galaxy-commits April 2011

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112 discussions

commit/galaxy-central: fubar: typo in selected for gcbias. Still broken on test - no idea why - wonder if it's an old version of picard?
by Bitbucket 28 Apr '11

28 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/d6aa5ad56d2b/ changeset: r5480:d6aa5ad56d2b user: fubar date: 2011-04-29 03:14:46 summary: typo in selected for gcbias. Still broken on test - no idea why - wonder if it's an old version of picard? affected #: 1 file (16 bytes) --- a/tools/picard/rgPicardGCBiasMetrics.xml Thu Apr 28 19:57:32 2011 -0400 +++ b/tools/picard/rgPicardGCBiasMetrics.xml Thu Apr 28 21:14:46 2011 -0400 @@ -44,7 +44,7 @@ <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" selected="true" >8GB - should generally work...</option> + <option value="8G" >8GB - should generally work...</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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commit/galaxy-central: fubar: gcbias still failing - try 2GB of java heap...
by Bitbucket 28 Apr '11

28 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/8f1cabffa8f8/ changeset: r5479:8f1cabffa8f8 user: fubar date: 2011-04-29 01:57:32 summary: gcbias still failing - try 2GB of java heap... affected #: 1 file (25 bytes) --- a/tools/picard/rgPicardGCBiasMetrics.xml Thu Apr 28 19:30:48 2011 -0400 +++ b/tools/picard/rgPicardGCBiasMetrics.xml Thu Apr 28 19:57:32 2011 -0400 @@ -41,10 +41,11 @@ 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"> + <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" selected="true" >8GB - should generally work...</option><option value="16G">16GB - try this if 8GB fails</option> - <option value="32G">32GB - please use only if absolutely necessary</option></param></inputs> 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: 2 new changesets
by Bitbucket 28 Apr '11

28 Apr '11

2 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/a1b017b9743f/ changeset: r5477:a1b017b9743f user: fubar date: 2011-04-28 23:28:07 summary: collectgcbias metrics is bitten by the header length bug again - try fakefasta solution again affected #: 1 file (149 bytes) --- a/tools/picard/picard_wrapper.py Thu Apr 28 16:25:09 2011 -0400 +++ b/tools/picard/picard_wrapper.py Thu Apr 28 17:28:07 2011 -0400 @@ -475,7 +475,8 @@ elif pic.picname == 'CollectGcBiasMetrics': assert os.path.isfile(ref_file_name),'PicardGC needs a reference sequence - cannot read %s' % ref_file_name - """ + # 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: @@ -484,13 +485,12 @@ s = '## unable to symlink %s to %s - different devices? May need to replace with shutil.copy' info = s shutil.copy(ref_file_name,fakefasta) - """ x = 'rgPicardGCBiasMetrics' pdfname = '%s.pdf' % x jpgname = '%s.jpg' % x tempout = os.path.join(opts.outdir,'rgPicardGCBiasMetrics.out') temppdf = os.path.join(opts.outdir,pdfname) - cl.append('R=%s' % ref_file_name) + cl.append('R=%s' % fakefasta) cl.append('WINDOW_SIZE=%s' % opts.windowsize) cl.append('MINIMUM_GENOME_FRACTION=%s' % opts.mingenomefrac) cl.append('INPUT=%s' % opts.input) http://bitbucket.org/galaxy/galaxy-central/changeset/c6eed447f43b/ changeset: r5478:c6eed447f43b user: fubar date: 2011-04-29 01:30:48 summary: tweaks to fasta locations for tests for ASM and insertsize affected #: 3 files (62 bytes) --- a/lib/galaxy/web/controllers/dataset.py Thu Apr 28 17:28:07 2011 -0400 +++ b/lib/galaxy/web/controllers/dataset.py Thu Apr 28 19:30:48 2011 -0400 @@ -507,7 +507,7 @@ # If data is binary or an image, stream without template; otherwise, use display template. # TODO: figure out a way to display images in display template. - if isinstance(dataset.datatype, datatypes.binary.Binary) or isinstance(dataset.datatype, datatypes.images.Image): + if isinstance(dataset.datatype, datatypes.binary.Binary) or isinstance(dataset.datatype, datatypes.images.Image) or isinstance(dataset.datatype, datatypes.images.Html): mime = trans.app.datatypes_registry.get_mimetype_by_extension( dataset.extension.lower() ) trans.response.set_content_type( mime ) return open( dataset.file_name ) --- a/tools/picard/rgPicardASMetrics.xml Thu Apr 28 17:28:07 2011 -0400 +++ b/tools/picard/rgPicardASMetrics.xml Thu Apr 28 19:30:48 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 ), $__app__.tool_data_tables[ 'all_fasta' ].get_fields() )[0][-1] }" + --ref "${ filter( lambda x: str( x[0] ) == str( $genomeSource.index ), $__app__.tool_data_tables[ 'srma_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="all_fasta"> + <options from_data_table="srma_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/rgPicardInsertSize.xml Thu Apr 28 17:28:07 2011 -0400 +++ b/tools/picard/rgPicardInsertSize.xml Thu Apr 28 19:30:48 2011 -0400 @@ -31,7 +31,7 @@ <param name="tailLimit" value="10000" /><param name="histWidth" value="0" /><param name="minPct" value="0.01" /> - <output name="html_file" file="picard_output_insertsize_tinysam.html" ftype="html" lines_diff="25" /> + <output name="html_file" file="picard_output_insertsize_tinysam.html" ftype="html" lines_diff="30" /></test></tests><help> 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: fix for missing html ref in picard_reordersam and for data index srma_indexes in gcbias
by Bitbucket 28 Apr '11

28 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/d2032d37013f/ changeset: r5476:d2032d37013f user: fubar date: 2011-04-28 22:25:09 summary: fix for missing html ref in picard_reordersam and for data index srma_indexes in gcbias affected #: 3 files (41 bytes) --- a/tools/picard/picard_ReorderSam.xml Thu Apr 28 13:40:41 2011 -0400 +++ b/tools/picard/picard_ReorderSam.xml Thu Apr 28 16:25:09 2011 -0400 @@ -121,7 +121,7 @@ **Picard documentation** -This is a Galaxy interface for Picard-tool_'s ReorderSam tool, a part of Picard-tools_, which is supported by SAMTools_. +This is a Galaxy interface for Picard-tools_'s ReorderSam tool, a part of Picard-tools_, which is supported by SAMTools_. .. _Picard-tools: http://picard.sourceforge.net/index.shtml .. _SAMTools: http://samtools.sourceforge.net/ --- a/tools/picard/rgPicardGCBiasMetrics.xml Thu Apr 28 13:40:41 2011 -0400 +++ b/tools/picard/rgPicardGCBiasMetrics.xml Thu Apr 28 16:25:09 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 ), $__app__.tool_data_tables[ 'srma_index' ].get_fields() )[0][-1] }" + --ref "${ filter( lambda x: str( x[0] ) == str( $genomeSource.index ), $__app__.tool_data_tables[ 'srma_indexes' ].get_fields() )[0][-1] }" #end if </command> @@ -25,7 +25,7 @@ </param><when value="indexed"><param name="index" type="select" label="Select a reference genome"> - <options from_data_table="srma_index"> + <options from_data_table="srma_indexes"><filter type="data_meta" ref="input_file" key="dbkey" column="dbkey" multiple="True" separator=","/><validator type="no_options" message="No reference sequences are available for the build associated with the selected input data"/></options> --- a/tools/rgenetics/rgfakePhe.xml Thu Apr 28 13:40:41 2011 -0400 +++ b/tools/rgenetics/rgfakePhe.xml Thu Apr 28 16:25:09 2011 -0400 @@ -1,6 +1,5 @@ <tool id="fakePhe1" name="Null phenotypes"><description>for testing</description> - <code file="rgfakePhe_code.py"/><command interpreter="python">rgfakePhe.py '$infile1.extra_files_path/$infile1.metadata.base_name' "$title1" '$ppheout' '$ppheout.files_path' '$script_file' </command> 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: 2 new changesets
by Bitbucket 28 Apr '11

28 Apr '11

2 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/493c62279136/ changeset: r5474:493c62279136 user: fubar date: 2011-04-28 19:40:20 summary: odd problem with gcbias on test - may be due to missing picard_index.loc - sample only is there so shifting to srma_index for testing affected #: 2 files (21 bytes) --- a/tools/picard/picard_wrapper.py Thu Apr 28 12:11:27 2011 -0400 +++ b/tools/picard/picard_wrapper.py Thu Apr 28 13:40:20 2011 -0400 @@ -475,6 +475,7 @@ elif pic.picname == 'CollectGcBiasMetrics': assert os.path.isfile(ref_file_name),'PicardGC needs a reference sequence - cannot read %s' % ref_file_name + """ fakefasta = os.path.join(opts.outdir,'%s_fake.fasta' % os.path.basename(ref_file_name)) pic.delme.append(fakefasta) try: @@ -483,13 +484,13 @@ s = '## unable to symlink %s to %s - different devices? May need to replace with shutil.copy' info = s shutil.copy(ref_file_name,fakefasta) - + """ x = 'rgPicardGCBiasMetrics' pdfname = '%s.pdf' % x jpgname = '%s.jpg' % x tempout = os.path.join(opts.outdir,'rgPicardGCBiasMetrics.out') temppdf = os.path.join(opts.outdir,pdfname) - cl.append('R=%s' % fakefasta) + cl.append('R=%s' % ref_file_name) cl.append('WINDOW_SIZE=%s' % opts.windowsize) cl.append('MINIMUM_GENOME_FRACTION=%s' % opts.mingenomefrac) cl.append('INPUT=%s' % opts.input) --- a/tools/picard/rgPicardGCBiasMetrics.xml Thu Apr 28 12:11:27 2011 -0400 +++ b/tools/picard/rgPicardGCBiasMetrics.xml Thu Apr 28 13:40:20 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 ), $__app__.tool_data_tables[ 'all_fasta' ].get_fields() )[0][-1] }" + --ref "${ filter( lambda x: str( x[0] ) == str( $genomeSource.index ), $__app__.tool_data_tables[ 'srma_index' ].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="all_fasta"> + <options from_data_table="srma_index"><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> http://bitbucket.org/galaxy/galaxy-central/changeset/2b057869b72f/ changeset: r5475:2b057869b72f user: fubar date: 2011-04-28 19:40:41 summary: branch merge affected #: 1 file (11 bytes) --- a/lib/galaxy/visualization/tracks/data_providers.py Thu Apr 28 13:40:20 2011 -0400 +++ b/lib/galaxy/visualization/tracks/data_providers.py Thu Apr 28 13:40:41 2011 -0400 @@ -417,7 +417,7 @@ return filters -class TabixDataProvider( TracksDataProvider, FilterableMixin ): +class TabixDataProvider( FilterableMixin, TracksDataProvider ): """ Tabix index data provider for the Galaxy track browser. """ @@ -448,7 +448,7 @@ iterator = self.get_iterator( chrom, start, end ) return self.process_data(iterator, **kwargs) -class GffDataProvider( TracksDataProvider, FilterableMixin ): +class IntervalIndexDataProvider( FilterableMixin, TracksDataProvider ): col_name_data_attr_mapping = { 4 : { 'index': 4 , 'name' : 'Score' } } def write_data_to_file( self, chrom, start, end, filename ): @@ -653,7 +653,7 @@ # is original dataset type. TODO: This needs to be more flexible. dataset_type_name_to_data_provider = { "tabix": { Vcf: VcfDataProvider, Bed: BedDataProvider, "default" : TabixDataProvider }, - "interval_index": { Gff: GffDataProvider, Gtf: GffDataProvider }, + "interval_index": IntervalIndexDataProvider, "bai": BamDataProvider, "summary_tree": SummaryTreeDataProvider, "bigwig": BigWigDataProvider, 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: kanwei: trackster: Fix filters, restore name of IntervalIndex provider
by Bitbucket 28 Apr '11

28 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/0cb1f1f68a86/ changeset: r5473:0cb1f1f68a86 user: kanwei date: 2011-04-28 19:17:51 summary: trackster: Fix filters, restore name of IntervalIndex provider affected #: 1 file (11 bytes) --- a/lib/galaxy/visualization/tracks/data_providers.py Thu Apr 28 12:11:27 2011 -0400 +++ b/lib/galaxy/visualization/tracks/data_providers.py Thu Apr 28 13:17:51 2011 -0400 @@ -417,7 +417,7 @@ return filters -class TabixDataProvider( TracksDataProvider, FilterableMixin ): +class TabixDataProvider( FilterableMixin, TracksDataProvider ): """ Tabix index data provider for the Galaxy track browser. """ @@ -448,7 +448,7 @@ iterator = self.get_iterator( chrom, start, end ) return self.process_data(iterator, **kwargs) -class GffDataProvider( TracksDataProvider, FilterableMixin ): +class IntervalIndexDataProvider( FilterableMixin, TracksDataProvider ): col_name_data_attr_mapping = { 4 : { 'index': 4 , 'name' : 'Score' } } def write_data_to_file( self, chrom, start, end, filename ): @@ -653,7 +653,7 @@ # is original dataset type. TODO: This needs to be more flexible. dataset_type_name_to_data_provider = { "tabix": { Vcf: VcfDataProvider, Bed: BedDataProvider, "default" : TabixDataProvider }, - "interval_index": { Gff: GffDataProvider, Gtf: GffDataProvider }, + "interval_index": IntervalIndexDataProvider, "bai": BamDataProvider, "summary_tree": SummaryTreeDataProvider, "bigwig": BigWigDataProvider, 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: The Buildbot tells me that it's easiest to install FastQC under tool-data/shared/jars - adjusted the tool appropriately
by Bitbucket 28 Apr '11

28 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/d6be25b05259/ changeset: r5472:d6be25b05259 user: fubar date: 2011-04-28 18:11:27 summary: The Buildbot tells me that it's easiest to install FastQC under tool-data/shared/jars - adjusted the tool appropriately affected #: 1 file (5 bytes) --- a/tools/rgenetics/rgFastQC.xml Thu Apr 28 11:48:52 2011 -0400 +++ b/tools/rgenetics/rgFastQC.xml Thu Apr 28 12:11:27 2011 -0400 @@ -1,7 +1,7 @@ <tool name="Fastqc: Fastqc QC" id="fastqc" version="0.1"><description>using FastQC from Babraham</description><command interpreter="python"> - rgFastQC.py -i $input_file -d $html_file.files_path -o $html_file -n "$out_prefix" -f $input_file.ext -e ${GALAXY_DATA_INDEX_DIR}/shared/FastQC/fastqc + rgFastQC.py -i $input_file -d $html_file.files_path -o $html_file -n "$out_prefix" -f $input_file.ext -e ${GALAXY_DATA_INDEX_DIR}/shared/jars/FastQC/fastqc #if $contaminants.dataset and str($contaminants) > '' -c "$contaminants" #end if 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: 2 new changesets
by Bitbucket 28 Apr '11

28 Apr '11

2 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/871ae4a9e95c/ changeset: r5470:871ae4a9e95c user: fubar date: 2011-04-28 17:48:37 summary: missing quote in picard_wrapper affected #: 1 file (1 byte) --- a/tools/picard/picard_wrapper.py Thu Apr 28 11:10:41 2011 -0400 +++ b/tools/picard/picard_wrapper.py Thu Apr 28 11:48:37 2011 -0400 @@ -527,7 +527,7 @@ s,stdouts = pic.runCL(cl=cl2,output_dir=opts.outdir) else: s = 'Unable to find expected pdf file %s<br/>\n' % pdfpath - s += This <b>always happens if single ended data was provided</b> to this tool,\n' + s += 'This <b>always happens if single ended data was provided</b> to this tool,\n' s += 'so please double check that your input data really is paired-end NGS data.<br/>\n' s += 'If your input was paired data this may be a bug worth reporting to the galaxy-bugs list\n<br/>' stdouts = '' http://bitbucket.org/galaxy/galaxy-central/changeset/ea9a898b73be/ changeset: r5471:ea9a898b73be user: fubar date: 2011-04-28 17:48:52 summary: branch merge affected #: 5 files (3.6 KB) --- a/lib/galaxy/web/controllers/user.py Thu Apr 28 11:48:37 2011 -0400 +++ b/lib/galaxy/web/controllers/user.py Thu Apr 28 11:48:52 2011 -0400 @@ -735,6 +735,38 @@ webapp=webapp, message=message, status=status ) + # For REMOTE_USER, we need the ability to just edit the username + @web.expose + @web.require_login( "to manage the public name" ) + def edit_username( self, trans, cntrller, **kwd ): + params = util.Params( kwd ) + is_admin = cntrller == 'admin' and trans.user_is_admin() + webapp = params.get( 'webapp', 'galaxy' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + user_id = params.get( 'user_id', None ) + if user_id and is_admin: + user = trans.sa_session.query( trans.app.model.User ).get( trans.security.decode_id( user_id ) ) + else: + user = trans.user + if user and params.get( 'change_username_button', False ): + username = kwd.get( 'username', '' ) + if username: + message = self.__validate_username( trans, username, user ) + if message: + status = 'error' + else: + user.username = username + trans.sa_session.add( user ) + trans.sa_session.flush() + message = 'The username has been updated with the changes.' + return trans.fill_template( '/user/username.mako', + cntrller=cntrller, + user=user, + username=user.username, + webapp=webapp, + message=message, + status=status ) @web.expose def edit_info( self, trans, cntrller, **kwd ): params = util.Params( kwd ) @@ -743,12 +775,15 @@ message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) user_id = params.get( 'user_id', None ) - #new_kwd = dict( webapp=webapp ) - if user_id: + if user_id and is_admin: user = trans.sa_session.query( trans.app.model.User ).get( trans.security.decode_id( user_id ) ) + elif user_id and ( not trans.user or trans.user.id != trans.security.decode_id( user_id ) ): + message = 'Invalid user id' + status = 'error' + user = None else: user = trans.user - if params.get( 'login_info_button', False ): + if user and params.get( 'login_info_button', False ): # Editing email and username email = util.restore_text( params.get( 'email', '' ) ) username = util.restore_text( params.get( 'username', '' ) ).lower() @@ -769,7 +804,7 @@ trans.sa_session.add_all( ( user, private_role ) ) trans.sa_session.flush() message = 'The login information has been updated with the changes.' - elif params.get( 'change_password_button', False ): + elif user and params.get( 'change_password_button', False ): # Editing password. Do not sanitize passwords, so get from kwd # and not params (which were sanitized). password = kwd.get( 'password', '' ) @@ -794,7 +829,7 @@ trans.sa_session.flush() trans.log_event( "User change password" ) message = 'The password has been changed.' - elif params.get( 'edit_user_info_button', False ): + elif user and params.get( 'edit_user_info_button', False ): # Edit user information - webapp MUST BE 'galaxy' user_type_fd_id = params.get( 'user_type_fd_id', 'none' ) if user_type_fd_id not in [ 'none' ]: @@ -809,7 +844,7 @@ else: values = {} flush_needed = False - if user.values: + if user.values: # Editing the user info of an existing user with existing user info user.values.content = values trans.sa_session.add( user.values ) @@ -823,7 +858,7 @@ trans.sa_session.add( user ) trans.sa_session.flush() message = "The user information has been updated with the changes." - if webapp == 'galaxy' and is_admin: + if user and webapp == 'galaxy' and is_admin: kwd[ 'user_id' ] = trans.security.encode_id( user.id ) kwd[ 'id' ] = user_id if message: --- a/lib/galaxy/web/framework/__init__.py Thu Apr 28 11:48:37 2011 -0400 +++ b/lib/galaxy/web/framework/__init__.py Thu Apr 28 11:48:52 2011 -0400 @@ -437,10 +437,18 @@ 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] 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 + # 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 + while ( self.sa_session.query( self.app.model.User ).filter_by( username=(username + '-' + str(i) ) ).first() ): + i += 1 + username += '-' + str(i) + user.username = username self.sa_session.add( user ) self.sa_session.flush() self.app.security_agent.create_private_user_role( user ) --- a/lib/galaxy/web/framework/middleware/remoteuser.py Thu Apr 28 11:48:37 2011 -0400 +++ b/lib/galaxy/web/framework/middleware/remoteuser.py Thu Apr 28 11:48:52 2011 -0400 @@ -97,6 +97,8 @@ pass # admins can create users elif path_info.startswith( '/user/api_keys' ): pass # api keys can be managed when remote_user is in use + elif path_info.startswith( '/user/edit_username' ): + pass # username can be managed when remote_user is in use elif path_info.startswith( '/user/dbkeys' ): pass # dbkeys can be managed when remote_user is in use elif path_info.startswith( '/user' ): --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/user/username.mako Thu Apr 28 11:48:52 2011 -0400 @@ -0,0 +1,23 @@ +<%inherit file="/base.mako"/> + +<% is_admin = cntrller == 'admin' and trans.user_is_admin() %> + +<h2>Manage Public Name</h2> +<div class="toolForm"> + <form name="username" id="username" action="${h.url_for( controller='user', action='edit_username', cntrller=cntrller, user_id=trans.security.encode_id( user.id ) )}" method="post" > + <input type="hidden" name="webapp" value="${webapp}" size="40"/> + <div class="toolFormTitle">Login Information</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> + </div> + <div class="form-row"> + <input type="submit" name="change_username_button" value="Save"/> + </div> + </form> +</div> --- a/templates/webapps/galaxy/base_panels.mako Thu Apr 28 11:48:37 2011 -0400 +++ b/templates/webapps/galaxy/base_panels.mako Thu Apr 28 11:48:52 2011 -0400 @@ -149,6 +149,8 @@ menu_options.append( [ 'Saved Pages', h.url_for( controller='/page', action='list' ), "_top" ] ) if app.config.enable_api: menu_options.append( [ 'API Keys', h.url_for( controller='/user', action='api_keys', cntrller='user' ), "galaxy_main" ] ) + if app.config.use_remote_user: + menu_options.append( [ 'Public Name', h.url_for( controller='/user', action='edit_username', cntrller='user' ), "galaxy_main" ] ) extra_class = "loggedin-only" visible = ( trans.user != None ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: natefoo: Set and allow modification of the public username if use_remote_user = True
by Bitbucket 28 Apr '11

28 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/7c101a11d261/ changeset: r5469:7c101a11d261 user: natefoo date: 2011-04-28 17:33:07 summary: Set and allow modification of the public username if use_remote_user = True affected #: 5 files (2.5 KB) --- a/lib/galaxy/web/controllers/user.py Thu Apr 28 11:10:41 2011 -0400 +++ b/lib/galaxy/web/controllers/user.py Thu Apr 28 11:33:07 2011 -0400 @@ -735,6 +735,38 @@ webapp=webapp, message=message, status=status ) + # For REMOTE_USER, we need the ability to just edit the username + @web.expose + @web.require_login( "to manage the public name" ) + def edit_username( self, trans, cntrller, **kwd ): + params = util.Params( kwd ) + is_admin = cntrller == 'admin' and trans.user_is_admin() + webapp = params.get( 'webapp', 'galaxy' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + user_id = params.get( 'user_id', None ) + if user_id and is_admin: + user = trans.sa_session.query( trans.app.model.User ).get( trans.security.decode_id( user_id ) ) + else: + user = trans.user + if user and params.get( 'change_username_button', False ): + username = kwd.get( 'username', '' ) + if username: + message = self.__validate_username( trans, username, user ) + if message: + status = 'error' + else: + user.username = username + trans.sa_session.add( user ) + trans.sa_session.flush() + message = 'The username has been updated with the changes.' + return trans.fill_template( '/user/username.mako', + cntrller=cntrller, + user=user, + username=user.username, + webapp=webapp, + message=message, + status=status ) @web.expose def edit_info( self, trans, cntrller, **kwd ): params = util.Params( kwd ) @@ -743,12 +775,15 @@ message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) user_id = params.get( 'user_id', None ) - #new_kwd = dict( webapp=webapp ) - if user_id: + if user_id and is_admin: user = trans.sa_session.query( trans.app.model.User ).get( trans.security.decode_id( user_id ) ) + elif user_id and ( not trans.user or trans.user.id != trans.security.decode_id( user_id ) ): + message = 'Invalid user id' + status = 'error' + user = None else: user = trans.user - if params.get( 'login_info_button', False ): + if user and params.get( 'login_info_button', False ): # Editing email and username email = util.restore_text( params.get( 'email', '' ) ) username = util.restore_text( params.get( 'username', '' ) ).lower() @@ -769,7 +804,7 @@ trans.sa_session.add_all( ( user, private_role ) ) trans.sa_session.flush() message = 'The login information has been updated with the changes.' - elif params.get( 'change_password_button', False ): + elif user and params.get( 'change_password_button', False ): # Editing password. Do not sanitize passwords, so get from kwd # and not params (which were sanitized). password = kwd.get( 'password', '' ) @@ -794,7 +829,7 @@ trans.sa_session.flush() trans.log_event( "User change password" ) message = 'The password has been changed.' - elif params.get( 'edit_user_info_button', False ): + elif user and params.get( 'edit_user_info_button', False ): # Edit user information - webapp MUST BE 'galaxy' user_type_fd_id = params.get( 'user_type_fd_id', 'none' ) if user_type_fd_id not in [ 'none' ]: @@ -809,7 +844,7 @@ else: values = {} flush_needed = False - if user.values: + if user.values: # Editing the user info of an existing user with existing user info user.values.content = values trans.sa_session.add( user.values ) @@ -823,7 +858,7 @@ trans.sa_session.add( user ) trans.sa_session.flush() message = "The user information has been updated with the changes." - if webapp == 'galaxy' and is_admin: + if user and webapp == 'galaxy' and is_admin: kwd[ 'user_id' ] = trans.security.encode_id( user.id ) kwd[ 'id' ] = user_id if message: --- a/lib/galaxy/web/framework/__init__.py Thu Apr 28 11:10:41 2011 -0400 +++ b/lib/galaxy/web/framework/__init__.py Thu Apr 28 11:33:07 2011 -0400 @@ -437,10 +437,18 @@ 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] 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 + # 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 + while ( self.sa_session.query( self.app.model.User ).filter_by( username=(username + '-' + str(i) ) ).first() ): + i += 1 + username += '-' + str(i) + user.username = username self.sa_session.add( user ) self.sa_session.flush() self.app.security_agent.create_private_user_role( user ) --- a/lib/galaxy/web/framework/middleware/remoteuser.py Thu Apr 28 11:10:41 2011 -0400 +++ b/lib/galaxy/web/framework/middleware/remoteuser.py Thu Apr 28 11:33:07 2011 -0400 @@ -97,6 +97,8 @@ pass # admins can create users elif path_info.startswith( '/user/api_keys' ): pass # api keys can be managed when remote_user is in use + elif path_info.startswith( '/user/edit_username' ): + pass # username can be managed when remote_user is in use elif path_info.startswith( '/user/dbkeys' ): pass # dbkeys can be managed when remote_user is in use elif path_info.startswith( '/user' ): --- a/templates/webapps/galaxy/base_panels.mako Thu Apr 28 11:10:41 2011 -0400 +++ b/templates/webapps/galaxy/base_panels.mako Thu Apr 28 11:33:07 2011 -0400 @@ -149,6 +149,8 @@ menu_options.append( [ 'Saved Pages', h.url_for( controller='/page', action='list' ), "_top" ] ) if app.config.enable_api: menu_options.append( [ 'API Keys', h.url_for( controller='/user', action='api_keys', cntrller='user' ), "galaxy_main" ] ) + if app.config.use_remote_user: + menu_options.append( [ 'Public Name', h.url_for( controller='/user', action='edit_username', cntrller='user' ), "galaxy_main" ] ) extra_class = "loggedin-only" visible = ( trans.user != None ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: fubar: clean up of accidentally added test detritus
by Bitbucket 28 Apr '11

28 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/9c63ae1f7cef/ changeset: r5468:9c63ae1f7cef user: fubar date: 2011-04-28 17:10:41 summary: clean up of accidentally added test detritus affected #: 1 file (0 bytes) Diff too large to display. 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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galaxy-commits April 2011