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galaxy-dist commit 7de1adaf5628: Add SAM indel filter tool to tool_conf.xml.sample
by commits-noreply＠bitbucket.org 08 Jun '10

08 Jun '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kelly Vincent <kpvincent(a)bx.psu.edu> # Date 1275939020 14400 # Node ID 7de1adaf5628e04e2da0d948f03d08cb5ce5d7f3 # Parent 5ba6a1d980ac4d446478d8a4d054234d6342a979 Add SAM indel filter tool to tool_conf.xml.sample --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -253,6 +253,7 @@ </section><section name="NGS: SAM Tools" id="samtools"><tool file="samtools/sam_bitwise_flag_filter.xml" /> + <tool file="samtools/sam_indel_filter.xml" /><tool file="samtools/sam2interval.xml" /><tool file="samtools/sam_to_bam.xml" /><tool file="samtools/sam_merge.xml" />

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galaxy-dist commit 5ba6a1d980ac: merged SAM indel filter tool commit
by commits-noreply＠bitbucket.org 08 Jun '10

08 Jun '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kelly Vincent <kpvincent(a)bx.psu.edu> # Date 1275938865 14400 # Node ID 5ba6a1d980ac4d446478d8a4d054234d6342a979 # Parent 1ab9d6b0ddfc65bc6e58c77891c57ef99e1e12cb # Parent c3ced3ed4fee6e0bdb5acbc7bdc2518995f97e7a merged SAM indel filter tool commit

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galaxy-dist commit c3ced3ed4fee: Adding SAM indel filter tool with test files
by commits-noreply＠bitbucket.org 08 Jun '10

08 Jun '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kelly Vincent <kpvincent(a)bx.psu.edu> # Date 1275938612 14400 # Node ID c3ced3ed4fee6e0bdb5acbc7bdc2518995f97e7a # Parent f7cf88978f1f848b97c5da1bfe6e48aeb1930378 Adding SAM indel filter tool with test files --- /dev/null +++ b/test-data/sam_indel_filter_out1.sam @@ -0,0 +1,3 @@ +1378_28_770 89 chr11.nib:1-134452384 72131356 37 17M1I5M = 72131356 0 CACACTGTGACAGACAGCGCAGC 00/02!!0//1200210AA44/1 XT:A:U CM:i:2 SM:i:37 AM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:22 +1378_69_800 16 chr11.nib:1-125234658 241 255 15M1D8M * 0 0 CGTGGCCGGCGGGCCGAAGGCAT IIIIIIIIIICCCCIII?IIIII +1378_72_1612 151 chrY.nib:1-124295114 190342418 37 19M1I3M = 190342418 0 TCTAACTTAGCCTCATAATAGCT /<<!"0/4//7//00/BC0121/ XT:A:U CM:i:2 SM:i:37 AM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:22 --- /dev/null +++ b/tools/samtools/sam_indel_filter.xml @@ -0,0 +1,74 @@ +<tool id="sam_indel_filter" name="Filter SAM" version="1.0.0"> + <description>for indels</description> + <command interpreter="python"> + sam_indel_filter.py + --input=$input1 + --quality_threshold=$quality_threshold + --adjacent_bases=$adjacent_bases + --output=$out_file1 + </command> + <inputs> + <param format="sam" name="input1" type="data" label="Select dataset to filter" /> + <param name="quality_threshold" type="integer" value="40" label="Quality threshold for adjacent bases" help="You need to give the true value, not offset (see chart below), regardless of source FASTQ type" /> + <param name="adjacent_bases" type="integer" value="5" label="The number of adjacent bases to match on either side of the indel" help="If one side is shorter than this width, it will still match if the long-enough side matches" /> + </inputs> + <outputs> + <data format="sam" name="out_file1" /> + </outputs> + <tests> + <test> + <param name="input1" value="sam_indel_filter_in1.sam" ftype="sam"/> + <param name="quality_threshold" value="47"/> + <param name="adjacent_bases" value="2"/> + <output name="out_file1" file="sam_indel_filter_out1.sam" ftype="sam"/> + </test> + <test> + <param name="input1" value="sam_indel_filter_in1.sam" ftype="sam"/> + <param name="quality_threshold" value="62"/> + <param name="adjacent_bases" value="5"/> + <output name="out_file1" file="sam_indel_filter_out2.sam" ftype="sam"/> + </test> + </tests> + <help> + +**What it does** + +Allows extracting indels from SAM. Currently it can handle SAM with alignments with only one insertion or one deletion, and will throw an error if it encounters an alignment with more than one. It matches CIGAR strings (column 6 in the SAM file) like 5M3I5M or 4M2D10M, so there must be a match or mismatch of sufficient length on either side of the indel. + +----- + +**Example** + +Suppose you have the following:: + + r770 89 ref 116 37 17M1I5M = 72131356 0 CACACTGTGACAGACAGCGCAGC 00/02!!0//1200210AA44/1 XT:A:U CM:i:2 SM:i:37 AM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:22 + r770 181 ref 116 0 24M = 72131356 0 TTGGTGCGCGCGGTTGAGGGTTGG $$(#%%#$%#%####$%%##$### + r1945 113 ref 181247988 0 23M 41710908 41710908 0 GAGAGAGAGAGAGAGAGAGAGAG PQRVUMNXYRPUXYXWXSOSZ]M XT:A:R CM:i:0 SM:i:0 AM:i:0 X0:i:163148 XM:i:0 XO:i:0 XG:i:0 MD:Z:23 + r1945 177 ref 41710908 0 23M 190342418 181247988 0 AGAGAGAGAGAGAGAGAGAGAGA SQQWZYURVYWX]]YXTSY]]ZM XT:A:R CM:i:0 SM:i:0 AM:i:0 X0:i:163148 XM:i:0 XO:i:0 XG:i:0 MD:Z:23 + r2363 115 ref 19671878 0 23M = 19671877 -1 AGAGAGAGAGAGAGAGAGAGTCT 77543:<55#"4!&=964518A> XT:A:R CM:i:2 SM:i:0 AM:i:0 X0:i:4 X1:i:137 XM:i:2 XO:i:0 XG:i:0 MD:Z:23 + r2363 179 ref 19671877 0 23M = 19671878 1 GAGAGAGAGAGAGAGAGAGAGTC LE7402DD34FL:27AKE>;432 XT:A:R CM:i:0 SM:i:0 AM:i:0 X0:i:265 XM:i:0 XO:i:0 XG:i:0 MD:Z:23 + r3671 117 ref 190342418 0 24M = 190342418 0 CTGGCGTTCTCGGCGTGGATGGGT #####$$##$#%#%%###%$#$## + r3671 153 ref 190342418 37 16M1I6M = 190342418 0 TCTAACTTAGCCTCATAATAGCT /<<!"0///////00/!!0121/ XT:A:U CM:i:2 SM:i:37 AM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:22 + r3824 117 ref 80324999 0 24M = 80324999 0 TCCAGTCGCGTTGTTAGGTTCGGA #$#$$$#####%##%%###**#+/ + r3824 153 ref 80324999 37 8M1I14M = 80324999 0 TTTAGCCCGAAATGCCTAGAGCA 4;6//11!"11100110////00 XT:A:U CM:i:2 SM:i:37 AM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:22 + r4795 81 ref 26739130 0 23M 57401793 57401793 0 TGGCATTCCTGTAGGCAGAGAGG AZWWZS]!"QNXZ]VQ]]]/2]] XT:A:R CM:i:2 SM:i:0 AM:i:0 X0:i:3 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:23 + r4795 161 ref 57401793 37 23M 26739130 26739130 0 GATCACCCAGGTGATGTAACTCC ]WV]]]]WW]]]]]]]]]]PU]] XT:A:U CM:i:0 SM:i:37 AM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:23 + r4800 16 ref 241 255 15M1D8M * 0 0 CGTGGCCGGCGGGCCGAAGGCAT IIIIIIIIIICCCCIII?IIIII + r5377 170 ref 59090793 37 23M 26739130 26739130 0 TATCAATAAGGTGATGTAACTCG ]WV]ABAWW]]]]]P]P//GU]] XT:A:U CM:i:0 SM:i:37 AM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:23 + r5612 151 ref 190342418 37 19M1I3M = 190342418 0 TCTAACTTAGCCTCATAATAGCT /<<!"0/4//7//00/BC0121/ XT:A:U CM:i:2 SM:i:37 AM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:22 + + +To select only alignments with indels, you need to determine the minimum quality you want the adjacent bases to have, as well as the number of adjacent bases to check. If you set the quality threshold to 47 and the number of bases to check to 2, you will get the following output:: + + r770 89 ref 116 37 17M1I5M = 72131356 0 CACACTGTGACAGACAGCGCAGC 00/02!!0//1200210AA44/1 XT:A:U CM:i:2 SM:i:37 AM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:22 + r4800 16 ref 241 255 15M1D8M * 0 0 CGTGGCCGGCGGGCCGAAGGCAT IIIIIIIIIICCCCIII?IIIII + r5612 151 ref 190342418 37 19M1I3M = 190342418 0 TCTAACTTAGCCTCATAATAGCT /<<!"0/4//7//00/BC0121/ XT:A:U CM:i:2 SM:i:37 AM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:22 + + +For more information on SAM, please consult the `SAM format description`__. + +.. __: http://www.ncbi.nlm.nih.gov/pubmed/19505943 + + + </help> +</tool> --- /dev/null +++ b/tools/samtools/sam_indel_filter.py @@ -0,0 +1,83 @@ +#!/usr/bin/env python + +""" +Allows user to filter out non-indels from SAM. + +usage: %prog [options] + -i, --input=i: Input SAM file to be filtered + -q, --quality_threshold=q: Minimum quality value for adjacent bases + -a, --adjacent_bases=a: Number of adjacent bases on each size to check qualities + -o, --output=o: Filtered output SAM file +""" + +import re, sys +from galaxy import eggs +import pkg_resources; pkg_resources.require( "bx-python" ) +from bx.cookbook import doc_optparse + + +def stop_err( msg ): + sys.stderr.write( '%s\n' % msg ) + sys.exit() + +def __main__(): + #Parse Command Line + options, args = doc_optparse.parse( __doc__ ) + # prep output file + output = open( options.output, 'wb' ) + # patterns + pat_indel = re.compile( '(?P<before_match>(\d+[MIDNSHP])*)(?P<lmatch>\d+)M(?P<ins_del_width>\d+)(?P<ins_del>[ID])(?P<rmatch>\d+)M' ) + pat_matches = re.compile( '\d+[MIDNSHP]' ) + qual_thresh = int( options.quality_threshold ) + adj_bases = int( options.adjacent_bases ) + # go through all lines in input file + for line in open( options.input, 'rb' ): + if line and not line.startswith( '#' ) and not line.startswith( '@' ) : + split_line = line.split( '\t' ) + cigar = split_line[5] + # find all possible matches, like 3M2D7M and 7M3I10M in 3M2D7M3I10M + cigar_copy = cigar[:] + matches = [] + while len( cigar_copy ) >= 6: # nMnInM or nMnDnM + m = pat_indel.match( cigar_copy ) + if not m: + break + else: + parts = m.groupdict() + parts[ 'start' ] = m.start() + matches.append( parts ) + cigar_copy = cigar_copy[ len( parts[ 'lmatch' ] ) : ] + # see if matches meet filter requirements + if len( matches ) == 1: + start = int( matches[0][ 'start' ] ) + left = int( matches[0][ 'lmatch' ] ) + right = int( matches[0][ 'rmatch' ] ) + if matches[0][ 'ins_del' ] == 'D': + middle = int( matches[0][ 'ins_del_width' ] ) + else: + middle = 0 + # if there are enough adjacent bases to check, then do so + if left >= adj_bases and right >= adj_bases: + qual = split_line[10] + left_bases = qual[ start : start + left + 1 ][ -adj_bases : ] + right_bases = qual[ start + left + middle : start + left + middle + right + 1 ][ : adj_bases ] + qual_thresh_met = True + for l in left_bases: + if ord( l ) < qual_thresh: + qual_thresh_met = False + break + if qual_thresh_met: + for r in right_bases: + if ord( r ) < qual_thresh: + qual_thresh_met = False + break + # if filter reqs met, output line + if qual_thresh_met: + output.write( line ) + # error if there are multiple indels + elif len( matches ) > 1: + stop_err( 'There is more than one indel present in the alignment:\n%s' % line ) + # close out file + output.close() + +if __name__=="__main__": __main__() --- /dev/null +++ b/test-data/sam_indel_filter_out2.sam @@ -0,0 +1,1 @@ +1378_69_800 16 chr11.nib:1-125234658 241 255 15M1D8M * 0 0 CGTGGCCGGCGGGCCGAAGGCAT IIIIIIIIIICCCCIII?IIIII --- /dev/null +++ b/test-data/sam_indel_filter_in1.sam @@ -0,0 +1,15 @@ +1378_28_770 89 chr11.nib:1-134452384 72131356 37 17M1I5M = 72131356 0 CACACTGTGACAGACAGCGCAGC 00/02!!0//1200210AA44/1 XT:A:U CM:i:2 SM:i:37 AM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:22 +1378_28_770 181 chr11.nib:1-134452384 72131356 0 24M = 72131356 0 TTGGTGCGCGCGGTTGAGGGTTGG $$(#%%#$%#%####$%%##$### +1378_33_1945 113 chr2.nib:1-242951149 181247988 0 23M chr12.nib:1-132349534 41710908 0 GAGAGAGAGAGAGAGAGAGAGAG PQRVUMNXYRPUXYXWXSOSZ]M XT:A:R CM:i:0 SM:i:0 AM:i:0 X0:i:163148 XM:i:0 XO:i:0 XG:i:0 MD:Z:23 +1378_33_1945 177 chr12.nib:1-132349534 41710908 0 23M chr2.nib:1-242951149 181247988 0 AGAGAGAGAGAGAGAGAGAGAGA SQQWZYURVYWX]]YXTSY]]ZM XT:A:R CM:i:0 SM:i:0 AM:i:0 X0:i:163148 XM:i:0 XO:i:0 XG:i:0 MD:Z:23 +1378_35_263 115 chr16.nib:1-88827254 19671878 0 23M = 19671877 -1 AGAGAGAGAGAGAGAGAGAGTCT 77543:<55#"4!&=964518A> XT:A:R CM:i:2 SM:i:0 AM:i:0 X0:i:4 X1:i:137 XM:i:2 XO:i:0 XG:i:0 MD:Z:23 +1378_35_263 179 chr16.nib:1-88827254 19671877 0 23M = 19671878 1 GAGAGAGAGAGAGAGAGAGAGTC LE7402DD34FL:27AKE>;432 XT:A:R CM:i:0 SM:i:0 AM:i:0 X0:i:265 XM:i:0 XO:i:0 XG:i:0 MD:Z:23 +1378_51_1671 117 chr2.nib:1-242951149 190342418 0 24M = 190342418 0 CTGGCGTTCTCGGCGTGGATGGGT #####$$##$#%#%%###%$#$## +1378_51_1671 153 chr2.nib:1-242951149 190342418 37 16M1I6M = 190342418 0 TCTAACTTAGCCTCATAATAGCT /<<!"0///////00/!!0121/ XT:A:U CM:i:2 SM:i:37 AM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:22 +1378_56_324 117 chr2.nib:1-242951149 80324999 0 24M = 80324999 0 TCCAGTCGCGTTGTTAGGTTCGGA #$#$$$#####%##%%###**#+/ +1378_56_324 153 chr2.nib:1-242951149 80324999 37 8M1I14M = 80324999 0 TTTAGCCCGAAATGCCTAGAGCA 4;6//11!"11100110////00 XT:A:U CM:i:2 SM:i:37 AM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:22 +1378_67_1795 81 chr16.nib:1-88827254 26739130 0 23M chrY.nib:1-57772954 57401793 0 TGGCATTCCTGTAGGCAGAGAGG AZWWZS]!"QNXZ]VQ]]]/2]] XT:A:R CM:i:2 SM:i:0 AM:i:0 X0:i:3 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:23 +1378_67_1795 161 chrY.nib:1-57772954 57401793 37 23M chr16.nib:1-88827254 26739130 0 GATCACCCAGGTGATGTAACTCC ]WV]]]]WW]]]]]]]]]]PU]] XT:A:U CM:i:0 SM:i:37 AM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:23 +1378_69_800 16 chr11.nib:1-125234658 241 255 15M1D8M * 0 0 CGTGGCCGGCGGGCCGAAGGCAT IIIIIIIIIICCCCIII?IIIII +1378_69_1777 170 chrX.nib:1-59090954 59090793 37 23M chr16.nib:1-88827254 26739130 0 TATCAATAAGGTGATGTAACTCG ]WV]ABAWW]]]]]P]P//GU]] XT:A:U CM:i:0 SM:i:37 AM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:23 +1378_72_1612 151 chrY.nib:1-124295114 190342418 37 19M1I3M = 190342418 0 TCTAACTTAGCCTCATAATAGCT /<<!"0/4//7//00/BC0121/ XT:A:U CM:i:2 SM:i:37 AM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:22

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galaxy-dist commit ada54c10540a: Bugfix for 4fb747f317d0, open tar file as stream
by commits-noreply＠bitbucket.org 07 Jun '10

07 Jun '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Nate Coraor <nate(a)bx.psu.edu> # Date 1275926267 14400 # Node ID ada54c10540ae10f308a1f2e8683bcbe779057f1 # Parent 1f70816084ae18122f3af9a5efb588f9ace6cd11 Bugfix for 4fb747f317d0, open tar file as stream --- a/lib/galaxy/web/controllers/library_common.py +++ b/lib/galaxy/web/controllers/library_common.py @@ -1382,7 +1382,7 @@ class LibraryCommon( BaseController ): archive.add = lambda x, y: archive.write( x, y.encode('CP437') ) elif action == 'tgz': if trans.app.config.upstream_gzip: - archive = util.streamball.StreamBall( 'w' ) + archive = util.streamball.StreamBall( 'w|' ) outext = 'tar' else: archive = util.streamball.StreamBall( 'w|gz' )

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galaxy-dist commit 1ab9d6b0ddfc: Yet another fix fo creating the history link on the library dataset information page - since it is possible to have an hda that does not have an associated history, we need to handle it.
by commits-noreply＠bitbucket.org 07 Jun '10

07 Jun '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Greg Von Kuster <greg(a)bx.psu.edu> # Date 1275930847 14400 # Node ID 1ab9d6b0ddfc65bc6e58c77891c57ef99e1e12cb # Parent f415eee0950c78ccf103bde9d4adc8a853e55a1e Yet another fix fo creating the history link on the library dataset information page - since it is possible to have an hda that does not have an associated history, we need to handle it. --- a/templates/library/common/ldda_info.mako +++ b/templates/library/common/ldda_info.mako @@ -149,20 +149,17 @@ %for hda in associated_hdas: <tr><td> - <% - hda_hist = trans.sa_session.query( trans.model.History ).get( hda.history_id ) - %> - %if hda_hist: - <a target="_blank" href="${h.url_for( controller='history', action='view', id=trans.security.encode_id( hda_hist.id ) )}">${hda_hist.get_display_name()}</a> + %if hda.history: + <a target="_blank" href="${h.url_for( controller='history', action='view', id=trans.security.encode_id( hda.history_id ) )}">${hda.history.get_display_name()}</a> %else: - error getting history + no history %endif </td><td>${hda.get_display_name()}</td><td>${time_ago( hda.update_time )}</td><td> - %if hda_hist and hda_hist.user: - ${hda_hist.user.email} + %if hda.history and hda.history.user: + ${hda.history.user.email} %else: anonymous %endif

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galaxy-dist commit 1f70816084ae: Fix bug in 48ec25db21c3
by commits-noreply＠bitbucket.org 07 Jun '10

07 Jun '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Nate Coraor <nate(a)bx.psu.edu> # Date 1275924969 14400 # Node ID 1f70816084ae18122f3af9a5efb588f9ace6cd11 # Parent 2c99bd86765fc2665cfa6bea98b4ebae7fc3d6c8 Fix bug in 48ec25db21c3 --- a/lib/galaxy/web/controllers/page.py +++ b/lib/galaxy/web/controllers/page.py @@ -129,7 +129,7 @@ class HistoryDatasetAssociationSelection model_class = model.HistoryDatasetAssociation columns = [ ItemSelectionGrid.NameColumn( "Name", key="name", model_class=model.HistoryDatasetAssociation, filterable="advanced" ), - grids.IndividualTagsColumn( "Tags", "tags", model_class=model.HistoryDatasetAssociation, model.HistoryDatasetAssociationTagAssociation, filterable="advanced"), + grids.IndividualTagsColumn( "Tags", "tags", model.HistoryDatasetAssociation, model.HistoryDatasetAssociationTagAssociation, filterable="advanced"), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), # Columns that are valid for filtering but are not visible. grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ),

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galaxy-dist commit f415eee0950c: Being extremely cautious when displaying history atibutes associated with an hda in the library dataset info page.
by commits-noreply＠bitbucket.org 07 Jun '10

07 Jun '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Greg Von Kuster <greg(a)bx.psu.edu> # Date 1275929498 14400 # Node ID f415eee0950c78ccf103bde9d4adc8a853e55a1e # Parent ada54c10540ae10f308a1f2e8683bcbe779057f1 Being extremely cautious when displaying history atibutes associated with an hda in the library dataset info page. --- a/templates/library/common/ldda_info.mako +++ b/templates/library/common/ldda_info.mako @@ -148,12 +148,21 @@ </thead> %for hda in associated_hdas: <tr> - <td><a target="_blank" href="${h.url_for( controller='history', action='view', id=trans.security.encode_id( hda.history_id ) )}">${hda.history.get_display_name()}</a></td> + <td> + <% + hda_hist = trans.sa_session.query( trans.model.History ).get( hda.history_id ) + %> + %if hda_hist: + <a target="_blank" href="${h.url_for( controller='history', action='view', id=trans.security.encode_id( hda_hist.id ) )}">${hda_hist.get_display_name()}</a> + %else: + error getting history + %endif + </td><td>${hda.get_display_name()}</td><td>${time_ago( hda.update_time )}</td><td> - %if hda.history.user: - ${hda.history.user.email} + %if hda_hist and hda_hist.user: + ${hda_hist.user.email} %else: anonymous %endif

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galaxy-dist commit 48ec25db21c3: Fix model_class typo.
by commits-noreply＠bitbucket.org 07 Jun '10

07 Jun '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1275923167 14400 # Node ID 48ec25db21c3bd76b52bcd68a1301f777eea280e # Parent f47ab71b2df3c27c7d231522c848b5e5ee2d2fe7 Fix model_class typo. --- a/lib/galaxy/web/controllers/page.py +++ b/lib/galaxy/web/controllers/page.py @@ -129,7 +129,7 @@ class HistoryDatasetAssociationSelection model_class = model.HistoryDatasetAssociation columns = [ ItemSelectionGrid.NameColumn( "Name", key="name", model_class=model.HistoryDatasetAssociation, filterable="advanced" ), - grids.IndividualTagsColumn( "Tags", "tags", model.StoredWorkflow, model.HistoryDatasetAssociationTagAssociation, filterable="advanced"), + grids.IndividualTagsColumn( "Tags", "tags", model_class=model.HistoryDatasetAssociation, model.HistoryDatasetAssociationTagAssociation, filterable="advanced"), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), # Columns that are valid for filtering but are not visible. grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ),

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galaxy-dist commit 4fb747f317d0: When using gzip compression in the upstream proxy, do not gzip compress library tar.gz or zip archives. bz2 then remains as the only compression perfomed in Galaxy itself.
by commits-noreply＠bitbucket.org 07 Jun '10

07 Jun '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Nate Coraor <nate(a)bx.psu.edu> # Date 1275924249 14400 # Node ID 4fb747f317d0b2c36ffb5fbf4b815caf4cb6ace1 # Parent 48ec25db21c3bd76b52bcd68a1301f777eea280e When using gzip compression in the upstream proxy, do not gzip compress library tar.gz or zip archives. bz2 then remains as the only compression perfomed in Galaxy itself. --- a/templates/library/common/common.mako +++ b/templates/library/common/common.mako @@ -382,15 +382,15 @@ # This condition should not contain an else clause because the user is not authorized # to manage dataset permissions unless the default action is 'manage_permissions' %endif - %if 'bz2' in comptypes: - <option value="tbz" + %if 'gz' in comptypes: + <option value="tgz" %if default_action == 'download': selected %endif> - >Download as a .tar.bz2 file</option> + >Download as a .tar.gz file</option> %endif - %if 'gz' in comptypes: - <option value="tgz">Download as a .tar.gz file</option> + %if 'bz2' in comptypes: + <option value="tbz">Download as a .tar.bz2 file</option> %endif %if 'zip' in comptypes: <option value="zip">Download as a .zip file</option> --- a/lib/galaxy/web/controllers/library_common.py +++ b/lib/galaxy/web/controllers/library_common.py @@ -1364,14 +1364,22 @@ class LibraryCommon( BaseController ): # Can't use mkstemp - the file must not exist first tmpd = tempfile.mkdtemp() tmpf = os.path.join( tmpd, 'library_download.' + action ) - if ziptype == '64': + if ziptype == '64' and trans.app.config.upstream_gzip: + archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_STORED, True ) + elif ziptype == '64': archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_DEFLATED, True ) + elif trans.app.config.upstream_gzip: + archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_STORED ) else: archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_DEFLATED ) archive.add = lambda x, y: archive.write( x, y.encode('CP437') ) elif action == 'tgz': - archive = util.streamball.StreamBall( 'w|gz' ) - outext = 'tgz' + if trans.app.config.upstream_gzip: + archive = util.streamball.StreamBall( 'w' ) + outext = 'tar' + else: + archive = util.streamball.StreamBall( 'w|gz' ) + outext = 'tgz' elif action == 'tbz': archive = util.streamball.StreamBall( 'w|bz2' ) outext = 'tbz2' --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -99,6 +99,7 @@ class Configuration( object ): raise ConfigurationError( "user_library_import_dir specified in config (%s) does not exist" % self.user_library_import_dir ) self.allow_library_path_paste = kwargs.get( 'allow_library_path_paste', False ) # Configuration options for taking advantage of nginx features + self.upstream_gzip = string_as_bool( kwargs.get( 'upstream_gzip', False ) ) self.apache_xsendfile = kwargs.get( 'apache_xsendfile', False ) self.nginx_x_accel_redirect_base = kwargs.get( 'nginx_x_accel_redirect_base', False ) self.nginx_x_archive_files_base = kwargs.get( 'nginx_x_archive_files_base', False ) --- a/templates/library/common/browse_library.mako +++ b/templates/library/common/browse_library.mako @@ -507,12 +507,16 @@ TIP: Multiple compression options are available for downloading library datasets: </p><ul style="padding-left: 1em; list-style-type: disc;"> + %if 'gz' in comptypes: + <li>gzip: Compression is fastest and yields a larger file, making it more suitable for fast network connections. + %if trans.app.config.upstream_gzip: + NOTE: The file you receive will be an uncompressed .tar file - this is because the Galaxy server compresses it and your browser decompresses it on the fly. + %endif + </li> + %endif %if 'bz2' in comptypes: <li>bzip2: Compression takes the most time but is better for slower network connections (that transfer slower than the rate of compression) since the resulting file size is smallest.</li> %endif - %if 'gz' in comptypes: - <li>gzip: Compression is faster and yields a larger file, making it more suitable for fast network connections.</li> - %endif %if 'zip' in comptypes: <li>ZIP: Not recommended but is provided as an option for those on Windows without WinZip (since WinZip can read .bz2 and .gz files).</li> %endif

1 0

galaxy-dist commit f47ab71b2df3: Fix autocomplete select not closing after dragging text inside, and holding arrow keys not triggering multiple times in firefox. Cleanup JS
by commits-noreply＠bitbucket.org 07 Jun '10

07 Jun '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kanwei Li <kanwei(a)gmail.com> # Date 1275864909 14400 # Node ID f47ab71b2df3c27c7d231522c848b5e5ee2d2fe7 # Parent 9114bd0887769b9ffe570b71f90ab95be68baa44 Fix autocomplete select not closing after dragging text inside, and holding arrow keys not triggering multiple times in firefox. Cleanup JS --- a/static/scripts/galaxy.base.js +++ b/static/scripts/galaxy.base.js @@ -147,7 +147,7 @@ function naturalSort(a, b){ // Replace select box with a text input box + autocomplete. function replace_big_select_inputs(min_length) { // To do replace, jQuery's autocomplete plugin must be loaded. - if (typeof jQuery().autocomplete == "undefined") + if (!jQuery().autocomplete) return; // Set default for min_length. @@ -174,10 +174,10 @@ function replace_big_select_inputs(min_l text_input_elt.attr('id', select_elt.attr('id')); text_input_elt.click( function() { // Show all. Also provide note that load is happening since this can be slow. - var cur_value = $(this).attr('value'); - $(this).attr('value', 'Loading...'); + var cur_value = $(this).val(); + $(this).val('Loading...'); $(this).showAllInCache(); - $(this).attr('value', cur_value); + $(this).val(cur_value); $(this).select(); }); --- a/static/scripts/jquery.autocomplete.js +++ b/static/scripts/jquery.autocomplete.js @@ -17,819 +17,817 @@ String.prototype.endsWith = function(str var return_key_pressed_for_autocomplete = false; ;(function($) { - + $.fn.extend({ - autocomplete: function(urlOrData, options) { - var isUrl = typeof urlOrData == "string"; - options = $.extend({}, $.Autocompleter.defaults, { - url: isUrl ? urlOrData : null, - data: isUrl ? null : urlOrData, - delay: isUrl ? $.Autocompleter.defaults.delay : 10, - max: options && !options.scroll ? 10 : 150 - }, options); - - // if highlight is set to false, replace it with a do-nothing function - options.highlight = options.highlight || function(value) { return value; }; - - // if the formatMatch option is not specified, then use formatItem for backwards compatibility - options.formatMatch = options.formatMatch || options.formatItem; - - return this.each(function() { - new $.Autocompleter(this, options); - }); - }, - result: function(handler) { - return this.bind("result", handler); - }, - search: function(handler) { - return this.trigger("search", [handler]); - }, - flushCache: function() { + autocomplete: function(urlOrData, options) { + var isUrl = typeof urlOrData == "string"; + options = $.extend({}, $.Autocompleter.defaults, { + url: isUrl ? urlOrData : null, + data: isUrl ? null : urlOrData, + delay: isUrl ? $.Autocompleter.defaults.delay : 10, + max: options && !options.scroll ? 10 : 150 + }, options); + + // if highlight is set to false, replace it with a do-nothing function + options.highlight = options.highlight || function(value) { return value; }; + + // if the formatMatch option is not specified, then use formatItem for backwards compatibility + options.formatMatch = options.formatMatch || options.formatItem; + + return this.each(function() { + new $.Autocompleter(this, options); + }); + }, + result: function(handler) { + return this.bind("result", handler); + }, + search: function(handler) { + return this.trigger("search", [handler]); + }, + flushCache: function() { return this.trigger("flushCache"); - }, - setOptions: function(options){ - return this.trigger("setOptions", [options]); - }, - unautocomplete: function() { - return this.trigger("unautocomplete"); - }, - // JG: add method to show all data in cache. + }, + setOptions: function(options){ + return this.trigger("setOptions", [options]); + }, + unautocomplete: function() { + return this.trigger("unautocomplete"); + }, + // JG: add method to show all data in cache. showAllInCache: function() { - return this.trigger("showAllInCache"); - } + return this.trigger("showAllInCache"); + } }); $.Autocompleter = function(input, options) { - var KEY = { - UP: 38, - DOWN: 40, - DEL: 46, - TAB: 9, - RETURN: 13, - ESC: 27, - COMMA: 188, - PAGEUP: 33, - PAGEDOWN: 34, - BACKSPACE: 8, - COLON: 16 - }; + var KEY = { + UP: 38, + DOWN: 40, + DEL: 46, + TAB: 9, + RETURN: 13, + ESC: 27, + COMMA: 188, + PAGEUP: 33, + PAGEDOWN: 34, + BACKSPACE: 8, + COLON: 16 + }; - // Create $ object for input element - var $input = $(input).attr("autocomplete", "off").addClass(options.inputClass); + // Create $ object for input element + var $input = $(input).attr("autocomplete", "off").addClass(options.inputClass); - var timeout; - var previousValue = ""; - var cache = $.Autocompleter.Cache(options); - var hasFocus = 0; - var lastKeyPressCode; - var config = { - mouseDownOnSelect: false - }; - var select = $.Autocompleter.Select(options, input, selectCurrent, config); - - var blockSubmit; - - // prevent form submit in opera when selecting with return key - $.browser.opera && $(input.form).bind("submit.autocomplete", function() { - if (blockSubmit) { - blockSubmit = false; - return false; - } - }); - - // only opera doesn't trigger keydown multiple times while pressed, others don't work with keypress at all - $input.bind(($.browser.opera ? "keypress" : "keydown") + ".autocomplete", function(event) { - // track last key pressed - lastKeyPressCode = event.keyCode; - switch(event.keyCode) { - - case KEY.UP: - event.preventDefault(); - if ( select.visible() ) { - select.prev(); - } else { - onChange(0, true); - } - break; - - case KEY.DOWN: - event.preventDefault(); - if ( select.visible() ) { - select.next(); - } else { - onChange(0, true); - } - break; - - case KEY.PAGEUP: - event.preventDefault(); - if ( select.visible() ) { - select.pageUp(); - } else { - onChange(0, true); - } - break; - - case KEY.PAGEDOWN: - event.preventDefault(); - if ( select.visible() ) { - select.pageDown(); - } else { - onChange(0, true); - } - break; - - // matches also semicolon - case options.multiple && $.trim(options.multipleSeparator) == "," && KEY.COMMA: - case KEY.TAB: - case KEY.RETURN: - if (event.keyCode == KEY.RETURN) - return_key_pressed_for_autocomplete = false; - if( selectCurrent() ) { - // stop default to prevent a form submit, Opera needs special handling - event.preventDefault(); - blockSubmit = true; - - // JG: set flag to indicate that a selection just occurred using the return key. FYI: - // event.stopPropagation() does not work. - if (event.keyCode == KEY.RETURN) - return_key_pressed_for_autocomplete = true; - - return false; - } - - case KEY.ESC: - select.hide(); - break; - case KEY.COLON: - break; - - default: - clearTimeout(timeout); - timeout = setTimeout(onChange, options.delay); - break; - } - }).focus(function(){ - // track whether the field has focus, we shouldn't process any - // results if the field no longer has focus - hasFocus++; - }).blur(function() { - hasFocus = 0; - if (!config.mouseDownOnSelect) { - // JG: if blur and user is not selecting with mouse, hide - // object. - select.hide(); - } - return this; - }).click(function() { - // show select when clicking in a focused field - if ( hasFocus++ > 1 && !select.visible() ) { - onChange(0, true); - } - return this; - }).bind("search", function() { - // TODO why not just specifying both arguments? - var fn = (arguments.length > 1) ? arguments[1] : null; - function findValueCallback(q, data) { - var result; - if( data && data.length ) { - for (var i=0; i < data.length; i++) { - if( data[i].result.toLowerCase() == q.toLowerCase() ) { - result = data[i]; - break; - } - } - } - if( typeof fn == "function" ) fn(result); - else $input.trigger("result", result && [result.data, result.value]); - } - $.each(trimWords($input.val()), function(i, value) { - request(value, findValueCallback, findValueCallback); - }); + var timeout; + var previousValue = ""; + var cache = $.Autocompleter.Cache(options); + var hasFocus = 0; + var lastKeyPressCode; + var config = { + mouseDownOnSelect: false + }; + var select = $.Autocompleter.Select(options, input, selectCurrent, config); + + var blockSubmit; + + // prevent form submit in opera when selecting with return key + $.browser.opera && $(input.form).bind("submit.autocomplete", function() { + if (blockSubmit) { + blockSubmit = false; + return false; + } + }); + + // Firefox only triggers holding down a key with keypress + $input.bind(($.browser.mozilla ? "keypress" : "keydown") + ".autocomplete", function(event) { + // track last key pressed + lastKeyPressCode = event.keyCode; + switch(event.keyCode) { + + case KEY.UP: + event.preventDefault(); + if ( select.visible() ) { + select.prev(); + } else { + onChange(0, true); + } + break; + + case KEY.DOWN: + event.preventDefault(); + if ( select.visible() ) { + select.next(); + } else { + onChange(0, true); + } + break; + + case KEY.PAGEUP: + event.preventDefault(); + if ( select.visible() ) { + select.pageUp(); + } else { + onChange(0, true); + } + break; + + case KEY.PAGEDOWN: + event.preventDefault(); + if ( select.visible() ) { + select.pageDown(); + } else { + onChange(0, true); + } + break; + + // matches also semicolon + case options.multiple && $.trim(options.multipleSeparator) == "," && KEY.COMMA: + case KEY.TAB: + case KEY.RETURN: + if (event.keyCode == KEY.RETURN) + return_key_pressed_for_autocomplete = false; + if( selectCurrent() ) { + // stop default to prevent a form submit, Opera needs special handling + event.preventDefault(); + blockSubmit = true; + + // JG: set flag to indicate that a selection just occurred using the return key. FYI: + // event.stopPropagation() does not work. + if (event.keyCode == KEY.RETURN) + return_key_pressed_for_autocomplete = true; + + return false; + } + + case KEY.ESC: + select.hide(); + break; + case KEY.COLON: + break; + + default: + clearTimeout(timeout); + timeout = setTimeout(onChange, options.delay); + break; + } + }).focus(function(){ + // track whether the field has focus, we shouldn't process any + // results if the field no longer has focus + hasFocus++; + }).blur(function() { + hasFocus = 0; + if (!config.mouseDownOnSelect) { + // JG: if blur and user is not selecting with mouse, hide + // object. + select.hide(); + } + return this; + }).click(function() { + // show select when clicking in a focused field + if ( hasFocus++ > 1 && !select.visible() ) { + onChange(0, true); + } + return this; + }).bind("search", function() { + // TODO why not just specifying both arguments? + var fn = (arguments.length > 1) ? arguments[1] : null; + function findValueCallback(q, data) { + var result; + if( data && data.length ) { + for (var i=0; i < data.length; i++) { + if( data[i].result.toLowerCase() == q.toLowerCase() ) { + result = data[i]; + break; + } + } + } + if( typeof fn == "function" ) fn(result); + else $input.trigger("result", result && [result.data, result.value]); + } + $.each(trimWords($input.val()), function(i, value) { + request(value, findValueCallback, findValueCallback); + }); - return this; - }).bind("flushCache", function() { - cache.flush(); - }).bind("setOptions", function() { - $.extend(options, arguments[1]); - // if we've updated the data, repopulate - if ( "data" in arguments[1] ) - cache.populate(); - }).bind("unautocomplete", function() { - select.unbind(); - $input.unbind(); - $(input.form).unbind(".autocomplete"); - }) - // JG: Show all data in cache. - .bind("showAllInCache", function() { - receiveData('', cache.load('')); - }); - - - function selectCurrent() { - var selected = select.selected(); - if( !selected ) - return false; - - var v = selected.result; - previousValue = v; - - if ( options.multiple ) { - var words = trimWords($input.val()); - if ( words.length > 1 ) { - v = words.slice(0, words.length - 1).join( options.multipleSeparator ) + options.multipleSeparator + v; - } - v += options.multipleSeparator; - } - - $input.val(v); - hideResultsNow(); - $input.trigger("result", [selected.data, selected.value]); - return true; - } - - function onChange(crap, skipPrevCheck) { - if( lastKeyPressCode == KEY.DEL ) { - select.hide(); - return; - } + return this; + }).bind("flushCache", function() { + cache.flush(); + }).bind("setOptions", function() { + $.extend(options, arguments[1]); + // if we've updated the data, repopulate + if ( "data" in arguments[1] ) + cache.populate(); + }).bind("unautocomplete", function() { + select.unbind(); + $input.unbind(); + $(input.form).unbind(".autocomplete"); + }) + // JG: Show all data in cache. + .bind("showAllInCache", function() { + receiveData('', cache.load('')); + }); + + function selectCurrent() { + var selected = select.selected(); + if( !selected ) + return false; + + var v = selected.result; + previousValue = v; + + if ( options.multiple ) { + var words = trimWords($input.val()); + if ( words.length > 1 ) { + v = words.slice(0, words.length - 1).join( options.multipleSeparator ) + options.multipleSeparator + v; + } + v += options.multipleSeparator; + } + + $input.val(v); + hideResultsNow(); + $input.trigger("result", [selected.data, selected.value]); + return true; + } + + function onChange(crap, skipPrevCheck) { + if( lastKeyPressCode == KEY.DEL ) { + select.hide(); + return; + } - var currentValue = $input.val(); - - if ( !skipPrevCheck && currentValue == previousValue ) - return; - - previousValue = currentValue; - - currentValue = lastWord(currentValue); - if ( currentValue.length >= options.minChars) { - $input.addClass(options.loadingClass); - if (!options.matchCase) - currentValue = currentValue.toLowerCase(); - request(currentValue, receiveData, hideResultsNow); - } else { - stopLoading(); - select.hide(); - } - }; - - function trimWords(value) { - if ( !value ) { - return [""]; - } - var words = value.split( options.multipleSeparator ); - var result = []; - $.each(words, function(i, value) { - if ( $.trim(value) ) - result[i] = $.trim(value); - }); - return result; - } - - function lastWord(value) { - if ( !options.multiple ) - return value; - var words = trimWords(value); - return words[words.length - 1]; - } - - // fills in the input box w/the first match (assumed to be the best match) - // q: the term entered - // sValue: the first matching result - function autoFill(q, sValue){ - // autofill in the complete box w/the first match as long as the user hasn't entered in more data - // if the last user key pressed was backspace, don't autofill - if( options.autoFill && (lastWord($input.val()).toLowerCase() == q.toLowerCase()) && lastKeyPressCode != KEY.BACKSPACE ) { - // fill in the value (keep the case the user has typed) - $input.val($input.val() + sValue.substring(lastWord(previousValue).length)); - // select the portion of the value not typed by the user (so the next character will erase) - $.Autocompleter.Selection(input, previousValue.length, previousValue.length + sValue.length); - } - }; + var currentValue = $input.val(); + + if ( !skipPrevCheck && currentValue == previousValue ) + return; + + previousValue = currentValue; + + currentValue = lastWord(currentValue); + if ( currentValue.length >= options.minChars) { + $input.addClass(options.loadingClass); + if (!options.matchCase) + currentValue = currentValue.toLowerCase(); + request(currentValue, receiveData, hideResultsNow); + } else { + stopLoading(); + select.hide(); + } + }; + + function trimWords(value) { + if ( !value ) { + return [""]; + } + var words = value.split( options.multipleSeparator ); + var result = []; + $.each(words, function(i, value) { + if ( $.trim(value) ) + result[i] = $.trim(value); + }); + return result; + } + + function lastWord(value) { + if ( !options.multiple ) + return value; + var words = trimWords(value); + return words[words.length - 1]; + } + + // fills in the input box w/the first match (assumed to be the best match) + // q: the term entered + // sValue: the first matching result + function autoFill(q, sValue){ + // autofill in the complete box w/the first match as long as the user hasn't entered in more data + // if the last user key pressed was backspace, don't autofill + if( options.autoFill && (lastWord($input.val()).toLowerCase() == q.toLowerCase()) && lastKeyPressCode != KEY.BACKSPACE ) { + // fill in the value (keep the case the user has typed) + $input.val($input.val() + sValue.substring(lastWord(previousValue).length)); + // select the portion of the value not typed by the user (so the next character will erase) + $.Autocompleter.Selection(input, previousValue.length, previousValue.length + sValue.length); + } + }; - function hideResults() { - clearTimeout(timeout); - timeout = setTimeout(hideResultsNow, 200); - }; + function hideResults() { + clearTimeout(timeout); + timeout = setTimeout(hideResultsNow, 200); + }; - function hideResultsNow() { - var wasVisible = select.visible(); - select.hide(); - clearTimeout(timeout); - stopLoading(); - if (options.mustMatch) { - // call search and run callback - $input.search( - function (result){ - // if no value found, clear the input box - if( !result ) { - if (options.multiple) { - var words = trimWords($input.val()).slice(0, -1); - $input.val( words.join(options.multipleSeparator) + (words.length ? options.multipleSeparator : "") ); - } - else - $input.val( "" ); - } - } - ); - } - if (wasVisible) - // position cursor at end of input field - $.Autocompleter.Selection(input, input.value.length, input.value.length); - }; + function hideResultsNow() { + var wasVisible = select.visible(); + select.hide(); + clearTimeout(timeout); + stopLoading(); + if (options.mustMatch) { + // call search and run callback + $input.search( + function (result){ + // if no value found, clear the input box + if( !result ) { + if (options.multiple) { + var words = trimWords($input.val()).slice(0, -1); + $input.val( words.join(options.multipleSeparator) + (words.length ? options.multipleSeparator : "") ); + } + else + $input.val( "" ); + } + } + ); + } + if (wasVisible) + // position cursor at end of input field + $.Autocompleter.Selection(input, input.value.length, input.value.length); + }; - function receiveData(q, data) { - if ( data && data.length && hasFocus ) { - stopLoading(); - select.display(data, q); - autoFill(q, data[0].value); - select.show(); - } else { - hideResultsNow(); - } - }; + function receiveData(q, data) { + if ( data && data.length && hasFocus ) { + stopLoading(); + select.display(data, q); + autoFill(q, data[0].value); + select.show(); + } else { + hideResultsNow(); + } + }; - function request(term, success, failure) { - if (!options.matchCase) - term = term.toLowerCase(); - var data = cache.load(term); + function request(term, success, failure) { + if (!options.matchCase) + term = term.toLowerCase(); + var data = cache.load(term); - // JG: hack: if term ends with ':', kill data to force an ajax request. - if (term.endsWith(":")) - data = null; + // JG: hack: if term ends with ':', kill data to force an ajax request. + if (term.endsWith(":")) + data = null; - // recieve the cached data - if (data && data.length) { - success(term, data); - // if an AJAX url has been supplied, try loading the data now - } else if( (typeof options.url == "string") && (options.url.length > 0) ){ - var extraParams = { - timestamp: +new Date() - }; - $.each(options.extraParams, function(key, param) { - extraParams[key] = typeof param == "function" ? param() : param; - }); - - $.ajax({ - // try to leverage ajaxQueue plugin to abort previous requests - mode: "abort", - // limit abortion to this input - port: "autocomplete" + input.name, - dataType: options.dataType, - url: options.url, - data: $.extend({ - q: lastWord(term), - limit: options.max - }, extraParams), - success: function(data) { - var parsed = options.parse && options.parse(data) || parse(data); - cache.add(term, parsed); - success(term, parsed); - } - }); - } else { - // if we have a failure, we need to empty the list -- this prevents the the [TAB] key from selecting the last successful match - select.emptyList(); - failure(term); - } - }; - - function parse(data) { - var parsed = []; - var rows = data.split("\n"); - for (var i=0; i < rows.length; i++) { - var row = $.trim(rows[i]); - if (row) { - row = row.split("|"); - parsed[parsed.length] = { - data: row, - value: row[0], - result: options.formatResult && options.formatResult(row, row[0]) || row[0] - }; - } - } - return parsed; - }; + // recieve the cached data + if (data && data.length) { + success(term, data); + // if an AJAX url has been supplied, try loading the data now + } else if( (typeof options.url == "string") && (options.url.length > 0) ){ + var extraParams = { + timestamp: +new Date() + }; + $.each(options.extraParams, function(key, param) { + extraParams[key] = typeof param == "function" ? param() : param; + }); + + $.ajax({ + // try to leverage ajaxQueue plugin to abort previous requests + mode: "abort", + // limit abortion to this input + port: "autocomplete" + input.name, + dataType: options.dataType, + url: options.url, + data: $.extend({ + q: lastWord(term), + limit: options.max + }, extraParams), + success: function(data) { + var parsed = options.parse && options.parse(data) || parse(data); + cache.add(term, parsed); + success(term, parsed); + } + }); + } else { + // if we have a failure, we need to empty the list -- this prevents the the [TAB] key from selecting the last successful match + select.emptyList(); + failure(term); + } + }; + + function parse(data) { + var parsed = []; + var rows = data.split("\n"); + for (var i=0; i < rows.length; i++) { + var row = $.trim(rows[i]); + if (row) { + row = row.split("|"); + parsed[parsed.length] = { + data: row, + value: row[0], + result: options.formatResult && options.formatResult(row, row[0]) || row[0] + }; + } + } + return parsed; + }; - function stopLoading() { - $input.removeClass(options.loadingClass); - }; + function stopLoading() { + $input.removeClass(options.loadingClass); + }; }; $.Autocompleter.defaults = { - inputClass: "ac_input", - resultsClass: "ac_results", - loadingClass: "ac_loading", - minChars: 1, - delay: 400, - matchCase: false, - matchSubset: true, - matchContains: false, - cacheLength: 10, - max: 100, - mustMatch: false, - extraParams: {}, - selectFirst: true, - formatItem: function(row) { return row[0]; }, - formatMatch: null, - autoFill: false, - width: 0, - multiple: false, - multipleSeparator: ", ", - highlight: function(value, term) { - // JG: short-circuit highlighting if term is empty string. - if (term == "") - return value; - return value.replace(new RegExp("(?![^&;]+;)(?!<[^<>]*)(" + term.replace(/([\^\$\[\]\{\}\*\.\+\?\|\\])/gi, "\\$1") + ")(?![^<>]*>)(?![^&;]+;)", "gi"), "<strong>$1</strong>"); - }, + inputClass: "ac_input", + resultsClass: "ac_results", + loadingClass: "ac_loading", + minChars: 1, + delay: 400, + matchCase: false, + matchSubset: true, + matchContains: false, + cacheLength: 10, + max: 100, + mustMatch: false, + extraParams: {}, + selectFirst: true, + formatItem: function(row) { return row[0]; }, + formatMatch: null, + autoFill: false, + width: 0, + multiple: false, + multipleSeparator: ", ", + highlight: function(value, term) { + // JG: short-circuit highlighting if term is empty string. + if (term == "") + return value; + return value.replace(new RegExp("(?![^&;]+;)(?!<[^<>]*)(" + term.replace(/([\^\$\[\]\{\}\*\.\+\?\|\\])/gi, "\\$1") + ")(?![^<>]*>)(?![^&;]+;)", "gi"), "<strong>$1</strong>"); + }, scroll: true, scrollHeight: 180 }; $.Autocompleter.Cache = function(options) { - var data = {}; - var length = 0; + var data = {}; + var length = 0; - function matchSubset(s, sub) { - if (!options.matchCase) - s = s.toLowerCase(); - var i = s.indexOf(sub); - if (i == -1) return false; - return i == 0 || options.matchContains; - }; - - function add(q, value) { - if (length > options.cacheLength){ - flush(); - } - if (!data[q]){ - length++; - } - data[q] = value; - } - - function populate(){ - if( !options.data ) return false; - // track the matches - var stMatchSets = {}, - nullData = 0; + function matchSubset(s, sub) { + if (!options.matchCase) + s = s.toLowerCase(); + var i = s.indexOf(sub); + if (i == -1) return false; + return i == 0 || options.matchContains; + }; + + function add(q, value) { + if (length > options.cacheLength){ + flush(); + } + if (!data[q]){ + length++; + } + data[q] = value; + } + + function populate(){ + if( !options.data ) return false; + // track the matches + var stMatchSets = {}, + nullData = 0; - // no url was specified, we need to adjust the cache length to make sure it fits the local data store - if( !options.url ) options.cacheLength = 1; - - // track all options for minChars = 0 - stMatchSets[""] = []; - - // loop through the array and create a lookup structure - for ( var i = 0, ol = options.data.length; i < ol; i++ ) { - var rawValue = options.data[i]; - // if rawValue is a string, make an array otherwise just reference the array - rawValue = (typeof rawValue == "string") ? [rawValue] : rawValue; - - var value = options.formatMatch(rawValue, i+1, options.data.length); - if ( value === false ) - continue; - - var firstChar = value.charAt(0).toLowerCase(); - // if no lookup array for this character exists, look it up now - if( !stMatchSets[firstChar] ) - stMatchSets[firstChar] = []; + // no url was specified, we need to adjust the cache length to make sure it fits the local data store + if( !options.url ) options.cacheLength = 1; + + // track all options for minChars = 0 + stMatchSets[""] = []; + + // loop through the array and create a lookup structure + for ( var i = 0, ol = options.data.length; i < ol; i++ ) { + var rawValue = options.data[i]; + // if rawValue is a string, make an array otherwise just reference the array + rawValue = (typeof rawValue == "string") ? [rawValue] : rawValue; + + var value = options.formatMatch(rawValue, i+1, options.data.length); + if ( value === false ) + continue; + + var firstChar = value.charAt(0).toLowerCase(); + // if no lookup array for this character exists, look it up now + if( !stMatchSets[firstChar] ) + stMatchSets[firstChar] = []; - // if the match is a string - var row = { - value: value, - data: rawValue, - result: options.formatResult && options.formatResult(rawValue) || value - }; - - // push the current match into the set list - stMatchSets[firstChar].push(row); + // if the match is a string + var row = { + value: value, + data: rawValue, + result: options.formatResult && options.formatResult(rawValue) || value + }; + + // push the current match into the set list + stMatchSets[firstChar].push(row); - // keep track of minChars zero items - if ( nullData++ < options.max ) { - stMatchSets[""].push(row); - } - }; + // keep track of minChars zero items + if ( nullData++ < options.max ) { + stMatchSets[""].push(row); + } + }; - // add the data items to the cache - $.each(stMatchSets, function(i, value) { - // increase the cache size - options.cacheLength++; - // add to the cache - add(i, value); - }); - } - - // populate any existing data - setTimeout(populate, 25); - - function flush(){ - data = {}; - length = 0; - } - - return { - flush: flush, - add: add, - populate: populate, - load: function(q) { - if (!options.cacheLength || !length) - return null; + // add the data items to the cache + $.each(stMatchSets, function(i, value) { + // increase the cache size + options.cacheLength++; + // add to the cache + add(i, value); + }); + } + + // populate any existing data + setTimeout(populate, 25); + + function flush(){ + data = {}; + length = 0; + } + + return { + flush: flush, + add: add, + populate: populate, + load: function(q) { + if (!options.cacheLength || !length) + return null; - /* - * if dealing w/local data and matchContains than we must make sure - * to loop through all the data collections looking for matches - */ - if( !options.url && options.matchContains ){ - // track all matches - var csub = []; - // loop through all the data grids for matches - for( var k in data ){ - // don't search through the stMatchSets[""] (minChars: 0) cache - // this prevents duplicates - if( k.length > 0 ){ - var c = data[k]; - $.each(c, function(i, x) { - // if we've got a match, add it to the array - if (matchSubset(x.value, q)) { - csub.push(x); - } - }); - } - } - return csub; - } else - // if the exact item exists, use it - if (data[q]){ - return data[q]; - } else - if (options.matchSubset) { - for (var i = q.length - 1; i >= options.minChars; i--) { - var c = data[q.substr(0, i)]; - if (c) { - var csub = []; - $.each(c, function(i, x) { - if ( (x.data.indexOf("#Header") == 0) || - (matchSubset(x.value, q)) ) { - csub[csub.length] = x; - } - }); - return csub; - } - } + /* + * if dealing w/local data and matchContains than we must make sure + * to loop through all the data collections looking for matches + */ + if( !options.url && options.matchContains ) { + // track all matches + var csub = []; + // loop through all the data grids for matches + for( var k in data ) { + // don't search through the stMatchSets[""] (minChars: 0) cache + // this prevents duplicates + if( k.length > 0 ){ + var c = data[k]; + $.each(c, function(i, x) { + // if we've got a match, add it to the array + if (matchSubset(x.value, q)) { + csub.push(x); + } + }); + } + } + return csub; + } else + // if the exact item exists, use it + if (data[q]) { + return data[q]; + } else + if (options.matchSubset) { + for (var i = q.length - 1; i >= options.minChars; i--) { + var c = data[q.substr(0, i)]; + if (c) { + var csub = []; + $.each(c, function(i, x) { + if ( (x.data.indexOf("#Header") == 0) || + (matchSubset(x.value, q)) ) { + csub[csub.length] = x; + } + }); + return csub; + } + } - } - return null; - } - }; + } + return null; + } + }; }; $.Autocompleter.Select = function (options, input, select, config) { - var CLASSES = { - ACTIVE: "ac_over" - }; - - var listItems, - active = -1, - data, - term = "", - needsInit = true, - element, - list; - - // Create results - function init() { - if (!needsInit) - return; - element = $("<div/>") - .hide() - .addClass(options.resultsClass) - .css("position", "absolute") - .appendTo(document.body); - - list = $("<ul/>").appendTo(element).mouseover( function(event) { - if(target(event).nodeName && target(event).nodeName.toUpperCase() == 'LI') { - active = $("li", list).removeClass(CLASSES.ACTIVE).index(target(event)); - // JG: Only add active class if target is not a header. - if (!headerAtPosition(active)) - $(target(event)).addClass(CLASSES.ACTIVE); - } - }).click(function(event) { - // JG: Ignore click on header. - active = $("li", list).index(target(event)); - if (headerAtPosition(active)) - return; + var CLASSES = { + ACTIVE: "ac_over" + }; + + var listItems, + active = -1, + data, + term = "", + needsInit = true, + element, + list; + + // Create results + function init() { + if (!needsInit) + return; + + element = $("<div/>") + .hide() + .addClass(options.resultsClass) + .css("position", "absolute") + .bind("mouseleave", function() { + element.hide(); + }) + .appendTo(document.body); - // Handle click on autocomplete options. - $(target(event)).addClass(CLASSES.ACTIVE); - select(); - // TODO provide option to avoid setting focus again after selection? useful for cleanup-on-focus - input.focus(); - return false; - }).mousedown(function() { - config.mouseDownOnSelect = true; - }).mouseup(function() { - config.mouseDownOnSelect = false; - }); - - if( options.width > 0 ) - element.css("width", options.width); - - needsInit = false; - } - - function target(event) { - var element = event.target; - while(element && element.tagName != "LI") - element = element.parentNode; - // more fun with IE, sometimes event.target is empty, just ignore it then - if(!element) - return []; - return element; - } + list = $("<ul/>").appendTo(element).mouseover( function(event) { + if(target(event).nodeName && target(event).nodeName.toUpperCase() == 'LI') { + active = $("li", list).removeClass(CLASSES.ACTIVE).index(target(event)); + // JG: Only add active class if target is not a header. + if (!headerAtPosition(active)) + $(target(event)).addClass(CLASSES.ACTIVE); + } + }).click(function(event) { + // JG: Ignore click on header. + active = $("li", list).index(target(event)); + if (headerAtPosition(active)) + return; - // JG: Returns true iff there is a header element at the given position. - function headerAtPosition(position) - { - dataAtPosition = data[position].data; - return (dataAtPosition[0].indexOf("#Header") == 0); - } + // Handle click on autocomplete options. + $(target(event)).addClass(CLASSES.ACTIVE); + select(); + // TODO provide option to avoid setting focus again after selection? useful for cleanup-on-focus + input.focus(); + return false; + }).mousedown(function() { + config.mouseDownOnSelect = true; + }).mouseup(function() { + config.mouseDownOnSelect = false; + }); - function moveSelect(step) { - listItems.slice(active, active + 1).removeClass(CLASSES.ACTIVE); - // JG: while active item is a header, continue stepping. - var isHeader = false; - do - { - movePosition(step); - isHeader = headerAtPosition(active); - } - while (isHeader); - var activeItem = listItems.slice(active, active + 1).addClass(CLASSES.ACTIVE); + if( options.width > 0 ) + element.css("width", options.width); + needsInit = false; + } + + function target(event) { + var element = event.target; + while(element && element.tagName != "LI") + element = element.parentNode; + // more fun with IE, sometimes event.target is empty, just ignore it then + if(!element) + return []; + return element; + } + + // JG: Returns true iff there is a header element at the given position. + function headerAtPosition(position) { + dataAtPosition = data[position].data; + return (dataAtPosition[0].indexOf("#Header") == 0); + } + + function moveSelect(step) { + listItems.slice(active, active + 1).removeClass(CLASSES.ACTIVE); + // JG: while active item is a header, continue stepping. + var isHeader = false; + do { + movePosition(step); + isHeader = headerAtPosition(active); + } + while (isHeader); + var activeItem = listItems.slice(active, active + 1).addClass(CLASSES.ACTIVE); if(options.scroll) { var offset = 0; listItems.slice(0, active).each(function() { - offset += this.offsetHeight; - }); + offset += this.offsetHeight; + }); if((offset + activeItem[0].offsetHeight - list.scrollTop()) > list[0].clientHeight) { list.scrollTop(offset + activeItem[0].offsetHeight - list.innerHeight()); } else if(offset < list.scrollTop()) { list.scrollTop(offset); } } - }; - - function movePosition(step) { - active += step; - if (active < 0) { - active = listItems.size() - 1; - } else if (active >= listItems.size()) { - active = 0; - } - } - - function limitNumberOfItems(available) { - return options.max && options.max < available - ? options.max - : available; - } - - function fillList() { - list.empty(); - var max = limitNumberOfItems(data.length); - for (var i=0; i < max; i++) { - if (!data[i]) - continue; - var formatted = options.formatItem(data[i].data, i+1, max, data[i].value, term); - if ( formatted === false ) - continue; + }; + + function movePosition(step) { + active += step; + if (active < 0) { + active = listItems.size() - 1; + } else if (active >= listItems.size()) { + active = 0; + } + } + + function limitNumberOfItems(available) { + return options.max && options.max < available + ? options.max + : available; + } + + function fillList() { + list.empty(); + var max = limitNumberOfItems(data.length); + for (var i=0; i < max; i++) { + if (!data[i]) + continue; + + var formatted = options.formatItem(data[i].data, i+1, max, data[i].value, term); + if ( formatted === false ) + continue; - // JG: Build list item by formatting the item and choosing a CSS class. - if (headerAtPosition(i)) - { - // Found header element; only add header if there are subsequent elements. - if (i != max-1) - var li = $("<li/>").html(data[i].data[1]).addClass("ac_header").appendTo(list)[0]; - } - else - { - // Found completion element. - var li = $("<li/>").html(options.highlight(formatted, term)).addClass(i%2 == 0 ? "ac_even" : "ac_odd").appendTo(list)[0]; - } + // JG: Build list item by formatting the item and choosing a CSS class. + if (headerAtPosition(i)) { + // Found header element; only add header if there are subsequent elements. + if (i != max-1) + var li = $("<li/>").html(data[i].data[1]).addClass("ac_header").appendTo(list)[0]; + } else { + // Found completion element. + var li = $("<li/>").html(options.highlight(formatted, term)).addClass(i%2 == 0 ? "ac_even" : "ac_odd").appendTo(list)[0]; + } - $.data(li, "ac_data", data[i]); - } - listItems = list.find("li"); - if ( options.selectFirst ) { - listItems.slice(0, 1).addClass(CLASSES.ACTIVE); - active = 0; - } - // apply bgiframe if available - if ( $.fn.bgiframe ) - list.bgiframe(); - } - - return { - display: function(d, q) { - init(); - data = d; - term = q; - fillList(); - }, - next: function() { - moveSelect(1); - }, - prev: function() { - moveSelect(-1); - }, - pageUp: function() { - if (active != 0 && active - 8 < 0) { - moveSelect( -active ); - } else { - moveSelect(-8); - } - }, - pageDown: function() { - if (active != listItems.size() - 1 && active + 8 > listItems.size()) { - moveSelect( listItems.size() - 1 - active ); - } else { - moveSelect(8); - } - }, - hide: function() { - element && element.hide(); - listItems && listItems.removeClass(CLASSES.ACTIVE); - active = -1; - }, - visible : function() { - return element && element.is(":visible"); - }, - current: function() { - return this.visible() && (listItems.filter("." + CLASSES.ACTIVE)[0] || options.selectFirst && listItems[0]); - }, - show: function() { - var offset = $(input).offset(); - element.css({ - width: typeof options.width == "string" || options.width > 0 ? options.width : $(input).width(), - top: offset.top + input.offsetHeight, - left: offset.left - }).show(); + $.data(li, "ac_data", data[i]); + } + listItems = list.find("li"); + if ( options.selectFirst ) { + listItems.slice(0, 1).addClass(CLASSES.ACTIVE); + active = 0; + } + // apply bgiframe if available + if ( $.fn.bgiframe ) + list.bgiframe(); + } + + return { + display: function(d, q) { + init(); + data = d; + term = q; + fillList(); + }, + next: function() { + moveSelect(1); + }, + prev: function() { + moveSelect(-1); + }, + pageUp: function() { + if (active != 0 && active - 8 < 0) { + moveSelect( -active ); + } else { + moveSelect(-8); + } + }, + pageDown: function() { + if (active != listItems.size() - 1 && active + 8 > listItems.size()) { + moveSelect( listItems.size() - 1 - active ); + } else { + moveSelect(8); + } + }, + hide: function() { + element && element.hide(); + listItems && listItems.removeClass(CLASSES.ACTIVE); + active = -1; + }, + visible : function() { + return element && element.is(":visible"); + }, + current: function() { + return this.visible() && (listItems.filter("." + CLASSES.ACTIVE)[0] || options.selectFirst && listItems[0]); + }, + show: function() { + var offset = $(input).offset(); + element.css({ + width: typeof options.width == "string" || options.width > 0 ? options.width : $(input).width(), + top: offset.top + input.offsetHeight, + left: offset.left + }).show(); if(options.scroll) { list.scrollTop(0); list.css({ - maxHeight: options.scrollHeight, - overflow: 'auto' - }); - + maxHeight: options.scrollHeight, + overflow: 'auto' + }); + if($.browser.msie && typeof document.body.style.maxHeight === "undefined") { - var listHeight = 0; - listItems.each(function() { - listHeight += this.offsetHeight; - }); - var scrollbarsVisible = listHeight > options.scrollHeight; + var listHeight = 0; + listItems.each(function() { + listHeight += this.offsetHeight; + }); + var scrollbarsVisible = listHeight > options.scrollHeight; list.css('height', scrollbarsVisible ? options.scrollHeight : listHeight ); - if (!scrollbarsVisible) { - // IE doesn't recalculate width when scrollbar disappears - listItems.width( list.width() - parseInt(listItems.css("padding-left")) - parseInt(listItems.css("padding-right")) ); - } + if (!scrollbarsVisible) { + // IE doesn't recalculate width when scrollbar disappears + listItems.width( list.width() - parseInt(listItems.css("padding-left")) - parseInt(listItems.css("padding-right")) ); + } } } - }, - selected: function() { - var selected = listItems && listItems.filter("." + CLASSES.ACTIVE).removeClass(CLASSES.ACTIVE); - return selected && selected.length && $.data(selected[0], "ac_data"); - }, - emptyList: function (){ - list && list.empty(); - }, - unbind: function() { - element && element.remove(); - } - }; + }, + selected: function() { + var selected = listItems && listItems.filter("." + CLASSES.ACTIVE).removeClass(CLASSES.ACTIVE); + return selected && selected.length && $.data(selected[0], "ac_data"); + }, + emptyList: function (){ + list && list.empty(); + }, + unbind: function() { + element && element.remove(); + } + }; }; $.Autocompleter.Selection = function(field, start, end) { - if( field.createTextRange ){ - var selRange = field.createTextRange(); - selRange.collapse(true); - selRange.moveStart("character", start); - selRange.moveEnd("character", end); - selRange.select(); - } else if( field.setSelectionRange ){ - field.setSelectionRange(start, end); - } else { - if( field.selectionStart ){ - field.selectionStart = start; - field.selectionEnd = end; - } - } - field.focus(); + if( field.createTextRange ){ + var selRange = field.createTextRange(); + selRange.collapse(true); + selRange.moveStart("character", start); + selRange.moveEnd("character", end); + selRange.select(); + } else if( field.setSelectionRange ){ + field.setSelectionRange(start, end); + } else { + if( field.selectionStart ){ + field.selectionStart = start; + field.selectionEnd = end; + } + } + field.focus(); }; })(jQuery); --- a/static/scripts/packed/galaxy.base.js +++ b/static/scripts/packed/galaxy.base.js @@ -1,1 +1,1 @@ -$(document).ready(function(){replace_big_select_inputs()});$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};function ensure_popup_helper(){if($("#popup-helper").length===0){$("<div id='popup-helper'/>").css({background:"white",opacity:0,zIndex:15000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function attach_popupmenu(b,d){var a=function(){d.unbind().hide();$("#popup-helper").unbind("click.popupmenu").hide()};var c=function(g){$("#popup-helper").bind("click.popupmenu",a).show();d.click(a).css({left:0,top:-1000}).show();var f=g.pageX-d.width()/2;f=Math.min(f,$(document).scrollLeft()+$(window).width()-$(d).width()-20);f=Math.max(f,$(document).scrollLeft()+20);d.css({top:g.pageY-5,left:f});return false};$(b).click(c)}function make_popupmenu (c,b){ensure_popup_helper();var a=$("<ul id='"+c.attr("id")+"-menu'></ul>");$.each(b,function(f,e){if(e){$("<li/>").html(f).click(e).appendTo(a)}else{$("<li class='head'/>").html(f).appendTo(a)}});var d=$("<div class='popmenu-wrapper'>");d.append(a).append("<div class='overlay-border'>").css("position","absolute").appendTo("body").hide();attach_popupmenu(c,d)}function make_popup_menus(){jQuery("div[popupmenu]").each(function(){var c={};$(this).find("a").each(function(){var 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