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commit/galaxy-central: natefoo: Decrease user disk usage when files are removed from disk by the cleanup_datasets.py.
by Bitbucket 22 Aug '11

22 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/126c7f11415b/ changeset: 126c7f11415b user: natefoo date: 2011-08-22 22:19:49 summary: Decrease user disk usage when files are removed from disk by the cleanup_datasets.py. affected #: 1 file (473 bytes) --- a/scripts/cleanup_datasets/cleanup_datasets.py Mon Aug 22 16:07:23 2011 -0400 +++ b/scripts/cleanup_datasets/cleanup_datasets.py Mon Aug 22 16:19:49 2011 -0400 @@ -453,6 +453,13 @@ # Remove associated extra files from disk if they exist if dataset.extra_files_path and os.path.exists( dataset.extra_files_path ): shutil.rmtree( dataset.extra_files_path ) #we need to delete the directory and its contents; os.unlink would always fail on a directory + usage_users = [] + for hda in dataset.history_associations: + if not hda.purged and hda.history.user is not None and hda.history.user not in usage_users: + usage_users.append( hda.history.user ) + for user in usage_users: + user.total_disk_usage -= dataset.total_size + app.sa_session.add( user ) print "Purging dataset id", dataset.id dataset.purged = True app.sa_session.add( dataset ) 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: Allow FASTQ Groomer tool to work on Color Space files that contain a fake/dummy quality score for the adapter base (e.g. files obtained from the SRA). The Groomer will remove the dummy/fake quality score from the read.
by Bitbucket 22 Aug '11

22 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/77b20b28d89c/ changeset: 77b20b28d89c user: dan date: 2011-08-22 22:07:23 summary: Allow FASTQ Groomer tool to work on Color Space files that contain a fake/dummy quality score for the adapter base (e.g. files obtained from the SRA). The Groomer will remove the dummy/fake quality score from the read. affected #: 4 files (1.6 KB) --- a/lib/galaxy_utils/sequence/fastq.py Mon Aug 22 14:58:51 2011 -0400 +++ b/lib/galaxy_utils/sequence/fastq.py Mon Aug 22 16:07:23 2011 -0400 @@ -153,6 +153,8 @@ rval.quality = reversed( rval.get_decimal_quality_scores() ) rval.quality = "%s " % " ".join( map( str, rval.quality ) ) return rval + def apply_galaxy_conventions( self ): + pass class fastqSangerRead( fastqSequencingRead ): format = 'sanger' @@ -206,7 +208,7 @@ if self.has_adapter_base(): qual_len = len( self.get_ascii_quality_scores() ) seq_len = len( self.sequence ) - assert qual_len + 1 == seq_len, "Invalid FASTQ file: quality score length (%i) does not match sequence length (%i with adapter base)" % ( qual_len, seq_len ) + assert ( qual_len + 1 == seq_len ) or ( qual_len == seq_len ), "Invalid FASTQ file: quality score length (%i) does not match sequence length (%i with adapter base)" % ( qual_len, seq_len ) #SRA adds FAKE/DUMMY quality scores to the adapter base, we'll allow the reading of the Improper score here, but remove it in the Reader when "apply_galaxy_conventions" is set to True else: return fastqSequencingRead.assert_sequence_quality_lengths( self ) def get_sequence( self ): @@ -262,7 +264,12 @@ elif new_adapter: rval.sequence = "%s%s" % ( new_adapter, rval.sequence ) return rval - + def apply_galaxy_conventions( self ): + if self.has_adapter_base() and len( self.sequence ) == len( self.get_ascii_quality_scores() ): #SRA adds FAKE/DUMMY quality scores to the adapter base, we remove them here + if self.is_ascii_encoded(): + self.quality = self.quality[1:] + else: + self.quality = " ".join( map( str, self.get_decimal_quality_scores()[1:] ) ) FASTQ_FORMATS = {} for format in [ fastqIlluminaRead, fastqSolexaRead, fastqSangerRead, fastqCSSangerRead ]: @@ -417,9 +424,10 @@ return column_stats class fastqReader( object ): - def __init__( self, fh, format = 'sanger' ): + def __init__( self, fh, format = 'sanger', apply_galaxy_conventions = False ): self.file = fh self.format = format + self.apply_galaxy_conventions = apply_galaxy_conventions def close( self ): return self.file.close() def next(self): @@ -450,6 +458,8 @@ break rval.append_quality( line ) rval.assert_sequence_quality_lengths() + if self.apply_galaxy_conventions: + rval.apply_galaxy_conventions() return rval def __iter__( self ): while True: @@ -494,13 +504,14 @@ raise e class fastqNamedReader( object ): - def __init__( self, fh, format = 'sanger' ): + def __init__( self, fh, format = 'sanger', apply_galaxy_conventions = False ): self.file = fh self.format = format self.reader = fastqReader( self.file, self.format ) #self.last_offset = self.file.tell() self.offset_dict = {} self.eof = False + self.apply_galaxy_conventions = apply_galaxy_conventions def close( self ): return self.file.close() def get( self, sequence_id ): @@ -531,6 +542,8 @@ if fastq_read.identifier not in self.offset_dict: self.offset_dict[ fastq_read.identifier ] = [] self.offset_dict[ fastq_read.identifier ].append( offset ) + if rval is not None and self.apply_galaxy_conventions: + rval.apply_galaxy_conventions() return rval def has_data( self ): #returns a string representation of remaining data, or empty string (False) if no data remaining --- a/tools/fastq/fastq_groomer.py Mon Aug 22 14:58:51 2011 -0400 +++ b/tools/fastq/fastq_groomer.py Mon Aug 22 16:07:23 2011 -0400 @@ -19,7 +19,7 @@ reader = fastqVerboseErrorReader else: reader = fastqReader - for read_count, fastq_read in enumerate( reader( open( input_filename ), format = input_type ) ): + for read_count, fastq_read in enumerate( reader( open( input_filename ), format = input_type, apply_galaxy_conventions = True ) ): if summarize_input: aggregator.consume_read( fastq_read ) out.write( fastq_read ) --- a/tools/fastq/fastq_groomer.xml Mon Aug 22 14:58:51 2011 -0400 +++ b/tools/fastq/fastq_groomer.xml Mon Aug 22 16:07:23 2011 -0400 @@ -1,4 +1,4 @@ -<tool id="fastq_groomer" name="FASTQ Groomer" version="1.0.3"> +<tool id="fastq_groomer" name="FASTQ Groomer" version="1.0.4"><description>convert between various FASTQ quality formats</description><command interpreter="python">fastq_groomer.py '$input_file' '$input_type' '$output_file' #if str( $options_type['options_type_selector'] ) == 'basic': @@ -240,6 +240,15 @@ <param name="summarize_input" value="summarize_input" /><output name="output_file" file="sanger_full_range_as_solexa.fastqsolexa" /></test> + <test> + <param name="input_file" value="sanger_full_range_as_cssanger_adapter_base_with_quality_score.fastqcssanger_fake_score" ftype="fastq" /> + <param name="input_type" value="cssanger" /> + <param name="options_type_selector" value="advanced" /> + <param name="output_type" value="cssanger" /> + <param name="force_quality_encoding" value="None" /> + <param name="summarize_input" value="summarize_input" /> + <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" /> + </test><test><param name="input_file" value="wrapping_original_sanger.fastqsanger" ftype="fastq" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dan: Add FIMO to tool_conf.xml.sample.
by Bitbucket 22 Aug '11

22 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/a82d009cb8ee/ changeset: a82d009cb8ee user: dan date: 2011-08-22 20:58:51 summary: Add FIMO to tool_conf.xml.sample. affected #: 1 file (33 bytes) --- a/tool_conf.xml.sample Mon Aug 22 14:52:11 2011 -0400 +++ b/tool_conf.xml.sample Mon Aug 22 14:58:51 2011 -0400 @@ -208,6 +208,7 @@ </section><section name="Motif Tools" id="motifs"><tool file="meme/meme.xml"/> + <tool file="meme/fimo.xml"/><tool file="rgenetics/rgWebLogo3.xml" /></section><section name="Multiple Alignments" id="clustal"> 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: Add FIMO tool from MEME suite.
by Bitbucket 22 Aug '11

22 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/00c1fa7a0c28/ changeset: 00c1fa7a0c28 user: dan date: 2011-08-22 20:52:11 summary: Add FIMO tool from MEME suite. affected #: 12 files (710 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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commit/galaxy-central: natefoo: Fix FTP upload when uploading only a single file and its name contains a comma. util.listify assumes that a string with commas should be split into a list, so don't use listify for this value. Thanks Ilya Chorny.
by Bitbucket 22 Aug '11

22 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/94688ff06248/ changeset: 94688ff06248 user: natefoo date: 2011-08-22 20:47:10 summary: Fix FTP upload when uploading only a single file and its name contains a comma. util.listify assumes that a string with commas should be split into a list, so don't use listify for this value. Thanks Ilya Chorny. affected #: 1 file (84 bytes) --- a/lib/galaxy/tools/parameters/basic.py Mon Aug 22 14:03:57 2011 -0400 +++ b/lib/galaxy/tools/parameters/basic.py Mon Aug 22 14:47:10 2011 -0400 @@ -454,7 +454,11 @@ user_ftp_dir = os.path.join( trans.app.config.ftp_upload_dir, trans.user.email ) return form_builder.FTPFileField( self.name, user_ftp_dir, trans.app.config.ftp_upload_site, value = value ) def from_html( self, value, trans=None, other_values={} ): - return util.listify( value ) + try: + assert type( value ) is list + except: + value = [ value ] + return value def to_string( self, value, app ): if value in [ None, '' ]: return None 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: pdate EuPathDB datasource configuration file. Contributed by Mark Heiges.
by Bitbucket 22 Aug '11

22 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/9de21817a7a5/ changeset: 9de21817a7a5 user: dan date: 2011-08-22 20:03:57 summary: pdate EuPathDB datasource configuration file. Contributed by Mark Heiges. affected #: 1 file (4 bytes) --- a/tools/data_source/eupathdb.xml Mon Aug 22 10:45:22 2011 -0400 +++ b/tools/data_source/eupathdb.xml Mon Aug 22 14:03:57 2011 -0400 @@ -7,7 +7,7 @@ </inputs><uihints minwidth="800"/><outputs> - <data name="output" format="txt" /> + <data name="output" format="tabular" /></outputs><options sanitize="False" refresh="True"/></tool> 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: Add helper.py (posted to the -dev list as "galaxythinger.py" in the past), a command line tool for performing a couple common operations like encoding/decoding IDs and getting the disk path of HDAs.
by Bitbucket 22 Aug '11

22 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/0f878ea61e98/ changeset: 0f878ea61e98 user: natefoo date: 2011-08-22 16:45:22 summary: Add helper.py (posted to the -dev list as "galaxythinger.py" in the past), a command line tool for performing a couple common operations like encoding/decoding IDs and getting the disk path of HDAs. 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: kanwei: Spacing fix
by Bitbucket 20 Aug '11

20 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/fa7159dcb42e/ changeset: fa7159dcb42e user: kanwei date: 2011-08-20 08:56:33 summary: Spacing fix affected #: 2 files (0 bytes) --- a/lib/galaxy/web/form_builder.py Sat Aug 20 14:27:30 2011 +1000 +++ b/lib/galaxy/web/form_builder.py Sat Aug 20 02:56:33 2011 -0400 @@ -191,9 +191,9 @@ def get_html( self, prefix="" ): rval = FTPFileField.thead if self.dir is None: - rval += '<tr><td colspan="3"><em>Please <a href="%s">create</a> or <a href="%s">log in to</a> a Galaxy account to view files uploaded via FTP.</em></td></tr>' % ( url_for( controller='user', action='create', cntrller='user', referer=url_for( controller='root' ) ), url_for( controller='user', action='login', cntrller='user', referer=url_for( controller='root' ) ) ) + rval += '<tr><td colspan="4"><em>Please <a href="%s">create</a> or <a href="%s">log in to</a> a Galaxy account to view files uploaded via FTP.</em></td></tr>' % ( url_for( controller='user', action='create', cntrller='user', referer=url_for( controller='root' ) ), url_for( controller='user', action='login', cntrller='user', referer=url_for( controller='root' ) ) ) elif not os.path.exists( self.dir ): - rval += '<tr><td colspan="3"><em>Your FTP upload directory contains no files.</em></td></tr>' + rval += '<tr><td colspan="4"><em>Your FTP upload directory contains no files.</em></td></tr>' else: uploads = [] for ( dirpath, dirnames, filenames ) in os.walk( self.dir ): @@ -204,7 +204,7 @@ size=nice_size( statinfo.st_size ), ctime=time.strftime( "%m/%d/%Y %I:%M:%S %p", time.localtime( statinfo.st_ctime ) ) ) ) if not uploads: - rval += '<tr><td colspan="3"><em>Your FTP upload directory contains no files.</em></td></tr>' + rval += '<tr><td colspan="4"><em>Your FTP upload directory contains no files.</em></td></tr>' for upload in uploads: rval += FTPFileField.trow % ( prefix, self.name, upload['path'], upload['path'], upload['size'], upload['ctime'] ) rval += FTPFileField.tfoot --- a/tools/data_source/upload.xml Sat Aug 20 14:27:30 2011 +1000 +++ b/tools/data_source/upload.xml Sat Aug 20 02:56:33 2011 -0400 @@ -177,7 +177,7 @@ **MAF** -TBA and multiz multiple alignment format. The first line of a .maf file begins with ##maf. This word is followed by white-space-separated "variable=value pairs". There should be no white space surrounding the "=". +TBA and multiz multiple alignment format. The first line of a .maf file begins with ##maf. This word is followed by white-space-separated "variable=value" pairs. There should be no white space surrounding the "=". ----- 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: WebLogo3 wrapper repair to a string format edge case. Reports are good for finding these - user hadn't reported...
by Bitbucket 20 Aug '11

20 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/a9b3f9b82e84/ changeset: a9b3f9b82e84 user: fubar date: 2011-08-20 06:27:30 summary: WebLogo3 wrapper repair to a string format edge case. Reports are good for finding these - user hadn't reported... affected #: 1 file (7 bytes) --- a/tools/rgenetics/rgWebLogo3.py Fri Aug 19 14:37:51 2011 -0400 +++ b/tools/rgenetics/rgWebLogo3.py Sat Aug 20 14:27:30 2011 +1000 @@ -43,11 +43,6 @@ tlf = open(templog,'w') process = subprocess.Popen(cl, shell=True, stderr=tlf, stdout=tlf) rval = process.wait() - if rval <> 0: - print >> sys.stderr, '## rgWebLogo3.py error - executing %s returned error code %d' % cl - print >> sys.stderr, '## This may be a data problem or a tool dependency (%s) installation problem' % WEBLOGO - print >> sys.stderr, '## Please ensure %s is correctly installed and working on the command line -see http://code.google.com/p/weblogo' % WEBLOGO - sys.exit(1) tlf.close() tlogs = ''.join(open(templog,'r').readlines()) if len(tlogs) > 1: @@ -55,6 +50,11 @@ else: s = '## executing %s returned status %d. Nothing appeared on stderr/stdout\n' % (cl,rval) os.unlink(templog) # always + if rval <> 0: + print >> sys.stderr, '## rgWebLogo3.py error - executing %s returned error code %d' % (cl,rval) + print >> sys.stderr, '## This may be a data problem or a tool dependency (%s) installation problem' % WEBLOGO + print >> sys.stderr, '## Please ensure %s is correctly installed and working on the command line -see http://code.google.com/p/weblogo' % WEBLOGO + sys.exit(1) return s 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: 3 new changesets
by Bitbucket 19 Aug '11

19 Aug '11

3 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/c5fa48633c0b/ changeset: c5fa48633c0b branch: job_scripts user: peterjc date: 2011-07-29 15:18:15 summary: Catch problems creating job script affected #: 1 file (248 bytes) --- a/lib/galaxy/jobs/runners/drmaa.py Thu Jul 28 11:50:56 2011 -0400 +++ b/lib/galaxy/jobs/runners/drmaa.py Fri Jul 29 14:18:15 2011 +0100 @@ -156,10 +156,15 @@ jt.nativeSpecification = native_spec script = drm_template % (job_wrapper.galaxy_lib_dir, os.path.abspath( job_wrapper.working_directory ), command_line) - fh = file( jt.remoteCommand, "w" ) - fh.write( script ) - fh.close() - os.chmod( jt.remoteCommand, 0750 ) + try: + fh = file( jt.remoteCommand, "w" ) + fh.write( script ) + fh.close() + os.chmod( jt.remoteCommand, 0750 ) + except: + job_wrapper.fail( "failure preparing job script", exception=True ) + log.exception("failure running job %s" % job_wrapper.get_id_tag()) + return # job was deleted while we were preparing it if job_wrapper.get_state() == model.Job.states.DELETED: http://bitbucket.org/galaxy/galaxy-central/changeset/769e04ccce29/ changeset: 769e04ccce29 branch: job_scripts user: natefoo date: 2011-08-19 19:30:21 summary: Closed branch job_scripts affected #: 0 files (0 bytes) http://bitbucket.org/galaxy/galaxy-central/changeset/8d8d9e8ef1a0/ changeset: 8d8d9e8ef1a0 user: natefoo date: 2011-08-19 19:30:36 summary: merge affected #: 1 file (248 bytes) --- a/lib/galaxy/jobs/runners/drmaa.py Thu Aug 18 14:20:48 2011 -0400 +++ b/lib/galaxy/jobs/runners/drmaa.py Fri Aug 19 13:30:36 2011 -0400 @@ -156,10 +156,15 @@ jt.nativeSpecification = native_spec script = drm_template % (job_wrapper.galaxy_lib_dir, os.path.abspath( job_wrapper.working_directory ), command_line) - fh = file( jt.remoteCommand, "w" ) - fh.write( script ) - fh.close() - os.chmod( jt.remoteCommand, 0750 ) + try: + fh = file( jt.remoteCommand, "w" ) + fh.write( script ) + fh.close() + os.chmod( jt.remoteCommand, 0750 ) + except: + job_wrapper.fail( "failure preparing job script", exception=True ) + log.exception("failure running job %s" % job_wrapper.get_id_tag()) + return # job was deleted while we were preparing it if job_wrapper.get_state() == model.Job.states.DELETED: 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: jgoecks: Add wrapper for Trinity, the de novo RNA-seq transcript assembler (http://http://trinityrnaseq.sourceforge.net/).
by Bitbucket 18 Aug '11

18 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/c4a82d645370/ changeset: c4a82d645370 user: jgoecks date: 2011-08-18 20:20:48 summary: Add wrapper for Trinity, the de novo RNA-seq transcript assembler (http://http://trinityrnaseq.sourceforge.net/) affected #: 2 files (105 bytes) --- a/tool_conf.xml.sample Thu Aug 18 14:01:28 2011 -0400 +++ b/tool_conf.xml.sample Thu Aug 18 14:20:48 2011 -0400 @@ -335,6 +335,8 @@ <tool file="ngs_rna/cufflinks_wrapper.xml" /><tool file="ngs_rna/cuffcompare_wrapper.xml" /><tool file="ngs_rna/cuffdiff_wrapper.xml" /> + <label text="De novo Assembly" id="de_novo_assembly "/> + <tool file="ngs_rna/trinity_all.xml" /><label text="Filtering" id="filtering" /><tool file="ngs_rna/filter_transcripts_via_tracking.xml" /></section> 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: Quota display nice_size bugfixes.
by Bitbucket 18 Aug '11

18 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/59beb8e9290d/ changeset: 59beb8e9290d user: natefoo date: 2011-08-18 20:01:28 summary: Quota display nice_size bugfixes. affected #: 1 file (72 bytes) --- a/lib/galaxy/quota/__init__.py Thu Aug 18 13:51:02 2011 -0400 +++ b/lib/galaxy/quota/__init__.py Thu Aug 18 14:01:28 2011 -0400 @@ -60,11 +60,13 @@ use_default = True max = 0 adjustment = 0 + rval = 0 for quota in quotas: if quota.deleted: continue if quota.operation == '=' and quota.bytes == -1: - return None + rval = None + break elif quota.operation == '=': use_default = False if quota.bytes > max: @@ -76,16 +78,17 @@ if use_default: max = self.default_registered_quota if max is None: - return None - quota = max + adjustment - if quota <= 0: - quota = 0 + rval = None + if rval is not None: + rval = max + adjustment + if rval <= 0: + rval = 0 if nice_size: - if quota is not None: - quota = util.nice_size( quota ) + if rval is not None: + rval = util.nice_size( rval ) else: - quota = 'unlimited' - return quota + rval = 'unlimited' + return rval @property def default_unregistered_quota( self ): return self._default_quota( self.model.DefaultQuotaAssociation.types.UNREGISTERED ) 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: Enhancements and fixes for working with versions of repository tools in the tool shed.
by Bitbucket 18 Aug '11

18 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/4e3494acdb97/ changeset: 4e3494acdb97 user: greg date: 2011-08-18 19:51:02 summary: Enhancements and fixes for working with versions of repository tools in the tool shed. affected #: 13 files (6.6 KB) --- a/lib/galaxy/webapps/community/controllers/admin.py Thu Aug 18 13:13:35 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/admin.py Thu Aug 18 13:51:02 2011 -0400 @@ -347,7 +347,7 @@ title = "Repository Metadata" model_class = model.RepositoryMetadata template='/webapps/community/repository/grid.mako' - default_sort_key = "repository_id" + default_sort_key = "name" columns = [ IdColumn( "Id", visible=False, @@ -355,8 +355,8 @@ NameColumn( "Name", key="name", model_class=model.Repository, - link=( lambda item: dict( operation="view_or_manage_repository", - id=item.repository.id, + link=( lambda item: dict( operation="view_or_manage_repository_revision", + id=item.id, webapp="community" ) ), attach_popup=True ), RevisionColumn( "Revision", @@ -396,7 +396,15 @@ operation = kwd[ 'operation' ].lower() if operation == "delete": return self.delete_repository_metadata( trans, **kwd ) - if operation == "view_or_manage_repository": + if operation == "view_or_manage_repository_revision": + # The received id is a RepositoryMetadata object id, so we need to get the + # associated Repository and redirect to view_or_manage_repository with the + # changeset_revision. + repository_metadata = get_repository_metadata_by_id( trans, kwd[ 'id' ] ) + repository = repository_metadata.repository + kwd[ 'id' ] = trans.security.encode_id( repository.id ) + kwd[ 'changeset_revision' ] = repository_metadata.changeset_revision + kwd[ 'operation' ] = 'view_or_manage_repository' return trans.response.send_redirect( web.url_for( controller='repository', action='browse_repositories', **kwd ) ) --- a/lib/galaxy/webapps/community/controllers/common.py Thu Aug 18 13:13:35 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/common.py Thu Aug 18 13:51:02 2011 -0400 @@ -81,13 +81,24 @@ def get_repository_metadata_by_id( trans, id ): """Get repository metadata from the database""" return trans.sa_session.query( trans.model.RepositoryMetadata ).get( trans.security.decode_id( id ) ) +def get_revision_label( trans, repository, changeset_revision ): + """ + Return a string consisting of the human read-able + changeset rev and the changeset revision string. + """ + repo = hg.repository( get_configured_ui(), repository.repo_path ) + ctx = get_changectx_for_changeset( trans, repo, changeset_revision ) + if ctx: + return "%s:%s" % ( str( ctx.rev() ), changeset_revision ) + else: + return "-1:%s" % changeset_revision def get_latest_repository_metadata( trans, id ): """Get last metadata defined for a specified repository from the database""" return trans.sa_session.query( trans.model.RepositoryMetadata ) \ .filter( trans.model.RepositoryMetadata.table.c.repository_id == trans.security.decode_id( id ) ) \ .order_by( trans.model.RepositoryMetadata.table.c.update_time.desc() ) \ .first() -def generate_workflow_metadata( trans, id, change_set_revision, exported_workflow_dict, metadata_dict ): +def generate_workflow_metadata( trans, id, changeset_revision, exported_workflow_dict, metadata_dict ): """ Update the received metadata_dict with changes that have been applied to the received exported_workflow_dict. Store everything except the @@ -120,7 +131,7 @@ # The received metadata_dict includes no metadata for workflows, so a new repository_metadata table # record is not needed. return False -def generate_tool_metadata( trans, id, change_set_revision, root, name, tool, metadata_dict ): +def generate_tool_metadata( trans, id, changeset_revision, root, name, tool, metadata_dict ): """ Update the received metadata_dict with changes that have been applied to the received tool. @@ -163,15 +174,25 @@ if repository_metadata: metadata = repository_metadata.metadata if metadata and 'tools' in metadata: + saved_tool_ids = [] # The metadata for one or more tools was successfully generated in the past - # for this repository, so we compare the version string for each tool id + # for this repository, so we first compare the version string for each tool id # in metadata_dict with what was previously saved to see if we need to create # a new table record or if we can simply update the existing record. for new_tool_metadata_dict in metadata_dict[ 'tools' ]: for saved_tool_metadata_dict in metadata[ 'tools' ]: + if saved_tool_metadata_dict[ 'id' ] not in saved_tool_ids: + saved_tool_ids.append( saved_tool_metadata_dict[ 'id' ] ) if new_tool_metadata_dict[ 'id' ] == saved_tool_metadata_dict[ 'id' ]: if new_tool_metadata_dict[ 'version' ] != saved_tool_metadata_dict[ 'version' ]: return True + # So far, a new metadata record is not required, but we still have to check to see if + # any new tool ids exist in metadata_dict that are not in the saved metadata. We do + # this because if a new tarball was uploaded to a repository that included tools, it + # may have removed existing tool files if they were not included in the uploaded tarball. + for new_tool_metadata_dict in metadata_dict[ 'tools' ]: + if new_tool_metadata_dict[ 'id' ] not in saved_tool_ids: + return True else: # We have repository metadata that does not include metadata for any tools in the # repository, so we can update the existing repository metadata. @@ -183,7 +204,7 @@ # The received metadata_dict includes no metadata for tools, so a new repository_metadata table # record is not needed. return False -def set_repository_metadata( trans, id, change_set_revision, **kwd ): +def set_repository_metadata( trans, id, changeset_revision, **kwd ): """Set repository metadata""" message = '' status = 'done' @@ -191,7 +212,7 @@ repo_dir = repository.repo_path repo = hg.repository( get_configured_ui(), repo_dir ) invalid_files = [] - ctx = get_changectx_for_changeset( trans, repo, change_set_revision ) + ctx = get_changectx_for_changeset( trans, repo, changeset_revision ) if ctx is not None: metadata_dict = {} for root, dirs, files in os.walk( repo_dir ): @@ -211,7 +232,7 @@ tool = load_tool( trans, full_path ) if tool is not None: # Update the list metadata dictionaries for tools in metadata_dict. - metadata_dict = generate_tool_metadata( trans, id, change_set_revision, root, name, tool, metadata_dict ) + metadata_dict = generate_tool_metadata( trans, id, changeset_revision, root, name, tool, metadata_dict ) except Exception, e: invalid_files.append( ( name, str( e ) ) ) # Find all exported workflows @@ -224,27 +245,28 @@ fp.close() exported_workflow_dict = from_json_string( workflow_text ) # Update the list of metadata dictionaries for workflows in metadata_dict. - metadata_dict = generate_workflow_metadata( trans, id, change_set_revision, exported_workflow_dict, metadata_dict ) + metadata_dict = generate_workflow_metadata( trans, id, changeset_revision, exported_workflow_dict, metadata_dict ) except Exception, e: invalid_files.append( ( name, str( e ) ) ) if metadata_dict: if new_tool_metadata_required( trans, id, metadata_dict ) or new_workflow_metadata_required( trans, id, metadata_dict ): # Create a new repository_metadata table row. - repository_metadata = trans.model.RepositoryMetadata( repository.id, change_set_revision, metadata_dict ) + repository_metadata = trans.model.RepositoryMetadata( repository.id, changeset_revision, metadata_dict ) trans.sa_session.add( repository_metadata ) trans.sa_session.flush() else: - # Update the last saved repository_metadata table row. - repository_metadata = get_latest_repository_metadata( trans, id ) - repository_metadata.metadata = metadata_dict - trans.sa_session.add( repository_metadata ) - trans.sa_session.flush() + # Update the last saved repository_metadata table row. + repository_metadata = get_latest_repository_metadata( trans, id ) + repository_metadata.changeset_revision = changeset_revision + repository_metadata.metadata = metadata_dict + trans.sa_session.add( repository_metadata ) + trans.sa_session.flush() else: # change_set is None - message = "Repository does not include changeset revision '%s'." % str( change_set_revision ) + message = "Repository does not include changeset revision '%s'." % str( changeset_revision ) status = 'error' if invalid_files: - message = "Metadata cannot be defined for change set revision '%s'. Correct the following problems and reset metadata.<br/>" % str( change_set_revision ) + message = "Metadata cannot be defined for change set revision '%s'. Correct the following problems and reset metadata.<br/>" % str( changeset_revision ) for itc_tup in invalid_files: tool_file = itc_tup[0] exception_msg = itc_tup[1] @@ -284,16 +306,16 @@ def get_repository_by_name( trans, name ): """Get a repository from the database via name""" return trans.sa_session.query( app.model.Repository ).filter_by( name=name ).one() -def get_changectx_for_changeset( trans, repo, change_set_revision, **kwd ): +def get_changectx_for_changeset( trans, repo, changeset_revision, **kwd ): """Retrieve a specified changectx from a repository""" for changeset in repo.changelog: ctx = repo.changectx( changeset ) - if str( ctx ) == change_set_revision: + if str( ctx ) == changeset_revision: return ctx return None -def change_set_is_malicious( trans, id, change_set_revision, **kwd ): +def change_set_is_malicious( trans, id, changeset_revision, **kwd ): """Check the malicious flag in repository metadata for a specified change set""" - repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, change_set_revision ) + repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) if repository_metadata: return repository_metadata.malicious return False @@ -440,8 +462,7 @@ refresh_on_change_values = [] for repository_metadata in repository.downloadable_revisions: changeset_revision = repository_metadata.changeset_revision - ctx = get_changectx_for_changeset( trans, repo, changeset_revision ) - revision_label = "%s:%s" % ( str( ctx.rev() ), changeset_revision ) + revision_label = get_revision_label( trans, repository, changeset_revision ) options.append( ( revision_label, changeset_revision ) ) refresh_on_change_values.append( changeset_revision ) if add_id_to_name: --- a/lib/galaxy/webapps/community/controllers/repository.py Thu Aug 18 13:13:35 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/repository.py Thu Aug 18 13:51:02 2011 -0400 @@ -83,7 +83,9 @@ strings of all downloadable_revisions of this repository. """ select_field = build_changeset_revision_select_field( trans, repository ) - return select_field.get_html() + if len( select_field.options ) > 1: + return select_field.get_html() + return repository.revision class DescriptionColumn( grids.TextColumn ): def get_value( self, trans, grid, repository ): return repository.description @@ -220,7 +222,7 @@ if 'operation' in kwd: operation = kwd['operation'].lower() if operation == "view_or_manage_repository": - repository_id = kwd.get( 'id', None ) + repository_id = kwd[ 'id' ] repository = get_repository( trans, repository_id ) is_admin = trans.user_is_admin() if is_admin or repository.user == trans.user: @@ -582,8 +584,7 @@ repository, selected_value=changeset_revision, add_id_to_name=False ) - ctx = get_changectx_for_changeset( trans, repo, changeset_revision ) - revision_label = "%s:%s" % ( str( ctx.rev() ), changeset_revision ) + revision_label = get_revision_label( trans, repository, changeset_revision ) repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) if repository_metadata: metadata = repository_metadata.metadata @@ -721,8 +722,7 @@ repository, selected_value=changeset_revision, add_id_to_name=False ) - ctx = get_changectx_for_changeset( trans, repo, changeset_revision ) - revision_label = "%s:%s" % ( str( ctx.rev() ), changeset_revision ) + revision_label = get_revision_label( trans, repository, changeset_revision ) repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) if repository_metadata: metadata = repository_metadata.metadata @@ -989,8 +989,6 @@ # Reload the tool_data_table_conf entries trans.app.tool_data_tables = galaxy.tools.data.ToolDataTableManager( trans.app.config.tool_data_table_config_path ) message = "The new entry has been added to the tool_data_table_conf.xml file, so click the <b>Reset metadata</b> button below." - # TODO: what if ~/tool-data/<loc_filename> doesn't exist? We need to figure out how to - # force the user to upload it's sample to the repository in order to generate metadata. return trans.response.send_redirect( web.url_for( controller='repository', action='manage_repository', id=repository_id, @@ -1025,29 +1023,56 @@ break return column_fields @web.expose - def display_tool( self, trans, repository_id, tool_config, **kwd ): + def display_tool( self, trans, repository_id, tool_config, changeset_revision, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) repository = get_repository( trans, repository_id ) + old_version_msg = "Your selected version of this tool does not exist in the repository tip, so it " + \ + "cannot be previewed, but you can inspect the tool version's metadata using it's pop-up menu and " + \ + "you can download your selected version of this tool from the <b>Repository Actions</b> menu." try: tool = load_tool( trans, os.path.abspath( tool_config ) ) - tool_state = self.__new_state( trans ) - is_malicious = change_set_is_malicious( trans, repository_id, repository.tip ) - return trans.fill_template( "/webapps/community/repository/tool_form.mako", - repository=repository, - tool=tool, - tool_state=tool_state, - is_malicious=is_malicious, - message=message, - status=status ) + can_preview = True + if changeset_revision != repository.tip: + # See if we are attempting to preview an old version of a tool. + # TODO: Previewing an old version of a tool is not currently supported because + # the received tool_config is a file on the file system. We need to implement + # an enhancement here to look at the repository manifest files if previewing an + # old version of a tool. + repo_changeset_repository_metadata = get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) + repo_changeset_metadata = repo_changeset_repository_metadata.metadata + if 'tools' in repo_changeset_metadata: + for tool_metadata_dict in repo_changeset_metadata[ 'tools' ]: + if tool_metadata_dict[ 'id' ] == tool.id: + if tool_metadata_dict[ 'version' ] != tool.version: + can_preview = False + message = old_version_msg + if can_preview: + tool_state = self.__new_state( trans ) + is_malicious = change_set_is_malicious( trans, repository_id, repository.tip ) + return trans.fill_template( "/webapps/community/repository/tool_form.mako", + repository=repository, + tool=tool, + tool_state=tool_state, + is_malicious=is_malicious, + message=message, + status=status ) except Exception, e: - message = 'Error loading tool: %s. Click <b>Reset metadata</b> to correct this error.' % str( e ) - return trans.response.send_redirect( web.url_for( controller='repository', - action='manage_repository', - id=repository_id, - message=message, - status='error' ) ) + # TODO: enhance this to check the repository manifest for the files and + # display the tool using them. + exception_str = str( e ) + if exception_str.find( 'No such file or directory' ) >= 0: + message = old_version_msg + else: + message = "Error loading tool: %s. Click <b>Reset metadata</b> to correct this error." % exception_str + return trans.response.send_redirect( web.url_for( controller='repository', + action='browse_repositories', + operation='view_or_manage_repository', + id=repository_id, + changeset_revision=changeset_revision, + message=message, + status='error' ) ) def __new_state( self, trans, all_pages=False ): """ Create a new `DefaultToolState` for this tool. It will not be initialized @@ -1067,18 +1092,25 @@ repository = get_repository( trans, repository_id ) metadata = {} tool = None + revision_label = get_revision_label( trans, repository, changeset_revision ) repository_metadata = get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ).metadata if 'tools' in repository_metadata: for tool_metadata_dict in repository_metadata[ 'tools' ]: if tool_metadata_dict[ 'id' ] == tool_id: metadata = tool_metadata_dict - tool = load_tool( trans, os.path.abspath( metadata[ 'tool_config' ] ) ) + try: + # We may be attempting to load a tool that no longer exists in the repository tip. + tool = load_tool( trans, os.path.abspath( metadata[ 'tool_config' ] ) ) + except: + tool = None break is_malicious = change_set_is_malicious( trans, repository_id, repository.tip ) return trans.fill_template( "/webapps/community/repository/view_tool_metadata.mako", repository=repository, tool=tool, metadata=metadata, + changeset_revision=changeset_revision, + revision_label=revision_label, is_malicious=is_malicious, message=message, status=status ) @@ -1147,6 +1179,7 @@ action='browse_repositories', operation="view_or_manage_repository", id=trans.security.encode_id( repository.id ), + changeset_revision=repository.tip, status=status, message=message ) ) return output.split() --- a/templates/webapps/community/repository/add_tool_data_table_entry.mako Thu Aug 18 13:13:35 2011 -0400 +++ b/templates/webapps/community/repository/add_tool_data_table_entry.mako Thu Aug 18 13:51:02 2011 -0400 @@ -46,9 +46,9 @@ <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> %endif %if can_download: - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='zip' )}">Download as a zip file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='gz' )}">Download as a .tar.gz file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='bz2' )}">Download as a .tar.bz2 file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='zip' )}">Download as a zip file</a> %endif </div> %endif --- a/templates/webapps/community/repository/browse_repository.mako Thu Aug 18 13:13:35 2011 -0400 +++ b/templates/webapps/community/repository/browse_repository.mako Thu Aug 18 13:51:02 2011 -0400 @@ -68,9 +68,9 @@ <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> %if can_manage: - <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ) )}">Manage repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ) )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View repository</a> %endif %if can_upload: <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> @@ -82,9 +82,9 @@ <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a> %endif %if can_download: - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='zip' )}">Download as a zip file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='gz' )}">Download as a .tar.gz file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='bz2' )}">Download as a .tar.bz2 file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='zip' )}">Download as a zip file</a> %endif </div> %endif --- a/templates/webapps/community/repository/manage_repository.mako Thu Aug 18 13:13:35 2011 -0400 +++ b/templates/webapps/community/repository/manage_repository.mako Thu Aug 18 13:51:02 2011 -0400 @@ -97,26 +97,28 @@ ${render_msg( message, status )} %endif -<div class="toolForm"> - <div class="toolFormTitle">Revision</div> - <div class="toolFormBody"> - <form name="change_revision" id="change_revision" action="${h.url_for( controller='repository', action='manage_repository', id=trans.security.encode_id( repository.id ) )}" method="post" > - <div class="form-row"> - <% - if changeset_revision == repository.tip: - tip_str = 'repository tip' - else: - tip_str = '' - %> - ${changeset_revision_select_field.get_html()} <i>${tip_str}</i> - <div class="toolParamHelp" style="clear: both;"> - Select a revision to preview download-able versions of tools from this repository. +%if len( changeset_revision_select_field.options ) > 1: + <div class="toolForm"> + <div class="toolFormTitle">Repository revision</div> + <div class="toolFormBody"> + <form name="change_revision" id="change_revision" action="${h.url_for( controller='repository', action='manage_repository', id=trans.security.encode_id( repository.id ) )}" method="post" > + <div class="form-row"> + <% + if changeset_revision == repository.tip: + tip_str = 'repository tip' + else: + tip_str = '' + %> + ${changeset_revision_select_field.get_html()} <i>${tip_str}</i> + <div class="toolParamHelp" style="clear: both;"> + Select a revision to inspect and download versions of tools from this repository. + </div></div> - </div> - </form> + </form> + </div></div> -</div> -<p/> + <p/> +%endif <div class="toolForm"><div class="toolFormTitle">${repository.name}</div><div class="toolFormBody"> @@ -181,7 +183,7 @@ %if can_set_metadata: <p/><div class="toolForm"> - <div class="toolFormTitle">Preview tools and inspect metadata</div> + <div class="toolFormTitle">Preview tools in repository tip and inspect metadata by tool version</div><div class="toolFormBody"> %if metadata: %if 'tools' in metadata: @@ -205,12 +207,12 @@ <tr><td><div style="float: left; margin-left: 1px;" class="menubutton split popup" id="tool-${tool_dict[ 'id' ].replace( ' ', '_' )}-popup"> - <a class="view-info" href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=tool_dict[ 'tool_config' ] )}"> + <a class="view-info" href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=tool_dict[ 'tool_config' ], changeset_revision=changeset_revision )}"> ${tool_dict[ 'name' ]} </a></div><div popupmenu="tool-${tool_dict[ 'id' ].replace( ' ', '_' )}-popup"> - <a class="action-button" href="${h.url_for( controller='repository', action='view_tool_metadata', repository_id=trans.security.encode_id( repository.id ), changeset_revision=changeset_revision, tool_id=tool_dict[ 'id' ] )}">View all metadata for this tool</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_tool_metadata', repository_id=trans.security.encode_id( repository.id ), changeset_revision=changeset_revision, tool_id=tool_dict[ 'id' ] )}">View tool metadata</a></div></td><td>${tool_dict[ 'description' ]}</td> @@ -269,16 +271,20 @@ <div style="clear: both"></div> %endif %endif - <form name="set_metadata" action="${h.url_for( controller='repository', action='set_metadata', id=trans.security.encode_id( repository.id ), ctx_str=changeset_revision )}" method="post"> - <div class="form-row"> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="submit" name="set_metadata_button" value="Reset metadata"/> + %if repository.tip == changeset_revision: + ## TODO: when we support previewing older versions of tools, we + ## should allow resetting metadata on the older versions as well. + <form name="set_metadata" action="${h.url_for( controller='repository', action='set_metadata', id=trans.security.encode_id( repository.id ), ctx_str=changeset_revision )}" method="post"> + <div class="form-row"> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input type="submit" name="set_metadata_button" value="Reset metadata"/> + </div> + <div class="toolParamHelp" style="clear: both;"> + Inspect the repository and reset the above attributes for the repository tip. + </div></div> - <div class="toolParamHelp" style="clear: both;"> - Inspect the repository and reset the above attributes for the repository tip. - </div> - </div> - </form> + </form> + %endif </div></div> %endif --- a/templates/webapps/community/repository/rate_repository.mako Thu Aug 18 13:13:35 2011 -0400 +++ b/templates/webapps/community/repository/rate_repository.mako Thu Aug 18 13:51:02 2011 -0400 @@ -75,9 +75,9 @@ <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> %if can_manage: - <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ) )}">Manage repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ) )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View repository</a> %endif %if can_upload: <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> @@ -89,9 +89,9 @@ <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> %endif %if can_download: - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='zip' )}">Download as a zip file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='gz' )}">Download as a .tar.gz file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='bz2' )}">Download as a .tar.bz2 file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='zip' )}">Download as a zip file</a> %endif </div> %endif --- a/templates/webapps/community/repository/tool_form.mako Thu Aug 18 13:13:35 2011 -0400 +++ b/templates/webapps/community/repository/tool_form.mako Thu Aug 18 13:51:02 2011 -0400 @@ -115,9 +115,9 @@ <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> %if can_manage: - <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ) )}">Manage repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ) )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View repository</a> %endif %if can_upload: <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> @@ -132,9 +132,9 @@ <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a> %endif %if can_download: - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='zip' )}">Download as a zip file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='gz' )}">Download as a .tar.gz file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='bz2' )}">Download as a .tar.bz2 file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='zip' )}">Download as a zip file</a> %endif </div> %endif @@ -145,7 +145,7 @@ %endif <div class="toolForm" id="${tool.id}"> - <div class="toolFormTitle">${tool.name}</div> + <div class="toolFormTitle">${tool.name} ${tool.version}</div><div class="toolFormBody"><form id="tool_form" name="tool_form" action="" method="get"><input type="hidden" name="tool_state" value="${util.object_to_string( tool_state.encode( tool, app ) )}"> --- a/templates/webapps/community/repository/upload.mako Thu Aug 18 13:13:35 2011 -0400 +++ b/templates/webapps/community/repository/upload.mako Thu Aug 18 13:51:02 2011 -0400 @@ -48,9 +48,9 @@ <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> %if can_manage: - <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ) )}">Manage repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ) )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View repository</a> %endif %if can_view_change_log: <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> --- a/templates/webapps/community/repository/view_changelog.mako Thu Aug 18 13:13:35 2011 -0400 +++ b/templates/webapps/community/repository/view_changelog.mako Thu Aug 18 13:51:02 2011 -0400 @@ -46,9 +46,9 @@ <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> %endif %if can_manage: - <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ) )}">Manage repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ) )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View repository</a> %endif %if can_rate: <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a> @@ -57,9 +57,9 @@ <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> %endif %if can_download: - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='zip' )}">Download as a zip file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='gz' )}">Download as a .tar.gz file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='bz2' )}">Download as a .tar.bz2 file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='zip' )}">Download as a zip file</a> %endif </div></ul> --- a/templates/webapps/community/repository/view_changeset.mako Thu Aug 18 13:13:35 2011 -0400 +++ b/templates/webapps/community/repository/view_changeset.mako Thu Aug 18 13:51:02 2011 -0400 @@ -47,9 +47,9 @@ <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> %endif %if can_manage: - <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ) )}">Manage repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ) )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View repository</a> %endif %if can_view_change_log: <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> @@ -61,9 +61,9 @@ <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> %endif %if can_download: - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='zip' )}">Download as a zip file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='gz' )}">Download as a .tar.gz file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='bz2' )}">Download as a .tar.bz2 file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='zip' )}">Download as a zip file</a> %endif </div></ul> --- a/templates/webapps/community/repository/view_repository.mako Thu Aug 18 13:13:35 2011 -0400 +++ b/templates/webapps/community/repository/view_repository.mako Thu Aug 18 13:51:02 2011 -0400 @@ -94,26 +94,28 @@ ${render_msg( message, status )} %endif -<div class="toolForm"> - <div class="toolFormTitle">Revision</div> - <div class="toolFormBody"> - <form name="change_revision" id="change_revision" action="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ) )}" method="post" > - <div class="form-row"> - <% - if changeset_revision == repository.tip: - tip_str = 'repository tip' - else: - tip_str = '' - %> - ${changeset_revision_select_field.get_html()} <i>${tip_str}</i> - <div class="toolParamHelp" style="clear: both;"> - Select a revision to preview download-able versions of tools from this repository. +%if len( changeset_revision_select_field.options ) > 1: + <div class="toolForm"> + <div class="toolFormTitle">Repository revision</div> + <div class="toolFormBody"> + <form name="change_revision" id="change_revision" action="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ) )}" method="post" > + <div class="form-row"> + <% + if changeset_revision == repository.tip: + tip_str = 'repository tip' + else: + tip_str = '' + %> + ${changeset_revision_select_field.get_html()} <i>${tip_str}</i> + <div class="toolParamHelp" style="clear: both;"> + Select a revision to inspect and download versions of tools from this repository. + </div></div> - </div> - </form> + </form> + </div></div> -</div> -<p/> + <p/> +%endif <div class="toolForm"><div class="toolFormTitle">${repository.name}</div><div class="toolFormBody"> @@ -173,7 +175,7 @@ %if metadata: <p/><div class="toolForm"> - <div class="toolFormTitle">Preview tools and inspect metadata</div> + <div class="toolFormTitle">Preview tools in repository tip and inspect metadata by tool version</div><div class="toolFormBody"> %if 'tools' in metadata: <div class="form-row"> @@ -196,12 +198,12 @@ <tr><td><div style="float: left; margin-left: 1px;" class="menubutton split popup" id="tool-${tool_dict[ 'id' ].replace( ' ', '_' )}-popup"> - <a class="view-info" href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=tool_dict[ 'tool_config' ] )}"> + <a class="view-info" href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=tool_dict[ 'tool_config' ], changeset_revision=changeset_revision )}"> ${tool_dict[ 'name' ]} </a></div><div popupmenu="tool-${tool_dict[ 'id' ].replace( ' ', '_' )}-popup"> - <a class="action-button" href="${h.url_for( controller='repository', action='view_tool_metadata', repository_id=trans.security.encode_id( repository.id ), changeset_revision=changeset_revision, tool_id=tool_dict[ 'id' ] )}">View all metadata for this tool</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_tool_metadata', repository_id=trans.security.encode_id( repository.id ), changeset_revision=changeset_revision, tool_id=tool_dict[ 'id' ] )}">View tool metadata</a></div></td><td>${tool_dict[ 'description' ]}</td> --- a/templates/webapps/community/repository/view_tool_metadata.mako Thu Aug 18 13:13:35 2011 -0400 +++ b/templates/webapps/community/repository/view_tool_metadata.mako Thu Aug 18 13:51:02 2011 -0400 @@ -38,9 +38,9 @@ <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> %if can_manage: - <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ) )}">Manage repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ) )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">View repository</a> %endif %if can_upload: <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> @@ -52,9 +52,9 @@ <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> %endif %if can_download: - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='zip' )}">Download as a zip file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='gz' )}">Download as a .tar.gz file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='bz2' )}">Download as a .tar.bz2 file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='zip' )}">Download as a zip file</a> %endif </div> %endif @@ -64,6 +64,20 @@ ${render_msg( message, status )} %endif +<div class="toolForm"> + <div class="toolFormTitle">Repository revision</div> + <div class="toolFormBody"> + <div class="form-row"> + <label>Revision:</label> + %if can_view_change_log: + <a href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">${revision_label}</a> + %else: + ${revision_label} + %endif + </div> + </div> +</div> +<p/> %if can_download: <div class="toolForm"><div class="toolFormTitle">${repository.name}</div> @@ -85,7 +99,7 @@ <div class="toolFormBody"><div class="form-row"><label>Name:</label> - <a href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=metadata[ 'tool_config' ] )}">${metadata[ 'name' ]}</a> + <a href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=metadata[ 'tool_config' ], changeset_revision=changeset_revision )}">${metadata[ 'name' ]}</a><div style="clear: both"></div></div> %if 'description' in metadata: @@ -116,31 +130,33 @@ <div style="clear: both"></div></div> %endif - <div class="form-row"> - <label>Command:</label> - <pre>${tool.command}</pre> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <label>Interpreter:</label> - ${tool.interpreter} - <div style="clear: both"></div> - </div> - <div class="form-row"> - <label>Is multi-byte:</label> - ${tool.is_multi_byte} - <div style="clear: both"></div> - </div> - <div class="form-row"> - <label>Forces a history refresh:</label> - ${tool.force_history_refresh} - <div style="clear: both"></div> - </div> - <div class="form-row"> - <label>Parallelism:</label> - ${tool.parallelism} - <div style="clear: both"></div> - </div> + %if tool: + <div class="form-row"> + <label>Command:</label> + <pre>${tool.command}</pre> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Interpreter:</label> + ${tool.interpreter} + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Is multi-byte:</label> + ${tool.is_multi_byte} + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Forces a history refresh:</label> + ${tool.force_history_refresh} + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Parallelism:</label> + ${tool.parallelism} + <div style="clear: both"></div> + </div> + %endif <% if 'requirements' in metadata: requirements = metadata[ 'requirements' ] Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: natefoo: Don't count library datasets against the creating user upon dataset creation.
by Bitbucket 18 Aug '11

18 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/5710c02b60ca/ changeset: 5710c02b60ca user: natefoo date: 2011-08-18 19:13:35 summary: Don't count library datasets against the creating user upon dataset creation. affected #: 1 file (30 bytes) --- a/lib/galaxy/jobs/__init__.py Thu Aug 18 13:08:39 2011 -0400 +++ b/lib/galaxy/jobs/__init__.py Thu Aug 18 13:13:35 2011 -0400 @@ -681,7 +681,7 @@ bytes = 0 # Once datasets are collected, set the total dataset size (includes extra files) - for dataset_assoc in job.output_datasets + job.output_library_datasets: + for dataset_assoc in job.output_datasets: dataset_assoc.dataset.dataset.set_total_size() bytes += dataset_assoc.dataset.dataset.get_total_size() 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: Decrease disk usage and actually remove datasets (if applicable) when purging a history.
by Bitbucket 18 Aug '11

18 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/3c87cb241165/ changeset: 3c87cb241165 user: natefoo date: 2011-08-18 19:08:39 summary: Decrease disk usage and actually remove datasets (if applicable) when purging a history. affected #: 1 file (167 bytes) --- a/lib/galaxy/web/controllers/history.py Thu Aug 18 11:08:47 2011 -0400 +++ b/lib/galaxy/web/controllers/history.py Thu Aug 18 13:08:39 2011 -0400 @@ -271,9 +271,12 @@ n_deleted += 1 if purge and trans.app.config.allow_user_dataset_purge: for hda in history.datasets: + if trans.user: + trans.user.total_disk_usage -= hda.quota_amount( trans.user ) hda.purged = True trans.sa_session.add( hda ) trans.log_event( "HDA id %s has been purged" % hda.id ) + trans.sa_session.flush() if hda.dataset.user_can_purge: try: hda.dataset.full_delete() @@ -1207,4 +1210,4 @@ def get_item( self, trans, id ): return self.get_history( trans, id ) - \ No newline at end of file + 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: Monkeypatch BigInt(eger) into SQLAlchemy 0.5 and make the bytes column in the quota table a bigint.
by Bitbucket 18 Aug '11

18 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/d6fa346d5460/ changeset: d6fa346d5460 user: natefoo date: 2011-08-18 17:08:47 summary: Monkeypatch BigInt(eger) into SQLAlchemy 0.5 and make the bytes column in the quota table a bigint. affected #: 3 files (1.8 KB) --- a/lib/galaxy/model/custom_types.py Wed Aug 17 16:32:09 2011 -0400 +++ b/lib/galaxy/model/custom_types.py Thu Aug 18 11:08:47 2011 -0400 @@ -8,6 +8,11 @@ from galaxy.util.bunch import Bunch from galaxy.util.aliaspickler import AliasPickleModule +# For monkeypatching BIGINT +import sqlalchemy.databases.sqlite +import sqlalchemy.databases.postgres +import sqlalchemy.databases.mysql + import logging log = logging.getLogger( __name__ ) @@ -87,3 +92,53 @@ value = value[0:self.impl.length] return value + +class BigInteger( Integer ): + """ + A type for bigger ``int`` integers. + + Typically generates a ``BIGINT`` in DDL, and otherwise acts like + a normal :class:`Integer` on the Python side. + + """ + +class BIGINT( BigInteger ): + """The SQL BIGINT type.""" + +class DBBigInteger( BigInteger ): + def get_col_spec( self ): + return "BIGINT" + +sqlalchemy.databases.postgres.PGBigInteger = DBBigInteger +sqlalchemy.databases.postgres.colspecs[BigInteger] = DBBigInteger +sqlalchemy.databases.sqlite.SLBigInteger = DBBigInteger +sqlalchemy.databases.sqlite.colspecs[BigInteger] = DBBigInteger + +class MSBigInteger( BigInteger, sqlalchemy.databases.mysql.MSInteger ): + """MySQL BIGINTEGER type.""" + + def __init__(self, display_width=None, **kw): + """Construct a BIGINTEGER. + + :param display_width: Optional, maximum display width for this number. + + :param unsigned: a boolean, optional. + + :param zerofill: Optional. If true, values will be stored as strings + left-padded with zeros. Note that this does not effect the values + returned by the underlying database API, which continue to be + numeric. + + """ + self.display_width = display_width + sqlalchemy.databases.mysql._NumericType.__init__(self, kw) + BigInteger.__init__(self, **kw) + + def get_col_spec(self): + if self.display_width is not None: + return self._extend("BIGINT(%(display_width)s)" % {'display_width': self.display_width}) + else: + return self._extend("BIGINT") + +sqlalchemy.databases.mysql.MSBigInteger = MSBigInteger +sqlalchemy.databases.mysql.colspecs[BigInteger] = MSBigInteger --- a/lib/galaxy/model/mapping.py Wed Aug 17 16:32:09 2011 -0400 +++ b/lib/galaxy/model/mapping.py Thu Aug 18 11:08:47 2011 -0400 @@ -217,7 +217,7 @@ Column( "update_time", DateTime, default=now, onupdate=now ), Column( "name", String( 255 ), index=True, unique=True ), Column( "description", TEXT ), - Column( "bytes", Integer ), + Column( "bytes", BigInteger ), Column( "operation", String( 8 ) ), Column( "deleted", Boolean, index=True, default=False ) ) --- a/lib/galaxy/model/migrate/versions/0080_quota_tables.py Wed Aug 17 16:32:09 2011 -0400 +++ b/lib/galaxy/model/migrate/versions/0080_quota_tables.py Thu Aug 18 11:08:47 2011 -0400 @@ -7,6 +7,7 @@ from migrate import * from migrate.changeset import * from galaxy.model.orm.ext.assignmapper import * +from galaxy.model.custom_types import * import datetime now = datetime.datetime.utcnow @@ -25,7 +26,7 @@ Column( "update_time", DateTime, default=now, onupdate=now ), Column( "name", String( 255 ), index=True, unique=True ), Column( "description", TEXT ), - Column( "bytes", Integer ), + Column( "bytes", BigInteger ), Column( "operation", String( 8 ) ), Column( "deleted", Boolean, index=True, default=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: Backed out changeset 6ca0a743296b, Alchemy 0.5 has no BigInteger...
by Bitbucket 17 Aug '11

17 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/a6bfc06dbc20/ changeset: a6bfc06dbc20 user: natefoo date: 2011-08-17 22:32:09 summary: Backed out changeset 6ca0a743296b, Alchemy 0.5 has no BigInteger... affected #: 2 files (6 bytes) --- a/lib/galaxy/model/mapping.py Wed Aug 17 16:25:34 2011 -0400 +++ b/lib/galaxy/model/mapping.py Wed Aug 17 16:32:09 2011 -0400 @@ -217,7 +217,7 @@ Column( "update_time", DateTime, default=now, onupdate=now ), Column( "name", String( 255 ), index=True, unique=True ), Column( "description", TEXT ), - Column( "bytes", BigInteger ), + Column( "bytes", Integer ), Column( "operation", String( 8 ) ), Column( "deleted", Boolean, index=True, default=False ) ) --- a/lib/galaxy/model/migrate/versions/0080_quota_tables.py Wed Aug 17 16:25:34 2011 -0400 +++ b/lib/galaxy/model/migrate/versions/0080_quota_tables.py Wed Aug 17 16:32:09 2011 -0400 @@ -25,7 +25,7 @@ Column( "update_time", DateTime, default=now, onupdate=now ), Column( "name", String( 255 ), index=True, unique=True ), Column( "description", TEXT ), - Column( "bytes", BigInteger ), + Column( "bytes", Integer ), Column( "operation", String( 8 ) ), Column( "deleted", Boolean, index=True, default=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: Make the bytes column in the quota table a bigint
by Bitbucket 17 Aug '11

17 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/6ca0a743296b/ changeset: 6ca0a743296b user: natefoo date: 2011-08-17 22:25:34 summary: Make the bytes column in the quota table a bigint affected #: 2 files (6 bytes) --- a/lib/galaxy/model/mapping.py Wed Aug 17 11:15:05 2011 -0400 +++ b/lib/galaxy/model/mapping.py Wed Aug 17 16:25:34 2011 -0400 @@ -217,7 +217,7 @@ Column( "update_time", DateTime, default=now, onupdate=now ), Column( "name", String( 255 ), index=True, unique=True ), Column( "description", TEXT ), - Column( "bytes", Integer ), + Column( "bytes", BigInteger ), Column( "operation", String( 8 ) ), Column( "deleted", Boolean, index=True, default=False ) ) --- a/lib/galaxy/model/migrate/versions/0080_quota_tables.py Wed Aug 17 11:15:05 2011 -0400 +++ b/lib/galaxy/model/migrate/versions/0080_quota_tables.py Wed Aug 17 16:25:34 2011 -0400 @@ -25,7 +25,7 @@ Column( "update_time", DateTime, default=now, onupdate=now ), Column( "name", String( 255 ), index=True, unique=True ), Column( "description", TEXT ), - Column( "bytes", Integer ), + Column( "bytes", BigInteger ), Column( "operation", String( 8 ) ), Column( "deleted", Boolean, index=True, default=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: greg: Add the ability for tool shed users to select repository revisions whose tools can all be successfully loaded into a Galaxy instance in order to view / preview / download various tool versions from a specified repository.
by Bitbucket 17 Aug '11

17 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/5ce088df9264/ changeset: 5ce088df9264 user: greg date: 2011-08-17 17:15:05 summary: Add the ability for tool shed users to select repository revisions whose tools can all be successfully loaded into a Galaxy instance in order to view / preview / download various tool versions from a specified repository. affected #: 6 files (9.5 KB) --- a/lib/galaxy/webapps/community/controllers/admin.py Wed Aug 17 08:59:56 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/admin.py Wed Aug 17 11:15:05 2011 -0400 @@ -3,9 +3,11 @@ from galaxy.model.orm import * from galaxy.web.framework.helpers import time_ago, iff, grids from galaxy.util import inflector -from common import get_category, get_repository, get_repository_metadata_by_id +from common import * from repository import RepositoryListGrid, CategoryListGrid +from mercurial import hg import logging + log = logging.getLogger( __name__ ) class UserListGrid( grids.Grid ): @@ -299,11 +301,11 @@ class AdminRepositoryListGrid( RepositoryListGrid ): operations = [ operation for operation in RepositoryListGrid.operations ] operations.append( grids.GridOperation( "Delete", - allow_multiple=True, + allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=False ) ) operations.append( grids.GridOperation( "Undelete", - allow_multiple=True, + allow_multiple=False, condition=( lambda item: item.deleted ), async_compatible=False ) ) standard_filters = [] @@ -312,12 +314,15 @@ class IdColumn( grids.IntegerColumn ): def get_value( self, trans, grid, repository_metadata ): return repository_metadata.id - class RepositoryIdColumn( grids.IntegerColumn ): + class NameColumn( grids.TextColumn ): def get_value( self, trans, grid, repository_metadata ): - return repository_metadata.repository_id - class ChangesetRevisionColumn( grids.TextColumn ): + return repository_metadata.repository.name + class RevisionColumn( grids.TextColumn ): def get_value( self, trans, grid, repository_metadata ): - return repository_metadata.changeset_revision + repository = repository_metadata.repository + repo = hg.repository( get_configured_ui(), repository.repo_path ) + ctx = get_changectx_for_changeset( trans, repo, repository_metadata.changeset_revision ) + return "%s:%s" % ( str( ctx.rev() ), repository_metadata.changeset_revision ) class MetadataColumn( grids.TextColumn ): def get_value( self, trans, grid, repository_metadata ): metadata_str = '' @@ -347,25 +352,33 @@ IdColumn( "Id", visible=False, attach_popup=False ), - RepositoryIdColumn( "Repository Id", - key="repository_id", - attach_popup=False ), - ChangesetRevisionColumn( "Revision", - attach_popup=False ), + NameColumn( "Name", + key="name", + model_class=model.Repository, + link=( lambda item: dict( operation="view_or_manage_repository", + id=item.repository.id, + webapp="community" ) ), + attach_popup=True ), + RevisionColumn( "Revision", + attach_popup=False ), MetadataColumn( "Metadata", attach_popup=False ), MaliciousColumn( "Malicious", attach_popup=False ) ] operations = [ grids.GridOperation( "Delete", - allow_multiple=True ) ] + allow_multiple=False, + allow_popup=True, + async_compatible=False, + confirm="Repository metadata records cannot be recovered after they are deleted. Click OK to delete the selected items." ) ] standard_filters = [] default_filter = {} num_rows_per_page = 50 preserve_state = False use_paging = True def build_initial_query( self, trans, **kwd ): - return trans.sa_session.query( self.model_class ) + return trans.sa_session.query( self.model_class ) \ + .join( model.Repository.table ) class AdminController( BaseController, Admin ): @@ -383,12 +396,15 @@ operation = kwd[ 'operation' ].lower() if operation == "delete": return self.delete_repository_metadata( trans, **kwd ) + if operation == "view_or_manage_repository": + return trans.response.send_redirect( web.url_for( controller='repository', + action='browse_repositories', + **kwd ) ) # Render the list view return self.repository_metadata_list_grid( trans, **kwd ) @web.expose @web.require_admin def delete_repository_metadata( self, trans, **kwd ): - # TODO: Add a javascript confirm before this method executes.... params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) @@ -460,6 +476,23 @@ return self.mark_repository_deleted( trans, **kwd ) elif operation == "undelete": return self.undelete_repository( trans, **kwd ) + # The changeset_revision_select_field in the RepositoryListGrid performs a refresh_on_change + # which sends in request parameters like changeset_revison_1, changeset_revision_2, etc. One + # of the many select fields on the grid performed the refresh_on_change, so we loop through + # all of the received values to see which value is not the repository tip. If we find it, we + # know the refresh_on_change occurred, and we have the necessary repository id and change set + # revision to pass on. + for k, v in kwd.items(): + changset_revision_str = 'changeset_revision_' + if k.startswith( changset_revision_str ): + repository_id = trans.security.encode_id( int( k.lstrip( changset_revision_str ) ) ) + repository = get_repository( trans, repository_id ) + if repository.tip != v: + return trans.response.send_redirect( web.url_for( controller='repository', + action='browse_repositories', + operation='view_or_manage_repository', + id=trans.security.encode_id( repository.id ), + changeset_revision=v ) ) # Render the list view return self.repository_list_grid( trans, **kwd ) @web.expose --- a/lib/galaxy/webapps/community/controllers/common.py Wed Aug 17 08:59:56 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/common.py Wed Aug 17 11:15:05 2011 -0400 @@ -190,9 +190,9 @@ repository = get_repository( trans, id ) repo_dir = repository.repo_path repo = hg.repository( get_configured_ui(), repo_dir ) - change_set = get_change_set( trans, repo, change_set_revision ) invalid_files = [] - if change_set is not None: + ctx = get_changectx_for_changeset( trans, repo, change_set_revision ) + if ctx is not None: metadata_dict = {} for root, dirs, files in os.walk( repo_dir ): if not root.find( '.hg' ) >= 0 and not root.find( 'hgrc' ) >= 0: @@ -284,8 +284,8 @@ def get_repository_by_name( trans, name ): """Get a repository from the database via name""" return trans.sa_session.query( app.model.Repository ).filter_by( name=name ).one() -def get_change_set( trans, repo, change_set_revision, **kwd ): - """Retrieve a specified change set from a repository""" +def get_changectx_for_changeset( trans, repo, change_set_revision, **kwd ): + """Retrieve a specified changectx from a repository""" for changeset in repo.changelog: ctx = repo.changectx( changeset ) if str( ctx ) == change_set_revision: @@ -430,3 +430,28 @@ ToolClass = Tool return ToolClass( config_file, root, trans.app ) return None +def build_changeset_revision_select_field( trans, repository, selected_value=None, add_id_to_name=True ): + """ + Build a SelectField whose options are the changeset_revision + strings of all downloadable_revisions of the received repository. + """ + repo = hg.repository( get_configured_ui(), repository.repo_path ) + options = [] + refresh_on_change_values = [] + for repository_metadata in repository.downloadable_revisions: + changeset_revision = repository_metadata.changeset_revision + ctx = get_changectx_for_changeset( trans, repo, changeset_revision ) + revision_label = "%s:%s" % ( str( ctx.rev() ), changeset_revision ) + options.append( ( revision_label, changeset_revision ) ) + refresh_on_change_values.append( changeset_revision ) + if add_id_to_name: + name = 'changeset_revision_%d' % repository.id + else: + name = 'changeset_revision' + select_field = SelectField( name=name, + refresh_on_change=True, + refresh_on_change_values=refresh_on_change_values ) + for option_tup in options: + selected = selected_value and option_tup[1] == selected_value + select_field.add_option( option_tup[0], option_tup[1], selected=selected ) + return select_field --- a/lib/galaxy/webapps/community/controllers/repository.py Wed Aug 17 08:59:56 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/repository.py Wed Aug 17 11:15:05 2011 -0400 @@ -74,9 +74,16 @@ class NameColumn( grids.TextColumn ): def get_value( self, trans, grid, repository ): return repository.name - class RevisionColumn( grids.TextColumn ): + class RevisionColumn( grids.GridColumn ): + def __init__( self, col_name ): + grids.GridColumn.__init__( self, col_name ) def get_value( self, trans, grid, repository ): - return repository.revision + """ + Display a SelectField whose options are the changeset_revision + strings of all downloadable_revisions of this repository. + """ + select_field = build_changeset_revision_select_field( trans, repository ) + return select_field.get_html() class DescriptionColumn( grids.TextColumn ): def get_value( self, trans, grid, repository ): return repository.description @@ -121,13 +128,14 @@ columns = [ NameColumn( "Name", key="name", - link=( lambda item: dict( operation="view_or_manage_repository", id=item.id, webapp="community" ) ), - attach_popup=False ), + link=( lambda item: dict( operation="view_or_manage_repository", + id=item.id, + webapp="community" ) ), + attach_popup=True ), DescriptionColumn( "Synopsis", key="description", attach_popup=False ), - RevisionColumn( "Revision", - attach_popup=False ), + RevisionColumn( "Revision" ), CategoryColumn( "Category", model_class=model.Category, key="Category.name", @@ -159,7 +167,7 @@ visible=False, filterable="standard" ) ) operations = [ grids.GridOperation( "Receive email alerts", - allow_multiple=True, + allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=False ) ] standard_filters = [] @@ -257,12 +265,32 @@ category = get_category( trans, category_id ) kwd[ 'f-Category.name' ] = category.name elif operation == "receive email alerts": - if kwd[ 'id' ]: + if trans.user: + if kwd[ 'id' ]: + return trans.response.send_redirect( web.url_for( controller='repository', + action='set_email_alerts', + **kwd ) ) + else: + kwd[ 'message' ] = 'You must be logged in to set email alerts.' + kwd[ 'status' ] = 'error' + del kwd[ 'operation' ] + # The changeset_revision_select_field in the RepositoryListGrid performs a refresh_on_change + # which sends in request parameters like changeset_revison_1, changeset_revision_2, etc. One + # of the many select fields on the grid performed the refresh_on_change, so we loop through + # all of the received values to see which value is not the repository tip. If we find it, we + # know the refresh_on_change occurred, and we have the necessary repository id and change set + # revision to pass on. + for k, v in kwd.items(): + changset_revision_str = 'changeset_revision_' + if k.startswith( changset_revision_str ): + repository_id = trans.security.encode_id( int( k.lstrip( changset_revision_str ) ) ) + repository = get_repository( trans, repository_id ) + if repository.tip != v: return trans.response.send_redirect( web.url_for( controller='repository', - action='set_email_alerts', - **kwd ) ) - else: - del kwd[ 'operation' ] + action='browse_repositories', + operation='view_or_manage_repository', + id=trans.security.encode_id( repository.id ), + changeset_revision=v ) ) # Render the list view return self.repository_list_grid( trans, **kwd ) @web.expose @@ -524,6 +552,7 @@ repository = get_repository( trans, id ) repo = hg.repository( get_configured_ui(), repository.repo_path ) avg_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, repository, webapp_model=trans.model ) + changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip ) ) display_reviews = util.string_as_bool( params.get( 'display_reviews', False ) ) alerts = params.get( 'alerts', '' ) alerts_checked = CheckboxField.is_checked( alerts ) @@ -549,7 +578,13 @@ trans.sa_session.flush() checked = alerts_checked or ( user and user.email in email_alerts ) alerts_check_box = CheckboxField( 'alerts', checked=checked ) - repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, repository.tip ) + changeset_revision_select_field = build_changeset_revision_select_field( trans, + repository, + selected_value=changeset_revision, + add_id_to_name=False ) + ctx = get_changectx_for_changeset( trans, repo, changeset_revision ) + revision_label = "%s:%s" % ( str( ctx.rev() ), changeset_revision ) + repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) if repository_metadata: metadata = repository_metadata.metadata else: @@ -569,6 +604,9 @@ display_reviews=display_reviews, num_ratings=num_ratings, alerts_check_box=alerts_check_box, + changeset_revision=changeset_revision, + changeset_revision_select_field=changeset_revision_select_field, + revision_label=revision_label, is_malicious=is_malicious, message=message, status=status ) @@ -582,6 +620,7 @@ repo_dir = repository.repo_path repo = hg.repository( get_configured_ui(), repo_dir ) repo_name = util.restore_text( params.get( 'repo_name', repository.name ) ) + changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip ) ) description = util.restore_text( params.get( 'description', repository.description ) ) long_description = util.restore_text( params.get( 'long_description', repository.long_description ) ) avg_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, repository, webapp_model=trans.model ) @@ -678,7 +717,13 @@ allow_push_select_field = self.__build_allow_push_select_field( trans, current_allow_push_list ) checked = alerts_checked or user.email in email_alerts alerts_check_box = CheckboxField( 'alerts', checked=checked ) - repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, repository.tip ) + changeset_revision_select_field = build_changeset_revision_select_field( trans, + repository, + selected_value=changeset_revision, + add_id_to_name=False ) + ctx = get_changectx_for_changeset( trans, repo, changeset_revision ) + revision_label = "%s:%s" % ( str( ctx.rev() ), changeset_revision ) + repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) if repository_metadata: metadata = repository_metadata.metadata is_malicious = repository_metadata.malicious @@ -702,6 +747,9 @@ allow_push_select_field=allow_push_select_field, repo=repo, repository=repository, + changeset_revision=changeset_revision, + changeset_revision_select_field=changeset_revision_select_field, + revision_label=revision_label, selected_categories=selected_categories, categories=categories, metadata=metadata, @@ -750,7 +798,7 @@ status = params.get( 'status', 'done' ) repository = get_repository( trans, id ) repo = hg.repository( get_configured_ui(), repository.repo_path ) - ctx = get_change_set( trans, repo, ctx_str ) + ctx = get_changectx_for_changeset( trans, repo, ctx_str ) if ctx is None: message = "Repository does not include changeset revision '%s'." % str( ctx_str ) status = 'error' @@ -878,6 +926,7 @@ return trans.response.send_redirect( web.url_for( controller='repository', action='manage_repository', id=id, + changeset_revision=ctx_str, malicious=malicious, message=message, status=status ) ) @@ -1034,7 +1083,7 @@ message=message, status=status ) @web.expose - def download( self, trans, repository_id, file_type, **kwd ): + def download( self, trans, repository_id, changeset_revision, file_type, **kwd ): # Download an archive of the repository files compressed as zip, gz or bz2. params = util.Params( kwd ) repository = get_repository( trans, repository_id ) @@ -1043,11 +1092,11 @@ # [web] # allow_archive = bz2, gz, zip if file_type == 'zip': - file_type_str = 'tip.zip' + file_type_str = '%s.zip' % changeset_revision elif file_type == 'bz2': - file_type_str = 'tip.tar.bz2' + file_type_str = '%s.tar.bz2' % changeset_revision elif file_type == 'gz': - file_type_str = 'tip.tar.gz' + file_type_str = '%s.tar.gz' % changeset_revision repository.times_downloaded += 1 trans.sa_session.add( repository ) trans.sa_session.flush() @@ -1081,7 +1130,6 @@ def print_ticks( d ): pass cmd = "ls -p '%s'" % folder_path - # Handle the authentication message if keys are not set - the message is output = pexpect.run( cmd, events={ pexpect.TIMEOUT : print_ticks }, timeout=10 ) --- a/lib/galaxy/webapps/community/model/mapping.py Wed Aug 17 08:59:56 2011 -0400 +++ b/lib/galaxy/webapps/community/model/mapping.py Wed Aug 17 11:15:05 2011 -0400 @@ -193,7 +193,8 @@ properties = dict( categories=relation( RepositoryCategoryAssociation ), ratings=relation( RepositoryRatingAssociation, order_by=desc( RepositoryRatingAssociation.table.c.update_time ), backref="repositories" ), - user=relation( User.mapper ) ) ) + user=relation( User.mapper ), + downloadable_revisions=relation( RepositoryMetadata, order_by=desc( RepositoryMetadata.table.c.update_time ) ) ) ) assign_mapper( context, RepositoryMetadata, RepositoryMetadata.table, properties=dict( repository=relation( Repository ) ) ) --- a/templates/webapps/community/repository/manage_repository.mako Wed Aug 17 08:59:56 2011 -0400 +++ b/templates/webapps/community/repository/manage_repository.mako Wed Aug 17 11:15:05 2011 -0400 @@ -85,9 +85,9 @@ <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> %endif %if can_download: - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='zip' )}">Download as a zip file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='gz' )}">Download as a .tar.gz file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='bz2' )}">Download as a .tar.bz2 file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='zip' )}">Download as a zip file</a> %endif </div> %endif @@ -98,6 +98,26 @@ %endif <div class="toolForm"> + <div class="toolFormTitle">Revision</div> + <div class="toolFormBody"> + <form name="change_revision" id="change_revision" action="${h.url_for( controller='repository', action='manage_repository', id=trans.security.encode_id( repository.id ) )}" method="post" > + <div class="form-row"> + <% + if changeset_revision == repository.tip: + tip_str = 'repository tip' + else: + tip_str = '' + %> + ${changeset_revision_select_field.get_html()} <i>${tip_str}</i> + <div class="toolParamHelp" style="clear: both;"> + Select a revision to preview download-able versions of tools from this repository. + </div> + </div> + </form> + </div> +</div> +<p/> +<div class="toolForm"><div class="toolFormTitle">${repository.name}</div><div class="toolFormBody"><form name="edit_repository" id="edit_repository" action="${h.url_for( controller='repository', action='manage_repository', id=trans.security.encode_id( repository.id ) )}" method="post" > @@ -129,9 +149,9 @@ <div class="form-row"><label>Revision:</label> %if can_view_change_log: - <a href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">${repository.revision}</a> + <a href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">${revision_label}</a> %else: - ${repository.revision} + ${revision_label} %endif </div><div class="form-row"> @@ -190,7 +210,7 @@ </a></div><div popupmenu="tool-${tool_dict[ 'id' ].replace( ' ', '_' )}-popup"> - <a class="action-button" href="${h.url_for( controller='repository', action='view_tool_metadata', repository_id=trans.security.encode_id( repository.id ), changeset_revision=repository.tip, tool_id=tool_dict[ 'id' ] )}">View all metadata for this tool</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_tool_metadata', repository_id=trans.security.encode_id( repository.id ), changeset_revision=changeset_revision, tool_id=tool_dict[ 'id' ] )}">View all metadata for this tool</a></div></td><td>${tool_dict[ 'description' ]}</td> @@ -249,7 +269,7 @@ <div style="clear: both"></div> %endif %endif - <form name="set_metadata" action="${h.url_for( controller='repository', action='set_metadata', id=trans.security.encode_id( repository.id ), ctx_str=repository.tip )}" method="post"> + <form name="set_metadata" action="${h.url_for( controller='repository', action='set_metadata', id=trans.security.encode_id( repository.id ), ctx_str=changeset_revision )}" method="post"><div class="form-row"><div style="float: left; width: 250px; margin-right: 10px;"><input type="submit" name="set_metadata_button" value="Reset metadata"/> @@ -406,7 +426,7 @@ <div class="toolForm"><div class="toolFormTitle">Malicious repository tip</div><div class="toolFormBody"> - <form name="malicious" id="malicious" action="${h.url_for( controller='repository', action='set_metadata', id=trans.security.encode_id( repository.id ), ctx_str=repository.tip )}" method="post"> + <form name="malicious" id="malicious" action="${h.url_for( controller='repository', action='set_metadata', id=trans.security.encode_id( repository.id ), ctx_str=changeset_revision )}" method="post"><div class="form-row"><label>Define repository tip as malicious:</label> ${malicious_check_box.get_html()} --- a/templates/webapps/community/repository/view_repository.mako Wed Aug 17 08:59:56 2011 -0400 +++ b/templates/webapps/community/repository/view_repository.mako Wed Aug 17 11:15:05 2011 -0400 @@ -82,9 +82,9 @@ <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> %endif %if can_download: - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='zip' )}">Download as a zip file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='gz' )}">Download as a .tar.gz file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='bz2' )}">Download as a .tar.bz2 file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='zip' )}">Download as a zip file</a> %endif </div> %endif @@ -95,6 +95,26 @@ %endif <div class="toolForm"> + <div class="toolFormTitle">Revision</div> + <div class="toolFormBody"> + <form name="change_revision" id="change_revision" action="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ) )}" method="post" > + <div class="form-row"> + <% + if changeset_revision == repository.tip: + tip_str = 'repository tip' + else: + tip_str = '' + %> + ${changeset_revision_select_field.get_html()} <i>${tip_str}</i> + <div class="toolParamHelp" style="clear: both;"> + Select a revision to preview download-able versions of tools from this repository. + </div> + </div> + </form> + </div> +</div> +<p/> +<div class="toolForm"><div class="toolFormTitle">${repository.name}</div><div class="toolFormBody"> %if can_download: @@ -125,9 +145,9 @@ <div class="form-row"><label>Revision:</label> %if can_view_change_log: - <a href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">${repository.revision}</a> + <a href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">${revision_label}</a> %else: - ${repository.revision} + ${revision_label} %endif </div><div class="form-row"> @@ -181,7 +201,7 @@ </a></div><div popupmenu="tool-${tool_dict[ 'id' ].replace( ' ', '_' )}-popup"> - <a class="action-button" href="${h.url_for( controller='repository', action='view_tool_metadata', repository_id=trans.security.encode_id( repository.id ), changeset_revision=repository.tip, tool_id=tool_dict[ 'id' ] )}">View all metadata for this tool</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_tool_metadata', repository_id=trans.security.encode_id( repository.id ), changeset_revision=changeset_revision, tool_id=tool_dict[ 'id' ] )}">View all metadata for this tool</a></div></td><td>${tool_dict[ 'description' ]}</td> 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: Added missing wiki link referred to for eample config settings per Dave & Jen.
by Bitbucket 17 Aug '11

17 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/0ea888b70d11/ changeset: 0ea888b70d11 user: greg date: 2011-08-17 14:59:56 summary: Added missing wiki link referred to for eample config settings per Dave & Jen. affected #: 1 file (43 bytes) --- a/universe_wsgi.ini.sample Tue Aug 16 13:03:10 2011 -0400 +++ b/universe_wsgi.ini.sample Wed Aug 17 08:59:56 2011 -0400 @@ -9,7 +9,9 @@ # Throughout this sample configuration file, except where stated otherwise, # uncommented values override the default if left unset, whereas commented # values are set to the default value. -# examples of many of these options are explained in more detail in the wiki: +# Examples of many of these options are explained in more detail in the wiki: +# +# http://wiki.g2.bx.psu.edu/Admin/Config # # Config hackers are encouraged to check there before asking for 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.

1 0

commit/galaxy-central: natefoo: A missing flush caused the test for whether a dataset could be removed from disk on user purge to always return False.
by Bitbucket 16 Aug '11

16 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/1b78e2c9aff5/ changeset: 1b78e2c9aff5 user: natefoo date: 2011-08-16 19:03:10 summary: A missing flush caused the test for whether a dataset could be removed from disk on user purge to always return False. affected #: 1 file (37 bytes) --- a/lib/galaxy/web/controllers/dataset.py Tue Aug 16 12:33:35 2011 -0400 +++ b/lib/galaxy/web/controllers/dataset.py Tue Aug 16 13:03:10 2011 -0400 @@ -950,6 +950,7 @@ hda.purged = True trans.sa_session.add( hda ) trans.log_event( "HDA id %s has been purged" % hda.id ) + trans.sa_session.flush() # Don't delete anything if there are active HDAs or any LDDAs, even if # the LDDAs are deleted. Let the cleanup scripts get it in the latter # case. 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.

1 0

commit/galaxy-central: dannon: Histories API (jdlogicman) and cleanup.
by Bitbucket 16 Aug '11

16 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/cd508c0ef8fa/ changeset: cd508c0ef8fa user: dannon date: 2011-08-16 18:33:35 summary: Histories API (jdlogicman) and cleanup. affected #: 6 files (2.1 KB) --- a/lib/galaxy/model/__init__.py Tue Aug 16 12:02:34 2011 -0400 +++ b/lib/galaxy/model/__init__.py Tue Aug 16 12:33:35 2011 -0400 @@ -58,7 +58,7 @@ # Relationships self.histories = [] self.credentials = [] - + def set_password_cleartext( self, cleartext ): """Set 'self.password' to the digest of 'cleartext'.""" self.password = new_secure_hash( text_type=cleartext ) @@ -93,7 +93,7 @@ dataset_ids.append( hda.dataset.id ) total += hda.dataset.get_total_size() return total - + class Job( object ): """ A job represents a request to run a tool given input datasets, tool @@ -126,7 +126,7 @@ self.job_runner_external_id = None self.post_job_actions = [] self.imported = False - + def add_parameter( self, name, value ): self.parameters.append( JobParameter( name, value ) ) def add_input_dataset( self, name, dataset ): @@ -230,12 +230,12 @@ def __init__( self, name, value ): self.name = name self.value = value - + class JobToInputDatasetAssociation( object ): def __init__( self, name, dataset ): self.name = name self.dataset = dataset - + class JobToOutputDatasetAssociation( object ): def __init__( self, name, dataset ): self.name = name @@ -257,7 +257,7 @@ self.output_name = output_name self.action_arguments = action_arguments self.workflow_step = workflow_step - + class PostJobActionAssociation( object ): def __init__(self, pja, job): self.job = job @@ -277,7 +277,7 @@ elif self.library_dataset_dataset_association: return self.library_dataset_dataset_association return None - + class JobExportHistoryArchive( object ): def __init__( self, job=None, history=None, dataset=None, compressed=False, \ history_attrs_filename=None, datasets_attrs_filename=None, @@ -289,7 +289,7 @@ self.history_attrs_filename = history_attrs_filename self.datasets_attrs_filename = datasets_attrs_filename self.jobs_attrs_filename = jobs_attrs_filename - + class JobImportHistoryArchive( object ): def __init__( self, job=None, history=None, archive_dir=None ): self.job = job @@ -332,7 +332,7 @@ return True else: return False - + class Group( object ): def __init__( self, name = None ): self.name = name @@ -344,6 +344,8 @@ self.group = group class History( object, UsesAnnotations ): + api_collection_visible_keys = ( 'id', 'name' ) + api_element_visible_keys = ( 'id', 'name' ) def __init__( self, id=None, name=None, user=None ): self.id = id self.name = name or "Unnamed history" @@ -410,7 +412,7 @@ db_session = object_session( self ) db_session.add( new_history ) db_session.flush() - + # Copy annotation. self.copy_item_annotation( db_session, self.user, self, target_user, new_history ) @@ -424,7 +426,7 @@ new_hda = hda.copy( copy_children=True ) new_history.add_dataset( new_hda, set_hid = False, quota=quota ) db_session.add( new_hda ) - db_session.flush() + db_session.flush() # Copy annotation. self.copy_item_annotation( db_session, self.user, hda, target_user, new_hda ) new_history.hid_counter = self.hid_counter @@ -441,6 +443,23 @@ if isinstance(history_name, str): history_name = unicode(history_name, 'utf-8') return history_name + + def get_api_value( self, view='collection', value_mapper = None ): + if value_mapper is None: + value_mapper = {} + rval = {} + try: + visible_keys = self.__getattribute__( 'api_' + view + '_visible_keys' ) + except AttributeError: + raise Exception( 'Unknown API view: %s' % view ) + for key in visible_keys: + try: + rval[key] = self.__getattribute__( key ) + if key in value_mapper: + rval[key] = value_mapper.get( key )( rval[key] ) + except AttributeError: + rval[key] = None + return rval @property def get_disk_size_bytes( self ): return self.get_disk_size( nice_size=False ) @@ -633,7 +652,7 @@ file_name = property( get_file_name, set_file_name ) @property def extra_files_path( self ): - if self._extra_files_path: + if self._extra_files_path: path = self._extra_files_path else: path = os.path.join( self.file_path, "dataset_%d_files" % self.id ) @@ -734,7 +753,7 @@ """A base class for all 'dataset instances', HDAs, LDAs, etc""" states = Dataset.states permitted_actions = Dataset.permitted_actions - def __init__( self, id=None, hid=None, name=None, info=None, blurb=None, peek=None, extension=None, + def __init__( self, id=None, hid=None, name=None, info=None, blurb=None, peek=None, extension=None, dbkey=None, metadata=None, history=None, dataset=None, deleted=False, designation=None, parent_id=None, validation_errors=None, visible=True, create_dataset=False, sa_session=None ): self.name = name or "Unnamed dataset" @@ -800,9 +819,9 @@ return dbkey[0] def set_dbkey( self, value ): if "dbkey" in self.datatype.metadata_spec: - if not isinstance(value, list): + if not isinstance(value, list): self.metadata.dbkey = [value] - else: + else: self.metadata.dbkey = value dbkey = property( get_dbkey, set_dbkey ) def change_datatype( self, new_ext ): @@ -879,22 +898,18 @@ # See if we can convert the dataset if target_ext not in self.get_converter_types(): raise NoConverterException("Conversion from '%s' to '%s' not possible" % (self.extension, target_ext) ) - deps = {} # List of string of dependencies try: depends_list = trans.app.datatypes_registry.converter_deps[self.extension][target_ext] except KeyError: depends_list = [] - # See if converted dataset already exists converted_dataset = self.get_converted_files_by_type( target_ext ) if converted_dataset: return converted_dataset - # Conversion is possible but hasn't been done yet, run converter. # Check if we have dependencies - try: for dependency in depends_list: dep_dataset = self.get_converted_dataset(trans, dependency) @@ -905,14 +920,12 @@ raise ConverterDependencyException("A dependency (%s) was in an error state." % dependency) elif dep_dataset.state != trans.app.model.Job.states.OK: # Pending - return None - + return None deps[dependency] = dep_dataset except NoConverterException: raise NoConverterException("A dependency (%s) is missing a converter." % dependency) except KeyError: pass # No deps - assoc = ImplicitlyConvertedDatasetAssociation( parent=self, file_type=target_ext, metadata_safe=False ) new_dataset = self.datatype.convert_dataset( trans, self, target_ext, return_output=True, visible=False, deps=deps, set_output_history=False ).values()[0] new_dataset.name = self.name @@ -1115,6 +1128,28 @@ for child in self.children: rval += child.get_disk_usage( user ) return rval + def get_api_value( self, view='collection' ): + # Since this class is a proxy to rather complex attributes we want to + # display in other objects, we can't use the simpler method used by + # other model classes. + hda = self + rval = dict( name = hda.name, + deleted = hda.deleted, + visible = hda.visible, + state = hda.state, + file_size = int( hda.get_size() ), + data_type = hda.ext, + genome_build = hda.dbkey, + misc_info = hda.info, + misc_blurb = hda.blurb ) + for name, spec in hda.metadata.spec.items(): + val = hda.metadata.get( name ) + if isinstance( val, MetadataFile ): + val = val.file_name + elif isinstance( val, list ): + val = ', '.join( [str(v) for v in val] ) + rval['metadata_' + name] = val + return rval class HistoryDatasetAssociationDisplayAtAuthorization( object ): def __init__( self, hda=None, user=None, site=None ): @@ -1264,7 +1299,7 @@ name = unicode( name, 'utf-8' ) return name def get_api_value( self, view='collection' ): - rval = super( LibraryFolder, self ).get_api_value( vew=view ) + rval = super( LibraryFolder, self ).get_api_value( view=view ) info_association, inherited = self.get_info_association() if info_association: if inherited: @@ -1332,7 +1367,7 @@ for field in template.fields: tmp_dict[field['label']] = content[field['name']] template_data[template.name] = tmp_dict - + rval = dict( name = ldda.name, file_name = ldda.file_name, uploaded_by = ldda.user.email, @@ -1479,7 +1514,7 @@ return template_data def templates_json( self ): return simplejson.dumps( self.templates_dict() ) - + def get_display_name( self ): """ LibraryDatasetDatasetAssociation name can be either a string or a unicode object. @@ -1588,7 +1623,7 @@ def set_disk_usage( self, bytes ): self.disk_usage = bytes total_disk_usage = property( get_disk_usage, set_disk_usage ) - + class GalaxySessionToHistoryAssociation( object ): def __init__( self, galaxy_session, history ): self.galaxy_session = galaxy_session @@ -1599,7 +1634,7 @@ self.id = None self.instance_id = None self.state = None - + class UCI( object ): def __init__( self ): self.id = None @@ -1615,7 +1650,7 @@ self.state = None self.public_dns = None self.availability_zone = None - + class CloudStore( object ): def __init__( self ): self.id = None @@ -1623,14 +1658,14 @@ self.user = None self.size = None self.availability_zone = None - + class CloudSnapshot( object ): def __init__( self ): self.id = None self.user = None self.store_id = None self.snapshot_id = None - + class CloudProvider( object ): def __init__( self ): self.id = None @@ -1665,7 +1700,7 @@ self.has_cycles = None self.has_errors = None self.steps = [] - + class WorkflowStep( object ): def __init__( self ): self.id = None @@ -1676,7 +1711,7 @@ self.position = None self.input_connections = [] self.config = None - + class WorkflowStepConnection( object ): def __init__( self ): self.output_step_id = None @@ -1688,7 +1723,7 @@ def __init__( self, workflow_step, output_name): self.workflow_step = workflow_step self.output_name = output_name - + class StoredWorkflowUserShareAssociation( object ): def __init__( self ): self.stored_workflow = None @@ -1849,12 +1884,12 @@ class FormDefinitionCurrent( object ): def __init__(self, form_definition=None): self.latest_form = form_definition - + class FormValues( object ): def __init__(self, form_def=None, content=None): self.form_definition = form_def self.content = content - + class Request( object, APIItem ): states = Bunch( NEW = 'New', SUBMITTED = 'In Progress', @@ -1938,7 +1973,7 @@ for sample in self.samples: if sample.bar_code: samples.append( sample ) - return samples + return samples def send_email_notification( self, trans, common_state, final_state=False ): # Check if an email notification is configured to be sent when the samples # are in this state @@ -2001,13 +2036,13 @@ trans.sa_session.add( event ) trans.sa_session.flush() return comments - + class RequestEvent( object ): def __init__(self, request=None, request_state=None, comment=''): self.request = request self.state = request_state self.comment = comment - + class ExternalService( object ): data_transfer_protocol = Bunch( HTTP = 'http', HTTPS = 'https', @@ -2045,7 +2080,7 @@ self.data_transfer[ self.data_transfer_protocol.HTTP ] = http_configs def populate_actions( self, trans, item, param_dict=None ): return self.get_external_service_type( trans ).actions.populate( self, item, param_dict=param_dict ) - + class RequestType( object, APIItem ): api_collection_visible_keys = ( 'id', 'name', 'desc' ) api_element_visible_keys = ( 'id', 'name', 'desc', 'request_form_id', 'sample_form_id' ) @@ -2120,18 +2155,18 @@ return template.get_widgets( trans.user, contents=info.content ) return template.get_widgets( trans.user ) return [] - + class RequestTypeExternalServiceAssociation( object ): def __init__( self, request_type, external_service ): self.request_type = request_type self.external_service = external_service - + class RequestTypePermissions( object ): def __init__( self, action, request_type, role ): self.action = action self.request_type = request_type self.role = role - + class Sample( object, APIItem ): # The following form_builder classes are supported by the Sample class. supported_field_types = [ CheckboxField, SelectField, TextField, WorkflowField, WorkflowMappingField, HistoryField ] @@ -2212,14 +2247,14 @@ def print_ticks( d ): pass error_msg = 'Error encountered in determining the file size of %s on the external_service.' % filepath - if not scp_configs[ 'host' ] or not scp_configs[ 'user_name' ] or not scp_configs[ 'password' ]: + if not scp_configs['host'] or not scp_configs['user_name'] or not scp_configs['password']: return error_msg login_str = '%s@%s' % ( scp_configs['user_name'], scp_configs['host'] ) cmd = 'ssh %s "du -sh \'%s\'"' % ( login_str, filepath ) try: output = pexpect.run( cmd, - events={ '.ssword:*' : scp_configs['password'] + '\r\n', - pexpect.TIMEOUT : print_ticks }, + events={ '.ssword:*': scp_configs['password']+'\r\n', + pexpect.TIMEOUT:print_ticks}, timeout=10 ) except Exception, e: return error_msg @@ -2277,7 +2312,7 @@ self.sample = sample self.state = sample_state self.comment = comment - + class SampleDataset( object ): transfer_status = Bunch( NOT_STARTED = 'Not started', IN_QUEUE = 'In queue', @@ -2366,7 +2401,7 @@ self.user = None self.title = None self.content = None - + class PageUserShareAssociation( object ): def __init__( self ): self.page = None @@ -2383,7 +2418,7 @@ self.revisions = [] if self.latest_revision: self.revisions.append( latest_revision ) - + def copy( self, user=None, title=None ): """ Provide copy of visualization with only its latest revision. @@ -2394,12 +2429,12 @@ # user who owns the datasets may delete them, making them inaccessible # for the current user. # TODO: a deep copy option is needed. - + if not user: user = self.user if not title: title = self.title - + copy_viz = Visualization( user=user, type=self.type, title=title, dbkey=self.dbkey ) copy_revision = self.latest_revision.copy( visualization=copy_viz ) copy_viz.latest_revision = copy_revision @@ -2412,26 +2447,26 @@ self.title = title self.dbkey = dbkey self.config = config - + def copy( self, visualization=None ): """ Returns a copy of this object. """ if not visualization: visualization = self.visualization - + return VisualizationRevision( visualization=visualization, title=self.title, dbkey=self.dbkey, config=self.config ) - + class VisualizationUserShareAssociation( object ): def __init__( self ): self.visualization = None self.user = None - + class TransferJob( object ): # These states are used both by the transfer manager's IPC and the object # state in the database. Not all states are used by both. @@ -2457,10 +2492,10 @@ self.type = type self.parent_id = parent_id self.name = name - + def __str__ ( self ): return "Tag(id=%s, type=%i, parent_id=%s, name=%s)" % ( self.id, self.type, self.parent_id, self.name ) - + class ItemTagAssociation ( object ): def __init__( self, id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None ): self.id = id @@ -2470,13 +2505,13 @@ self.user_tname = user_tname self.value = None self.user_value = None - + class HistoryTagAssociation ( ItemTagAssociation ): pass - + class DatasetTagAssociation ( ItemTagAssociation ): pass - + class HistoryDatasetAssociationTagAssociation ( ItemTagAssociation ): pass @@ -2485,13 +2520,13 @@ class WorkflowStepTagAssociation ( ItemTagAssociation ): pass - + class StoredWorkflowTagAssociation ( ItemTagAssociation ): pass - + class VisualizationTagAssociation ( ItemTagAssociation ): pass - + class ToolTagAssociation( ItemTagAssociation ): def __init__( self, id=None, user=None, tool_id=None, tag_id=None, user_tname=None, value=None ): self.id = id @@ -2503,50 +2538,50 @@ self.user_value = None # Item annotation classes. - + class HistoryAnnotationAssociation( object ): pass - + class HistoryDatasetAssociationAnnotationAssociation( object ): pass - + class StoredWorkflowAnnotationAssociation( object ): pass - + class WorkflowStepAnnotationAssociation( object ): pass - + class PageAnnotationAssociation( object ): pass - + class VisualizationAnnotationAssociation( object ): pass - + # Item rating classes. - + class ItemRatingAssociation( object ): def __init__( self, id=None, user=None, item=None, rating=0 ): self.id = id self.user = user self.item = item self.rating = rating - + def set_item( self, item ): """ Set association's item. """ pass - + class HistoryRatingAssociation( ItemRatingAssociation ): def set_item( self, history ): self.history = history - + class HistoryDatasetAssociationRatingAssociation( ItemRatingAssociation ): def set_item( self, history_dataset_association ): self.history_dataset_association = history_dataset_association - + class StoredWorkflowRatingAssociation( ItemRatingAssociation ): def set_item( self, stored_workflow ): self.stored_workflow = stored_workflow - + class PageRatingAssociation( ItemRatingAssociation ): def set_item( self, page ): self.page = page @@ -2554,12 +2589,12 @@ class VisualizationRatingAssociation( ItemRatingAssociation ): def set_item( self, visualization ): self.visualization = visualization - + class UserPreference ( object ): def __init__( self, name=None, value=None ): self.name = name self.value = value - + class UserAction( object ): def __init__( self, id=None, create_time=None, user_id=None, session_id=None, action=None, params=None, context=None): self.id = id --- a/lib/galaxy/web/api/contents.py Tue Aug 16 12:02:34 2011 -0400 +++ b/lib/galaxy/web/api/contents.py Tue Aug 16 12:33:35 2011 -0400 @@ -11,7 +11,7 @@ log = logging.getLogger( __name__ ) class ContentsController( BaseController ): - + @web.expose_api def index( self, trans, library_id, **kwd ): """ @@ -55,14 +55,14 @@ rval.append( dict( id = encoded_id, type = 'folder', name = '/', - url = url_for( 'content', library_id=library_id, id=encoded_id ) ) ) + url = url_for( 'library_content', library_id=library_id, id=encoded_id ) ) ) library.root_folder.api_path = '' for content in traverse( library.root_folder ): encoded_id = trans.security.encode_id( '%s.%s' % ( content.api_type, content.id ) ) rval.append( dict( id = encoded_id, type = content.api_type, name = content.api_path, - url = url_for( 'content', library_id=library_id, id=encoded_id, ) ) ) + url = url_for( 'library_content', library_id=library_id, id=encoded_id, ) ) ) return rval @web.expose_api @@ -150,5 +150,5 @@ encoded_id = trans.security.encode_id( create_type + '.' + str( v.id ) ) rval.append( dict( id = encoded_id, name = v.name, - url = url_for( 'content', library_id=library_id, id=encoded_id ) ) ) + url = url_for( 'library_content', library_id=library_id, id=encoded_id ) ) ) return rval --- a/lib/galaxy/web/api/libraries.py Tue Aug 16 12:02:34 2011 -0400 +++ b/lib/galaxy/web/api/libraries.py Tue Aug 16 12:33:35 2011 -0400 @@ -58,7 +58,8 @@ trans.response.status = 400 return "Invalid library id ( %s ) specified." % str( library_id ) item = library.get_api_value( view='element' ) - item['contents_url'] = url_for( 'contents', library_id=library_id ) + #item['contents_url'] = url_for( 'contents', library_id=library_id ) + item['contents_url'] = url_for( 'library_contents', library_id=library_id ) return item @web.expose_api --- a/lib/galaxy/web/buildapp.py Tue Aug 16 12:02:34 2011 -0400 +++ b/lib/galaxy/web/buildapp.py Tue Aug 16 12:33:35 2011 -0400 @@ -106,10 +106,18 @@ # If enabled, add the web API if asbool( kwargs.get( 'enable_api', False ) ): add_api_controllers( webapp, app ) - webapp.api_mapper.resource( 'content', - 'contents', + webapp.api_mapper.resource( 'content', + 'contents', + controller='contents', + name_prefix='library_', path_prefix='/api/libraries/:library_id', parent_resources=dict( member_name='library', collection_name='libraries' ) ) + webapp.api_mapper.resource( 'content', + 'contents', + controller='history_contents', + name_prefix='history_', + path_prefix='/api/histories/:history_id', + parent_resources=dict( member_name='history', collection_name='histories' ) ) webapp.api_mapper.resource( 'library', 'libraries', path_prefix='/api' ) webapp.api_mapper.resource( 'sample', 'samples', path_prefix='/api' ) webapp.api_mapper.resource( 'request', 'requests', path_prefix='/api' ) @@ -118,7 +126,9 @@ webapp.api_mapper.resource( 'role', 'roles', path_prefix='/api' ) webapp.api_mapper.resource( 'user', 'users', path_prefix='/api' ) webapp.api_mapper.resource( 'workflow', 'workflows', path_prefix='/api' ) - + webapp.api_mapper.resource( 'history', 'histories', path_prefix='/api' ) + #webapp.api_mapper.connect( 'run_workflow', '/api/workflow/{workflow_id}/library/{library_id}', controller='workflows', action='run', workflow_id=None, library_id=None, conditions=dict(method=["GET"]) ) + webapp.finalize_config() # Wrap the webapp in some useful middleware if kwargs.get( 'middleware', True ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: natefoo: Make nice_size able to display terabytes, and set a default cutoff for users in the user disk usage reports.
by Bitbucket 16 Aug '11

16 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/1aaa9f0338fb/ changeset: 1aaa9f0338fb user: natefoo date: 2011-08-16 18:02:34 summary: Make nice_size able to display terabytes, and set a default cutoff for users in the user disk usage reports. affected #: 2 files (7 bytes) --- a/lib/galaxy/util/__init__.py Tue Aug 16 10:40:10 2011 -0400 +++ b/lib/galaxy/util/__init__.py Tue Aug 16 12:02:34 2011 -0400 @@ -528,7 +528,7 @@ >>> nice_size(100000000) '95.4 Mb' """ - words = [ 'bytes', 'Kb', 'Mb', 'Gb' ] + words = [ 'bytes', 'Kb', 'Mb', 'Gb', 'Tb' ] try: size = float( size ) except: --- a/lib/galaxy/webapps/reports/controllers/users.py Tue Aug 16 10:40:10 2011 -0400 +++ b/lib/galaxy/webapps/reports/controllers/users.py Tue Aug 16 12:02:34 2011 -0400 @@ -120,7 +120,7 @@ @web.expose def user_disk_usage( self, trans, **kwd ): message = util.restore_text( kwd.get( 'message', '' ) ) - user_cutoff = int( kwd.get( 'user_cutoff', 0 ) ) + user_cutoff = int( kwd.get( 'user_cutoff', 60 ) ) # disk_usage isn't indexed users = sorted( trans.sa_session.query( galaxy.model.User ).all(), key=operator.attrgetter( 'disk_usage' ), reverse=True ) if user_cutoff: 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: Reports: Add a per-user disk usage report.
by Bitbucket 16 Aug '11

16 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/0d6106a6941f/ changeset: 0d6106a6941f user: natefoo date: 2011-08-16 16:40:10 summary: Reports: Add a per-user disk usage report. affected #: 3 files (827 bytes) --- a/lib/galaxy/webapps/reports/controllers/users.py Mon Aug 15 16:12:12 2011 -0400 +++ b/lib/galaxy/webapps/reports/controllers/users.py Tue Aug 16 10:40:10 2011 -0400 @@ -116,3 +116,16 @@ users=users, not_logged_in_for_days=not_logged_in_for_days, message=message ) + + @web.expose + def user_disk_usage( self, trans, **kwd ): + message = util.restore_text( kwd.get( 'message', '' ) ) + user_cutoff = int( kwd.get( 'user_cutoff', 0 ) ) + # disk_usage isn't indexed + users = sorted( trans.sa_session.query( galaxy.model.User ).all(), key=operator.attrgetter( 'disk_usage' ), reverse=True ) + if user_cutoff: + users = users[:user_cutoff] + return trans.fill_template( '/webapps/reports/users_user_disk_usage.mako', + users=users, + user_cutoff=user_cutoff, + message=message ) --- a/templates/webapps/reports/index.mako Mon Aug 15 16:12:12 2011 -0400 +++ b/templates/webapps/reports/index.mako Tue Aug 16 10:40:10 2011 -0400 @@ -87,6 +87,7 @@ <div class="toolSectionBg"><div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='users', action='registered_users' )}">Registered users</a></div><div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='users', action='last_access_date' )}">Date of last login</a></div> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='users', action='user_disk_usage' )}">User disk usage</a></div></div></div><div class="toolSectionPad"></div> 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: Add the ability for a tool shed admin to browse repository metadata, and implement fixes for setting repository metadata for repositories with multiple tools.
by Bitbucket 15 Aug '11

15 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/824c59db3c3a/ changeset: 824c59db3c3a user: greg date: 2011-08-15 22:12:12 summary: Add the ability for a tool shed admin to browse repository metadata, and implement fixes for setting repository metadata for repositories with multiple tools. affected #: 4 files (5.8 KB) --- a/lib/galaxy/webapps/community/controllers/admin.py Mon Aug 15 13:28:40 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/admin.py Mon Aug 15 16:12:12 2011 -0400 @@ -3,7 +3,7 @@ from galaxy.model.orm import * from galaxy.web.framework.helpers import time_ago, iff, grids from galaxy.util import inflector -from common import get_category, get_repository +from common import get_category, get_repository, get_repository_metadata_by_id from repository import RepositoryListGrid, CategoryListGrid import logging log = logging.getLogger( __name__ ) @@ -308,6 +308,65 @@ async_compatible=False ) ) standard_filters = [] +class RepositoryMetadataListGrid( grids.Grid ): + class IdColumn( grids.IntegerColumn ): + def get_value( self, trans, grid, repository_metadata ): + return repository_metadata.id + class RepositoryIdColumn( grids.IntegerColumn ): + def get_value( self, trans, grid, repository_metadata ): + return repository_metadata.repository_id + class ChangesetRevisionColumn( grids.TextColumn ): + def get_value( self, trans, grid, repository_metadata ): + return repository_metadata.changeset_revision + class MetadataColumn( grids.TextColumn ): + def get_value( self, trans, grid, repository_metadata ): + metadata_str = '' + if repository_metadata: + metadata = repository_metadata.metadata + if metadata: + if 'tools' in metadata: + metadata_str += '<b>Tools:</b><br/>' + for tool_metadata_dict in metadata[ 'tools' ]: + metadata_str += '%s <b>%s</b><br/>' % \ + ( tool_metadata_dict[ 'id' ], tool_metadata_dict[ 'version' ] ) + if 'workflows' in metadata: + metadata_str += '<b>Workflows:</b><br/>' + for workflow_metadata_dict in metadata[ 'workflows' ]: + metadata_str += '%s <b>%s</b><br/>' % \ + ( workflow_metadata_dict[ 'name' ], workflow_metadata_dict[ 'format-version' ] ) + return metadata_str + class MaliciousColumn( grids.BooleanColumn ): + def get_value( self, trans, grid, repository_metadata ): + return repository_metadata.malicious + # Grid definition + title = "Repository Metadata" + model_class = model.RepositoryMetadata + template='/webapps/community/repository/grid.mako' + default_sort_key = "repository_id" + columns = [ + IdColumn( "Id", + visible=False, + attach_popup=False ), + RepositoryIdColumn( "Repository Id", + key="repository_id", + attach_popup=False ), + ChangesetRevisionColumn( "Revision", + attach_popup=False ), + MetadataColumn( "Metadata", + attach_popup=False ), + MaliciousColumn( "Malicious", + attach_popup=False ) + ] + operations = [ grids.GridOperation( "Delete", + allow_multiple=True ) ] + standard_filters = [] + default_filter = {} + num_rows_per_page = 50 + preserve_state = False + use_paging = True + def build_initial_query( self, trans, **kwd ): + return trans.sa_session.query( self.model_class ) + class AdminController( BaseController, Admin ): user_list_grid = UserListGrid() @@ -315,9 +374,44 @@ group_list_grid = GroupListGrid() manage_category_list_grid = ManageCategoryListGrid() repository_list_grid = AdminRepositoryListGrid() + repository_metadata_list_grid = RepositoryMetadataListGrid() @web.expose @web.require_admin + def browse_repository_metadata( self, trans, **kwd ): + if 'operation' in kwd: + operation = kwd[ 'operation' ].lower() + if operation == "delete": + return self.delete_repository_metadata( trans, **kwd ) + # Render the list view + return self.repository_metadata_list_grid( trans, **kwd ) + @web.expose + @web.require_admin + def delete_repository_metadata( self, trans, **kwd ): + # TODO: Add a javascript confirm before this method executes.... + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + id = kwd.get( 'id', None ) + if id: + ids = util.listify( id ) + count = 0 + for repository_metadata_id in ids: + repository_metadata = get_repository_metadata_by_id( trans, repository_metadata_id ) + trans.sa_session.delete( repository_metadata ) + trans.sa_session.flush() + count += 1 + if count: + message = "Deleted %d repository metadata %s" % ( count, inflector.cond_plural( len( ids ), "record" ) ) + else: + message = "No repository metadata ids received for deleting." + status = 'error' + trans.response.send_redirect( web.url_for( controller='admin', + action='browse_repository_metadata', + message=util.sanitize_text( message ), + status=status ) ) + @web.expose + @web.require_admin def browse_repositories( self, trans, **kwd ): # We add params to the keyword dict in this method in order to rename the param # with an "f-" prefix, simulating filtering by clicking a search link. We have --- a/lib/galaxy/webapps/community/controllers/common.py Mon Aug 15 13:28:40 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/common.py Mon Aug 15 16:12:12 2011 -0400 @@ -78,52 +78,54 @@ .filter( and_( trans.model.RepositoryMetadata.table.c.repository_id == trans.security.decode_id( id ), trans.model.RepositoryMetadata.table.c.changeset_revision == changeset_revision ) ) \ .first() +def get_repository_metadata_by_id( trans, id ): + """Get repository metadata from the database""" + return trans.sa_session.query( trans.model.RepositoryMetadata ).get( trans.security.decode_id( id ) ) def get_latest_repository_metadata( trans, id ): """Get last metadata defined for a specified repository from the database""" return trans.sa_session.query( trans.model.RepositoryMetadata ) \ .filter( trans.model.RepositoryMetadata.table.c.repository_id == trans.security.decode_id( id ) ) \ .order_by( trans.model.RepositoryMetadata.table.c.update_time.desc() ) \ .first() -def set_workflowl_metadata( trans, id, change_set_revision, exported_workflow_dict, metadata_dict ): - # We'll store everything except the workflow steps in the database. - flush_needed = False +def generate_workflow_metadata( trans, id, change_set_revision, exported_workflow_dict, metadata_dict ): + """ + Update the received metadata_dict with changes that have been applied + to the received exported_workflow_dict. Store everything except the + workflow steps in the database. + """ workflow_dict = { 'a_galaxy_workflow' : exported_workflow_dict[ 'a_galaxy_workflow' ], 'name' :exported_workflow_dict[ 'name' ], 'annotation' : exported_workflow_dict[ 'annotation' ], 'format-version' : exported_workflow_dict[ 'format-version' ] } - repository_metadata = get_latest_repository_metadata( trans, id ) - if repository_metadata: - metadata = repository_metadata.metadata - if metadata and 'workflows' in metadata: - metadata_workflows = metadata[ 'workflows' ] - found = False - for workflow_metadata_dict in metadata_workflows: - if 'a_galaxy_workflow' in workflow_metadata_dict and util.string_as_bool( workflow_metadata_dict[ 'a_galaxy_workflow' ] ) and \ - 'name' in workflow_metadata_dict and workflow_metadata_dict[ 'name' ] == exported_workflow_dict[ 'name' ] and \ - 'annotation' in workflow_metadata_dict and workflow_metadata_dict[ 'annotation' ] == exported_workflow_dict[ 'annotation' ] and \ - 'format-version' in workflow_metadata_dict and workflow_metadata_dict[ 'format-version' ] == exported_workflow_dict[ 'format-version' ]: - found = True - break - if not found: - metadata_workflows.append( workflow_dict ) + if 'workflows' in metadata_dict: + metadata_dict[ 'workflows' ].append( workflow_dict ) + else: + metadata_dict[ 'workflows' ] = [ workflow_dict ] + return metadata_dict +def new_workflow_metadata_required( trans, id, metadata_dict ): + """ + TODO: Currently everything about an exported workflow except the name is hard-coded, so + there's no real way to differentiate versions of exported workflows. If this changes at + some future time, this method should be enhanced accordingly... + """ + if 'workflows' in metadata_dict: + repository_metadata = get_latest_repository_metadata( trans, id ) + if repository_metadata: + if repository_metadata.metadata: + # The repository has metadata, so update the workflows value - no new record is needed. + return False else: - if metadata is None: - repository_metadata.metadata = {} - repository_metadata.metadata[ 'workflows' ] = workflow_dict - repository_metadata.changeset_revision = change_set_revision - trans.sa_session.add( repository_metadata ) - if not flush_needed: - flush_needed = True - else: - if 'workflows' in metadata_dict: - metadata_dict[ 'workflows' ].append( workflow_dict ) - else: - metadata_dict[ 'workflows' ] = [ workflow_dict ] - return flush_needed, metadata_dict - -def set_tool_metadata( trans, id, change_set_revision, root, name, tool, metadata_dict ): + # There is no saved repository metadata, so we need to create a new repository_metadata table record. + return True + # The received metadata_dict includes no metadata for workflows, so a new repository_metadata table + # record is not needed. + return False +def generate_tool_metadata( trans, id, change_set_revision, root, name, tool, metadata_dict ): + """ + Update the received metadata_dict with changes that have been + applied to the received tool. + """ tool_requirements = [] - flush_needed = False for tr in tool.requirements: requirement_dict = dict( name=tr.name, type=tr.type, @@ -145,54 +147,42 @@ tool_config=os.path.join( root, name ), requirements=tool_requirements, tests=tool_tests ) - repository_metadata = get_latest_repository_metadata( trans, id ) - if repository_metadata: - # We have the last RepositoryMetadata record generated for this repository. - metadata = repository_metadata.metadata - if metadata and 'tools' in metadata: - # The metadata for 1 or more tools was successfully generated in the past for this repository.. - metadata_tools = metadata[ 'tools' ] - found = False - for tool_metadata_dict in metadata_tools: - if 'id' in tool_metadata_dict and tool_metadata_dict[ 'id' ] == tool.id and \ - 'version' in tool_metadata_dict and tool_metadata_dict[ 'version' ] == tool.version: - # We've found a record for the current tool id and version, so we'll - # update the metadata associated with the record. - found = True - tool_metadata_dict[ 'name' ] = tool.name - tool_metadata_dict[ 'description' ] = tool.description - tool_metadata_dict[ 'version_string_cmd' ] = tool.version_string_cmd - tool_metadata_dict[ 'tool_config' ] = os.path.join( root, name ) - tool_metadata_dict[ 'requirements' ] = tool_requirements - tool_metadata_dict[ 'tests' ] = tool_tests - if not flush_needed: - flush_needed = True - if found: - repository_metadata.changeset_revision = change_set_revision + if 'tools' in metadata_dict: + metadata_dict[ 'tools' ].append( tool_dict ) + else: + metadata_dict[ 'tools' ] = [ tool_dict ] + return metadata_dict +def new_tool_metadata_required( trans, id, metadata_dict ): + """ + Compare the last saved metadata for each tool in the repository with the new metadata + in metadata_dict to determine if a new repository_metadata table record is required, or + if the last saved metadata record can updated instead. + """ + if 'tools' in metadata_dict: + repository_metadata = get_latest_repository_metadata( trans, id ) + if repository_metadata: + metadata = repository_metadata.metadata + if metadata and 'tools' in metadata: + # The metadata for one or more tools was successfully generated in the past + # for this repository, so we compare the version string for each tool id + # in metadata_dict with what was previously saved to see if we need to create + # a new table record or if we can simply update the existing record. + for new_tool_metadata_dict in metadata_dict[ 'tools' ]: + for saved_tool_metadata_dict in metadata[ 'tools' ]: + if new_tool_metadata_dict[ 'id' ] == saved_tool_metadata_dict[ 'id' ]: + if new_tool_metadata_dict[ 'version' ] != saved_tool_metadata_dict[ 'version' ]: + return True else: - if 'tools' in metadata_dict: - metadata_dict[ 'tools' ].append( tool_dict ) - else: - metadata_dict[ 'tools' ] = [ tool_dict ] - if not flush_needed: - flush_needed = True - if not flush_needed: - flush_needed = True + # We have repository metadata that does not include metadata for any tools in the + # repository, so we can update the existing repository metadata. + return False else: - # Either the metadata is Null, or it does not include the key 'tools'. - if metadata is None: - repository_metadata.metadata = {} - repository_metadata.metadata[ 'tools' ] = [ tool_dict ] - repository_metadata.changeset_revision = change_set_revision - trans.sa_session.add( repository_metadata ) - if not flush_needed: - flush_needed = True - else: - if 'tools' in metadata_dict: - metadata_dict[ 'tools' ].append( tool_dict ) - else: - metadata_dict[ 'tools' ] = [ tool_dict ] - return flush_needed, metadata_dict + # There is no saved repository metadata, so we need to create a new repository_metadata + # table record. + return True + # The received metadata_dict includes no metadata for tools, so a new repository_metadata table + # record is not needed. + return False def set_repository_metadata( trans, id, change_set_revision, **kwd ): """Set repository metadata""" message = '' @@ -202,7 +192,6 @@ repo = hg.repository( get_configured_ui(), repo_dir ) change_set = get_change_set( trans, repo, change_set_revision ) invalid_files = [] - flush_needed = False if change_set is not None: metadata_dict = {} for root, dirs, files in os.walk( repo_dir ): @@ -221,7 +210,8 @@ full_path = os.path.abspath( os.path.join( root, name ) ) tool = load_tool( trans, full_path ) if tool is not None: - flush_needed, metadata_dict = set_tool_metadata( trans, id, change_set_revision, root, name, tool, metadata_dict ) + # Update the list metadata dictionaries for tools in metadata_dict. + metadata_dict = generate_tool_metadata( trans, id, change_set_revision, root, name, tool, metadata_dict ) except Exception, e: invalid_files.append( ( name, str( e ) ) ) # Find all exported workflows @@ -233,16 +223,22 @@ workflow_text = fp.read() fp.close() exported_workflow_dict = from_json_string( workflow_text ) - flush_needed, metadata_dict = set_workflowl_metadata( trans, id, change_set_revision, exported_workflow_dict, metadata_dict ) + # Update the list of metadata dictionaries for workflows in metadata_dict. + metadata_dict = generate_workflow_metadata( trans, id, change_set_revision, exported_workflow_dict, metadata_dict ) except Exception, e: invalid_files.append( ( name, str( e ) ) ) if metadata_dict: - # The metadata_dict dictionary will contain items only - # if the repository did not already have metadata set. - repository_metadata = trans.model.RepositoryMetadata( repository.id, change_set_revision, metadata_dict ) - trans.sa_session.add( repository_metadata ) - if not flush_needed: - flush_needed = True + if new_tool_metadata_required( trans, id, metadata_dict ) or new_workflow_metadata_required( trans, id, metadata_dict ): + # Create a new repository_metadata table row. + repository_metadata = trans.model.RepositoryMetadata( repository.id, change_set_revision, metadata_dict ) + trans.sa_session.add( repository_metadata ) + trans.sa_session.flush() + else: + # Update the last saved repository_metadata table row. + repository_metadata = get_latest_repository_metadata( trans, id ) + repository_metadata.metadata = metadata_dict + trans.sa_session.add( repository_metadata ) + trans.sa_session.flush() else: # change_set is None message = "Repository does not include changeset revision '%s'." % str( change_set_revision ) @@ -284,10 +280,6 @@ correction_msg = exception_msg message += "<b>%s</b> - %s<br/>" % ( tool_file, correction_msg ) status = 'error' - elif flush_needed: - # We only flush if there are no tool config errors, so change sets will only have metadata - # if everything in them is valid. - trans.sa_session.flush() return message, status def get_repository_by_name( trans, name ): """Get a repository from the database via name""" --- a/templates/webapps/community/admin/index.mako Mon Aug 15 13:28:40 2011 -0400 +++ b/templates/webapps/community/admin/index.mako Mon Aug 15 16:12:12 2011 -0400 @@ -43,14 +43,30 @@ <div class="page-container" style="padding: 10px;"><div class="toolMenu"><div class="toolSectionList"> - <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_categories', webapp='community' )}">Browse by category</a></div> - <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='admin', action='browse_repositories', webapp='community' )}">Browse all repositories</a></div> + <div class="toolSectionTitle"> + Repositories + </div> + <div class="toolSectionBody"> + <div class="toolSectionBg"> + <div class="toolTitle"> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_categories', webapp='community' )}">Browse by category</a> + </div> + <div class="toolTitle"> + <a target="galaxy_main" href="${h.url_for( controller='admin', action='browse_repositories', webapp='community' )}">Browse all repositories</a> + </div> + <div class="toolTitle"> + <a target="galaxy_main" href="${h.url_for( controller='admin', action='browse_repository_metadata', webapp='community' )}">Browse metadata</a> + </div> + </div> + </div><div class="toolSectionTitle"> Categories </div><div class="toolSectionBody"><div class="toolSectionBg"> - <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='admin', action='manage_categories', webapp='community' )}">Manage categories</a></div> + <div class="toolTitle"> + <a target="galaxy_main" href="${h.url_for( controller='admin', action='manage_categories', webapp='community' )}">Manage categories</a> + </div></div></div><div class="toolSectionPad"></div> @@ -59,9 +75,15 @@ </div><div class="toolSectionBody"><div class="toolSectionBg"> - <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='admin', action='users', webapp='community' )}">Manage users</a></div> - <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='admin', action='groups', webapp='community' )}">Manage groups</a></div> - <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='admin', action='roles', webapp='community' )}">Manage roles</a></div> + <div class="toolTitle"> + <a target="galaxy_main" href="${h.url_for( controller='admin', action='users', webapp='community' )}">Manage users</a> + </div> + <div class="toolTitle"> + <a target="galaxy_main" href="${h.url_for( controller='admin', action='groups', webapp='community' )}">Manage groups</a> + </div> + <div class="toolTitle"> + <a target="galaxy_main" href="${h.url_for( controller='admin', action='roles', webapp='community' )}">Manage roles</a> + </div></div></div></div> --- a/templates/webapps/community/index.mako Mon Aug 15 13:28:40 2011 -0400 +++ b/templates/webapps/community/index.mako Mon Aug 15 16:12:12 2011 -0400 @@ -45,13 +45,21 @@ <div class="toolMenu"><div class="toolSectionList"><div class="toolSectionPad"></div> - <div class="toolSectionTitle">Repositories</div> + <div class="toolSectionTitle"> + Repositories + </div><div class="toolSectionBody"><div class="toolSectionBg"> - <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_categories', webapp='community' )}">Browse by category</a></div> - <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories', webapp='community' )}">Browse all repositories</a></div> + <div class="toolTitle"> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_categories', webapp='community' )}">Browse by category</a> + </div> + <div class="toolTitle"> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories', webapp='community' )}">Browse all repositories</a> + </div> %if trans.user: - <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories', operation='my_repositories', webapp='community' )}">Browse my repositories</a></div> + <div class="toolTitle"> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories', operation='my_repositories', webapp='community' )}">Browse my repositories</a> + </div> %endif </div></div> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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