ --ref "${ filter( lambda x: str( x[0] ) == str( $genomeSource.index ), $__app__.tool_data_tables[ 'all_fasta' ].get_fields() )[0][-1] }"
#end if
</command>
@@ -25,7 +25,7 @@
</param><when value="indexed"><param name="index" type="select" label="Select a reference genome">
- <options from_data_table="bwa_indexes">
+ <options from_data_table="all_fasta"><filter type="data_meta" ref="input_file" key="dbkey" column="dbkey" multiple="True" separator=","/><validator type="no_options" message="No reference sequences are available for the build associated with the selected input data"/></options>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: fubar: Finally I think. fasta not .fa for asmetrics and gcbias
by Bitbucket
1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/640ff3d819e5/
changeset: r5481:640ff3d819e5
user: fubar
date: 2011-04-29 03:44:35
summary: Finally I think. fasta not .fa for asmetrics and gcbias
affected #: 2 files (29 bytes)
--- a/tools/picard/rgPicardASMetrics.xml Thu Apr 28 21:14:46 2011 -0400
+++ b/tools/picard/rgPicardASMetrics.xml Thu Apr 28 21:44:35 2011 -0400
@@ -8,7 +8,7 @@
--ref "$genomeSource.ownFile"
#end if
#if $genomeSource.refGenomeSource == "indexed":
- --ref "${ filter( lambda x: str( x[0] ) == str( $genomeSource.index ), $__app__.tool_data_tables[ 'srma_indexes' ].get_fields() )[0][-1] }"
+ --ref "${ filter( lambda x: str( x[0] ) == str( $genomeSource.index ), $__app__.tool_data_tables[ 'bwa_indexes' ].get_fields() )[0][-1] }"
#end if
</command><requirements><requirement type="package">picard</requirement></requirements>
@@ -25,7 +25,7 @@
</param><when value="indexed"><param name="index" type="select" label="Select a reference genome">
- <options from_data_table="srma_indexes">
+ <options from_data_table="bwa_indexes"><filter type="data_meta" ref="input_file" key="dbkey" column="dbkey" multiple="True" separator=","/><validator type="no_options" message="No reference sequences are available for the build associated with the selected input data"/></options>
--- a/tools/picard/rgPicardGCBiasMetrics.xml Thu Apr 28 21:14:46 2011 -0400
+++ b/tools/picard/rgPicardGCBiasMetrics.xml Thu Apr 28 21:44:35 2011 -0400
@@ -7,7 +7,7 @@
#if $genomeSource.refGenomeSource == "history":
--own_ref "$genomeSource.ownFile"
#else:
- --ref "${ filter( lambda x: str( x[0] ) == str( $genomeSource.index ), $__app__.tool_data_tables[ 'srma_indexes' ].get_fields() )[0][-1] }"
+ --ref "${ filter( lambda x: str( x[0] ) == str( $genomeSource.index ), $__app__.tool_data_tables[ 'bwa_indexes' ].get_fields() )[0][-1] }"
#end if
</command>
@@ -25,7 +25,7 @@
</param><when value="indexed"><param name="index" type="select" label="Select a reference genome">
- <options from_data_table="srma_indexes">
+ <options from_data_table="bwa_indexes"><filter type="data_meta" ref="input_file" key="dbkey" column="dbkey" multiple="True" separator=","/><validator type="no_options" message="No reference sequences are available for the build associated with the selected input data"/></options>
@@ -43,8 +43,8 @@
label="Java heap size. Java is a pig, the art is long but memory is short"><option value="1G">1GB: very small data</option><option value="2G" selected="true">2GB</option>
- <option value="4G">4GB will work for small sized datasets </option>
- <option value="8G" >8GB - should generally work...</option>
+ <option value="4G">4GB for larger datasets </option>
+ <option value="8G" >8GB use if 4GB fails</option><option value="16G">16GB - try this if 8GB fails</option></param>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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