galaxy-commits August 2012

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commit/galaxy-central: jgoecks: Add data placeholders so that BED files without all optional fields can be dynamically filtered.
by Bitbucket 22 Aug '12

22 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/863e1150c85b/ changeset: 863e1150c85b user: jgoecks date: 2012-08-22 20:42:05 summary: Add data placeholders so that BED files without all optional fields can be dynamically filtered. affected #: 1 file diff -r 931382e567f501ff8529cdd3c7b45c2d08d0ab23 -r 863e1150c85b7383a1b136c9b3c9376da81bc16b lib/galaxy/visualization/tracks/data_providers.py --- a/lib/galaxy/visualization/tracks/data_providers.py +++ b/lib/galaxy/visualization/tracks/data_providers.py @@ -484,6 +484,11 @@ # Score (filter data) if length >= 5 and filter_cols and filter_cols[0] == "Score": + # If dataset doesn't have name/strand/thick start/thick end/blocks, + # add placeholders. There should be 8 entries if all attributes + # are present. + payload.extend( [ None for i in range( 8 - len( payload ) ) ] ) + try: payload.append( float( feature[4] ) ) except: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Refactor GBrowse external display application. Update WormBase with latest builds and to be able to use reference sites.
by Bitbucket 22 Aug '12

22 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/931382e567f5/ changeset: 931382e567f5 user: dan date: 2012-08-22 18:35:23 summary: Refactor GBrowse external display application. Update WormBase with latest builds and to be able to use reference sites. affected #: 6 files diff -r 7eeee803345e111b9485cc9b9c2b397a6623fa5f -r 931382e567f501ff8529cdd3c7b45c2d08d0ab23 display_applications/gbrowse/gbrowse_gff.xml --- a/display_applications/gbrowse/gbrowse_gff.xml +++ b/display_applications/gbrowse/gbrowse_gff.xml @@ -1,16 +1,24 @@ <display id="gbrowse_gff" version="1.0.0" name="display at GBrowse"> - <dynamic_links from_file="tool-data/shared/gbrowse/gbrowse_build_sites.txt" skip_startswith="#" id="0" name="0"> + <dynamic_links from_file="tool-data/shared/gbrowse/gbrowse_build_sites.txt" skip_startswith="#" id="0" name="1"> + <dynamic_param name="site_id" value="0"/> - <dynamic_param name="gbrowse_link" value="1"/> - <dynamic_param name="builds" value="2" split="True" separator="," /> + <dynamic_param name="site_name" value="1"/> + <dynamic_param name="site_link" value="2"/> + <dynamic_param name="site_dbkeys" value="3" split="True" separator="," /> + <dynamic_param name="site_organisms" value="4" split="True" separator="," /> + <filter>${site_id in $APP.config.gbrowse_display_sites}</filter> - <filter>${dataset.dbkey in $builds}</filter> + <filter>${dataset.dbkey in $site_dbkeys}</filter> +  - <url>${gbrowse_link}/?${position}eurl=${gff_file.qp}</url> + <url>${site_link}${site_organism}/?${position}eurl=${gff_file.qp}</url><param type="data" name="gff_file" url="galaxy_${DATASET_HASH}.gff" /> + <param type="template" name="site_organism" strip="True" > + $site_organisms[ $site_dbkeys.index( $gff_file.dbkey ) ] + </param><param type="template" name="position" strip="True" > #set chrom, start, end = $gff_file.datatype.get_estimated_display_viewport( $gff_file ) #if $chrom is not None: diff -r 7eeee803345e111b9485cc9b9c2b397a6623fa5f -r 931382e567f501ff8529cdd3c7b45c2d08d0ab23 display_applications/gbrowse/gbrowse_interval_as_bed.xml --- a/display_applications/gbrowse/gbrowse_interval_as_bed.xml +++ b/display_applications/gbrowse/gbrowse_interval_as_bed.xml @@ -1,16 +1,24 @@ <display id="gbrowse_interval_as_bed" version="1.0.0" name="display at GBrowse"> - <dynamic_links from_file="tool-data/shared/gbrowse/gbrowse_build_sites.txt" skip_startswith="#" id="0" name="0"> + <dynamic_links from_file="tool-data/shared/gbrowse/gbrowse_build_sites.txt" skip_startswith="#" id="0" name="1"> + <dynamic_param name="site_id" value="0"/> - <dynamic_param name="gbrowse_link" value="1"/> - <dynamic_param name="builds" value="2" split="True" separator="," /> + <dynamic_param name="site_name" value="1"/> + <dynamic_param name="site_link" value="2"/> + <dynamic_param name="site_dbkeys" value="3" split="True" separator="," /> + <dynamic_param name="site_organisms" value="4" split="True" separator="," /> + <filter>${site_id in $APP.config.gbrowse_display_sites}</filter> - <filter>${dataset.dbkey in $builds}</filter> + <filter>${dataset.dbkey in $site_dbkeys}</filter> +  - <url>${gbrowse_link}/?${position}eurl=${bed_file.qp}</url> + <url>${site_link}${site_organism}/?${position}eurl=${bed_file.qp}</url><param type="data" name="bed_file" url="galaxy_${DATASET_HASH}.bed" format="bedstrict"/> + <param type="template" name="site_organism" strip="True" > + $site_organisms[ $site_dbkeys.index( $bed_file.dbkey ) ] + </param><param type="template" name="position" strip="True" > #set chrom, start, end = $bed_file.datatype.get_estimated_display_viewport( $bed_file ) #if $chrom is not None: diff -r 7eeee803345e111b9485cc9b9c2b397a6623fa5f -r 931382e567f501ff8529cdd3c7b45c2d08d0ab23 display_applications/gbrowse/gbrowse_wig.xml --- a/display_applications/gbrowse/gbrowse_wig.xml +++ b/display_applications/gbrowse/gbrowse_wig.xml @@ -1,16 +1,24 @@ <display id="gbrowse_wig" version="1.0.0" name="display at GBrowse"> - <dynamic_links from_file="tool-data/shared/gbrowse/gbrowse_build_sites.txt" skip_startswith="#" id="0" name="0"> + <dynamic_links from_file="tool-data/shared/gbrowse/gbrowse_build_sites.txt" skip_startswith="#" id="0" name="1"> + <dynamic_param name="site_id" value="0"/> - <dynamic_param name="gbrowse_link" value="1"/> - <dynamic_param name="builds" value="2" split="True" separator="," /> + <dynamic_param name="site_name" value="1"/> + <dynamic_param name="site_link" value="2"/> + <dynamic_param name="site_dbkeys" value="3" split="True" separator="," /> + <dynamic_param name="site_organisms" value="4" split="True" separator="," /> + <filter>${site_id in $APP.config.gbrowse_display_sites}</filter> - <filter>${dataset.dbkey in $builds}</filter> + <filter>${dataset.dbkey in $site_dbkeys}</filter> +  - <url>${gbrowse_link}/?${position}eurl=${wig_file.qp}</url> + <url>${site_link}${site_organism}/?${position}eurl=${wig_file.qp}</url><param type="data" name="wig_file" url="galaxy_${DATASET_HASH}.wig" format="wig"/> + <param type="template" name="site_organism" strip="True" > + $site_organisms[ $site_dbkeys.index( $wig_file.dbkey ) ] + </param><param type="template" name="position" strip="True" > #set chrom, start, end = $wig_file.datatype.get_estimated_display_viewport( $wig_file ) #if $chrom is not None: diff -r 7eeee803345e111b9485cc9b9c2b397a6623fa5f -r 931382e567f501ff8529cdd3c7b45c2d08d0ab23 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -132,7 +132,7 @@ self.log_events = string_as_bool( kwargs.get( 'log_events', 'False' ) ) self.sanitize_all_html = string_as_bool( kwargs.get( 'sanitize_all_html', True ) ) self.ucsc_display_sites = kwargs.get( 'ucsc_display_sites', "main,test,archaea,ucla" ).lower().split(",") - self.gbrowse_display_sites = kwargs.get( 'gbrowse_display_sites', "wormbase,tair,modencode_worm,modencode_fly,sgd_yeast" ).lower().split(",") + self.gbrowse_display_sites = kwargs.get( 'gbrowse_display_sites', "modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225" ).lower().split(",") self.genetrack_display_sites = kwargs.get( 'genetrack_display_sites', "main,test" ).lower().split(",") self.brand = kwargs.get( 'brand', None ) self.support_url = kwargs.get( 'support_url', 'http://wiki.g2.bx.psu.edu/Support' ) diff -r 7eeee803345e111b9485cc9b9c2b397a6623fa5f -r 931382e567f501ff8529cdd3c7b45c2d08d0ab23 tool-data/shared/gbrowse/gbrowse_build_sites.txt --- a/tool-data/shared/gbrowse/gbrowse_build_sites.txt +++ b/tool-data/shared/gbrowse/gbrowse_build_sites.txt @@ -1,14 +1,24 @@ -# wormbase sites / supported genomes -wormbase http://www.wormbase.org/db/gb2/gbrowse/c_elegans ce8,ce7,ce6,ce5,ce4,ce3,ce2,cb3,cb2,cb1,caeRem3,caeRem2,caeRem1,caePb2,caePb1,caeJap2,caeJap1 -#test http://dev.wormbase.org/db/seq/gbrowse/c_elegans/ ce8,ce7,ce6,ce5,ce4,ce3,ce2,cb3,cb2,cb1,caeRem3,caeRem2,caeRem1,caePb2,caePb1,caeJap2,caeJap1 +#GBrowse Sites +#site_id site_name site_link site_dbkeys site_organisms -# UCSC mirror that includes arabidopsis -tair http://arabidopsis.org/cgi-bin/gbrowse/ arabidopsis_tair8,arabidopsis +#WormBase +wormbase WormBase current http://www.wormbase.org/db/gb2/gbrowse/ ce10,ce9,ce8,ce7,ce6,ce5,ce4,ce3,ce2,cb4,cb3,cb2,cb1,caeRem4,caeRem3,caeRem2,caeRem1,caePb2,caePb1,caeJap4,caeJap3,caeJap2,caeJap1,caeAng1 c_elegans,c_elegans,c_elegans,c_elegans,c_elegans,c_elegans,c_elegans,c_elegans,c_elegans,c_briggsae,c_briggsae,c_briggsae,c_briggsae,c_remanei,c_remanei,c_remanei,c_remanei,c_brenneri,c_brenneri,c_japonica,c_japonica,c_japonica,c_japonica,c_angaria +wormbase_ws120 WormBase WS120 http://ws120.wormbase.org/db/seq/gbrowse/ ce2 wormbase +wormbase_ws140 WormBase WS140 http://ws140.wormbase.org/db/seq/gbrowse/ ce3 wormbase +wormbase_ws170 WormBase WS170 http://ws170.wormbase.org/db/seq/gbrowse/ ce4 wormbase +wormbase_ws180 WormBase WS180 http://ws180.wormbase.org/db/seq/gbrowse/ ce5 elegans +wormbase_ws190 WormBase WS190 http://ws190.wormbase.org/db/seq/gbrowse/ ce6 elegans +wormbase_ws200 WormBase WS200 http://ws200.wormbase.org/db/seq/gbrowse/ ce7 c_elegans +wormbase_ws204 WormBase WS204 http://ws204.wormbase.org/db/seq/gbrowse/ ce8 c_elegans +wormbase_ws210 WormBase WS210 http://ws210.wormbase.org/db/seq/gbrowse/ ce9 c_elegans +wormbase_ws220 WormBase WS220 http://ws220.wormbase.org/db/gb2/gbrowse/ ce10,caeRem4 c_elegans,c_remanei +wormbase_ws225 WormBase WS225 http://ws225.wormbase.org/db/gb2/gbrowse/ caeAng1,cb4 c_angaria,c_briggsae -# modENCODE worm and fly -modencode_worm http://modencode.oicr.on.ca/fgb2/gbrowse/worm ce6 -modencode_fly http://modencode.oicr.on.ca/fgb2/gbrowse/fly dm2 +#The Arabidopsis Information Resource (tair) +tair tair http://arabidopsis.org/cgi-bin/gbrowse/ arabidopsis_tair8,arabidopsis,Arabidopsis_thaliana_TAIR10 arabidopsis_tair8,arabidopsis_tair9,arabidopsis -#SGD -sgd_yeast http://browse.yeastgenome.org/fgb2/gbrowse/scgenome Saccharomyces_cerevisiae_S288C_SGD2010 +#modENCODE +modencode modENCODE http://modencode.oicr.on.ca/fgb2/gbrowse/ ce6,dm2 worm,fly +#Saccharomyces Genome Database (SGD) +sgd_yeast Saccharomyces Genome Database http://browse.yeastgenome.org/fgb2/gbrowse/ Saccharomyces_cerevisiae_S288C_SGD2010 scgenome diff -r 7eeee803345e111b9485cc9b9c2b397a6623fa5f -r 931382e567f501ff8529cdd3c7b45c2d08d0ab23 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -218,7 +218,7 @@ #ucsc_display_sites = main,test,archaea,ucla # GBrowse servers: tool-data/shared/gbrowse/gbrowse_build_sites.txt -#gbrowse_display_sites = wormbase,tair,modencode_worm,modencode_fly,yeast_sgd +#gbrowse_display_sites = modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225 # GeneTrack servers: tool-data/shared/genetrack/genetrack_sites.txt #genetrack_display_sites = main,test Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dan: Better handling of invalid dynamic external display application links.
by Bitbucket 22 Aug '12

22 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/7eeee803345e/ changeset: 7eeee803345e user: dan date: 2012-08-22 17:40:55 summary: Better handling of invalid dynamic external display application links. affected #: 1 file diff -r 9df126526d89979a7830bc48c7bff122555eaea9 -r 7eeee803345e111b9485cc9b9c2b397a6623fa5f lib/galaxy/datatypes/display_applications/application.py --- a/lib/galaxy/datatypes/display_applications/application.py +++ b/lib/galaxy/datatypes/display_applications/application.py @@ -98,8 +98,10 @@ for line in open( filename ): if not skip_startswith or not line.startswith( skip_startswith ): line = line.rstrip( '\n\r' ) + if not line: + continue fields = line.split( separator ) - if len( fields ) >= max_col: + if len( fields ) > max_col: new_elem = deepcopy( elem ) new_elem.set( 'id', fields[id_col] ) new_elem.set( 'name', fields[name_col] ) @@ -111,6 +113,8 @@ dynamic_values[key] = value #now populate rval.append( DisplayApplicationLink.from_elem( new_elem, display_application, other_values = dynamic_values ) ) + else: + log.warning( 'Invalid dynamic display application link specified in %s: "%s"' % ( filename, line ) ) self.links = rval def __iter__( self ): return iter( self.links ) 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: afgane: Rename an ObjectStore method not to be AWS-specific
by Bitbucket 22 Aug '12

22 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/9df126526d89/ changeset: 9df126526d89 user: afgane date: 2012-08-22 08:24:52 summary: Rename an ObjectStore method not to be AWS-specific affected #: 1 file diff -r 8c07fc133839d1c175aa85d37d43f2f9ce5c6182 -r 9df126526d89979a7830bc48c7bff122555eaea9 lib/galaxy/objectstore/__init__.py --- a/lib/galaxy/objectstore/__init__.py +++ b/lib/galaxy/objectstore/__init__.py @@ -608,13 +608,13 @@ log.error("Problem downloading key '%s' from S3 bucket '%s': %s" % (rel_path, self.bucket.name, ex)) return False - def _push_to_s3(self, rel_path, source_file=None, from_string=None): + def _push_to_os(self, rel_path, source_file=None, from_string=None): """ - Push the file pointed to by `rel_path` to S3 naming the key `rel_path`. - If `source_file` is provided, push that file instead while still using - `rel_path` as the key name. - If `from_string` is provided, set contents of the file to the value of - the string + Push the file pointed to by ``rel_path`` to the object store naming the key + ``rel_path``. If ``source_file`` is provided, push that file instead while + still using ``rel_path`` as the key name. + If ``from_string`` is provided, set contents of the file to the value of + the string. """ try: source_file = source_file if source_file else self._get_cache_path(rel_path) @@ -680,7 +680,7 @@ return False # TODO: Sync should probably not be done here. Add this to an async upload stack? if in_cache and not in_s3: - self._push_to_s3(rel_path, source_file=self._get_cache_path(rel_path)) + self._push_to_os(rel_path, source_file=self._get_cache_path(rel_path)) return True elif in_s3: return True @@ -713,12 +713,12 @@ # flat namespace), do so for consistency with the regular file system # S3 folders are marked by having trailing '/' so add it now # s3_dir = '%s/' % rel_path - # self._push_to_s3(s3_dir, from_string='') + # self._push_to_os(s3_dir, from_string='') # If instructed, create the dataset in cache & in S3 if not dir_only: rel_path = os.path.join(rel_path, alt_name if alt_name else "dataset_%s.dat" % obj.id) open(os.path.join(self.staging_path, rel_path), 'w').close() - self._push_to_s3(rel_path, from_string='') + self._push_to_os(rel_path, from_string='') def empty(self, obj, **kwargs): if self.exists(obj, **kwargs): @@ -832,7 +832,7 @@ else: source_file = self._get_cache_path(rel_path) # Update the file on S3 - self._push_to_s3(rel_path, source_file) + self._push_to_os(rel_path, source_file) else: raise ObjectNotFound() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by Bitbucket 22 Aug '12

22 Aug '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/f906603c475e/ changeset: f906603c475e user: afgane date: 2012-08-22 08:12:46 summary: Multipart upload to OpenStack Swift does not work with boto so don't use it affected #: 2 files diff -r 9e9e104ad5c93a2268bb00cfae09b57a31ece13c -r f906603c475e80f9d3171c18a4051c4b325b6e5b lib/galaxy/objectstore/__init__.py --- a/lib/galaxy/objectstore/__init__.py +++ b/lib/galaxy/objectstore/__init__.py @@ -631,7 +631,7 @@ # print "Pushing cache file '%s' of size %s bytes to key '%s'" % (source_file, os.path.getsize(source_file), rel_path) # print "+ Push started at '%s'" % start_time mb_size = os.path.getsize(source_file) / 1e6 - if mb_size < 60: + if mb_size < 60 or self.config.object_store == 'swift': self.transfer_progress = 0 # Reset transfer progress counter key.set_contents_from_filename(source_file, reduced_redundancy=self.use_rr, cb=self._transfer_cb, num_cb=10) @@ -649,12 +649,17 @@ return False def file_ready(self, obj, **kwargs): - """ A helper method that checks if a file corresponding to a dataset - is ready and available to be used. Return True if so, False otherwise.""" + """ + A helper method that checks if a file corresponding to a dataset is + ready and available to be used. Return ``True`` if so, ``False`` otherwise. + """ rel_path = self._construct_path(obj, **kwargs) # Make sure the size in cache is available in its entirety - if self._in_cache(rel_path) and os.path.getsize(self._get_cache_path(rel_path)) == self._get_size_in_s3(rel_path): - return True + if self._in_cache(rel_path): + if os.path.getsize(self._get_cache_path(rel_path)) == self._get_size_in_s3(rel_path): + return True + log.debug("Waiting for dataset {0} to transfer from OS: {1}/{2}".format(rel_path, + os.path.getsize(self._get_cache_path(rel_path)), self._get_size_in_s3(rel_path))) return False def exists(self, obj, **kwargs): diff -r 9e9e104ad5c93a2268bb00cfae09b57a31ece13c -r f906603c475e80f9d3171c18a4051c4b325b6e5b templates/root/history.mako --- a/templates/root/history.mako +++ b/templates/root/history.mako @@ -166,7 +166,7 @@ // $("<div/>").text("Data is loading from S3... please be patient").appendTo(link.parent()); $( '#historyItem-' + history_id).removeClass( "historyItem-ok" ); $( '#historyItem-' + history_id).addClass( "historyItem-running" ); - setTimeout(function(){check_transfer_status(link, history_id)}, 1000); + setTimeout(function(){check_transfer_status(link, history_id)}, 4000); } else { $( '#historyItem-' + history_id).removeClass( "historyItem-running" ); $( '#historyItem-' + history_id).addClass( "historyItem-ok" ); https://bitbucket.org/galaxy/galaxy-central/changeset/8c07fc133839/ changeset: 8c07fc133839 user: afgane date: 2012-08-22 08:13:51 summary: Merge affected #: 194 files 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: jgoecks: Final JS reorg to rename and move files so that all files follow standard conventions.
by Bitbucket 21 Aug '12

21 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/e27c236c05e5/ changeset: e27c236c05e5 user: jgoecks date: 2012-08-21 23:08:35 summary: Final JS reorg to rename and move files so that all files follow standard conventions. affected #: 29 files diff -r f076e439d46e1bd66a9a5dd0c75c69c0a11550ed -r e27c236c05e5d65f3ce92f271a712419e7fd73a5 static/scripts/autocomplete_tagging.js --- a/static/scripts/autocomplete_tagging.js +++ /dev/null @@ -1,374 +0,0 @@ -/** -* JQuery extension for tagging with autocomplete. -* @author: Jeremy Goecks -* @require: jquery.autocomplete plugin -*/ -// -// Initialize "tag click functions" for tags. -// -function init_tag_click_function(tag_elt, click_func) { - $(tag_elt).find('.tag-name').each( function() { - $(this).click( function() { - var tag_str = $(this).text(); - var tag_name_and_value = tag_str.split(":"); - click_func(tag_name_and_value[0], tag_name_and_value[1]); - return true; - }); - }); -} - -jQuery.fn.autocomplete_tagging = function(options) { - - var defaults = { - get_toggle_link_text_fn: function(tags) { - var text = ""; - var num_tags = obj_length(tags); - if (num_tags > 0) { - text = num_tags + (num_tags > 1 ? " Tags" : " Tag"); - } else { - text = "Add tags"; - } - return text; - }, - tag_click_fn : function (name, value) {}, - editable: true, - input_size: 20, - in_form: false, - tags : {}, - use_toggle_link: true, - item_id: "", - add_tag_img: "", - add_tag_img_rollover: "", - delete_tag_img: "", - ajax_autocomplete_tag_url: "", - ajax_retag_url: "", - ajax_delete_tag_url: "", - ajax_add_tag_url: "" - }; - - var settings = jQuery.extend(defaults, options); - - // - // Initalize object's elements. - // - - // Get elements for this object. For this_obj, assume the last element with the id is the "this"; this is somewhat of a hack to address the problem - // that there may be two tagging elements for a single item if there are both community and individual tags for an element. - var this_obj = $(this); - var tag_area = this_obj.find('.tag-area'); - var toggle_link = this_obj.find('.toggle-link'); - var tag_input_field = this_obj.find('.tag-input'); - var add_tag_button = this_obj.find('.add-tag-button'); - - // Initialize toggle link. - toggle_link.click( function() { - // Take special actions depending on whether toggle is showing or hiding link. - var after_toggle_fn; - if (tag_area.is(":hidden")) { - after_toggle_fn = function() { - // If there are no tags, go right to editing mode by generating a click on the area. - var num_tags = $(this).find('.tag-button').length; - if (num_tags === 0) { - tag_area.click(); - } - }; - } else { - after_toggle_fn = function() { - tag_area.blur(); - }; - } - tag_area.slideToggle("fast", after_toggle_fn); - return $(this); - }); - - // Initialize tag input field. - if (settings.editable) { - tag_input_field.hide(); - } - tag_input_field.keyup( function(e) { - if ( e.keyCode === 27 ) { - // Escape key - $(this).trigger( "blur" ); - } else if ( - ( e.keyCode === 13 ) || // Return Key - ( e.keyCode === 188 ) || // Comma - ( e.keyCode === 32 ) // Space - ) { - // - // Check input. - // - - var new_value = this.value; - - // Do nothing if return key was used to autocomplete. - if (return_key_pressed_for_autocomplete === true) { - return_key_pressed_for_autocomplete = false; - return false; - } - - // Suppress space after a ":" - if ( new_value.indexOf(": ", new_value.length - 2) !== -1) { - this.value = new_value.substring(0, new_value.length-1); - return false; - } - - // Remove trigger keys from input. - if ( (e.keyCode === 188) || (e.keyCode === 32) ) { - new_value = new_value.substring( 0 , new_value.length - 1 ); - } - - // Trim whitespace. - new_value = $.trim(new_value); - - // Too short? - if (new_value.length < 2) { - return false; - } - - // - // New tag OK - apply it. - // - - this.value = ""; // Reset text field now that tag is being added - - // Add button for tag after all other tag buttons. - var new_tag_button = build_tag_button(new_value); - var tag_buttons = tag_area.children(".tag-button"); - if (tag_buttons.length !== 0) { - var last_tag_button = tag_buttons.slice(tag_buttons.length-1); - last_tag_button.after(new_tag_button); - } else { - tag_area.prepend(new_tag_button); - } - - // Add tag to internal list. - var tag_name_and_value = new_value.split(":"); - settings.tags[tag_name_and_value[0]] = tag_name_and_value[1]; - - // Update toggle link text. - var new_text = settings.get_toggle_link_text_fn(settings.tags); - toggle_link.text(new_text); - - // Commit tag to server. - var zz = $(this); - $.ajax({ - url: settings.ajax_add_tag_url, - data: { new_tag: new_value }, - error: function() { - // Failed. Roll back changes and show alert. - new_tag_button.remove(); - delete settings.tags[tag_name_and_value[0]]; - var new_text = settings.get_toggle_link_text_fn(settings.tags); - toggle_link.text(new_text); - alert( "Add tag failed" ); - }, - success: function() { - // Flush autocomplete cache because it's not out of date. - // TODO: in the future, we could remove the particular item - // that was chosen from the cache rather than flush it. - zz.flushCache(); - } - }); - - return false; - } - }); - - // Add autocomplete to input. - var format_item_func = function(key, row_position, num_rows, value, search_term) { - var tag_name_and_value = value.split(":"); - return (tag_name_and_value.length === 1 ? tag_name_and_value[0] : tag_name_and_value[1]); - }; - var autocomplete_options = { selectFirst: false, formatItem: format_item_func, - autoFill: false, highlight: false }; - tag_input_field.autocomplete(settings.ajax_autocomplete_tag_url, autocomplete_options); - - - // Initialize delete tag images for current tags. - this_obj.find('.delete-tag-img').each(function() { - init_delete_tag_image( $(this) ); - }); - - - // Initialize tag click function. - init_tag_click_function($(this), settings.tag_click_fn); - - // Initialize "add tag" button. - add_tag_button.click( function() { - $(this).hide(); - - // Clicking on button is the same as clicking on the tag area. - tag_area.click(); - return false; - }); - - // - // Set up tag area interactions; these are needed only if tags are editable. - // - if (settings.editable) { - // When the tag area blurs, go to "view tag" mode. - tag_area.bind("blur", function(e) { - if (obj_length(settings.tags) > 0) { - add_tag_button.show(); - tag_input_field.hide(); - tag_area.removeClass("active-tag-area"); - tag_area.addClass("tooltip"); - } else { - // No tags, so do nothing to ensure that input is still visible. - } - }); - - // On click, enable user to add tags. - tag_area.click( function(e) { - var is_active = $(this).hasClass("active-tag-area"); - - // If a "delete image" object was pressed and area is inactive, do nothing. - if ($(e.target).hasClass("delete-tag-img") && !is_active) { - return false; - } - - // If a "tag name" object was pressed and area is inactive, do nothing. - if ($(e.target).hasClass("tag-name") && !is_active) { - return false; - } - - // Remove tooltip. - $(this).removeClass("tooltip"); - - // Hide add tag button, show tag_input field. Change background to show - // area is active. - $(this).addClass("active-tag-area"); - add_tag_button.hide(); - tag_input_field.show(); - tag_input_field.focus(); - - // Add handler to document that will call blur when the tag area is blurred; - // a tag area is blurred when a user clicks on an element outside the area. - var handle_document_click = function(e) { - var check_click = function(tag_area, target) { - var tag_area_id = tag_area.attr("id"); - // Blur the tag area if the element clicked on is not in the tag area. - if (target !== tag_area) { - tag_area.blur(); - $(window).unbind("click.tagging_blur"); - $(this).addClass("tooltip"); - } - }; - check_click(tag_area, $(e.target)); - }; - // TODO: we should attach the click handler to all frames in order to capture - // clicks outside the frame that this element is in. - //window.parent.document.onclick = handle_document_click; - //var temp = $(window.parent.document.body).contents().find("iframe").html(); - //alert(temp); - //$(document).parent().click(handle_document_click); - $(window).bind("click.tagging_blur", handle_document_click); - - return false; - }); - } - - // If using toggle link, hide the tag area. Otherwise, show the tag area. - if (settings.use_toggle_link) { - tag_area.hide(); - } - - // - // Helper functions. - // - - // - // Collapse tag name + value into a single string. - // - function build_tag_str(tag_name, tag_value) { - return tag_name + ( tag_value ? ":" + tag_value : ""); - } - - - // Initialize a "delete tag image": when click, delete tag from UI and send delete request to server. - function init_delete_tag_image(delete_img) { - $(delete_img).mouseenter( function () { - $(this).attr("src", settings.delete_tag_img_rollover); - }); - $(delete_img).mouseleave( function () { - $(this).attr("src", settings.delete_tag_img); - }); - $(delete_img).click( function () { - // Tag button is image's parent. - var tag_button = $(this).parent(); - - // Get tag name, value. - var tag_name_elt = tag_button.find(".tag-name").eq(0); - var tag_str = tag_name_elt.text(); - var tag_name_and_value = tag_str.split(":"); - var tag_name = tag_name_and_value[0]; - var tag_value = tag_name_and_value[1]; - - var prev_button = tag_button.prev(); - tag_button.remove(); - - // Remove tag from local list for consistency. - delete settings.tags[tag_name]; - - // Update toggle link text. - var new_text = settings.get_toggle_link_text_fn(settings.tags); - toggle_link.text(new_text); - - // Delete tag. - $.ajax({ - url: settings.ajax_delete_tag_url, - data: { tag_name: tag_name }, - error: function() { - // Failed. Roll back changes and show alert. - settings.tags[tag_name] = tag_value; - if (prev_button.hasClass("tag-button")) { - prev_button.after(tag_button); - } else { - tag_area.prepend(tag_button); - } - alert( "Remove tag failed" ); - - toggle_link.text(settings.get_toggle_link_text_fn(settings.tags)); - - // TODO: no idea why it's necessary to set this up again. - delete_img.mouseenter( function () { - $(this).attr("src", settings.delete_tag_img_rollover); - }); - delete_img.mouseleave( function () { - $(this).attr("src", settings.delete_tag_img); - }); - }, - success: function() {} - }); - - return true; - }); - } - - // - // Function that builds a tag button. - // - function build_tag_button(tag_str) { - // Build "delete tag" image. - var delete_img = $("<img/>").attr("src", settings.delete_tag_img).addClass("delete-tag-img"); - init_delete_tag_image(delete_img); - - // Build tag button. - var tag_name_elt = $("<span>").text(tag_str).addClass("tag-name"); - tag_name_elt.click( function() { - var tag_name_and_value = tag_str.split(":"); - settings.tag_click_fn(tag_name_and_value[0], tag_name_and_value[1]); - return true; - }); - - var tag_button = $("<span></span>").addClass("tag-button"); - tag_button.append(tag_name_elt); - // Allow delete only if element is editable. - if (settings.editable) { - tag_button.append(delete_img); - } - - return tag_button; - } - -}; diff -r f076e439d46e1bd66a9a5dd0c75c69c0a11550ed -r e27c236c05e5d65f3ce92f271a712419e7fd73a5 static/scripts/galaxy.autocom_tagging.js --- /dev/null +++ b/static/scripts/galaxy.autocom_tagging.js @@ -0,0 +1,374 @@ +/** +* JQuery extension for tagging with autocomplete. +* @author: Jeremy Goecks +* @require: jquery.autocomplete plugin +*/ +// +// Initialize "tag click functions" for tags. +// +function init_tag_click_function(tag_elt, click_func) { + $(tag_elt).find('.tag-name').each( function() { + $(this).click( function() { + var tag_str = $(this).text(); + var tag_name_and_value = tag_str.split(":"); + click_func(tag_name_and_value[0], tag_name_and_value[1]); + return true; + }); + }); +} + +jQuery.fn.autocomplete_tagging = function(options) { + + var defaults = { + get_toggle_link_text_fn: function(tags) { + var text = ""; + var num_tags = obj_length(tags); + if (num_tags > 0) { + text = num_tags + (num_tags > 1 ? " Tags" : " Tag"); + } else { + text = "Add tags"; + } + return text; + }, + tag_click_fn : function (name, value) {}, + editable: true, + input_size: 20, + in_form: false, + tags : {}, + use_toggle_link: true, + item_id: "", + add_tag_img: "", + add_tag_img_rollover: "", + delete_tag_img: "", + ajax_autocomplete_tag_url: "", + ajax_retag_url: "", + ajax_delete_tag_url: "", + ajax_add_tag_url: "" + }; + + var settings = jQuery.extend(defaults, options); + + // + // Initalize object's elements. + // + + // Get elements for this object. For this_obj, assume the last element with the id is the "this"; this is somewhat of a hack to address the problem + // that there may be two tagging elements for a single item if there are both community and individual tags for an element. + var this_obj = $(this); + var tag_area = this_obj.find('.tag-area'); + var toggle_link = this_obj.find('.toggle-link'); + var tag_input_field = this_obj.find('.tag-input'); + var add_tag_button = this_obj.find('.add-tag-button'); + + // Initialize toggle link. + toggle_link.click( function() { + // Take special actions depending on whether toggle is showing or hiding link. + var after_toggle_fn; + if (tag_area.is(":hidden")) { + after_toggle_fn = function() { + // If there are no tags, go right to editing mode by generating a click on the area. + var num_tags = $(this).find('.tag-button').length; + if (num_tags === 0) { + tag_area.click(); + } + }; + } else { + after_toggle_fn = function() { + tag_area.blur(); + }; + } + tag_area.slideToggle("fast", after_toggle_fn); + return $(this); + }); + + // Initialize tag input field. + if (settings.editable) { + tag_input_field.hide(); + } + tag_input_field.keyup( function(e) { + if ( e.keyCode === 27 ) { + // Escape key + $(this).trigger( "blur" ); + } else if ( + ( e.keyCode === 13 ) || // Return Key + ( e.keyCode === 188 ) || // Comma + ( e.keyCode === 32 ) // Space + ) { + // + // Check input. + // + + var new_value = this.value; + + // Do nothing if return key was used to autocomplete. + if (return_key_pressed_for_autocomplete === true) { + return_key_pressed_for_autocomplete = false; + return false; + } + + // Suppress space after a ":" + if ( new_value.indexOf(": ", new_value.length - 2) !== -1) { + this.value = new_value.substring(0, new_value.length-1); + return false; + } + + // Remove trigger keys from input. + if ( (e.keyCode === 188) || (e.keyCode === 32) ) { + new_value = new_value.substring( 0 , new_value.length - 1 ); + } + + // Trim whitespace. + new_value = $.trim(new_value); + + // Too short? + if (new_value.length < 2) { + return false; + } + + // + // New tag OK - apply it. + // + + this.value = ""; // Reset text field now that tag is being added + + // Add button for tag after all other tag buttons. + var new_tag_button = build_tag_button(new_value); + var tag_buttons = tag_area.children(".tag-button"); + if (tag_buttons.length !== 0) { + var last_tag_button = tag_buttons.slice(tag_buttons.length-1); + last_tag_button.after(new_tag_button); + } else { + tag_area.prepend(new_tag_button); + } + + // Add tag to internal list. + var tag_name_and_value = new_value.split(":"); + settings.tags[tag_name_and_value[0]] = tag_name_and_value[1]; + + // Update toggle link text. + var new_text = settings.get_toggle_link_text_fn(settings.tags); + toggle_link.text(new_text); + + // Commit tag to server. + var zz = $(this); + $.ajax({ + url: settings.ajax_add_tag_url, + data: { new_tag: new_value }, + error: function() { + // Failed. Roll back changes and show alert. + new_tag_button.remove(); + delete settings.tags[tag_name_and_value[0]]; + var new_text = settings.get_toggle_link_text_fn(settings.tags); + toggle_link.text(new_text); + alert( "Add tag failed" ); + }, + success: function() { + // Flush autocomplete cache because it's not out of date. + // TODO: in the future, we could remove the particular item + // that was chosen from the cache rather than flush it. + zz.flushCache(); + } + }); + + return false; + } + }); + + // Add autocomplete to input. + var format_item_func = function(key, row_position, num_rows, value, search_term) { + var tag_name_and_value = value.split(":"); + return (tag_name_and_value.length === 1 ? tag_name_and_value[0] : tag_name_and_value[1]); + }; + var autocomplete_options = { selectFirst: false, formatItem: format_item_func, + autoFill: false, highlight: false }; + tag_input_field.autocomplete(settings.ajax_autocomplete_tag_url, autocomplete_options); + + + // Initialize delete tag images for current tags. + this_obj.find('.delete-tag-img').each(function() { + init_delete_tag_image( $(this) ); + }); + + + // Initialize tag click function. + init_tag_click_function($(this), settings.tag_click_fn); + + // Initialize "add tag" button. + add_tag_button.click( function() { + $(this).hide(); + + // Clicking on button is the same as clicking on the tag area. + tag_area.click(); + return false; + }); + + // + // Set up tag area interactions; these are needed only if tags are editable. + // + if (settings.editable) { + // When the tag area blurs, go to "view tag" mode. + tag_area.bind("blur", function(e) { + if (obj_length(settings.tags) > 0) { + add_tag_button.show(); + tag_input_field.hide(); + tag_area.removeClass("active-tag-area"); + tag_area.addClass("tooltip"); + } else { + // No tags, so do nothing to ensure that input is still visible. + } + }); + + // On click, enable user to add tags. + tag_area.click( function(e) { + var is_active = $(this).hasClass("active-tag-area"); + + // If a "delete image" object was pressed and area is inactive, do nothing. + if ($(e.target).hasClass("delete-tag-img") && !is_active) { + return false; + } + + // If a "tag name" object was pressed and area is inactive, do nothing. + if ($(e.target).hasClass("tag-name") && !is_active) { + return false; + } + + // Remove tooltip. + $(this).removeClass("tooltip"); + + // Hide add tag button, show tag_input field. Change background to show + // area is active. + $(this).addClass("active-tag-area"); + add_tag_button.hide(); + tag_input_field.show(); + tag_input_field.focus(); + + // Add handler to document that will call blur when the tag area is blurred; + // a tag area is blurred when a user clicks on an element outside the area. + var handle_document_click = function(e) { + var check_click = function(tag_area, target) { + var tag_area_id = tag_area.attr("id"); + // Blur the tag area if the element clicked on is not in the tag area. + if (target !== tag_area) { + tag_area.blur(); + $(window).unbind("click.tagging_blur"); + $(this).addClass("tooltip"); + } + }; + check_click(tag_area, $(e.target)); + }; + // TODO: we should attach the click handler to all frames in order to capture + // clicks outside the frame that this element is in. + //window.parent.document.onclick = handle_document_click; + //var temp = $(window.parent.document.body).contents().find("iframe").html(); + //alert(temp); + //$(document).parent().click(handle_document_click); + $(window).bind("click.tagging_blur", handle_document_click); + + return false; + }); + } + + // If using toggle link, hide the tag area. Otherwise, show the tag area. + if (settings.use_toggle_link) { + tag_area.hide(); + } + + // + // Helper functions. + // + + // + // Collapse tag name + value into a single string. + // + function build_tag_str(tag_name, tag_value) { + return tag_name + ( tag_value ? ":" + tag_value : ""); + } + + + // Initialize a "delete tag image": when click, delete tag from UI and send delete request to server. + function init_delete_tag_image(delete_img) { + $(delete_img).mouseenter( function () { + $(this).attr("src", settings.delete_tag_img_rollover); + }); + $(delete_img).mouseleave( function () { + $(this).attr("src", settings.delete_tag_img); + }); + $(delete_img).click( function () { + // Tag button is image's parent. + var tag_button = $(this).parent(); + + // Get tag name, value. + var tag_name_elt = tag_button.find(".tag-name").eq(0); + var tag_str = tag_name_elt.text(); + var tag_name_and_value = tag_str.split(":"); + var tag_name = tag_name_and_value[0]; + var tag_value = tag_name_and_value[1]; + + var prev_button = tag_button.prev(); + tag_button.remove(); + + // Remove tag from local list for consistency. + delete settings.tags[tag_name]; + + // Update toggle link text. + var new_text = settings.get_toggle_link_text_fn(settings.tags); + toggle_link.text(new_text); + + // Delete tag. + $.ajax({ + url: settings.ajax_delete_tag_url, + data: { tag_name: tag_name }, + error: function() { + // Failed. Roll back changes and show alert. + settings.tags[tag_name] = tag_value; + if (prev_button.hasClass("tag-button")) { + prev_button.after(tag_button); + } else { + tag_area.prepend(tag_button); + } + alert( "Remove tag failed" ); + + toggle_link.text(settings.get_toggle_link_text_fn(settings.tags)); + + // TODO: no idea why it's necessary to set this up again. + delete_img.mouseenter( function () { + $(this).attr("src", settings.delete_tag_img_rollover); + }); + delete_img.mouseleave( function () { + $(this).attr("src", settings.delete_tag_img); + }); + }, + success: function() {} + }); + + return true; + }); + } + + // + // Function that builds a tag button. + // + function build_tag_button(tag_str) { + // Build "delete tag" image. + var delete_img = $("<img/>").attr("src", settings.delete_tag_img).addClass("delete-tag-img"); + init_delete_tag_image(delete_img); + + // Build tag button. + var tag_name_elt = $("<span>").text(tag_str).addClass("tag-name"); + tag_name_elt.click( function() { + var tag_name_and_value = tag_str.split(":"); + settings.tag_click_fn(tag_name_and_value[0], tag_name_and_value[1]); + return true; + }); + + var tag_button = $("<span></span>").addClass("tag-button"); + tag_button.append(tag_name_elt); + // Allow delete only if element is editable. + if (settings.editable) { + tag_button.append(delete_img); + } + + return tag_button; + } + +}; diff -r f076e439d46e1bd66a9a5dd0c75c69c0a11550ed -r e27c236c05e5d65f3ce92f271a712419e7fd73a5 static/scripts/libs/jquery/jquery.ui.core.js --- /dev/null +++ b/static/scripts/libs/jquery/jquery.ui.core.js @@ -0,0 +1,519 @@ +/* + * jQuery UI 1.7.1 + * + * Copyright (c) 2009 AUTHORS.txt (http://jqueryui.com/about) + * Dual licensed under the MIT (MIT-LICENSE.txt) + * and GPL (GPL-LICENSE.txt) licenses. + * + * http://docs.jquery.com/UI + */ +;jQuery.ui || (function($) { + +var _remove = $.fn.remove, + isFF2 = $.browser.mozilla && (parseFloat($.browser.version) < 1.9); + +//Helper functions and ui object +$.ui = { + version: "1.7.1", + + // $.ui.plugin is deprecated. Use the proxy pattern instead. + plugin: { + add: function(module, option, set) { + var proto = $.ui[module].prototype; + for(var i in set) { + proto.plugins[i] = proto.plugins[i] || []; + proto.plugins[i].push([option, set[i]]); + } + }, + call: function(instance, name, args) { + var set = instance.plugins[name]; + if(!set || !instance.element[0].parentNode) { return; } + + for (var i = 0; i < set.length; i++) { + if (instance.options[set[i][0]]) { + set[i][1].apply(instance.element, args); + } + } + } + }, + + contains: function(a, b) { + return document.compareDocumentPosition + ? a.compareDocumentPosition(b) & 16 + : a !== b && a.contains(b); + }, + + hasScroll: function(el, a) { + + //If overflow is hidden, the element might have extra content, but the user wants to hide it + if ($(el).css('overflow') == 'hidden') { return false; } + + var scroll = (a && a == 'left') ? 'scrollLeft' : 'scrollTop', + has = false; + + if (el[scroll] > 0) { return true; } + + // TODO: determine which cases actually cause this to happen + // if the element doesn't have the scroll set, see if it's possible to + // set the scroll + el[scroll] = 1; + has = (el[scroll] > 0); + el[scroll] = 0; + return has; + }, + + isOverAxis: function(x, reference, size) { + //Determines when x coordinate is over "b" element axis + return (x > reference) && (x < (reference + size)); + }, + + isOver: function(y, x, top, left, height, width) { + //Determines when x, y coordinates is over "b" element + return $.ui.isOverAxis(y, top, height) && $.ui.isOverAxis(x, left, width); + }, + + keyCode: { + BACKSPACE: 8, + CAPS_LOCK: 20, + COMMA: 188, + CONTROL: 17, + DELETE: 46, + DOWN: 40, + END: 35, + ENTER: 13, + ESCAPE: 27, + HOME: 36, + INSERT: 45, + LEFT: 37, + NUMPAD_ADD: 107, + NUMPAD_DECIMAL: 110, + NUMPAD_DIVIDE: 111, + NUMPAD_ENTER: 108, + NUMPAD_MULTIPLY: 106, + NUMPAD_SUBTRACT: 109, + PAGE_DOWN: 34, + PAGE_UP: 33, + PERIOD: 190, + RIGHT: 39, + SHIFT: 16, + SPACE: 32, + TAB: 9, + UP: 38 + } +}; + +// WAI-ARIA normalization +if (isFF2) { + var attr = $.attr, + removeAttr = $.fn.removeAttr, + ariaNS = "http://www.w3.org/2005/07/aaa", + ariaState = /^aria-/, + ariaRole = /^wairole:/; + + $.attr = function(elem, name, value) { + var set = value !== undefined; + + return (name == 'role' + ? (set + ? attr.call(this, elem, name, "wairole:" + value) + : (attr.apply(this, arguments) || "").replace(ariaRole, "")) + : (ariaState.test(name) + ? (set + ? elem.setAttributeNS(ariaNS, + name.replace(ariaState, "aaa:"), value) + : attr.call(this, elem, name.replace(ariaState, "aaa:"))) + : attr.apply(this, arguments))); + }; + + $.fn.removeAttr = function(name) { + return (ariaState.test(name) + ? this.each(function() { + this.removeAttributeNS(ariaNS, name.replace(ariaState, "")); + }) : removeAttr.call(this, name)); + }; +} + +//jQuery plugins +$.fn.extend({ + remove: function() { + // Safari has a native remove event which actually removes DOM elements, + // so we have to use triggerHandler instead of trigger (#3037). + $("*", this).add(this).each(function() { + $(this).triggerHandler("remove"); + }); + return _remove.apply(this, arguments ); + }, + + enableSelection: function() { + return this + .attr('unselectable', 'off') + .css('MozUserSelect', '') + .unbind('selectstart.ui'); + }, + + disableSelection: function() { + return this + .attr('unselectable', 'on') + .css('MozUserSelect', 'none') + .bind('selectstart.ui', function() { return false; }); + }, + + scrollParent: function() { + var scrollParent; + if(($.browser.msie && (/(static|relative)/).test(this.css('position'))) || (/absolute/).test(this.css('position'))) { + scrollParent = this.parents().filter(function() { + return (/(relative|absolute|fixed)/).test($.curCSS(this,'position',1)) && (/(auto|scroll)/).test($.curCSS(this,'overflow',1)+$.curCSS(this,'overflow-y',1)+$.curCSS(this,'overflow-x',1)); + }).eq(0); + } else { + scrollParent = this.parents().filter(function() { + return (/(auto|scroll)/).test($.curCSS(this,'overflow',1)+$.curCSS(this,'overflow-y',1)+$.curCSS(this,'overflow-x',1)); + }).eq(0); + } + + return (/fixed/).test(this.css('position')) || !scrollParent.length ? $(document) : scrollParent; + } +}); + + +//Additional selectors +$.extend($.expr[':'], { + data: function(elem, i, match) { + return !!$.data(elem, match[3]); + }, + + focusable: function(element) { + var nodeName = element.nodeName.toLowerCase(), + tabIndex = $.attr(element, 'tabindex'); + return (/input|select|textarea|button|object/.test(nodeName) + ? !element.disabled + : 'a' == nodeName || 'area' == nodeName + ? element.href || !isNaN(tabIndex) + : !isNaN(tabIndex)) + // the element and all of its ancestors must be visible + // the browser may report that the area is hidden + && !$(element)['area' == nodeName ? 'parents' : 'closest'](':hidden').length; + }, + + tabbable: function(element) { + var tabIndex = $.attr(element, 'tabindex'); + return (isNaN(tabIndex) || tabIndex >= 0) && $(element).is(':focusable'); + } +}); + + +// $.widget is a factory to create jQuery plugins +// taking some boilerplate code out of the plugin code +function getter(namespace, plugin, method, args) { + function getMethods(type) { + var methods = $[namespace][plugin][type] || []; + return (typeof methods == 'string' ? methods.split(/,?\s+/) : methods); + } + + var methods = getMethods('getter'); + if (args.length == 1 && typeof args[0] == 'string') { + methods = methods.concat(getMethods('getterSetter')); + } + return ($.inArray(method, methods) != -1); +} + +$.widget = function(name, prototype) { + var namespace = name.split(".")[0]; + name = name.split(".")[1]; + + // create plugin method + $.fn[name] = function(options) { + var isMethodCall = (typeof options == 'string'), + args = Array.prototype.slice.call(arguments, 1); + + // prevent calls to internal methods + if (isMethodCall && options.substring(0, 1) == '_') { + return this; + } + + // handle getter methods + if (isMethodCall && getter(namespace, name, options, args)) { + var instance = $.data(this[0], name); + return (instance ? instance[options].apply(instance, args) + : undefined); + } + + // handle initialization and non-getter methods + return this.each(function() { + var instance = $.data(this, name); + + // constructor + (!instance && !isMethodCall && + $.data(this, name, new $[namespace][name](this, options))._init()); + + // method call + (instance && isMethodCall && $.isFunction(instance[options]) && + instance[options].apply(instance, args)); + }); + }; + + // create widget constructor + $[namespace] = $[namespace] || {}; + $[namespace][name] = function(element, options) { + var self = this; + + this.namespace = namespace; + this.widgetName = name; + this.widgetEventPrefix = $[namespace][name].eventPrefix || name; + this.widgetBaseClass = namespace + '-' + name; + + this.options = $.extend({}, + $.widget.defaults, + $[namespace][name].defaults, + $.metadata && $.metadata.get(element)[name], + options); + + this.element = $(element) + .bind('setData.' + name, function(event, key, value) { + if (event.target == element) { + return self._setData(key, value); + } + }) + .bind('getData.' + name, function(event, key) { + if (event.target == element) { + return self._getData(key); + } + }) + .bind('remove', function() { + return self.destroy(); + }); + }; + + // add widget prototype + $[namespace][name].prototype = $.extend({}, $.widget.prototype, prototype); + + // TODO: merge getter and getterSetter properties from widget prototype + // and plugin prototype + $[namespace][name].getterSetter = 'option'; +}; + +$.widget.prototype = { + _init: function() {}, + destroy: function() { + this.element.removeData(this.widgetName) + .removeClass(this.widgetBaseClass + '-disabled' + ' ' + this.namespace + '-state-disabled') + .removeAttr('aria-disabled'); + }, + + option: function(key, value) { + var options = key, + self = this; + + if (typeof key == "string") { + if (value === undefined) { + return this._getData(key); + } + options = {}; + options[key] = value; + } + + $.each(options, function(key, value) { + self._setData(key, value); + }); + }, + _getData: function(key) { + return this.options[key]; + }, + _setData: function(key, value) { + this.options[key] = value; + + if (key == 'disabled') { + this.element + [value ? 'addClass' : 'removeClass']( + this.widgetBaseClass + '-disabled' + ' ' + + this.namespace + '-state-disabled') + .attr("aria-disabled", value); + } + }, + + enable: function() { + this._setData('disabled', false); + }, + disable: function() { + this._setData('disabled', true); + }, + + _trigger: function(type, event, data) { + var callback = this.options[type], + eventName = (type == this.widgetEventPrefix + ? type : this.widgetEventPrefix + type); + + event = $.Event(event); + event.type = eventName; + + // copy original event properties over to the new event + // this would happen if we could call $.event.fix instead of $.Event + // but we don't have a way to force an event to be fixed multiple times + if (event.originalEvent) { + for (var i = $.event.props.length, prop; i;) { + prop = $.event.props[--i]; + event[prop] = event.originalEvent[prop]; + } + } + + this.element.trigger(event, data); + + return !($.isFunction(callback) && callback.call(this.element[0], event, data) === false + || event.isDefaultPrevented()); + } +}; + +$.widget.defaults = { + disabled: false +}; + + +/** Mouse Interaction Plugin **/ + +$.ui.mouse = { + _mouseInit: function() { + var self = this; + + this.element + .bind('mousedown.'+this.widgetName, function(event) { + return self._mouseDown(event); + }) + .bind('click.'+this.widgetName, function(event) { + if(self._preventClickEvent) { + self._preventClickEvent = false; + event.stopImmediatePropagation(); + return false; + } + }); + + // Prevent text selection in IE + if ($.browser.msie) { + this._mouseUnselectable = this.element.attr('unselectable'); + this.element.attr('unselectable', 'on'); + } + + this.started = false; + }, + + // TODO: make sure destroying one instance of mouse doesn't mess with + // other instances of mouse + _mouseDestroy: function() { + this.element.unbind('.'+this.widgetName); + + // Restore text selection in IE + ($.browser.msie + && this.element.attr('unselectable', this._mouseUnselectable)); + }, + + _mouseDown: function(event) { + // don't let more than one widget handle mouseStart + // TODO: figure out why we have to use originalEvent + event.originalEvent = event.originalEvent || {}; + if (event.originalEvent.mouseHandled) { return; } + + // we may have missed mouseup (out of window) + (this._mouseStarted && this._mouseUp(event)); + + this._mouseDownEvent = event; + + var self = this, + btnIsLeft = (event.which == 1), + elIsCancel = (typeof this.options.cancel == "string" ? $(event.target).parents().add(event.target).filter(this.options.cancel).length : false); + if (!btnIsLeft || elIsCancel || !this._mouseCapture(event)) { + return true; + } + + this.mouseDelayMet = !this.options.delay; + if (!this.mouseDelayMet) { + this._mouseDelayTimer = setTimeout(function() { + self.mouseDelayMet = true; + }, this.options.delay); + } + + if (this._mouseDistanceMet(event) && this._mouseDelayMet(event)) { + this._mouseStarted = (this._mouseStart(event) !== false); + if (!this._mouseStarted) { + event.preventDefault(); + return true; + } + } + + // these delegates are required to keep context + this._mouseMoveDelegate = function(event) { + return self._mouseMove(event); + }; + this._mouseUpDelegate = function(event) { + return self._mouseUp(event); + }; + $(document) + .bind('mousemove.'+this.widgetName, this._mouseMoveDelegate) + .bind('mouseup.'+this.widgetName, this._mouseUpDelegate); + + // preventDefault() is used to prevent the selection of text here - + // however, in Safari, this causes select boxes not to be selectable + // anymore, so this fix is needed + ($.browser.safari || event.preventDefault()); + + event.originalEvent.mouseHandled = true; + return true; + }, + + _mouseMove: function(event) { + // IE mouseup check - mouseup happened when mouse was out of window + if ($.browser.msie && !event.button) { + return this._mouseUp(event); + } + + if (this._mouseStarted) { + this._mouseDrag(event); + return event.preventDefault(); + } + + if (this._mouseDistanceMet(event) && this._mouseDelayMet(event)) { + this._mouseStarted = + (this._mouseStart(this._mouseDownEvent, event) !== false); + (this._mouseStarted ? this._mouseDrag(event) : this._mouseUp(event)); + } + + return !this._mouseStarted; + }, + + _mouseUp: function(event) { + $(document) + .unbind('mousemove.'+this.widgetName, this._mouseMoveDelegate) + .unbind('mouseup.'+this.widgetName, this._mouseUpDelegate); + + if (this._mouseStarted) { + this._mouseStarted = false; + this._preventClickEvent = (event.target == this._mouseDownEvent.target); + this._mouseStop(event); + } + + return false; + }, + + _mouseDistanceMet: function(event) { + return (Math.max( + Math.abs(this._mouseDownEvent.pageX - event.pageX), + Math.abs(this._mouseDownEvent.pageY - event.pageY) + ) >= this.options.distance + ); + }, + + _mouseDelayMet: function(event) { + return this.mouseDelayMet; + }, + + // These are placeholder methods, to be overriden by extending plugin + _mouseStart: function(event) {}, + _mouseDrag: function(event) {}, + _mouseStop: function(event) {}, + _mouseCapture: function(event) { return true; } +}; + +$.ui.mouse.defaults = { + cancel: null, + distance: 1, + delay: 0 +}; + +})(jQuery); diff -r f076e439d46e1bd66a9a5dd0c75c69c0a11550ed -r e27c236c05e5d65f3ce92f271a712419e7fd73a5 static/scripts/packed/autocomplete_tagging.js --- a/static/scripts/packed/autocomplete_tagging.js +++ /dev/null @@ -1,1 +0,0 @@ -function init_tag_click_function(b,a){$(b).find(".tag-name").each(function(){$(this).click(function(){var d=$(this).text();var c=d.split(":");a(c[0],c[1]);return true})})}jQuery.fn.autocomplete_tagging=function(m){var f={get_toggle_link_text_fn:function(n){var p="";var o=obj_length(n);if(o>0){p=o+(o>1?" 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false}if((t.keyCode===188)||(t.keyCode===32)){s=s.substring(0,s.length-1)}s=$.trim(s);if(s.length<2){return false}this.value="";var q=j(s);var p=b.children(".tag-button");if(p.length!==0){var u=p.slice(p.length-1);u.after(q)}else{b.prepend(q)}var o=s.split(":");d.tags[o[0]]=o[1];var r=d.get_toggle_link_text_fn(d.tags);e.text(r);var n=$(this);$.ajax({url:d.ajax_add_tag_url,data:{new_tag:s},error:function(){q.remove();delete d.tags[o[0]];var v=d.get_toggle_link_text_fn(d.tags);e.text(v);alert("Add tag failed")},success:function(){n.flushCache()}});return false}}});var i=function(q,p,o,s,r){var n=s.split(":");return(n.length===1?n[0]:n[1])};var h={selectFirst:false,formatItem:i,autoFill:false,highlight:false};a.autocomplete(d.ajax_autocomplete_tag_url,h);g.find(".delete-tag-img").each(function(){c($(this))});init_tag_click_function($(this),d.tag_click_fn);l.click(function(){$(this).hide();b.click();return false});if(d.editable){b.bind("blur",function(n){if(obj_length(d.tags)>0){l.show();a.hide();b.removeClass("active-tag-area");b.addClass("tooltip")}else{}});b.click(function(p){var o=$(this).hasClass("active-tag-area");if($(p.target).hasClass("delete-tag-img")&&!o){return false}if($(p.target).hasClass("tag-name")&&!o){return false}$(this).removeClass("tooltip");$(this).addClass("active-tag-area");l.hide();a.show();a.focus();var n=function(r){var q=function(s,u){var t=s.attr("id");if(u!==s){s.blur();$(window).unbind("click.tagging_blur");$(this).addClass("tooltip")}};q(b,$(r.target))};$(window).bind("click.tagging_blur",n);return false})}if(d.use_toggle_link){b.hide()}function k(o,n){return o+(n?":"+n:"")}function c(n){$(n).mouseenter(function(){$(this).attr("src",d.delete_tag_img_rollover)});$(n).mouseleave(function(){$(this).attr("src",d.delete_tag_img)});$(n).click(function(){var t=$(this).parent();var s=t.find(".tag-name").eq(0);var r=s.text();var p=r.split(":");var v=p[0];var 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Use the proxy pattern instead. - plugin: { - add: function(module, option, set) { - var proto = $.ui[module].prototype; - for(var i in set) { - proto.plugins[i] = proto.plugins[i] || []; - proto.plugins[i].push([option, set[i]]); - } - }, - call: function(instance, name, args) { - var set = instance.plugins[name]; - if(!set || !instance.element[0].parentNode) { return; } - - for (var i = 0; i < set.length; i++) { - if (instance.options[set[i][0]]) { - set[i][1].apply(instance.element, args); - } - } - } - }, - - contains: function(a, b) { - return document.compareDocumentPosition - ? a.compareDocumentPosition(b) & 16 - : a !== b && a.contains(b); - }, - - hasScroll: function(el, a) { - - //If overflow is hidden, the element might have extra content, but the user wants to hide it - if ($(el).css('overflow') == 'hidden') { return false; } - - var scroll = (a && a == 'left') ? 'scrollLeft' : 'scrollTop', - has = false; - - if (el[scroll] > 0) { return true; } - - // TODO: determine which cases actually cause this to happen - // if the element doesn't have the scroll set, see if it's possible to - // set the scroll - el[scroll] = 1; - has = (el[scroll] > 0); - el[scroll] = 0; - return has; - }, - - isOverAxis: function(x, reference, size) { - //Determines when x coordinate is over "b" element axis - return (x > reference) && (x < (reference + size)); - }, - - isOver: function(y, x, top, left, height, width) { - //Determines when x, y coordinates is over "b" element - return $.ui.isOverAxis(y, top, height) && $.ui.isOverAxis(x, left, width); - }, - - keyCode: { - BACKSPACE: 8, - CAPS_LOCK: 20, - COMMA: 188, - CONTROL: 17, - DELETE: 46, - DOWN: 40, - END: 35, - ENTER: 13, - ESCAPE: 27, - HOME: 36, - INSERT: 45, - LEFT: 37, - NUMPAD_ADD: 107, - NUMPAD_DECIMAL: 110, - NUMPAD_DIVIDE: 111, - NUMPAD_ENTER: 108, - NUMPAD_MULTIPLY: 106, - NUMPAD_SUBTRACT: 109, - PAGE_DOWN: 34, - PAGE_UP: 33, - PERIOD: 190, - RIGHT: 39, - SHIFT: 16, - SPACE: 32, - TAB: 9, - UP: 38 - } -}; - -// WAI-ARIA normalization -if (isFF2) { - var attr = $.attr, - removeAttr = $.fn.removeAttr, - ariaNS = "http://www.w3.org/2005/07/aaa", - ariaState = /^aria-/, - ariaRole = /^wairole:/; - - $.attr = function(elem, name, value) { - var set = value !== undefined; - - return (name == 'role' - ? (set - ? attr.call(this, elem, name, "wairole:" + value) - : (attr.apply(this, arguments) || "").replace(ariaRole, "")) - : (ariaState.test(name) - ? (set - ? elem.setAttributeNS(ariaNS, - name.replace(ariaState, "aaa:"), value) - : attr.call(this, elem, name.replace(ariaState, "aaa:"))) - : attr.apply(this, arguments))); - }; - - $.fn.removeAttr = function(name) { - return (ariaState.test(name) - ? this.each(function() { - this.removeAttributeNS(ariaNS, name.replace(ariaState, "")); - }) : removeAttr.call(this, name)); - }; -} - -//jQuery plugins -$.fn.extend({ - remove: function() { - // Safari has a native remove event which actually removes DOM elements, - // so we have to use triggerHandler instead of trigger (#3037). - $("*", this).add(this).each(function() { - $(this).triggerHandler("remove"); - }); - return _remove.apply(this, arguments ); - }, - - enableSelection: function() { - return this - .attr('unselectable', 'off') - .css('MozUserSelect', '') - .unbind('selectstart.ui'); - }, - - disableSelection: function() { - return this - .attr('unselectable', 'on') - .css('MozUserSelect', 'none') - .bind('selectstart.ui', function() { return false; }); - }, - - scrollParent: function() { - var scrollParent; - if(($.browser.msie && (/(static|relative)/).test(this.css('position'))) || (/absolute/).test(this.css('position'))) { - scrollParent = this.parents().filter(function() { - return (/(relative|absolute|fixed)/).test($.curCSS(this,'position',1)) && (/(auto|scroll)/).test($.curCSS(this,'overflow',1)+$.curCSS(this,'overflow-y',1)+$.curCSS(this,'overflow-x',1)); - }).eq(0); - } else { - scrollParent = this.parents().filter(function() { - return (/(auto|scroll)/).test($.curCSS(this,'overflow',1)+$.curCSS(this,'overflow-y',1)+$.curCSS(this,'overflow-x',1)); - }).eq(0); - } - - return (/fixed/).test(this.css('position')) || !scrollParent.length ? $(document) : scrollParent; - } -}); - - -//Additional selectors -$.extend($.expr[':'], { - data: function(elem, i, match) { - return !!$.data(elem, match[3]); - }, - - focusable: function(element) { - var nodeName = element.nodeName.toLowerCase(), - tabIndex = $.attr(element, 'tabindex'); - return (/input|select|textarea|button|object/.test(nodeName) - ? !element.disabled - : 'a' == nodeName || 'area' == nodeName - ? element.href || !isNaN(tabIndex) - : !isNaN(tabIndex)) - // the element and all of its ancestors must be visible - // the browser may report that the area is hidden - && !$(element)['area' == nodeName ? 'parents' : 'closest'](':hidden').length; - }, - - tabbable: function(element) { - var tabIndex = $.attr(element, 'tabindex'); - return (isNaN(tabIndex) || tabIndex >= 0) && $(element).is(':focusable'); - } -}); - - -// $.widget is a factory to create jQuery plugins -// taking some boilerplate code out of the plugin code -function getter(namespace, plugin, method, args) { - function getMethods(type) { - var methods = $[namespace][plugin][type] || []; - return (typeof methods == 'string' ? methods.split(/,?\s+/) : methods); - } - - var methods = getMethods('getter'); - if (args.length == 1 && typeof args[0] == 'string') { - methods = methods.concat(getMethods('getterSetter')); - } - return ($.inArray(method, methods) != -1); -} - -$.widget = function(name, prototype) { - var namespace = name.split(".")[0]; - name = name.split(".")[1]; - - // create plugin method - $.fn[name] = function(options) { - var isMethodCall = (typeof options == 'string'), - args = Array.prototype.slice.call(arguments, 1); - - // prevent calls to internal methods - if (isMethodCall && options.substring(0, 1) == '_') { - return this; - } - - // handle getter methods - if (isMethodCall && getter(namespace, name, options, args)) { - var instance = $.data(this[0], name); - return (instance ? instance[options].apply(instance, args) - : undefined); - } - - // handle initialization and non-getter methods - return this.each(function() { - var instance = $.data(this, name); - - // constructor - (!instance && !isMethodCall && - $.data(this, name, new $[namespace][name](this, options))._init()); - - // method call - (instance && isMethodCall && $.isFunction(instance[options]) && - instance[options].apply(instance, args)); - }); - }; - - // create widget constructor - $[namespace] = $[namespace] || {}; - $[namespace][name] = function(element, options) { - var self = this; - - this.namespace = namespace; - this.widgetName = name; - this.widgetEventPrefix = $[namespace][name].eventPrefix || name; - this.widgetBaseClass = namespace + '-' + name; - - this.options = $.extend({}, - $.widget.defaults, - $[namespace][name].defaults, - $.metadata && $.metadata.get(element)[name], - options); - - this.element = $(element) - .bind('setData.' + name, function(event, key, value) { - if (event.target == element) { - return self._setData(key, value); - } - }) - .bind('getData.' + name, function(event, key) { - if (event.target == element) { - return self._getData(key); - } - }) - .bind('remove', function() { - return self.destroy(); - }); - }; - - // add widget prototype - $[namespace][name].prototype = $.extend({}, $.widget.prototype, prototype); - - // TODO: merge getter and getterSetter properties from widget prototype - // and plugin prototype - $[namespace][name].getterSetter = 'option'; -}; - -$.widget.prototype = { - _init: function() {}, - destroy: function() { - this.element.removeData(this.widgetName) - .removeClass(this.widgetBaseClass + '-disabled' + ' ' + this.namespace + '-state-disabled') - .removeAttr('aria-disabled'); - }, - - option: function(key, value) { - var options = key, - self = this; - - if (typeof key == "string") { - if (value === undefined) { - return this._getData(key); - } - options = {}; - options[key] = value; - } - - $.each(options, function(key, value) { - self._setData(key, value); - }); - }, - _getData: function(key) { - return this.options[key]; - }, - _setData: function(key, value) { - this.options[key] = value; - - if (key == 'disabled') { - this.element - [value ? 'addClass' : 'removeClass']( - this.widgetBaseClass + '-disabled' + ' ' + - this.namespace + '-state-disabled') - .attr("aria-disabled", value); - } - }, - - enable: function() { - this._setData('disabled', false); - }, - disable: function() { - this._setData('disabled', true); - }, - - _trigger: function(type, event, data) { - var callback = this.options[type], - eventName = (type == this.widgetEventPrefix - ? type : this.widgetEventPrefix + type); - - event = $.Event(event); - event.type = eventName; - - // copy original event properties over to the new event - // this would happen if we could call $.event.fix instead of $.Event - // but we don't have a way to force an event to be fixed multiple times - if (event.originalEvent) { - for (var i = $.event.props.length, prop; i;) { - prop = $.event.props[--i]; - event[prop] = event.originalEvent[prop]; - } - } - - this.element.trigger(event, data); - - return !($.isFunction(callback) && callback.call(this.element[0], event, data) === false - || event.isDefaultPrevented()); - } -}; - -$.widget.defaults = { - disabled: false -}; - - -/** Mouse Interaction Plugin **/ - -$.ui.mouse = { - _mouseInit: function() { - var self = this; - - this.element - .bind('mousedown.'+this.widgetName, function(event) { - return self._mouseDown(event); - }) - .bind('click.'+this.widgetName, function(event) { - if(self._preventClickEvent) { - self._preventClickEvent = false; - event.stopImmediatePropagation(); - return false; - } - }); - - // Prevent text selection in IE - if ($.browser.msie) { - this._mouseUnselectable = this.element.attr('unselectable'); - this.element.attr('unselectable', 'on'); - } - - this.started = false; - }, - - // TODO: make sure destroying one instance of mouse doesn't mess with - // other instances of mouse - _mouseDestroy: function() { - this.element.unbind('.'+this.widgetName); - - // Restore text selection in IE - ($.browser.msie - && this.element.attr('unselectable', this._mouseUnselectable)); - }, - - _mouseDown: function(event) { - // don't let more than one widget handle mouseStart - // TODO: figure out why we have to use originalEvent - event.originalEvent = event.originalEvent || {}; - if (event.originalEvent.mouseHandled) { return; } - - // we may have missed mouseup (out of window) - (this._mouseStarted && this._mouseUp(event)); - - this._mouseDownEvent = event; - - var self = this, - btnIsLeft = (event.which == 1), - elIsCancel = (typeof this.options.cancel == "string" ? $(event.target).parents().add(event.target).filter(this.options.cancel).length : false); - if (!btnIsLeft || elIsCancel || !this._mouseCapture(event)) { - return true; - } - - this.mouseDelayMet = !this.options.delay; - if (!this.mouseDelayMet) { - this._mouseDelayTimer = setTimeout(function() { - self.mouseDelayMet = true; - }, this.options.delay); - } - - if (this._mouseDistanceMet(event) && this._mouseDelayMet(event)) { - this._mouseStarted = (this._mouseStart(event) !== false); - if (!this._mouseStarted) { - event.preventDefault(); - return true; - } - } - - // these delegates are required to keep context - this._mouseMoveDelegate = function(event) { - return self._mouseMove(event); - }; - this._mouseUpDelegate = function(event) { - return self._mouseUp(event); - }; - $(document) - .bind('mousemove.'+this.widgetName, this._mouseMoveDelegate) - .bind('mouseup.'+this.widgetName, this._mouseUpDelegate); - - // preventDefault() is used to prevent the selection of text here - - // however, in Safari, this causes select boxes not to be selectable - // anymore, so this fix is needed - ($.browser.safari || event.preventDefault()); - - event.originalEvent.mouseHandled = true; - return true; - }, - - _mouseMove: function(event) { - // IE mouseup check - mouseup happened when mouse was out of window - if ($.browser.msie && !event.button) { - return this._mouseUp(event); - } - - if (this._mouseStarted) { - this._mouseDrag(event); - return event.preventDefault(); - } - - if (this._mouseDistanceMet(event) && this._mouseDelayMet(event)) { - this._mouseStarted = - (this._mouseStart(this._mouseDownEvent, event) !== false); - (this._mouseStarted ? this._mouseDrag(event) : this._mouseUp(event)); - } - - return !this._mouseStarted; - }, - - _mouseUp: function(event) { - $(document) - .unbind('mousemove.'+this.widgetName, this._mouseMoveDelegate) - .unbind('mouseup.'+this.widgetName, this._mouseUpDelegate); - - if (this._mouseStarted) { - this._mouseStarted = false; - this._preventClickEvent = (event.target == this._mouseDownEvent.target); - this._mouseStop(event); - } - - return false; - }, - - _mouseDistanceMet: function(event) { - return (Math.max( - Math.abs(this._mouseDownEvent.pageX - event.pageX), - Math.abs(this._mouseDownEvent.pageY - event.pageY) - ) >= this.options.distance - ); - }, - - _mouseDelayMet: function(event) { - return this.mouseDelayMet; - }, - - // These are placeholder methods, to be overriden by extending plugin - _mouseStart: function(event) {}, - _mouseDrag: function(event) {}, - _mouseStop: function(event) {}, - _mouseCapture: function(event) { return true; } -}; - -$.ui.mouse.defaults = { - cancel: null, - distance: 1, - delay: 0 -}; - -})(jQuery); diff -r f076e439d46e1bd66a9a5dd0c75c69c0a11550ed -r e27c236c05e5d65f3ce92f271a712419e7fd73a5 templates/admin/data_admin/data_form.mako --- a/templates/admin/data_admin/data_form.mako +++ b/templates/admin/data_admin/data_form.mako @@ -27,7 +27,7 @@ </%def><%def name="javascripts()"> ${parent.javascripts()} - ${h.js("libs/jquery/jquery.autocomplete", "autocomplete_tagging" )} + ${h.js("libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging" )} </%def> ## ## Override methods from base.mako and base_panels.mako diff -r f076e439d46e1bd66a9a5dd0c75c69c0a11550ed -r e27c236c05e5d65f3ce92f271a712419e7fd73a5 templates/admin/data_admin/generic_error.mako --- a/templates/admin/data_admin/generic_error.mako +++ b/templates/admin/data_admin/generic_error.mako @@ -27,7 +27,7 @@ </%def><%def name="javascripts()"> ${parent.javascripts()} - ${h.js("libs/jquery/jquery.autocomplete", "autocomplete_tagging" )} + ${h.js("libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging" )} </%def> ## ## Override methods from base.mako and base_panels.mako diff -r f076e439d46e1bd66a9a5dd0c75c69c0a11550ed -r e27c236c05e5d65f3ce92f271a712419e7fd73a5 templates/admin/data_admin/local_data.mako --- a/templates/admin/data_admin/local_data.mako +++ b/templates/admin/data_admin/local_data.mako @@ -27,7 +27,7 @@ </%def><%def name="javascripts()"> ${parent.javascripts()} - ${h.js("libs/jquery/jquery.autocomplete", "autocomplete_tagging" )} + ${h.js("libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging" )} </%def> ## ## Override methods from base.mako and base_panels.mako diff -r f076e439d46e1bd66a9a5dd0c75c69c0a11550ed -r e27c236c05e5d65f3ce92f271a712419e7fd73a5 templates/admin/requests/select_datasets_to_transfer.mako --- a/templates/admin/requests/select_datasets_to_transfer.mako +++ b/templates/admin/requests/select_datasets_to_transfer.mako @@ -8,7 +8,7 @@ ${common_javascripts()} </%def> -${h.js( "ui.core", "libs/jquery/jquery.cookie", "libs/jquery/jquery.dynatree" )} +${h.js( "libs/jquery/jquery.ui.core", "libs/jquery/jquery.cookie", "libs/jquery/jquery.dynatree" )} ${h.css( "dynatree_skin/ui.dynatree" )} <script type="text/javascript"> diff -r f076e439d46e1bd66a9a5dd0c75c69c0a11550ed -r e27c236c05e5d65f3ce92f271a712419e7fd73a5 templates/admin/tool_shed_repository/browse_repository.mako --- a/templates/admin/tool_shed_repository/browse_repository.mako +++ b/templates/admin/tool_shed_repository/browse_repository.mako @@ -9,7 +9,7 @@ <%def name="javascripts()"> ${parent.javascripts()} - ${h.js( "ui.core", "libs/jquery/jquery.dynatree" )} + ${h.js( "libs/jquery/jquery.ui.core", "libs/jquery/jquery.dynatree" )} ${browse_files(repository.name, repository.repo_files_directory(trans.app))} </%def> diff -r f076e439d46e1bd66a9a5dd0c75c69c0a11550ed -r e27c236c05e5d65f3ce92f271a712419e7fd73a5 templates/admin/tool_shed_repository/browse_tool_dependency.mako --- a/templates/admin/tool_shed_repository/browse_tool_dependency.mako +++ b/templates/admin/tool_shed_repository/browse_tool_dependency.mako @@ -9,7 +9,7 @@ <%def name="javascripts()"> ${parent.javascripts()} - ${h.js( "ui.core", "libs/jquery/jquery.dynatree" )} + ${h.js( "libs/jquery/jquery.ui.core", "libs/jquery/jquery.dynatree" )} ${browse_files(tool_dependency.name, tool_dependency.installation_directory( trans.app ))} </%def> diff -r f076e439d46e1bd66a9a5dd0c75c69c0a11550ed -r e27c236c05e5d65f3ce92f271a712419e7fd73a5 templates/dataset/edit_attributes.mako --- a/templates/dataset/edit_attributes.mako +++ b/templates/dataset/edit_attributes.mako @@ -11,7 +11,7 @@ <%def name="javascripts()"> ${parent.javascripts()} ${message_ns.javascripts()} - ${h.js( "galaxy.base", "libs/jquery/jquery.autocomplete", "autocomplete_tagging" )} + ${h.js( "galaxy.base", "libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging" )} </%def><%def name="datatype( dataset, datatypes )"> diff -r f076e439d46e1bd66a9a5dd0c75c69c0a11550ed -r e27c236c05e5d65f3ce92f271a712419e7fd73a5 templates/display_base.mako --- a/templates/display_base.mako +++ b/templates/display_base.mako @@ -33,7 +33,7 @@ <%def name="javascripts()"> ${parent.javascripts()} ${h.js( "libs/jquery/jquery", "libs/bootstrap", "galaxy.base", "libs/json2", "libs/jquery/jstorage", "libs/jquery/jquery.autocomplete", "libs/jquery/jquery.rating", - "autocomplete_tagging", "viz/trackster", "viz/trackster_ui", "libs/jquery/jquery.event.drag", "libs/jquery/jquery.mousewheel", + "galaxy.autocom_tagging", "viz/trackster", "viz/trackster_ui", "libs/jquery/jquery.event.drag", "libs/jquery/jquery.mousewheel", "libs/jquery/jquery.autocomplete", "libs/jquery/jquery.ui.sortable.slider", "libs/farbtastic", "mvc/data", "viz/visualization" )} <script type="text/javascript"> diff -r f076e439d46e1bd66a9a5dd0c75c69c0a11550ed -r e27c236c05e5d65f3ce92f271a712419e7fd73a5 templates/grid_base.mako --- a/templates/grid_base.mako +++ b/templates/grid_base.mako @@ -52,7 +52,7 @@ </%def><%def name="grid_javascripts()"> - ${h.js("libs/jquery/jquery.autocomplete", "autocomplete_tagging", "libs/jquery/jquery.rating" )} + ${h.js("libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging", "libs/jquery/jquery.rating" )} <script type="text/javascript"> // This is necessary so that, when nested arrays are used in ajax/post/get methods, square brackets ('[]') are // not appended to the identifier of a nested array. diff -r f076e439d46e1bd66a9a5dd0c75c69c0a11550ed -r e27c236c05e5d65f3ce92f271a712419e7fd73a5 templates/library/common/ldda_edit_info.mako --- a/templates/library/common/ldda_edit_info.mako +++ b/templates/library/common/ldda_edit_info.mako @@ -5,7 +5,7 @@ <%def name="javascripts()"> ${parent.javascripts()} - ${h.js("libs/jquery/jquery.autocomplete", "autocomplete_tagging" )} + ${h.js("libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging" )} </%def><%def name="stylesheets()"> diff -r f076e439d46e1bd66a9a5dd0c75c69c0a11550ed -r e27c236c05e5d65f3ce92f271a712419e7fd73a5 templates/library/common/move_library_item.mako --- a/templates/library/common/move_library_item.mako +++ b/templates/library/common/move_library_item.mako @@ -3,7 +3,7 @@ <%def name="javascripts()"> ${parent.javascripts()} - ${h.js("libs/jquery/jquery.autocomplete", "autocomplete_tagging" )} + ${h.js("libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging" )} </%def><%def name="stylesheets()"> diff -r f076e439d46e1bd66a9a5dd0c75c69c0a11550ed -r e27c236c05e5d65f3ce92f271a712419e7fd73a5 templates/library/common/upload.mako --- a/templates/library/common/upload.mako +++ b/templates/library/common/upload.mako @@ -13,7 +13,7 @@ <%def name="javascripts()"> ${parent.javascripts()} - ${h.js("libs/jquery/jquery.autocomplete", "autocomplete_tagging" )} + ${h.js("libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging" )} </%def><%def name="stylesheets()"> diff -r f076e439d46e1bd66a9a5dd0c75c69c0a11550ed -r e27c236c05e5d65f3ce92f271a712419e7fd73a5 templates/page/editor.mako --- a/templates/page/editor.mako +++ b/templates/page/editor.mako @@ -22,7 +22,7 @@ <%def name="javascripts()"> ${parent.javascripts()} ${h.js( "libs/jquery/jquery.event.drag", "libs/jquery/jquery.event.drop", "libs/jquery/jquery.event.hover", "libs/jquery/jquery.form", "libs/json2", "libs/jquery/jstorage", - "galaxy.base", "libs/jquery/jquery.wymeditor", "libs/jquery/jquery.autocomplete", "autocomplete_tagging")} + "galaxy.base", "libs/jquery/jquery.wymeditor", "libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging")} <script type="text/javascript"> // Useful Galaxy stuff. diff -r f076e439d46e1bd66a9a5dd0c75c69c0a11550ed -r e27c236c05e5d65f3ce92f271a712419e7fd73a5 templates/requests/common/create_request.mako --- a/templates/requests/common/create_request.mako +++ b/templates/requests/common/create_request.mako @@ -3,7 +3,7 @@ <%def name="javascripts()"> ${parent.javascripts()} - ${h.js("libs/jquery/jquery.autocomplete", "autocomplete_tagging" )} + ${h.js("libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging" )} </%def><%def name="stylesheets()"> diff -r f076e439d46e1bd66a9a5dd0c75c69c0a11550ed -r e27c236c05e5d65f3ce92f271a712419e7fd73a5 templates/requests/common/find_samples.mako --- a/templates/requests/common/find_samples.mako +++ b/templates/requests/common/find_samples.mako @@ -3,7 +3,7 @@ <%def name="javascripts()"> ${parent.javascripts()} - ${h.js("libs/jquery/jquery.autocomplete", "autocomplete_tagging" )} + ${h.js("libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging" )} </%def><%def name="stylesheets()"> diff -r f076e439d46e1bd66a9a5dd0c75c69c0a11550ed -r e27c236c05e5d65f3ce92f271a712419e7fd73a5 templates/root/history.mako --- a/templates/root/history.mako +++ b/templates/root/history.mako @@ -17,7 +17,7 @@ <meta http-equiv="Pragma" content="no-cache"> ${h.css( "base", "history", "autocomplete_tagging" )} -${h.js( "libs/jquery/jquery", "libs/bootstrap", "galaxy.base", "libs/json2", "libs/jquery/jstorage", "libs/jquery/jquery.autocomplete", "autocomplete_tagging" )} +${h.js( "libs/jquery/jquery", "libs/bootstrap", "galaxy.base", "libs/json2", "libs/jquery/jstorage", "libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging" )} <script type="text/javascript"> diff -r f076e439d46e1bd66a9a5dd0c75c69c0a11550ed -r e27c236c05e5d65f3ce92f271a712419e7fd73a5 templates/root/tool_menu.mako --- a/templates/root/tool_menu.mako +++ b/templates/root/tool_menu.mako @@ -17,7 +17,7 @@ <%def name="javascripts()"> ${parent.javascripts()} ${h.templates( "tool_link", "panel_section", "tool_search" )} - ${h.js( "galaxy.base", "libs/json2", "autocomplete_tagging", "mvc/tools", "libs/bootstrap" )} + ${h.js( "galaxy.base", "libs/json2", "galaxy.autocom_tagging", "mvc/tools", "libs/bootstrap" )} <% # Set up for creating tool panel. diff -r f076e439d46e1bd66a9a5dd0c75c69c0a11550ed -r e27c236c05e5d65f3ce92f271a712419e7fd73a5 templates/webapps/community/repository/browse_repository.mako --- a/templates/webapps/community/repository/browse_repository.mako +++ b/templates/webapps/community/repository/browse_repository.mako @@ -57,7 +57,7 @@ <%def name="javascripts()"> ${parent.javascripts()} - ${h.js( "libs/jquery/jquery.rating", "ui.core", "libs/jquery/jquery.cookie", "libs/jquery/jquery.dynatree" )} + ${h.js( "libs/jquery/jquery.rating", "libs/jquery/jquery.ui.core", "libs/jquery/jquery.cookie", "libs/jquery/jquery.dynatree" )} ${common_javascripts(repository)} </%def> diff -r f076e439d46e1bd66a9a5dd0c75c69c0a11550ed -r e27c236c05e5d65f3ce92f271a712419e7fd73a5 templates/webapps/community/repository/upload.mako --- a/templates/webapps/community/repository/upload.mako +++ b/templates/webapps/community/repository/upload.mako @@ -28,7 +28,7 @@ <%def name="javascripts()"> ${parent.javascripts()} - ${h.js( "ui.core", "libs/jquery/jquery.cookie", "libs/jquery/jquery.dynatree" )} + ${h.js( "libs/jquery/jquery.ui.core", "libs/jquery/jquery.cookie", "libs/jquery/jquery.dynatree" )} ${common_javascripts(repository)} <script type="text/javascript"> $( function() { diff -r f076e439d46e1bd66a9a5dd0c75c69c0a11550ed -r e27c236c05e5d65f3ce92f271a712419e7fd73a5 templates/workflow/edit_attributes.mako --- a/templates/workflow/edit_attributes.mako +++ b/templates/workflow/edit_attributes.mako @@ -9,7 +9,7 @@ <%def name="javascripts()"> ${parent.javascripts()} - ${h.js( "galaxy.base", "libs/jquery/jquery.autocomplete", "autocomplete_tagging" )} + ${h.js( "galaxy.base", "libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging" )} </%def> %if msg: diff -r f076e439d46e1bd66a9a5dd0c75c69c0a11550ed -r e27c236c05e5d65f3ce92f271a712419e7fd73a5 templates/workflow/editor.mako --- a/templates/workflow/editor.mako +++ b/templates/workflow/editor.mako @@ -36,7 +36,7 @@ "galaxy.base", "galaxy.workflow_editor.canvas", "libs/jquery/jquery.autocomplete", - "autocomplete_tagging")} + "galaxy.autocom_tagging")} <!--[if lt IE 7]><script type='text/javascript'> 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: More JS file reorganization: (a) move IE and rgenetics into their own directories; (b) move additional external libraries to libs.
by Bitbucket 21 Aug '12

21 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/f076e439d46e/ changeset: f076e439d46e user: jgoecks date: 2012-08-21 22:54:19 summary: More JS file reorganization: (a) move IE and rgenetics into their own directories; (b) move additional external libraries to libs. affected #: 57 files 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: dan: Remove blastxml from datatypes_conf.xml.sample.
by Bitbucket 21 Aug '12

21 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/11a52ade55cd/ changeset: 11a52ade55cd user: dan date: 2012-08-21 22:05:55 summary: Remove blastxml from datatypes_conf.xml.sample. affected #: 1 file diff -r 0548e6380f5ae342f8745c4ee49aba624c618c5d -r 11a52ade55cdcdb1bb6b97741c2f123a3410a2f0 datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -169,7 +169,6 @@ <datatype extension="linecount" type="galaxy.datatypes.data:LineCount" display_in_upload="false"/><datatype extension="memexml" type="galaxy.datatypes.xml:MEMEXml" mimetype="application/xml" display_in_upload="true"/><datatype extension="cisml" type="galaxy.datatypes.xml:CisML" mimetype="application/xml" display_in_upload="true"/> - <datatype extension="blastxml" type="galaxy.datatypes.xml:BlastXml" mimetype="application/xml" display_in_upload="true"/><datatype extension="xml" type="galaxy.datatypes.xml:GenericXml" mimetype="application/xml" display_in_upload="true"/><datatype extension="vcf" type="galaxy.datatypes.tabular:Vcf" display_in_upload="true"><converter file="vcf_to_bgzip_converter.xml" target_datatype="bgzip"/> @@ -246,7 +245,6 @@ <sniffer type="galaxy.datatypes.binary:TwoBit"/><sniffer type="galaxy.datatypes.binary:Bam"/><sniffer type="galaxy.datatypes.binary:Sff"/> - <sniffer type="galaxy.datatypes.xml:BlastXml"/><sniffer type="galaxy.datatypes.xml:GenericXml"/><sniffer type="galaxy.datatypes.sequence:Maf"/><sniffer type="galaxy.datatypes.sequence:Lav"/> 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: Move most jQuery files into own libs directory.
by Bitbucket 21 Aug '12

21 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/0548e6380f5a/ changeset: 0548e6380f5a user: jgoecks date: 2012-08-21 21:52:50 summary: Move most jQuery files into own libs directory. affected #: 104 files 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: jgoecks: JavaScript cleanup: (a) create backbone lib in scripts/lib and use for backbone libraries; (b) clean up history.js; (c) pack scripts.
by Bitbucket 21 Aug '12

21 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/6ac6c3d4b907/ changeset: 6ac6c3d4b907 user: jgoecks date: 2012-08-21 20:27:18 summary: JavaScript cleanup: (a) create backbone lib in scripts/lib and use for backbone libraries; (b) clean up history.js; (c) pack scripts. affected #: 19 files 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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