1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/862d562e3167/ changeset: 862d562e3167 user: dan date: 2011-12-08 17:44:22 summary: Escape backslashes and quotes in name attributes for UCSC external display applications which use bigDataUrls. Remove no longer required strip_https attribute. Resolves #627. affected #: 3 files diff -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca -r 862d562e31670dd22a6bd575b2fa79328acabb4d display_applications/ucsc/bam.xml --- a/display_applications/ucsc/bam.xml +++ b/display_applications/ucsc/bam.xml @@ -10,8 +10,8 @@ <filter>${dataset.dbkey in $builds}</filter><!-- We define url and params as normal, but values defined in dynamic_param are available by specified name --><url>${ucsc_link}db=${qp($bam_file.dbkey)}&hgt.customText=${qp($track.url)}</url> - <param type="data" name="bam_file" url="galaxy_${DATASET_HASH}.bam" strip_https="True" /> - <param type="data" name="bai_file" url="galaxy_${DATASET_HASH}.bam.bai" metadata="bam_index" strip_https="True" /><!-- UCSC expects index file to exist as bam_file_name.bai --> - <param type="template" name="track" viewable="True" strip_https="True">track type=bam name="${bam_file.name}" bigDataUrl=${bam_file.url} db=${bam_file.dbkey}</param> + <param type="data" name="bam_file" url="galaxy_${DATASET_HASH}.bam" /> + <param type="data" name="bai_file" url="galaxy_${DATASET_HASH}.bam.bai" metadata="bam_index" /><!-- UCSC expects index file to exist as bam_file_name.bai --> + <param type="template" name="track" viewable="True">track type="bam" name="${bam_file.name.replace( '\\', '\\\\' ).replace( '"', '\\"' )}" bigDataUrl="${bam_file.url}" db="${bam_file.dbkey}"</param></dynamic_links></display> diff -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca -r 862d562e31670dd22a6bd575b2fa79328acabb4d display_applications/ucsc/bigbed.xml --- a/display_applications/ucsc/bigbed.xml +++ b/display_applications/ucsc/bigbed.xml @@ -10,7 +10,7 @@ <filter>${dataset.dbkey in $builds}</filter><!-- We define url and params as normal, but values defined in dynamic_param are available by specified name --><url>${ucsc_link}db=${qp($bigbed_file.dbkey)}&hgt.customText=${qp($track.url)}</url> - <param type="data" name="bigbed_file" url="galaxy_${DATASET_HASH}.bigbed" strip_https="True" /> - <param type="template" name="track" viewable="True" strip_https="True">track type=bigBed name="${bigbed_file.name}" bigDataUrl=${bigbed_file.url} db=${bigbed_file.dbkey}</param> + <param type="data" name="bigbed_file" url="galaxy_${DATASET_HASH}.bigbed" /> + <param type="template" name="track" viewable="True">track type="bigBed" name="${bigbed_file.name.replace( '\\', '\\\\' ).replace( '"', '\\"' )}" bigDataUrl="${bigbed_file.url}" db="${bigbed_file.dbkey}"</param></dynamic_links></display> diff -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca -r 862d562e31670dd22a6bd575b2fa79328acabb4d display_applications/ucsc/bigwig.xml --- a/display_applications/ucsc/bigwig.xml +++ b/display_applications/ucsc/bigwig.xml @@ -10,7 +10,7 @@ <filter>${dataset.dbkey in $builds}</filter><!-- We define url and params as normal, but values defined in dynamic_param are available by specified name --><url>${ucsc_link}db=${qp($bigwig_file.dbkey)}&hgt.customText=${qp($track.url)}</url> - <param type="data" name="bigwig_file" url="galaxy_${DATASET_HASH}.bigwig" strip_https="True" /> - <param type="template" name="track" viewable="True" strip_https="True">track type=bigWig name="${bigwig_file.name}" bigDataUrl=${bigwig_file.url} db=${bigwig_file.dbkey}</param> + <param type="data" name="bigwig_file" url="galaxy_${DATASET_HASH}.bigwig" /> + <param type="template" name="track" viewable="True">track type="bigWig" name="${bigwig_file.name.replace( '\\', '\\\\' ).replace( '"', '\\"' )}" bigDataUrl="${bigwig_file.url}" db="${bigwig_file.dbkey}"</param></dynamic_links></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.