April 2011 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: fubar: second test for picard asmetrics fails on buildbot. This fix works on my own testbed - but then, it worked before too...
by Bitbucket 29 Apr '11

29 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/6dc381fe8af9/ changeset: r5490:6dc381fe8af9 user: fubar date: 2011-04-29 23:32:33 summary: second test for picard asmetrics fails on buildbot. This fix works on my own testbed - but then, it worked before too... affected #: 1 file (42 bytes) --- a/tools/picard/rgPicardASMetrics.xml Fri Apr 29 17:23:06 2011 -0400 +++ b/tools/picard/rgPicardASMetrics.xml Fri Apr 29 17:32:33 2011 -0400 @@ -62,6 +62,7 @@ <param name="sorted" value="true" /><param name="adaptors" value="" /><param name="maxinsert" value="100000" /> + <param name="index" value="hg18" /><param name="refGenomeSource" value="indexed" /><param name="index" value="hg18" /><param name="input_file" value="picard_input_sorted_pair.sam" dbkey="hg18" /> 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.

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commit/galaxy-central: dan: Show rerun and info buttons in dataset previews for additional states.
by Bitbucket 29 Apr '11

29 Apr '11

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

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commit/galaxy-central: dan: Only allow a user to rerun if they have access permissions on the dataset.
by Bitbucket 29 Apr '11

29 Apr '11

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

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commit/galaxy-central: greg: Apply patch from taoliu - ticket #529 - Missing controller when creating user with require_login & allow_user_creatio is on.
by Bitbucket 29 Apr '11

29 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/3496a98f9cbe/ changeset: r5487:3496a98f9cbe user: greg date: 2011-04-29 21:32:04 summary: Apply patch from taoliu - ticket #529 - Missing controller when creating user with require_login & allow_user_creatio is on. affected #: 1 file (17 bytes) --- a/lib/galaxy/web/controllers/user.py Fri Apr 29 13:59:11 2011 -0400 +++ b/lib/galaxy/web/controllers/user.py Fri Apr 29 15:32:04 2011 -0400 @@ -371,7 +371,7 @@ redirect_url = url_for( '/' ) if not user and trans.app.config.require_login: if trans.app.config.allow_user_creation: - header = require_login_creation_template % web.url_for( action='create' ) + header = require_login_creation_template % web.url_for( action='create', cntrller='user' ) else: header = require_login_nocreation_template return trans.fill_template( '/user/login.mako', 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.

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commit/galaxy-central: natefoo: New pysam w/o ctypes dependency.
by Bitbucket 29 Apr '11

29 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/27dfee4fccaf/ changeset: r5486:27dfee4fccaf user: natefoo date: 2011-04-29 19:59:11 summary: New pysam w/o ctypes dependency. affected #: 1 file (0 bytes) 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.

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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 29 Apr '11

29 Apr '11

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

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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 29 Apr '11

29 Apr '11

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

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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 29 Apr '11

29 Apr '11

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

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commit/galaxy-central: fubar: ok. back to all_fasta.loc - they must be somewhere
by Bitbucket 28 Apr '11

28 Apr '11

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

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commit/galaxy-central: fubar: Finally I think. fasta not .fa for asmetrics and gcbias
by Bitbucket 28 Apr '11

28 Apr '11

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

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