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commit/galaxy-central: dan: Better determination in tests if a provided input is a DataToolParameter to better handle .gz and .zip uploads and allowing uploads from a sub-directory of test-data/.
by Bitbucket 28 Feb '11

28 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/4d2d7c952d87/ changeset: r5142:4d2d7c952d87 user: dan date: 2011-02-28 18:16:28 summary: Better determination in tests if a provided input is a DataToolParameter to better handle .gz and .zip uploads and allowing uploads from a sub-directory of test-data/. affected #: 16 files (2.5 KB) --- a/lib/galaxy/tools/test.py Mon Feb 28 09:59:30 2011 -0500 +++ b/lib/galaxy/tools/test.py Mon Feb 28 12:16:28 2011 -0500 @@ -1,4 +1,5 @@ import new, sys +import os.path import galaxy.util import parameters from parameters import basic @@ -12,7 +13,7 @@ """ Encapsulates information about a tool test, and allows creation of a dynamic TestCase class (the unittest framework is very class oriented, - doing dynamic tests in this was allows better integration) + doing dynamic tests in this way allows better integration) """ def __init__( self, tool, name, maxseconds ): self.tool = tool @@ -26,19 +27,17 @@ def add_param( self, name, value, extra ): try: if name not in self.tool.inputs: + found_parameter = False for input_name, input_value in self.tool.inputs.items(): - if isinstance( input_value, grouping.Conditional ) or isinstance( input_value, grouping.Repeat ): - self.__expand_grouping_for_data_input(name, value, extra, input_name, input_value) - elif isinstance( self.tool.inputs[name], parameters.DataToolParameter ) and ( value, extra ) not in self.required_files: - name_change = [ att for att in extra.get( 'edit_attributes', [] ) if att.get( 'type' ) == 'name' ] - if name_change: - name_change = name_change[-1].get( 'value' ) #only the last name change really matters - if value is None and not name_change: - assert self.tool.inputs[name].optional, '%s is not optional. You must provide a valid filename.' % name - else: - self.required_files.append( ( value, extra ) ) #these files will be uploaded - if name_change: - value = name_change #change value for select to renamed uploaded file for e.g. composite dataset + if isinstance( input_value, grouping.Group ): + found_parameter, new_value = self.__expand_grouping_for_data_input(name, value, extra, input_name, input_value) + if found_parameter: + value = new_value + break + if not found_parameter: + raise ValueError( "Unable to determine parameter type of test input '%s'. Ensure that the parameter exists and that any container groups are defined first." % name ) + elif isinstance( self.tool.inputs[name], basic.DataToolParameter ): + value = self.__add_uploaded_dataset( name, value, extra, self.tool.inputs[name] ) except Exception, e: log.debug( "Error in add_param for %s: %s" % ( name, e ) ) self.inputs.append( ( name, value, extra ) ) @@ -47,27 +46,65 @@ def __expand_grouping_for_data_input( self, name, value, extra, grouping_name, grouping_value ): # Currently handles grouping.Conditional and grouping.Repeat if isinstance( grouping_value, grouping.Conditional ): - if name != grouping_value.test_param.name: - for case in grouping_value.cases: - for case_input_name, case_input_value in case.inputs.items(): - if case_input_name == name and isinstance( case_input_value, basic.DataToolParameter ) and ( value, extra ) not in self.required_files: - if value is None: - assert case_input_value.optional, '%s is not optional. You must provide a valid filename.' % name - else: - self.required_files.append( ( value, extra ) ) - return True - elif isinstance( case_input_value, grouping.Conditional ): - self.__expand_grouping_for_data_input(name, value, extra, case_input_name, case_input_value) + if name == grouping_value.test_param.name: + return True, value + case_test_param_value = None + for input in self.inputs: + if input[0] == grouping_value.test_param.name: + case_test_param_value = input[1] + break + if case_test_param_value is None: + #case for this group has not been set yet + return False, value + for case in grouping_value.cases: + if case.value == case_test_param_value: + break + if case.value != case_test_param_value: + return False, value + #assert case.value == case_test_param_value, "Current case could not be determined for parameter '%s'. Provided value '%s' could not be found in '%s'." % ( grouping_value.name, value, grouping_value.test_param.name ) + if name in case.inputs: + if isinstance( case.inputs[name], basic.DataToolParameter ): + return True, self.__add_uploaded_dataset( name, value, extra, case.inputs[name] ) + else: + return True, value + else: + for input_name, input_parameter in case.inputs.iteritems(): + if isinstance( input_parameter, grouping.Group ): + found_parameter, new_value = self.__expand_grouping_for_data_input( name, value, extra, input_name, input_parameter ) + if found_parameter: + return True, new_value elif isinstance( grouping_value, grouping.Repeat ): # FIXME: grouping.Repeat can only handle 1 repeat param element since the param name # is something like "input2" and the expanded page display is something like "queries_0|input2". # The problem is that the only param name on the page is "input2", and adding more test input params - # with the same name ( "input2" ) is not yet supported in our test code ( the lat one added is the only - # one used ). - for input_name, input_value in grouping_value.inputs.items(): - if input_name == name and isinstance( input_value, basic.DataToolParameter ) and ( value, extra ) not in self.required_files: - if value is None: - assert input_value.optional, '%s is not optional. You must provide a valid filename.' % name - else: - self.required_files.append( ( value, extra ) ) - return True + # with the same name ( "input2" ) is not yet supported in our test code ( the last one added is the only + # one used ). + if name in grouping_value.inputs: + if isinstance( grouping_value.inputs[name], basic.DataToolParameter ): + return True, self.__add_uploaded_dataset( name, value, extra, grouping_value.inputs[name] ) + else: + return True, value + else: + for input_name, input_parameter in grouping_value.inputs.iteritems(): + if isinstance( input_parameter, grouping.Group ): + found_parameter, new_value = self.__expand_grouping_for_data_input( name, value, extra, input_name, input_parameter ) + if found_parameter: + return True, new_value + return False, value + def __add_uploaded_dataset( self, name, value, extra, input_parameter ): + if value is None: + assert input_parameter.optional, '%s is not optional. You must provide a valid filename.' % name + return value + if ( value, extra ) not in self.required_files: + self.required_files.append( ( value, extra ) ) #these files will be uploaded + name_change = [ att for att in extra.get( 'edit_attributes', [] ) if att.get( 'type' ) == 'name' ] + if name_change: + name_change = name_change[-1].get( 'value' ) #only the last name change really matters + value = name_change #change value for select to renamed uploaded file for e.g. composite dataset + else: + for end in [ '.zip', '.gz' ]: + if value.endswith( end ): + value = value[ :-len( end ) ] + break + value = os.path.basename( value ) #if uploading a file in a path other than root of test-data + return value --- a/test/functional/test_toolbox.py Mon Feb 28 09:59:30 2011 -0500 +++ b/test/functional/test_toolbox.py Mon Feb 28 12:16:28 2011 -0500 @@ -1,5 +1,4 @@ import sys, new -import os.path from galaxy.tools.parameters import grouping from galaxy.tools.parameters import basic from base.twilltestcase import TwillTestCase @@ -56,12 +55,6 @@ # tool will have uncompressed it on the fly. all_inputs = {} for name, value, _ in testdef.inputs: - if value: - for end in [ '.zip', '.gz' ]: - if value.endswith( end ): - value = value[ :-len( end ) ] - break - value = os.path.basename( value ) #if uploading a file in a path other than root of test-data all_inputs[ name ] = value # See if we have a grouping.Repeat element repeat_name = None --- a/tools/human_genome_variation/ldtools.xml Mon Feb 28 09:59:30 2011 -0500 +++ b/tools/human_genome_variation/ldtools.xml Mon Feb 28 12:16:28 2011 -0500 @@ -24,7 +24,7 @@ <param name="input" value="ldInput1.txt" /><param name="rsquare" value="0.64" /><param name="freq" value="0.00" /> - <param name="output" file="ldOutput1.txt" /> + <output name="output" file="ldOutput1.txt" /></test></tests> --- a/tools/maf/maf_to_fasta.xml Mon Feb 28 09:59:30 2011 -0500 +++ b/tools/maf/maf_to_fasta.xml Mon Feb 28 12:16:28 2011 -0500 @@ -38,15 +38,15 @@ <tests><test><param name="input1" value="3.maf" ftype="maf"/> + <param name="fasta_type" value="concatenated"/><param name="species" value="canFam1"/> - <param name="fasta_type" value="concatenated"/><output name="out_file1" file="cf_maf2fasta_concat.dat" ftype="fasta"/></test><test><param name="input1" value="4.maf" ftype="maf"/> + <param name="fasta_type" value="multiple"/><param name="species" value="hg17,panTro1,rheMac2,rn3,mm7,canFam2,bosTau2,dasNov1"/><param name="complete_blocks" value="partial_allowed"/> - <param name="fasta_type" value="multiple"/><output name="out_file1" file="cf_maf2fasta_new.dat" ftype="fasta"/></test></tests> --- a/tools/new_operations/intersect.xml Mon Feb 28 09:59:30 2011 -0500 +++ b/tools/new_operations/intersect.xml Mon Feb 28 12:16:28 2011 -0500 @@ -38,7 +38,6 @@ <code file="operation_filter.py"/><tests><test> - <param name="type" value="Interval"/><param name="input1" value="1.bed" /><param name="input2" value="2.bed" /><param name="min" value="1" /> @@ -46,7 +45,6 @@ <output name="output" file="gops_intersect_out.bed" /></test><test> - <param name="type" value="Interval"/><param name="input1" value="1.bed" /><param name="input2" value="2_mod.bed" ftype="interval"/><param name="min" value="1" /> --- a/tools/next_gen_conversion/solid2fastq.xml Mon Feb 28 09:59:30 2011 -0500 +++ b/tools/next_gen_conversion/solid2fastq.xml Mon Feb 28 12:16:28 2011 -0500 @@ -54,9 +54,9 @@ <test><param name="input1" value="fr.csfasta" ftype="csfasta"/><param name="input2" value="fr.qualsolid" ftype="qualsolid" /> + <param name="paired" value="yes"/><param name="input3" value="rr.csfasta" ftype="csfasta"/><param name="input4" value="rr.qualsolid" ftype="qualsolid" /> - <param name="paired" value="yes"/><param name="qual" value="0" /><param name="trim_first_base" value="No" /><param name="trim_name" value="Yes" /> --- a/tools/peak_calling/macs_wrapper.xml Mon Feb 28 09:59:30 2011 -0500 +++ b/tools/peak_calling/macs_wrapper.xml Mon Feb 28 12:16:28 2011 -0500 @@ -140,10 +140,10 @@ </configfiles><tests><test> + <param name="input_type_selector" value="single_end" /><param name="input_chipseq_file1" value="chipseq_enriched.bed.gz" ftype="bed" /><param name="input_control_file1" value="chipseq_input.bed.gz" ftype="bed" /><param name="experiment_name" value="Galaxy Test Run" /> - <param name="input_type_selector" value="single_end" /><param name="tsize" value="36" /><param name="mfold" value="13" /><param name="gsize" value="2.7e+9" /> @@ -166,10 +166,10 @@ </output></test><test> + <param name="input_type_selector" value="single_end" /><param name="input_chipseq_file1" value="chipseq_enriched.bed.gz" ftype="bed" /><param name="input_control_file1" value="chipseq_input.bed.gz" ftype="bed" /><param name="experiment_name" value="Galaxy Test Run" /> - <param name="input_type_selector" value="single_end" /><param name="tsize" value="36" /><param name="mfold" value="13" /><param name="gsize" value="2.7e+9" /> @@ -190,10 +190,10 @@ </output></test><param name="input1" value="3.bam" ftype="bam" /> - <param name="output1" file="bam_to_sam_out2.sam" sorted="True" /> + <output name="output1" file="bam_to_sam_out2.sam" sorted="True" /></test></tests><help> --- a/tools/samtools/sam2interval.xml Mon Feb 28 09:59:30 2011 -0500 +++ b/tools/samtools/sam2interval.xml Mon Feb 28 12:16:28 2011 -0500 @@ -15,13 +15,11 @@ <tests><test><param name="input1" value="sam_bioinf_example.sam" ftype="sam"/> - <param name="flags" value="Read is mapped in a proper pair"/><param name="print_all" value="Yes"/><output name="out_file1" file="sam2interval_printAll.dat" ftype="interval"/></test><test><param name="input1" value="sam_bioinf_example.sam" ftype="sam"/> - <param name="flags" value="Read is mapped in a proper pair"/><param name="print_all" value="No"/><output name="out_file1" file="sam2interval_noprintAll.dat" ftype="interval"/></test> --- a/tools/samtools/sam_to_bam.xml Mon Feb 28 09:59:30 2011 -0500 +++ b/tools/samtools/sam_to_bam.xml Mon Feb 28 12:16:28 2011 -0500 @@ -60,7 +60,7 @@ --><param name="index_source" value="cached" /><param name="input1" value="3.sam" ftype="sam" dbkey="equCab2" /> - <param name="output1" file="sam_to_bam_out2.bam" /> + <output name="output1" file="sam_to_bam_out2.bam" /></test></tests><help> --- a/tools/samtools/samtools_flagstat.xml Mon Feb 28 09:59:30 2011 -0500 +++ b/tools/samtools/samtools_flagstat.xml Mon Feb 28 12:16:28 2011 -0500 @@ -14,7 +14,7 @@ <tests><test><param name="input1" value="3.bam" ftype="bam" /> - <param name="output1" file="samtools_flagstat_out1.txt" /> + <output name="output1" file="samtools_flagstat_out1.txt" /></test></tests><help> --- a/tools/sr_mapping/bfast_wrapper.xml Mon Feb 28 09:59:30 2011 -0500 +++ b/tools/sr_mapping/bfast_wrapper.xml Mon Feb 28 12:16:28 2011 -0500 @@ -368,8 +368,6 @@ <param name="indices" value="phiX_nt_50" /><param name="source_select" value="pre_set" /><param name="suppressHeader" value="False" /> - <param name="indexing_repeatmasker" value="" /> - <param name="indexing_option_selector" value="default" /><output name="output" ftype="sam" file="bfast_out3.sam" lines_diff="2" /></test></tests> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Fix bad value in cufflinks functional test.
by Bitbucket 28 Feb '11

28 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/4146f64da13d/ changeset: r5141:4146f64da13d user: jgoecks date: 2011-02-28 15:59:30 summary: Fix bad value in cufflinks functional test. affected #: 1 file (4 bytes) --- a/tools/ngs_rna/cufflinks_wrapper.xml Mon Feb 28 09:52:17 2011 -0500 +++ b/tools/ngs_rna/cufflinks_wrapper.xml Mon Feb 28 09:59:30 2011 -0500 @@ -103,7 +103,7 @@ Simple test that uses test data included with cufflinks. --><test> - <param name="sPaired" value="single"/> + <param name="sPaired" value="No"/><param name="input" value="cufflinks_in.sam"/><param name="mean_inner_distance" value="20"/><param name="max_intron_len" value="300000"/> 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: Bugfix for the last commit when running functional tests with sqlite.
by Bitbucket 28 Feb '11

28 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/2e88578ef7e1/ changeset: r5140:2e88578ef7e1 user: natefoo date: 2011-02-28 15:52:17 summary: Bugfix for the last commit when running functional tests with sqlite. affected #: 1 file (49 bytes) --- a/scripts/functional_tests.py Mon Feb 28 09:35:36 2011 -0500 +++ b/scripts/functional_tests.py Mon Feb 28 09:52:17 2011 -0500 @@ -139,13 +139,15 @@ if psu_production: global_conf = None + if not database_connection.startswith( 'sqlite://' ): + kwargs['database_engine_option_max_overflow'] = '20' + # Build the Universe Application app = UniverseApplication( job_queue_workers = 5, id_secret = 'changethisinproductiontoo', template_path = "templates", database_connection = database_connection, database_engine_option_pool_size = '10', - database_engine_option_max_overflow = '20', file_path = file_path, new_file_path = new_file_path, tool_path = tool_path, 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: Require ctypes egg before pysam on Python 2.4
by Bitbucket 28 Feb '11

28 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/b9b772f2e4eb/ changeset: r5139:b9b772f2e4eb user: natefoo date: 2011-02-28 15:35:36 summary: Require ctypes egg before pysam on Python 2.4 affected #: 2 files (157 bytes) --- a/lib/galaxy/datatypes/converters/bam_to_summary_tree_converter.py Mon Feb 28 08:33:48 2011 -0500 +++ b/lib/galaxy/datatypes/converters/bam_to_summary_tree_converter.py Mon Feb 28 09:35:36 2011 -0500 @@ -4,7 +4,11 @@ import sys from galaxy import eggs -import pkg_resources; pkg_resources.require( "pysam" ) +import pkg_resources + +if sys.version_info[:2] == (2, 4): + pkg_resources.require( "ctypes" ) +pkg_resources.require( "pysam" ) from pysam import csamtools from galaxy.visualization.tracks.summary import * @@ -24,4 +28,4 @@ st.write(out_fname) if __name__ == "__main__": - main() \ No newline at end of file + main() --- a/lib/galaxy/visualization/tracks/data_providers.py Mon Feb 28 08:33:48 2011 -0500 +++ b/lib/galaxy/visualization/tracks/data_providers.py Mon Feb 28 09:35:36 2011 -0500 @@ -2,9 +2,14 @@ Data providers for tracks visualizations. """ +import sys from math import floor, ceil, log, pow import pkg_resources -pkg_resources.require( "bx-python" ); pkg_resources.require( "pysam" ); pkg_resources.require( "numpy" ) +pkg_resources.require( "bx-python" ) +if sys.version_info[:2] == (2, 4): + pkg_resources.require( "ctypes" ) +pkg_resources.require( "pysam" ) +pkg_resources.require( "numpy" ) from galaxy.datatypes.util.gff_util import * from bx.interval_index_file import Indexes from bx.arrays.array_tree import FileArrayTreeDict @@ -671,4 +676,4 @@ blocks = zip( block_sizes, block_starts ) payload.append( [ ( feature.start + block[1], feature.start + block[1] + block[0] ) for block in blocks ] ) - return payload \ No newline at end of file + return payload 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 ccat_configurations.loc to buildbot_setup.sh
by Bitbucket 28 Feb '11

28 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/16cafc8da6f3/ changeset: r5138:16cafc8da6f3 user: natefoo date: 2011-02-28 14:33:48 summary: Add ccat_configurations.loc to buildbot_setup.sh affected #: 1 file (46 bytes) --- a/buildbot_setup.sh Mon Feb 28 07:58:52 2011 -0500 +++ b/buildbot_setup.sh Mon Feb 28 08:33:48 2011 -0500 @@ -40,6 +40,7 @@ /galaxy/data/location/bowtie_indices_color.loc /galaxy/data/location/bwa_index.loc /galaxy/data/location/bwa_index_color.loc +/galaxy/data/location/ccat_configurations.loc /galaxy/data/location/codingSnps.loc /galaxy/data/location/encode_datasets.loc /galaxy/home/universe/encode_feature_partitions 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: Increase the SQLAlchemy SuquePool limits for functional tests.
by Bitbucket 28 Feb '11

28 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/5bced201f40a/ changeset: r5137:5bced201f40a user: natefoo date: 2011-02-28 13:58:52 summary: Increase the SQLAlchemy SuquePool limits for functional tests. affected #: 1 file (155 bytes) --- a/scripts/functional_tests.py Sun Feb 27 14:48:23 2011 -0500 +++ b/scripts/functional_tests.py Mon Feb 28 07:58:52 2011 -0500 @@ -144,6 +144,8 @@ id_secret = 'changethisinproductiontoo', template_path = "templates", database_connection = database_connection, + database_engine_option_pool_size = '10', + database_engine_option_max_overflow = '20', file_path = file_path, new_file_path = new_file_path, tool_path = tool_path, 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: Suppress most logging for cufflinks and cuffdiff as the logging can generate output that is incompatible with UTF-8 format used by database.
by Bitbucket 27 Feb '11

27 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/9bcf6ac08839/ changeset: r5136:9bcf6ac08839 user: jgoecks date: 2011-02-27 20:48:23 summary: Suppress most logging for cufflinks and cuffdiff as the logging can generate output that is incompatible with UTF-8 format used by database. affected #: 2 files (136 bytes) --- a/tools/ngs_rna/cuffdiff_wrapper.py Sat Feb 26 13:12:44 2011 -0500 +++ b/tools/ngs_rna/cuffdiff_wrapper.py Sun Feb 27 14:48:23 2011 -0500 @@ -135,8 +135,8 @@ # Build command. - # Base. - cmd = "cuffdiff" + # Base; always use quiet mode to avoid problems with storing log output. + cmd = "cuffdiff -q" # Add options. if options.inner_dist_std_dev: --- a/tools/ngs_rna/cufflinks_wrapper.py Sat Feb 26 13:12:44 2011 -0500 +++ b/tools/ngs_rna/cufflinks_wrapper.py Sun Feb 27 14:48:23 2011 -0500 @@ -84,8 +84,8 @@ # Build command. - # Base. - cmd = "cufflinks" + # Base; always use quiet mode to avoid problems with storing log output. + cmd = "cufflinks -q" # Add options. if options.inner_dist_std_dev: 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 mosaik index location file to buildbot setup.
by Bitbucket 26 Feb '11

26 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/e58da3d454f2/ changeset: r5135:e58da3d454f2 user: natefoo date: 2011-02-26 19:12:44 summary: Add mosaik index location file to buildbot setup. affected #: 1 file (39 bytes) --- a/buildbot_setup.sh Sat Feb 26 10:53:50 2011 -0500 +++ b/buildbot_setup.sh Sat Feb 26 13:12:44 2011 -0500 @@ -48,6 +48,7 @@ /galaxy/data/location/maf_index.loc /galaxy/data/location/maf_pairwise.loc /galaxy/data/location/microbes/microbial_data.loc +/galaxy/data/location/mosaik_index.loc /galaxy/data/location/perm_base_index.loc /galaxy/data/location/perm_color_index.loc /galaxy/data/location/phastOdds.loc 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: dannon: Basic Freebayes test added.
by Bitbucket 26 Feb '11

26 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/71c61850ea7a/ changeset: r5134:71c61850ea7a user: dannon date: 2011-02-26 16:53:50 summary: Basic Freebayes test added. affected #: 3 files (277 bytes) --- a/tools/human_genome_variation/freebayes.xml Fri Feb 25 17:53:58 2011 -0500 +++ b/tools/human_genome_variation/freebayes.xml Sat Feb 26 10:53:50 2011 -0500 @@ -112,6 +112,10 @@ </outputs><tests><test> + <param name="reference" ftype="fasta" value="mosaik_test_ref.fasta"/> + <param name="bamfile" ftype="bam" value="freebayes_in.bam"/> + <param name="source_select" value="pre_set"/> + <output name="output" ftype="vcf" file="freebayes_out.vcf" lines_diff="4"/></test></tests><help> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Freebayes and Mosaik updates
by Bitbucket 25 Feb '11

25 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/6537337eeb50/ changeset: r5133:6537337eeb50 user: dannon date: 2011-02-25 23:53:58 summary: Freebayes and Mosaik updates affected #: 5 files (742 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: rc: Fixed adding an external service to a request type in edit_request_type
by Bitbucket 25 Feb '11

25 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/cad3884b8729/ changeset: r5132:cad3884b8729 user: rc date: 2011-02-25 22:25:54 summary: Fixed adding an external service to a request type in edit_request_type affected #: 1 file (37 bytes) --- a/lib/galaxy/web/controllers/request_type.py Fri Feb 25 16:12:17 2011 -0500 +++ b/lib/galaxy/web/controllers/request_type.py Fri Feb 25 16:25:54 2011 -0500 @@ -244,7 +244,7 @@ sample_form_id = params.get( 'sample_form_id', 'none' ) external_service_id = params.get( 'external_service_id', 'none' ) # validate - if not name or request_form_id == 'none' or sample_form_id == 'none' or not kwd.has_key( 'state_name_0' ): + if not name or request_form_id == 'none' or sample_form_id == 'none': message = 'Enter the name, request form, sample form and at least one sample state associated with this request type.' return trans.response.send_redirect( web.url_for( controller='request_type', action=action, 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: rc: Bug fix: do not show sample field widgets in the view request page
by Bitbucket 25 Feb '11

25 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/67f76a732e97/ changeset: r5131:67f76a732e97 user: rc date: 2011-02-25 22:12:17 summary: Bug fix: do not show sample field widgets in the view request page affected #: 4 files (49 bytes) --- a/templates/requests/common/add_samples.mako Fri Feb 25 15:58:13 2011 -0500 +++ b/templates/requests/common/add_samples.mako Fri Feb 25 16:12:17 2011 -0500 @@ -71,7 +71,7 @@ ## Render the other grids <% trans.sa_session.refresh( request.type.sample_form ) %> %for grid_index, grid_name in enumerate( request.type.sample_form.layout ): - ${render_request_type_sample_form_grids( grid_index, grid_name, request.type.sample_form.grid_fields( grid_index ), displayable_sample_widgets=displayable_sample_widgets, adding_new_samples=True )} + ${render_request_type_sample_form_grids( grid_index, grid_name, request.type.sample_form.grid_fields( grid_index ), displayable_sample_widgets=displayable_sample_widgets, show_saved_samples_read_only=True )} %endfor %else: <label>There are no samples.</label> --- a/templates/requests/common/common.mako Fri Feb 25 15:58:13 2011 -0500 +++ b/templates/requests/common/common.mako Fri Feb 25 16:12:17 2011 -0500 @@ -606,7 +606,7 @@ </tr></%def> -<%def name="render_request_type_sample_form_grids( grid_index, grid_name, fields_dict, displayable_sample_widgets, adding_new_samples )"> +<%def name="render_request_type_sample_form_grids( grid_index, grid_name, fields_dict, displayable_sample_widgets, show_saved_samples_read_only )"><% if not grid_name: grid_name = "Sample form layout %s" % str( grid_index ) @@ -629,7 +629,7 @@ <% trans.sa_session.refresh( request ) %> %for sample_index, sample in enumerate( displayable_sample_widgets ): <% - if not adding_new_samples or sample_index >= len( request.samples ): + if not show_saved_samples_read_only or sample_index >= len( request.samples ): display_only = False else: display_only = True --- a/templates/requests/common/edit_samples.mako Fri Feb 25 15:58:13 2011 -0500 +++ b/templates/requests/common/edit_samples.mako Fri Feb 25 16:12:17 2011 -0500 @@ -120,7 +120,7 @@ ## Render the other grids <% trans.sa_session.refresh( request.type.sample_form ) %> %for grid_index, grid_name in enumerate( request.type.sample_form.layout ): - ${render_request_type_sample_form_grids( grid_index, grid_name, request.type.sample_form.grid_fields( grid_index ), displayable_sample_widgets=displayable_sample_widgets, adding_new_samples=False )} + ${render_request_type_sample_form_grids( grid_index, grid_name, request.type.sample_form.grid_fields( grid_index ), displayable_sample_widgets=displayable_sample_widgets, show_saved_samples_read_only=False )} %endfor %else: <label>There are no samples.</label> --- a/templates/requests/common/view_request.mako Fri Feb 25 15:58:13 2011 -0500 +++ b/templates/requests/common/view_request.mako Fri Feb 25 16:12:17 2011 -0500 @@ -162,7 +162,7 @@ ## Render the other grids <% trans.sa_session.refresh( request.type.sample_form ) %> %for grid_index, grid_name in enumerate( request.type.sample_form.layout ): - ${render_request_type_sample_form_grids( grid_index, grid_name, request.type.sample_form.grid_fields( grid_index ), displayable_sample_widgets=displayable_sample_widgets, adding_new_samples=False )} + ${render_request_type_sample_form_grids( grid_index, grid_name, request.type.sample_form.grid_fields( grid_index ), displayable_sample_widgets=displayable_sample_widgets, show_saved_samples_read_only=True )} %endfor %else: There are no samples. 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: rc: First pass of extract & filter VCF tools.
by Bitbucket 25 Feb '11

25 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/69338ee03d1d/ changeset: r5130:69338ee03d1d user: rc date: 2011-02-25 21:58:13 summary: First pass of extract & filter VCF tools. affected #: 6 files (22 bytes) --- a/tools/vcf_tools/annotate.xml Fri Feb 25 14:58:35 2011 -0500 +++ b/tools/vcf_tools/annotate.xml Fri Feb 25 15:58:13 2011 -0500 @@ -1,5 +1,5 @@ -<tool id="vcf_annotate" name="Annotate a VCF file" version="1.0.0"> - <description></description> +<tool id="vcf_annotate" name="Annotate" version="1.0.0"> + <description>a VCF file (dbSNP, hapmap)</description><command interpreter="python"> vcfPytools.py annotate @@ -27,7 +27,7 @@ </conditional></inputs><outputs> - <data format="vcf" name="output1" label="${tool.name} on ${on_string}" /> + <data format="vcf" name="output1" label="${tool.name} ${on_string}" /></outputs><tests><test> --- a/tools/vcf_tools/intersect.xml Fri Feb 25 14:58:35 2011 -0500 +++ b/tools/vcf_tools/intersect.xml Fri Feb 25 15:58:13 2011 -0500 @@ -1,4 +1,4 @@ -<tool id="vcf_intersect" name="Intersect VCF Files" version="1.0.0"> +<tool id="vcf_intersect" name="Intersect" version="1.0.0"><description>Generate the intersection of two VCF files</description><command interpreter="python"> vcfPytools.py 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: Update test-data files for meme 4.6.0
by Bitbucket 25 Feb '11

25 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/e448ba0e8843/ changeset: r5129:e448ba0e8843 user: kanwei date: 2011-02-25 20:58:35 summary: Update test-data files for meme 4.6.0 affected #: 4 files (2.8 KB) --- a/test-data/meme/meme/meme_output_html_1.html Fri Feb 25 13:35:27 2011 -0500 +++ b/test-data/meme/meme/meme_output_html_1.html Fri Feb 25 14:58:35 2011 -0500 @@ -4,6 +4,8 @@ <meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><title>MEME</title><style type="text/css"> + + /* START INCLUDED FILE "meme.css" */ /* The following is the content of meme.css */ body { background-color:white; font-size: 12px; font-family: Verdana, Arial, Helvetica, sans-serif;} @@ -13,6 +15,7 @@ padding: 0px; width: 12px; height: 13px; + cursor: pointer; background-image: url("help.gif"); background-image: url("data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAwAAAANAQMAAACn5x0BAAAAAXNSR0IArs4c6QAAAAZQTFRFAAAAnp6eqp814gAAAAF0Uk5TAEDm2GYAAAABYktHRACIBR1IAAAACXBIWXMAAAsTAAALEwEAmpwYAAAAB3RJTUUH2gMJBQgGYqhNZQAAACZJREFUCNdj+P+BoUGAoV+AYeYEEGoWYGgTYGgRAAm2gRGQ8f8DAOnhC2lYnqs6AAAAAElFTkSuQmCC"); } @@ -123,8 +126,12 @@ padding:0px 10px; } + /* END INCLUDED FILE "meme.css" */ + </style><script type="text/javascript"> + + /* START INCLUDED FILE "motif_logo.js" */ //====================================================================== // start Alphabet object //====================================================================== @@ -337,7 +344,9 @@ //====================================================================== // start Pspm object //====================================================================== - function Pspm(pssm, name) { + function Pspm(pssm, name, ltrim, rtrim) { + if (ltrim === undefined) ltrim = 0; + if (rtrim === undefined) rtrim = 0; //variable prototype this.alph_length = 0; this.motif_length = 0; @@ -345,6 +354,8 @@ this.name = (typeof name == "string" ? name : ""); this.nsites = 0; this.evalue = 0; + this.ltrim = ltrim; + this.rtrim = rtrim; //function prototype this.copy = Pspm_copy; this.reverse_complement = Pspm_reverse_complement; @@ -352,10 +363,11 @@ this.get_stack_ic = Pspm_get_stack_ic; this.get_motif_length = Pspm_get_motif_length; this.get_alph_length = Pspm_get_alph_length; + this.get_left_trim = Pspm_get_left_trim; + this.get_right_trim = Pspm_get_right_trim; this.toString = Pspm_to_string; //construct var pspm_header = /letter-probability matrix:\s+alength=\s+(\d+)\s+w=\s+(\d+)(\s+nsites=\s+(\S+))?(\s+E=\s+(\S+))?\s*/; - var is_prob = /^((1(\.0+)?)|(0(\.\d+)?))$/; var is_empty = /^\s*$/; var lines = pssm.split(/\s*\n\s*/); var read_pssm = false; @@ -392,11 +404,14 @@ if (!parts.hasOwnProperty(part_index) || parts[part_index] === undefined) continue; var prob = parts[part_index]; - if (!is_prob.test(prob)) continue; if (col_num >= this.alph_length) { throw "TOO_MANY_COLS"; } this.pspm[line_num][col_num] = (+prob); + //check the probability is within bounds + if (this.pspm[line_num][col_num] > 1 || this.pspm[line_num][col_num] < 0) { + throw "NUM_NOT_PROB"; + } col_num++; } if (col_num != this.alph_length) { @@ -417,6 +432,11 @@ //so far only a shallow copy, need to copy everything clone.alph_length = (0+this.alph_length); clone.motif_length = (0+this.motif_length); + clone.name = (""+this.name); + clone.nsites = (0+this.nsites); + clone.evalue = (0+this.evalue); + clone.ltrim = (0+this.ltrim); + clone.rtrim = (0+this.rtrim); clone.pspm = new Array(this.motif_length); for (row = 0; row < this.motif_length; row++) { clone.pspm[row] = new Array(this.alph_length); @@ -460,6 +480,10 @@ row[c_index] = row[g_index]; row[g_index] = temp; } + //swap triming + var temp_trim = this.ltrim; + this.ltrim = this.rtrim; + this.rtrim = temp_trim; //note that ambigs are ignored because they don't effect motifs return this; //allow function chaining... } @@ -515,6 +539,14 @@ return this.alph_length; } + function Pspm_get_left_trim() { + return this.ltrim; + } + + function Pspm_get_right_trim() { + return this.rtrim; + } + function Pspm_to_string() { var str = ""; for (row_index in this.pspm) { @@ -1036,6 +1068,62 @@ pos = pos - sym_height; } } + + function draw_dashed_line(ctx, pattern, start, x1, y1, x2, y2) { + var x, y, len, i; + var dx = x2 - x1; + var dy = y2 - y1; + var tlen = Math.pow(dx*dx + dy*dy, 0.5); + var theta = Math.atan2(dy,dx); + var mulx = Math.cos(theta); + var muly = Math.sin(theta); + var lx = []; + var ly = []; + for (i = 0; i < pattern; ++i) { + lx.push(pattern[i] * mulx); + ly.push(pattern[i] * muly); + } + i = start; + x = x1; + y = y1; + len = 0; + ctx.beginPath(); + while (len + pattern[i] < tlen) { + ctx.moveTo(x, y); + x += lx[i]; + y += ly[i]; + ctx.lineTo(x, y); + len += pattern[i]; + i = (i + 1) % pattern.length; + x += lx[i]; + y += ly[i]; + len += pattern[i]; + i = (i + 1) % pattern.length; + } + if (len < tlen) { + ctx.moveTo(x, y); + x += mulx * (tlen - len); + y += muly * (tlen - len); + ctx.lineTo(x, y); + } + ctx.stroke(); + } + + function draw_trim_background(ctx, metrics, pspm, offset) { + var lwidth = metrics.stack_width * pspm.get_left_trim(); + var rwidth = metrics.stack_width * pspm.get_right_trim(); + var mwidth = metrics.stack_width * pspm.get_motif_length(); + var rstart = mwidth - rwidth; + ctx.save();//s8 + ctx.translate(offset * metrics.stack_width, 0); + ctx.fillStyle = "rgb(240, 240, 240)"; + if (pspm.get_left_trim() > 0) ctx.fillRect(0, 0, lwidth, metrics.stack_height); + if (pspm.get_right_trim() > 0) ctx.fillRect(rstart, 0, rwidth, metrics.stack_height); + ctx.fillStyle = "rgb(51, 51, 51)"; + if (pspm.get_left_trim() > 0) draw_dashed_line(ctx, [3], 0, lwidth-0.5, 0, lwidth-0.5, metrics.stack_height); + if (pspm.get_right_trim() > 0) draw_dashed_line(ctx, [3], 0, rstart+0.5, 0, rstart+0.5, metrics.stack_height); + ctx.restore();//s8 + } function draw_logo_on_canvas(logo, canvas, show_names, scale) { var draw_name = (typeof show_names == "boolean" ? show_names : (logo.get_rows() > 1)); @@ -1089,6 +1177,10 @@ //translate across past the scale ctx.translate(metrics.y_label_height + metrics.y_label_spacer + metrics.y_num_width + metrics.y_tic_width, 0); + //draw the trimming background + if (pspm.get_left_trim() > 0 || pspm.get_right_trim() > 0) { + draw_trim_background(ctx, metrics, pspm, offset); + } //draw letters ctx.translate(0, metrics.y_num_height / 2); for (var col_index = 0; col_index < logo.get_columns(); col_index++) { @@ -1211,15 +1303,8 @@ element.parentNode.replaceChild(canvas, element); } - //example code for creating a logo - //function do_load() { - // var alphabet = new Alphabet(document.getElementById("alphabet").value, document.getElementById("bgfreq").value); - // var pspm = new Pspm(document.getElementById("pspm1").value); - // var pspm_rc = pspm.copy().reverse_complement(alphabet); - // draw_logo(pspm, alphabet, "Motif 1", "logo1"); - // draw_logo(pspm_rc, alphabet, "Motif 1 Reverse Complement", "logo_rc1"); - //} - + /* END INCLUDED FILE "motif_logo.js" */ + function setup() { var motif_count = 1; @@ -1377,15 +1462,15 @@ } </script></head> -<body onload="javascript:setup()"><form enctype="application/x-www-form-urlencoded" method="post" target="_new" action="http://dan/meme_request.cgi"> +<body onload="javascript:setup()"><form enctype="application/x-www-form-urlencoded" method="post" target="_new" action="http://straub/meme/cgi-bin/meme_request.cgi"> -<input type="hidden" name="version" value="MEME version 4.5.0"> +<input type="hidden" name="version" value="MEME version 4.6.0"><input type="hidden" name="alphabet" id="alphabet" value="ACDEFGHIKLMNPQRSTVWY"><input type="hidden" name="strands" value="none"><input type="hidden" name="bgfreq" id="bgfreq" value="A 0.291 C 0.229 D 0.001 E 0.001 F 0.001 G 0.255 H 0.001 I 0.001 K 0.001 L 0.001 M 0.001 N 0.001 P 0.001 Q 0.001 R 0.001 S 0.001 T 0.215 V 0.001 W 0.001 Y 0.001"> -<input type="hidden" name="name" value="dan.dat"> +<input type="hidden" name="name" value="dataset_3.dat"><input type="hidden" name="combinedblock" value=" chr21_19617074_19617124_+ 1.22e-03 1 50 1 39 3.06e-05 chr21_26934381_26934431_+ 2.21e-03 1 50 1 27 5.52e-05 @@ -2179,12 +2264,12 @@ </tbody></table></div> -<p>Time 1.6 secs.</p> +<p>Time 2.1 secs.</p></div><div class="bar"><div style="text-align:right;"><a href="#top_buttons">Top</a></div><div class="subsection"> -<a name="version"></a><h5>MEME version</h5>4.5.0 (Release date: Thu Oct 14 08:44:28 EST 2010) +<a name="version"></a><h5>MEME version</h5>4.6.0 (Release date: Thu Jan 20 14:06:48 PST 2011) </div><div class="subsection"><a name="reference"></a><h5>Reference</h5> @@ -2196,7 +2281,7 @@ </div><a name="sequences"></a><a href="javascript:showHidden('trainingseq')" id="trainingseq_activator">show training set...</a><div class="subsection" id="trainingseq_data" style="display:none;"><h5>Training set:</h5> - Datafile = dan.dat<br> + Datafile = dataset_3.dat<br> Alphabet = ACDEFGHIKLMNPQRSTVWY<br><table><col><col> @@ -2387,19 +2472,19 @@ </div><a href="javascript:hideShown('trainingseq')" style="display:none;" id="trainingseq_deactivator">hide training set...</a><div class="subsection"><a name="command"></a><h5>Command line summary</h5> -<textarea rows="1" style="width:100%;" readonly>meme dan.dat -o /dataset_dan_files -nostatus </textarea><br> +<textarea rows="1" style="width:100%;" readonly>meme dataset_3.dat -o dataset_4_files -nostatus </textarea><br> Letter frequencies in dataset<br><div style="margin-left:25px;">A: 0.294 C: 0.231 D: 0.000 E: 0.000 F: 0.000 G: 0.257 H: 0.000 I: 0.000 K: 0.000 L: 0.000 M: 0.000 N: 0.000 P: 0.000 Q: 0.000 R: 0.000 S: 0.000 T: 0.217 V: 0.000 W: 0.000 Y: 0.000</div><br> Background letter frequencies (from dataset with add-one prior applied):<br><div style="margin-left:25px;">A: 0.291 C: 0.229 D: 0.001 E: 0.001 F: 0.001 G: 0.255 H: 0.001 I: 0.001 K: 0.001 L: 0.001 M: 0.001 N: 0.001 P: 0.001 Q: 0.001 R: 0.001 S: 0.001 T: 0.215 V: 0.001 W: 0.001 Y: 0.001</div><br></div><div class="subsection"> -<a name="stopped"></a><h5>Stopping Reason</h5>Stopped because nmotifs = 1 reached. Program ran on <i>dan</i>. +<a name="stopped"></a><h5>Stopping Reason</h5>Stopped because nmotifs = 1 reached. Program ran on <i>scofield</i>. </div><a href="javascript:showHidden('model')" id="model_activator">show model parameters...</a><div class="subsection" id="model_data" style="display:none;"><h5>Model parameters</h5><textarea style="width:100%;" rows="28" readonly> -host = dan +host = scofield type = zoops nmotifs = 1 evalue_threshold = inf --- a/test-data/meme/meme/meme_output_txt_1.txt Fri Feb 25 13:35:27 2011 -0500 +++ b/test-data/meme/meme/meme_output_txt_1.txt Fri Feb 25 14:58:35 2011 -0500 @@ -1,7 +1,7 @@ ******************************************************************************** MEME - Motif discovery tool ******************************************************************************** -MEME version 4.5.0 (Release date: Thu Oct 14 08:44:28 EST 2010) +MEME version 4.6.0 (Release date: Thu Jan 20 14:06:48 PST 2011) For further information on how to interpret these results or to get a copy of the MEME software please access http://meme.nbcr.net. @@ -28,7 +28,7 @@ ******************************************************************************** TRAINING SET ******************************************************************************** -DATAFILE= dan.dat +DATAFILE= dataset_3.dat ALPHABET= ACDEFGHIKLMNPQRSTVWY Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ @@ -55,7 +55,7 @@ This information can also be useful in the event you wish to report a problem with the MEME software. -command: meme dan.dat -o dan/dataset_dan_files -nostatus +command: meme dataset_3.dat -o dataset_4_files -nostatus model: mod= zoops nmotifs= 1 evt= inf object function= E-value of product of p-values @@ -267,7 +267,7 @@ -Time 1.56 secs. +Time 2.13 secs. ******************************************************************************** @@ -320,6 +320,6 @@ Stopped because nmotifs = 1 reached. ******************************************************************************** -CPU: dan +CPU: scofield ******************************************************************************** --- a/test-data/meme/meme/meme_output_xml_1.xml Fri Feb 25 13:35:27 2011 -0500 +++ b/test-data/meme/meme/meme_output_xml_1.xml Fri Feb 25 14:58:35 2011 -0500 @@ -157,8 +157,8 @@ ]> -<MEME version="4.5.0" release="Thu Oct 14 08:44:28 EST 2010"> -<training_set datafile="/dan_110.dat" length="30"> +<MEME version="4.6.0" release="Thu Jan 20 14:06:48 PST 2011"> +<training_set datafile="dataset_3.dat" length="30"><alphabet id="amino-acid" length="20"><letter id="letter_A" symbol="A"/><letter id="letter_C" symbol="C"/> @@ -183,6 +183,8 @@ </alphabet><ambigs><letter id="letter_B" symbol="B"/> +<letter id="letter_J" symbol="J"/> +<letter id="letter_O" symbol="O"/><letter id="letter_U" symbol="U"/><letter id="letter_X" symbol="X"/><letter id="letter_Z" symbol="Z"/> @@ -245,8 +247,8 @@ </letter_frequencies></training_set><model> -<command_line>meme /dan.dat -o /dataset_dan_files -nostatus </command_line> -<host>dan</host> +<command_line>meme dataset_3.dat -o dataset_4_files -nostatus </command_line> +<host>scofield</host><type>zoops</type><nmotifs>1</nmotifs><evalue_threshold>inf</evalue_threshold> @@ -300,7 +302,7 @@ </background_frequencies></model><motifs> -<motif id="motif_1" name="1" width="11" sites="25" ic="40.0" re="13.8" llr="239" e_value="2.4e-011" bayes_threshold="5.33554" elapsed_time="1.563760"> +<motif id="motif_1" name="1" width="11" sites="25" ic="40.0" re="13.8" llr="239" e_value="2.4e-011" bayes_threshold="5.33554" elapsed_time="2.128133"><scores><alphabet_matrix><alphabet_array> --- a/tools/meme/meme.xml Fri Feb 25 13:35:27 2011 -0500 +++ b/tools/meme/meme.xml Fri Feb 25 14:58:35 2011 -0500 @@ -319,7 +319,7 @@ <param name="input1" value="meme_input_1.fasta" ftype="fasta" dbkey="hg19"/><param name="options_type_selector" value="basic"/><param name="non_commercial_use" value="True"/> - <output name="html_outfile" file="meme/meme/meme_output_html_1.html" lines_diff="14"/> + <output name="html_outfile" file="meme/meme/meme_output_html_1.html" lines_diff="12"/><output name="txt_outfile" file="meme/meme/meme_output_txt_1.txt" lines_diff="12"/><output name="xml_outfile" file="meme/meme/meme_output_xml_1.xml" lines_diff="8"/></test> 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: Typos
by Bitbucket 25 Feb '11

25 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/5215215c3659/ changeset: r5128:5215215c3659 user: kanwei date: 2011-02-25 19:35:27 summary: Typos affected #: 4 files (21 bytes) --- a/tools/filters/fileGrep.xml Thu Feb 24 19:07:41 2011 -0500 +++ b/tools/filters/fileGrep.xml Fri Feb 25 13:35:27 2011 -0500 @@ -1,19 +1,19 @@ -<tool id="fileGrep1" name="Match"> - <description>a column from one Query against another Query</description> - <command>cut -f $col $input1 | grep -f - $match $input2 > $out_file1</command> - <inputs> - <param name="col" size="2" type="text" value="1" label="Match content of column"/> - <param format="tabular" name="input1" type="data" label="From Query1"/> +<tool id="fileGrep1" name="Match"> + <description>a column from one Query against another Query</description> + <command>cut -f $col $input1 | grep -f - $match $input2 > $out_file1</command> + <inputs> + <param name="col" size="2" type="text" value="1" label="Match content of column"/> + <param format="tabular" name="input1" type="data" label="From Query1"/><param format="tabular" name="input2" type="data" label="Against Query2"/> - <param name="match" type="select" label="and return rows that"> - <option value="">Match</option> - <option value="-v">Do not match</option> - </param> - </inputs> - <outputs> + <param name="match" type="select" label="and return rows that"> + <option value="">Match</option> + <option value="-v">Do not match</option> + </param> + </inputs> + <outputs><data format="input" name="out_file1" metadata_source="input2" /> - </outputs> - <help> + </outputs> + <help> This tool is based on UNIX command grep with option -f. It matches content of one query against another. For example, assume you have two queries - one that contains EST accession numbers and some other information:: AA001229 12 12 @@ -32,11 +32,11 @@ chr7 115443243 115443347 DB331869_exon_0_0_chr7_115443244_f 0 + chr7 115443347 115443373 DB331869_exon_1_0_chr7_115443348_f 0 + -Using this tool you will bne able to tell how many ESTs in Query1 are also preset in Query2 and will output this:: +Using this tool you will be able to tell how many ESTs in Query1 are also preset in Query2 and will output this:: chr7 115443239 115443802 AA001842_exon_0_0_chr7_115443240_f 0 if **Match** option is chosen. -</help> +</help></tool> \ No newline at end of file --- a/tools/ngs_rna/cuffdiff_wrapper.xml Thu Feb 24 19:07:41 2011 -0500 +++ b/tools/ngs_rna/cuffdiff_wrapper.xml Fri Feb 25 13:35:27 2011 -0500 @@ -209,7 +209,7 @@ 1. Transcript FPKM expression tracking. 2. Gene FPKM expression tracking; tracks the summed FPKM of transcripts sharing each gene_id 3. Primary transcript FPKM tracking; tracks the summed FPKM of transcripts sharing each tss_id -4. Coding sequence FPKM tracking; tracks the summed FPKM of transcripts sharing each p_id, indepedent of tss_id +4. Coding sequence FPKM tracking; tracks the summed FPKM of transcripts sharing each p_id, independent of tss_id 5. Transcript differential FPKM. 6. Gene differential FPKM. Tests difference sin the summed FPKM of transcripts sharing each gene_id 7. Primary transcript differential FPKM. Tests difference sin the summed FPKM of transcripts sharing each tss_id @@ -233,7 +233,7 @@ -m INT This is the expected (mean) inner distance between mate pairs. For, example, for paired end runs with fragments selected at 300bp, where each end is 50bp, you should set -r to be 200. The default is 45bp. -s INT The standard deviation for the distribution on inner distances between mate pairs. The default is 20bp. -Q Instructs Cufflinks to ignore alignments with a SAM mapping quality lower than this number. The default is 0. - -c INT The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples. If no testing is performed, changes in the locus are deemed not signficant, and the locus' observed changes don't contribute to correction for multiple testing. The default is 1,000 fragment alignments (up to 2,000 paired reads). + -c INT The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples. If no testing is performed, changes in the locus are deemed not significant, and the locus' observed changes don't contribute to correction for multiple testing. The default is 1,000 fragment alignments (up to 2,000 paired reads). --FDR FLOAT The allowed false discovery rate. The default is 0.05. --num-importance-samples INT Sets the number of importance samples generated for each locus during abundance estimation. Default: 1000 --max-mle-iterations INT Sets the number of iterations allowed during maximum likelihood estimation of abundances. Default: 5000 --- a/tools/ngs_rna/tophat_wrapper.xml Thu Feb 24 19:07:41 2011 -0500 +++ b/tools/ngs_rna/tophat_wrapper.xml Fri Feb 25 13:35:27 2011 -0500 @@ -25,7 +25,7 @@ ## First input file always required. --input1=$singlePaired.input1 - ## Set parms based on whether reads are single-end or paired. + ## Set params based on whether reads are single-end or paired. #if $singlePaired.sPaired == "single": --settings=$singlePaired.sParams.sSettingsType #if $singlePaired.sParams.sSettingsType == "full": @@ -171,7 +171,7 @@ <option value="full">Full parameter list</option></param><when value="preSet" /> -  + <when value="full"><param name="library_type" type="select" label="Library Type" help="TopHat will treat the reads as strand specific. Every read alignment will have an XS attribute tag. Consider supplying library type options below to select the correct RNA-seq protocol."><option value="fr-unstranded">FR Unstranded</option> @@ -277,7 +277,7 @@ <option value="full">Full parameter list</option></param><when value="preSet" /> -  + <when value="full"><param name="library_type" type="select" label="Library Type" help="TopHat will treat the reads as strand specific. Every read alignment will have an XS attribute tag. Consider supplying library type options below to select the correct RNA-seq protocol."><option value="fr-unstranded">FR Unstranded</option> @@ -435,7 +435,7 @@ <test><param name="genomeSource" value="history"/> --- a/tools/sr_mapping/lastz_wrapper.xml Thu Feb 24 19:07:41 2011 -0500 +++ b/tools/sr_mapping/lastz_wrapper.xml Fri Feb 25 13:35:27 2011 -0500 @@ -504,7 +504,7 @@ up 65 thousand --census32[=<output_file>] count and report how many times each target bas aligns, up to 4 billion - --writecapsule=<capsule_file> just write out a targegt capsule file and quit; don't + --writecapsule=<capsule_file> just write out a target capsule file and quit; don't search for seeds or perform subsequent stages --verbosity=<level> set info level (0 is minimum, 10 is everything) (default is 0) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: kanwei: Only lowercase columns if starting with "c".. fixes issue where "None" was lowercased to "none". Fixes subtract_query tests
by Bitbucket 24 Feb '11

24 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/88a118487292/ changeset: r5127:88a118487292 user: kanwei date: 2011-02-25 01:07:41 summary: Only lowercase columns if starting with "c".. fixes issue where "None" was lowercased to "none". Fixes subtract_query tests affected #: 1 file (28 bytes) --- a/lib/galaxy/tools/parameters/basic.py Thu Feb 24 18:21:46 2011 -0500 +++ b/lib/galaxy/tools/parameters/basic.py Thu Feb 24 19:07:41 2011 -0500 @@ -845,9 +845,8 @@ removes the 'c' when entered into a workflow. """ def _strip_c( column ): - column = column.strip().lower() if column.startswith( 'c' ): - column = column[1:] + column = column.strip().lower()[1:] return column if self.multiple: #split on newline and , 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: dannon: workflows: Will never collapse steps containing workflow parameters by default now.
by Bitbucket 24 Feb '11

24 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/6e72905f5119/ changeset: r5126:6e72905f5119 user: dannon date: 2011-02-25 00:21:46 summary: workflows: Will never collapse steps containing workflow parameters by default now. affected #: 1 file (10 bytes) --- a/templates/workflow/run.mako Thu Feb 24 18:08:15 2011 -0500 +++ b/templates/workflow/run.mako Thu Feb 24 18:21:46 2011 -0500 @@ -27,7 +27,7 @@ toggle_tool_body($(this)); }); // Collapse non-interactive run-workflow panels by default. - $("div.toolFormBody:not(:has(select, textarea, input[type!=hidden]))").hide().parent().css('border-bottom-width', '0px'); + $("div.toolFormBody:not(:has(select, textarea, input[type!=hidden], .wfpspan))").hide().parent().css('border-bottom-width', '0px'); $("#show_all_tool_body").click(function(){ $("div.toolFormTitle").each(function(){ show_tool_body($(this)); 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: dannon: workflows: Fix parameter replacement in long inputs where the parameter isn't the whole value.
by Bitbucket 24 Feb '11

24 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/5e552f7d9a17/ changeset: r5125:5e552f7d9a17 user: dannon date: 2011-02-25 00:08:15 summary: workflows: Fix parameter replacement in long inputs where the parameter isn't the whole value. affected #: 1 file (11 bytes) --- a/templates/workflow/run.mako Thu Feb 24 17:23:16 2011 -0500 +++ b/templates/workflow/run.mako Thu Feb 24 18:08:15 2011 -0500 @@ -126,7 +126,7 @@ <div class="form-title-row"><b>${input.title} ${i + 1}</b></div> ${do_inputs( input.inputs, repeat_values[ i ], rep_errors, prefix + input.name + "_" + str(index) + "|", step, other_values )} ## <div class="form-row"><input type="submit" name="${step.id}|${prefix}${input.name}_${i}_remove" value="Remove ${input.title} ${i+1}" /></div> - </div> + </div> %endfor ## <div class="form-row"><input type="submit" name="${step.id}|${prefix}${input.name}_add" value="Add new ${input.title}" /></div></div> @@ -209,7 +209,7 @@ <div style="width: 300px;"><img style="vertical-align: middle;" src="${h.url_for('/static/style/error_small.png')}"> <span style="vertical-align: middle;">${error_dict[param.name]}</span></div></div> %endif - <div style="clear: both"></div> + <div style="clear: both"></div></div></%def> @@ -262,7 +262,7 @@ $('.wfpspan.wf_parm__'+tag_id).text(new_text); // Now set the hidden input to the generated text. $('.wfpspan.wf_parm__'+tag_id).not('.pja_wfp').each(function(){ - // var new_text = $(this).parent().text(); + var new_text = $(this).parent().text(); $(this).parent().siblings().children().val(new_text); }); } 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: Update jQuery to 1.5.1, and also jquery.form as old one was incompatible with 1.5
by Bitbucket 24 Feb '11

24 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/632a7a0f3caa/ changeset: r5124:632a7a0f3caa user: kanwei date: 2011-02-24 23:23:16 summary: Update jQuery to 1.5.1, and also jquery.form as old one was incompatible with 1.5 affected #: 4 files (7.5 KB) --- a/static/scripts/jquery.form.js Thu Feb 24 16:19:03 2011 -0500 +++ b/static/scripts/jquery.form.js Thu Feb 24 17:23:16 2011 -0500 @@ -1,632 +1,803 @@ -/* - * jQuery Form Plugin - * version: 2.21 (08-FEB-2009) - * @requires jQuery v1.2.2 or later - * - * Examples and documentation at: http://malsup.com/jquery/form/ - * Dual licensed under the MIT and GPL licenses: - * http://www.opensource.org/licenses/mit-license.php - * http://www.gnu.org/licenses/gpl.html - */ -;(function($) { - -/* - Usage Note: - ----------- - Do not use both ajaxSubmit and ajaxForm on the same form. These - functions are intended to be exclusive. Use ajaxSubmit if you want - to bind your own submit handler to the form. For example, - - $(document).ready(function() { - $('#myForm').bind('submit', function() { - $(this).ajaxSubmit({ - target: '#output' - }); - return false; // <-- important! - }); - }); - - Use ajaxForm when you want the plugin to manage all the event binding - for you. For example, - - $(document).ready(function() { - $('#myForm').ajaxForm({ - target: '#output' - }); - }); - - When using ajaxForm, the ajaxSubmit function will be invoked for you - at the appropriate time. -*/ - -/** - * ajaxSubmit() provides a mechanism for immediately submitting - * an HTML form using AJAX. - */ -$.fn.ajaxSubmit = function(options) { - // fast fail if nothing selected (http://dev.jquery.com/ticket/2752) - if (!this.length) { - log('ajaxSubmit: skipping submit process - no element selected'); - return this; - } - - if (typeof options == 'function') - options = { success: options }; - - options = $.extend({ - url: this.attr('action') || window.location.toString(), - type: this.attr('method') || 'GET' - }, options || {}); - - // hook for manipulating the form data before it is extracted; - // convenient for use with rich editors like tinyMCE or FCKEditor - var veto = {}; - this.trigger('form-pre-serialize', [this, options, veto]); - if (veto.veto) { - log('ajaxSubmit: submit vetoed via form-pre-serialize trigger'); - return this; - } - - // provide opportunity to alter form data before it is serialized - if (options.beforeSerialize && options.beforeSerialize(this, options) === false) { - log('ajaxSubmit: submit aborted via beforeSerialize callback'); - return this; - } - - var a = this.formToArray(options.semantic); - if (options.data) { - options.extraData = options.data; - for (var n in options.data) { - if(options.data[n] instanceof Array) { - for (var k in options.data[n]) - a.push( { name: n, value: options.data[n][k] } ) - } - else - a.push( { name: n, value: options.data[n] } ); - } - } - - // give pre-submit callback an opportunity to abort the submit - if (options.beforeSubmit && options.beforeSubmit(a, this, options) === false) { - log('ajaxSubmit: submit aborted via beforeSubmit callback'); - return this; - } - - // fire vetoable 'validate' event - this.trigger('form-submit-validate', [a, this, options, veto]); - if (veto.veto) { - log('ajaxSubmit: submit vetoed via form-submit-validate trigger'); - return this; - } - - var q = $.param(a); - - if (options.type.toUpperCase() == 'GET') { - options.url += (options.url.indexOf('?') >= 0 ? '&' : '?') + q; - options.data = null; // data is null for 'get' - } - else - options.data = q; // data is the query string for 'post' - - var $form = this, callbacks = []; - if (options.resetForm) callbacks.push(function() { $form.resetForm(); }); - if (options.clearForm) callbacks.push(function() { $form.clearForm(); }); - - // perform a load on the target only if dataType is not provided - if (!options.dataType && options.target) { - var oldSuccess = options.success || function(){}; - callbacks.push(function(data) { - $(options.target).html(data).each(oldSuccess, arguments); - }); - } - else if (options.success) - callbacks.push(options.success); - - options.success = function(data, status) { - for (var i=0, max=callbacks.length; i < max; i++) - callbacks[i].apply(options, [data, status, $form]); - }; - - // are there files to upload? - var files = $('input:file', this).fieldValue(); - var found = false; - for (var j=0; j < files.length; j++) - if (files[j]) - found = true; - - // options.iframe allows user to force iframe mode - if (options.iframe || found) { - // hack to fix Safari hang (thanks to Tim Molendijk for this) - // see: http://groups.google.com/group/jquery-dev/browse_thread/thread/36395b7ab510… - if (options.closeKeepAlive) - $.get(options.closeKeepAlive, fileUpload); - else - fileUpload(); - } - else - $.ajax(options); - - // fire 'notify' event - this.trigger('form-submit-notify', [this, options]); - return this; - - - // private function for handling file uploads (hat tip to YAHOO!) - function fileUpload() { - var form = $form[0]; - - if ($(':input[name=submit]', form).length) { - alert('Error: Form elements must not be named "submit".'); - return; - } - - var opts = $.extend({}, $.ajaxSettings, options); - var s = jQuery.extend(true, {}, $.extend(true, {}, $.ajaxSettings), opts); - - var id = 'jqFormIO' + (new Date().getTime()); - var $io = $('<iframe id="' + id + '" name="' + id + '" src="about:blank" />'); - var io = $io[0]; - - $io.css({ position: 'absolute', top: '-1000px', left: '-1000px' }); - - var xhr = { // mock object - aborted: 0, - responseText: null, - responseXML: null, - status: 0, - statusText: 'n/a', - getAllResponseHeaders: function() {}, - getResponseHeader: function() {}, - setRequestHeader: function() {}, - abort: function() { - this.aborted = 1; - $io.attr('src','about:blank'); // abort op in progress - } - }; - - var g = opts.global; - // trigger ajax global events so that activity/block indicators work like normal - if (g && ! $.active++) $.event.trigger("ajaxStart"); - if (g) $.event.trigger("ajaxSend", [xhr, opts]); - - if (s.beforeSend && s.beforeSend(xhr, s) === false) { - s.global && jQuery.active--; - return; - } - if (xhr.aborted) - return; - - var cbInvoked = 0; - var timedOut = 0; - - // add submitting element to data if we know it - var sub = form.clk; - if (sub) { - var n = sub.name; - if (n && !sub.disabled) { - options.extraData = options.extraData || {}; - options.extraData[n] = sub.value; - if (sub.type == "image") { - options.extraData[name+'.x'] = form.clk_x; - options.extraData[name+'.y'] = form.clk_y; - } - } - } - - // take a breath so that pending repaints get some cpu time before the upload starts - setTimeout(function() { - // make sure form attrs are set - var t = $form.attr('target'), a = $form.attr('action'); - - // update form attrs in IE friendly way - form.setAttribute('target',id); - if (form.getAttribute('method') != 'POST') - form.setAttribute('method', 'POST'); - if (form.getAttribute('action') != opts.url) - form.setAttribute('action', opts.url); - - // ie borks in some cases when setting encoding - if (! options.skipEncodingOverride) { - $form.attr({ - encoding: 'multipart/form-data', - enctype: 'multipart/form-data' - }); - } - - // support timout - if (opts.timeout) - setTimeout(function() { timedOut = true; cb(); }, opts.timeout); - - // add "extra" data to form if provided in options - var extraInputs = []; - try { - if (options.extraData) - for (var n in options.extraData) - extraInputs.push( - $('<input type="hidden" name="'+n+'" value="'+options.extraData[n]+'" />') - .appendTo(form)[0]); - - // add iframe to doc and submit the form - $io.appendTo('body'); - io.attachEvent ? io.attachEvent('onload', cb) : io.addEventListener('load', cb, false); - form.submit(); - } - finally { - // reset attrs and remove "extra" input elements - form.setAttribute('action',a); - t ? form.setAttribute('target', t) : $form.removeAttr('target'); - $(extraInputs).remove(); - } - }, 10); - - var nullCheckFlag = 0; - - function cb() { - if (cbInvoked++) return; - - io.detachEvent ? io.detachEvent('onload', cb) : io.removeEventListener('load', cb, false); - - var ok = true; - try { - if (timedOut) throw 'timeout'; - // extract the server response from the iframe - var data, doc; - - doc = io.contentWindow ? io.contentWindow.document : io.contentDocument ? io.contentDocument : io.document; - - if ((doc.body == null || doc.body.innerHTML == '') && !nullCheckFlag) { - // in some browsers (cough, Opera 9.2.x) the iframe DOM is not always traversable when - // the onload callback fires, so we give them a 2nd chance - nullCheckFlag = 1; - cbInvoked--; - setTimeout(cb, 100); - return; - } - - xhr.responseText = doc.body ? doc.body.innerHTML : null; - xhr.responseXML = doc.XMLDocument ? doc.XMLDocument : doc; - xhr.getResponseHeader = function(header){ - var headers = {'content-type': opts.dataType}; - return headers[header]; - }; - - if (opts.dataType == 'json' || opts.dataType == 'script') { - var ta = doc.getElementsByTagName('textarea')[0]; - xhr.responseText = ta ? ta.value : xhr.responseText; - } - else if (opts.dataType == 'xml' && !xhr.responseXML && xhr.responseText != null) { - xhr.responseXML = toXml(xhr.responseText); - } - data = $.httpData(xhr, opts.dataType); - } - catch(e){ - ok = false; - $.handleError(opts, xhr, 'error', e); - } - - // ordering of these callbacks/triggers is odd, but that's how $.ajax does it - if (ok) { - opts.success(data, 'success'); - if (g) $.event.trigger("ajaxSuccess", [xhr, opts]); - } - if (g) $.event.trigger("ajaxComplete", [xhr, opts]); - if (g && ! --$.active) $.event.trigger("ajaxStop"); - if (opts.complete) opts.complete(xhr, ok ? 'success' : 'error'); - - // clean up - setTimeout(function() { - $io.remove(); - xhr.responseXML = null; - }, 100); - }; - - function toXml(s, doc) { - if (window.ActiveXObject) { - doc = new ActiveXObject('Microsoft.XMLDOM'); - doc.async = 'false'; - doc.loadXML(s); - } - else - doc = (new DOMParser()).parseFromString(s, 'text/xml'); - return (doc && doc.documentElement && doc.documentElement.tagName != 'parsererror') ? doc : null; - }; - }; -}; - -/** - * ajaxForm() provides a mechanism for fully automating form submission. - * - * The advantages of using this method instead of ajaxSubmit() are: - * - * 1: This method will include coordinates for <input type="image" /> elements (if the element - * is used to submit the form). - * 2. This method will include the submit element's name/value data (for the element that was - * used to submit the form). - * 3. This method binds the submit() method to the form for you. - * - * The options argument for ajaxForm works exactly as it does for ajaxSubmit. ajaxForm merely - * passes the options argument along after properly binding events for submit elements and - * the form itself. - */ -$.fn.ajaxForm = function(options) { - return this.ajaxFormUnbind().bind('submit.form-plugin',function() { - $(this).ajaxSubmit(options); - return false; - }).each(function() { - // store options in hash - $(":submit,input:image", this).bind('click.form-plugin',function(e) { - var form = this.form; - form.clk = this; - if (this.type == 'image') { - if (e.offsetX != undefined) { - form.clk_x = e.offsetX; - form.clk_y = e.offsetY; - } else if (typeof $.fn.offset == 'function') { // try to use dimensions plugin - var offset = $(this).offset(); - form.clk_x = e.pageX - offset.left; - form.clk_y = e.pageY - offset.top; - } else { - form.clk_x = e.pageX - this.offsetLeft; - form.clk_y = e.pageY - this.offsetTop; - } - } - // clear form vars - setTimeout(function() { form.clk = form.clk_x = form.clk_y = null; }, 10); - }); - }); -}; - -// ajaxFormUnbind unbinds the event handlers that were bound by ajaxForm -$.fn.ajaxFormUnbind = function() { - this.unbind('submit.form-plugin'); - return this.each(function() { - $(":submit,input:image", this).unbind('click.form-plugin'); - }); - -}; - -/** - * formToArray() gathers form element data into an array of objects that can - * be passed to any of the following ajax functions: $.get, $.post, or load. - * Each object in the array has both a 'name' and 'value' property. An example of - * an array for a simple login form might be: - * - * [ { name: 'username', value: 'jresig' }, { name: 'password', value: 'secret' } ] - * - * It is this array that is passed to pre-submit callback functions provided to the - * ajaxSubmit() and ajaxForm() methods. - */ -$.fn.formToArray = function(semantic) { - var a = []; - if (this.length == 0) return a; - - var form = this[0]; - var els = semantic ? form.getElementsByTagName('*') : form.elements; - if (!els) return a; - for(var i=0, max=els.length; i < max; i++) { - var el = els[i]; - var n = el.name; - if (!n) continue; - - if (semantic && form.clk && el.type == "image") { - // handle image inputs on the fly when semantic == true - if(!el.disabled && form.clk == el) - a.push({name: n+'.x', value: form.clk_x}, {name: n+'.y', value: form.clk_y}); - continue; - } - - var v = $.fieldValue(el, true); - if (v && v.constructor == Array) { - for(var j=0, jmax=v.length; j < jmax; j++) - a.push({name: n, value: v[j]}); - } - else if (v !== null && typeof v != 'undefined') - a.push({name: n, value: v}); - } - - if (!semantic && form.clk) { - // input type=='image' are not found in elements array! handle them here - var inputs = form.getElementsByTagName("input"); - for(var i=0, max=inputs.length; i < max; i++) { - var input = inputs[i]; - var n = input.name; - if(n && !input.disabled && input.type == "image" && form.clk == input) - a.push({name: n+'.x', value: form.clk_x}, {name: n+'.y', value: form.clk_y}); - } - } - return a; -}; - -/** - * Serializes form data into a 'submittable' string. This method will return a string - * in the format: name1=value1&name2=value2 - */ -$.fn.formSerialize = function(semantic) { - //hand off to jQuery.param for proper encoding - return $.param(this.formToArray(semantic)); -}; - -/** - * Serializes all field elements in the jQuery object into a query string. - * This method will return a string in the format: name1=value1&name2=value2 - */ -$.fn.fieldSerialize = function(successful) { - var a = []; - this.each(function() { - var n = this.name; - if (!n) return; - var v = $.fieldValue(this, successful); - if (v && v.constructor == Array) { - for (var i=0,max=v.length; i < max; i++) - a.push({name: n, value: v[i]}); - } - else if (v !== null && typeof v != 'undefined') - a.push({name: this.name, value: v}); - }); - //hand off to jQuery.param for proper encoding - return $.param(a); -}; - -/** - * Returns the value(s) of the element in the matched set. For example, consider the following form: - * - * <form><fieldset> - * <input name="A" type="text" /> - * <input name="A" type="text" /> - * <input name="B" type="checkbox" value="B1" /> - * <input name="B" type="checkbox" value="B2"/> - * <input name="C" type="radio" value="C1" /> - * <input name="C" type="radio" value="C2" /> - * </fieldset></form> - * - * var v = $(':text').fieldValue(); - * // if no values are entered into the text inputs - * v == ['',''] - * // if values entered into the text inputs are 'foo' and 'bar' - * v == ['foo','bar'] - * - * var v = $(':checkbox').fieldValue(); - * // if neither checkbox is checked - * v === undefined - * // if both checkboxes are checked - * v == ['B1', 'B2'] - * - * var v = $(':radio').fieldValue(); - * // if neither radio is checked - * v === undefined - * // if first radio is checked - * v == ['C1'] - * - * The successful argument controls whether or not the field element must be 'successful' - * (per http://www.w3.org/TR/html4/interact/forms.html#successful-controls) - * The default value of the successful argument is true. If this value is false the value(s) - * for each element is returned. - * - * Note: This method *always* returns an array. If no valid value can be determined the - * array will be empty, otherwise it will contain one or more values. - */ -$.fn.fieldValue = function(successful) { - for (var val=[], i=0, max=this.length; i < max; i++) { - var el = this[i]; - var v = $.fieldValue(el, successful); - if (v === null || typeof v == 'undefined' || (v.constructor == Array && !v.length)) - continue; - v.constructor == Array ? $.merge(val, v) : val.push(v); - } - return val; -}; - -/** - * Returns the value of the field element. - */ -$.fieldValue = function(el, successful) { - var n = el.name, t = el.type, tag = el.tagName.toLowerCase(); - if (typeof successful == 'undefined') successful = true; - - if (successful && (!n || el.disabled || t == 'reset' || t == 'button' || - (t == 'checkbox' || t == 'radio') && !el.checked || - (t == 'submit' || t == 'image') && el.form && el.form.clk != el || - tag == 'select' && el.selectedIndex == -1)) - return null; - - if (tag == 'select') { - var index = el.selectedIndex; - if (index < 0) return null; - var a = [], ops = el.options; - var one = (t == 'select-one'); - var max = (one ? index+1 : ops.length); - for(var i=(one ? index : 0); i < max; i++) { - var op = ops[i]; - if (op.selected) { - var v = op.value; - if (!v) // extra pain for IE... - v = (op.attributes && op.attributes['value'] && !(op.attributes['value'].specified)) ? op.text : op.value; - if (one) return v; - a.push(v); - } - } - return a; - } - return el.value; -}; - -/** - * Clears the form data. Takes the following actions on the form's input fields: - * - input text fields will have their 'value' property set to the empty string - * - select elements will have their 'selectedIndex' property set to -1 - * - checkbox and radio inputs will have their 'checked' property set to false - * - inputs of type submit, button, reset, and hidden will *not* be effected - * - button elements will *not* be effected - */ -$.fn.clearForm = function() { - return this.each(function() { - $('input,select,textarea', this).clearFields(); - }); -}; - -/** - * Clears the selected form elements. - */ -$.fn.clearFields = $.fn.clearInputs = function() { - return this.each(function() { - var t = this.type, tag = this.tagName.toLowerCase(); - if (t == 'text' || t == 'password' || tag == 'textarea') - this.value = ''; - else if (t == 'checkbox' || t == 'radio') - this.checked = false; - else if (tag == 'select') - this.selectedIndex = -1; - }); -}; - -/** - * Resets the form data. Causes all form elements to be reset to their original value. - */ -$.fn.resetForm = function() { - return this.each(function() { - // guard against an input with the name of 'reset' - // note that IE reports the reset function as an 'object' - if (typeof this.reset == 'function' || (typeof this.reset == 'object' && !this.reset.nodeType)) - this.reset(); - }); -}; - -/** - * Enables or disables any matching elements. - */ -$.fn.enable = function(b) { - if (b == undefined) b = true; - return this.each(function() { - this.disabled = !b - }); -}; - -/** - * Checks/unchecks any matching checkboxes or radio buttons and - * selects/deselects and matching option elements. - */ -$.fn.selected = function(select) { - if (select == undefined) select = true; - return this.each(function() { - var t = this.type; - if (t == 'checkbox' || t == 'radio') - this.checked = select; - else if (this.tagName.toLowerCase() == 'option') { - var $sel = $(this).parent('select'); - if (select && $sel[0] && $sel[0].type == 'select-one') { - // deselect all other options - $sel.find('option').selected(false); - } - this.selected = select; - } - }); -}; - -// helper fn for console logging -// set $.fn.ajaxSubmit.debug to true to enable debug logging -function log() { - if ($.fn.ajaxSubmit.debug && window.console && window.console.log) - window.console.log('[jquery.form] ' + Array.prototype.join.call(arguments,'')); -}; - -})(jQuery); +/*! + * jQuery Form Plugin + * version: 2.63 (29-JAN-2011) + * @requires jQuery v1.3.2 or later + * + * Examples and documentation at: http://malsup.com/jquery/form/ + * Dual licensed under the MIT and GPL licenses: + * http://www.opensource.org/licenses/mit-license.php + * http://www.gnu.org/licenses/gpl.html + */ +;(function($) { + +/* + Usage Note: + ----------- + Do not use both ajaxSubmit and ajaxForm on the same form. These + functions are intended to be exclusive. Use ajaxSubmit if you want + to bind your own submit handler to the form. For example, + + $(document).ready(function() { + $('#myForm').bind('submit', function(e) { + e.preventDefault(); // <-- important + $(this).ajaxSubmit({ + target: '#output' + }); + }); + }); + + Use ajaxForm when you want the plugin to manage all the event binding + for you. For example, + + $(document).ready(function() { + $('#myForm').ajaxForm({ + target: '#output' + }); + }); + + When using ajaxForm, the ajaxSubmit function will be invoked for you + at the appropriate time. +*/ + +/** + * ajaxSubmit() provides a mechanism for immediately submitting + * an HTML form using AJAX. + */ +$.fn.ajaxSubmit = function(options) { + // fast fail if nothing selected (http://dev.jquery.com/ticket/2752) + if (!this.length) { + log('ajaxSubmit: skipping submit process - no element selected'); + return this; + } + + if (typeof options == 'function') { + options = { success: options }; + } + + var action = this.attr('action'); + var url = (typeof action === 'string') ? $.trim(action) : ''; + if (url) { + // clean url (don't include hash vaue) + url = (url.match(/^([^#]+)/)||[])[1]; + } + url = url || window.location.href || ''; + + options = $.extend(true, { + url: url, + type: this[0].getAttribute('method') || 'GET', // IE7 massage (see issue 57) + iframeSrc: /^https/i.test(window.location.href || '') ? 'javascript:false' : 'about:blank' + }, options); + + // hook for manipulating the form data before it is extracted; + // convenient for use with rich editors like tinyMCE or FCKEditor + var veto = {}; + this.trigger('form-pre-serialize', [this, options, veto]); + if (veto.veto) { + log('ajaxSubmit: submit vetoed via form-pre-serialize trigger'); + return this; + } + + // provide opportunity to alter form data before it is serialized + if (options.beforeSerialize && options.beforeSerialize(this, options) === false) { + log('ajaxSubmit: submit aborted via beforeSerialize callback'); + return this; + } + + var n,v,a = this.formToArray(options.semantic); + if (options.data) { + options.extraData = options.data; + for (n in options.data) { + if(options.data[n] instanceof Array) { + for (var k in options.data[n]) { + a.push( { name: n, value: options.data[n][k] } ); + } + } + else { + v = options.data[n]; + v = $.isFunction(v) ? v() : v; // if value is fn, invoke it + a.push( { name: n, value: v } ); + } + } + } + + // give pre-submit callback an opportunity to abort the submit + if (options.beforeSubmit && options.beforeSubmit(a, this, options) === false) { + log('ajaxSubmit: submit aborted via beforeSubmit callback'); + return this; + } + + // fire vetoable 'validate' event + this.trigger('form-submit-validate', [a, this, options, veto]); + if (veto.veto) { + log('ajaxSubmit: submit vetoed via form-submit-validate trigger'); + return this; + } + + var q = $.param(a); + + if (options.type.toUpperCase() == 'GET') { + options.url += (options.url.indexOf('?') >= 0 ? '&' : '?') + q; + options.data = null; // data is null for 'get' + } + else { + options.data = q; // data is the query string for 'post' + } + + var $form = this, callbacks = []; + if (options.resetForm) { + callbacks.push(function() { $form.resetForm(); }); + } + if (options.clearForm) { + callbacks.push(function() { $form.clearForm(); }); + } + + // perform a load on the target only if dataType is not provided + if (!options.dataType && options.target) { + var oldSuccess = options.success || function(){}; + callbacks.push(function(data) { + var fn = options.replaceTarget ? 'replaceWith' : 'html'; + $(options.target)[fn](data).each(oldSuccess, arguments); + }); + } + else if (options.success) { + callbacks.push(options.success); + } + + options.success = function(data, status, xhr) { // jQuery 1.4+ passes xhr as 3rd arg + var context = options.context || options; // jQuery 1.4+ supports scope context + for (var i=0, max=callbacks.length; i < max; i++) { + callbacks[i].apply(context, [data, status, xhr || $form, $form]); + } + }; + + // are there files to upload? + var fileInputs = $('input:file', this).length > 0; + var mp = 'multipart/form-data'; + var multipart = ($form.attr('enctype') == mp || $form.attr('encoding') == mp); + + // options.iframe allows user to force iframe mode + // 06-NOV-09: now defaulting to iframe mode if file input is detected + if (options.iframe !== false && (fileInputs || options.iframe || multipart)) { + // hack to fix Safari hang (thanks to Tim Molendijk for this) + // see: http://groups.google.com/group/jquery-dev/browse_thread/thread/36395b7ab510… + if (options.closeKeepAlive) { + $.get(options.closeKeepAlive, fileUpload); + } + else { + fileUpload(); + } + } + else { + $.ajax(options); + } + + // fire 'notify' event + this.trigger('form-submit-notify', [this, options]); + return this; + + + // private function for handling file uploads (hat tip to YAHOO!) + function fileUpload() { + var form = $form[0]; + + if ($(':input[name=submit],:input[id=submit]', form).length) { + // if there is an input with a name or id of 'submit' then we won't be + // able to invoke the submit fn on the form (at least not x-browser) + alert('Error: Form elements must not have name or id of "submit".'); + return; + } + + var s = $.extend(true, {}, $.ajaxSettings, options); + s.context = s.context || s; + var id = 'jqFormIO' + (new Date().getTime()), fn = '_'+id; + var $io = $('<iframe id="' + id + '" name="' + id + '" src="'+ s.iframeSrc +'" />'); + var io = $io[0]; + + $io.css({ position: 'absolute', top: '-1000px', left: '-1000px' }); + + var xhr = { // mock object + aborted: 0, + responseText: null, + responseXML: null, + status: 0, + statusText: 'n/a', + getAllResponseHeaders: function() {}, + getResponseHeader: function() {}, + setRequestHeader: function() {}, + abort: function() { + this.aborted = 1; + $io.attr('src', s.iframeSrc); // abort op in progress + } + }; + + var g = s.global; + // trigger ajax global events so that activity/block indicators work like normal + if (g && ! $.active++) { + $.event.trigger("ajaxStart"); + } + if (g) { + $.event.trigger("ajaxSend", [xhr, s]); + } + + if (s.beforeSend && s.beforeSend.call(s.context, xhr, s) === false) { + if (s.global) { + $.active--; + } + return; + } + if (xhr.aborted) { + return; + } + + var timedOut = 0; + + // add submitting element to data if we know it + var sub = form.clk; + if (sub) { + var n = sub.name; + if (n && !sub.disabled) { + s.extraData = s.extraData || {}; + s.extraData[n] = sub.value; + if (sub.type == "image") { + s.extraData[n+'.x'] = form.clk_x; + s.extraData[n+'.y'] = form.clk_y; + } + } + } + + // take a breath so that pending repaints get some cpu time before the upload starts + function doSubmit() { + // make sure form attrs are set + var t = $form.attr('target'), a = $form.attr('action'); + + // update form attrs in IE friendly way + form.setAttribute('target',id); + if (form.getAttribute('method') != 'POST') { + form.setAttribute('method', 'POST'); + } + if (form.getAttribute('action') != s.url) { + form.setAttribute('action', s.url); + } + + // ie borks in some cases when setting encoding + if (! s.skipEncodingOverride) { + $form.attr({ + encoding: 'multipart/form-data', + enctype: 'multipart/form-data' + }); + } + + // support timout + if (s.timeout) { + setTimeout(function() { timedOut = true; cb(); }, s.timeout); + } + + // add "extra" data to form if provided in options + var extraInputs = []; + try { + if (s.extraData) { + for (var n in s.extraData) { + extraInputs.push( + $('<input type="hidden" name="'+n+'" value="'+s.extraData[n]+'" />') + .appendTo(form)[0]); + } + } + + // add iframe to doc and submit the form + $io.appendTo('body'); + io.attachEvent ? io.attachEvent('onload', cb) : io.addEventListener('load', cb, false); + form.submit(); + } + finally { + // reset attrs and remove "extra" input elements + form.setAttribute('action',a); + if(t) { + form.setAttribute('target', t); + } else { + $form.removeAttr('target'); + } + $(extraInputs).remove(); + } + } + + if (s.forceSync) { + doSubmit(); + } + else { + setTimeout(doSubmit, 10); // this lets dom updates render + } + + var data, doc, domCheckCount = 50; + + function cb() { + doc = io.contentWindow ? io.contentWindow.document : io.contentDocument ? io.contentDocument : io.document; + if (!doc || doc.location.href == s.iframeSrc) { + // response not received yet + return; + } + io.detachEvent ? io.detachEvent('onload', cb) : io.removeEventListener('load', cb, false); + + var ok = true; + try { + if (timedOut) { + throw 'timeout'; + } + + var isXml = s.dataType == 'xml' || doc.XMLDocument || $.isXMLDoc(doc); + log('isXml='+isXml); + if (!isXml && window.opera && (doc.body == null || doc.body.innerHTML == '')) { + if (--domCheckCount) { + // in some browsers (Opera) the iframe DOM is not always traversable when + // the onload callback fires, so we loop a bit to accommodate + log('requeing onLoad callback, DOM not available'); + setTimeout(cb, 250); + return; + } + // let this fall through because server response could be an empty document + //log('Could not access iframe DOM after mutiple tries.'); + //throw 'DOMException: not available'; + } + + //log('response detected'); + xhr.responseText = doc.body ? doc.body.innerHTML : doc.documentElement ? doc.documentElement.innerHTML : null; + xhr.responseXML = doc.XMLDocument ? doc.XMLDocument : doc; + xhr.getResponseHeader = function(header){ + var headers = {'content-type': s.dataType}; + return headers[header]; + }; + + var scr = /(json|script)/.test(s.dataType); + if (scr || s.textarea) { + // see if user embedded response in textarea + var ta = doc.getElementsByTagName('textarea')[0]; + if (ta) { + xhr.responseText = ta.value; + } + else if (scr) { + // account for browsers injecting pre around json response + var pre = doc.getElementsByTagName('pre')[0]; + var b = doc.getElementsByTagName('body')[0]; + if (pre) { + xhr.responseText = pre.textContent; + } + else if (b) { + xhr.responseText = b.innerHTML; + } + } + } + else if (s.dataType == 'xml' && !xhr.responseXML && xhr.responseText != null) { + xhr.responseXML = toXml(xhr.responseText); + } + + data = httpData(xhr, s.dataType, s); + } + catch(e){ + log('error caught:',e); + ok = false; + xhr.error = e; + s.error.call(s.context, xhr, 'error', e); + g && $.event.trigger("ajaxError", [xhr, s, e]); + } + + if (xhr.aborted) { + log('upload aborted'); + ok = false; + } + + // ordering of these callbacks/triggers is odd, but that's how $.ajax does it + if (ok) { + s.success.call(s.context, data, 'success', xhr); + g && $.event.trigger("ajaxSuccess", [xhr, s]); + } + + g && $.event.trigger("ajaxComplete", [xhr, s]); + + if (g && ! --$.active) { + $.event.trigger("ajaxStop"); + } + + s.complete && s.complete.call(s.context, xhr, ok ? 'success' : 'error'); + + // clean up + setTimeout(function() { + $io.removeData('form-plugin-onload'); + $io.remove(); + xhr.responseXML = null; + }, 100); + } + + var toXml = $.parseXML || function(s, doc) { // use parseXML if available (jQuery 1.5+) + if (window.ActiveXObject) { + doc = new ActiveXObject('Microsoft.XMLDOM'); + doc.async = 'false'; + doc.loadXML(s); + } + else { + doc = (new DOMParser()).parseFromString(s, 'text/xml'); + } + return (doc && doc.documentElement && doc.documentElement.nodeName != 'parsererror') ? doc : null; + }; + var parseJSON = $.parseJSON || function(s) { + return window['eval']('(' + s + ')'); + }; + + var httpData = function( xhr, type, s ) { // mostly lifted from jq1.4.4 + var ct = xhr.getResponseHeader('content-type') || '', + xml = type === 'xml' || !type && ct.indexOf('xml') >= 0, + data = xml ? xhr.responseXML : xhr.responseText; + + if (xml && data.documentElement.nodeName === 'parsererror') { + $.error && $.error('parsererror'); + } + if (s && s.dataFilter) { + data = s.dataFilter(data, type); + } + if (typeof data === 'string') { + if (type === 'json' || !type && ct.indexOf('json') >= 0) { + data = parseJSON(data); + } else if (type === "script" || !type && ct.indexOf("javascript") >= 0) { + $.globalEval(data); + } + } + return data; + }; + } +}; + +/** + * ajaxForm() provides a mechanism for fully automating form submission. + * + * The advantages of using this method instead of ajaxSubmit() are: + * + * 1: This method will include coordinates for <input type="image" /> elements (if the element + * is used to submit the form). + * 2. This method will include the submit element's name/value data (for the element that was + * used to submit the form). + * 3. This method binds the submit() method to the form for you. + * + * The options argument for ajaxForm works exactly as it does for ajaxSubmit. ajaxForm merely + * passes the options argument along after properly binding events for submit elements and + * the form itself. + */ +$.fn.ajaxForm = function(options) { + // in jQuery 1.3+ we can fix mistakes with the ready state + if (this.length === 0) { + var o = { s: this.selector, c: this.context }; + if (!$.isReady && o.s) { + log('DOM not ready, queuing ajaxForm'); + $(function() { + $(o.s,o.c).ajaxForm(options); + }); + return this; + } + // is your DOM ready? http://docs.jquery.com/Tutorials:Introducing_$(document).ready() + log('terminating; zero elements found by selector' + ($.isReady ? '' : ' (DOM not ready)')); + return this; + } + + return this.ajaxFormUnbind().bind('submit.form-plugin', function(e) { + if (!e.isDefaultPrevented()) { // if event has been canceled, don't proceed + e.preventDefault(); + $(this).ajaxSubmit(options); + } + }).bind('click.form-plugin', function(e) { + var target = e.target; + var $el = $(target); + if (!($el.is(":submit,input:image"))) { + // is this a child element of the submit el? (ex: a span within a button) + var t = $el.closest(':submit'); + if (t.length == 0) { + return; + } + target = t[0]; + } + var form = this; + form.clk = target; + if (target.type == 'image') { + if (e.offsetX != undefined) { + form.clk_x = e.offsetX; + form.clk_y = e.offsetY; + } else if (typeof $.fn.offset == 'function') { // try to use dimensions plugin + var offset = $el.offset(); + form.clk_x = e.pageX - offset.left; + form.clk_y = e.pageY - offset.top; + } else { + form.clk_x = e.pageX - target.offsetLeft; + form.clk_y = e.pageY - target.offsetTop; + } + } + // clear form vars + setTimeout(function() { form.clk = form.clk_x = form.clk_y = null; }, 100); + }); +}; + +// ajaxFormUnbind unbinds the event handlers that were bound by ajaxForm +$.fn.ajaxFormUnbind = function() { + return this.unbind('submit.form-plugin click.form-plugin'); +}; + +/** + * formToArray() gathers form element data into an array of objects that can + * be passed to any of the following ajax functions: $.get, $.post, or load. + * Each object in the array has both a 'name' and 'value' property. An example of + * an array for a simple login form might be: + * + * [ { name: 'username', value: 'jresig' }, { name: 'password', value: 'secret' } ] + * + * It is this array that is passed to pre-submit callback functions provided to the + * ajaxSubmit() and ajaxForm() methods. + */ +$.fn.formToArray = function(semantic) { + var a = []; + if (this.length === 0) { + return a; + } + + var form = this[0]; + var els = semantic ? form.getElementsByTagName('*') : form.elements; + if (!els) { + return a; + } + + var i,j,n,v,el,max,jmax; + for(i=0, max=els.length; i < max; i++) { + el = els[i]; + n = el.name; + if (!n) { + continue; + } + + if (semantic && form.clk && el.type == "image") { + // handle image inputs on the fly when semantic == true + if(!el.disabled && form.clk == el) { + a.push({name: n, value: $(el).val()}); + a.push({name: n+'.x', value: form.clk_x}, {name: n+'.y', value: form.clk_y}); + } + continue; + } + + v = $.fieldValue(el, true); + if (v && v.constructor == Array) { + for(j=0, jmax=v.length; j < jmax; j++) { + a.push({name: n, value: v[j]}); + } + } + else if (v !== null && typeof v != 'undefined') { + a.push({name: n, value: v}); + } + } + + if (!semantic && form.clk) { + // input type=='image' are not found in elements array! handle it here + var $input = $(form.clk), input = $input[0]; + n = input.name; + if (n && !input.disabled && input.type == 'image') { + a.push({name: n, value: $input.val()}); + a.push({name: n+'.x', value: form.clk_x}, {name: n+'.y', value: form.clk_y}); + } + } + return a; +}; + +/** + * Serializes form data into a 'submittable' string. This method will return a string + * in the format: name1=value1&name2=value2 + */ +$.fn.formSerialize = function(semantic) { + //hand off to jQuery.param for proper encoding + return $.param(this.formToArray(semantic)); +}; + +/** + * Serializes all field elements in the jQuery object into a query string. + * This method will return a string in the format: name1=value1&name2=value2 + */ +$.fn.fieldSerialize = function(successful) { + var a = []; + this.each(function() { + var n = this.name; + if (!n) { + return; + } + var v = $.fieldValue(this, successful); + if (v && v.constructor == Array) { + for (var i=0,max=v.length; i < max; i++) { + a.push({name: n, value: v[i]}); + } + } + else if (v !== null && typeof v != 'undefined') { + a.push({name: this.name, value: v}); + } + }); + //hand off to jQuery.param for proper encoding + return $.param(a); +}; + +/** + * Returns the value(s) of the element in the matched set. For example, consider the following form: + * + * <form><fieldset> + * <input name="A" type="text" /> + * <input name="A" type="text" /> + * <input name="B" type="checkbox" value="B1" /> + * <input name="B" type="checkbox" value="B2"/> + * <input name="C" type="radio" value="C1" /> + * <input name="C" type="radio" value="C2" /> + * </fieldset></form> + * + * var v = $(':text').fieldValue(); + * // if no values are entered into the text inputs + * v == ['',''] + * // if values entered into the text inputs are 'foo' and 'bar' + * v == ['foo','bar'] + * + * var v = $(':checkbox').fieldValue(); + * // if neither checkbox is checked + * v === undefined + * // if both checkboxes are checked + * v == ['B1', 'B2'] + * + * var v = $(':radio').fieldValue(); + * // if neither radio is checked + * v === undefined + * // if first radio is checked + * v == ['C1'] + * + * The successful argument controls whether or not the field element must be 'successful' + * (per http://www.w3.org/TR/html4/interact/forms.html#successful-controls) + * The default value of the successful argument is true. If this value is false the value(s) + * for each element is returned. + * + * Note: This method *always* returns an array. If no valid value can be determined the + * array will be empty, otherwise it will contain one or more values. + */ +$.fn.fieldValue = function(successful) { + for (var val=[], i=0, max=this.length; i < max; i++) { + var el = this[i]; + var v = $.fieldValue(el, successful); + if (v === null || typeof v == 'undefined' || (v.constructor == Array && !v.length)) { + continue; + } + v.constructor == Array ? $.merge(val, v) : val.push(v); + } + return val; +}; + +/** + * Returns the value of the field element. + */ +$.fieldValue = function(el, successful) { + var n = el.name, t = el.type, tag = el.tagName.toLowerCase(); + if (successful === undefined) { + successful = true; + } + + if (successful && (!n || el.disabled || t == 'reset' || t == 'button' || + (t == 'checkbox' || t == 'radio') && !el.checked || + (t == 'submit' || t == 'image') && el.form && el.form.clk != el || + tag == 'select' && el.selectedIndex == -1)) { + return null; + } + + if (tag == 'select') { + var index = el.selectedIndex; + if (index < 0) { + return null; + } + var a = [], ops = el.options; + var one = (t == 'select-one'); + var max = (one ? index+1 : ops.length); + for(var i=(one ? index : 0); i < max; i++) { + var op = ops[i]; + if (op.selected) { + var v = op.value; + if (!v) { // extra pain for IE... + v = (op.attributes && op.attributes['value'] && !(op.attributes['value'].specified)) ? op.text : op.value; + } + if (one) { + return v; + } + a.push(v); + } + } + return a; + } + return $(el).val(); +}; + +/** + * Clears the form data. Takes the following actions on the form's input fields: + * - input text fields will have their 'value' property set to the empty string + * - select elements will have their 'selectedIndex' property set to -1 + * - checkbox and radio inputs will have their 'checked' property set to false + * - inputs of type submit, button, reset, and hidden will *not* be effected + * - button elements will *not* be effected + */ +$.fn.clearForm = function() { + return this.each(function() { + $('input,select,textarea', this).clearFields(); + }); +}; + +/** + * Clears the selected form elements. + */ +$.fn.clearFields = $.fn.clearInputs = function() { + return this.each(function() { + var t = this.type, tag = this.tagName.toLowerCase(); + if (t == 'text' || t == 'password' || tag == 'textarea') { + this.value = ''; + } + else if (t == 'checkbox' || t == 'radio') { + this.checked = false; + } + else if (tag == 'select') { + this.selectedIndex = -1; + } + }); +}; + +/** + * Resets the form data. Causes all form elements to be reset to their original value. + */ +$.fn.resetForm = function() { + return this.each(function() { + // guard against an input with the name of 'reset' + // note that IE reports the reset function as an 'object' + if (typeof this.reset == 'function' || (typeof this.reset == 'object' && !this.reset.nodeType)) { + this.reset(); + } + }); +}; + +/** + * Enables or disables any matching elements. + */ +$.fn.enable = function(b) { + if (b === undefined) { + b = true; + } + return this.each(function() { + this.disabled = !b; + }); +}; + +/** + * Checks/unchecks any matching checkboxes or radio buttons and + * selects/deselects and matching option elements. + */ +$.fn.selected = function(select) { + if (select === undefined) { + select = true; + } + return this.each(function() { + var t = this.type; + if (t == 'checkbox' || t == 'radio') { + this.checked = select; + } + else if (this.tagName.toLowerCase() == 'option') { + var $sel = $(this).parent('select'); + if (select && $sel[0] && $sel[0].type == 'select-one') { + // deselect all other options + $sel.find('option').selected(false); + } + this.selected = select; + } + }); +}; + +// helper fn for console logging +// set $.fn.ajaxSubmit.debug to true to enable debug logging +function log() { + if ($.fn.ajaxSubmit.debug) { + var msg = '[jquery.form] ' + Array.prototype.join.call(arguments,''); + if (window.console && window.console.log) { + window.console.log(msg); + } + else if (window.opera && window.opera.postError) { + window.opera.postError(msg); + } + } +}; + +})(jQuery); --- a/static/scripts/jquery.js Thu Feb 24 16:19:03 2011 -0500 +++ b/static/scripts/jquery.js Thu Feb 24 17:23:16 2011 -0500 @@ -1,5 +1,5 @@ -/* - * jQuery JavaScript Library v1.5 +/*! + * jQuery JavaScript Library v1.5.1 * http://jquery.com/ * * Copyright 2011, John Resig @@ -11,7 +11,7 @@ * Copyright 2011, The Dojo Foundation * Released under the MIT, BSD, and GPL Licenses. * - * Date: Mon Jan 31 08:31:29 2011 -0500 + * Date: Wed Feb 23 13:55:29 2011 -0500 */ (function( window, undefined ) { @@ -202,7 +202,7 @@ selector: "", // The current version of jQuery being used - jquery: "1.5", + jquery: "1.5.1", // The default length of a jQuery object is 0 length: 0, @@ -313,7 +313,7 @@ jQuery.fn.init.prototype = jQuery.fn; jQuery.extend = jQuery.fn.extend = function() { - var options, name, src, copy, copyIsArray, clone, + var options, name, src, copy, copyIsArray, clone, target = arguments[0] || {}, i = 1, length = arguments.length, @@ -585,10 +585,8 @@ if ( data && rnotwhite.test(data) ) { // Inspired by code by Andrea Giammarchi // http://webreflection.blogspot.com/2007/08/global-scope-evaluation-and-dom.h… - var head = document.getElementsByTagName("head")[0] || document.documentElement, - script = document.createElement("script"); - - script.type = "text/javascript"; + var head = document.head || document.getElementsByTagName( "head" )[0] || document.documentElement, + script = document.createElement( "script" ); if ( jQuery.support.scriptEval() ) { script.appendChild( document.createTextNode( data ) ); @@ -864,6 +862,12 @@ callbacks.shift().apply( context, args ); } } + // We have to add a catch block for + // IE prior to 8 or else the finally + // block will never get executed + catch (e) { + throw e; + } finally { fired = [ context, args ]; firing = 0; @@ -911,22 +915,22 @@ isRejected: failDeferred.isResolved, // Get a promise for this deferred // If obj is provided, the promise aspect is added to the object - promise: function( obj , i /* internal */ ) { + promise: function( obj ) { if ( obj == null ) { if ( promise ) { return promise; } promise = obj = {}; } - i = promiseMethods.length; + var i = promiseMethods.length; while( i-- ) { - obj[ promiseMethods[ i ] ] = deferred[ promiseMethods[ i ] ]; + obj[ promiseMethods[i] ] = deferred[ promiseMethods[i] ]; } return obj; } } ); // Make sure only one callback list will be used - deferred.then( failDeferred.cancel, deferred.cancel ); + deferred.done( failDeferred.cancel ).fail( deferred.cancel ); // Unexpose cancel delete deferred.cancel; // Call given func if any @@ -938,24 +942,34 @@ // Deferred helper when: function( object ) { - var args = arguments, - length = args.length, - deferred = length <= 1 && object && jQuery.isFunction( object.promise ) ? + var lastIndex = arguments.length, + deferred = lastIndex <= 1 && object && jQuery.isFunction( object.promise ) ? object : jQuery.Deferred(), - promise = deferred.promise(), - resolveArray; - - if ( length > 1 ) { - resolveArray = new Array( length ); - jQuery.each( args, function( index, element ) { - jQuery.when( element ).then( function( value ) { - resolveArray[ index ] = arguments.length > 1 ? slice.call( arguments, 0 ) : value; - if( ! --length ) { - deferred.resolveWith( promise, resolveArray ); - } - }, deferred.reject ); - } ); + promise = deferred.promise(); + + if ( lastIndex > 1 ) { + var array = slice.call( arguments, 0 ), + count = lastIndex, + iCallback = function( index ) { + return function( value ) { + array[ index ] = arguments.length > 1 ? slice.call( arguments, 0 ) : value; + if ( !( --count ) ) { + deferred.resolveWith( promise, array ); + } + }; + }; + while( ( lastIndex-- ) ) { + object = array[ lastIndex ]; + if ( object && jQuery.isFunction( object.promise ) ) { + object.promise().then( iCallback(lastIndex), deferred.reject ); + } else { + --count; + } + } + if ( !count ) { + deferred.resolveWith( promise, array ); + } } else if ( deferred !== object ) { deferred.resolve( object ); } @@ -1071,7 +1085,7 @@ } // Expose jQuery to the global object -return (window.jQuery = window.$ = jQuery); +return jQuery; })(); @@ -1088,7 +1102,8 @@ var all = div.getElementsByTagName("*"), a = div.getElementsByTagName("a")[0], select = document.createElement("select"), - opt = select.appendChild( document.createElement("option") ); + opt = select.appendChild( document.createElement("option") ), + input = div.getElementsByTagName("input")[0]; // Can't get basic test support if ( !all || !all.length || !a ) { @@ -1127,7 +1142,7 @@ // Make sure that if no value is specified for a checkbox // that it defaults to "on". // (WebKit defaults to "" instead) - checkOn: div.getElementsByTagName("input")[0].value === "on", + checkOn: input.value === "on", // Make sure that a selected-by-default option has a working selected property. // (WebKit defaults to false instead of true, IE too, if it's in an optgroup) @@ -1137,26 +1152,29 @@ deleteExpando: true, optDisabled: false, checkClone: false, - _scriptEval: null, noCloneEvent: true, + noCloneChecked: true, boxModel: null, inlineBlockNeedsLayout: false, shrinkWrapBlocks: false, reliableHiddenOffsets: true }; + input.checked = true; + jQuery.support.noCloneChecked = input.cloneNode( true ).checked; + // Make sure that the options inside disabled selects aren't marked as disabled // (WebKit marks them as diabled) select.disabled = true; jQuery.support.optDisabled = !opt.disabled; + var _scriptEval = null; jQuery.support.scriptEval = function() { - if ( jQuery.support._scriptEval === null ) { + if ( _scriptEval === null ) { var root = document.documentElement, script = document.createElement("script"), id = "script" + jQuery.now(); - script.type = "text/javascript"; try { script.appendChild( document.createTextNode( "window." + id + "=1;" ) ); } catch(e) {} @@ -1167,10 +1185,10 @@ // tag with appendChild/createTextNode // (IE doesn't support this, fails, and uses .text instead) if ( window[ id ] ) { - jQuery.support._scriptEval = true; + _scriptEval = true; delete window[ id ]; } else { - jQuery.support._scriptEval = false; + _scriptEval = false; } root.removeChild( script ); @@ -1178,7 +1196,7 @@ root = script = id = null; } - return jQuery.support._scriptEval; + return _scriptEval; }; // Test to see if it's possible to delete an expando from an element @@ -1190,7 +1208,7 @@ jQuery.support.deleteExpando = false; } - if ( div.attachEvent && div.fireEvent ) { + if ( !div.addEventListener && div.attachEvent && div.fireEvent ) { div.attachEvent("onclick", function click() { // Cloning a node shouldn't copy over any // bound event handlers (IE does this) @@ -1321,7 +1339,7 @@ hasData: function( elem ) { elem = elem.nodeType ? jQuery.cache[ elem[jQuery.expando] ] : elem[ jQuery.expando ]; - return !!elem && !jQuery.isEmptyObject(elem); + return !!elem && !isEmptyDataObject( elem ); }, data: function( elem, name, data, pvt /* Internal Use Only */ ) { @@ -1361,11 +1379,18 @@ if ( !cache[ id ] ) { cache[ id ] = {}; + + // TODO: This is a hack for 1.5 ONLY. Avoids exposing jQuery + // metadata on plain JS objects when the object is serialized using + // JSON.stringify + if ( !isNode ) { + cache[ id ].toJSON = jQuery.noop; + } } // An object can be passed to jQuery.data instead of a key/value pair; this gets // shallow copied over onto the existing cache - if ( typeof name === "object" ) { + if ( typeof name === "object" || typeof name === "function" ) { if ( pvt ) { cache[ id ][ internalKey ] = jQuery.extend(cache[ id ][ internalKey ], name); } else { @@ -1427,7 +1452,7 @@ // If there is no data left in the cache, we want to continue // and let the cache object itself get destroyed - if ( !jQuery.isEmptyObject(thisCache) ) { + if ( !isEmptyDataObject(thisCache) ) { return; } } @@ -1439,7 +1464,7 @@ // Don't destroy the parent cache unless the internal data object // had been the only thing left in it - if ( !jQuery.isEmptyObject(cache[ id ]) ) { + if ( !isEmptyDataObject(cache[ id ]) ) { return; } } @@ -1460,6 +1485,13 @@ // data if it existed if ( internalCache ) { cache[ id ] = {}; + // TODO: This is a hack for 1.5 ONLY. Avoids exposing jQuery + // metadata on plain JS objects when the object is serialized using + // JSON.stringify + if ( !isNode ) { + cache[ id ].toJSON = jQuery.noop; + } + cache[ id ][ internalKey ] = internalCache; // Otherwise, we need to eliminate the expando on the node to avoid @@ -1588,6 +1620,19 @@ return data; } +// TODO: This is a hack for 1.5 ONLY to allow objects with a single toJSON +// property to be considered empty objects; this property always exists in +// order to make sure JSON.stringify does not expose internal metadata +function isEmptyDataObject( obj ) { + for ( var name in obj ) { + if ( name !== "toJSON" ) { + return false; + } + } + + return true; +} + @@ -1888,6 +1933,11 @@ } } + // Fixes Bug #2551 -- select.val() broken in IE after form.reset() + if ( one && !values.length && options.length ) { + return jQuery( options[ index ] ).val(); + } + return values; } @@ -2081,8 +2131,7 @@ rescape = /[^\w\s.|`]/g, fcleanup = function( nm ) { return nm.replace(rescape, "\\$&"); - }, - eventKey = "events"; + }; /* * A number of helper functions used for managing events. @@ -2098,17 +2147,22 @@ return; } - // For whatever reason, IE has trouble passing the window object - // around, causing it to be cloned in the process - if ( jQuery.isWindow( elem ) && ( elem !== window && !elem.frameElement ) ) { - elem = window; - } + // TODO :: Use a try/catch until it's safe to pull this out (likely 1.6) + // Minor release fix for bug #8018 + try { + // For whatever reason, IE has trouble passing the window object + // around, causing it to be cloned in the process + if ( jQuery.isWindow( elem ) && ( elem !== window && !elem.frameElement ) ) { + elem = window; + } + } + catch ( e ) {} if ( handler === false ) { handler = returnFalse; } else if ( !handler ) { // Fixes bug #7229. Fix recommended by jdalton - return; + return; } var handleObjIn, handleObj; @@ -2132,23 +2186,10 @@ return; } - var events = elemData[ eventKey ], + var events = elemData.events, eventHandle = elemData.handle; - if ( typeof events === "function" ) { - // On plain objects events is a fn that holds the the data - // which prevents this data from being JSON serialized - // the function does not need to be called, it just contains the data - eventHandle = events.handle; - events = events.events; - - } else if ( !events ) { - if ( !elem.nodeType ) { - // On plain objects, create a fn that acts as the holder - // of the values to avoid JSON serialization of event data - elemData[ eventKey ] = elemData = function(){}; - } - + if ( !events ) { elemData.events = events = {}; } @@ -2249,17 +2290,12 @@ var ret, type, fn, j, i = 0, all, namespaces, namespace, special, eventType, handleObj, origType, elemData = jQuery.hasData( elem ) && jQuery._data( elem ), - events = elemData && elemData[ eventKey ]; + events = elemData && elemData.events; if ( !elemData || !events ) { return; } - if ( typeof events === "function" ) { - elemData = events; - events = events.events; - } - // types is actually an event object here if ( types && types.type ) { handler = types.handler; @@ -2359,10 +2395,7 @@ delete elemData.events; delete elemData.handle; - if ( typeof elemData === "function" ) { - jQuery.removeData( elem, eventKey, true ); - - } else if ( jQuery.isEmptyObject( elemData ) ) { + if ( jQuery.isEmptyObject( elemData ) ) { jQuery.removeData( elem, undefined, true ); } } @@ -2403,7 +2436,7 @@ // points to jQuery.expando var internalKey = jQuery.expando, internalCache = this[ internalKey ]; - if ( internalCache && internalCache.events && internalCache.events[type] ) { + if ( internalCache && internalCache.events && internalCache.events[ type ] ) { jQuery.event.trigger( event, data, internalCache.handle.elem ); } }); @@ -2429,9 +2462,7 @@ event.currentTarget = elem; // Trigger the event, it is assumed that "handle" is a function - var handle = elem.nodeType ? - jQuery._data( elem, "handle" ) : - (jQuery._data( elem, eventKey ) || {}).handle; + var handle = jQuery._data( elem, "handle" ); if ( handle ) { handle.apply( elem, data ); @@ -2509,11 +2540,7 @@ event.namespace = event.namespace || namespace_sort.join("."); - events = jQuery._data(this, eventKey); - - if ( typeof events === "function" ) { - events = events.events; - } + events = jQuery._data(this, "events"); handlers = (events || {})[ event.type ]; @@ -2680,7 +2707,7 @@ // Events bubbling up the document may have been marked as prevented // by a handler lower down the tree; reflect the correct value. - this.isDefaultPrevented = (src.defaultPrevented || src.returnValue === false || + this.isDefaultPrevented = (src.defaultPrevented || src.returnValue === false || src.getPreventDefault && src.getPreventDefault()) ? returnTrue : returnFalse; // Event type @@ -2755,6 +2782,12 @@ // Firefox sometimes assigns relatedTarget a XUL element // which we cannot access the parentNode property of try { + + // Chrome does something similar, the parentNode property + // can be accessed but is null. + if ( parent !== document && !parent.parentNode ) { + return; + } // Traverse up the tree while ( parent && parent !== this ) { parent = parent.parentNode; @@ -2805,8 +2838,7 @@ type = elem.type; if ( (type === "submit" || type === "image") && jQuery( elem ).closest("form").length ) { - e.liveFired = undefined; - return trigger( "submit", this, arguments ); + trigger( "submit", this, arguments ); } }); @@ -2815,8 +2847,7 @@ type = elem.type; if ( (type === "text" || type === "password") && jQuery( elem ).closest("form").length && e.keyCode === 13 ) { - e.liveFired = undefined; - return trigger( "submit", this, arguments ); + trigger( "submit", this, arguments ); } }); @@ -2879,7 +2910,7 @@ if ( data != null || val ) { e.type = "change"; e.liveFired = undefined; - return jQuery.event.trigger( e, arguments[1], elem ); + jQuery.event.trigger( e, arguments[1], elem ); } }; @@ -2893,7 +2924,7 @@ var elem = e.target, type = elem.type; if ( type === "radio" || type === "checkbox" || elem.nodeName.toLowerCase() === "select" ) { - return testChange.call( this, e ); + testChange.call( this, e ); } }, @@ -2905,7 +2936,7 @@ if ( (e.keyCode === 13 && elem.nodeName.toLowerCase() !== "textarea") || (e.keyCode === 32 && (type === "checkbox" || type === "radio")) || type === "select-multiple" ) { - return testChange.call( this, e ); + testChange.call( this, e ); } }, @@ -2944,8 +2975,18 @@ } function trigger( type, elem, args ) { - args[0].type = type; - return jQuery.event.handle.apply( elem, args ); + // Piggyback on a donor event to simulate a different one. + // Fake originalEvent to avoid donor's stopPropagation, but if the + // simulated event prevents default then we do the same on the donor. + // Don't pass args or remember liveFired; they apply to the donor event. + var event = jQuery.extend( {}, args[ 0 ] ); + event.type = type; + event.originalEvent = {}; + event.liveFired = undefined; + jQuery.event.handle.call( elem, event ); + if ( event.isDefaultPrevented() ) { + args[ 0 ].preventDefault(); + } } // Create "bubbling" focus and blur events @@ -2954,8 +2995,8 @@ jQuery.event.special[ fix ] = { setup: function() { this.addEventListener( orig, handler, true ); - }, - teardown: function() { + }, + teardown: function() { this.removeEventListener( orig, handler, true ); } }; @@ -3148,11 +3189,7 @@ var stop, maxLevel, related, match, handleObj, elem, j, i, l, data, close, namespace, ret, elems = [], selectors = [], - events = jQuery._data( this, eventKey ); - - if ( typeof events === "function" ) { - events = events.events; - } + events = jQuery._data( this, "events" ); // Make sure we avoid non-left-click bubbling in Firefox (#3861) and disabled elements in IE (#6911) if ( event.liveFired === this || !events || !events.live || event.target.disabled || event.button && event.type === "click" ) { @@ -3186,7 +3223,7 @@ for ( j = 0; j < live.length; j++ ) { handleObj = live[j]; - if ( close.selector === handleObj.selector && (!namespace || namespace.test( handleObj.namespace )) ) { + if ( close.selector === handleObj.selector && (!namespace || namespace.test( handleObj.namespace )) && !close.elem.disabled ) { elem = close.elem; related = null; @@ -3269,7 +3306,9 @@ done = 0, toString = Object.prototype.toString, hasDuplicate = false, - baseHasDuplicate = true; + baseHasDuplicate = true, + rBackslash = /\\/g, + rNonWord = /\W/; // Here we check if the JavaScript engine is using some sort of // optimization where it does not always call our comparision @@ -3468,7 +3507,7 @@ match.splice( 1, 1 ); if ( left.substr( left.length - 1 ) !== "\\" ) { - match[1] = (match[1] || "").replace(/\\/g, ""); + match[1] = (match[1] || "").replace( rBackslash, "" ); set = Expr.find[ type ]( match, context, isXML ); if ( set != null ) { @@ -3607,13 +3646,16 @@ attrHandle: { href: function( elem ) { return elem.getAttribute( "href" ); + }, + type: function( elem ) { + return elem.getAttribute( "type" ); } }, relative: { "+": function(checkSet, part){ var isPartStr = typeof part === "string", - isTag = isPartStr && !/\W/.test( part ), + isTag = isPartStr && !rNonWord.test( part ), isPartStrNotTag = isPartStr && !isTag; if ( isTag ) { @@ -3641,7 +3683,7 @@ i = 0, l = checkSet.length; - if ( isPartStr && !/\W/.test( part ) ) { + if ( isPartStr && !rNonWord.test( part ) ) { part = part.toLowerCase(); for ( ; i < l; i++ ) { @@ -3675,7 +3717,7 @@ doneName = done++, checkFn = dirCheck; - if ( typeof part === "string" && !/\W/.test(part) ) { + if ( typeof part === "string" && !rNonWord.test( part ) ) { part = part.toLowerCase(); nodeCheck = part; checkFn = dirNodeCheck; @@ -3689,7 +3731,7 @@ doneName = done++, checkFn = dirCheck; - if ( typeof part === "string" && !/\W/.test( part ) ) { + if ( typeof part === "string" && !rNonWord.test( part ) ) { part = part.toLowerCase(); nodeCheck = part; checkFn = dirNodeCheck; @@ -3732,7 +3774,7 @@ }, preFilter: { CLASS: function( match, curLoop, inplace, result, not, isXML ) { - match = " " + match[1].replace(/\\/g, "") + " "; + match = " " + match[1].replace( rBackslash, "" ) + " "; if ( isXML ) { return match; @@ -3755,11 +3797,11 @@ }, ID: function( match ) { - return match[1].replace(/\\/g, ""); + return match[1].replace( rBackslash, "" ); }, TAG: function( match, curLoop ) { - return match[1].toLowerCase(); + return match[1].replace( rBackslash, "" ).toLowerCase(); }, CHILD: function( match ) { @@ -3790,14 +3832,14 @@ }, ATTR: function( match, curLoop, inplace, result, not, isXML ) { - var name = match[1] = match[1].replace(/\\/g, ""); + var name = match[1] = match[1].replace( rBackslash, "" ); if ( !isXML && Expr.attrMap[name] ) { match[1] = Expr.attrMap[name]; } // Handle if an un-quoted value was used - match[4] = ( match[4] || match[5] || "" ).replace(/\\/g, ""); + match[4] = ( match[4] || match[5] || "" ).replace( rBackslash, "" ); if ( match[2] === "~=" ) { match[4] = " " + match[4] + " "; @@ -3852,7 +3894,9 @@ selected: function( elem ) { // Accessing this property makes selected-by-default // options in Safari work properly - elem.parentNode.selectedIndex; + if ( elem.parentNode ) { + elem.parentNode.selectedIndex; + } return elem.selected === true; }, @@ -3874,7 +3918,9 @@ }, text: function( elem ) { - return "text" === elem.type; + // IE6 and 7 will map elem.type to 'text' for new HTML5 types (search, etc) + // use getAttribute instead to test this case + return "text" === elem.getAttribute( 'type' ); }, radio: function( elem ) { return "radio" === elem.type; @@ -4407,7 +4453,8 @@ // and working up from there (Thanks to Andrew Dupont for the technique) // IE 8 doesn't work on object elements } else if ( context.nodeType === 1 && context.nodeName.toLowerCase() !== "object" ) { - var old = context.getAttribute( "id" ), + var oldContext = context, + old = context.getAttribute( "id" ), nid = old || id, hasParent = context.parentNode, relativeHierarchySelector = /^\s*[+~]/.test( query ); @@ -4429,7 +4476,7 @@ } catch(pseudoError) { } finally { if ( !old ) { - context.removeAttribute( "id" ); + oldContext.removeAttribute( "id" ); } } } @@ -4845,11 +4892,11 @@ }, function( name, fn ) { jQuery.fn[ name ] = function( until, selector ) { var ret = jQuery.map( this, fn, until ), - // The variable 'args' was introduced in - // https://github.com/jquery/jquery/commit/52a0238 - // to work around a bug in Chrome 10 (Dev) and should be removed when the bug is fixed. - // http://code.google.com/p/v8/issues/detail?id=1050 - args = slice.call(arguments); + // The variable 'args' was introduced in + // https://github.com/jquery/jquery/commit/52a0238 + // to work around a bug in Chrome 10 (Dev) and should be removed when the bug is fixed. + // http://code.google.com/p/v8/issues/detail?id=1050 + args = slice.call(arguments); if ( !runtil.test( name ) ) { selector = until; @@ -4959,7 +5006,7 @@ rtbody = /<tbody/i, rhtml = /<|&#?\w+;/, rnocache = /<(?:script|object|embed|option|style)/i, - // checked="checked" or checked (html5) + // checked="checked" or checked rchecked = /checked\s*(?:[^=]|=\s*.checked.)/i, wrapMap = { option: [ 1, "<select multiple='multiple'>", "</select>" ], @@ -5111,7 +5158,7 @@ } if ( elem.parentNode ) { - elem.parentNode.removeChild( elem ); + elem.parentNode.removeChild( elem ); } } } @@ -5136,7 +5183,7 @@ }, clone: function( dataAndEvents, deepDataAndEvents ) { - dataAndEvents = dataAndEvents == null ? true : dataAndEvents; + dataAndEvents = dataAndEvents == null ? false : dataAndEvents; deepDataAndEvents = deepDataAndEvents == null ? dataAndEvents : deepDataAndEvents; return this.map( function () { @@ -5305,8 +5352,8 @@ } var internalKey = jQuery.expando, - oldData = jQuery.data( src ), - curData = jQuery.data( dest, oldData ); + oldData = jQuery.data( src ), + curData = jQuery.data( dest, oldData ); // Switch to use the internal data object, if it exists, for the next // stage of data copying @@ -5320,7 +5367,7 @@ for ( var type in events ) { for ( var i = 0, l = events[ type ].length; i < l; i++ ) { - jQuery.event.add( dest, type, events[ type ][ i ], events[ type ][ i ].data ); + jQuery.event.add( dest, type + ( events[ type ][ i ].namespace ? "." : "" ) + events[ type ][ i ].namespace, events[ type ][ i ], events[ type ][ i ].data ); } } } @@ -5441,6 +5488,18 @@ }; }); +function getAll( elem ) { + if ( "getElementsByTagName" in elem ) { + return elem.getElementsByTagName( "*" ); + + } else if ( "querySelectorAll" in elem ) { + return elem.querySelectorAll( "*" ); + + } else { + return []; + } +} + jQuery.extend({ clone: function( elem, dataAndEvents, deepDataAndEvents ) { var clone = elem.cloneNode(true), @@ -5448,17 +5507,20 @@ destElements, i; - if ( !jQuery.support.noCloneEvent && (elem.nodeType === 1 || elem.nodeType === 11) && !jQuery.isXMLDoc(elem) ) { + if ( (!jQuery.support.noCloneEvent || !jQuery.support.noCloneChecked) && + (elem.nodeType === 1 || elem.nodeType === 11) && !jQuery.isXMLDoc(elem) ) { // IE copies events bound via attachEvent when using cloneNode. // Calling detachEvent on the clone will also remove the events // from the original. In order to get around this, we use some // proprietary methods to clear the events. Thanks to MooTools // guys for this hotness. + cloneFixAttributes( elem, clone ); + // Using Sizzle here is crazy slow, so we use getElementsByTagName // instead - srcElements = elem.getElementsByTagName("*"); - destElements = clone.getElementsByTagName("*"); + srcElements = getAll( elem ); + destElements = getAll( clone ); // Weird iteration because IE will replace the length property // with an element if you are cloning the body and one of the @@ -5466,30 +5528,25 @@ for ( i = 0; srcElements[i]; ++i ) { cloneFixAttributes( srcElements[i], destElements[i] ); } - - cloneFixAttributes( elem, clone ); } // Copy the events from the original to the clone if ( dataAndEvents ) { - cloneCopyEvent( elem, clone ); - if ( deepDataAndEvents && "getElementsByTagName" in elem ) { - - srcElements = elem.getElementsByTagName("*"); - destElements = clone.getElementsByTagName("*"); - - if ( srcElements.length ) { - for ( i = 0; srcElements[i]; ++i ) { - cloneCopyEvent( srcElements[i], destElements[i] ); - } - } - } - } + if ( deepDataAndEvents ) { + srcElements = getAll( elem ); + destElements = getAll( clone ); + + for ( i = 0; srcElements[i]; ++i ) { + cloneCopyEvent( srcElements[i], destElements[i] ); + } + } + } + // Return the cloned set return clone; - }, +}, clean: function( elems, context, fragment, scripts ) { context = context || document; @@ -5910,7 +5967,7 @@ if ( document.documentElement.currentStyle ) { currentStyle = function( elem, name ) { - var left, + var left, ret = elem.currentStyle && elem.currentStyle[ name ], rsLeft = elem.runtimeStyle && elem.runtimeStyle[ name ], style = elem.style; @@ -5988,8 +6045,10 @@ rbracket = /\[\]$/, rCRLF = /\r?\n/g, rhash = /#.*$/, - rheaders = /^(.*?):\s*(.*?)\r?$/mg, // IE leaves an \r character at EOL + rheaders = /^(.*?):[ \t]*([^\r\n]*)\r?$/mg, // IE leaves an \r character at EOL rinput = /^(?:color|date|datetime|email|hidden|month|number|password|range|search|tel|text|time|url|week)$/i, + // #7653, #8125, #8152: local protocol detection + rlocalProtocol = /(?:^file|^widget|\-extension):$/, rnoContent = /^(?:GET|HEAD)$/, rprotocol = /^\/\//, rquery = /\?/, @@ -5997,7 +6056,11 @@ rselectTextarea = /^(?:select|textarea)/i, rspacesAjax = /\s+/, rts = /([?&])_=[^&]*/, - rurl = /^(\w+:)\/\/([^\/?#:]+)(?::(\d+))?/, + rucHeaders = /(^|\-)([a-z])/g, + rucHeadersFunc = function( _, $1, $2 ) { + return $1 + $2.toUpperCase(); + }, + rurl = /^([\w\+\.\-]+:)\/\/([^\/?#:]*)(?::(\d+))?/, // Keep a copy of the old load method _load = jQuery.fn.load, @@ -6018,7 +6081,28 @@ * 2) the catchall symbol "*" can be used * 3) selection will start with transport dataType and THEN go to "*" if needed */ - transports = {}; + transports = {}, + + // Document location + ajaxLocation, + + // Document location segments + ajaxLocParts; + +// #8138, IE may throw an exception when accessing +// a field from document.location if document.domain has been set +try { + ajaxLocation = document.location.href; +} catch( e ) { + // Use the href attribute of an A element + // since IE will modify it given document.location + ajaxLocation = document.createElement( "a" ); + ajaxLocation.href = ""; + ajaxLocation = ajaxLocation.href; +} + +// Segment location into parts +ajaxLocParts = rurl.exec( ajaxLocation.toLowerCase() ); // Base "constructor" for jQuery.ajaxPrefilter and jQuery.ajaxTransport function addToPrefiltersOrTransports( structure ) { @@ -6057,7 +6141,7 @@ } //Base inspection function for prefilters and transports -function inspectPrefiltersOrTransports( structure, options, originalOptions, jXHR, +function inspectPrefiltersOrTransports( structure, options, originalOptions, jqXHR, dataType /* internal */, inspected /* internal */ ) { dataType = dataType || options.dataTypes[ 0 ]; @@ -6072,16 +6156,16 @@ selection; for(; i < length && ( executeOnly || !selection ); i++ ) { - selection = list[ i ]( options, originalOptions, jXHR ); + selection = list[ i ]( options, originalOptions, jqXHR ); // If we got redirected to another dataType - // we try there if not done already + // we try there if executing only and not done already if ( typeof selection === "string" ) { - if ( inspected[ selection ] ) { + if ( !executeOnly || inspected[ selection ] ) { selection = undefined; } else { options.dataTypes.unshift( selection ); selection = inspectPrefiltersOrTransports( - structure, options, originalOptions, jXHR, selection, inspected ); + structure, options, originalOptions, jqXHR, selection, inspected ); } } } @@ -6089,7 +6173,7 @@ // we try the catchall dataType if not done already if ( ( executeOnly || !selection ) && !inspected[ "*" ] ) { selection = inspectPrefiltersOrTransports( - structure, options, originalOptions, jXHR, "*", inspected ); + structure, options, originalOptions, jqXHR, "*", inspected ); } // unnecessary when only executing (prefilters) // but it'll be ignored by the caller in that case @@ -6121,7 +6205,7 @@ if ( jQuery.isFunction( params ) ) { // We assume that it's the callback callback = params; - params = null; + params = undefined; // Otherwise, build a param string } else if ( typeof params === "object" ) { @@ -6139,14 +6223,14 @@ dataType: "html", data: params, // Complete callback (responseText is used internally) - complete: function( jXHR, status, responseText ) { - // Store the response as specified by the jXHR object - responseText = jXHR.responseText; + complete: function( jqXHR, status, responseText ) { + // Store the response as specified by the jqXHR object + responseText = jqXHR.responseText; // If successful, inject the HTML into all the matched elements - if ( jXHR.isResolved() ) { + if ( jqXHR.isResolved() ) { // #4825: Get the actual response in case // a dataFilter is present in ajaxSettings - jXHR.done(function( r ) { + jqXHR.done(function( r ) { responseText = r; }); // See if a selector was specified @@ -6165,7 +6249,7 @@ } if ( callback ) { - self.each( callback, [ responseText, status, jXHR ] ); + self.each( callback, [ responseText, status, jqXHR ] ); } } }); @@ -6213,7 +6297,7 @@ if ( jQuery.isFunction( data ) ) { type = type || callback; callback = data; - data = null; + data = undefined; } return jQuery.ajax({ @@ -6229,22 +6313,39 @@ jQuery.extend({ getScript: function( url, callback ) { - return jQuery.get( url, null, callback, "script" ); + return jQuery.get( url, undefined, callback, "script" ); }, getJSON: function( url, data, callback ) { return jQuery.get( url, data, callback, "json" ); }, - ajaxSetup: function( settings ) { - jQuery.extend( true, jQuery.ajaxSettings, settings ); - if ( settings.context ) { - jQuery.ajaxSettings.context = settings.context; - } + // Creates a full fledged settings object into target + // with both ajaxSettings and settings fields. + // If target is omitted, writes into ajaxSettings. + ajaxSetup: function ( target, settings ) { + if ( !settings ) { + // Only one parameter, we extend ajaxSettings + settings = target; + target = jQuery.extend( true, jQuery.ajaxSettings, settings ); + } else { + // target was provided, we extend into it + jQuery.extend( true, target, jQuery.ajaxSettings, settings ); + } + // Flatten fields we don't want deep extended + for( var field in { context: 1, url: 1 } ) { + if ( field in settings ) { + target[ field ] = settings[ field ]; + } else if( field in jQuery.ajaxSettings ) { + target[ field ] = jQuery.ajaxSettings[ field ]; + } + } + return target; }, ajaxSettings: { - url: location.href, + url: ajaxLocation, + isLocal: rlocalProtocol.test( ajaxLocParts[ 1 ] ), global: true, type: "GET", contentType: "application/x-www-form-urlencoded", @@ -6306,9 +6407,8 @@ // Main method ajax: function( url, options ) { - // If options is not an object, - // we simulate pre-1.5 signature - if ( typeof options !== "object" ) { + // If url is an object, simulate pre-1.5 signature + if ( typeof url === "object" ) { options = url; url = undefined; } @@ -6317,19 +6417,22 @@ options = options || {}; var // Create the final options object - s = jQuery.extend( true, {}, jQuery.ajaxSettings, options ), - // Callbacks contexts - // We force the original context if it exists - // or take it from jQuery.ajaxSettings otherwise - // (plain objects used as context get extended) - callbackContext = - ( s.context = ( "context" in options ? options : jQuery.ajaxSettings ).context ) || s, - globalEventContext = callbackContext === s ? jQuery.event : jQuery( callbackContext ), + s = jQuery.ajaxSetup( {}, options ), + // Callbacks context + callbackContext = s.context || s, + // Context for global events + // It's the callbackContext if one was provided in the options + // and if it's a DOM node or a jQuery collection + globalEventContext = callbackContext !== s && + ( callbackContext.nodeType || callbackContext instanceof jQuery ) ? + jQuery( callbackContext ) : jQuery.event, // Deferreds deferred = jQuery.Deferred(), completeDeferred = jQuery._Deferred(), // Status-dependent callbacks statusCode = s.statusCode || {}, + // ifModified key + ifModifiedKey, // Headers (they are sent all at once) requestHeaders = {}, // Response headers @@ -6340,22 +6443,22 @@ // timeout handle timeoutTimer, // Cross-domain detection vars - loc = document.location, - protocol = loc.protocol || "http:", parts, - // The jXHR state + // The jqXHR state state = 0, + // To know if global events are to be dispatched + fireGlobals, // Loop variable i, // Fake xhr - jXHR = { + jqXHR = { readyState: 0, // Caches the header setRequestHeader: function( name, value ) { - if ( state === 0 ) { - requestHeaders[ name.toLowerCase() ] = value; + if ( !state ) { + requestHeaders[ name.toLowerCase().replace( rucHeaders, rucHeadersFunc ) ] = value; } return this; }, @@ -6377,7 +6480,15 @@ } match = responseHeaders[ key.toLowerCase() ]; } - return match || null; + return match === undefined ? null : match; + }, + + // Overrides response content-type header + overrideMimeType: function( type ) { + if ( !state ) { + s.mimeType = type; + } + return this; }, // Cancel the request @@ -6394,7 +6505,7 @@ // Callback for when everything is done // It is defined here because jslint complains if it is declared // at the end of the function (which would be more logical and readable) - function done( status, statusText, responses, headers) { + function done( status, statusText, responses, headers ) { // Called once if ( state === 2 ) { @@ -6410,19 +6521,19 @@ } // Dereference transport for early garbage collection - // (no matter how long the jXHR object will be used) + // (no matter how long the jqXHR object will be used) transport = undefined; // Cache response headers responseHeadersString = headers || ""; // Set readyState - jXHR.readyState = status ? 4 : 0; + jqXHR.readyState = status ? 4 : 0; var isSuccess, success, error, - response = responses ? ajaxHandleResponses( s, jXHR, responses ) : undefined, + response = responses ? ajaxHandleResponses( s, jqXHR, responses ) : undefined, lastModified, etag; @@ -6432,11 +6543,11 @@ // Set the If-Modified-Since and/or If-None-Match header, if in ifModified mode. if ( s.ifModified ) { - if ( ( lastModified = jXHR.getResponseHeader( "Last-Modified" ) ) ) { - jQuery.lastModified[ s.url ] = lastModified; + if ( ( lastModified = jqXHR.getResponseHeader( "Last-Modified" ) ) ) { + jQuery.lastModified[ ifModifiedKey ] = lastModified; } - if ( ( etag = jXHR.getResponseHeader( "Etag" ) ) ) { - jQuery.etag[ s.url ] = etag; + if ( ( etag = jqXHR.getResponseHeader( "Etag" ) ) ) { + jQuery.etag[ ifModifiedKey ] = etag; } } @@ -6463,7 +6574,7 @@ // We extract error from statusText // then normalize statusText and status for non-aborts error = statusText; - if( status ) { + if( !statusText || status ) { statusText = "error"; if ( status < 0 ) { status = 0; @@ -6472,30 +6583,30 @@ } // Set data for the fake xhr object - jXHR.status = status; - jXHR.statusText = statusText; + jqXHR.status = status; + jqXHR.statusText = statusText; // Success/Error if ( isSuccess ) { - deferred.resolveWith( callbackContext, [ success, statusText, jXHR ] ); + deferred.resolveWith( callbackContext, [ success, statusText, jqXHR ] ); } else { - deferred.rejectWith( callbackContext, [ jXHR, statusText, error ] ); + deferred.rejectWith( callbackContext, [ jqXHR, statusText, error ] ); } // Status-dependent callbacks - jXHR.statusCode( statusCode ); + jqXHR.statusCode( statusCode ); statusCode = undefined; - if ( s.global ) { + if ( fireGlobals ) { globalEventContext.trigger( "ajax" + ( isSuccess ? "Success" : "Error" ), - [ jXHR, s, isSuccess ? success : error ] ); + [ jqXHR, s, isSuccess ? success : error ] ); } // Complete - completeDeferred.resolveWith( callbackContext, [ jXHR, statusText ] ); - - if ( s.global ) { - globalEventContext.trigger( "ajaxComplete", [ jXHR, s] ); + completeDeferred.resolveWith( callbackContext, [ jqXHR, statusText ] ); + + if ( fireGlobals ) { + globalEventContext.trigger( "ajaxComplete", [ jqXHR, s] ); // Handle the global AJAX counter if ( !( --jQuery.active ) ) { jQuery.event.trigger( "ajaxStop" ); @@ -6504,13 +6615,13 @@ } // Attach deferreds - deferred.promise( jXHR ); - jXHR.success = jXHR.done; - jXHR.error = jXHR.fail; - jXHR.complete = completeDeferred.done; + deferred.promise( jqXHR ); + jqXHR.success = jqXHR.done; + jqXHR.error = jqXHR.fail; + jqXHR.complete = completeDeferred.done; // Status-dependent callbacks - jXHR.statusCode = function( map ) { + jqXHR.statusCode = function( map ) { if ( map ) { var tmp; if ( state < 2 ) { @@ -6518,8 +6629,8 @@ statusCode[ tmp ] = [ statusCode[tmp], map[tmp] ]; } } else { - tmp = map[ jXHR.status ]; - jXHR.then( tmp, tmp ); + tmp = map[ jqXHR.status ]; + jqXHR.then( tmp, tmp ); } } return this; @@ -6528,7 +6639,7 @@ // Remove hash character (#7531: and string promotion) // Add protocol if not provided (#5866: IE7 issue with protocol-less urls) // We also use the url parameter if available - s.url = ( "" + ( url || s.url ) ).replace( rhash, "" ).replace( rprotocol, protocol + "//" ); + s.url = ( ( url || s.url ) + "" ).replace( rhash, "" ).replace( rprotocol, ajaxLocParts[ 1 ] + "//" ); // Extract dataTypes list s.dataTypes = jQuery.trim( s.dataType || "*" ).toLowerCase().split( rspacesAjax ); @@ -6537,9 +6648,9 @@ if ( !s.crossDomain ) { parts = rurl.exec( s.url.toLowerCase() ); s.crossDomain = !!( parts && - ( parts[ 1 ] != protocol || parts[ 2 ] != loc.hostname || + ( parts[ 1 ] != ajaxLocParts[ 1 ] || parts[ 2 ] != ajaxLocParts[ 2 ] || ( parts[ 3 ] || ( parts[ 1 ] === "http:" ? 80 : 443 ) ) != - ( loc.port || ( protocol === "http:" ? 80 : 443 ) ) ) + ( ajaxLocParts[ 3 ] || ( ajaxLocParts[ 1 ] === "http:" ? 80 : 443 ) ) ) ); } @@ -6549,7 +6660,15 @@ } // Apply prefilters - inspectPrefiltersOrTransports( prefilters, s, options, jXHR ); + inspectPrefiltersOrTransports( prefilters, s, options, jqXHR ); + + // If request was aborted inside a prefiler, stop there + if ( state === 2 ) { + return false; + } + + // We can fire global events as of now if asked to + fireGlobals = s.global; // Uppercase the type s.type = s.type.toUpperCase(); @@ -6558,7 +6677,7 @@ s.hasContent = !rnoContent.test( s.type ); // Watch for a new set of requests - if ( s.global && jQuery.active++ === 0 ) { + if ( fireGlobals && jQuery.active++ === 0 ) { jQuery.event.trigger( "ajaxStart" ); } @@ -6570,6 +6689,9 @@ s.url += ( rquery.test( s.url ) ? "&" : "?" ) + s.data; } + // Get ifModifiedKey before adding the anti-cache parameter + ifModifiedKey = s.url; + // Add anti-cache in url if needed if ( s.cache === false ) { @@ -6584,77 +6706,77 @@ // Set the correct header, if data is being sent if ( s.data && s.hasContent && s.contentType !== false || options.contentType ) { - requestHeaders[ "content-type" ] = s.contentType; + requestHeaders[ "Content-Type" ] = s.contentType; } // Set the If-Modified-Since and/or If-None-Match header, if in ifModified mode. if ( s.ifModified ) { - if ( jQuery.lastModified[ s.url ] ) { - requestHeaders[ "if-modified-since" ] = jQuery.lastModified[ s.url ]; - } - if ( jQuery.etag[ s.url ] ) { - requestHeaders[ "if-none-match" ] = jQuery.etag[ s.url ]; + ifModifiedKey = ifModifiedKey || s.url; + if ( jQuery.lastModified[ ifModifiedKey ] ) { + requestHeaders[ "If-Modified-Since" ] = jQuery.lastModified[ ifModifiedKey ]; + } + if ( jQuery.etag[ ifModifiedKey ] ) { + requestHeaders[ "If-None-Match" ] = jQuery.etag[ ifModifiedKey ]; } } // Set the Accepts header for the server, depending on the dataType - requestHeaders.accept = s.dataTypes[ 0 ] && s.accepts[ s.dataTypes[0] ] ? + requestHeaders.Accept = s.dataTypes[ 0 ] && s.accepts[ s.dataTypes[0] ] ? s.accepts[ s.dataTypes[0] ] + ( s.dataTypes[ 0 ] !== "*" ? ", */*; q=0.01" : "" ) : s.accepts[ "*" ]; // Check for headers option for ( i in s.headers ) { - requestHeaders[ i.toLowerCase() ] = s.headers[ i ]; + jqXHR.setRequestHeader( i, s.headers[ i ] ); } // Allow custom headers/mimetypes and early abort - if ( s.beforeSend && ( s.beforeSend.call( callbackContext, jXHR, s ) === false || state === 2 ) ) { + if ( s.beforeSend && ( s.beforeSend.call( callbackContext, jqXHR, s ) === false || state === 2 ) ) { // Abort if not done already - done( 0, "abort" ); - // Return false - jXHR = false; - + jqXHR.abort(); + return false; + + } + + // Install callbacks on deferreds + for ( i in { success: 1, error: 1, complete: 1 } ) { + jqXHR[ i ]( s[ i ] ); + } + + // Get transport + transport = inspectPrefiltersOrTransports( transports, s, options, jqXHR ); + + // If no transport, we auto-abort + if ( !transport ) { + done( -1, "No Transport" ); } else { - - // Install callbacks on deferreds - for ( i in { success: 1, error: 1, complete: 1 } ) { - jXHR[ i ]( s[ i ] ); - } - - // Get transport - transport = inspectPrefiltersOrTransports( transports, s, options, jXHR ); - - // If no transport, we auto-abort - if ( !transport ) { - done( -1, "No Transport" ); - } else { - // Set state as sending - state = jXHR.readyState = 1; - // Send global event - if ( s.global ) { - globalEventContext.trigger( "ajaxSend", [ jXHR, s ] ); - } - // Timeout - if ( s.async && s.timeout > 0 ) { - timeoutTimer = setTimeout( function(){ - jXHR.abort( "timeout" ); - }, s.timeout ); - } - - try { - transport.send( requestHeaders, done ); - } catch (e) { - // Propagate exception as error if not done - if ( status < 2 ) { - done( -1, e ); - // Simply rethrow otherwise - } else { - jQuery.error( e ); - } - } - } - } - return jXHR; + jqXHR.readyState = 1; + // Send global event + if ( fireGlobals ) { + globalEventContext.trigger( "ajaxSend", [ jqXHR, s ] ); + } + // Timeout + if ( s.async && s.timeout > 0 ) { + timeoutTimer = setTimeout( function(){ + jqXHR.abort( "timeout" ); + }, s.timeout ); + } + + try { + state = 1; + transport.send( requestHeaders, done ); + } catch (e) { + // Propagate exception as error if not done + if ( status < 2 ) { + done( -1, e ); + // Simply rethrow otherwise + } else { + jQuery.error( e ); + } + } + } + + return jqXHR; }, // Serialize an array of form elements or a set of @@ -6673,7 +6795,7 @@ } // If an array was passed in, assume that it is an array of form elements. - if ( jQuery.isArray( a ) || a.jquery ) { + if ( jQuery.isArray( a ) || ( a.jquery && !jQuery.isPlainObject( a ) ) ) { // Serialize the form elements jQuery.each( a, function() { add( this.name, this.value ); @@ -6720,9 +6842,9 @@ // Serialize object item. } else { - jQuery.each( obj, function( k, v ) { - buildParams( prefix + "[" + k + "]", v, traditional, add ); - }); + for ( var name in obj ) { + buildParams( prefix + "[" + name + "]", obj[ name ], traditional, add ); + } } } else { @@ -6749,7 +6871,7 @@ * - finds the right dataType (mediates between content-type and expected dataType) * - returns the corresponding response */ -function ajaxHandleResponses( s, jXHR, responses ) { +function ajaxHandleResponses( s, jqXHR, responses ) { var contents = s.contents, dataTypes = s.dataTypes, @@ -6762,7 +6884,7 @@ // Fill responseXXX fields for( type in responseFields ) { if ( type in responses ) { - jXHR[ responseFields[type] ] = responses[ type ]; + jqXHR[ responseFields[type] ] = responses[ type ]; } } @@ -6770,7 +6892,7 @@ while( dataTypes[ 0 ] === "*" ) { dataTypes.shift(); if ( ct === undefined ) { - ct = jXHR.getResponseHeader( "content-type" ); + ct = s.mimeType || jqXHR.getResponseHeader( "content-type" ); } } @@ -6822,8 +6944,9 @@ } var dataTypes = s.dataTypes, - converters = s.converters, + converters = {}, i, + key, length = dataTypes.length, tmp, // Current and previous dataTypes @@ -6840,6 +6963,16 @@ // For each dataType in the chain for( i = 1; i < length; i++ ) { + // Create converters map + // with lowercased keys + if ( i === 1 ) { + for( key in s.converters ) { + if( typeof key === "string" ) { + converters[ key.toLowerCase() ] = s.converters[ key ]; + } + } + } + // Get the dataTypes prev = current; current = dataTypes[ i ]; @@ -6902,9 +7035,9 @@ }); // Detect, normalize options and install callbacks for jsonp requests -jQuery.ajaxPrefilter( "json jsonp", function( s, originalSettings, dataIsString /* internal */ ) { - - dataIsString = ( typeof s.data === "string" ); +jQuery.ajaxPrefilter( "json jsonp", function( s, originalSettings, jqXHR ) { + + var dataIsString = ( typeof s.data === "string" ); if ( s.dataTypes[ 0 ] === "jsonp" || originalSettings.jsonpCallback || @@ -6918,7 +7051,15 @@ previous = window[ jsonpCallback ], url = s.url, data = s.data, - replace = "$1" + jsonpCallback + "$2"; + replace = "$1" + jsonpCallback + "$2", + cleanUp = function() { + // Set callback back to previous value + window[ jsonpCallback ] = previous; + // Call if it was a function and we have a response + if ( responseContainer && jQuery.isFunction( previous ) ) { + window[ jsonpCallback ]( responseContainer[ 0 ] ); + } + }; if ( s.jsonp !== false ) { url = url.replace( jsre, replace ); @@ -6936,32 +7077,17 @@ s.url = url; s.data = data; + // Install callback window[ jsonpCallback ] = function( response ) { responseContainer = [ response ]; }; - s.complete = [ function() { - - // Set callback back to previous value - window[ jsonpCallback ] = previous; - - // Call if it was a function and we have a response - if ( previous) { - if ( responseContainer && jQuery.isFunction( previous ) ) { - window[ jsonpCallback ] ( responseContainer[ 0 ] ); - } - } else { - // else, more memory leak avoidance - try{ - delete window[ jsonpCallback ]; - } catch( e ) {} - } - - }, s.complete ]; + // Install cleanUp function + jqXHR.then( cleanUp, cleanUp ); // Use data converter to retrieve json after script execution s.converters["script json"] = function() { - if ( ! responseContainer ) { + if ( !responseContainer ) { jQuery.error( jsonpCallback + " was not called" ); } return responseContainer[ 0 ]; @@ -6981,10 +7107,10 @@ // Install script dataType jQuery.ajaxSetup({ accepts: { - script: "text/javascript, application/javascript" + script: "text/javascript, application/javascript, application/ecmascript, application/x-ecmascript" }, contents: { - script: /javascript/ + script: /javascript|ecmascript/ }, converters: { "text script": function( text ) { @@ -7012,7 +7138,7 @@ if ( s.crossDomain ) { var script, - head = document.getElementsByTagName( "head" )[ 0 ] || document.documentElement; + head = document.head || document.getElementsByTagName( "head" )[0] || document.documentElement; return { @@ -7067,18 +7193,36 @@ -var // Next active xhr id +var // #5280: next active xhr id and list of active xhrs' callbacks xhrId = jQuery.now(), - - // active xhrs - xhrs = {}, - - // #5280: see below - xhrUnloadAbortInstalled, + xhrCallbacks, // XHR used to determine supports properties testXHR; +// #5280: Internet Explorer will keep connections alive if we don't abort on unload +function xhrOnUnloadAbort() { + jQuery( window ).unload(function() { + // Abort all pending requests + for ( var key in xhrCallbacks ) { + xhrCallbacks[ key ]( 0, 1 ); + } + }); +} + +// Functions to create xhrs +function createStandardXHR() { + try { + return new window.XMLHttpRequest(); + } catch( e ) {} +} + +function createActiveXHR() { + try { + return new window.ActiveXObject( "Microsoft.XMLHTTP" ); + } catch( e ) {} +} + // Create the request object // (This is still attached to ajaxSettings for backward compatibility) jQuery.ajaxSettings.xhr = window.ActiveXObject ? @@ -7089,27 +7233,13 @@ * we need a fallback. */ function() { - if ( window.location.protocol !== "file:" ) { - try { - return new window.XMLHttpRequest(); - } catch( xhrError ) {} - } - - try { - return new window.ActiveXObject("Microsoft.XMLHTTP"); - } catch( activeError ) {} + return !this.isLocal && createStandardXHR() || createActiveXHR(); } : // For all other browsers, use the standard XMLHttpRequest object - function() { - return new window.XMLHttpRequest(); - }; + createStandardXHR; // Test if we can create an xhr object -try { - testXHR = jQuery.ajaxSettings.xhr(); -} catch( xhrCreationException ) {} - -//Does this browser support XHR requests? +testXHR = jQuery.ajaxSettings.xhr(); jQuery.support.ajax = !!testXHR; // Does this browser support crossDomain XHR requests @@ -7130,26 +7260,10 @@ return { send: function( headers, complete ) { - // #5280: we need to abort on unload or IE will keep connections alive - if ( !xhrUnloadAbortInstalled ) { - - xhrUnloadAbortInstalled = 1; - - jQuery(window).bind( "unload", function() { - - // Abort all pending requests - jQuery.each( xhrs, function( _, xhr ) { - if ( xhr.onreadystatechange ) { - xhr.onreadystatechange( 1 ); - } - } ); - - } ); - } - // Get a new xhr var xhr = s.xhr(), - handle; + handle, + i; // Open the socket // Passing null username, generates a login popup on Opera (#2865) @@ -7159,19 +7273,31 @@ xhr.open( s.type, s.url, s.async ); } + // Apply custom fields if provided + if ( s.xhrFields ) { + for ( i in s.xhrFields ) { + xhr[ i ] = s.xhrFields[ i ]; + } + } + + // Override mime type if needed + if ( s.mimeType && xhr.overrideMimeType ) { + xhr.overrideMimeType( s.mimeType ); + } + // Requested-With header // Not set for crossDomain requests with no content // (see why at http://trac.dojotoolkit.org/ticket/9486) // Won't change header if already provided - if ( !( s.crossDomain && !s.hasContent ) && !headers["x-requested-with"] ) { - headers[ "x-requested-with" ] = "XMLHttpRequest"; + if ( !( s.crossDomain && !s.hasContent ) && !headers["X-Requested-With"] ) { + headers[ "X-Requested-With" ] = "XMLHttpRequest"; } // Need an extra try/catch for cross domain requests in Firefox 3 try { - jQuery.each( headers, function( key, value ) { - xhr.setRequestHeader( key, value ); - } ); + for ( i in headers ) { + xhr.setRequestHeader( i, headers[ i ] ); + } } catch( _ ) {} // Do send the request @@ -7182,75 +7308,79 @@ // Listener callback = function( _, isAbort ) { - // Was never called and is aborted or complete - if ( callback && ( isAbort || xhr.readyState === 4 ) ) { - - // Only called once - callback = 0; - - // Do not keep as active anymore - if ( handle ) { - xhr.onreadystatechange = jQuery.noop; - delete xhrs[ handle ]; + var status, + statusText, + responseHeaders, + responses, + xml; + + // Firefox throws exceptions when accessing properties + // of an xhr when a network error occured + // http://helpful.knobs-dials.com/index.php/Component_returned_failure_code:_0… + try { + + // Was never called and is aborted or complete + if ( callback && ( isAbort || xhr.readyState === 4 ) ) { + + // Only called once + callback = undefined; + + // Do not keep as active anymore + if ( handle ) { + xhr.onreadystatechange = jQuery.noop; + delete xhrCallbacks[ handle ]; + } + + // If it's an abort + if ( isAbort ) { + // Abort it manually if needed + if ( xhr.readyState !== 4 ) { + xhr.abort(); + } + } else { + status = xhr.status; + responseHeaders = xhr.getAllResponseHeaders(); + responses = {}; + xml = xhr.responseXML; + + // Construct response list + if ( xml && xml.documentElement /* #4958 */ ) { + responses.xml = xml; + } + responses.text = xhr.responseText; + + // Firefox throws an exception when accessing + // statusText for faulty cross-domain requests + try { + statusText = xhr.statusText; + } catch( e ) { + // We normalize with Webkit giving an empty statusText + statusText = ""; + } + + // Filter status for non standard behaviors + + // If the request is local and we have data: assume a success + // (success with no data won't get notified, that's the best we + // can do given current implementations) + if ( !status && s.isLocal && !s.crossDomain ) { + status = responses.text ? 200 : 404; + // IE - #1450: sometimes returns 1223 when it should be 204 + } else if ( status === 1223 ) { + status = 204; + } + } } - - // If it's an abort - if ( isAbort ) { - // Abort it manually if needed - if ( xhr.readyState !== 4 ) { - xhr.abort(); - } - } else { - // Get info - var status = xhr.status, - statusText, - responseHeaders = xhr.getAllResponseHeaders(), - responses = {}, - xml = xhr.responseXML; - - // Construct response list - if ( xml && xml.documentElement /* #4958 */ ) { - responses.xml = xml; - } - responses.text = xhr.responseText; - - // Firefox throws an exception when accessing - // statusText for faulty cross-domain requests - try { - statusText = xhr.statusText; - } catch( e ) { - // We normalize with Webkit giving an empty statusText - statusText = ""; - } - - // Filter status for non standard behaviours - status = - // Opera returns 0 when it should be 304 - // Webkit returns 0 for failing cross-domain no matter the real status - status === 0 ? - ( - // Webkit, Firefox: filter out faulty cross-domain requests - !s.crossDomain || statusText ? - ( - // Opera: filter out real aborts #6060 - responseHeaders ? - 304 : - 0 - ) : - // We assume 302 but could be anything cross-domain related - 302 - ) : - ( - // IE sometimes returns 1223 when it should be 204 (see #1450) - status == 1223 ? - 204 : - status - ); - - // Call complete - complete( status, statusText, responses, responseHeaders ); + } catch( firefoxAccessException ) { + if ( !isAbort ) { + complete( -1, firefoxAccessException ); } } + + // Call complete if needed + if ( responses ) { + complete( status, statusText, responses, responseHeaders ); + } }; // if we're in sync mode or it's in cache @@ -7259,10 +7389,15 @@ if ( !s.async || xhr.readyState === 4 ) { callback(); } else { - // Add to list of active xhrs + // Create the active xhrs callbacks list if needed + // and attach the unload handler + if ( !xhrCallbacks ) { + xhrCallbacks = {}; + xhrOnUnloadAbort(); + } + // Add to list of active xhrs callbacks handle = xhrId++; - xhrs[ handle ] = xhr; - xhr.onreadystatechange = callback; + xhr.onreadystatechange = xhrCallbacks[ handle ] = callback; } }, @@ -7464,11 +7599,11 @@ } else { var parts = rfxnum.exec(val), - start = e.cur() || 0; + start = e.cur(); if ( parts ) { var end = parseFloat( parts[2] ), - unit = parts[3] || "px"; + unit = parts[3] || ( jQuery.cssNumber[ name ] ? "" : "px" ); // We need to compute starting value if ( unit !== "px" ) { @@ -7615,8 +7750,12 @@ return this.elem[ this.prop ]; } - var r = parseFloat( jQuery.css( this.elem, this.prop ) ); - return r || 0; + var parsed, + r = jQuery.css( this.elem, this.prop ); + // Empty strings, null, undefined and "auto" are converted to 0, + // complex values such as "rotate(1rad)" are returned as is, + // simple values such as "10px" are parsed to Float. + return isNaN( parsed = parseFloat( r ) ) ? !r || r === "auto" ? 0 : r : parsed; }, // Start an animation from one number to another @@ -7627,7 +7766,7 @@ this.startTime = jQuery.now(); this.start = from; this.end = to; - this.unit = unit || this.unit || "px"; + this.unit = unit || this.unit || ( jQuery.cssNumber[ this.prop ] ? 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commit/galaxy-central: kanwei: Updated bigBed test file
by Bitbucket 24 Feb '11

24 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/818f94014a76/ changeset: r5123:818f94014a76 user: kanwei date: 2011-02-24 22:19:03 summary: Updated bigBed test file affected #: 1 file (0 bytes) Binary file test-data/7.bigbed has changed 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 options to Tophat wrapper to support v1.2.0 functionality: (a) allow indel search; (b) max insertion and max deletion lengths; and (c) library type. Update functional tests to tests new options. Also update function that checks from_work_dir output attribute to use real path to prevent mishandling of symbolic links.
by Bitbucket 24 Feb '11

24 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/c0d6d17fc7db/ changeset: r5122:c0d6d17fc7db user: jgoecks date: 2011-02-24 21:24:52 summary: Add options to Tophat wrapper to support v1.2.0 functionality: (a) allow indel search; (b) max insertion and max deletion lengths; and (c) library type. Update functional tests to tests new options. Also update function that checks from_work_dir output attribute to use real path to prevent mishandling of symbolic links. affected #: 5 files (6.0 KB) --- a/lib/galaxy/jobs/__init__.py Thu Feb 24 15:23:21 2011 -0500 +++ b/lib/galaxy/jobs/__init__.py Thu Feb 24 15:24:52 2011 -0500 @@ -505,10 +505,14 @@ return job_context = ExpressionContext( dict( stdout = stdout, stderr = stderr ) ) job_tool = self.app.toolbox.tools_by_id.get( job.tool_id, None ) - def file_in_dir( file_path, a_dir ): - """ Returns true if file is in directory. """ - abs_file_path = os.path.abspath( file_path ) - return os.path.split( abs_file_path )[0] == os.path.abspath( a_dir ) + def in_directory( file, directory ): + # Make both absolute. + directory = os.path.realpath( directory ) + file = os.path.realpath( file ) + + #Return true, if the common prefix of both is equal to directory + #e.g. /a/b/c/d.rst and directory is /a/b, the common prefix is /a/b + return os.path.commonprefix( [ file, directory ] ) == directory for dataset_assoc in job.output_datasets + job.output_library_datasets: context = self.get_dataset_finish_context( job_context, dataset_assoc.dataset.dataset ) #should this also be checking library associations? - can a library item be added from a history before the job has ended? - lets not allow this to occur @@ -523,7 +527,7 @@ if hda_tool_output and hda_tool_output.from_work_dir: # Copy from working dir to HDA. source_file = os.path.join( os.path.abspath( self.working_directory ), hda_tool_output.from_work_dir ) - if file_in_dir( source_file, self.working_directory ): + if in_directory( source_file, self.working_directory ): try: shutil.move( source_file, dataset.file_name ) log.debug( "finish(): Moved %s to %s as directed by from_work_dir" % ( source_file, dataset.file_name ) ) --- a/tools/ngs_rna/tophat_wrapper.py Thu Feb 24 15:23:21 2011 -0500 +++ b/tools/ngs_rna/tophat_wrapper.py Thu Feb 24 15:24:52 2011 -0500 @@ -30,6 +30,10 @@ parser.add_option( '-g', '--max_multihits', dest='max_multihits', help='Maximum number of alignments to be allowed' ) parser.add_option( '', '--seg-mismatches', dest='seg_mismatches', help='Number of mismatches allowed in each segment alignment for reads mapped independently' ) parser.add_option( '', '--seg-length', dest='seg_length', help='Minimum length of read segments' ) + parser.add_option( '', '--library-type', dest='library_type', help='TopHat will treat the reads as strand specific. Every read alignment will have an XS attribute tag. Consider supplying library type options below to select the correct RNA-seq protocol.' ) + parser.add_option( '', '--allow-indels', action="store_true", help='Allow indel search. Indel search is disabled by default.' ) + parser.add_option( '', '--max-insertion-length', dest='max_insertion_length', help='The maximum insertion length. The default is 3.' ) + parser.add_option( '', '--max-deletion-length', dest='max_deletion_length', help='The maximum deletion length. The default is 3.' ) # Options for supplying own junctions parser.add_option( '-G', '--GTF', dest='gene_model_annotations', help='Supply TopHat with a list of gene model annotations. \ @@ -115,8 +119,7 @@ index_path = options.index_path # Build tophat command. - tmp_output_dir = tempfile.mkdtemp() - cmd = 'tophat -o %s %s %s %s' + cmd = 'tophat %s %s %s' reads = options.input1 if options.input2: reads += ' ' + options.input2 @@ -124,7 +127,7 @@ if options.single_paired == 'paired': opts += ' -r %s' % options.mate_inner_dist if options.settings == 'preSet': - cmd = cmd % ( tmp_output_dir, opts, index_path, reads ) + cmd = cmd % ( opts, index_path, reads ) else: try: if int( options.min_anchor_length ) >= 3: @@ -144,6 +147,13 @@ opts += ' -j %s' % options.raw_juncs if options.no_novel_juncs: opts += ' --no-novel-juncs' + if options.library_type: + opts += ' --library-type %s' % options.library_type + if options.allow_indels: + # Max options do not work for Tophat v1.2.0, despite documentation to the contrary. + opts += ' --allow-indels' + #opts += ' --allow-indels --max-insertion-length %i --max-deletion-length %i' % ( int( options.max_insertion_length ), int( options.max_deletion_length ) ) + # Search type options. if options.coverage_search: @@ -166,23 +176,21 @@ opts += ' --min-segment-intron %d' % int(options.min_segment_intron) if options.max_segment_intron: opts += ' --max-segment-intron %d' % int(options.max_segment_intron) - cmd = cmd % ( tmp_output_dir, opts, index_path, reads ) + cmd = cmd % ( opts, index_path, reads ) except Exception, e: # Clean up temp dirs if os.path.exists( tmp_index_dir ): shutil.rmtree( tmp_index_dir ) - if os.path.exists( tmp_output_dir ): - shutil.rmtree( tmp_output_dir ) stop_err( 'Something is wrong with the alignment parameters and the alignment could not be run\n' + str( e ) ) print cmd # Run try: - tmp_out = tempfile.NamedTemporaryFile( dir=tmp_output_dir ).name + tmp_out = tempfile.NamedTemporaryFile().name tmp_stdout = open( tmp_out, 'wb' ) - tmp_err = tempfile.NamedTemporaryFile( dir=tmp_output_dir ).name + tmp_err = tempfile.NamedTemporaryFile().name tmp_stderr = open( tmp_err, 'wb' ) - proc = subprocess.Popen( args=cmd, shell=True, cwd=tmp_output_dir, stdout=tmp_stdout, stderr=tmp_stderr ) + proc = subprocess.Popen( args=cmd, shell=True, cwd=".", stdout=tmp_stdout, stderr=tmp_stderr ) returncode = proc.wait() tmp_stderr.close() # get stderr, allowing for case where it's very large @@ -202,17 +210,11 @@ raise Exception, stderr # TODO: look for errors in program output. - - # Copy output files from tmp directory to specified files. - shutil.copyfile( os.path.join( tmp_output_dir, "junctions.bed" ), options.junctions_output_file ) - shutil.copyfile( os.path.join( tmp_output_dir, "accepted_hits.bam" ), options.accepted_hits_output_file ) except Exception, e: stop_err( 'Error in tophat:\n' + str( e ) ) # Clean up temp dirs if os.path.exists( tmp_index_dir ): shutil.rmtree( tmp_index_dir ) - if os.path.exists( tmp_output_dir ): - shutil.rmtree( tmp_output_dir ) if __name__=="__main__": __main__() --- a/tools/ngs_rna/tophat_wrapper.xml Thu Feb 24 15:23:21 2011 -0500 +++ b/tools/ngs_rna/tophat_wrapper.xml Thu Feb 24 15:24:52 2011 -0500 @@ -39,6 +39,14 @@ --max-segment-intron $singlePaired.sParams.max_segment_intron --seg-mismatches=$singlePaired.sParams.seg_mismatches --seg-length=$singlePaired.sParams.seg_length + --library-type=$singlePaired.sParams.library_type + + ## Indel search. + #if $singlePaired.sParams.indel_search.allow_indel_search == "Yes": + --allow-indels + --max-insertion-length $singlePaired.sParams.indel_search.max_insertion_length + --max-deletion-length $singlePaired.sParams.indel_search.max_deletion_length + #end if ## Supplying junctions parameters. #if $singlePaired.sParams.own_junctions.use_junctions == "Yes": @@ -90,6 +98,14 @@ --max-segment-intron $singlePaired.pParams.max_segment_intron --seg-mismatches=$singlePaired.pParams.seg_mismatches --seg-length=$singlePaired.pParams.seg_length + --library-type=$singlePaired.pParams.library_type + + ## Indel search. + #if $singlePaired.pParams.indel_search.allow_indel_search == "Yes": + --allow-indels + --max-insertion-length $singlePaired.pParams.indel_search.max_insertion_length + --max-deletion-length $singlePaired.pParams.indel_search.max_deletion_length + #end if ## Supplying junctions parameters. #if $singlePaired.pParams.own_junctions.use_junctions == "Yes": @@ -157,10 +173,26 @@ <when value="preSet" /><when value="full"> + <param name="library_type" type="select" label="Library Type" help="TopHat will treat the reads as strand specific. Every read alignment will have an XS attribute tag. Consider supplying library type options below to select the correct RNA-seq protocol."> + <option value="fr-unstranded">FR Unstranded</option> + <option value="fr-firststrand">FR First Strand</option> + <option value="fr-secondstrand">FR Second Strand</option> + </param><param name="anchor_length" type="integer" value="8" label="Anchor length (at least 3)" help="Report junctions spanned by reads with at least this many bases on each side of the junction." /><param name="splice_mismatches" type="integer" value="0" label="Maximum number of mismatches that can appear in the anchor region of spliced alignment" /><param name="min_intron_length" type="integer" value="70" label="The minimum intron length" help="TopHat will ignore donor/acceptor pairs closer than this many bases apart." /><param name="max_intron_length" type="integer" value="500000" label="The maximum intron length" help="When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read." /> + <conditional name="indel_search"> + <param name="allow_indel_search" type="select" label="Allow indel search"> + <option value="No">No</option> + <option value="Yes">Yes</option> + </param> + <when value="No"/> + <when value="Yes"> + <param name="max_insertion_length" type="integer" value="3" label="Max insertion length." help="The maximum insertion length." /> + <param name="max_deletion_length" type="integer" value="3" label="Max deletion length." help="The maximum deletion length." /> + </when> + </conditional><param name="junction_filter" type="float" value="0.15" label="Minimum isoform fraction: filter out junctions supported by too few alignments (number of reads divided by average depth of coverage)" help="0.0 to 1.0 (0 to turn off)" /><param name="max_multihits" type="integer" value="40" label="Maximum number of alignments to be allowed" /><param name="min_segment_intron" type="integer" value="50" label="Minimum intron length that may be found during split-segment (default) search" /> @@ -247,11 +279,27 @@ <when value="preSet" /><when value="full"> + <param name="library_type" type="select" label="Library Type" help="TopHat will treat the reads as strand specific. Every read alignment will have an XS attribute tag. Consider supplying library type options below to select the correct RNA-seq protocol."> + <option value="fr-unstranded">FR Unstranded</option> + <option value="fr-firststrand">FR First Strand</option> + <option value="fr-secondstrand">FR Second Strand</option> + </param><param name="mate_std_dev" type="integer" value="20" label="Std. Dev for Distance between Mate Pairs" help="The standard deviation for the distribution on inner distances between mate pairs."/><param name="anchor_length" type="integer" value="8" label="Anchor length (at least 3)" help="Report junctions spanned by reads with at least this many bases on each side of the junction." /><param name="splice_mismatches" type="integer" value="0" label="Maximum number of mismatches that can appear in the anchor region of spliced alignment" /><param name="min_intron_length" type="integer" value="70" label="The minimum intron length" help="TopHat will ignore donor/acceptor pairs closer than this many bases apart." /><param name="max_intron_length" type="integer" value="500000" label="The maximum intron length" help="When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read." /> + <conditional name="indel_search"> + <param name="allow_indel_search" type="select" label="Allow indel search"> + <option value="No">No</option> + <option value="Yes">Yes</option> + </param> + <when value="No"/> + <when value="Yes"> + <param name="max_insertion_length" type="integer" value="3" label="Max insertion length." help="The maximum insertion length." /> + <param name="max_deletion_length" type="integer" value="3" label="Max deletion length." help="The maximum deletion length." /> + </when> + </conditional><param name="junction_filter" type="float" value="0.15" label="Minimum isoform fraction: filter out junctions supported by too few alignments (number of reads divided by average depth of coverage)" help="0.0 to 1.0 (0 to turn off)" /><param name="max_multihits" type="integer" value="40" label="Maximum number of alignments to be allowed" /><param name="min_segment_intron" type="integer" value="50" label="Minimum intron length that may be found during split-segment (default) search" /> @@ -329,8 +377,28 @@ </inputs><outputs> - <data format="bed" name="junctions" label="${tool.name} on ${on_string}: splice junctions"/> - <data format="bam" name="accepted_hits" label="${tool.name} on ${on_string}: accepted_hits"/> + <data format="bed" name="insertions" label="${tool.name} on ${on_string}: insertions" from_work_dir="tophat_out/insertions.bed"> + <filter> + ( + ( ( 'sParams' in singlePaired ) and ( 'indel_search' in singlePaired['sParams'] ) and + ( singlePaired['sParams']['indel_search']['allow_indel_search'] == 'Yes' ) ) or + ( ( 'pParams' in singlePaired ) and ( 'indel_search' in singlePaired['pParams'] ) and + ( singlePaired['pParams']['indel_search']['allow_indel_search'] == 'Yes' ) ) + ) + </filter> + </data> + <data format="bed" name="deletions" label="${tool.name} on ${on_string}: deletions" from_work_dir="tophat_out/deletions.bed"> + <filter> + ( + ( ( 'sParams' in singlePaired ) and ( 'indel_search' in singlePaired['sParams'] ) and + ( singlePaired['sParams']['indel_search']['allow_indel_search'] == 'Yes' ) ) or + ( ( 'pParams' in singlePaired ) and ( 'indel_search' in singlePaired['pParams'] ) and + ( singlePaired['pParams']['indel_search']['allow_indel_search'] == 'Yes' ) ) + ) + </filter> + </data> + <data format="bed" name="junctions" label="${tool.name} on ${on_string}: splice junctions" from_work_dir="tophat_out/junctions.bed"/> + <data format="bam" name="accepted_hits" label="${tool.name} on ${on_string}: accepted_hits" from_work_dir="tophat_out/accepted_hits.bam"/></outputs><tests> @@ -367,7 +435,7 @@ <test><param name="genomeSource" value="history"/> @@ -375,6 +443,7 @@ <param name="sPaired" value="single"/><param name="input1" ftype="fastqsanger" value="tophat_in2.fastqsanger"/><param name="sSettingsType" value="full"/> + <param name="library_type" value="FR Unstranded"/><param name="anchor_length" value="8"/><param name="splice_mismatches" value="0"/><param name="min_intron_length" value="70"/> @@ -386,6 +455,9 @@ <param name="max_segment_intron" value="500000" /><param name="seg_mismatches" value="2"/><param name="seg_length" value="25"/> + <param name="allow_indel_search" value="Yes"/> + <param name="max_insertion_length" value="3"/> + <param name="max_deletion_length" value="3"/><param name="use_junctions" value="Yes" /><param name="use_annotations" value="No" /><param name="use_juncs" value="No" /> @@ -398,6 +470,8 @@ <param name="min_coverage_intron" value="50" /><param name="max_coverage_intron" value="20000" /><param name="microexon_search" value="Yes" /> + <output name="insertions" file="tophat_out3i.bed" ftype="bed"/> + <output name="deletions" file="tophat_out3d.bed" ftype="bed"/><output name="junctions" file="tophat_out3j.bed" ftype="bed" /><output name="accepted_hits" file="tophat_out3h.bam" compare="sim_size" ftype="bam" /></test> @@ -414,6 +488,7 @@ <param name="input2" ftype="fastqsanger" value="tophat_in3.fastqsanger"/><param name="mate_inner_distance" value="20"/><param name="pSettingsType" value="full"/> + <param name="library_type" value="FR Unstranded"/><param name="mate_std_dev" value="20"/><param name="anchor_length" value="8"/><param name="splice_mismatches" value="0"/> @@ -426,6 +501,7 @@ <param name="max_segment_intron" value="500000" /><param name="seg_mismatches" value="2"/><param name="seg_length" value="25"/> + <param name="allow_indel_search" value="No"/><param name="use_junctions" value="Yes" /><param name="use_annotations" value="No" /><param name="use_juncs" value="No" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: kanwei: Fix bed_to_bigBed test
by Bitbucket 24 Feb '11

24 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/1a544e327b3d/ changeset: r5121:1a544e327b3d user: kanwei date: 2011-02-24 21:23:21 summary: Fix bed_to_bigBed test affected #: 2 files (18 bytes) --- a/buildbot_setup.sh Thu Feb 24 15:07:46 2011 -0500 +++ b/buildbot_setup.sh Thu Feb 24 15:23:21 2011 -0500 @@ -109,7 +109,7 @@ fi done -# for wig_to_bigWig +# for wig_to_bigWig and bed_to_bigBed if [ ! -f "tool-data/shared/ucsc/chrom/hg17.len" -a -f "test-data/wig_to_bigwig_hg17.len" ]; then mkdir -p tool-data/shared/ucsc/chrom cp test-data/wig_to_bigwig_hg17.len tool-data/shared/ucsc/chrom/hg17.len --- a/tools/filters/bed_to_bigbed.xml Thu Feb 24 15:07:46 2011 -0500 +++ b/tools/filters/bed_to_bigbed.xml Thu Feb 24 15:23:21 2011 -0500 @@ -31,7 +31,7 @@ </outputs><tests><test> - <param name="input1" value="7.bed" dbkey="hg18" /> + <param name="input1" value="7.bed" dbkey="hg17" /><param name="settingsType" value="full" /><param name="blockSize" value="256" /><param name="itemsPerSlot" value="512" /> @@ -39,7 +39,7 @@ <output name="out_file1" file="7.bigbed"/></test><test> - <param name="input1" value="7.bed" dbkey="hg18" /> + <param name="input1" value="7.bed" dbkey="hg17" /><param name="settingsType" value="preset" /><output name="out_file1" file="7.bigbed"/></test> 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: Fix BLAST+ test
by Bitbucket 24 Feb '11

24 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/fb51941391ed/ changeset: r5120:fb51941391ed user: kanwei date: 2011-02-24 21:07:46 summary: Fix BLAST+ test affected #: 1 file (1 byte) --- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Thu Feb 24 12:27:37 2011 -0500 +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Thu Feb 24 15:07:46 2011 -0500 @@ -1,7 +1,7 @@ <tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.8"><description>Search translated nucleotide database with protein query sequence(s)</description><command interpreter="python">hide_stderr.py -# The command is a Cheetah template which allows some Python based syntax. +## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces tblastn -query "$query" 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: Fix debugging output on BLASTX+ failure
by Bitbucket 24 Feb '11

24 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/dd3c21ebfa4a/ changeset: r5119:dd3c21ebfa4a user: kanwei date: 2011-02-24 18:27:37 summary: Fix debugging output on BLASTX+ failure affected #: 1 file (164 bytes) --- a/tools/ncbi_blast_plus/hide_stderr.py Thu Feb 24 12:16:33 2011 -0500 +++ b/tools/ncbi_blast_plus/hide_stderr.py Thu Feb 24 12:27:37 2011 -0500 @@ -23,6 +23,13 @@ #Avoid using shell=True when we call subprocess to ensure if the Python #script is killed, so too is the BLAST process. try: + words = [] + for w in sys.argv[1:]: + if " " in w: + words.append('"%s"' % w) + else: + words.append(w) + cmd = " ".join(words) child = subprocess.Popen(sys.argv[1:], stdout=subprocess.PIPE, stderr=subprocess.PIPE) except Exception, err: 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: rc: Adding ftype attribute to vcf tool tests
by Bitbucket 24 Feb '11

24 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/07275d9052af/ changeset: r5118:07275d9052af user: rc date: 2011-02-24 18:16:33 summary: Adding ftype attribute to vcf tool tests affected #: 3 files (142 bytes) --- a/lib/galaxy/tools/parameters/basic.py Thu Feb 24 09:17:50 2011 -0500 +++ b/lib/galaxy/tools/parameters/basic.py Thu Feb 24 12:16:33 2011 -0500 @@ -202,7 +202,7 @@ except: raise ValueError( "An integer is required" ) elif self.value is None: - raise ValueError( "The settings for this field require a 'value' setting and optionally a default value which must be an integer" ) + raise ValueError( "The settings for the field named '%s' require a 'value' setting and optionally a default value which must be an integer" % self.name ) self.min = elem.get( 'min' ) self.max = elem.get( 'max' ) if self.min: --- a/tools/vcf_tools/annotate.xml Thu Feb 24 09:17:50 2011 -0500 +++ b/tools/vcf_tools/annotate.xml Thu Feb 24 12:16:33 2011 -0500 @@ -31,15 +31,15 @@ </outputs><tests><test> - <param name="input1" value="test.small.vcf" /> + <param name="input1" value="test.small.vcf" ftype="vcf" /><param name="annotate" value="dbsnp" /> - <param name="input2" value="dbsnp.small.vcf" /> + <param name="input2" value="dbsnp.small.vcf" ftype="vcf" /><output name="output" file="test_annotated_dbsnp.vcf" lines_diff="6" ftype="vcf" /></test><test> - <param name="input1" value="test.small.vcf" /> + <param name="input1" value="test.small.vcf" ftype="vcf" /><param name="annotate" value="hapmap" /> - <param name="input2" value="hapmap.small.vcf" /> + <param name="input2" value="hapmap.small.vcf" ftype="vcf" /><output name="output" file="test_annotated_hapmap.vcf" lines_diff="6" ftype="vcf" /></test></tests> --- a/tools/vcf_tools/intersect.xml Thu Feb 24 09:17:50 2011 -0500 +++ b/tools/vcf_tools/intersect.xml Thu Feb 24 12:16:33 2011 -0500 @@ -41,23 +41,23 @@ </outputs><tests><test> - <param name="input1" value="1.vcf" /> + <param name="input1" value="1.vcf" ftype="vcf" /><param name="format" value="vcf" /> - <param name="input2" value="2.vcf" /> + <param name="input2" value="2.vcf" ftype="vcf" /><param name="priority_file" value="none" /><output name="output" file="1_2_intersect_priority_0.vcf" lines_diff="2" ftype="vcf" /></test><test> - <param name="input1" value="1.vcf" /> + <param name="input1" value="1.vcf" ftype="vcf" /><param name="format" value="vcf" /> - <param name="input2" value="2.vcf" /> + <param name="input2" value="2.vcf" ftype="vcf" /><param name="priority_file" value="first_file" /><output name="output" file="1_2_intersect_priority_1.vcf" lines_diff="2" ftype="vcf" /></test><test> - <param name="input1" value="1.vcf" /> + <param name="input1" value="1.vcf" ftype="vcf" /><param name="format" value="vcf" /> - <param name="input2" value="2.vcf" /> + <param name="input2" value="2.vcf" ftype="vcf" /><param name="priority_file" value="second_file" /><output name="output" file="1_2_intersect_priority_2.vcf" lines_diff="2" ftype="vcf" /></test> 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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