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commit/galaxy-central: fubar: Fixes to rgManQQ.py to handle chromosome oddities like 'chr1' and X.
by Bitbucket 19 Jul '11

19 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/2b55d3bd13d4/ changeset: 2b55d3bd13d4 user: fubar date: 2011-07-20 04:17:43 summary: Fixes to rgManQQ.py to handle chromosome oddities like 'chr1' and X. Also cleaned up redundant file recreation - the code passes column numbers to R so the raw data can be read as supplied by Galaxy Thanks to Alison Harrill for exposing some more input edge cases... affected #: 3 files (1.3 KB) --- a/test-data/rgtestouts/rgManQQ/rgManQQtest1.html Tue Jul 19 21:22:07 2011 -0400 +++ b/test-data/rgtestouts/rgManQQ/rgManQQtest1.html Wed Jul 20 12:17:43 2011 +1000 @@ -13,8 +13,8 @@ <h1>rgManQQtest1</h1><table> -<tr><td><a href="Allelep_manhattan.png"><img src="Allelep_manhattan.png" alt="Allelep_manhattan.png hspace="10" width="400"><br>(Click to download image Allelep_manhattan.png)</a></td></tr> -<tr><td><a href="Allelep_qqplot.png"><img src="Allelep_qqplot.png" alt="Allelep_qqplot.png hspace="10" width="400"><br>(Click to download image Allelep_qqplot.png)</a></td></tr> +<tr><td><a href="Allelep_manhattan.png"><img src="Allelep_manhattan.png" title="Allelep_manhattan.png hspace="10" width="400"><br>(Click to download image Allelep_manhattan.png)</a></td></tr> +<tr><td><a href="Allelep_qqplot.png"><img src="Allelep_qqplot.png" title="Allelep_qqplot.png hspace="10" width="400"><br>(Click to download image Allelep_qqplot.png)</a></td></tr><tr><td><a href="rgManQQtest1.R">rgManQQtest1.R</a></td></tr><tr><td><a href="rgManQQtest1.R.log">rgManQQtest1.R.log</a></td></tr></table> @@ -35,7 +35,7 @@ - round_any + rename, round_any @@ -43,11 +43,11 @@ Loading required package: proto -[1] "### 101 values read from /tmp/rgManQQtemplYC5wa read - now running plots" +[1] "### 101 values read from /data/tmp/tmpTPXdE1/database/files/000/dataset_1.dat read - now running plots" [1] "## qqplot on Allelep done" -[1] "## manhattan on Allelep starting 1 2 3" +[1] "## manhattan on Allelep starting 2 3 8" [1] "## manhattan plot on Allelep done" @@ -72,26 +72,30 @@ library(ggplot2) coloursTouse = c('firebrick','darkblue','goldenrod','darkgreen') -# not too fugly but need a colour expert please... +# not too ugly but need a colour expert please... -manhattan = function(chrom=NULL,offset=NULL,pvals=NULL, title=NULL, max.y="max", - suggestiveline=0, genomewide=T, size.x.labels=9, size.y.labels=10, annotate=F, SNPlist=NULL,grey=0) { - +DrawManhattan = function(pvals=Null,chrom=Null,offset=Null,title=NULL, max.y="max",suggestiveline=0, genomewide=T, size.x.labels=9, + size.y.labels=10, annotate=F, SNPlist=NULL,grey=0) { if (annotate & is.null(SNPlist)) stop("You requested annotation but provided no SNPlist!") genomewideline=NULL # was genomewideline=-log10(5e-8) if (genomewide) { # use bonferroni since might be only a small region? genomewideline = -log10(0.05/length(pvals)) } - d=data.frame(CHR=chrom,BP=offset,P=pvals) - - #limit to only chrs 1-23? - d=d[d$CHR %in% 1:23, ] - + chro = sub('chr','',chrom, ignore.case = T) # just in case + chro = sub(':','',chro, ignore.case = T) # ugh + chro = sub('X',23,chro, ignore.case = T) + chro = sub('Y',24,chro, ignore.case = T) + chro = sub('Mt',25,chro, ignore.case = T) + offset = as.integer(offset) + pvals = as.double(pvals) + chro = as.integer(chro) + d=data.frame(CHR=chro,BP=offset,P=pvals) + #limit to only chrs 1-22, x=23,y=24,Mt=25? + d=d[d$CHR %in% 1:25, ] if ("CHR" %in% names(d) & "BP" %in% names(d) & "P" %in% names(d) ) { - d=na.omit(d) + #d=na.omit(d) d=d[d$P>0 & d$P<=1, ] - d$logp = -log10(d$P) - + d$logp = as.double(-log10(d$P)) d$pos=NA ticks=NULL lastbase=0 @@ -107,7 +111,11 @@ lastchr = chrlist[x-1] # previous whatever the list lastbase=lastbase+tail(subset(d,CHR==lastchr)$BP, 1) d[d$CHR==i, ]$pos=d[d$CHR==i, ]$BP+lastbase + if (sum(is.na(lastchr),is.na(lastbase),is.na(d[d$CHR==i, ]$pos))) { + cat(paste('manhattan: For',title,'chrlistx=',i,'lastchr=',lastchr,'lastbase=',lastbase,'pos=',d[d$CHR==i,]$pos)) + } tks=c(tks, d[d$CHR==i, ]$pos[floor(length(d[d$CHR==i, ]$pos)/2)+1]) + } ticklim=c(min(d$pos),max(d$pos)) xlabs = chrlist @@ -129,8 +137,6 @@ if (max.y=="max") maxy=ceiling(max(d$logp)) else maxy=max.y maxy = max(maxy,1.1*genomewideline) - # if (maxy<8) maxy=8 - # only makes sense if genome wide is assumed - we could have a fine mapping region? if (annotate) d.annotate=d[as.numeric(substr(d$SNP,3,100)) %in% SNPlist, ] if (nchr >= 2) { manplot=qplot(pos,logp,data=d, ylab=expression(-log[10](italic(p))) , colour=factor(CHR)) @@ -149,9 +155,6 @@ axis.text.y=theme_text(size=size.y.labels, colour="grey50"), axis.ticks=theme_segment(colour=NA) ) - #manplot = manplot + opts(panel.grid.y.minor=theme_blank(),panel.grid.y.major=theme_blank()) - #manplot = manplot + opts(panel.grid.major=theme_blank()) - if (suggestiveline) manplot=manplot+geom_hline(yintercept=suggestiveline,colour="blue", alpha=I(1/3)) if (genomewideline) manplot=manplot+geom_hline(yintercept=genomewideline,colour="red") manplot @@ -178,7 +181,8 @@ if (spartan) plot=plot+opts(panel.background=theme_rect(col="grey50"), panel.grid.minor=theme_blank()) qq } -rgqqMan = function(infile="/tmp/rgManQQtemplYC5wa",chromcolumn=1, offsetcolumn=2, pvalscolumns=c(3), + +rgqqMan = function(infile="/data/tmp/tmpTPXdE1/database/files/000/dataset_1.dat",chromcolumn=2, offsetcolumn=3, pvalscolumns=c(8), title="rgManQQtest1",grey=0) { rawd = read.table(infile,head=T,sep='\t') dn = names(rawd) @@ -206,7 +210,7 @@ doreorder = 0 } print(paste('## manhattan on',cname,'starting',chromcolumn,offsetcolumn,pvalscolumn)) - mymanplot= manhattan(chrom=rawd[,chromcolumn],offset=rawd[,offsetcolumn],pvals=rawd[,pvalscolumn],title=mytitle,grey=grey) + mymanplot= DrawManhattan(chrom=rawd[,chromcolumn],offset=rawd[,offsetcolumn],pvals=rawd[,pvalscolumn],title=mytitle,grey=grey) print(paste('## manhattan plot on',cname,'done')) ggsave(filename=paste(myfname,"manhattan.png",sep='_'),mymanplot,width=6,height=4,dpi=100) } @@ -227,6 +231,6 @@ </pre> -<h3><a href="http://rgenetics.org">Rgenetics</a> tool rgManQQ.py run at 07/11/2010 20:04:20</h3> +<b><a href="http://rgenetics.org">Galaxy Rgenetics</a> tool output rgManQQ.py run at 20/07/2011 12:08:46</b><br/></div></body></html> --- a/tools/rgenetics/rgManQQ.py Tue Jul 19 21:22:07 2011 -0400 +++ b/tools/rgenetics/rgManQQ.py Wed Jul 20 12:17:43 2011 +1000 @@ -1,5 +1,7 @@ #!/usr/local/bin/python - +# rgmanqq updated july 19 to deal with x,y and mt +# lots of fixes +# ross lazarus import sys,math,shutil,subprocess,os,time,tempfile,string from os.path import abspath from rgutils import timenow, RRun, galhtmlprefix, galhtmlpostfix, galhtmlattr @@ -18,7 +20,7 @@ # http://StephenTurner.us/ # http://GettingGeneticsDone.blogspot.com/ -# Last updated: Tuesday, December 22, 2009 +# Last updated: 19 July 2011 by Ross Lazarus # R code for making manhattan plots and QQ plots from plink output files. # With GWAS data this can take a lot of memory. Recommended for use on # 64bit machines only, for now. @@ -28,26 +30,30 @@ library(ggplot2) coloursTouse = c('firebrick','darkblue','goldenrod','darkgreen') -# not too fugly but need a colour expert please... +# not too ugly but need a colour expert please... -manhattan = function(chrom=NULL,offset=NULL,pvals=NULL, title=NULL, max.y="max", - suggestiveline=0, genomewide=T, size.x.labels=9, size.y.labels=10, annotate=F, SNPlist=NULL,grey=0) { - +DrawManhattan = function(pvals=Null,chrom=Null,offset=Null,title=NULL, max.y="max",suggestiveline=0, genomewide=T, size.x.labels=9, + size.y.labels=10, annotate=F, SNPlist=NULL,grey=0) { if (annotate & is.null(SNPlist)) stop("You requested annotation but provided no SNPlist!") genomewideline=NULL # was genomewideline=-log10(5e-8) if (genomewide) { # use bonferroni since might be only a small region? genomewideline = -log10(0.05/length(pvals)) } - d=data.frame(CHR=chrom,BP=offset,P=pvals) - - #limit to only chrs 1-23? - d=d[d$CHR %in% 1:23, ] - + chro = sub('chr','',chrom, ignore.case = T) # just in case + chro = sub(':','',chro, ignore.case = T) # ugh + chro = sub('X',23,chro, ignore.case = T) + chro = sub('Y',24,chro, ignore.case = T) + chro = sub('Mt',25,chro, ignore.case = T) + offset = as.integer(offset) + pvals = as.double(pvals) + chro = as.integer(chro) + d=data.frame(CHR=chro,BP=offset,P=pvals) + #limit to only chrs 1-22, x=23,y=24,Mt=25? + d=d[d$CHR %in% 1:25, ] if ("CHR" %in% names(d) & "BP" %in% names(d) & "P" %in% names(d) ) { - d=na.omit(d) + #d=na.omit(d) d=d[d$P>0 & d$P<=1, ] - d$logp = -log10(d$P) - + d$logp = as.double(-log10(d$P)) d$pos=NA ticks=NULL lastbase=0 @@ -63,7 +69,11 @@ lastchr = chrlist[x-1] # previous whatever the list lastbase=lastbase+tail(subset(d,CHR==lastchr)$BP, 1) d[d$CHR==i, ]$pos=d[d$CHR==i, ]$BP+lastbase + if (sum(is.na(lastchr),is.na(lastbase),is.na(d[d$CHR==i, ]$pos))) { + cat(paste('manhattan: For',title,'chrlistx=',i,'lastchr=',lastchr,'lastbase=',lastbase,'pos=',d[d$CHR==i,]$pos)) + } tks=c(tks, d[d$CHR==i, ]$pos[floor(length(d[d$CHR==i, ]$pos)/2)+1]) + } ticklim=c(min(d$pos),max(d$pos)) xlabs = chrlist @@ -85,8 +95,6 @@ if (max.y=="max") maxy=ceiling(max(d$logp)) else maxy=max.y maxy = max(maxy,1.1*genomewideline) - # if (maxy<8) maxy=8 - # only makes sense if genome wide is assumed - we could have a fine mapping region? if (annotate) d.annotate=d[as.numeric(substr(d$SNP,3,100)) %in% SNPlist, ] if (nchr >= 2) { manplot=qplot(pos,logp,data=d, ylab=expression(-log[10](italic(p))) , colour=factor(CHR)) @@ -105,9 +113,6 @@ axis.text.y=theme_text(size=size.y.labels, colour="grey50"), axis.ticks=theme_segment(colour=NA) ) - #manplot = manplot + opts(panel.grid.y.minor=theme_blank(),panel.grid.y.major=theme_blank()) - #manplot = manplot + opts(panel.grid.major=theme_blank()) - if (suggestiveline) manplot=manplot+geom_hline(yintercept=suggestiveline,colour="blue", alpha=I(1/3)) if (genomewideline) manplot=manplot+geom_hline(yintercept=genomewideline,colour="red") manplot @@ -134,12 +139,13 @@ if (spartan) plot=plot+opts(panel.background=theme_rect(col="grey50"), panel.grid.minor=theme_blank()) qq } + """ # we need another string to avoid confusion over string substitutions with %in% # instantiate rcode2 string with infile,chromcol,offsetcol,pvalscols,title before saving and running -rcode2 = """rgqqMan = function(infile="%s",chromcolumn=%s, offsetcolumn=%s, pvalscolumns=%s, +rcode2 = """rgqqMan = function(infile="%s",chromcolumn=%d, offsetcolumn=%d, pvalscolumns=c(%s), title="%s",grey=%d) { rawd = read.table(infile,head=T,sep='\\t') dn = names(rawd) @@ -167,7 +173,7 @@ doreorder = 0 } print(paste('## manhattan on',cname,'starting',chromcolumn,offsetcolumn,pvalscolumn)) - mymanplot= manhattan(chrom=rawd[,chromcolumn],offset=rawd[,offsetcolumn],pvals=rawd[,pvalscolumn],title=mytitle,grey=grey) + mymanplot= DrawManhattan(chrom=rawd[,chromcolumn],offset=rawd[,offsetcolumn],pvals=rawd[,pvalscolumn],title=mytitle,grey=grey) print(paste('## manhattan plot on',cname,'done')) ggsave(filename=paste(myfname,"manhattan.png",sep='_'),mymanplot,width=6,height=4,dpi=100) } @@ -198,50 +204,13 @@ this can be called externally, I guess...for QC eg? """ if debug: - print 'doManQQ',input_fname,chrom_col,offset_col,pval_cols,title,grey,ctitle,outdir - ffd,filtered_fname = tempfile.mkstemp(prefix='rgManQQtemp') - f = open(filtered_fname,'w') - inf = open(input_fname,'r') - ohead = inf.readline().strip().split('\t') # see if we have a header - inf.seek(0) # rewind - newhead = ['pval%d' % (x+1) for x in pval_cols] - newhead.insert(0,'Offset') - newhead.insert(0,'Chrom') - havehead = 0 - wewant = [chrom_col,offset_col] - wewant += pval_cols - try: - allnums = ['%d' % x for x in ohead] # this should barf if non numerics == header row? - f.write('\t'.join(newhead)) # for R to read - f.write('\n') - except: - havehead = 1 - newhead = [ohead[chrom_col],ohead[offset_col]] - newhead += [ohead[x] for x in pval_cols] - f.write('\t'.join(newhead)) # use the original head - f.write('\n') - for i,row in enumerate(inf): - if i == 0 and havehead: - continue # ignore header - sr = row.strip().split('\t') - if len(sr) > 1: - if sr[chrom_col].lower().find('chr') <> -1: - sr[chrom_col] = sr[chrom_col][3:] - newr = [sr[x] for x in wewant] # grab cols we need - s = '\t'.join(newr) - f.write(s) - f.write('\n') - f.close() - pvc = [x+3 for x in range(len(pval_cols))] # 2 for offset and chrom, 1 for r offset start - pvc = 'c(%s)' % (','.join(map(str,pvc))) - rcmd = '%s%s' % (rcode,rcode2 % (filtered_fname,'1','2',pvc,title,grey)) + print 'doManQQ',input_fname,chrom_col,offset_col,pval_cols,title,grey,ctitle,outdir + rcmd = '%s%s' % (rcode,rcode2 % (input_fname,chrom_col,offset_col,pval_cols,title,grey)) if debug: - print 'running\n%s\n' % rcmd + print 'running\n%s\n' % rcmd rlog,flist = RRun(rcmd=rcmd,title=ctitle,outdir=outdir) rlog.append('## R script=') rlog.append(rcmd) - if beTidy: - os.unlink(filtered_fname) return rlog,flist @@ -272,19 +241,20 @@ offset_col = -1 p = sys.argv[7].strip().split(',') try: - p = [int(x) for x in p] + q = [int(x) for x in p] except: - p = [-1] + p = -1 if chrom_col == -1 or offset_col == -1: # was passed as zero - do not do manhattan plots chrom_col = -1 offset_col = -1 grey = 0 if (sys.argv[8].lower() in ['1','true']): grey = 1 - if p == [-1]: + if p == -1: print >> sys.stderr,'## Cannot run rgManQQ - missing pval column' sys.exit(1) - rlog,flist = doManQQ(input_fname,chrom_col,offset_col,p,title,grey,ctitle,outdir) + p = ['%d' % (int(x) + 1) for x in p] + rlog,flist = doManQQ(input_fname,chrom_col+1,offset_col+1,','.join(p),title,grey,ctitle,outdir) flist.sort() html = [galhtmlprefix % progname,] html.append('<h1>%s</h1>' % title) @@ -294,7 +264,7 @@ fname,expl = row # RRun returns pairs of filenames fiddled for the log and R script e = os.path.splitext(fname)[-1] if e in ['.png','.jpg']: - s= '<tr><td><a href="%s"><img src="%s" alt="%s hspace="10" width="400"><br>(Click to download image %s)</a></td></tr>' \ + s= '<tr><td><a href="%s"><img src="%s" title="%s hspace="10" width="400"><br>(Click to download image %s)</a></td></tr>' \ % (fname,fname,expl,expl ) html.append(s) else: @@ -317,3 +287,4 @@ if __name__ == "__main__": main() + --- a/tools/rgenetics/rgManQQ.xml Tue Jul 19 21:22:07 2011 -0400 +++ b/tools/rgenetics/rgManQQ.xml Wed Jul 20 12:17:43 2011 +1000 @@ -1,4 +1,4 @@ -<tool id="rgManQQ1" name="Manhattan/QQ:" version="1.0.1"> +<tool id="rgManQQ1" name="Manhattan/QQ:" version="1.0.2"><code file="rgManQQ_code.py"/><description>Plots for WGA P values</description> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: kanwei: Fix LibraryField grouping issue by adding prefix
by Bitbucket 19 Jul '11

19 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/f5f352f7099d/ changeset: f5f352f7099d user: kanwei date: 2011-07-20 03:22:07 summary: Fix LibraryField grouping issue by adding prefix affected #: 1 file (21 bytes) --- a/lib/galaxy/web/form_builder.py Tue Jul 19 15:10:11 2011 -0400 +++ b/lib/galaxy/web/form_builder.py Tue Jul 19 21:22:07 2011 -0400 @@ -658,7 +658,7 @@ self.name = name self.ldda = value self.trans = trans - def get_html( self, disabled=False ): + def get_html( self, prefix="", disabled=False ): if not self.ldda: ldda = "" text = "Choose a library dataset" @@ -666,7 +666,7 @@ ldda = self.trans.security.encode_id(self.ldda.id) text = self.ldda.name return '<a href="javascript:void(0);" class="add-librarydataset">%s</a> \ - <input type="hidden" name="%s" value="%s">' % ( text, self.name, escape( str(ldda), quote=True ) ) + <input type="hidden" name="%s%s" value="%s">' % ( text, prefix, self.name, escape( str(ldda), quote=True ) ) def get_display_text(self): if self.ldda: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fix for message display when setting tool shed repository metadata.
by Bitbucket 19 Jul '11

19 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/9d17faf3398a/ changeset: 9d17faf3398a user: greg date: 2011-07-19 21:10:11 summary: Fix for message display when setting tool shed repository metadata. affected #: 1 file (64 bytes) --- a/lib/galaxy/webapps/community/controllers/common.py Tue Jul 19 13:48:42 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/common.py Tue Jul 19 15:10:11 2011 -0400 @@ -230,6 +230,8 @@ correction_msg += "Upload a file named <b>%s</b> to the repository to correct this error." % sample_loc_file else: correction_msg += "Upload a file named <b>%s</b> to the repository to correct this error." % missing_file + else: + correction_msg = exception_msg message += "<b>%s</b> - %s<br/>" % ( tool_file, correction_msg ) status = 'error' elif flush_needed: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Add exception handling around all mercurial api commit calls. On Linux, the mercurial api's commit seems to bump into issues intermittently, throws an exception, and rolls back the transaction. Although I can reproduce it on Linux, I cannot produce this behavior on a Mac. The exception handler uses a different approach to committing the changes. I've also added this code to the update_for_browsing method.
by Bitbucket 19 Jul '11

19 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/f9ef2aecaecd/ changeset: f9ef2aecaecd user: greg date: 2011-07-19 19:48:42 summary: Add exception handling around all mercurial api commit calls. On Linux, the mercurial api's commit seems to bump into issues intermittently, throws an exception, and rolls back the transaction. Although I can reproduce it on Linux, I cannot produce this behavior on a Mac. The exception handler uses a different approach to committing the changes. I've also added this code to the update_for_browsing method. affected #: 3 files (1.9 KB) --- a/lib/galaxy/webapps/community/controllers/common.py Tue Jul 19 11:27:16 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/common.py Tue Jul 19 13:48:42 2011 -0400 @@ -297,7 +297,7 @@ util.send_mail( frm, to, subject, body, trans.app.config ) except Exception, e: log.exception( "An error occurred sending a tool shed repository update alert by email." ) -def update_for_browsing( repository, current_working_dir ): +def update_for_browsing( repository, current_working_dir, commit_message='' ): # Make a copy of a repository's files for browsing. repo_dir = repository.repo_path repo = hg.repository( ui.ui(), repo_dir ) @@ -316,12 +316,15 @@ # ! = deleted, but still tracked # ? = not tracked # I = ignored - # We'll remove all files that are not tracked or ignored. files_to_remove_from_disk = [] + files_to_commit = [] for status_and_file_name in status_and_file_names: if status_and_file_name.startswith( '?' ) or status_and_file_name.startswith( 'I' ): files_to_remove_from_disk.append( os.path.abspath( os.path.join( repo_dir, status_and_file_name.split()[1] ) ) ) + elif status_and_file_name.startswith( 'M' ) or status_and_file_name.startswith( 'A' ) or status_and_file_name.startswith( 'R' ): + files_to_commit.append( os.path.abspath( os.path.join( repo_dir, status_and_file_name.split()[1] ) ) ) for full_path in files_to_remove_from_disk: + # We'll remove all files that are not tracked or ignored. if os.path.isdir( full_path ): try: os.rmdir( full_path ) @@ -336,6 +339,11 @@ except OSError, e: # The directory is not empty pass + if files_to_commit: + if not commit_message: + commit_message = 'Committed changes to: %s' % ', '.join( files_to_commit ) + repo.dirstate.write() + repo.commit( text=commit_message ) os.chdir( repo_dir ) os.system( 'hg update > /dev/null 2>&1' ) os.chdir( current_working_dir ) --- a/lib/galaxy/webapps/community/controllers/repository.py Tue Jul 19 11:27:16 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/repository.py Tue Jul 19 13:48:42 2011 -0400 @@ -425,7 +425,7 @@ repository = get_repository( trans, id ) repo = hg.repository( ui.ui(), repository.repo_path ) current_working_dir = os.getcwd() - update_for_browsing( repository, current_working_dir ) + update_for_browsing( repository, current_working_dir, commit_message=commit_message ) return trans.fill_template( '/webapps/community/repository/browse_repository.mako', repo=repo, repository=repository, @@ -454,11 +454,17 @@ # Commit the change set. if not commit_message: commit_message = 'Deleted selected files' - # Commit the changes. - commands.commit( repo.ui, repo, repo_dir, user=trans.user.username, message=commit_message ) + try: + commands.commit( repo.ui, repo, repo_dir, user=trans.user.username, message=commit_message ) + except Exception, e: + # I never have a problem with commands.commit on a Mac, but in the test/production + # tool shed environment, it occasionally throws a "TypeError: array item must be char" + # exception. If this happens, we'll try the following. + repo.dirstate.write() + repo.commit( text=commit_message ) handle_email_alerts( trans, repository ) # Update the repository files for browsing. - update_for_browsing( repository, current_working_dir ) + update_for_browsing( repository, current_working_dir, commit_message=commit_message ) # Get the new repository tip. repo = hg.repository( ui.ui(), repo_dir ) if tip != repository.tip: --- a/lib/galaxy/webapps/community/controllers/upload.py Tue Jul 19 11:27:16 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/upload.py Tue Jul 19 13:48:42 2011 -0400 @@ -87,7 +87,16 @@ # Move the uploaded file to the load_point within the repository hierarchy. shutil.move( uploaded_file_name, full_path ) commands.add( repo.ui, repo, full_path ) - commands.commit( repo.ui, repo, full_path, user=trans.user.username, message=commit_message ) + """ + try: + commands.commit( repo.ui, repo, full_path, user=trans.user.username, message=commit_message ) + except Exception, e: + # I never have a problem with commands.commit on a Mac, but in the test/production + # tool shed environment, it occasionally throws a "TypeError: array item must be char" + # exception. If this happens, we'll try the following. + repo.dirstate.write() + repo.commit( text=commit_message ) + """ if full_path.endswith( '.loc.sample' ): # Handle the special case where a xxx.loc.sample file is # being uploaded by copying it to ~/tool-data/xxx.loc. @@ -96,7 +105,7 @@ if ok: # Update the repository files for browsing, a by-product of doing this # is eliminating unwanted files from the repository directory. - update_for_browsing( repository, current_working_dir ) + update_for_browsing( repository, current_working_dir, commit_message=commit_message ) # Get the new repository tip. if tip != repository.tip: if ( isgzip or isbz2 ) and uncompress_file: @@ -183,8 +192,14 @@ # Handle the special case where a xxx.loc.sample file is # being uploaded by copying it to ~/tool-data/xxx.loc. copy_sample_loc_file( trans, filename_in_archive ) - # Commit the changes. - commands.commit( repo.ui, repo, full_path, user=trans.user.username, message=commit_message ) + try: + commands.commit( repo.ui, repo, full_path, user=trans.user.username, message=commit_message ) + except Exception, e: + # I never have a problem with commands.commit on a Mac, but in the test/production + # tool shed environment, it occasionally throws a "TypeError: array item must be char" + # exception. If this happens, we'll try the following. + repo.dirstate.write() + repo.commit( text=commit_message ) handle_email_alerts( trans, repository ) return True, '', files_to_remove def uncompress( self, repository, uploaded_file_name, uploaded_file_filename, isgzip, isbz2 ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Various tool shed fixes and enhancements:
by Bitbucket 19 Jul '11

19 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/98ef4f135243/ changeset: 98ef4f135243 user: greg date: 2011-07-19 17:27:16 summary: Various tool shed fixes and enhancements: 1) Fix for uploading empty files to a repository 2) Better error messages when setting repository metadata fails 3) Automatically copy uploaded xxx.loc.sample files to ~/tool-data/xxx.loc 4) Fix for setting the value of the upload_point when uploading files to a repository affected #: 4 files (3.3 KB) --- a/lib/galaxy/webapps/community/controllers/common.py Mon Jul 18 21:56:23 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/common.py Tue Jul 19 11:27:16 2011 -0400 @@ -214,7 +214,23 @@ if invalid_files: message = "Metadata cannot be defined for change set revision '%s'. Correct the following problems and reset metadata.<br/>" % str( change_set_revision ) for itc_tup in invalid_files: - message += "<b>%s</b> - %s<br/>" % ( itc_tup[0], itc_tup[1] ) + # Handle the special case where a tool depends on a missing xxx.loc file by telliing + # the user to upload xxx.loc.sample to the repository so that it can be copied to + # ~/tool-data/xxx.loc. In this case, itc_tup[1] will be a message looking something like: + # [Errno 2] No such file or directory: '/Users/gvk/central/tool-data/blast2go.loc' + tool_file = itc_tup[0] + exception_msg = itc_tup[1] + if exception_msg.find( 'No such file or directory' ) >= 0: + exception_items = exception_msg.split() + missing_file_items = exception_items[7].split( '/' ) + missing_file = missing_file_items[-1].rstrip( '\'' ) + correction_msg = "This file refers to a missing file <b>%s</b>. " % str( missing_file ) + if exception_msg.find( '.loc' ) >= 0: + sample_loc_file = '%s.sample' % str( missing_file ) + correction_msg += "Upload a file named <b>%s</b> to the repository to correct this error." % sample_loc_file + else: + correction_msg += "Upload a file named <b>%s</b> to the repository to correct this error." % missing_file + message += "<b>%s</b> - %s<br/>" % ( tool_file, correction_msg ) status = 'error' elif flush_needed: # We only flush if there are no tool config errors, so change sets will only have metadata @@ -231,6 +247,14 @@ if str( ctx ) == change_set_revision: return ctx return None +def copy_sample_loc_file( trans, filename ): + """Copy xxx.loc.sample to ~/tool-data/xxx.loc""" + sample_loc_file = os.path.split( filename )[1] + loc_file = os.path.split( filename )[1].rstrip( '.sample' ) + tool_data_path = os.path.abspath( trans.app.config.tool_data_path ) + if not ( os.path.exists( os.path.join( tool_data_path, loc_file ) ) or os.path.exists( os.path.join( tool_data_path, sample_loc_file ) ) ): + shutil.copy( os.path.abspath( filename ), os.path.join( tool_data_path, sample_loc_file ) ) + shutil.copy( os.path.abspath( filename ), os.path.join( tool_data_path, loc_file ) ) def get_user( trans, id ): """Get a user from the database""" return trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( id ) ) --- a/lib/galaxy/webapps/community/controllers/upload.py Mon Jul 18 21:56:23 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/upload.py Tue Jul 19 11:27:16 2011 -0400 @@ -45,6 +45,7 @@ uploaded_file = file_data.file uploaded_file_name = uploaded_file.name uploaded_file_filename = file_data.filename + isempty = os.path.getsize( os.path.abspath( uploaded_file_name ) ) == 0 if uploaded_file: isgzip = False isbz2 = False @@ -53,17 +54,21 @@ if not isgzip: isbz2 = is_bz2( uploaded_file_name ) ok = True - # Determine what we have - a single file or an archive - try: - if ( isgzip or isbz2 ) and uncompress_file: - # Open for reading with transparent compression. - tar = tarfile.open( uploaded_file_name, 'r:*' ) - else: - tar = tarfile.open( uploaded_file_name ) - istar = True - except tarfile.ReadError, e: + if isempty: tar = None istar = False + else: + # Determine what we have - a single file or an archive + try: + if ( isgzip or isbz2 ) and uncompress_file: + # Open for reading with transparent compression. + tar = tarfile.open( uploaded_file_name, 'r:*' ) + else: + tar = tarfile.open( uploaded_file_name ) + istar = True + except tarfile.ReadError, e: + tar = None + istar = False if istar: ok, message, files_to_remove = self.upload_tar( trans, repository, @@ -83,6 +88,10 @@ shutil.move( uploaded_file_name, full_path ) commands.add( repo.ui, repo, full_path ) commands.commit( repo.ui, repo, full_path, user=trans.user.username, message=commit_message ) + if full_path.endswith( '.loc.sample' ): + # Handle the special case where a xxx.loc.sample file is + # being uploaded by copying it to ~/tool-data/xxx.loc. + copy_sample_loc_file( trans, full_path ) handle_email_alerts( trans, repository ) if ok: # Update the repository files for browsing, a by-product of doing this @@ -170,6 +179,10 @@ commands.remove( repo.ui, repo, repo_file ) for filename_in_archive in filenames_in_archive: commands.add( repo.ui, repo, filename_in_archive ) + if filename_in_archive.endswith( '.loc.sample' ): + # Handle the special case where a xxx.loc.sample file is + # being uploaded by copying it to ~/tool-data/xxx.loc. + copy_sample_loc_file( trans, filename_in_archive ) # Commit the changes. commands.commit( repo.ui, repo, full_path, user=trans.user.username, message=commit_message ) handle_email_alerts( trans, repository ) --- a/templates/webapps/community/repository/common.mako Mon Jul 18 21:56:23 2011 -0400 +++ b/templates/webapps/community/repository/common.mako Tue Jul 19 11:27:16 2011 -0400 @@ -44,7 +44,7 @@ } // The following is used only in ~/templates/webapps/community/repository/upload.mako. if (document.forms["upload_form"]) { - document.upload_form.upload_point.value = selKeys[0]; + document.upload_form.upload_point.value = selKeys.slice(-1); } }, onActivate: function(dtnode) { --- a/templates/webapps/community/repository/upload.mako Mon Jul 18 21:56:23 2011 -0400 +++ b/templates/webapps/community/repository/upload.mako Tue Jul 19 11:27:16 2011 -0400 @@ -64,96 +64,96 @@ <div class="toolForm"><div class="toolFormTitle">Upload a single file or a tarball</div><div class="toolFormBody"> - ## TODO: nginx - <form id="upload_form" name="upload_form" action="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}" enctype="multipart/form-data" method="post"> - <div class="form-row"> - <label>File:</label> - <div class="form-row-input"> - <input type="file" name="file_data"/> - </div> - <div style="clear: both"></div> - </div> - - <div class="form-row"> - <% - if uncompress_file: - yes_selected = 'selected' - no_selected = '' - else: - yes_selected = '' - no_selected = 'selected' - %> - <label>Uncompress files?</label> - <div class="form-row-input"> - <select name="uncompress_file"> - <option value="true" ${yes_selected}>Yes - <option value="false" ${no_selected}>No - </select> - </div> - <div class="toolParamHelp" style="clear: both;"> - Supported compression types are gz and bz2. If <b>Yes</b> is selected, the uploaded file will be uncompressed. However, - if the uploaded file is an archive that contains compressed files, the contained files will not be uncompressed. For - example, if the uploaded compressed file is some_file.tar.gz, some_file.tar will be uncompressed and extracted, but if - some_file.tar contains some_contained_file.gz, the contained file will not be uncompressed. - </div> - </div> - %if not is_new: - <div class="form-row"> - <% - if remove_repo_files_not_in_tar: - yes_selected = 'selected' - no_selected = '' - else: - yes_selected = '' - no_selected = 'selected' - %> - <label>Remove files in the repository (relative to the root or selected upload point) that are not in the uploaded archive?</label> - <div class="form-row-input"> - <select name="remove_repo_files_not_in_tar"> - <option value="true" ${yes_selected}>Yes - <option value="false" ${no_selected}>No - </select> + ## TODO: nginx + <form id="upload_form" name="upload_form" action="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}" enctype="multipart/form-data" method="post"> + <div class="form-row"> + <label>File:</label> + <div class="form-row-input"> + <input type="file" name="file_data"/> + </div> + <div style="clear: both"></div></div> - <div class="toolParamHelp" style="clear: both;"> - This selection pertains only to uploaded tar archives, not to single file uploads. If <b>Yes</b> is selected, files - that exist in the repository (relative to the root or selected upload point) but that are not in the uploaded archive - will be removed from the repository. Otherwise, all existing repository files will remain and the uploaded archive - files will be added to the repository. + + <div class="form-row"> + <% + if uncompress_file: + yes_selected = 'selected' + no_selected = '' + else: + yes_selected = '' + no_selected = 'selected' + %> + <label>Uncompress files?</label> + <div class="form-row-input"> + <select name="uncompress_file"> + <option value="true" ${yes_selected}>Yes + <option value="false" ${no_selected}>No + </select> + </div> + <div class="toolParamHelp" style="clear: both;"> + Supported compression types are gz and bz2. If <b>Yes</b> is selected, the uploaded file will be uncompressed. However, + if the uploaded file is an archive that contains compressed files, the contained files will not be uncompressed. For + example, if the uploaded compressed file is some_file.tar.gz, some_file.tar will be uncompressed and extracted, but if + some_file.tar contains some_contained_file.gz, the contained file will not be uncompressed. + </div></div> - </div> - %endif - <div class="form-row"> - <label>Change set commit message:</label> - <div class="form-row-input"> - %if commit_message: - <pre><textarea name="commit_message" rows="3" cols="35">${commit_message}</textarea></pre> - %else: - <textarea name="commit_message" rows="3" cols="35"></textarea> + %if not is_new: + <div class="form-row"> + <% + if remove_repo_files_not_in_tar: + yes_selected = 'selected' + no_selected = '' + else: + yes_selected = '' + no_selected = 'selected' + %> + <label>Remove files in the repository (relative to the root or selected upload point) that are not in the uploaded archive?</label> + <div class="form-row-input"> + <select name="remove_repo_files_not_in_tar"> + <option value="true" ${yes_selected}>Yes + <option value="false" ${no_selected}>No + </select> + </div> + <div class="toolParamHelp" style="clear: both;"> + This selection pertains only to uploaded tar archives, not to single file uploads. If <b>Yes</b> is selected, files + that exist in the repository (relative to the root or selected upload point) but that are not in the uploaded archive + will be removed from the repository. Otherwise, all existing repository files will remain and the uploaded archive + files will be added to the repository. + </div> + </div> %endif - </div> - <div class="toolParamHelp" style="clear: both;"> - This is the commit message for the mercurial change set that will be created by this upload. - </div> - <div style="clear: both"></div> - </div> - %if not repository.is_new: - <div class="form-row" > - <label>Contents:</label> - <div id="tree" > - Loading... + <div class="form-row"> + <label>Change set commit message:</label> + <div class="form-row-input"> + %if commit_message: + <pre><textarea name="commit_message" rows="3" cols="35">${commit_message}</textarea></pre> + %else: + <textarea name="commit_message" rows="3" cols="35"></textarea> + %endif + </div> + <div class="toolParamHelp" style="clear: both;"> + This is the commit message for the mercurial change set that will be created by this upload. + </div> + <div style="clear: both"></div></div> - <input type="hidden" id="upload_point" name="upload_point" value=""/> - <div class="toolParamHelp" style="clear: both;"> - Select a location within the repository to upload your files by clicking a check box next to the location. The - selected location is considered the upload point. If a location is not selected, the upload point will be the - repository root. + %if not repository.is_new: + <div class="form-row" > + <label>Contents:</label> + <div id="tree" > + Loading... + </div> + <input type="hidden" id="upload_point" name="upload_point" value=""/> + <div class="toolParamHelp" style="clear: both;"> + Select a location within the repository to upload your files by clicking a check box next to the location. The + selected location is considered the upload point. If a location is not selected, the upload point will be the + repository root. + </div> + <div style="clear: both"></div> + </div> + %endif + <div class="form-row"> + <input type="submit" class="primary-button" name="upload_button" value="Upload"></div> - <div style="clear: both"></div> - </div> - %endif - <div class="form-row"> - <input type="submit" class="primary-button" name="upload_button" value="Upload"> - </div> - </form> + </form></div></div> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: kanwei: Tools: Add new LibraryDataset tool parameter to expose LDDAs to tools. Use trackster's modal popup interface for item selection. Add new InputWrapper that exposes LDDA templates as well.
by Bitbucket 18 Jul '11

18 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/8553b02ce9ee/ changeset: 8553b02ce9ee user: kanwei date: 2011-07-19 03:56:23 summary: Tools: Add new LibraryDataset tool parameter to expose LDDAs to tools. Use trackster's modal popup interface for item selection. Add new InputWrapper that exposes LDDA templates as well. Refactor tool_form.mako to use base_panels.mako instead of its own custom HTML. affected #: 9 files (4.1 KB) --- a/lib/galaxy/tools/__init__.py Mon Jul 18 15:02:37 2011 -0400 +++ b/lib/galaxy/tools/__init__.py Mon Jul 18 21:56:23 2011 -0400 @@ -1463,6 +1463,11 @@ elif isinstance( input, SelectToolParameter ): input_values[ input.name ] = SelectToolParameterWrapper( input, input_values[ input.name ], self.app, other_values = param_dict ) + + elif isinstance( input, LibraryDatasetToolParameter ): + input_values[ input.name ] = LibraryDatasetValueWrapper( + input, input_values[ input.name ], param_dict ) + else: input_values[ input.name ] = InputValueWrapper( input, input_values[ input.name ], param_dict ) @@ -2013,6 +2018,31 @@ def __getattr__( self, key ): return getattr( self.obj, key ) +class LibraryDatasetValueWrapper( object ): + """ + Wraps an input so that __str__ gives the "param_dict" representation. + """ + def __init__( self, input, value, other_values={} ): + self.input = input + self.value = value + self._other_values = other_values + def __str__( self ): + return self.value.name + def templates( self ): + if not self.value: + return None + template_data = {} + for temp_info in self.value.info_association: + template = temp_info.template + content = temp_info.info.content + tmp_dict = {} + for field in template.fields: + tmp_dict[field['label']] = content[field['name']] + template_data[template.name] = tmp_dict + return template_data + def __getattr__( self, key ): + return getattr( self.value, key ) + class InputValueWrapper( object ): """ Wraps an input so that __str__ gives the "param_dict" representation. --- a/lib/galaxy/tools/parameters/basic.py Mon Jul 18 15:02:37 2011 -0400 +++ b/lib/galaxy/tools/parameters/basic.py Mon Jul 18 21:56:23 2011 -0400 @@ -1272,7 +1272,7 @@ displayed as radio buttons and multiple selects as a set of checkboxes TODO: The following must be fixed to test correctly for the new security_check tag in the DataToolParameter ( the last test below is broken ) - Nate's next passs at the dataset security stuff will dramatically alter this anyway. + Nate's next pass at the dataset security stuff will dramatically alter this anyway. """ def __init__( self, tool, elem ): @@ -1522,6 +1522,38 @@ ref = ref() return ref +class LibraryDatasetToolParameter( ToolParameter ): + """ + Parameter that lets users select a LDDA from a modal window, then use it within the wrapper. + """ + + def __init__( self, tool, elem ): + ToolParameter.__init__( self, tool, elem ) + + def get_html_field( self, trans=None, value=None, other_values={} ): + return form_builder.LibraryField( self.name, value=value, trans=trans ) + + def get_initial_value( self, trans, context ): + return None + + def from_html( self, value, trans, other_values={} ): + if not value: + return None + elif isinstance( value, trans.app.model.LibraryDatasetDatasetAssociation ): + return value + else: + return trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( value ) ) + + def to_string( self, value, app ): + if not value: + return None + return value.id + + def to_python( self, value, app ): + if not value: + return value + return app.model.context.query( app.model.LibraryDatasetDatasetAssociation ).get( value ) + # class RawToolParameter( ToolParameter ): # """ # Completely nondescript parameter, HTML representation is provided as text @@ -1570,19 +1602,20 @@ # self.html = form_builder.HiddenField( self.name, trans.history.id ).get_html() # return self.html -parameter_types = dict( text = TextToolParameter, - integer = IntegerToolParameter, - float = FloatToolParameter, - boolean = BooleanToolParameter, - genomebuild = GenomeBuildParameter, - select = SelectToolParameter, - data_column = ColumnListParameter, - hidden = HiddenToolParameter, - baseurl = BaseURLToolParameter, - file = FileToolParameter, - ftpfile = FTPFileToolParameter, - data = DataToolParameter, - drill_down = DrillDownSelectToolParameter ) +parameter_types = dict( text = TextToolParameter, + integer = IntegerToolParameter, + float = FloatToolParameter, + boolean = BooleanToolParameter, + genomebuild = GenomeBuildParameter, + select = SelectToolParameter, + data_column = ColumnListParameter, + hidden = HiddenToolParameter, + baseurl = BaseURLToolParameter, + file = FileToolParameter, + ftpfile = FTPFileToolParameter, + data = DataToolParameter, + library_data = LibraryDatasetToolParameter, + drill_down = DrillDownSelectToolParameter ) class UnvalidatedValue( object ): """ --- a/lib/galaxy/web/form_builder.py Mon Jul 18 15:02:37 2011 -0400 +++ b/lib/galaxy/web/form_builder.py Mon Jul 18 21:56:23 2011 -0400 @@ -652,6 +652,27 @@ return self.value else: return '-' + +class LibraryField( BaseField ): + def __init__( self, name, value=None, trans=None ): + self.name = name + self.ldda = value + self.trans = trans + def get_html( self, disabled=False ): + if not self.ldda: + ldda = "" + text = "Choose a library dataset" + else: + ldda = self.trans.security.encode_id(self.ldda.id) + text = self.ldda.name + return '<a href="javascript:void(0);" class="add-librarydataset">%s</a> \ + <input type="hidden" name="%s" value="%s">' % ( text, self.name, escape( str(ldda), quote=True ) ) + + def get_display_text(self): + if self.ldda: + return self.ldda.name + else: + return 'None' def get_suite(): """Get unittest suite for this module""" --- a/static/scripts/galaxy.base.js Mon Jul 18 15:02:37 2011 -0400 +++ b/static/scripts/galaxy.base.js Mon Jul 18 21:56:23 2011 -0400 @@ -725,4 +725,5 @@ } return anchor; }); + }); --- a/static/scripts/galaxy.panels.js Mon Jul 18 15:02:37 2011 -0400 +++ b/static/scripts/galaxy.panels.js Mon Jul 18 21:56:23 2011 -0400 @@ -214,7 +214,7 @@ init_fn(); } }; - + function show_in_overlay( options ) { var width = options.width || '600'; var height = options.height || '400'; @@ -226,9 +226,9 @@ show_modal( null, $( "<div style='margin: -5px;'><img id='close_button' style='position:absolute;right:-17px;top:-15px;src='" + image_path + "/closebox.png'><iframe style='margin: 0; padding: 0;' src='" + options.url + "' width='" + width + "' height='" + height + "' scrolling='" + scroll + "' frameborder='0'></iframe></div>" ) ); $("#close_button").bind( "click", function() { hide_modal(); } ); } - + // Tab management - + $(function() { $(".tab").each( function() { var submenu = $(this).children( ".submenu" ); --- a/templates/base.mako Mon Jul 18 15:02:37 2011 -0400 +++ b/templates/base.mako Mon Jul 18 21:56:23 2011 -0400 @@ -1,15 +1,13 @@ <% _=n_ %><!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd"><html> - -<head> -<title>${self.title()}</title> -<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> -${self.metas()} -${self.stylesheets()} -${self.javascripts()} -</head> - + <head> + <title>${self.title()}</title> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + ${self.metas()} + ${self.stylesheets()} + ${self.javascripts()} + </head><body> ${next.body()} </body> --- a/templates/base_panels.mako Mon Jul 18 15:02:37 2011 -0400 +++ b/templates/base_panels.mako Mon Jul 18 21:56:23 2011 -0400 @@ -155,13 +155,13 @@ ## Override </%def> -<%def name="overlay( title='', content='' )"> +<%def name="overlay( title='', content='', visible=False )"><%def name="title()"></%def><%def name="content()"></%def><div id="overlay" - %if not self.overlay_visible: - style="display: none;" + %if not visible: + style="display: none;" %endif > ## @@ -169,21 +169,21 @@ ## Need a table here for centering in IE6 <table class="dialog-box-container" border="0" cellpadding="0" cellspacing="0" - %if not self.overlay_visible: + %if not visible: style="display: none;" %endif ><tr><td><div class="dialog-box-wrapper"><div class="dialog-box"> - <div class="unified-panel-header"> - <div class="unified-panel-header-inner"><span class='title'>${title}</span></div> - </div> - <div class="body">${content}</div> - <div> - <div class="buttons" style="display: none; float: right;"></div> - <div class="extra_buttons" style="display: none; padding: 5px;"></div> - <div style="clear: both;"></div> - </div> + <div class="unified-panel-header"> + <div class="unified-panel-header-inner"><span class='title'>${title}</span></div> + </div> + <div class="body">${content}</div> + <div> + <div class="buttons" style="display: none; float: right;"></div> + <div class="extra_buttons" style="display: none; padding: 5px;"></div> + <div style="clear: both;"></div> + </div></div></div></td></tr></table> @@ -198,45 +198,45 @@ <html> ${self.init()} <head> - <title>${self.title()}</title> - <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> - <meta name = "viewport" content = "maximum-scale=1.0"> - ${self.stylesheets()} - ${self.javascripts()} + <title>${self.title()}</title> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + <meta name = "viewport" content = "maximum-scale=1.0"> + ${self.stylesheets()} + ${self.javascripts()} </head><body scroll="no" class="${self.body_class}"> - <div id="everything" style="position: absolute; top: 0; left: 0; width: 100%; height: 100%; min-width: 600px;"> - ## Background displays first - <div id="background"></div> - ## Layer iframes over backgrounds - <div id="masthead"> - ${self.masthead()} - </div> - <div id="messagebox" class="panel-${self.message_box_class}-message"> - %if self.message_box_visible: - ${self.message_box_content()} + <div id="everything" style="position: absolute; top: 0; left: 0; width: 100%; height: 100%; min-width: 600px;"> + ## Background displays first + <div id="background"></div> + ## Layer iframes over backgrounds + <div id="masthead"> + ${self.masthead()} + </div> + <div id="messagebox" class="panel-${self.message_box_class}-message"> + %if self.message_box_visible: + ${self.message_box_content()} + %endif + </div> + ${self.overlay(visible=self.overlay_visible)} + %if self.has_left_panel: + <div id="left"> + ${self.left_panel()} + </div> + <div id="left-border"> + <div id="left-border-inner" style="display: none;"></div> + </div> + %endif + <div id="center"> + ${self.center_panel()} + </div> + %if self.has_right_panel: + <div id="right-border"><div id="right-border-inner" style="display: none;"></div></div> + <div id="right"> + ${self.right_panel()} + </div> %endif </div> - ${self.overlay()} - %if self.has_left_panel: - <div id="left"> - ${self.left_panel()} - </div> - <div id="left-border"> - <div id="left-border-inner" style="display: none;"></div> - </div> - %endif - <div id="center"> - ${self.center_panel()} - </div> - %if self.has_right_panel: - <div id="right-border"><div id="right-border-inner" style="display: none;"></div></div> - <div id="right"> - ${self.right_panel()} - </div> - %endif - </div> ## Allow other body level elements </body> ## Scripts can be loaded later since they progressively add features to --- a/templates/root/index.mako Mon Jul 18 15:02:37 2011 -0400 +++ b/templates/root/index.mako Mon Jul 18 21:56:23 2011 -0400 @@ -174,14 +174,14 @@ <%def name="init()"><% - if trans.app.config.cloud_controller_instance: - self.has_left_panel=False - self.has_right_panel=False - self.active_view="cloud" - else: - self.has_left_panel=True - self.has_right_panel=True - self.active_view="analysis" + if trans.app.config.cloud_controller_instance: + self.has_left_panel=False + self.has_right_panel=False + self.active_view="cloud" + else: + self.has_left_panel=True + self.has_right_panel=True + self.active_view="analysis" %> %if trans.app.config.require_login and not trans.user: <script type="text/javascript"> @@ -219,7 +219,7 @@ elif m_c is not None: center_url = h.url_for( controller=m_c, action=m_a ) elif trans.app.config.cloud_controller_instance: - center_url = h.url_for( controller='cloud', action='list' ) + center_url = h.url_for( controller='cloud', action='list' ) else: center_url = h.url_for( '/static/welcome.html' ) %> --- a/templates/tool_form.mako Mon Jul 18 15:02:37 2011 -0400 +++ b/templates/tool_form.mako Mon Jul 18 21:56:23 2011 -0400 @@ -1,203 +1,230 @@ - -<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd"> +<%inherit file="/base.mako"/> +<%namespace file="/base_panels.mako" import="overlay" /> -<% -from galaxy.util.expressions import ExpressionContext -%> +<%def name="stylesheets()"> + ${h.css( "autocomplete_tagging", "panel_layout", "base", "library" )} +</%def> -<html> +<%def name="javascripts()"> + ${h.js( "jquery", "galaxy.panels", "galaxy.base", "jquery.autocomplete", "jstorage" )} + <script type="text/javascript"> + $(function() { + $(window).bind("refresh_on_change", function() { + $(':file').each( function() { + var file = $(this); + var file_value = file.val(); + if (file_value) { + // disable file input, since we don't want to upload the file on refresh + var file_name = $(this).attr("name"); + file.attr( { name: 'replaced_file_input_' + file_name, disabled: true } ); + // create a new hidden field which stores the filename and has the original name of the file input + var new_file_input = $(document.createElement('input')); + new_file_input.attr( { "type": "hidden", "value": file_value, "name": file_name } ); + file.after(new_file_input); + } + }); + }); -<head> -<title>Galaxy</title> -<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> -${h.css( "base", "autocomplete_tagging" )} -${h.js( "jquery", "galaxy.base", "jquery.autocomplete" )} -<script type="text/javascript"> -$(function() { - $(window).bind("refresh_on_change", function() { - $(':file').each( function() { - var file = $(this); - var file_value = file.val(); - if (file_value) { - // disable file input, since we don't want to upload the file on refresh - var file_name = $(this).attr("name"); - file.attr( { name: 'replaced_file_input_' + file_name, disabled: true } ); - // create a new hidden field which stores the filename and has the original name of the file input - var new_file_input = $(document.createElement('input')); - new_file_input.attr( { "type": "hidden", "value": file_value, "name": file_name } ); - file.after(new_file_input); + // For drilldown parameters: add expand/collapse buttons and collapse initially-collapsed elements + $( 'li ul.toolParameterExpandableCollapsable' ).each( function() { + var el = $(this), + parent_li = el.parent('li'), + sub_ul = el.remove(); + + parent_li.find( 'span' ).wrapInner( '<a/>' ).find( 'a' ).click( function() { + sub_ul.toggle(); + (this).html( sub_ul.is(":hidden") ? '[+]' : '[-]' ); + }); + parent_li.append( sub_ul ); + }); + + $( 'ul ul.toolParameterExpandableCollapsable' ).each( function(i) { + var el = $(this); + if (el.attr("default_state") === "collapsed") { + el.hide(); } }); + + function checkUncheckAll( name, check ) { + $("input[name='" + name + "'][type='checkbox']").attr('checked', !!check); + } + + // Inserts the Select All / Unselect All buttons for checkboxes + $("div.checkUncheckAllPlaceholder").each( function() { + var check_name = $(this).attr("checkbox_name"); + select_link = $("<a class='action-button'></a>").text("Select All").click(function() { + checkUncheckAll(check_name, true); + }); + unselect_link = $("<a class='action-button'></a>").text("Unselect All").click(function() { + checkUncheckAll(check_name, false); + }); + $(this).append(select_link).append(" ").append(unselect_link); + }); + + $(".add-librarydataset").live("click", function() { + var link = $(this); + $.ajax({ + url: "/tracks/list_libraries", + error: function(xhr, ajaxOptions, thrownError) { alert( "Grid failed" ); console.log(xhr, ajaxOptions, thrownError); }, + success: function(table_html) { + show_modal( + "Select Library Dataset", + table_html, { + "Cancel": function() { + hide_modal(); + }, + "Select": function() { + $('input[name=ldda_ids]:checked').each(function() { + var name = $.trim( $(this).siblings("div").find("a").text() ); + var id = $(this).val(); + link.text(name); + link.siblings("input[type=hidden]").val(id); + }); + hide_modal(); + } + } + ); + } + }); + }); }); - - // For drilldown parameters: add expand/collapse buttons and collapse initially-collapsed elements - $( 'li ul.toolParameterExpandableCollapsable' ).each( function() { - var el = $(this), - parent_li = el.parent('li'), - sub_ul = el.remove(); - - parent_li.find( 'span' ).wrapInner( '<a/>' ).find( 'a' ).click( function() { - sub_ul.toggle(); - (this).html( sub_ul.is(":hidden") ? '[+]' : '[-]' ); - }); - parent_li.append( sub_ul ); - }); - - $( 'ul ul.toolParameterExpandableCollapsable' ).each( function(i) { - var el = $(this); - if (el.attr("default_state") === "collapsed") { - el.hide(); + + %if not add_frame.debug: + if( window.name != "galaxy_main" ) { + location.replace( '${h.url_for( controller='root', action='index', tool_id=tool.id )}' ); } - }); - - function checkUncheckAll( name, check ) { - $("input[name='" + name + "'][type='checkbox']").attr('checked', !!check); - } - - // Inserts the Select All / Unselect All buttons for checkboxes - $("div.checkUncheckAllPlaceholder").each( function() { - var check_name = $(this).attr("checkbox_name"); - select_link = $("<a class='action-button'></a>").text("Select All").click(function() { - checkUncheckAll(check_name, true); - }); - unselect_link = $("<a class='action-button'></a>").text("Unselect All").click(function() { - checkUncheckAll(check_name, false); - }); - $(this).append(select_link).append(" ").append(unselect_link); - }); -}); + %endif -%if not add_frame.debug: - if( window.name != "galaxy_main" ) { - location.replace( '${h.url_for( controller='root', action='index', tool_id=tool.id )}' ); - } -%endif + </script> -</script> -</head> +</%def> -<body> - <%def name="do_inputs( inputs, tool_state, errors, prefix, other_values=None )"> - <% other_values = ExpressionContext( tool_state, other_values ) %> - %for input_index, input in enumerate( inputs.itervalues() ): - %if not input.visible: - <% pass %> - %elif input.type == "repeat": - <div class="repeat-group"> - <div class="form-title-row"><b>${input.title_plural}</b></div> - <% repeat_state = tool_state[input.name] %> - %for i in range( len( repeat_state ) ): - <div class="repeat-group-item"> - <% - if input.name in errors: - rep_errors = errors[input.name][i] - else: - rep_errors = dict() - index = repeat_state[i]['__index__'] - %> - <div class="form-title-row"><b>${input.title} ${i + 1}</b></div> - ${do_inputs( input.inputs, repeat_state[i], rep_errors, prefix + input.name + "_" + str(index) + "|", other_values )} - <div class="form-row"><input type="submit" name="${prefix}${input.name}_${index}_remove" value="Remove ${input.title} ${i+1}"></div> - </div> - %if rep_errors.has_key( '__index__' ): - <div><img style="vertical-align: middle;" src="${h.url_for('/static/style/error_small.png')}"> <span style="vertical-align: middle;">${rep_errors['__index__']}</span></div> - %endif - %endfor - <div class="form-row"><input type="submit" name="${prefix}${input.name}_add" value="Add new ${input.title}"></div> - </div> - %elif input.type == "conditional": - <% - group_state = tool_state[input.name] - group_errors = errors.get( input.name, {} ) - current_case = group_state['__current_case__'] - group_prefix = prefix + input.name + "|" - %> - %if input.value_ref_in_group: - ${row_for_param( group_prefix, input.test_param, group_state, group_errors, other_values )} - %endif - ${do_inputs( input.cases[current_case].inputs, group_state, group_errors, group_prefix, other_values )} - %elif input.type == "upload_dataset": - %if input.get_datatype( trans, other_values ).composite_type is None: #have non-composite upload appear as before +<%def name="do_inputs( inputs, tool_state, errors, prefix, other_values=None )"> + <% + from galaxy.util.expressions import ExpressionContext + other_values = ExpressionContext( tool_state, other_values ) + %> + %for input_index, input in enumerate( inputs.itervalues() ): + %if not input.visible: + <% pass %> + %elif input.type == "repeat": + <div class="repeat-group"> + <div class="form-title-row"><strong>${input.title_plural}</strong></div> + <% repeat_state = tool_state[input.name] %> + %for i in range( len( repeat_state ) ): + <div class="repeat-group-item"><% if input.name in errors: - rep_errors = errors[input.name][0] + rep_errors = errors[input.name][i] else: rep_errors = dict() + index = repeat_state[i]['__index__'] %> - ${do_inputs( input.inputs, tool_state[input.name][0], rep_errors, prefix + input.name + "_" + str( 0 ) + "|", other_values )} - %else: - <div class="repeat-group"> - <div class="form-title-row"><b>${input.group_title( other_values )}</b></div> - <% - repeat_state = tool_state[input.name] - %> - %for i in range( len( repeat_state ) ): - <div class="repeat-group-item"> - <% - if input.name in errors: - rep_errors = errors[input.name][i] - else: - rep_errors = dict() - index = repeat_state[i]['__index__'] - %> - <div class="form-title-row"><b>File Contents for ${input.title_by_index( trans, i, other_values )}</b></div> - ${do_inputs( input.inputs, repeat_state[i], rep_errors, prefix + input.name + "_" + str(index) + "|", other_values )} - ##<div class="form-row"><input type="submit" name="${prefix}${input.name}_${index}_remove" value="Remove ${input.title} ${i+1}"></div> - </div> - %endfor - ##<div class="form-row"><input type="submit" name="${prefix}${input.name}_add" value="Add new ${input.title}"></div> - </div> + <div class="form-title-row"><strong>${input.title} ${i + 1}</strong></div> + ${do_inputs( input.inputs, repeat_state[i], rep_errors, prefix + input.name + "_" + str(index) + "|", other_values )} + <div class="form-row"><input type="submit" name="${prefix}${input.name}_${index}_remove" value="Remove ${input.title} ${i+1}"></div> + </div> + %if rep_errors.has_key( '__index__' ): + <div><img style="vertical-align: middle;" src="${h.url_for('/static/style/error_small.png')}"> <span style="vertical-align: middle;">${rep_errors['__index__']}</span></div> %endif + %endfor + <div class="form-row"><input type="submit" name="${prefix}${input.name}_add" value="Add new ${input.title}"></div> + </div> + %elif input.type == "conditional": + <% + group_state = tool_state[input.name] + group_errors = errors.get( input.name, {} ) + current_case = group_state['__current_case__'] + group_prefix = prefix + input.name + "|" + %> + %if input.value_ref_in_group: + ${row_for_param( group_prefix, input.test_param, group_state, group_errors, other_values )} + %endif + ${do_inputs( input.cases[current_case].inputs, group_state, group_errors, group_prefix, other_values )} + %elif input.type == "upload_dataset": + %if input.get_datatype( trans, other_values ).composite_type is None: #have non-composite upload appear as before + <% + if input.name in errors: + rep_errors = errors[input.name][0] + else: + rep_errors = dict() + %> + ${do_inputs( input.inputs, tool_state[input.name][0], rep_errors, prefix + input.name + "_" + str( 0 ) + "|", other_values )} %else: - ${row_for_param( prefix, input, tool_state, errors, other_values )} - %endif - %endfor - </%def> - - <%def name="row_for_param( prefix, param, parent_state, parent_errors, other_values )"> - <% - if parent_errors.has_key( param.name ): - cls = "form-row form-row-error" - else: - cls = "form-row" - - label = param.get_label() - - field = param.get_html_field( trans, parent_state[ param.name ], other_values ) - field.refresh_on_change = param.refresh_on_change - - # Field may contain characters submitted by user and these characters may be unicode; handle non-ascii characters gracefully. - field_html = field.get_html( prefix ) - if type( field_html ) is not unicode: - field_html = unicode( field_html, 'utf-8' ) - - if param.type == "hidden": - return field_html - %> - <div class="${cls}"> - %if label: - <label for="${param.name}">${label}:</label> - %endif - <div class="form-row-input">${field_html}</div> - %if parent_errors.has_key( param.name ): - <div class="form-row-error-message"> - <div><img style="vertical-align: middle;" src="${h.url_for('/static/style/error_small.png')}"> <span style="vertical-align: middle;">${parent_errors[param.name]}</span></div> + <div class="repeat-group"> + <div class="form-title-row"><strong>${input.group_title( other_values )}</strong></div> + <% + repeat_state = tool_state[input.name] + %> + %for i in range( len( repeat_state ) ): + <div class="repeat-group-item"> + <% + if input.name in errors: + rep_errors = errors[input.name][i] + else: + rep_errors = dict() + index = repeat_state[i]['__index__'] + %> + <div class="form-title-row"><strong>File Contents for ${input.title_by_index( trans, i, other_values )}</strong></div> + ${do_inputs( input.inputs, repeat_state[i], rep_errors, prefix + input.name + "_" + str(index) + "|", other_values )} + ##<div class="form-row"><input type="submit" name="${prefix}${input.name}_${index}_remove" value="Remove ${input.title} ${i+1}"></div> + </div> + %endfor + ##<div class="form-row"><input type="submit" name="${prefix}${input.name}_add" value="Add new ${input.title}"></div></div> %endif - - %if param.help: - <div class="toolParamHelp" style="clear: both;"> - ${param.help} - </div> - %endif - - <div style="clear: both"></div> - - </div> - </%def> - - %if add_frame.from_noframe: - <div class="warningmessage"> + %else: + ${row_for_param( prefix, input, tool_state, errors, other_values )} + %endif + %endfor +</%def> + +<%def name="row_for_param( prefix, param, parent_state, parent_errors, other_values )"> + <% + if parent_errors.has_key( param.name ): + cls = "form-row form-row-error" + else: + cls = "form-row" + + label = param.get_label() + + field = param.get_html_field( trans, parent_state[ param.name ], other_values ) + field.refresh_on_change = param.refresh_on_change + + # Field may contain characters submitted by user and these characters may be unicode; handle non-ascii characters gracefully. + field_html = field.get_html( prefix ) + if type( field_html ) is not unicode: + field_html = unicode( field_html, 'utf-8' ) + + if param.type == "hidden": + return field_html + %> + <div class="${cls}"> + %if label: + <label for="${param.name}">${label}:</label> + %endif + <div class="form-row-input">${field_html}</div> + %if parent_errors.has_key( param.name ): + <div class="form-row-error-message"> + <div><img style="vertical-align: middle;" src="${h.url_for('/static/style/error_small.png')}"> <span style="vertical-align: middle;">${parent_errors[param.name]}</span></div> + </div> + %endif + + %if param.help: + <div class="toolParamHelp" style="clear: both;"> + ${param.help} + </div> + %endif + + <div style="clear: both;"></div> + + </div> +</%def> + +<% overlay(visible=False) %> + +%if add_frame.from_noframe: + <div class="warningmessage"><strong>Welcome to Galaxy</strong><hr/> It appears that you found this tool from a link outside of Galaxy. @@ -205,60 +232,59 @@ <a href="${h.url_for( controller='root' )}" target="_top">welcome page</a>. To learn more about what Galaxy is and what it can do for you, please visit the <a href="$add_frame.wiki_url" target="_top">Galaxy wiki</a>. - </div> - <br/> + </div> + <br/> +%endif + +## handle calculating the redict url for the special case where we have nginx proxy +## upload and need to do url_for on the redirect portion of the tool action +<% + try: + tool_url = h.url_for(tool.action) + except AttributeError: + assert len(tool.action) == 2 + tool_url = tool.action[0] + h.url_for(tool.action[1]) +%> +<div class="toolForm" id="${tool.id}"> + %if tool.has_multiple_pages: + <div class="toolFormTitle">${tool.name} (step ${tool_state.page+1} of ${tool.npages})</div> + %else: + <div class="toolFormTitle">${tool.name}</div> %endif - - ## handle calculating the redict url for the special case where we have nginx proxy - ## upload and need to do url_for on the redirect portion of the tool action - <% - try: - tool_url = h.url_for(tool.action) - except AttributeError: - assert len(tool.action) == 2 - tool_url = tool.action[0] + h.url_for(tool.action[1]) - %><div class="toolForm" id="${tool.id}"> - %if tool.has_multiple_pages: - <div class="toolFormTitle">${tool.name} (step ${tool_state.page+1} of ${tool.npages})</div> - %else: - <div class="toolFormTitle">${tool.name}</div> - %endif - <div class="toolFormBody"> - <form id="tool_form" name="tool_form" action="${tool_url}" enctype="${tool.enctype}" target="${tool.target}" method="${tool.method}"> - <input type="hidden" name="tool_id" value="${tool.id}"> - <input type="hidden" name="tool_state" value="${util.object_to_string( tool_state.encode( tool, app ) )}"> - %if tool.display_by_page[tool_state.page]: - ${trans.fill_template_string( tool.display_by_page[tool_state.page], context=tool.get_param_html_map( trans, tool_state.page, tool_state.inputs ) )} - <input type="submit" class="primary-button" name="runtool_btn" value="Execute"> - %else: - ${do_inputs( tool.inputs_by_page[ tool_state.page ], tool_state.inputs, errors, "" )} - <div class="form-row"> - %if tool_state.page == tool.last_page: - <input type="submit" class="primary-button" name="runtool_btn" value="Execute"> - %else: - <input type="submit" class="primary-button" name="runtool_btn" value="Next step"> - %endif - </div> - %endif - </form> + <div class="toolFormBody"> + <form id="tool_form" name="tool_form" action="${tool_url}" enctype="${tool.enctype}" target="${tool.target}" method="${tool.method}"> + <input type="hidden" name="tool_id" value="${tool.id}"> + <input type="hidden" name="tool_state" value="${util.object_to_string( tool_state.encode( tool, app ) )}"> + %if tool.display_by_page[tool_state.page]: + ${trans.fill_template_string( tool.display_by_page[tool_state.page], context=tool.get_param_html_map( trans, tool_state.page, tool_state.inputs ) )} + <input type="submit" class="primary-button" name="runtool_btn" value="Execute"> + %else: + ${do_inputs( tool.inputs_by_page[ tool_state.page ], tool_state.inputs, errors, "" )} + <div class="form-row"> + %if tool_state.page == tool.last_page: + <input type="submit" class="primary-button" name="runtool_btn" value="Execute"> + %else: + <input type="submit" class="primary-button" name="runtool_btn" value="Next step"> + %endif + </div> + %endif + </form> + </div> +</div> +%if tool.help: + <div class="toolHelp"> + <div class="toolHelpBody"> + <% + if tool.has_multiple_pages: + tool_help = tool.help_by_page[tool_state.page] + else: + tool_help = tool.help + + # Convert to unicode to display non-ascii characters. + if type( tool_help ) is not unicode: + tool_help = unicode( tool_help, 'utf-8') + %> + ${tool_help} </div></div> - %if tool.help: - <div class="toolHelp"> - <div class="toolHelpBody"> - <% - if tool.has_multiple_pages: - tool_help = tool.help_by_page[tool_state.page] - else: - tool_help = tool.help - - # Convert to unicode to display non-ascii characters. - if type( tool_help ) is not unicode: - tool_help = unicode( tool_help, 'utf-8') - %> - ${tool_help} - </div> - </div> - %endif -</body> -</html> +%endif Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: dannon: Case sensitivity note for login not found error.
by Bitbucket 18 Jul '11

18 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/8e05f9425723/ changeset: 8e05f9425723 user: dannon date: 2011-07-18 21:02:37 summary: Case sensitivity note for login not found error. affected #: 3 files (129 bytes) --- a/lib/galaxy/web/controllers/mobile.py Mon Jul 18 15:09:49 2011 +0200 +++ b/lib/galaxy/web/controllers/mobile.py Mon Jul 18 15:02:37 2011 -0400 @@ -47,7 +47,7 @@ error = password_error = None user = trans.sa_session.query( model.User ).filter_by( email = email ).first() if not user: - error = "No such user" + error = "No such user (please note that login is case sensitive)" elif user.deleted: error = "This account has been marked deleted, contact your Galaxy administrator to restore the account." elif user.external: --- a/lib/galaxy/web/controllers/user.py Mon Jul 18 15:09:49 2011 +0200 +++ b/lib/galaxy/web/controllers/user.py Mon Jul 18 15:02:37 2011 -0400 @@ -394,7 +394,7 @@ success = False user = trans.sa_session.query( trans.app.model.User ).filter( trans.app.model.User.table.c.email==email ).first() if not user: - message = "No such user" + message = "No such user (please note that login is case sensitive)" status = 'error' elif user.deleted: message = "This account has been marked deleted, contact your Galaxy administrator to restore the account." --- a/scripts/check_galaxy.py Mon Jul 18 15:09:49 2011 +0200 +++ b/scripts/check_galaxy.py Mon Jul 18 15:02:37 2011 -0400 @@ -292,7 +292,7 @@ self.in_span = False def handle_data(self, data): if self.in_span: - if data == "No such user": + if data == "No such user (please note that login is case sensitive)": self.no_user = True elif data == "Invalid password": self.bad_pw = True Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jgoecks: Trackster: show 'Add Datasets' button when there are no tracks in a visualization. Refactor and modularize add tracks code so that is can be used in multiple places.
by Bitbucket 18 Jul '11

18 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/27bac44e93f6/ changeset: 27bac44e93f6 user: jgoecks date: 2011-07-18 15:09:49 summary: Trackster: show 'Add Datasets' button when there are no tracks in a visualization. Refactor and modularize add tracks code so that is can be used in multiple places. affected #: 5 files (1.6 KB) --- a/static/june_2007_style/blue/trackster.css Fri Jul 15 10:33:02 2011 -0400 +++ b/static/june_2007_style/blue/trackster.css Mon Jul 18 15:09:49 2011 +0200 @@ -54,3 +54,5 @@ .icon{display:inline-block;width:16px;height:16px;} .icon.more-down{background:url('../images/fugue/arrow-transition-270-bw.png') no-repeat 0px 0px;} .icon.more-across{background:url('../images/fugue/arrow-transition-bw.png') no-repeat 0px 0px;} +.intro{padding:1em;} +.intro>.action-button{background-color:#CCC;padding:1em;} \ No newline at end of file --- a/static/june_2007_style/trackster.css.tmpl Fri Jul 15 10:33:02 2011 -0400 +++ b/static/june_2007_style/trackster.css.tmpl Mon Jul 18 15:09:49 2011 +0200 @@ -301,8 +301,14 @@ .icon.more-down { background:url('../images/fugue/arrow-transition-270-bw.png') no-repeat 0px 0px; } -.icon.more-across{ - background:url('../images/fugue/arrow-transition-bw.png') no-repeat 0px 0px; +.icon.more-across { + background: url('../images/fugue/arrow-transition-bw.png') no-repeat 0px 0px; +} +.intro { + padding: 1em; +} +.intro > .action-button { + background-color: #CCC; + padding: 1em; } - --- a/static/scripts/packed/trackster.js Fri Jul 15 10:33:02 2011 -0400 +++ b/static/scripts/packed/trackster.js Mon Jul 18 15:09:49 2011 +0200 @@ -1,1 +1,1 @@ -var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};a.extend=c};var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var trackster_module=function(f,T){var n=f("class").extend,p=f("slotting"),I=f("painters");var Z=function(aa,ab){this.document=aa;this.default_font=ab!==undefined?ab:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};n(Z.prototype,{load_pattern:function(aa,ae){var ab=this.patterns,ac=this.dummy_context,ad=new Image();ad.src=image_path+ae;ad.onload=function(){ab[aa]=ac.createPattern(ad,"repeat")}},get_pattern:function(aa){return this.patterns[aa]},new_canvas:function(){var aa=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(aa)}aa.manager=this;return aa}});var C=function(aa,ab){aa.bind("drag",{handle:ab,relative:true},function(af,ag){var ae=$(this).parent();var ad=ae.children();var ac;for(ac=0;ac<ad.length;ac++){if(ag.offsetY<$(ad.get(ac)).position().top){break}}if(ac===ad.length){if(this!==ad.get(ac-1)){ae.append(this)}}else{if(this!==ad.get(ac)){$(this).insertBefore(ad.get(ac))}}}).bind("dragstart",function(){$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css("border","0px")})};T.sortable=C;var D=9,A=18,O=D+2,w=100,F=12000,M=200,z=5,s=10,H=5000,t=100,m="There was an error in indexing this dataset. ",G="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",B="No data for this chrom/contig.",q="Currently indexing... please wait",v="Tool cannot be rerun: ",a="Loading data...",U="Ready for display",d=10,r=5,y=5;function u(aa){return Math.round(aa*1000)/1000}var c=function(aa){this.num_elements=aa;this.clear()};n(c.prototype,{get:function(ab){var aa=this.key_ary.indexOf(ab);if(aa!==-1){if(this.obj_cache[ab].stale){this.key_ary.splice(aa,1);delete this.obj_cache[ab]}else{this.move_key_to_end(ab,aa)}}return this.obj_cache[ab]},set:function(ab,ac){if(!this.obj_cache[ab]){if(this.key_ary.length>=this.num_elements){var aa=this.key_ary.shift();delete this.obj_cache[aa]}this.key_ary.push(ab)}this.obj_cache[ab]=ac;return ac},move_key_to_end:function(ab,aa){this.key_ary.splice(aa,1);this.key_ary.push(ab)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var N=function(ab,aa,ac){c.call(this,ab);this.track=aa;this.subset=(ac!==undefined?ac:true)};n(N.prototype,c.prototype,{load_data:function(aj,ae,ab,ag){var ai=this.track.view.chrom,ah=this.track.mode,ad={chrom:ai,low:aj,high:ae,mode:ah,resolution:ab,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ad,ag);if(this.track.filters_manager){var ak=[];var aa=this.track.filters_manager.filters;for(var af=0;af<aa.length;af++){ak[ak.length]=aa[af].name}ad.filter_cols=JSON.stringify(ak)}var ac=this;return $.getJSON(this.track.data_url,ad,function(al){ac.set_data(aj,ae,ah,al)})},get_data:function(aa,ae,ab,ad){var af=this.track.mode,ac=this.get_data_from_cache(aa,ae,af);if(ac){return ac}ac=this.load_data(aa,ae,ab,ad);this.set_data(aa,ae,af,ac);return ac},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(ah,ac,ab,af,ad){var ag=this.track.mode,ai=this.get_data_from_cache(ah,ac,ag);if(!ai){console.log("ERROR: no current data for: ",this.track,ah,ac,ab,af);return}ai.stale=true;if(ad===this.DEEP_DATA_REQ){$.extend(af,{start_val:ai.data.length+1})}else{if(ad===this.BROAD_DATA_REQ){ah=ai.data[ai.length-1][2]+1}}var aa=this,ae=this.load_data(ah,ac,ab,af);new_data_available=$.Deferred();this.set_data(ah,ac,ag,new_data_available);$.when(ae).then(function(aj){if(aj.data){aj.data=ai.data.concat(aj.data)}aa.set_data(ah,ac,ag,aj);new_data_available.resolve(aj)});return new_data_available},get_data_from_cache:function(aa,ab,ac){return this.get(this.gen_key(aa,ab,ac))},set_data:function(ab,ac,ad,aa){return this.set(this.gen_key(ab,ac,ad),aa)},gen_key:function(aa,ac,ad){var ab=aa+"_"+ac+"_"+ad;return ab},split_key:function(aa){return aa.split("_")}});var E=function(ab,aa,ac){N.call(this,ab,aa,ac)};n(E.prototype,N.prototype,c.prototype,{load_data:function(ac,aa,ae,af,ab,ad){if(ab>1){return}return N.prototype.load_data.call(this,ac,aa,ae,af,ab,ad)}});var Y=function(aa,ad,ac,ab,ae){this.container=aa;this.chrom=null;this.vis_id=ac;this.dbkey=ab;this.title=ad;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(ae);this.canvas_manager=new Z(aa.get(0).ownerDocument);this.reset()};n(Y.prototype,{init:function(ad){var ac=this.container,aa=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ac);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ac);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ac);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ab=function(ae){if(ae.type==="focusout"||(ae.keyCode||ae.which)===13||(ae.keyCode||ae.which)===27){if((ae.keyCode||ae.which)!==27){aa.go_to($(this).val())}$(this).hide();$(this).val("");aa.location_span.show();aa.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ab).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.bind("click",function(){aa.location_span.hide();aa.chrom_select.hide();aa.nav_input.val(aa.chrom+":"+aa.low+"-"+aa.high);aa.nav_input.css("display","inline-block");aa.nav_input.select();aa.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){aa.zoom_out();aa.redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){aa.zoom_in();aa.redraw()}).appendTo(this.nav_controls);this.load_chroms({low:0},ad);this.chrom_select.bind("change",function(){aa.change_chrom(aa.chrom_select.val())});this.intro_div.show();this.content_div.bind("click",function(ae){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(ae){aa.zoom_in(ae.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ae,af){this.current_x=af.offsetX}).bind("drag",function(ae,ag){var ah=ag.offsetX-this.current_x;this.current_x=ag.offsetX;var af=Math.round(ah/aa.viewport_container.width()*(aa.max_high-aa.max_low));aa.move_delta(-af)});this.overview_close.bind("click",function(){for(var af=0,ae=aa.tracks.length;af<ae;af++){aa.tracks[af].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",aa.overview_box.height());aa.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("draginit",function(ae,af){if(ae.clientX>aa.viewport_container.width()-16){return false}}).bind("dragstart",function(ae,af){af.original_low=aa.low;af.current_height=ae.clientY;af.current_x=af.offsetX}).bind("drag",function(ag,ai){var ae=$(this);var aj=ai.offsetX-ai.current_x;var af=ae.scrollTop()-(ag.clientY-ai.current_height);ae.scrollTop(af);ai.current_height=ag.clientY;ai.current_x=ai.offsetX;var ah=Math.round(aj/aa.viewport_container.width()*(aa.high-aa.low));aa.move_delta(ah)}).bind("mousewheel",function(ag,ai,af,ae){if(af){var ah=Math.round(-af/aa.viewport_container.width()*(aa.high-aa.low));aa.move_delta(ah)}});this.top_labeltrack.bind("dragstart",function(ae,af){return $("<div />").css({height:aa.content_div.height()+aa.top_labeltrack.height()+aa.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ai,aj){$(aj.proxy).css({left:Math.min(ai.pageX,aj.startX),width:Math.abs(ai.pageX-aj.startX)});var af=Math.min(ai.pageX,aj.startX)-aa.container.offset().left,ae=Math.max(ai.pageX,aj.startX)-aa.container.offset().left,ah=(aa.high-aa.low),ag=aa.viewport_container.width();aa.update_location(Math.round(af/ag*ah)+aa.low,Math.round(ae/ag*ah)+aa.low)}).bind("dragend",function(aj,ak){var af=Math.min(aj.pageX,ak.startX),ae=Math.max(aj.pageX,ak.startX),ah=(aa.high-aa.low),ag=aa.viewport_container.width(),ai=aa.low;aa.low=Math.round(af/ag*ah)+ai;aa.high=Math.round(ae/ag*ah)+ai;$(ak.proxy).remove();aa.redraw()});this.add_label_track(new X(this,this.top_labeltrack));this.add_label_track(new X(this,this.nav_labeltrack));$(window).bind("resize",function(){aa.resize_window()});$(document).bind("redraw",function(){aa.redraw()});this.reset();$(window).trigger("resize")},update_location:function(aa,ab){this.location_span.text(commatize(aa)+" - "+commatize(ab));this.nav_input.val(this.chrom+":"+commatize(aa)+"-"+commatize(ab))},load_chroms:function(ab,ac){ab.num=t;$.extend(ab,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var aa=this;$.ajax({url:chrom_url,data:ab,dataType:"json",success:function(ae){if(ae.chrom_info.length===0){alert("Invalid chromosome: "+ab.chrom);return}if(ae.reference){aa.add_label_track(new x(aa))}aa.chrom_data=ae.chrom_info;var ah='<option value="">Select Chrom/Contig</option>';for(var ag=0,ad=aa.chrom_data.length;ag<ad;ag++){var af=aa.chrom_data[ag].chrom;ah+='<option value="'+af+'">'+af+"</option>"}if(ae.prev_chroms){ah+='<option value="previous">Previous '+t+"</option>"}if(ae.next_chroms){ah+='<option value="next">Next '+t+"</option>"}aa.chrom_select.html(ah);if(ac){ac()}aa.chrom_start_index=ae.start_index},error:function(){alert("Could not load chroms for this dbkey:",aa.dbkey)}})},change_chrom:function(ae,ab,ag){if(!ae||ae==="None"){return}var ad=this;if(ae==="previous"){ad.load_chroms({low:this.chrom_start_index-t});return}if(ae==="next"){ad.load_chroms({low:this.chrom_start_index+t});return}var af=$.grep(ad.chrom_data,function(ai,aj){return ai.chrom===ae})[0];if(af===undefined){ad.load_chroms({chrom:ae},function(){ad.change_chrom(ae,ab,ag)});return}else{if(ae!==ad.chrom){ad.chrom=ae;if(!ad.chrom){ad.intro_div.show()}else{ad.intro_div.hide()}ad.chrom_select.val(ad.chrom);ad.max_high=af.len-1;ad.reset();ad.redraw(true);for(var ah=0,aa=ad.tracks.length;ah<aa;ah++){var ac=ad.tracks[ah];if(ac.init){ac.init()}}}if(ab!==undefined&&ag!==undefined){ad.low=Math.max(ab,0);ad.high=Math.min(ag,ad.max_high)}ad.reset_overview();ad.redraw()}},go_to:function(ae){var ai=this,aa,ad,ab=ae.split(":"),ag=ab[0],ah=ab[1];if(ah!==undefined){try{var af=ah.split("-");aa=parseInt(af[0].replace(/,/g,""),10);ad=parseInt(af[1].replace(/,/g,""),10)}catch(ac){return false}}ai.change_chrom(ag,aa,ad)},move_fraction:function(ac){var aa=this;var ab=aa.high-aa.low;this.move_delta(ac*ab)},move_delta:function(ac){var aa=this;var ab=aa.high-aa.low;if(aa.low-ac<aa.max_low){aa.low=aa.max_low;aa.high=aa.max_low+ab}else{if(aa.high-ac>aa.max_high){aa.high=aa.max_high;aa.low=aa.max_high-ab}else{aa.high-=ac;aa.low-=ac}}aa.redraw()},add_track:function(aa){aa.view=this;aa.track_id=this.track_id_counter;this.tracks.push(aa);if(aa.init){aa.init()}aa.container_div.attr("id","track_"+aa.track_id);C(aa.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(aa){aa.view=this;this.label_tracks.push(aa)},remove_track:function(aa){this.has_changes=true;aa.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(aa)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(ah){var ag=this.high-this.low,af=this.low,ab=this.high;if(af<this.max_low){af=this.max_low}if(ab>this.max_high){ab=this.max_high}if(this.high!==0&&ag<this.min_separation){ab=af+this.min_separation}this.low=Math.floor(af);this.high=Math.ceil(ab);this.resolution=Math.pow(z,Math.ceil(Math.log((this.high-this.low)/M)/Math.log(z)));this.zoom_res=Math.pow(s,Math.max(0,Math.ceil(Math.log(this.resolution,s)/Math.log(s))));var aa=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ae=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ai=13;this.overview_box.css({left:aa,width:Math.max(ai,ae)}).show();if(ae<ai){this.overview_box.css("left",aa-(ai-ae)/2)}if(this.overview_highlight){this.overview_highlight.css({left:aa,width:ae})}this.update_location(this.low,this.high);if(!ah){for(var ac=0,ad=this.tracks.length;ac<ad;ac++){if(this.tracks[ac]&&this.tracks[ac].enabled){this.tracks[ac].draw()}}for(ac=0,ad=this.label_tracks.length;ac<ad;ac++){this.label_tracks[ac].draw()}}},zoom_in:function(ab,ac){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ad=this.high-this.low,ae=ad/2+this.low,aa=(ad/this.zoom_factor)/2;if(ab){ae=ab/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ae-aa);this.high=Math.round(ae+aa);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var ab=this.high-this.low,ac=ab/2+this.low,aa=(ab*this.zoom_factor)/2;this.low=Math.round(ac-aa);this.high=Math.round(ac+aa);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide()}});var o=function(ac,ag){this.track=ac;this.name=ag.name;this.params=[];var an=ag.params;for(var ad=0;ad<an.length;ad++){var ai=an[ad],ab=ai.name,am=ai.label,ae=unescape(ai.html),ao=ai.value,ak=ai.type;if(ak==="number"){this.params[this.params.length]=new g(ab,am,ae,ao,ai.min,ai.max)}else{if(ak=="select"){this.params[this.params.length]=new K(ab,am,ae,ao)}else{console.log("WARNING: unrecognized tool parameter type:",ab,ak)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(aq){aq.stopPropagation()}).bind("click",function(aq){aq.stopPropagation()}).bind("dblclick",function(aq){aq.stopPropagation()});var al=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var aj=this.params;var ah=this;$.each(this.params,function(ar,av){var au=$("<div>").addClass("param-row").appendTo(ah.parent_div);var aq=$("<div>").addClass("param-label").text(av.label).appendTo(au);var at=$("<div/>").addClass("slider").html(av.html).appendTo(au);at.find(":input").val(av.value);$("<div style='clear: both;'/>").appendTo(au)});this.parent_div.find("input").click(function(){$(this).select()});var ap=$("<div>").addClass("param-row").appendTo(this.parent_div);var af=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ap);var aa=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ap);var ah=this;aa.click(function(){ah.run_on_region()});af.click(function(){ah.run_on_dataset()})};n(o.prototype,{get_param_values_dict:function(){var aa={};this.parent_div.find(":input").each(function(){var ab=$(this).attr("name"),ac=$(this).val();aa[ab]=JSON.stringify(ac)});return aa},get_param_values:function(){var ab=[];var aa={};this.parent_div.find(":input").each(function(){var ac=$(this).attr("name"),ad=$(this).val();if(ac){ab[ab.length]=ad}});return ab},run_on_dataset:function(){var aa=this;aa.run({dataset_id:this.track.original_dataset_id,tool_id:aa.name},function(ab){show_modal(aa.name+" is Running",aa.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var aa={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},ac=this.track,ab=aa.tool_id+ac.tool_region_and_parameters_str(aa.chrom,aa.low,aa.high),ad;if(ac instanceof e){ad=new Q(ab,view,ac.hda_ldda,undefined,{},{},ac);ad.change_mode(ac.mode)}this.track.add_track(ad);ad.content_div.text("Starting job.");this.run(aa,function(ae){ad.dataset_id=ae.dataset_id;ad.content_div.text("Running job.");ad.init()})},run:function(ab,ac){$.extend(ab,this.get_param_values_dict());var aa=function(){$.getJSON(rerun_tool_url,ab,function(ad){if(ad==="no converter"){new_track.container_div.addClass("error");new_track.content_div.text(G)}else{if(ad.error){new_track.container_div.addClass("error");new_track.content_div.text(v+ad.message)}else{if(ad==="pending"){new_track.container_div.addClass("pending");new_track.content_div.text("Converting input data so that it can be easily reused.");setTimeout(aa,2000)}else{ac(ad)}}}})};aa()}});var K=function(ab,aa,ac,ad){this.name=ab;this.label=aa;this.html=ac;this.value=ad};var g=function(ac,ab,ae,af,ad,aa){K.call(this,ac,ab,ae,af);this.min=ad;this.max=aa};var h=function(ab,aa,ac,ad){this.name=ab;this.index=aa;this.tool_id=ac;this.tool_exp_name=ad};var R=function(ab,aa,ac,ad){h.call(this,ab,aa,ac,ad);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};n(R.prototype,{applies_to:function(aa){if(aa.length>this.index){return true}return false},keep:function(aa){if(!this.applies_to(aa)){return true}var ab=parseInt(aa[this.index]);return(isNaN(ab)||(ab>=this.low&&ab<=this.high))},update_attrs:function(ab){var aa=false;if(!this.applies_to(ab)){return aa}if(ab[this.index]<this.min){this.min=Math.floor(ab[this.index]);aa=true}if(ab[this.index]>this.max){this.max=Math.ceil(ab[this.index]);aa=true}return aa},update_ui_elt:function(){var ac=function(af,ad){var ae=ad-af;return(ae<=2?0.01:1)};var ab=this.slider.slider("option","min"),aa=this.slider.slider("option","max");if(this.min<ab||this.max>aa){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",ac(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var W=function(ac,al){this.track=ac;this.filters=[];for(var ag=0;ag<al.length;ag++){var aa=al[ag],ab=aa.name,ak=aa.type,ai=aa.index,an=aa.tool_id,ad=aa.tool_exp_name;if(ak==="int"||ak==="float"){this.filters[ag]=new R(ab,ai,an,ad)}else{console.log("ERROR: unsupported filter: ",ab,ak)}}var aj=function(ao,ap,aq){ao.click(function(){var ar=ap.text();max=parseFloat(aq.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aq.slider("option","values")){input_size=2*input_size+1;multi_value=true}ap.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",ar).appendTo(ap).focus().select().click(function(at){at.stopPropagation()}).blur(function(){$(this).remove();ap.text(ar)}).keyup(function(ax){if(ax.keyCode===27){$(this).trigger("blur")}else{if(ax.keyCode===13){var av=aq.slider("option","min"),at=aq.slider("option","max"),aw=function(ay){return(isNaN(ay)||ay>at||ay<av)},au=$(this).val();if(!multi_value){au=parseFloat(au);if(aw(au)){alert("Parameter value must be in the range ["+av+"-"+at+"]");return $(this)}}else{au=au.split("-");au=[parseFloat(au[0]),parseFloat(au[1])];if(aw(au[0])||aw(au[1])){alert("Parameter value must be in the range ["+av+"-"+at+"]");return $(this)}}aq.slider((multi_value?"values":"value"),au)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(ao){ao.stopPropagation()}).bind("click",function(ao){ao.stopPropagation()}).bind("dblclick",function(ao){ao.stopPropagation()}).bind("keydown",function(ao){ao.stopPropagation()});var ae=this;$.each(this.filters,function(av,ap){var ar=$("<div/>").addClass("slider-row").appendTo(ae.parent_div);var ao=$("<div/>").addClass("slider-label").appendTo(ar);var ax=$("<span/>").addClass("slider-name").text(ap.name+" ").appendTo(ao);var aq=$("<span/>");var at=$("<span/>").addClass("slider-value").appendTo(ao).append("[").append(aq).append("]");var aw=$("<div/>").addClass("slider").appendTo(ar);ap.control_element=$("<div/>").attr("id",ap.name+"-filter-control").appendTo(aw);var au=[0,0];ap.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(ay,az){au=az.values;aq.text(az.values[0]+"-"+az.values[1]);setTimeout(function(){if(az.values[0]==au[0]&&az.values[1]==au[1]){var aA=az.values;aq.text(aA[0]+"-"+aA[1]);ap.low=aA[0];ap.high=aA[1];ae.track.draw(true,true)}},50)},change:function(ay,az){ap.control_element.slider("option","slide").call(ap.control_element,ay,az)}});ap.slider=ap.control_element;ap.slider_label=aq;aj(at,aq,ap.control_element);$("<div style='clear: both;'/>").appendTo(ar)});if(this.filters.length!=0){var am=$("<div>").addClass("param-row").appendTo(this.parent_div);var ah=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(am);var af=this;ah.click(function(){af.run_on_dataset()})}};n(W.prototype,{reset_filters:function(){for(var aa=0;aa<this.filters.length;aa++){filter=this.filters[aa];filter.slider.slider("option","values",[filter.min,filter.max])}},run_on_dataset:function(){var ai=function(am,ak,al){if(!(ak in am)){am[ak]=al}return am[ak]};var ac={},aa,ab,ad;for(var ae=0;ae<this.filters.length;ae++){aa=this.filters[ae];if(aa.tool_id){if(aa.min!=aa.low){ab=ai(ac,aa.tool_id,[]);ab[ab.length]=aa.tool_exp_name+" >= "+aa.low}if(aa.max!=aa.high){ab=ai(ac,aa.tool_id,[]);ab[ab.length]=aa.tool_exp_name+" <= "+aa.high}}}var ag=[];for(var aj in ac){ag[ag.length]=[aj,ac[aj]]}var ah=ag.length;(function af(aq,an){var al=an[0],am=al[0],ap=al[1],ao="("+ap.join(") and (")+")",ak={cond:ao,input:aq,target_dataset_id:aq,tool_id:am},an=an.slice(1);$.getJSON(run_tool_url,ak,function(ar){if(ar.error){show_modal("Filter Dataset","Error running tool "+am,{Close:hide_modal})}else{if(an.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{af(ar.dataset_id,an)}}})})(this.track.dataset_id,ag)}});var V=function(aa){this.track=aa.track;this.params=aa.params;this.values={};if(aa.saved_values){this.restore_values(aa.saved_values)}this.onchange=aa.onchange};n(V.prototype,{restore_values:function(aa){var ab=this;$.each(this.params,function(ac,ad){if(aa[ad.key]!==undefined){ab.values[ad.key]=aa[ad.key]}else{ab.values[ad.key]=ad.default_value}})},build_form:function(){var ab=this;var aa=$("<div />");$.each(this.params,function(af,ad){if(!ad.hidden){var ac="param_"+af;var ak=$("<div class='form-row' />").appendTo(aa);ak.append($("<label />").attr("for",ac).text(ad.label+":"));if(ad.type==="bool"){ak.append($('<input type="checkbox" />').attr("id",ac).attr("name",ac).attr("checked",ab.values[ad.key]))}else{if(ad.type==="color"){var ah=ab.values[ad.key];var ag=$("<input />").attr("id",ac).attr("name",ac).val(ah);var ai=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var ae=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ai);var aj=$("<div/>").appendTo(ae).farbtastic({width:100,height:100,callback:ag,color:ah});$("<div />").append(ag).append(ai).appendTo(ak).bind("click",function(al){ai.css({left:$(this).position().left+($(ag).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ai.hide();$(document).unbind("click.color-picker")});al.stopPropagation()})}else{ak.append($("<input />").attr("id",ac).attr("name",ac).val(ab.values[ad.key]))}}}});return aa},update_from_form:function(aa){var ac=this;var ab=false;$.each(this.params,function(ad,af){if(!af.hidden){var ag="param_"+ad;var ae=aa.find("#"+ag).val();if(af.type==="float"){ae=parseFloat(ae)}else{if(af.type==="int"){ae=parseInt(ae)}else{if(af.type==="bool"){ae=aa.find("#"+ag).is(":checked")}}}if(ae!==ac.values[af.key]){ac.values[af.key]=ae;ab=true}}});if(ab){this.onchange()}}});var b=function(ac,ab,aa){this.index=ac;this.low=ac*M*ab;this.high=(ac+1)*M*ab;this.resolution=ab;this.canvas=$("<div class='track-tile'/>").append(aa);this.stale=false};var l=function(ac,ab,aa,ad){b.call(this,ac,ab,aa);this.max_val=ad};var L=function(ac,ab,aa,ad){b.call(this,ac,ab,aa);this.message=ad};var j=function(ab,aa,ae,ac,ad){this.name=ab;this.view=aa;this.parent_element=ae;this.data_url=(ac?ac:default_data_url);this.data_url_extra_params={};this.data_query_wait=(ad?ad:H);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};n(j.prototype,{get_type:function(){if(this instanceof X){return"LabelTrack"}else{if(this instanceof x){return"ReferenceTrack"}else{if(this instanceof k){return"LineTrack"}else{if(this instanceof S){return"ReadTrack"}else{if(this instanceof Q){return"ToolDataFeatureTrack"}else{if(this instanceof P){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var aa=this;aa.enabled=false;aa.tile_cache.clear();aa.data_manager.clear();aa.initial_canvas=undefined;aa.content_div.css("height","auto");aa.container_div.removeClass("nodata error pending");if(!aa.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:aa.hda_ldda,dataset_id:aa.dataset_id,chrom:aa.view.chrom},function(ab){if(!ab||ab==="error"||ab.kind==="error"){aa.container_div.addClass("error");aa.content_div.text(m);if(ab.message){var ad=aa.view.tracks.indexOf(aa);var ac=$(" <a href='javascript:void(0);'></a>").text("View error").bind("click",function(){show_modal("Trackster Error","<pre>"+ab.message+"</pre>",{Close:hide_modal})});aa.content_div.append(ac)}}else{if(ab==="no converter"){aa.container_div.addClass("error");aa.content_div.text(G)}else{if(ab==="no data"||(ab.data!==undefined&&(ab.data===null||ab.data.length===0))){aa.container_div.addClass("nodata");aa.content_div.text(B)}else{if(ab==="pending"){aa.container_div.addClass("pending");aa.content_div.text(q);setTimeout(function(){aa.init()},aa.data_query_wait)}else{if(ab.status==="data"){if(ab.valid_chroms){aa.valid_chroms=ab.valid_chroms;aa.make_name_popup_menu()}aa.content_div.text(U);if(aa.view.chrom){aa.content_div.text("");aa.content_div.css("height",aa.height_px+"px");aa.enabled=true;$.when(aa.predraw_init()).done(function(){aa.container_div.removeClass("nodata error pending");aa.draw()})}}}}}}})},predraw_init:function(){},update_name:function(aa){this.old_name=this.name;this.name=aa;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var J=function(ah,af,ai){var ab=this,aj=ab.view;this.filters_manager=(ah!==undefined?new W(this,ah):undefined);this.filters_available=false;this.filters_visible=false;this.tool=(af!==undefined&&obj_length(af)>0?new o(this,af):undefined);this.parent_track=ai;this.child_tracks=[];if(ab.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}ab.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();ab.container_div.append(ab.child_tracks_container);if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}if(ab.display_modes!==undefined){if(ab.mode_div===undefined){ab.mode_div=$("<div class='right-float menubutton popup' />").appendTo(ab.header_div);var ac=(ab.track_config&&ab.track_config.values.mode?ab.track_config.values.mode:ab.display_modes[0]);ab.mode=ac;ab.mode_div.text(ac);var aa={};for(var ad=0,ag=ab.display_modes.length;ad<ag;ad++){var ae=ab.display_modes[ad];aa[ae]=function(ak){return function(){ab.change_mode(ak)}}(ae)}make_popupmenu(ab.mode_div,aa)}else{ab.mode_div.hide()}}this.make_name_popup_menu()};n(J.prototype,j.prototype,{change_mode:function(ab){var aa=this;aa.mode_div.text(ab);aa.mode=ab;aa.track_config.values.mode=ab;aa.tile_cache.clear();aa.draw()},make_name_popup_menu:function(){var ab=this;var aa={};aa["Edit configuration"]=function(){var ah=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},af=function(){ab.track_config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){af()}}};$(window).bind("keypress.check_enter_esc",ag);show_modal("Configure Track",ab.track_config.build_form(),{Cancel:ah,OK:af})};if(ab.filters_available>0){var ae=(ab.filters_div.is(":visible")?"Hide filters":"Show filters");aa[ae]=function(){ab.filters_visible=(ab.filters_div.is(":visible"));if(ab.filters_visible){ab.filters_manager.reset_filters()}ab.filters_div.toggle();ab.make_name_popup_menu()}}if(ab.tool){var ae=(ab.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");aa[ae]=function(){if(!ab.dynamic_tool_div.is(":visible")){ab.update_name(ab.name+ab.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";ab.revert_name()}ab.dynamic_tool_div.toggle();ab.make_name_popup_menu()}}if(ab.valid_chroms){aa["List chrom/contigs with data"]=function(){show_modal("Chrom/contigs with data","<p>"+ab.valid_chroms.join("<br/>")+"</p>",{Close:function(){hide_modal()}})}}var ac=view;var ad=function(){$("#no-tracks").show()};if(this.parent_track){ac=this.parent_track;ad=function(){}}aa.Remove=function(){ac.remove_track(ab);if(ac.num_tracks===0){ad()}};make_popupmenu(ab.name_div,aa)},draw:function(aa,ac){if(!this.dataset_id){return}var au=this.view.low,ag=this.view.high,ai=ag-au,ak=this.view.container.width(),ae=ak/ai,al=this.view.resolution,ad=$("<div style='position: relative;'></div>"),am=function(aw,ax,av){return aw+"_"+ax+"_"+av};if(!ac){this.content_div.children().remove()}this.content_div.append(ad);this.max_height=0;var ao=Math.floor(au/al/M);var af=[];var ap=0;while((ao*M*al)<ag){var at=am(ak,ae,ao);var ah=this.tile_cache.get(at);var aq=ao*M*this.view.resolution;var ab=aq+M*this.view.resolution;if(!aa&&ah){af[af.length]=ah;this.show_tile(ah,ad,ae)}else{this.delayed_draw(aa,at,ao,al,ad,ae,af)}ao+=1;ap++}var aj=this;var ar=setInterval(function(){if(af.length===ap){clearInterval(ar);if(ac){var aA=aj.content_div.children();var aB=false;for(var az=aA.length-1,aF=0;az>=aF;az--){var ay=$(aA[az]);if(aB){ay.remove()}else{if(ay.children().length!==0){aB=true}}}}if(aj instanceof e&&aj.mode=="Histogram"){var aE=-1;for(var az=0;az<af.length;az++){var aH=af[az].max_val;if(aH>aE){aE=aH}}for(var az=0;az<af.length;az++){if(af[az].max_val!==aE){var aG=af[az];aG.canvas.remove();aj.delayed_draw(true,am(ak,ae,aG.index),aG.index,aG.resolution,ad,ae,[],{max:aE})}}}if(aj.filters_manager){var ax=aj.filters_manager.filters;for(var aD=0;aD<ax.length;aD++){ax[aD].update_ui_elt()}var aC=false;if(aj.example_feature){for(var aD=0;aD<ax.length;aD++){if(ax[aD].applies_to(aj.example_feature)){aC=true;break}}}if(aj.filters_available!==aC){aj.filters_available=aC;if(!aj.filters_available){aj.filters_div.hide()}aj.make_name_popup_menu()}}var av=false;for(var aw=0;aw<af.length;aw++){if(af[aw].message){av=true;break}}if(av){for(var aw=0;aw<af.length;aw++){aG=af[aw];if(!aG.message){aG.canvas.css("padding-top",A)}}}}},50);for(var an=0;an<this.child_tracks.length;an++){this.child_tracks[an].draw(aa,ac)}},delayed_draw:function(ab,ai,ac,ae,aj,am,ak,af){var ad=this,ag=ac*M*ae,al=ag+M*ae;var ah=function(av,an,ap,ao,at,au,aq){var ar=ad.draw_tile(an,ap,ao,au,aq);ad.tile_cache.set(ai,ar);if(ar===undefined){return}ad.show_tile(ar,at,au);ak[ak.length]=ar};var aa=setTimeout(function(){if(ag<=ad.view.high&&al>=ad.view.low){var an=(ab?undefined:ad.tile_cache.get(ai));if(an){ad.show_tile(an,aj,am);ak[ak.length]=an}else{$.when(ad.data_manager.get_data(ag,al,ae,ad.data_url_extra_params)).then(function(ao){n(ao,af);if(view.reference_track&&am>view.canvas_manager.char_width_px){$.when(view.reference_track.data_manager.get_data(ag,al,ae,view.reference_track.data_url_extra_params)).then(function(ap){ah(aa,ao,ae,ac,aj,am,ap)})}else{ah(aa,ao,ae,ac,aj,am)}})}}},50)},show_tile:function(ag,ai,aj){var ab=this,aa=ag.canvas,ae=aa;if(ag.message){var ak=$("<div/>"),ah=$("<div/>").addClass("tile-message").text(ag.message).css({height:A-1,width:ag.canvas.width}).appendTo(ak),af=$("<div/>").text("Show more").addClass("action-button").css({"padding-top":0,"padding-bottom":0}).appendTo(ah);ak.append(aa);ae=ak;af.click(function(){ag.stale=true;ab.data_manager.get_more_data(ag.low,ag.high,ag.resolution,{},ab.data_manager.DEEP_DATA_REQ);ab.draw()}).dblclick(function(al){al.stopPropagation()})}var ad=this.view.high-this.view.low,ac=(ag.low-this.view.low)*aj;if(this.left_offset){ac-=this.left_offset}ae.css({position:"absolute",top:0,left:ac,height:""});ai.append(ae);ab.max_height=Math.max(ab.max_height,ae.height());ab.content_div.css("height",ab.max_height+"px");ai.children().css("height",ab.max_height+"px")},set_overview:function(){var aa=this.view;if(this.initial_canvas&&this.is_overview){aa.overview_close.show();aa.overview_viewport.append(this.initial_canvas);aa.overview_highlight.show().height(this.initial_canvas.height());aa.overview_viewport.height(this.initial_canvas.height()+aa.overview_box.height())}$(window).trigger("resize")},tool_region_and_parameters_str:function(ac,aa,ad){var ab=this,ae=(ac!==undefined&&aa!==undefined&&ad!==undefined?ac+":"+aa+"-"+ad:"all");return" - region=["+ae+"], parameters=["+ab.tool.get_param_values().join(", ")+"]"},add_track:function(aa){aa.track_id=this.track_id+"_"+this.child_tracks.length;aa.container_div.attr("id","track_"+aa.track_id);this.child_tracks_container.append(aa.container_div);C(aa.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(aa);this.view.has_changes=true},remove_track:function(aa){aa.container_div.fadeOut("slow",function(){$(this).remove()})}});var X=function(aa,ab){this.hidden=true;j.call(this,null,aa,ab);this.container_div.addClass("label-track")};n(X.prototype,j.prototype,{draw:function(){var ac=this.view,ad=ac.high-ac.low,ag=Math.floor(Math.pow(10,Math.floor(Math.log(ad)/Math.log(10)))),aa=Math.floor(ac.low/ag)*ag,ae=this.view.container.width(),ab=$("<div style='position: relative; height: 1.3em;'></div>");while(aa<ac.high){var af=(aa-ac.low)/ad*ae;ab.append($("<div class='label'>"+commatize(aa)+"</div>").css({position:"absolute",left:af-1}));aa+=ag}this.content_div.children(":first").remove();this.content_div.append(ab)}});var x=function(aa){this.hidden=true;j.call(this,null,aa,aa.top_labeltrack);J.call(this);aa.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:aa.dbkey};this.data_manager=new E(y,this,false);this.tile_cache=new c(r)};n(x.prototype,J.prototype,{draw_tile:function(ai,af,ab,ak){var ae=this,ac=M*af;if(ak>this.view.canvas_manager.char_width_px){if(ai===null){ae.content_div.css("height","0px");return}var ad=this.view.canvas_manager.new_canvas();var aj=ad.getContext("2d");ad.width=Math.ceil(ac*ak+ae.left_offset);ad.height=ae.height_px;aj.font=aj.canvas.manager.default_font;aj.textAlign="center";for(var ag=0,ah=ai.length;ag<ah;ag++){var aa=Math.round(ag*ak);aj.fillText(ai[ag],aa+ae.left_offset,10)}return new b(ab,af,ad)}this.content_div.css("height","0px")}});var k=function(ae,ac,af,aa,ad){var ab=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";j.call(this,ae,ac,ac.viewport_container);J.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=af;this.dataset_id=aa;this.original_dataset_id=aa;this.data_manager=new N(y,this);this.tile_cache=new c(r);this.track_config=new V({track:this,params:[{key:"color",label:"Color",type:"color",default_value:"black"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:ad,onchange:function(){ab.vertical_range=ab.prefs.max_value-ab.prefs.min_value;$("#linetrack_"+ab.track_id+"_minval").text(ab.prefs.min_value);$("#linetrack_"+ab.track_id+"_maxval").text(ab.prefs.max_value);ab.tile_cache.clear();ab.draw()}});this.prefs=this.track_config.values;this.height_px=this.track_config.values.height;this.vertical_range=this.track_config.values.max_value-this.track_config.values.min_value;this.add_resize_handle()};n(k.prototype,J.prototype,{add_resize_handle:function(){var aa=this;var ad=false;var ac=false;var ab=$("<div class='track-resize'>");$(aa.container_div).hover(function(){ad=true;ab.show()},function(){ad=false;if(!ac){ab.hide()}});ab.hide().bind("dragstart",function(ae,af){ac=true;af.original_height=$(aa.content_div).height()}).bind("drag",function(af,ag){var ae=Math.min(Math.max(ag.original_height+ag.deltaY,aa.min_height_px),aa.max_height_px);$(aa.content_div).css("height",ae);aa.height_px=ae;aa.draw(true)}).bind("dragend",function(ae,af){aa.tile_cache.clear();ac=false;if(!ad){ab.hide()}aa.track_config.values.height=aa.height_px}).appendTo(aa.container_div)},predraw_init:function(){var aa=this,ab=aa.view.tracks.indexOf(aa);aa.vertical_range=undefined;return $.getJSON(aa.data_url,{stats:true,chrom:aa.view.chrom,low:null,high:null,hda_ldda:aa.hda_ldda,dataset_id:aa.dataset_id},function(ac){aa.container_div.addClass("line-track");var ae=ac.data;if(isNaN(parseFloat(aa.prefs.min_value))||isNaN(parseFloat(aa.prefs.max_value))){aa.prefs.min_value=ae.min;aa.prefs.max_value=ae.max;$("#track_"+ab+"_minval").val(aa.prefs.min_value);$("#track_"+ab+"_maxval").val(aa.prefs.max_value)}aa.vertical_range=aa.prefs.max_value-aa.prefs.min_value;aa.total_frequency=ae.total_frequency;aa.container_div.find(".yaxislabel").remove();var af=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ab+"_minval").text(u(aa.prefs.min_value));var ad=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ab+"_maxval").text(u(aa.prefs.max_value));ad.css({position:"absolute",top:"24px",left:"10px"});ad.prependTo(aa.container_div);af.css({position:"absolute",bottom:"2px",left:"10px"});af.prependTo(aa.container_div)})},draw_tile:function(ak,ae,ab,aj){if(this.vertical_range===undefined){return}var af=ab*M*ae,ad=M*ae,aa=Math.ceil(ad*aj),ah=this.height_px;var ac=this.view.canvas_manager.new_canvas();ac.width=aa,ac.height=ah;var ai=ac.getContext("2d");var ag=new I.LinePainter(ak.data,af,af+ad,this.prefs,this.mode);ag.draw(ai,aa,ah);return new b(ab,ae,ac)}});var e=function(aa,af,ae,ai,ah,ac,ad,ag){var ab=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];this.track_config=new V({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ah,onchange:function(){ab.tile_cache.clear();ab.draw()}});this.prefs=this.track_config.values;j.call(this,aa,af,af.viewport_container);J.call(this,ac,ad,ag);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=ae;this.dataset_id=ai;this.original_dataset_id=ai;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new N(20,this);this.left_offset=200;this.painter=I.LinkedFeaturePainter};n(e.prototype,J.prototype,{update_auto_mode:function(aa){if(this.mode=="Auto"){if(aa=="no_detail"){aa="feature spans"}else{if(aa=="summary_tree"){aa="coverage histogram"}}this.mode_div.text("Auto ("+aa+")")}},incremental_slots:function(ae,ab,ad){var ac=this.view.canvas_manager.dummy_context,aa=this.inc_slots[ae];if(!aa||(aa.mode!==ad)){aa=new (p.FeatureSlotter)(ae,ad==="Pack",w,function(af){return ac.measureText(af)});aa.mode=ad;this.inc_slots[ae]=aa}return aa.slot_features(ab)},get_summary_tree_data:function(ae,ah,ac,ap){if(ap>ac-ah){ap=ac-ah}var al=Math.floor((ac-ah)/ap),ao=[],ad=0;var af=0,ag=0,ak,an=0,ai=[],am,aj;var ab=function(at,ar,au,aq){at[0]=ar+au*aq;at[1]=ar+(au+1)*aq};while(an<ap&&af!==ae.length){var aa=false;for(;an<ap&&!aa;an++){ab(ai,ah,an,al);for(ag=af;ag<ae.length;ag++){ak=ae[ag].slice(1,3);if(is_overlap(ak,ai)){aa=true;break}}if(aa){break}}data_start_index=ag;ao[ao.length]=am=[ai[0],0];for(;ag<ae.length;ag++){ak=ae[ag].slice(1,3);if(is_overlap(ak,ai)){am[1]++}else{break}}if(am[1]>ad){ad=am[1]}an++}return{max:ad,delta:al,data:ao}},draw_tile:function(an,av,az,aj,ad){var ar=this,aB=az*M*av,ab=(az+1)*M*av,ap=ab-aB,at=Math.ceil(ap*aj),aq=this.mode,aF=25,ae=this.left_offset,ao,af;if(aq==="Auto"){if(an.dataset_type==="summary_tree"){aq=an.dataset_type}else{if(an.extra_info==="no_detail"){aq="no_detail"}else{var aE=an.data;if(this.view.high-this.view.low>F){aq="Squish"}else{aq="Pack"}}}this.update_auto_mode(aq)}if(aq==="summary_tree"||aq==="Histogram"){af=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var aa=$("<div />").addClass("yaxislabel");aa.text(an.max);aa.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});aa.prependTo(this.container_div);var ac=this.view.canvas_manager.new_canvas();ac.width=at+ae;ac.height=af+O;if(an.dataset_type!="summary_tree"){var ak=this.get_summary_tree_data(an.data,aB,ab,200);if(an.max){ak.max=an.max}an=ak}var aC=new I.SummaryTreePainter(an,aB,ab,this.prefs);var au=ac.getContext("2d");au.translate(ae,O);aC.draw(au,at,af);return new l(az,av,ac,an.max)}var ao,ah=1;if(aq==="no_detail"||aq==="Squish"||aq==="Pack"){ah=this.incremental_slots(aj,an.data,aq);ao=this.inc_slots[aj].slots}var ai=[];if(an.data){var al=this.filters_manager.filters;for(var aw=0,ay=an.data.length;aw<ay;aw++){var ag=an.data[aw];var ax=false;var am;for(var aA=0,aD=al.length;aA<aD;aA++){am=al[aA];am.update_attrs(ag);if(!am.keep(ag)){ax=true;break}}if(!ax){ai.push(ag)}}}var aC=new (this.painter)(ai,aB,ab,this.prefs,aq,ad);var af=aC.get_required_height(ah);var ac=this.view.canvas_manager.new_canvas();ac.width=at+ae;ac.height=af;var au=ac.getContext("2d");au.fillStyle=this.prefs.block_color;au.font=au.canvas.manager.default_font;au.textAlign="right";this.container_div.find(".yaxislabel").remove();if(an.data){this.example_feature=(an.data.length?an.data[0]:undefined);au.translate(ae,0);aC.draw(au,at,af,ao)}return new L(az,av,ac,an.message)}});var P=function(ad,ab,af,aa,ac,ae){e.call(this,ad,ab,af,aa,ac,ae);this.painter=I.VariantPainter};n(P.prototype,J.prototype,e.prototype);var S=function(ad,ab,af,aa,ac,ae){e.call(this,ad,ab,af,aa,ac,ae);this.track_config=new V({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ac,onchange:function(){this.track.tile_cache.clear();this.track.draw()}});this.prefs=this.track_config.values;this.painter=I.ReadPainter;this.make_name_popup_menu()};n(S.prototype,J.prototype,e.prototype);var Q=function(ae,ac,ag,aa,ad,af,ab){e.call(this,ae,ac,ag,aa,ad,af,{},ab);this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};n(Q.prototype,J.prototype,e.prototype,{predraw_init:function(){var ab=this;var aa=function(){if(ab.data_manager.size()===0){setTimeout(aa,300)}else{ab.data_url=default_data_url;ab.data_query_wait=H;ab.dataset_state_url=converted_datasets_state_url;$.getJSON(ab.dataset_state_url,{dataset_id:ab.dataset_id,hda_ldda:ab.hda_ldda},function(ac){})}};aa()}});T.View=Y;T.LineTrack=k;T.FeatureTrack=e;T.ReadTrack=S};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(j,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=j;this.include_label=h;this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,s=this.slots,h=this.start_end_dct,y=[],A=[],n=0,z=this.max_rows;for(var w=0,x=m.length;w<x;w++){var l=m[w],o=l[0];if(s[o]!==undefined){n=Math.max(n,s[o]);A.push(s[o])}else{y.push(w)}}var q=function(G,H){for(var F=0;F<=z;F++){var D=false,I=h[F];if(I!==undefined){for(var C=0,E=I.length;C<E;C++){var B=I[C];if(H>B[0]&&G<B[1]){D=true;break}}}if(!D){return F}}return -1};for(var w=0,x=y.length;w<x;w++){var l=m[y[w]],o=l[0],u=l[1],f=l[2],r=l[3],g=Math.floor(u*p),k=Math.ceil(f*p),v=this.measureText(r).width,j;if(r!==undefined&&this.include_label){v+=(d+a);if(g-v>=0){g-=v;j="left"}else{k+=v;j="right"}}var t=q(g,k);if(t>=0){if(h[t]===undefined){h[t]=[]}h[t].push([g,k]);s[o]=t;n=Math.max(n,t)}else{}}return n+1}})};var painters_module=function(j,w){var t=j("class").extend;var o=function(H,z,F,y,E,C){if(C===undefined){C=4}var B=y-z;var A=E-F;var D=Math.floor(Math.sqrt(B*B+A*A)/C);var I=B/D;var G=A/D;var x;for(x=0;x<D;x++,z+=I,F+=G){if(x%2!==0){continue}H.fillRect(z,F,C,1)}};var p=function(A,z,x,D){var C=z-D/2,B=z+D/2,E=x-Math.sqrt(D*3/2);A.beginPath();A.moveTo(C,E);A.lineTo(B,E);A.lineTo(z,x);A.lineTo(C,E);A.strokeStyle=this.fillStyle;A.fill();A.stroke();A.closePath()};var m=function(z,B,x,y,A){this.data=z;this.view_start=B;this.view_end=x;this.prefs=t({},this.default_prefs,y);this.mode=A};m.prototype.default_prefs={};var u=function(z,B,x,y,A){m.call(this,z,B,x,y,A)};u.prototype.default_prefs={show_counts:false};u.prototype.draw=function(M,z,L){var E=this.view_start,O=this.view_end-this.view_start,N=z/O;var J=this.data.data,I=this.data.delta,G=this.data.max,B=L;delta_x_px=Math.ceil(I*N);M.save();for(var C=0,D=J.length;C<D;C++){var H=Math.floor((J[C][0]-E)*N);var F=J[C][1];if(!F){continue}var K=F/G*L;if(F!==0&&K<1){K=1}M.fillStyle=this.prefs.block_color;M.fillRect(H,B-K,delta_x_px,K);var A=4;if(this.prefs.show_counts&&(M.measureText(F).width+A)<delta_x_px){M.fillStyle=this.prefs.label_color;M.textAlign="center";M.fillText(F,H+(delta_x_px/2),10)}}M.restore()};var 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N.prototype.load_data.call(this,ac,aa,ae,af,ab,ad)}});var Y=function(aa,ad,ac,ab,ae){this.container=aa;this.chrom=null;this.vis_id=ac;this.dbkey=ab;this.title=ad;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(ae);this.canvas_manager=new Z(aa.get(0).ownerDocument);this.reset()};n(Y.prototype,{init:function(ae){var ac=this.container,aa=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ac);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ac);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ac);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ad=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ab=function(af){if(af.type==="focusout"||(af.keyCode||af.which)===13||(af.keyCode||af.which)===27){if((af.keyCode||af.which)!==27){aa.go_to($(this).val())}$(this).hide();$(this).val("");aa.location_span.show();aa.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ab).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.bind("click",function(){aa.location_span.hide();aa.chrom_select.hide();aa.nav_input.val(aa.chrom+":"+aa.low+"-"+aa.high);aa.nav_input.css("display","inline-block");aa.nav_input.select();aa.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){aa.zoom_out();aa.redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){aa.zoom_in();aa.redraw()}).appendTo(this.nav_controls);this.load_chroms({low:0},ae);this.chrom_select.bind("change",function(){aa.change_chrom(aa.chrom_select.val())});this.content_div.bind("click",function(af){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(af){aa.zoom_in(af.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(af,ag){this.current_x=ag.offsetX}).bind("drag",function(af,ah){var ai=ah.offsetX-this.current_x;this.current_x=ah.offsetX;var ag=Math.round(ai/aa.viewport_container.width()*(aa.max_high-aa.max_low));aa.move_delta(-ag)});this.overview_close.bind("click",function(){for(var ag=0,af=aa.tracks.length;ag<af;ag++){aa.tracks[ag].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",aa.overview_box.height());aa.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("draginit",function(af,ag){if(af.clientX>aa.viewport_container.width()-16){return false}}).bind("dragstart",function(af,ag){ag.original_low=aa.low;ag.current_height=af.clientY;ag.current_x=ag.offsetX}).bind("drag",function(ah,aj){var af=$(this);var ak=aj.offsetX-aj.current_x;var ag=af.scrollTop()-(ah.clientY-aj.current_height);af.scrollTop(ag);aj.current_height=ah.clientY;aj.current_x=aj.offsetX;var ai=Math.round(ak/aa.viewport_container.width()*(aa.high-aa.low));aa.move_delta(ai)}).bind("mousewheel",function(ah,aj,ag,af){if(ag){var ai=Math.round(-ag/aa.viewport_container.width()*(aa.high-aa.low));aa.move_delta(ai)}});this.top_labeltrack.bind("dragstart",function(af,ag){return $("<div />").css({height:aa.content_div.height()+aa.top_labeltrack.height()+aa.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(aj,ak){$(ak.proxy).css({left:Math.min(aj.pageX,ak.startX),width:Math.abs(aj.pageX-ak.startX)});var ag=Math.min(aj.pageX,ak.startX)-aa.container.offset().left,af=Math.max(aj.pageX,ak.startX)-aa.container.offset().left,ai=(aa.high-aa.low),ah=aa.viewport_container.width();aa.update_location(Math.round(ag/ah*ai)+aa.low,Math.round(af/ah*ai)+aa.low)}).bind("dragend",function(ak,al){var ag=Math.min(ak.pageX,al.startX),af=Math.max(ak.pageX,al.startX),ai=(aa.high-aa.low),ah=aa.viewport_container.width(),aj=aa.low;aa.low=Math.round(ag/ah*ai)+aj;aa.high=Math.round(af/ah*ai)+aj;$(al.proxy).remove();aa.redraw()});this.add_label_track(new X(this,this.top_labeltrack));this.add_label_track(new X(this,this.nav_labeltrack));$(window).bind("resize",function(){aa.resize_window()});$(document).bind("redraw",function(){aa.redraw()});this.reset();$(window).trigger("resize");this.update_intro_div()},update_intro_div:function(){if(this.num_tracks===0){this.intro_div.show()}else{this.intro_div.hide()}},update_location:function(aa,ab){this.location_span.text(commatize(aa)+" - "+commatize(ab));this.nav_input.val(this.chrom+":"+commatize(aa)+"-"+commatize(ab))},load_chroms:function(ab,ac){ab.num=t;$.extend(ab,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var aa=this;$.ajax({url:chrom_url,data:ab,dataType:"json",success:function(ae){if(ae.chrom_info.length===0){alert("Invalid chromosome: "+ab.chrom);return}if(ae.reference){aa.add_label_track(new x(aa))}aa.chrom_data=ae.chrom_info;var ah='<option value="">Select Chrom/Contig</option>';for(var ag=0,ad=aa.chrom_data.length;ag<ad;ag++){var af=aa.chrom_data[ag].chrom;ah+='<option value="'+af+'">'+af+"</option>"}if(ae.prev_chroms){ah+='<option value="previous">Previous '+t+"</option>"}if(ae.next_chroms){ah+='<option value="next">Next '+t+"</option>"}aa.chrom_select.html(ah);if(ac){ac()}aa.chrom_start_index=ae.start_index},error:function(){alert("Could not load chroms for this dbkey:",aa.dbkey)}})},change_chrom:function(ae,ab,ag){if(!ae||ae==="None"){return}var ad=this;if(ae==="previous"){ad.load_chroms({low:this.chrom_start_index-t});return}if(ae==="next"){ad.load_chroms({low:this.chrom_start_index+t});return}var af=$.grep(ad.chrom_data,function(ai,aj){return ai.chrom===ae})[0];if(af===undefined){ad.load_chroms({chrom:ae},function(){ad.change_chrom(ae,ab,ag)});return}else{if(ae!==ad.chrom){ad.chrom=ae;ad.chrom_select.val(ad.chrom);ad.max_high=af.len-1;ad.reset();ad.redraw(true);for(var ah=0,aa=ad.tracks.length;ah<aa;ah++){var ac=ad.tracks[ah];if(ac.init){ac.init()}}}if(ab!==undefined&&ag!==undefined){ad.low=Math.max(ab,0);ad.high=Math.min(ag,ad.max_high)}ad.reset_overview();ad.redraw()}},go_to:function(ae){var ai=this,aa,ad,ab=ae.split(":"),ag=ab[0],ah=ab[1];if(ah!==undefined){try{var af=ah.split("-");aa=parseInt(af[0].replace(/,/g,""),10);ad=parseInt(af[1].replace(/,/g,""),10)}catch(ac){return false}}ai.change_chrom(ag,aa,ad)},move_fraction:function(ac){var aa=this;var ab=aa.high-aa.low;this.move_delta(ac*ab)},move_delta:function(ac){var aa=this;var ab=aa.high-aa.low;if(aa.low-ac<aa.max_low){aa.low=aa.max_low;aa.high=aa.max_low+ab}else{if(aa.high-ac>aa.max_high){aa.high=aa.max_high;aa.low=aa.max_high-ab}else{aa.high-=ac;aa.low-=ac}}aa.redraw()},add_track:function(aa){aa.view=this;aa.track_id=this.track_id_counter;this.tracks.push(aa);if(aa.init){aa.init()}aa.container_div.attr("id","track_"+aa.track_id);C(aa.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1;this.update_intro_div()},add_label_track:function(aa){aa.view=this;this.label_tracks.push(aa)},remove_track:function(ab){this.has_changes=true;delete this.tracks[this.tracks.indexOf(ab)];this.num_tracks-=1;var aa=this;ab.container_div.fadeOut("slow",function(){$(this).remove();aa.update_intro_div()})},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(ah){var ag=this.high-this.low,af=this.low,ab=this.high;if(af<this.max_low){af=this.max_low}if(ab>this.max_high){ab=this.max_high}if(this.high!==0&&ag<this.min_separation){ab=af+this.min_separation}this.low=Math.floor(af);this.high=Math.ceil(ab);this.resolution=Math.pow(z,Math.ceil(Math.log((this.high-this.low)/M)/Math.log(z)));this.zoom_res=Math.pow(s,Math.max(0,Math.ceil(Math.log(this.resolution,s)/Math.log(s))));var aa=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ae=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ai=13;this.overview_box.css({left:aa,width:Math.max(ai,ae)}).show();if(ae<ai){this.overview_box.css("left",aa-(ai-ae)/2)}if(this.overview_highlight){this.overview_highlight.css({left:aa,width:ae})}this.update_location(this.low,this.high);if(!ah){for(var ac=0,ad=this.tracks.length;ac<ad;ac++){if(this.tracks[ac]&&this.tracks[ac].enabled){this.tracks[ac].draw()}}for(ac=0,ad=this.label_tracks.length;ac<ad;ac++){this.label_tracks[ac].draw()}}},zoom_in:function(ab,ac){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ad=this.high-this.low,ae=ad/2+this.low,aa=(ad/this.zoom_factor)/2;if(ab){ae=ab/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ae-aa);this.high=Math.round(ae+aa);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var ab=this.high-this.low,ac=ab/2+this.low,aa=(ab*this.zoom_factor)/2;this.low=Math.round(ac-aa);this.high=Math.round(ac+aa);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide()}});var o=function(ac,ag){this.track=ac;this.name=ag.name;this.params=[];var an=ag.params;for(var ad=0;ad<an.length;ad++){var ai=an[ad],ab=ai.name,am=ai.label,ae=unescape(ai.html),ao=ai.value,ak=ai.type;if(ak==="number"){this.params[this.params.length]=new g(ab,am,ae,ao,ai.min,ai.max)}else{if(ak=="select"){this.params[this.params.length]=new K(ab,am,ae,ao)}else{console.log("WARNING: unrecognized tool parameter type:",ab,ak)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(aq){aq.stopPropagation()}).bind("click",function(aq){aq.stopPropagation()}).bind("dblclick",function(aq){aq.stopPropagation()});var al=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var aj=this.params;var ah=this;$.each(this.params,function(ar,av){var au=$("<div>").addClass("param-row").appendTo(ah.parent_div);var aq=$("<div>").addClass("param-label").text(av.label).appendTo(au);var at=$("<div/>").addClass("slider").html(av.html).appendTo(au);at.find(":input").val(av.value);$("<div style='clear: both;'/>").appendTo(au)});this.parent_div.find("input").click(function(){$(this).select()});var ap=$("<div>").addClass("param-row").appendTo(this.parent_div);var af=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ap);var aa=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ap);var ah=this;aa.click(function(){ah.run_on_region()});af.click(function(){ah.run_on_dataset()})};n(o.prototype,{get_param_values_dict:function(){var aa={};this.parent_div.find(":input").each(function(){var ab=$(this).attr("name"),ac=$(this).val();aa[ab]=JSON.stringify(ac)});return aa},get_param_values:function(){var ab=[];var aa={};this.parent_div.find(":input").each(function(){var ac=$(this).attr("name"),ad=$(this).val();if(ac){ab[ab.length]=ad}});return ab},run_on_dataset:function(){var aa=this;aa.run({dataset_id:this.track.original_dataset_id,tool_id:aa.name},function(ab){show_modal(aa.name+" is Running",aa.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var aa={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},ac=this.track,ab=aa.tool_id+ac.tool_region_and_parameters_str(aa.chrom,aa.low,aa.high),ad;if(ac instanceof e){ad=new Q(ab,view,ac.hda_ldda,undefined,{},{},ac);ad.change_mode(ac.mode)}this.track.add_track(ad);ad.content_div.text("Starting job.");this.run(aa,function(ae){ad.dataset_id=ae.dataset_id;ad.content_div.text("Running job.");ad.init()})},run:function(ab,ac){$.extend(ab,this.get_param_values_dict());var aa=function(){$.getJSON(rerun_tool_url,ab,function(ad){if(ad==="no converter"){new_track.container_div.addClass("error");new_track.content_div.text(G)}else{if(ad.error){new_track.container_div.addClass("error");new_track.content_div.text(v+ad.message)}else{if(ad==="pending"){new_track.container_div.addClass("pending");new_track.content_div.text("Converting input data so that it can be easily reused.");setTimeout(aa,2000)}else{ac(ad)}}}})};aa()}});var K=function(ab,aa,ac,ad){this.name=ab;this.label=aa;this.html=ac;this.value=ad};var g=function(ac,ab,ae,af,ad,aa){K.call(this,ac,ab,ae,af);this.min=ad;this.max=aa};var h=function(ab,aa,ac,ad){this.name=ab;this.index=aa;this.tool_id=ac;this.tool_exp_name=ad};var R=function(ab,aa,ac,ad){h.call(this,ab,aa,ac,ad);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};n(R.prototype,{applies_to:function(aa){if(aa.length>this.index){return true}return false},keep:function(aa){if(!this.applies_to(aa)){return true}var ab=parseInt(aa[this.index]);return(isNaN(ab)||(ab>=this.low&&ab<=this.high))},update_attrs:function(ab){var aa=false;if(!this.applies_to(ab)){return aa}if(ab[this.index]<this.min){this.min=Math.floor(ab[this.index]);aa=true}if(ab[this.index]>this.max){this.max=Math.ceil(ab[this.index]);aa=true}return aa},update_ui_elt:function(){var ac=function(af,ad){var ae=ad-af;return(ae<=2?0.01:1)};var ab=this.slider.slider("option","min"),aa=this.slider.slider("option","max");if(this.min<ab||this.max>aa){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",ac(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var W=function(ac,al){this.track=ac;this.filters=[];for(var ag=0;ag<al.length;ag++){var aa=al[ag],ab=aa.name,ak=aa.type,ai=aa.index,an=aa.tool_id,ad=aa.tool_exp_name;if(ak==="int"||ak==="float"){this.filters[ag]=new R(ab,ai,an,ad)}else{console.log("ERROR: unsupported filter: ",ab,ak)}}var aj=function(ao,ap,aq){ao.click(function(){var ar=ap.text();max=parseFloat(aq.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aq.slider("option","values")){input_size=2*input_size+1;multi_value=true}ap.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",ar).appendTo(ap).focus().select().click(function(at){at.stopPropagation()}).blur(function(){$(this).remove();ap.text(ar)}).keyup(function(ax){if(ax.keyCode===27){$(this).trigger("blur")}else{if(ax.keyCode===13){var av=aq.slider("option","min"),at=aq.slider("option","max"),aw=function(ay){return(isNaN(ay)||ay>at||ay<av)},au=$(this).val();if(!multi_value){au=parseFloat(au);if(aw(au)){alert("Parameter value must be in the range ["+av+"-"+at+"]");return $(this)}}else{au=au.split("-");au=[parseFloat(au[0]),parseFloat(au[1])];if(aw(au[0])||aw(au[1])){alert("Parameter value must be in the range ["+av+"-"+at+"]");return $(this)}}aq.slider((multi_value?"values":"value"),au)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(ao){ao.stopPropagation()}).bind("click",function(ao){ao.stopPropagation()}).bind("dblclick",function(ao){ao.stopPropagation()}).bind("keydown",function(ao){ao.stopPropagation()});var ae=this;$.each(this.filters,function(av,ap){var ar=$("<div/>").addClass("slider-row").appendTo(ae.parent_div);var ao=$("<div/>").addClass("slider-label").appendTo(ar);var ax=$("<span/>").addClass("slider-name").text(ap.name+" ").appendTo(ao);var aq=$("<span/>");var at=$("<span/>").addClass("slider-value").appendTo(ao).append("[").append(aq).append("]");var aw=$("<div/>").addClass("slider").appendTo(ar);ap.control_element=$("<div/>").attr("id",ap.name+"-filter-control").appendTo(aw);var au=[0,0];ap.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(ay,az){au=az.values;aq.text(az.values[0]+"-"+az.values[1]);setTimeout(function(){if(az.values[0]==au[0]&&az.values[1]==au[1]){var aA=az.values;aq.text(aA[0]+"-"+aA[1]);ap.low=aA[0];ap.high=aA[1];ae.track.draw(true,true)}},50)},change:function(ay,az){ap.control_element.slider("option","slide").call(ap.control_element,ay,az)}});ap.slider=ap.control_element;ap.slider_label=aq;aj(at,aq,ap.control_element);$("<div style='clear: both;'/>").appendTo(ar)});if(this.filters.length!=0){var am=$("<div>").addClass("param-row").appendTo(this.parent_div);var ah=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(am);var af=this;ah.click(function(){af.run_on_dataset()})}};n(W.prototype,{reset_filters:function(){for(var aa=0;aa<this.filters.length;aa++){filter=this.filters[aa];filter.slider.slider("option","values",[filter.min,filter.max])}},run_on_dataset:function(){var ai=function(am,ak,al){if(!(ak in am)){am[ak]=al}return am[ak]};var ac={},aa,ab,ad;for(var ae=0;ae<this.filters.length;ae++){aa=this.filters[ae];if(aa.tool_id){if(aa.min!=aa.low){ab=ai(ac,aa.tool_id,[]);ab[ab.length]=aa.tool_exp_name+" >= "+aa.low}if(aa.max!=aa.high){ab=ai(ac,aa.tool_id,[]);ab[ab.length]=aa.tool_exp_name+" <= "+aa.high}}}var ag=[];for(var aj in ac){ag[ag.length]=[aj,ac[aj]]}var ah=ag.length;(function af(aq,an){var al=an[0],am=al[0],ap=al[1],ao="("+ap.join(") and (")+")",ak={cond:ao,input:aq,target_dataset_id:aq,tool_id:am},an=an.slice(1);$.getJSON(run_tool_url,ak,function(ar){if(ar.error){show_modal("Filter Dataset","Error running tool "+am,{Close:hide_modal})}else{if(an.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{af(ar.dataset_id,an)}}})})(this.track.dataset_id,ag)}});var V=function(aa){this.track=aa.track;this.params=aa.params;this.values={};if(aa.saved_values){this.restore_values(aa.saved_values)}this.onchange=aa.onchange};n(V.prototype,{restore_values:function(aa){var ab=this;$.each(this.params,function(ac,ad){if(aa[ad.key]!==undefined){ab.values[ad.key]=aa[ad.key]}else{ab.values[ad.key]=ad.default_value}})},build_form:function(){var ab=this;var aa=$("<div />");$.each(this.params,function(af,ad){if(!ad.hidden){var ac="param_"+af;var ak=$("<div class='form-row' />").appendTo(aa);ak.append($("<label />").attr("for",ac).text(ad.label+":"));if(ad.type==="bool"){ak.append($('<input type="checkbox" />').attr("id",ac).attr("name",ac).attr("checked",ab.values[ad.key]))}else{if(ad.type==="color"){var ah=ab.values[ad.key];var ag=$("<input />").attr("id",ac).attr("name",ac).val(ah);var ai=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var ae=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ai);var aj=$("<div/>").appendTo(ae).farbtastic({width:100,height:100,callback:ag,color:ah});$("<div />").append(ag).append(ai).appendTo(ak).bind("click",function(al){ai.css({left:$(this).position().left+($(ag).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ai.hide();$(document).unbind("click.color-picker")});al.stopPropagation()})}else{ak.append($("<input />").attr("id",ac).attr("name",ac).val(ab.values[ad.key]))}}}});return aa},update_from_form:function(aa){var ac=this;var ab=false;$.each(this.params,function(ad,af){if(!af.hidden){var ag="param_"+ad;var ae=aa.find("#"+ag).val();if(af.type==="float"){ae=parseFloat(ae)}else{if(af.type==="int"){ae=parseInt(ae)}else{if(af.type==="bool"){ae=aa.find("#"+ag).is(":checked")}}}if(ae!==ac.values[af.key]){ac.values[af.key]=ae;ab=true}}});if(ab){this.onchange()}}});var b=function(ac,ab,aa){this.index=ac;this.low=ac*M*ab;this.high=(ac+1)*M*ab;this.resolution=ab;this.canvas=$("<div class='track-tile'/>").append(aa);this.stale=false};var l=function(ac,ab,aa,ad){b.call(this,ac,ab,aa);this.max_val=ad};var L=function(ac,ab,aa,ad){b.call(this,ac,ab,aa);this.message=ad};var j=function(ab,aa,ae,ac,ad){this.name=ab;this.view=aa;this.parent_element=ae;this.data_url=(ac?ac:default_data_url);this.data_url_extra_params={};this.data_query_wait=(ad?ad:H);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};n(j.prototype,{get_type:function(){if(this instanceof X){return"LabelTrack"}else{if(this instanceof x){return"ReferenceTrack"}else{if(this instanceof k){return"LineTrack"}else{if(this instanceof S){return"ReadTrack"}else{if(this instanceof Q){return"ToolDataFeatureTrack"}else{if(this instanceof P){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var aa=this;aa.enabled=false;aa.tile_cache.clear();aa.data_manager.clear();aa.initial_canvas=undefined;aa.content_div.css("height","auto");aa.container_div.removeClass("nodata error pending");if(!aa.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:aa.hda_ldda,dataset_id:aa.dataset_id,chrom:aa.view.chrom},function(ab){if(!ab||ab==="error"||ab.kind==="error"){aa.container_div.addClass("error");aa.content_div.text(m);if(ab.message){var ad=aa.view.tracks.indexOf(aa);var ac=$(" <a href='javascript:void(0);'></a>").text("View error").bind("click",function(){show_modal("Trackster Error","<pre>"+ab.message+"</pre>",{Close:hide_modal})});aa.content_div.append(ac)}}else{if(ab==="no converter"){aa.container_div.addClass("error");aa.content_div.text(G)}else{if(ab==="no data"||(ab.data!==undefined&&(ab.data===null||ab.data.length===0))){aa.container_div.addClass("nodata");aa.content_div.text(B)}else{if(ab==="pending"){aa.container_div.addClass("pending");aa.content_div.text(q);setTimeout(function(){aa.init()},aa.data_query_wait)}else{if(ab.status==="data"){if(ab.valid_chroms){aa.valid_chroms=ab.valid_chroms;aa.make_name_popup_menu()}aa.content_div.text(U);if(aa.view.chrom){aa.content_div.text("");aa.content_div.css("height",aa.height_px+"px");aa.enabled=true;$.when(aa.predraw_init()).done(function(){aa.container_div.removeClass("nodata error pending");aa.draw()})}}}}}}})},predraw_init:function(){},update_name:function(aa){this.old_name=this.name;this.name=aa;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var J=function(ah,af,ai){var ab=this,aj=ab.view;this.filters_manager=(ah!==undefined?new W(this,ah):undefined);this.filters_available=false;this.filters_visible=false;this.tool=(af!==undefined&&obj_length(af)>0?new o(this,af):undefined);this.parent_track=ai;this.child_tracks=[];if(ab.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}ab.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();ab.container_div.append(ab.child_tracks_container);if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}if(ab.display_modes!==undefined){if(ab.mode_div===undefined){ab.mode_div=$("<div class='right-float menubutton popup' />").appendTo(ab.header_div);var ac=(ab.track_config&&ab.track_config.values.mode?ab.track_config.values.mode:ab.display_modes[0]);ab.mode=ac;ab.mode_div.text(ac);var aa={};for(var ad=0,ag=ab.display_modes.length;ad<ag;ad++){var ae=ab.display_modes[ad];aa[ae]=function(ak){return function(){ab.change_mode(ak)}}(ae)}make_popupmenu(ab.mode_div,aa)}else{ab.mode_div.hide()}}this.make_name_popup_menu()};n(J.prototype,j.prototype,{change_mode:function(ab){var aa=this;aa.mode_div.text(ab);aa.mode=ab;aa.track_config.values.mode=ab;aa.tile_cache.clear();aa.draw()},make_name_popup_menu:function(){var ab=this;var aa={};aa["Edit configuration"]=function(){var ah=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},af=function(){ab.track_config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){af()}}};$(window).bind("keypress.check_enter_esc",ag);show_modal("Configure Track",ab.track_config.build_form(),{Cancel:ah,OK:af})};if(ab.filters_available>0){var ae=(ab.filters_div.is(":visible")?"Hide filters":"Show filters");aa[ae]=function(){ab.filters_visible=(ab.filters_div.is(":visible"));if(ab.filters_visible){ab.filters_manager.reset_filters()}ab.filters_div.toggle();ab.make_name_popup_menu()}}if(ab.tool){var ae=(ab.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");aa[ae]=function(){if(!ab.dynamic_tool_div.is(":visible")){ab.update_name(ab.name+ab.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";ab.revert_name()}ab.dynamic_tool_div.toggle();ab.make_name_popup_menu()}}if(ab.valid_chroms){aa["List chrom/contigs with data"]=function(){show_modal("Chrom/contigs with data","<p>"+ab.valid_chroms.join("<br/>")+"</p>",{Close:function(){hide_modal()}})}}var ac=view;var ad=function(){$("#no-tracks").show()};if(this.parent_track){ac=this.parent_track;ad=function(){}}aa.Remove=function(){ac.remove_track(ab);if(ac.num_tracks===0){ad()}};make_popupmenu(ab.name_div,aa)},draw:function(aa,ac){if(!this.dataset_id){return}var au=this.view.low,ag=this.view.high,ai=ag-au,ak=this.view.container.width(),ae=ak/ai,al=this.view.resolution,ad=$("<div style='position: relative;'></div>"),am=function(aw,ax,av){return aw+"_"+ax+"_"+av};if(!ac){this.content_div.children().remove()}this.content_div.append(ad);this.max_height=0;var ao=Math.floor(au/al/M);var af=[];var ap=0;while((ao*M*al)<ag){var at=am(ak,ae,ao);var ah=this.tile_cache.get(at);var aq=ao*M*this.view.resolution;var ab=aq+M*this.view.resolution;if(!aa&&ah){af[af.length]=ah;this.show_tile(ah,ad,ae)}else{this.delayed_draw(aa,at,ao,al,ad,ae,af)}ao+=1;ap++}var aj=this;var ar=setInterval(function(){if(af.length===ap){clearInterval(ar);if(ac){var aA=aj.content_div.children();var aB=false;for(var az=aA.length-1,aF=0;az>=aF;az--){var ay=$(aA[az]);if(aB){ay.remove()}else{if(ay.children().length!==0){aB=true}}}}if(aj instanceof e&&aj.mode=="Histogram"){var aE=-1;for(var az=0;az<af.length;az++){var aH=af[az].max_val;if(aH>aE){aE=aH}}for(var az=0;az<af.length;az++){if(af[az].max_val!==aE){var aG=af[az];aG.canvas.remove();aj.delayed_draw(true,am(ak,ae,aG.index),aG.index,aG.resolution,ad,ae,[],{max:aE})}}}if(aj.filters_manager){var ax=aj.filters_manager.filters;for(var aD=0;aD<ax.length;aD++){ax[aD].update_ui_elt()}var aC=false;if(aj.example_feature){for(var aD=0;aD<ax.length;aD++){if(ax[aD].applies_to(aj.example_feature)){aC=true;break}}}if(aj.filters_available!==aC){aj.filters_available=aC;if(!aj.filters_available){aj.filters_div.hide()}aj.make_name_popup_menu()}}var av=false;for(var aw=0;aw<af.length;aw++){if(af[aw].message){av=true;break}}if(av){for(var aw=0;aw<af.length;aw++){aG=af[aw];if(!aG.message){aG.canvas.css("padding-top",A)}}}}},50);for(var an=0;an<this.child_tracks.length;an++){this.child_tracks[an].draw(aa,ac)}},delayed_draw:function(ab,ai,ac,ae,aj,am,ak,af){var ad=this,ag=ac*M*ae,al=ag+M*ae;var ah=function(av,an,ap,ao,at,au,aq){var ar=ad.draw_tile(an,ap,ao,au,aq);ad.tile_cache.set(ai,ar);if(ar===undefined){return}ad.show_tile(ar,at,au);ak[ak.length]=ar};var aa=setTimeout(function(){if(ag<=ad.view.high&&al>=ad.view.low){var an=(ab?undefined:ad.tile_cache.get(ai));if(an){ad.show_tile(an,aj,am);ak[ak.length]=an}else{$.when(ad.data_manager.get_data(ag,al,ae,ad.data_url_extra_params)).then(function(ao){n(ao,af);if(view.reference_track&&am>view.canvas_manager.char_width_px){$.when(view.reference_track.data_manager.get_data(ag,al,ae,view.reference_track.data_url_extra_params)).then(function(ap){ah(aa,ao,ae,ac,aj,am,ap)})}else{ah(aa,ao,ae,ac,aj,am)}})}}},50)},show_tile:function(ah,aj,ak){var ac=this,ab=ah.canvas,ag=ab;if(ah.message){var al=$("<div/>"),ai=$("<div/>").addClass("tile-message").text(ah.message).css({height:A-1,width:ah.canvas.width}).appendTo(al),ae=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(ai),aa=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(ai);al.append(ab);ag=al;ae.click(function(){ah.stale=true;ac.data_manager.get_more_data(ah.low,ah.high,ah.resolution,{},ac.data_manager.DEEP_DATA_REQ);ac.draw()}).dblclick(function(am){am.stopPropagation()});aa.click(function(){ah.stale=true;ac.data_manager.get_more_data(ah.low,ah.high,ah.resolution,{},ac.data_manager.BROAD_DATA_REQ);ac.draw()}).dblclick(function(am){am.stopPropagation()})}var af=this.view.high-this.view.low,ad=(ah.low-this.view.low)*ak;if(this.left_offset){ad-=this.left_offset}ag.css({position:"absolute",top:0,left:ad,height:""});aj.append(ag);ac.max_height=Math.max(ac.max_height,ag.height());ac.content_div.css("height",ac.max_height+"px");aj.children().css("height",ac.max_height+"px")},set_overview:function(){var aa=this.view;if(this.initial_canvas&&this.is_overview){aa.overview_close.show();aa.overview_viewport.append(this.initial_canvas);aa.overview_highlight.show().height(this.initial_canvas.height());aa.overview_viewport.height(this.initial_canvas.height()+aa.overview_box.height())}$(window).trigger("resize")},tool_region_and_parameters_str:function(ac,aa,ad){var ab=this,ae=(ac!==undefined&&aa!==undefined&&ad!==undefined?ac+":"+aa+"-"+ad:"all");return" - region=["+ae+"], parameters=["+ab.tool.get_param_values().join(", ")+"]"},add_track:function(aa){aa.track_id=this.track_id+"_"+this.child_tracks.length;aa.container_div.attr("id","track_"+aa.track_id);this.child_tracks_container.append(aa.container_div);C(aa.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(aa);this.view.has_changes=true},remove_track:function(aa){aa.container_div.fadeOut("slow",function(){$(this).remove()})}});var X=function(aa,ab){this.hidden=true;j.call(this,null,aa,ab);this.container_div.addClass("label-track")};n(X.prototype,j.prototype,{draw:function(){var ac=this.view,ad=ac.high-ac.low,ag=Math.floor(Math.pow(10,Math.floor(Math.log(ad)/Math.log(10)))),aa=Math.floor(ac.low/ag)*ag,ae=this.view.container.width(),ab=$("<div style='position: relative; height: 1.3em;'></div>");while(aa<ac.high){var af=(aa-ac.low)/ad*ae;ab.append($("<div class='label'>"+commatize(aa)+"</div>").css({position:"absolute",left:af-1}));aa+=ag}this.content_div.children(":first").remove();this.content_div.append(ab)}});var x=function(aa){this.hidden=true;j.call(this,null,aa,aa.top_labeltrack);J.call(this);aa.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:aa.dbkey};this.data_manager=new E(y,this,false);this.tile_cache=new c(r)};n(x.prototype,J.prototype,{draw_tile:function(ai,af,ab,ak){var ae=this,ac=M*af;if(ak>this.view.canvas_manager.char_width_px){if(ai===null){ae.content_div.css("height","0px");return}var ad=this.view.canvas_manager.new_canvas();var aj=ad.getContext("2d");ad.width=Math.ceil(ac*ak+ae.left_offset);ad.height=ae.height_px;aj.font=aj.canvas.manager.default_font;aj.textAlign="center";for(var ag=0,ah=ai.length;ag<ah;ag++){var aa=Math.round(ag*ak);aj.fillText(ai[ag],aa+ae.left_offset,10)}return new b(ab,af,ad)}this.content_div.css("height","0px")}});var k=function(ae,ac,af,aa,ad){var ab=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";j.call(this,ae,ac,ac.viewport_container);J.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=af;this.dataset_id=aa;this.original_dataset_id=aa;this.data_manager=new N(y,this);this.tile_cache=new c(r);this.track_config=new V({track:this,params:[{key:"color",label:"Color",type:"color",default_value:"black"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:ad,onchange:function(){ab.vertical_range=ab.prefs.max_value-ab.prefs.min_value;$("#linetrack_"+ab.track_id+"_minval").text(ab.prefs.min_value);$("#linetrack_"+ab.track_id+"_maxval").text(ab.prefs.max_value);ab.tile_cache.clear();ab.draw()}});this.prefs=this.track_config.values;this.height_px=this.track_config.values.height;this.vertical_range=this.track_config.values.max_value-this.track_config.values.min_value;this.add_resize_handle()};n(k.prototype,J.prototype,{add_resize_handle:function(){var aa=this;var ad=false;var ac=false;var ab=$("<div class='track-resize'>");$(aa.container_div).hover(function(){ad=true;ab.show()},function(){ad=false;if(!ac){ab.hide()}});ab.hide().bind("dragstart",function(ae,af){ac=true;af.original_height=$(aa.content_div).height()}).bind("drag",function(af,ag){var ae=Math.min(Math.max(ag.original_height+ag.deltaY,aa.min_height_px),aa.max_height_px);$(aa.content_div).css("height",ae);aa.height_px=ae;aa.draw(true)}).bind("dragend",function(ae,af){aa.tile_cache.clear();ac=false;if(!ad){ab.hide()}aa.track_config.values.height=aa.height_px}).appendTo(aa.container_div)},predraw_init:function(){var aa=this,ab=aa.view.tracks.indexOf(aa);aa.vertical_range=undefined;return $.getJSON(aa.data_url,{stats:true,chrom:aa.view.chrom,low:null,high:null,hda_ldda:aa.hda_ldda,dataset_id:aa.dataset_id},function(ac){aa.container_div.addClass("line-track");var ae=ac.data;if(isNaN(parseFloat(aa.prefs.min_value))||isNaN(parseFloat(aa.prefs.max_value))){aa.prefs.min_value=ae.min;aa.prefs.max_value=ae.max;$("#track_"+ab+"_minval").val(aa.prefs.min_value);$("#track_"+ab+"_maxval").val(aa.prefs.max_value)}aa.vertical_range=aa.prefs.max_value-aa.prefs.min_value;aa.total_frequency=ae.total_frequency;aa.container_div.find(".yaxislabel").remove();var af=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ab+"_minval").text(u(aa.prefs.min_value));var ad=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ab+"_maxval").text(u(aa.prefs.max_value));ad.css({position:"absolute",top:"24px",left:"10px"});ad.prependTo(aa.container_div);af.css({position:"absolute",bottom:"2px",left:"10px"});af.prependTo(aa.container_div)})},draw_tile:function(ak,ae,ab,aj){if(this.vertical_range===undefined){return}var af=ab*M*ae,ad=M*ae,aa=Math.ceil(ad*aj),ah=this.height_px;var ac=this.view.canvas_manager.new_canvas();ac.width=aa,ac.height=ah;var ai=ac.getContext("2d");var ag=new I.LinePainter(ak.data,af,af+ad,this.prefs,this.mode);ag.draw(ai,aa,ah);return new b(ab,ae,ac)}});var e=function(aa,af,ae,ai,ah,ac,ad,ag){var ab=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];this.track_config=new V({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ah,onchange:function(){ab.tile_cache.clear();ab.draw()}});this.prefs=this.track_config.values;j.call(this,aa,af,af.viewport_container);J.call(this,ac,ad,ag);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=ae;this.dataset_id=ai;this.original_dataset_id=ai;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new N(20,this);this.left_offset=200;this.painter=I.LinkedFeaturePainter};n(e.prototype,J.prototype,{update_auto_mode:function(aa){if(this.mode=="Auto"){if(aa=="no_detail"){aa="feature spans"}else{if(aa=="summary_tree"){aa="coverage histogram"}}this.mode_div.text("Auto ("+aa+")")}},incremental_slots:function(ae,ab,ad){var ac=this.view.canvas_manager.dummy_context,aa=this.inc_slots[ae];if(!aa||(aa.mode!==ad)){aa=new (p.FeatureSlotter)(ae,ad==="Pack",w,function(af){return ac.measureText(af)});aa.mode=ad;this.inc_slots[ae]=aa}return aa.slot_features(ab)},get_summary_tree_data:function(ae,ah,ac,ap){if(ap>ac-ah){ap=ac-ah}var al=Math.floor((ac-ah)/ap),ao=[],ad=0;var af=0,ag=0,ak,an=0,ai=[],am,aj;var ab=function(at,ar,au,aq){at[0]=ar+au*aq;at[1]=ar+(au+1)*aq};while(an<ap&&af!==ae.length){var aa=false;for(;an<ap&&!aa;an++){ab(ai,ah,an,al);for(ag=af;ag<ae.length;ag++){ak=ae[ag].slice(1,3);if(is_overlap(ak,ai)){aa=true;break}}if(aa){break}}data_start_index=ag;ao[ao.length]=am=[ai[0],0];for(;ag<ae.length;ag++){ak=ae[ag].slice(1,3);if(is_overlap(ak,ai)){am[1]++}else{break}}if(am[1]>ad){ad=am[1]}an++}return{max:ad,delta:al,data:ao}},draw_tile:function(an,av,az,aj,ad){var ar=this,aB=az*M*av,ab=(az+1)*M*av,ap=ab-aB,at=Math.ceil(ap*aj),aq=this.mode,aF=25,ae=this.left_offset,ao,af;if(aq==="Auto"){if(an.dataset_type==="summary_tree"){aq=an.dataset_type}else{if(an.extra_info==="no_detail"){aq="no_detail"}else{var aE=an.data;if(this.view.high-this.view.low>F){aq="Squish"}else{aq="Pack"}}}this.update_auto_mode(aq)}if(aq==="summary_tree"||aq==="Histogram"){af=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var aa=$("<div />").addClass("yaxislabel");aa.text(an.max);aa.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});aa.prependTo(this.container_div);var ac=this.view.canvas_manager.new_canvas();ac.width=at+ae;ac.height=af+O;if(an.dataset_type!="summary_tree"){var ak=this.get_summary_tree_data(an.data,aB,ab,200);if(an.max){ak.max=an.max}an=ak}var aC=new I.SummaryTreePainter(an,aB,ab,this.prefs);var au=ac.getContext("2d");au.translate(ae,O);aC.draw(au,at,af);return new l(az,av,ac,an.max)}var ao,ah=1;if(aq==="no_detail"||aq==="Squish"||aq==="Pack"){ah=this.incremental_slots(aj,an.data,aq);ao=this.inc_slots[aj].slots}var ai=[];if(an.data){var al=this.filters_manager.filters;for(var aw=0,ay=an.data.length;aw<ay;aw++){var ag=an.data[aw];var ax=false;var am;for(var aA=0,aD=al.length;aA<aD;aA++){am=al[aA];am.update_attrs(ag);if(!am.keep(ag)){ax=true;break}}if(!ax){ai.push(ag)}}}var aC=new (this.painter)(ai,aB,ab,this.prefs,aq,ad);var af=aC.get_required_height(ah);var ac=this.view.canvas_manager.new_canvas();ac.width=at+ae;ac.height=af;var au=ac.getContext("2d");au.fillStyle=this.prefs.block_color;au.font=au.canvas.manager.default_font;au.textAlign="right";this.container_div.find(".yaxislabel").remove();if(an.data){this.example_feature=(an.data.length?an.data[0]:undefined);au.translate(ae,0);aC.draw(au,at,af,ao)}return new L(az,av,ac,an.message)}});var P=function(ad,ab,af,aa,ac,ae){e.call(this,ad,ab,af,aa,ac,ae);this.painter=I.VariantPainter};n(P.prototype,J.prototype,e.prototype);var S=function(ad,ab,af,aa,ac,ae){e.call(this,ad,ab,af,aa,ac,ae);this.track_config=new V({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ac,onchange:function(){this.track.tile_cache.clear();this.track.draw()}});this.prefs=this.track_config.values;this.painter=I.ReadPainter;this.make_name_popup_menu()};n(S.prototype,J.prototype,e.prototype);var Q=function(ae,ac,ag,aa,ad,af,ab){e.call(this,ae,ac,ag,aa,ad,af,{},ab);this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};n(Q.prototype,J.prototype,e.prototype,{predraw_init:function(){var ab=this;var aa=function(){if(ab.data_manager.size()===0){setTimeout(aa,300)}else{ab.data_url=default_data_url;ab.data_query_wait=H;ab.dataset_state_url=converted_datasets_state_url;$.getJSON(ab.dataset_state_url,{dataset_id:ab.dataset_id,hda_ldda:ab.hda_ldda},function(ac){})}};aa()}});T.View=Y;T.LineTrack=k;T.FeatureTrack=e;T.ReadTrack=S};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(j,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=j;this.include_label=h;this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,s=this.slots,h=this.start_end_dct,y=[],A=[],n=0,z=this.max_rows;for(var w=0,x=m.length;w<x;w++){var l=m[w],o=l[0];if(s[o]!==undefined){n=Math.max(n,s[o]);A.push(s[o])}else{y.push(w)}}var q=function(G,H){for(var F=0;F<=z;F++){var D=false,I=h[F];if(I!==undefined){for(var C=0,E=I.length;C<E;C++){var B=I[C];if(H>B[0]&&G<B[1]){D=true;break}}}if(!D){return F}}return -1};for(var w=0,x=y.length;w<x;w++){var l=m[y[w]],o=l[0],u=l[1],f=l[2],r=l[3],g=Math.floor(u*p),k=Math.ceil(f*p),v=this.measureText(r).width,j;if(r!==undefined&&this.include_label){v+=(d+a);if(g-v>=0){g-=v;j="left"}else{k+=v;j="right"}}var t=q(g,k);if(t>=0){if(h[t]===undefined){h[t]=[]}h[t].push([g,k]);s[o]=t;n=Math.max(n,t)}else{}}return n+1}})};var painters_module=function(j,w){var t=j("class").extend;var o=function(H,z,F,y,E,C){if(C===undefined){C=4}var B=y-z;var A=E-F;var D=Math.floor(Math.sqrt(B*B+A*A)/C);var I=B/D;var G=A/D;var x;for(x=0;x<D;x++,z+=I,F+=G){if(x%2!==0){continue}H.fillRect(z,F,C,1)}};var p=function(A,z,x,D){var C=z-D/2,B=z+D/2,E=x-Math.sqrt(D*3/2);A.beginPath();A.moveTo(C,E);A.lineTo(B,E);A.lineTo(z,x);A.lineTo(C,E);A.strokeStyle=this.fillStyle;A.fill();A.stroke();A.closePath()};var m=function(z,B,x,y,A){this.data=z;this.view_start=B;this.view_end=x;this.prefs=t({},this.default_prefs,y);this.mode=A};m.prototype.default_prefs={};var u=function(z,B,x,y,A){m.call(this,z,B,x,y,A)};u.prototype.default_prefs={show_counts:false};u.prototype.draw=function(M,z,L){var E=this.view_start,O=this.view_end-this.view_start,N=z/O;var J=this.data.data,I=this.data.delta,G=this.data.max,B=L;delta_x_px=Math.ceil(I*N);M.save();for(var C=0,D=J.length;C<D;C++){var H=Math.floor((J[C][0]-E)*N);var F=J[C][1];if(!F){continue}var K=F/G*L;if(F!==0&&K<1){K=1}M.fillStyle=this.prefs.block_color;M.fillRect(H,B-K,delta_x_px,K);var A=4;if(this.prefs.show_counts&&(M.measureText(F).width+A)<delta_x_px){M.fillStyle=this.prefs.label_color;M.textAlign="center";M.fillText(F,H+(delta_x_px/2),10)}}M.restore()};var c=function(x,B,D,E,z){m.call(this,x,B,D,E,z);if(this.prefs.min_value===undefined){var F=Infinity;for(var y=0,A=this.data.length;y<A;y++){F=Math.min(F,this.data[y][1])}this.prefs.min_value=F}if(this.prefs.max_value===undefined){var C=-Infinity;for(var y=0,A=this.data.length;y<A;y++){C=Math.max(C,this.data[y][1])}this.prefs.max_value=C}};c.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};c.prototype.draw=function(M,L,J){var E=false,G=this.prefs.min_value,C=this.prefs.max_value,I=C-G,x=J,z=this.view_start,K=this.view_end-this.view_start,A=L/K,H=this.mode,S=this.data;M.save();var T=Math.round(J+G/I*J);if(H!=="Intensity"){M.fillStyle="#aaa";M.fillRect(0,T,L,1)}M.beginPath();var Q,D,B;if(S.length>1){B=Math.ceil((S[1][0]-S[0][0])*A)}else{B=10}for(var N=0,O=S.length;N<O;N++){M.fillStyle=this.prefs.color;Q=Math.round((S[N][0]-z)*A);D=S[N][1];var P=false,F=false;if(D===null){if(E&&H==="Filled"){M.lineTo(Q,x)}E=false;continue}if(D<G){F=true;D=G}else{if(D>C){P=true;D=C}}if(H==="Histogram"){D=Math.round(D/I*x);M.fillRect(Q,T,B,-D)}else{if(H==="Intensity"){D=255-Math.floor((D-G)/I*255);M.fillStyle="rgb("+D+","+D+","+D+")";M.fillRect(Q,0,B,x)}else{D=Math.round(x-(D-G)/I*x);if(E){M.lineTo(Q,D)}else{E=true;if(H==="Filled"){M.moveTo(Q,x);M.lineTo(Q,D)}else{M.moveTo(Q,D)}}}}M.fillStyle=this.prefs.overflow_color;if(P||F){var R;if(H==="Histogram"||H==="Intensity"){R=B}else{Q-=2;R=4}if(P){M.fillRect(Q,0,R,3)}if(F){M.fillRect(Q,x-3,R,3)}}M.fillStyle=this.prefs.color}if(H==="Filled"){if(E){M.lineTo(Q,T);M.lineTo(0,T)}M.fill()}else{M.stroke()}M.restore()};var n=function(z,B,x,y,A){m.call(this,z,B,x,y,A)};n.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};t(n.prototype,{get_required_height:function(y){var x=y_scale=this.get_row_height(),z=this.mode;if(z==="no_detail"||z==="Squish"||z==="Pack"){x=y*y_scale}return x+Math.max(Math.round(y_scale/2),5)},draw:function(J,A,I,F){var D=this.data,G=this.view_start,K=this.view_end;J.save();J.fillStyle=this.prefs.block_color;J.textAlign="right";var N=this.view_end-this.view_start,M=A/N,z=this.get_row_height();for(var C=0,E=D.length;C<E;C++){var L=D[C],B=L[0],x=L[1],y=L[2],H=(F&&F[B]!==undefined?F[B]:null);if((x<K&&y>G)&&(this.mode=="Dense"||H!==null)){this.draw_element(J,this.mode,L,H,G,K,M,z,A)}}J.restore()},draw_element:function(D,z,F,B,A,C,E,y,x){}});var d=10,h=3,l=5,v=10,f=1,r=3,e=3,a=9,k=2,g="#ccc";var q=function(z,B,x,y,A){n.call(this,z,B,x,y,A)};t(q.prototype,n.prototype,{get_row_height:function(){var y=this.mode,x;if(y==="Dense"){x=d}else{if(y==="no_detail"){x=h}else{if(y==="Squish"){x=l}else{x=v}}}return x},draw_element:function(J,C,R,E,L,ab,af,ag,x){var O=R[0],ad=R[1],V=R[2],M=R[3],W=Math.floor(Math.max(0,(ad-L)*af)),K=Math.ceil(Math.min(x,Math.max(0,(V-L)*af))),U=(C==="Dense"?0:(0+E))*ag,I,Z,N=null,ah=null,A=this.prefs.block_color,Y=this.prefs.label_color;if(C=="Dense"){E=1}if(C==="no_detail"){J.fillStyle=A;J.fillRect(W,U+5,K-W,f)}else{var H=R[4],T=R[5],X=R[6],B=R[7];if(T&&X){N=Math.floor(Math.max(0,(T-L)*af));ah=Math.ceil(Math.min(x,Math.max(0,(X-L)*af)))}var ae,P;if(C==="Squish"||C==="Dense"){ae=1;P=e}else{ae=5;P=a}if(!B){if(R.strand){if(R.strand==="+"){J.fillStyle=J.canvas.manager.get_pattern("right_strand_inv")}else{if(R.strand==="-"){J.fillStyle=J.canvas.manager.get_pattern("left_strand_inv")}}}else{J.fillStyle=A}J.fillRect(W,U,K-W,P)}else{var G,Q;if(C==="Squish"||C==="Dense"){J.fillStyle=g;G=U+Math.floor(e/2)+1;Q=1}else{if(H){var G=U;var Q=P;if(H==="+"){J.fillStyle=J.canvas.manager.get_pattern("right_strand")}else{if(H==="-"){J.fillStyle=J.canvas.manager.get_pattern("left_strand")}}}else{J.fillStyle=g;G+=(e/2)+1;Q=1}}J.fillRect(W,G,K-W,Q);for(var ac=0,z=B.length;ac<z;ac++){var D=B[ac],y=Math.floor(Math.max(0,(D[0]-L)*af)),S=Math.ceil(Math.min(x,Math.max((D[1]-L)*af)));if(y>S){continue}J.fillStyle=A;J.fillRect(y,U+(P-ae)/2+1,S-y,ae);if(N!==undefined&&X>T&&!(y>ah||S<N)){var aa=Math.max(y,N),F=Math.min(S,ah);J.fillRect(aa,U+1,F-aa,P);if(B.length==1&&C=="Pack"){if(H==="+"){J.fillStyle=J.canvas.manager.get_pattern("right_strand_inv")}else{if(H==="-"){J.fillStyle=J.canvas.manager.get_pattern("left_strand_inv")}}if(aa+14<F){aa+=2;F-=2}J.fillRect(aa,U+1,F-aa,P)}}}}if(C==="Pack"&&ad>L){J.fillStyle=Y;if(L===0&&W-J.measureText(M).width<0){J.textAlign="left";J.fillText(M,K+k,U+8)}else{J.textAlign="right";J.fillText(M,W-k,U+8)}J.fillStyle=A}}}});var b=function(z,B,x,y,A){n.call(this,z,B,x,y,A)};t(b.prototype,n.prototype,{draw_element:function(Q,L,F,B,T,z,I,R,O){var F=data[i],H=F[0],P=F[1],A=F[2],K=F[3],D=Math.floor(Math.max(0,(P-T)*I)),G=Math.ceil(Math.min(O,Math.max(0,(A-T)*I))),C=(L==="Dense"?0:(0+B))*R,x,U,y=null,J=null;if(no_label){Q.fillStyle=block_color;Q.fillRect(D+left_offset,C+5,G-D,1)}else{var S=F[4],N=F[5],E=F[6];x=9;U=1;Q.fillRect(D+left_offset,C,G-D,x);if(L!=="Dense"&&K!==undefined&&P>T){Q.fillStyle=label_color;if(T===0&&D-Q.measureText(K).width<0){Q.textAlign="left";Q.fillText(K,G+2+left_offset,C+8)}else{Q.textAlign="right";Q.fillText(K,D-2+left_offset,C+8)}Q.fillStyle=block_color}var M=S+" / "+N;if(P>T&&Q.measureText(M).width<(G-D)){Q.fillStyle="white";Q.textAlign="center";Q.fillText(M,left_offset+D+(G-D)/2,C+8);Q.fillStyle=block_color}}}});var s=function(A,C,x,z,B,y){n.call(this,A,C,x,z,B);this.ref_seq=y};s.prototype.default_prefs=t({},n.prototype.default_prefs,{show_insertions:false});t(s.prototype,n.prototype,{get_row_height:function(){var x,y=this.mode;if(y==="Dense"){x=d}else{if(y==="Squish"){x=l}else{x=v;if(this.prefs.show_insertions){x*=2}}}return x},draw_read:function(T,O,K,Y,z,S,H,E,D){T.textAlign="center";var R=this,y=[Y,z],N=0,U=0,Q=0;ref_seq=this.ref_seq,char_width_px=T.canvas.manager.char_width_px;var ad=[];if((O==="Pack"||this.mode==="Auto")&&E!==undefined&&K>char_width_px){Q=Math.round(K/2)}if(!H){H=[[0,E.length]]}for(var L=0,W=H.length;L<W;L++){var I=H[L],A="MIDNSHP=X"[I[0]],M=I[1];if(A==="H"||A==="S"){N-=M}var F=S+N,ac=Math.floor(Math.max(0,(F-Y)*K)),G=Math.floor(Math.max(0,(F+M-Y)*K));if(ac===G){G+=1}switch(A){case"H":break;case"S":case"M":case"=":if(is_overlap([F,F+M],y)){var P=E.slice(U,U+M);if(Q>0){T.fillStyle=this.prefs.block_color;T.fillRect(ac-Q,D+1,G-ac,9);T.fillStyle=g;for(var aa=0,x=P.length;aa<x;aa++){if(this.prefs.show_differences&&ref_seq){var J=ref_seq[F-Y+aa];if(!J||J.toLowerCase()===P[aa].toLowerCase()){continue}}if(F+aa>=Y&&F+aa<=z){var ab=Math.floor(Math.max(0,(F+aa-Y)*K));T.fillText(P[aa],ab,D+9)}}}else{T.fillStyle=this.prefs.block_color;T.fillRect(ac,D+4,G-ac,e)}}U+=M;N+=M;break;case"N":T.fillStyle=g;T.fillRect(ac-Q,D+5,G-ac,1);N+=M;break;case"D":T.fillStyle="red";T.fillRect(ac-Q,D+4,G-ac,3);N+=M;break;case"P":break;case"I":var X=ac-Q;if(is_overlap([F,F+M],y)){var P=E.slice(U,U+M);if(this.prefs.show_insertions){var C=ac-(G-ac)/2;if((O==="Pack"||this.mode==="Auto")&&E!==undefined&&K>char_width_px){T.fillStyle="yellow";T.fillRect(C-Q,D-9,G-ac,9);ad[ad.length]={type:"triangle",data:[X,D+4,5]};T.fillStyle=g;switch(seq_tile_overlap){case (OVERLAP_START):P=P.slice(Y-F);break;case (OVERLAP_END):P=P.slice(0,F-z);break;case (CONTAINED_BY):break;case (CONTAINS):P=P.slice(Y-F,F-z);break}for(var aa=0,x=P.length;aa<x;aa++){var ab=Math.floor(Math.max(0,(F+aa-Y)*K));T.fillText(P[aa],ab-(G-ac)/2,D)}}else{T.fillStyle="yellow";T.fillRect(C,D+(this.mode!=="Dense"?2:5),G-ac,(O!=="Dense"?e:r))}}else{if((O==="Pack"||this.mode==="Auto")&&E!==undefined&&K>char_width_px){ad[ad.length]={type:"text",data:[P.length,X,D+9]}}else{}}}U+=M;break;case"X":U+=M;break}}T.fillStyle="yellow";var Z,B,ae;for(var V=0;V<ad.length;V++){Z=ad[V];B=Z.type;ae=Z.data;if(B==="text"){T.save();T.font="bold "+T.font;T.fillText(ae[0],ae[1],ae[2]);T.restore()}else{if(B=="triangle"){p(T,ae[0],ae[1],ae[2])}}}},draw_element:function(Q,L,D,A,T,y,H,R,O){var G=D[0],P=D[1],z=D[2],I=D[3],C=Math.floor(Math.max(0,(P-T)*H)),E=Math.ceil(Math.min(O,Math.max(0,(z-T)*H))),B=(L==="Dense"?0:(0+A))*R,U=this.prefs.block_color,F=this.prefs.label_color,N=0;if((L==="Pack"||this.mode==="Auto")&&H>Q.canvas.manager.char_width_px){var N=Math.round(H/2)}Q.fillStyle=U;if(D[5] instanceof Array){var M=Math.floor(Math.max(0,(D[4][0]-T)*H)),K=Math.ceil(Math.min(O,Math.max(0,(D[4][1]-T)*H))),J=Math.floor(Math.max(0,(D[5][0]-T)*H)),x=Math.ceil(Math.min(O,Math.max(0,(D[5][1]-T)*H)));if(D[4][1]>=T&&D[4][0]<=y&&D[4][2]){this.draw_read(Q,L,H,T,y,D[4][0],D[4][2],D[4][3],B)}if(D[5][1]>=T&&D[5][0]<=y&&D[5][2]){this.draw_read(Q,L,H,T,y,D[5][0],D[5][2],D[5][3],B)}if(J>K){Q.fillStyle=g;o(Q,K-N,B+5,J-N,B+5)}}else{Q.fillStyle=U;this.draw_read(Q,L,H,T,y,P,D[4],D[5],B)}if(L==="Pack"&&P>T){Q.fillStyle=this.prefs.label_color;var S=1;if(S===0&&C-Q.measureText(I).width<0){Q.textAlign="left";Q.fillText(I,E+k-N,B+8)}else{Q.textAlign="right";Q.fillText(I,C-k-N,B+8)}Q.fillStyle=U}}});w.SummaryTreePainter=u;w.LinePainter=c;w.LinkedFeaturePainter=q;w.ReadPainter=s;w.VariantPainter=b};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window); \ No newline at end of file --- a/static/scripts/trackster.js Fri Jul 15 10:33:02 2011 -0400 +++ b/static/scripts/trackster.js Mon Jul 18 15:09:49 2011 +0200 @@ -486,8 +486,11 @@ this.top_labeltrack = $("<div/>").addClass("top-labeltrack").appendTo(this.top_container); // Viewport for dragging tracks in center this.viewport_container = $("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div); - // Future overlay? - this.intro_div = $("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide(); + // Introduction div shown when there are no tracks. + this.intro_div = $("<div/>").addClass("intro").appendTo(this.viewport_container).hide(); + var add_tracks_button = $("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function () { + add_tracks(); + }); // Another label track at bottom this.nav_labeltrack = $("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container); // Navigation at top @@ -536,7 +539,6 @@ this.chrom_select.bind("change", function() { view.change_chrom(view.chrom_select.val()); }); - this.intro_div.show(); /* this.content_div.bind("mousewheel", function( e, delta ) { @@ -651,6 +653,16 @@ this.reset(); $(window).trigger("resize"); + this.update_intro_div(); + }, + /** Show or hide intro div depending on view state. */ + update_intro_div: function() { + if (this.num_tracks === 0) { + this.intro_div.show(); + } + else { + this.intro_div.hide(); + } }, update_location: function(low, high) { this.location_span.text( commatize(low) + ' - ' + commatize(high) ); @@ -735,12 +747,6 @@ // Switching to local chrom. if (chrom !== view.chrom) { view.chrom = chrom; - if (!view.chrom) { - // No chrom selected - view.intro_div.show(); - } else { - view.intro_div.hide(); - } view.chrom_select.val(view.chrom); view.max_high = found.len-1; // -1 because we're using 0-based indexing. view.reset(); @@ -810,6 +816,7 @@ sortable( track.container_div, '.draghandle' ); this.track_id_counter += 1; this.num_tracks += 1; + this.update_intro_div(); }, add_label_track: function (label_track) { label_track.view = this; @@ -817,9 +824,13 @@ }, remove_track: function(track) { this.has_changes = true; - track.container_div.fadeOut('slow', function() { $(this).remove(); }); delete this.tracks[this.tracks.indexOf(track)]; this.num_tracks -= 1; + var view = this; + track.container_div.fadeOut('slow', function() { + $(this).remove(); + view.update_intro_div(); + }); }, reset: function() { this.low = this.max_low; --- a/templates/tracks/browser.mako Fri Jul 15 10:33:02 2011 -0400 +++ b/templates/tracks/browser.mako Mon Jul 18 15:09:49 2011 +0200 @@ -86,6 +86,75 @@ return new_bookmark; }; + /** + * Use track data to add a track to a view. + * TODO: rename function? + */ + var add_async_success = function(track_data) { + var td = track_data, + new_track = new addable_track_types[track_data.track_type]( + track_data.name, view, track_data.hda_ldda, track_data.dataset_id, + track_data.prefs, track_data.filters, track_data.tool ); + view.add_track(new_track); + // Should replace with live event but can't get working + sortable(new_track.container_div, ".draghandle"); + view.has_changes = true; + $("#no-tracks").hide(); + }; + + /** + * Use a popup grid to add more tracks. + */ + var add_tracks = function() { + $.ajax({ + url: "${h.url_for( action='list_histories' )}", + data: { "f-dbkey": view.dbkey }, + error: function() { alert( "Grid failed" ); }, + success: function(table_html) { + show_modal( + "Select datasets for new tracks", + table_html, { + "Cancel": function() { + hide_modal(); + }, + "Insert": function() { + var requests = []; + $('input[name=id]:checked,input[name=ldda_ids]:checked').each(function() { + var data, + id = $(this).val(); + if ($(this).attr("name") === "id") { + data = { hda_id: id }; + } else { + data = { ldda_id: id}; + } + requests[requests.length] = $.ajax({ + url: "${h.url_for( action='add_track_async' )}", + data: data, + dataType: "json", + }); + }); + // To preserve order, wait until there are definitions for all tracks and then add + // them sequentially. + $.when.apply($, requests).then(function() { + // jQuery always returns an Array for arguments, so need to look at first element + // to determine whether multiple requests were made and consequently how to + // map arguments to track definitions. + var track_defs = (arguments[0] instanceof Array ? + $.map(arguments, function(arg) { return arg[0]; }) : + [ arguments[0] ] + ); + for (var i= 0; i < track_defs.length; i++) { + add_async_success(track_defs[i]); + } + }); + hide_modal(); + } + } + ); + } + }); + }; + $(function() { // Hide bookmarks by default right now. parent.force_right_panel("hide"); @@ -170,19 +239,7 @@ return "There are unsaved changes to your visualization which will be lost."; } }; - - var add_async_success = function(track_data) { - var td = track_data, - new_track = new addable_track_types[track_data.track_type]( - track_data.name, view, track_data.hda_ldda, track_data.dataset_id, - track_data.prefs, track_data.filters, track_data.tool ); - view.add_track(new_track); - // Should replace with live event but can't get working - sortable(new_track.container_div, ".draghandle"); - view.has_changes = true; - $("#no-tracks").hide(); - }; - + %if add_dataset is not None: $.ajax({ url: "${h.url_for( action='add_track_async' )}", @@ -195,56 +252,7 @@ $("#viz-options-button").css( "position", "relative" ); make_popupmenu( $("#viz-options-button"), { - "Add Tracks": function() { - // Use a popup grid to add more tracks - $.ajax({ - url: "${h.url_for( action='list_histories' )}", - data: { "f-dbkey": view.dbkey }, - error: function() { alert( "Grid failed" ); }, - success: function(table_html) { - show_modal( - "Select datasets for new tracks", - table_html, { - "Cancel": function() { - hide_modal(); - }, - "Insert": function() { - var requests = []; - $('input[name=id]:checked,input[name=ldda_ids]:checked').each(function() { - var data, - id = $(this).val(); - if ($(this).attr("name") === "id") { - data = { hda_id: id }; - } else { - data = { ldda_id: id}; - } - requests[requests.length] = $.ajax({ - url: "${h.url_for( action='add_track_async' )}", - data: data, - dataType: "json", - }); - }); - // To preserve order, wait until there are definitions for all tracks and then add - // them sequentially. - $.when.apply($, requests).then(function() { - // jQuery always returns an Array for arguments, so need to look at first element - // to determine whether multiple requests were made and consequently how to - // map arguments to track definitions. - var track_defs = (arguments[0] instanceof Array ? - $.map(arguments, function(arg) { return arg[0]; }) : - [ arguments[0] ] - ); - for (var i= 0; i < track_defs.length; i++) { - add_async_success(track_defs[i]); - } - }); - hide_modal(); - } - } - ); - } - }); - }, + "Add Tracks": add_tracks, "Save": function() { // Show saving dialog box show_modal("Saving...", "<img src='${h.url_for('/static/images/yui/rel_interstitial_loading.gif')}'/>"); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: guru: Fixed a bug in PCA tool - standard deviation & prop variance values are now sorted by PC order.
by Bitbucket 15 Jul '11

15 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/5952ac09af12/ changeset: 5952ac09af12 user: guru date: 2011-07-15 16:33:02 summary: Fixed a bug in PCA tool - standard deviation & prop variance values are now sorted by PC order. affected #: 4 files (70 bytes) --- a/test-data/pca_out1.tabular Thu Jul 14 22:54:43 2011 +0200 +++ b/test-data/pca_out1.tabular Fri Jul 15 10:33:02 2011 -0400 @@ -1,6 +1,6 @@ #Component 1 2 3 4 -#Std. deviation 0.9598 0.1436 0.3839 1.706 -#Proportion of variance explained 0.2303 0.005152 0.03684 0.7277 +#Std. deviation 1.706 0.9598 0.3839 0.1436 +#Proportion of variance explained 0.7277 0.2303 0.03684 0.005152 #Loadings 1 2 3 4 c1 0.5224 -0.3723 0.721 0.262 c2 -0.2634 -0.9256 -0.242 -0.1241 --- a/test-data/pca_out3.tabular Thu Jul 14 22:54:43 2011 +0200 +++ b/test-data/pca_out3.tabular Fri Jul 15 10:33:02 2011 -0400 @@ -1,6 +1,6 @@ #Component 1 2 3 4 -#Std. deviation 0.4905 0.1534 0.2793 2.049 -#Proportion of variance explained 0.05302 0.005183 0.01719 0.9246 +#Std. deviation 2.049 0.4905 0.2793 0.1534 +#Proportion of variance explained 0.9246 0.05302 0.01719 0.005183 #Loadings 1 2 3 4 c1 0.3616 -0.6565 0.581 0.3173 c2 -0.08227 -0.7297 -0.5964 -0.3241 --- a/tools/multivariate_stats/pca.py Thu Jul 14 22:54:43 2011 +0200 +++ b/tools/multivariate_stats/pca.py Fri Jul 15 10:33:02 2011 -0400 @@ -83,10 +83,12 @@ ncomps = len(summary['sdev']) if type(summary['sdev']) == type({}): - comps = summary['sdev'].keys() + comps_unsorted = summary['sdev'].keys() + comps=[] sd = summary['sdev'].values() for i in range(ncomps): - sd[comps.index('Comp.%s' %(i+1))] = summary['sdev'].values()[i] + sd[i] = summary['sdev'].values()[comps_unsorted.index('Comp.%s' %(i+1))] + comps.append('Comp.%s' %(i+1)) elif type(summary['sdev']) == type([]): comps=[] for i in range(ncomps): --- a/tools/multivariate_stats/pca.xml Thu Jul 14 22:54:43 2011 +0200 +++ b/tools/multivariate_stats/pca.xml Fri Jul 15 10:33:02 2011 -0400 @@ -1,4 +1,4 @@ -<tool id="pca1" name="Principal Component Analysis" version="1.0.1"> +<tool id="pca1" name="Principal Component Analysis" version="1.0.2"><description></description><command interpreter="python"> pca.py Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Fix bug in trackster filtering of GFF datasets.
by Bitbucket 14 Jul '11

14 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/f2638528e904/ changeset: f2638528e904 user: jgoecks date: 2011-07-14 22:54:43 summary: Fix bug in trackster filtering of GFF datasets. affected #: 1 file (0 bytes) --- a/lib/galaxy/visualization/tracks/data_providers.py Thu Jul 14 15:58:06 2011 -0400 +++ b/lib/galaxy/visualization/tracks/data_providers.py Thu Jul 14 22:54:43 2011 +0200 @@ -412,7 +412,7 @@ 'type': 'int', 'index': filter_col, 'tool_id': 'Filter1', - 'tool_exp_name': 'c5' } ] + 'tool_exp_name': 'c6' } ] filter_col += 1 if isinstance( self.original_dataset.datatype, Gtf ): # Create filters based on dataset metadata. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Another patch from Assaf Gordon for the cleanup_datasets.py script.
by Bitbucket 14 Jul '11

14 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/a3fc507f2b42/ changeset: a3fc507f2b42 user: greg date: 2011-07-14 21:58:06 summary: Another patch from Assaf Gordon for the cleanup_datasets.py script. This patch adds messages for the "purge histories" step: 1. A message is printed when processing a new history (so that the user can tell to which history the following dataset/hda messages belong). 2. in "info_only" mode, a message is printed about each deleted history 3. in "info_only" mode, a message is printed for each HDA that is checked 4. The message for HDA is changed to include the associated dataset id. affected #: 1 file (784 bytes) --- a/scripts/cleanup_datasets/cleanup_datasets.py Thu Jul 14 14:25:29 2011 -0400 +++ b/scripts/cleanup_datasets/cleanup_datasets.py Thu Jul 14 15:58:06 2011 -0400 @@ -170,6 +170,7 @@ app.model.History.table.c.update_time < cutoff_time ) ) \ .options( eagerload( 'datasets' ) ) for history in histories: + print "### Processing history id %d (%s)" % (history.id, history.name) for dataset_assoc in history.datasets: _purge_dataset_instance( dataset_assoc, app, remove_from_disk, info_only = info_only ) #mark a DatasetInstance as deleted, clear associated files, and mark the Dataset as deleted if it is deletable if not info_only: @@ -182,6 +183,8 @@ history.purged = True app.sa_session.add( history ) app.sa_session.flush() + else: + print "History id %d will be purged (without 'info_only' mode)" % history.id history_count += 1 stop = time.time() print 'Purged %d histories.' % history_count @@ -364,15 +367,24 @@ # A dataset_instance is either a HDA or an LDDA. Purging a dataset instance marks the instance as deleted, # and marks the associated dataset as deleted if it is not associated with another active DatsetInstance. if not info_only: - print "Marking as deleted: ", dataset_instance.__class__.__name__, " id ", dataset_instance.id + print "Marking as deleted: %s id %d (for dataset id %d)" % \ + ( dataset_instance.__class__.__name__, dataset_instance.id, dataset_instance.dataset.id ) dataset_instance.mark_deleted( include_children = include_children ) dataset_instance.clear_associated_files() app.sa_session.add( dataset_instance ) app.sa_session.flush() app.sa_session.refresh( dataset_instance.dataset ) + else: + print "%s id %d (for dataset id %d) will be marked as deleted (without 'info_only' mode)" % \ + ( dataset_instance.__class__.__name__, dataset_instance.id, dataset_instance.dataset.id ) if is_deletable or _dataset_is_deletable( dataset_instance.dataset ): # Calling methods may have already checked _dataset_is_deletable, if so, is_deletable should be True _delete_dataset( dataset_instance.dataset, app, remove_from_disk, info_only=info_only, is_deletable=is_deletable ) + else: + if info_only: + print "Not deleting dataset ", dataset_instance.dataset.id, " (will be possibly deleted without 'info_only' mode)" + else: + print "Not deleting dataset %d (shared between multiple histories/libraries, at least one not deleted)" % dataset_instance.dataset.id #need to purge children here if include_children: for child in dataset_instance.children: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Change tool shed repository version to be revision, and some fixes for generating and saving repository metadata.
by Bitbucket 14 Jul '11

14 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/e43c31f9e64c/ changeset: e43c31f9e64c user: greg date: 2011-07-14 20:25:29 summary: Change tool shed repository version to be revision, and some fixes for generating and saving repository metadata. affected #: 6 files (984 bytes) --- a/lib/galaxy/webapps/community/controllers/common.py Thu Jul 14 12:12:55 2011 +0200 +++ b/lib/galaxy/webapps/community/controllers/common.py Thu Jul 14 14:25:29 2011 -0400 @@ -75,14 +75,14 @@ .filter( and_( trans.model.RepositoryMetadata.table.c.repository_id == trans.security.decode_id( id ), trans.model.RepositoryMetadata.table.c.changeset_revision == changeset_revision ) ) \ .first() -def set_repository_metadata( trans, id, ctx_str, **kwd ): +def set_repository_metadata( trans, id, change_set_revision, **kwd ): """Set repository metadata""" message = '' status = 'done' repository = get_repository( trans, id ) repo_dir = repository.repo_path repo = hg.repository( ui.ui(), repo_dir ) - change_set = get_change_set( trans, repo, ctx_str ) + change_set = get_change_set( trans, repo, change_set_revision ) invalid_files = [] flush_needed = False if change_set is not None: @@ -103,7 +103,6 @@ full_path = os.path.abspath( os.path.join( root, name ) ) tool = load_tool( trans, full_path ) if tool is not None: - repository_metadata = get_repository_metadata( trans, id, repository.tip ) tool_requirements = [] for tr in tool.requirements: requirement_dict = dict( name=tr.name, @@ -126,6 +125,7 @@ tool_config=os.path.join( root, name ), requirements=tool_requirements, tests=tool_tests ) + repository_metadata = get_repository_metadata( trans, id, change_set_revision ) if repository_metadata: metadata = repository_metadata.metadata if metadata and 'tools' in metadata: @@ -161,32 +161,39 @@ # Find all exported workflows elif name.endswith( '.ga' ): try: - repository_metadata = get_repository_metadata( trans, id, repository.tip ) full_path = os.path.abspath( os.path.join( root, name ) ) # Convert workflow data from json fp = open( full_path, 'rb' ) workflow_text = fp.read() fp.close() - workflow_dict = from_json_string( workflow_text ) + exported_workflow_dict = from_json_string( workflow_text ) + # We'll store everything except the workflow steps in the database. + workflow_dict = { 'a_galaxy_workflow' : exported_workflow_dict[ 'a_galaxy_workflow' ], + 'name' :exported_workflow_dict[ 'name' ], + 'annotation' : exported_workflow_dict[ 'annotation' ], + 'format-version' : exported_workflow_dict[ 'format-version' ] } + repository_metadata = get_repository_metadata( trans, id, change_set_revision ) if repository_metadata: metadata = repository_metadata.metadata - old_metadata_workflows = metadata[ 'workflows' ] - new_metadata_workflows = [] - for workflow_metadata_dict in old_metadata_workflows: - # TODO: what if 2 exported galaxy workflows have the same name, annotation, format-version? - if 'a_galaxy_workflow' in workflow_metadata_dict and util.string_as_bool( workflow_metadata_dict[ 'a_galaxy_workflow' ] ) and \ - 'name' in workflow_metadata_dict and workflow_metadata_dict[ 'name' ] == workflow_dict[ 'name' ] and \ - 'annotation' in workflow_metadata_dict and workflow_metadata_dict[ 'annotation' ] == workflow_dict[ 'annotation' ] and \ - 'format-version' in workflow_metadata_dict and workflow_metadata_dict[ 'format-version' ] == workflow_dict[ 'format-version' ]: - new_metadata_workflows.append( workflow_dict ) - else: - new_metadata_workflows.append( workflow_metadata_dict ) - if metadata is None: - repository_metadata.metadata = {} - repository_metadata.metadata[ 'workflows' ] = new_metadata_workflows - trans.sa_session.add( repository_metadata ) - if not flush_needed: - flush_needed = True + if metadata and 'workflows' in metadata: + metadata_workflows = metadata[ 'workflows' ] + found = False + for workflow_metadata_dict in metadata_workflows: + if 'a_galaxy_workflow' in workflow_metadata_dict and util.string_as_bool( workflow_metadata_dict[ 'a_galaxy_workflow' ] ) and \ + 'name' in workflow_metadata_dict and workflow_metadata_dict[ 'name' ] == exported_workflow_dict[ 'name' ] and \ + 'annotation' in workflow_metadata_dict and workflow_metadata_dict[ 'annotation' ] == exported_workflow_dict[ 'annotation' ] and \ + 'format-version' in workflow_metadata_dict and workflow_metadata_dict[ 'format-version' ] == exported_workflow_dict[ 'format-version' ]: + found = True + break + if not found: + metadata_workflows.append( workflow_dict ) + else: + if metadata is None: + repository_metadata.metadata = {} + repository_metadata.metadata[ 'workflows' ] = workflow_dict + trans.sa_session.add( repository_metadata ) + if not flush_needed: + flush_needed = True else: if 'workflows' in metadata_dict: metadata_dict[ 'workflows' ].append( workflow_dict ) @@ -202,10 +209,10 @@ if not flush_needed: flush_needed = True else: - message = "Repository does not include changeset revision '%s'." % str( ctx_str ) + message = "Repository does not include changeset revision '%s'." % str( change_set_revision ) status = 'error' if invalid_files: - message = "Metadata cannot be defined for change set revision '%s'. Correct the following problems and reset metadata.<br/>" % str( ctx_str ) + message = "Metadata cannot be defined for change set revision '%s'. Correct the following problems and reset metadata.<br/>" % str( change_set_revision ) for itc_tup in invalid_files: message += "<b>%s</b> - %s<br/>" % ( itc_tup[0], itc_tup[1] ) status = 'error' @@ -217,11 +224,11 @@ def get_repository_by_name( trans, name ): """Get a repository from the database via name""" return trans.sa_session.query( app.model.Repository ).filter_by( name=name ).one() -def get_change_set( trans, repo, ctx_str, **kwd ): +def get_change_set( trans, repo, change_set_revision, **kwd ): """Retrieve a specified change set from a repository""" for changeset in repo.changelog: ctx = repo.changectx( changeset ) - if str( ctx ) == ctx_str: + if str( ctx ) == change_set_revision: return ctx return None def get_user( trans, id ): --- a/lib/galaxy/webapps/community/controllers/repository.py Thu Jul 14 12:12:55 2011 +0200 +++ b/lib/galaxy/webapps/community/controllers/repository.py Thu Jul 14 14:25:29 2011 -0400 @@ -74,9 +74,9 @@ class NameColumn( grids.TextColumn ): def get_value( self, trans, grid, repository ): return repository.name - class VersionColumn( grids.TextColumn ): + class RevisionColumn( grids.TextColumn ): def get_value( self, trans, grid, repository ): - return repository.version + return repository.revision class DescriptionColumn( grids.TextColumn ): def get_value( self, trans, grid, repository ): return repository.description @@ -126,8 +126,8 @@ DescriptionColumn( "Synopsis", key="description", attach_popup=False ), - VersionColumn( "Version", - attach_popup=False ), + RevisionColumn( "Revision", + attach_popup=False ), CategoryColumn( "Category", model_class=model.Category, key="Category.name", @@ -878,7 +878,6 @@ folder_contents.append( node ) return folder_contents def __get_files( self, trans, repository, folder_path ): - ok = True def print_ticks( d ): pass cmd = "ls -p '%s'" % folder_path @@ -887,17 +886,22 @@ events={ pexpect.TIMEOUT : print_ticks }, timeout=10 ) if 'No such file or directory' in output: - status = 'error' - message = "No folder named (%s) exists." % folder_path - ok = False - if ok: - return output.split() - return trans.response.send_redirect( web.url_for( controller='repository', - action='browse_repositories', - operation="view_or_manage_repository", - id=trans.security.encode_id( repository.id ), - status=status, - message=message ) ) + if 'root' in output: + # The repository is empty + return [] + else: + # Some strange error occurred, the selected file was displayed, but + # does not exist in the sub-directory from which it was displayed. + # This should not happen... + status = 'error' + message = "No folder named (%s) exists." % folder_path + return trans.response.send_redirect( web.url_for( controller='repository', + action='browse_repositories', + operation="view_or_manage_repository", + id=trans.security.encode_id( repository.id ), + status=status, + message=message ) ) + return output.split() @web.json def get_file_contents( self, trans, file_path ): # Avoid caching --- a/lib/galaxy/webapps/community/model/__init__.py Thu Jul 14 12:12:55 2011 +0200 +++ b/lib/galaxy/webapps/community/model/__init__.py Thu Jul 14 14:25:29 2011 -0400 @@ -114,7 +114,7 @@ return config.get( "paths", option ) raise Exception( "Entry for repository %s missing in %s/hgweb.config file." % ( lhs, os.getcwd() ) ) @property - def version( self ): + def revision( self ): repo = hg.repository( ui.ui(), self.repo_path ) tip_ctx = repo.changectx( repo.changelog.tip() ) return "%s:%s" % ( str( tip_ctx.rev() ), str( repo.changectx( repo.changelog.tip() ) ) ) --- a/templates/webapps/community/repository/manage_repository.mako Thu Jul 14 12:12:55 2011 +0200 +++ b/templates/webapps/community/repository/manage_repository.mako Thu Jul 14 14:25:29 2011 -0400 @@ -122,9 +122,9 @@ <div class="form-row"><label>Version:</label> %if can_view_change_log: - <a href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">${repository.version}</a> + <a href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">${repository.revision}</a> %else: - ${repository.version} + ${repository.revision} %endif </div><div class="form-row"> --- a/templates/webapps/community/repository/rate_repository.mako Thu Jul 14 12:12:55 2011 +0200 +++ b/templates/webapps/community/repository/rate_repository.mako Thu Jul 14 14:25:29 2011 -0400 @@ -104,7 +104,7 @@ </div><div class="form-row"><label>Version:</label> - ${repository.version} + ${repository.revision} <div style="clear: both"></div></div><div class="form-row"> --- a/templates/webapps/community/repository/view_repository.mako Thu Jul 14 12:12:55 2011 +0200 +++ b/templates/webapps/community/repository/view_repository.mako Thu Jul 14 14:25:29 2011 -0400 @@ -120,9 +120,9 @@ <div class="form-row"><label>Version:</label> %if can_view_change_log: - <a href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">${repository.version}</a> + <a href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">${repository.revision}</a> %else: - ${repository.version} + ${repository.revision} %endif </div><div class="form-row"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Trackster: document FeaturePainter object and methods as abstract.
by Bitbucket 14 Jul '11

14 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/fd53d9688eb3/ changeset: fd53d9688eb3 user: jgoecks date: 2011-07-14 12:12:55 summary: Trackster: document FeaturePainter object and methods as abstract. affected #: 1 file (377 bytes) --- a/static/scripts/trackster.js Wed Jul 13 16:51:51 2011 -0400 +++ b/static/scripts/trackster.js Thu Jul 14 12:12:55 2011 +0200 @@ -3307,6 +3307,9 @@ ctx.restore(); } +/** + * Abstract object for painting feature tracks. Subclasses must implement draw_element() for painting to work. + */ var FeaturePainter = function( data, view_start, view_end, prefs, mode ) { Painter.call( this, data, view_start, view_end, prefs, mode ); } @@ -3327,7 +3330,6 @@ }, draw: function( ctx, width, height, slots ) { - var data = this.data, view_start = this.view_start, view_end = this.view_end; ctx.save(); @@ -3356,7 +3358,12 @@ } ctx.restore(); - } + }, + + /** + * Abstract function for drawing an individual feature. NOTE: this method must be implemented by subclasses for drawing to work. + */ + draw_element: function(ctx, mode, feature, slot, tile_low, tile_high, w_scale, y_scale, width ) {} }); // Constants specific to feature tracks moved here (HACKING, these should Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Add support for exproted Galaxy workflows when generating metadata for a tool shed repository.
by Bitbucket 13 Jul '11

13 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/31dda910849a/ changeset: 31dda910849a user: greg date: 2011-07-13 22:51:51 summary: Add support for exproted Galaxy workflows when generating metadata for a tool shed repository. affected #: 4 files (6.6 KB) --- a/lib/galaxy/webapps/community/controllers/common.py Wed Jul 13 09:39:02 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/common.py Wed Jul 13 16:51:51 2011 -0400 @@ -83,7 +83,7 @@ repo_dir = repository.repo_path repo = hg.repository( ui.ui(), repo_dir ) change_set = get_change_set( trans, repo, ctx_str ) - invalid_tool_configs = [] + invalid_files = [] flush_needed = False if change_set is not None: metadata_dict = {} @@ -110,12 +110,22 @@ type=tr.type, version=tr.version ) tool_requirements.append( requirement_dict ) - tool_dict = dict( id = tool.id, - name = tool.name, - version = tool.version, - description = tool.description, - tool_config = os.path.join( root, name ), - requirements = tool_requirements ) + tool_tests = [] + if tool.tests: + for ttb in tool.tests: + test_dict = dict( name=ttb.name, + required_files=ttb.required_files, + inputs=ttb.inputs, + outputs=ttb.outputs ) + tool_tests.append( test_dict ) + tool_dict = dict( id=tool.id, + name=tool.name, + version=tool.version, + description=tool.description, + version_string_cmd = tool.version_string_cmd, + tool_config=os.path.join( root, name ), + requirements=tool_requirements, + tests=tool_tests ) if repository_metadata: metadata = repository_metadata.metadata if metadata and 'tools' in metadata: @@ -127,8 +137,10 @@ found = True tool_metadata_dict[ 'name' ] = tool.name tool_metadata_dict[ 'description' ] = tool.description + tool_metadata_dict[ 'version_string_cmd' ] = tool.version_string_cmd tool_metadata_dict[ 'tool_config' ] = os.path.join( root, name ) tool_metadata_dict[ 'requirements' ] = tool_requirements + tool_metadata_dict[ 'tests' ] = tool_tests flush_needed = True if not found: metadata_tools.append( tool_dict ) @@ -145,7 +157,43 @@ else: metadata_dict[ 'tools' ] = [ tool_dict ] except Exception, e: - invalid_tool_configs.append( ( name, str( e ) ) ) + invalid_files.append( ( name, str( e ) ) ) + # Find all exported workflows + elif name.endswith( '.ga' ): + try: + repository_metadata = get_repository_metadata( trans, id, repository.tip ) + full_path = os.path.abspath( os.path.join( root, name ) ) + # Convert workflow data from json + fp = open( full_path, 'rb' ) + workflow_text = fp.read() + fp.close() + workflow_dict = from_json_string( workflow_text ) + if repository_metadata: + metadata = repository_metadata.metadata + old_metadata_workflows = metadata[ 'workflows' ] + new_metadata_workflows = [] + for workflow_metadata_dict in old_metadata_workflows: + # TODO: what if 2 exported galaxy workflows have the same name, annotation, format-version? + if 'a_galaxy_workflow' in workflow_metadata_dict and util.string_as_bool( workflow_metadata_dict[ 'a_galaxy_workflow' ] ) and \ + 'name' in workflow_metadata_dict and workflow_metadata_dict[ 'name' ] == workflow_dict[ 'name' ] and \ + 'annotation' in workflow_metadata_dict and workflow_metadata_dict[ 'annotation' ] == workflow_dict[ 'annotation' ] and \ + 'format-version' in workflow_metadata_dict and workflow_metadata_dict[ 'format-version' ] == workflow_dict[ 'format-version' ]: + new_metadata_workflows.append( workflow_dict ) + else: + new_metadata_workflows.append( workflow_metadata_dict ) + if metadata is None: + repository_metadata.metadata = {} + repository_metadata.metadata[ 'workflows' ] = new_metadata_workflows + trans.sa_session.add( repository_metadata ) + if not flush_needed: + flush_needed = True + else: + if 'workflows' in metadata_dict: + metadata_dict[ 'workflows' ].append( workflow_dict ) + else: + metadata_dict[ 'workflows' ] = [ workflow_dict ] + except Exception, e: + invalid_files.append( ( name, str( e ) ) ) if metadata_dict: # The metadata_dict dictionary will contain items only # if the repository did not already have metadata set. @@ -156,9 +204,9 @@ else: message = "Repository does not include changeset revision '%s'." % str( ctx_str ) status = 'error' - if invalid_tool_configs: + if invalid_files: message = "Metadata cannot be defined for change set revision '%s'. Correct the following problems and reset metadata.<br/>" % str( ctx_str ) - for itc_tup in invalid_tool_configs: + for itc_tup in invalid_files: message += "<b>%s</b> - %s<br/>" % ( itc_tup[0], itc_tup[1] ) status = 'error' elif flush_needed: --- a/templates/webapps/community/repository/manage_repository.mako Wed Jul 13 09:39:02 2011 -0400 +++ b/templates/webapps/community/repository/manage_repository.mako Wed Jul 13 16:51:51 2011 -0400 @@ -187,7 +187,13 @@ %if metadata: %if 'tools' in metadata: <div class="form-row"> - <label>Tools:</label> + <table width="100%"> + <tr bgcolor="#D8D8D8" width="100%"> + <td><label>Tools:</label></td> + </tr> + </table> + </div> + <div class="form-row"><% tool_dicts = metadata[ 'tools' ] %><table class="grid"><tr> @@ -226,6 +232,34 @@ </div><div style="clear: both"></div> %endif + %if 'workflows' in metadata: + <div class="form-row"> + <table width="100%"> + <tr bgcolor="#D8D8D8" width="100%"> + <td><label>Workflows:</label></td> + </tr> + </table> + </div> + <div style="clear: both"></div> + <div class="form-row"> + <% workflow_dicts = metadata[ 'workflows' ] %> + <table class="grid"> + <tr> + <td><b>name</b></td> + <td><b>format-version</b></td> + <td><b>annotation</b></td> + </tr> + %for workflow_dict in workflow_dicts: + <tr> + <td>${workflow_dict[ 'name' ]}</td> + <td>${workflow_dict[ 'format-version' ]}</td> + <td>${workflow_dict[ 'annotation' ]}</td> + </tr> + %endfor + </table> + </div> + <div style="clear: both"></div> + %endif %endif <form name="set_metadata" action="${h.url_for( controller='repository', action='set_metadata', id=trans.security.encode_id( repository.id ), ctx_str=repository.tip )}" method="post"><div class="form-row"> --- a/templates/webapps/community/repository/view_changelog.mako Wed Jul 13 09:39:02 2011 -0400 +++ b/templates/webapps/community/repository/view_changelog.mako Wed Jul 13 16:51:51 2011 -0400 @@ -94,7 +94,7 @@ %><% display_date = changeset[ 'display_date' ] %> %if test_date != display_date: - <tr colspan="2"><td bgcolor="#D8D8D8 ">${display_date}</td></tr> + <tr colspan="2"><td bgcolor="#D8D8D8">${display_date}</td></tr> %endif <tr><td> --- a/templates/webapps/community/repository/view_repository.mako Wed Jul 13 09:39:02 2011 -0400 +++ b/templates/webapps/community/repository/view_repository.mako Wed Jul 13 16:51:51 2011 -0400 @@ -166,7 +166,13 @@ <div class="toolFormBody"> %if 'tools' in metadata: <div class="form-row"> - <label>Tools:</label> + <table width="100%"> + <tr bgcolor="#D8D8D8" width="100%"> + <td><label>Tools:</label></td> + </tr> + </table> + </div> + <div class="form-row"><% tool_dicts = metadata[ 'tools' ] %><table class="grid"><tr> @@ -205,6 +211,34 @@ </div><div style="clear: both"></div> %endif + %if 'workflows' in metadata: + <div class="form-row"> + <table width="100%"> + <tr bgcolor="#D8D8D8" width="100%"> + <td><label>Workflows:</label></td> + </tr> + </table> + </div> + <div style="clear: both"></div> + <div class="form-row"> + <% workflow_dicts = metadata[ 'workflows' ] %> + <table class="grid"> + <tr> + <td><b>name</b></td> + <td><b>format-version</b></td> + <td><b>annotation</b></td> + </tr> + %for workflow_dict in workflow_dicts: + <tr> + <td>${workflow_dict[ 'name' ]}</td> + <td>${workflow_dict[ 'format-version' ]}</td> + <td>${workflow_dict[ 'annotation' ]}</td> + </tr> + %endfor + </table> + </div> + <div style="clear: both"></div> + %endif </div></div> %endif Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Add patch from Assaf Gordon to the cleanup_datasets.py script. The changes are:
by Bitbucket 13 Jul '11

13 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/b2f7abd50f6a/ changeset: b2f7abd50f6a user: greg date: 2011-07-13 15:39:02 summary: Add patch from Assaf Gordon to the cleanup_datasets.py script. The changes are: 1. If a dataset is skipped (because it's shared/cloned and was already process), no message is printed at all. 2. If a dataset can not be deleted because it is shared, and one instance is not marked as "deleted", a proper message is printed. 3. If a dataset has metadata files, the message is changed depending on "info_only" and "remove_from_disk" flags. 4. The final summary message is slightly changed. affected #: 1 file (514 bytes) --- a/scripts/cleanup_datasets/cleanup_datasets.py Tue Jul 12 18:14:56 2011 -0400 +++ b/scripts/cleanup_datasets/cleanup_datasets.py Wed Jul 13 09:39:02 2011 -0400 @@ -310,17 +310,21 @@ dataset_ids.extend( [ row.id for row in history_dataset_ids_query.execute() ] ) # Process each of the Dataset objects for dataset_id in dataset_ids: + dataset = app.sa_session.query( app.model.Dataset ).get( dataset_id ) + if dataset.id in skip: + continue + skip.append( dataset.id ) print "######### Processing dataset id:", dataset_id - dataset = app.sa_session.query( app.model.Dataset ).get( dataset_id ) - if dataset.id not in skip and _dataset_is_deletable( dataset ): - deleted_dataset_count += 1 - for dataset_instance in dataset.history_associations + dataset.library_associations: - # Mark each associated HDA as deleted - _purge_dataset_instance( dataset_instance, app, remove_from_disk, include_children=True, info_only=info_only, is_deletable=True ) - deleted_instance_count += 1 - skip.append( dataset.id ) + if not _dataset_is_deletable( dataset ): + print "Dataset is not deletable (shared between multiple histories/libraries, at least one is not deleted)" + continue + deleted_dataset_count += 1 + for dataset_instance in dataset.history_associations + dataset.library_associations: + # Mark each associated HDA as deleted + _purge_dataset_instance( dataset_instance, app, remove_from_disk, include_children=True, info_only=info_only, is_deletable=True ) + deleted_instance_count += 1 stop = time.time() - print "Examined %d datasets, marked %d as deleted and purged %d dataset instances" % ( len( skip ), deleted_dataset_count, deleted_instance_count ) + print "Examined %d datasets, marked %d datasets and %d dataset instances (HDA) as deleted" % ( len( skip ), deleted_dataset_count, deleted_instance_count ) print "Total elapsed time: ", stop - start print "##########################################" @@ -396,8 +400,13 @@ .filter( app.model.MetadataFile.table.c.lda_id==ldda.id ): metadata_files.append( metadata_file ) for metadata_file in metadata_files: - print "The following metadata files attached to associations of Dataset '%s' have been purged:" % dataset.id - if not info_only: + op_description = "marked as deleted" + if remove_from_disk: + op_description = op_description + " and purged from disk" + if info_only: + print "The following metadata files attached to associations of Dataset '%s' will be %s (without 'info_only' mode):" % ( dataset.id, op_description ) + else: + print "The following metadata files attached to associations of Dataset '%s' have been %s:" % ( dataset.id, op_description ) if remove_from_disk: try: print "Removing disk file ", metadata_file.file_name Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: kanwei: Improve BLAST parser tool error handling, and improve elementtree import as well.
by Bitbucket 12 Jul '11

12 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/26bffb1b7d57/ changeset: 26bffb1b7d57 user: kanwei date: 2011-07-13 00:14:56 summary: Improve BLAST parser tool error handling, and improve elementtree import as well. affected #: 3 files (260 bytes) --- a/tools/metag_tools/megablast_xml_parser.py Tue Jul 12 17:04:16 2011 -0400 +++ b/tools/metag_tools/megablast_xml_parser.py Tue Jul 12 18:14:56 2011 -0400 @@ -2,12 +2,12 @@ import sys, os, re -assert sys.version_info[:2] >= ( 2, 4 ) - if sys.version_info[:2] >= ( 2, 5 ): - import xml.etree.cElementTree as cElementTree + import xml.etree.cElementTree as ElementTree else: - import cElementTree + from galaxy import eggs + import pkg_resources; pkg_resources.require( "elementtree" ) + from elementtree import ElementTree def stop_err( msg ): sys.stderr.write( "%s\n" % msg ) @@ -34,7 +34,7 @@ # get an iterable try: - context = cElementTree.iterparse( source, events=( "start", "end" ) ) + context = ElementTree.iterparse( source, events=( "start", "end" ) ) except: stop_err( "Invalid data format." ) # turn it into an iterator @@ -46,7 +46,7 @@ stop_err( "Invalid data format." ) outfile = open( sys.argv[2], 'w' ) - try: + try: for event, elem in context: # for every <Iteration> tag if event == "end" and elem.tag == "Iteration": @@ -71,7 +71,7 @@ elem.clear() except: outfile.close() - stop_err( "The input data contains tags that are not recognizable by the tool." ) + stop_err( "The input data is malformed, or there is more than one dataset in the input file. Error: %s" % sys.exc_info()[1] ) outfile.close() --- a/tools/metag_tools/megablast_xml_parser.xml Tue Jul 12 17:04:16 2011 -0400 +++ b/tools/metag_tools/megablast_xml_parser.xml Tue Jul 12 18:14:56 2011 -0400 @@ -2,26 +2,23 @@ <description></description><command interpreter="python">megablast_xml_parser.py $input1 $output1</command><inputs> - <param name="input1" type="data" format="blastxml" label="Megablast XML output" /> + <param name="input1" type="data" format="blastxml" label="Megablast XML output" /></inputs><outputs> - <data name="output1" format="tabular"/> + <data name="output1" format="tabular"/></outputs> -<requirements> - <requirement type="python-module">cElementTree</requirement> -</requirements><tests> - <test> - <param name="input1" value="megablast_xml_parser_test1.gz" ftype="blastxml" /> - <output name="output1" file="megablast_xml_parser_test1_out.tabular" ftype="tabular" /> - </test> + <test> + <param name="input1" value="megablast_xml_parser_test1.gz" ftype="blastxml" /> + <output name="output1" file="megablast_xml_parser_test1_out.tabular" ftype="tabular" /> + </test></tests><help> **What it does** This tool processes the XML output of any NCBI blast tool (if you run your own blast jobs, the XML output can be generated with **-m 7** option). - + ----- **Output fields** --- a/tools/ncbi_blast_plus/blastxml_to_tabular.py Tue Jul 12 17:04:16 2011 -0400 +++ b/tools/ncbi_blast_plus/blastxml_to_tabular.py Tue Jul 12 18:14:56 2011 -0400 @@ -5,7 +5,7 @@ BLAST filename, output format (std for standard 12 columns, or ext for the extended 24 columns offered in the BLAST+ wrappers). -The 12 colums output are 'qseqid sseqid pident length mismatch gapopen qstart +The 12 columns output are 'qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore' or 'std' at the BLAST+ command line, which mean: @@ -51,22 +51,23 @@ Be aware that the sequence in the extended tabular output or XML direct from BLAST+ may or may not use XXXX masking on regions of low complexity. This can throw the off the calculation of percentage identity and gap openings. -[In fact, both BLAST 2.2.24+ and 2.2.25+ have a sutle bug in this regard, +[In fact, both BLAST 2.2.24+ and 2.2.25+ have a subtle bug in this regard, with these numbers changing depending on whether or not the low complexity filter is used.] -This script attempts to produce idential output to what BLAST+ would have done. +This script attempts to produce identical output to what BLAST+ would have done. However, check this with "diff -b ..." since BLAST+ sometimes includes an extra space character (probably a bug). """ import sys import re -assert sys.version_info[:2] >= ( 2, 4 ) if sys.version_info[:2] >= ( 2, 5 ): - import xml.etree.cElementTree as cElementTree + import xml.etree.cElementTree as ElementTree else: - import cElementTree + from galaxy import eggs + import pkg_resources; pkg_resources.require( "elementtree" ) + from elementtree import ElementTree def stop_err( msg ): sys.stderr.write("%s\n" % msg) @@ -90,7 +91,7 @@ # get an iterable try: - context = cElementTree.iterparse(in_file, events=("start", "end")) + context = ElementTree.iterparse(in_file, events=("start", "end")) except: stop_err("Invalid data format.") # turn it into an iterator Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: kanwei: Rename version_string -> version_command, update wrappers
by Bitbucket 12 Jul '11

12 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/12cb939a8147/ changeset: 12cb939a8147 user: kanwei date: 2011-07-12 23:04:16 summary: Rename version_string -> version_command, update wrappers affected #: 7 files (31 bytes) --- a/lib/galaxy/tools/__init__.py Thu Jul 07 11:19:33 2011 +0100 +++ b/lib/galaxy/tools/__init__.py Tue Jul 12 17:04:16 2011 -0400 @@ -397,8 +397,9 @@ self.description = util.xml_text(root, "description") # Versioning for tools self.version_string_cmd = None - if root.find("version_string") is not None: - self.version_string_cmd = root.find("version_string").text + version_cmd = root.find("version_command") + if version_cmd is not None: + self.version_string_cmd = version_cmd.text # Parallelism for tasks, read from tool config. parallelism = root.find("parallelism") if parallelism is not None and parallelism.get("method"): --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Thu Jul 07 11:19:33 2011 +0100 +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Tue Jul 12 17:04:16 2011 -0400 @@ -1,6 +1,6 @@ <tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.11"><description>Search nucleotide database with nucleotide query sequence(s)</description> - <version_string>blastn -version</version_string> + <version_command>blastn -version</version_command><command interpreter="python">hide_stderr.py ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces --- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Thu Jul 07 11:19:33 2011 +0100 +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Tue Jul 12 17:04:16 2011 -0400 @@ -1,6 +1,6 @@ <tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.0.11"><description>Search protein database with protein query sequence(s)</description> - <version_string>blastp -version</version_string> + <version_command>blastp -version</version_command><command interpreter="python">hide_stderr.py ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces --- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Thu Jul 07 11:19:33 2011 +0100 +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Tue Jul 12 17:04:16 2011 -0400 @@ -1,6 +1,6 @@ <tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="0.0.11"><description>Search protein database with translated nucleotide query sequence(s)</description> - <version_string>blastx -version</version_string> + <version_command>blastx -version</version_command><command interpreter="python">hide_stderr.py ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces --- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Thu Jul 07 11:19:33 2011 +0100 +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Tue Jul 12 17:04:16 2011 -0400 @@ -1,6 +1,6 @@ <tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.11"><description>Search translated nucleotide database with protein query sequence(s)</description> - <version_string>tblastn -version</version_string> + <version_command>tblastn -version</version_command><command interpreter="python">hide_stderr.py ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces --- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Thu Jul 07 11:19:33 2011 +0100 +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Tue Jul 12 17:04:16 2011 -0400 @@ -1,6 +1,6 @@ <tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="0.0.11"><description>Search translated nucleotide database with translated nucleotide query sequence(s)</description> - <version_string>tblastx -version</version_string> + <version_command>tblastx -version</version_command><command interpreter="python">hide_stderr.py ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces --- a/tools/ngs_rna/tophat_wrapper.xml Thu Jul 07 11:19:33 2011 +0100 +++ b/tools/ngs_rna/tophat_wrapper.xml Tue Jul 12 17:04:16 2011 -0400 @@ -1,6 +1,6 @@ <tool id="tophat" name="Tophat for Illumina" version="1.5.0"><description>Find splice junctions using RNA-seq data</description> - <version_string>tophat --version</version_string> + <version_command>tophat --version</version_command><requirements><requirement type="package">tophat</requirement></requirements> 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: peterjc: Support new tool version tag in NCBI BLAST+ wrappers
by Bitbucket 12 Jul '11

12 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/632d4c48d97c/ changeset: 632d4c48d97c user: peterjc date: 2011-07-07 12:19:33 summary: Support new tool version tag in NCBI BLAST+ wrappers affected #: 5 files (267 bytes) --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Tue Jul 12 15:02:37 2011 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Thu Jul 07 11:19:33 2011 +0100 @@ -1,5 +1,6 @@ -<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.10"> +<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.11"><description>Search nucleotide database with nucleotide query sequence(s)</description> + <version_string>blastn -version</version_string><command interpreter="python">hide_stderr.py ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces --- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Tue Jul 12 15:02:37 2011 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Thu Jul 07 11:19:33 2011 +0100 @@ -1,5 +1,6 @@ -<tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.0.10"> +<tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.0.11"><description>Search protein database with protein query sequence(s)</description> + <version_string>blastp -version</version_string><command interpreter="python">hide_stderr.py ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces --- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Tue Jul 12 15:02:37 2011 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Thu Jul 07 11:19:33 2011 +0100 @@ -1,5 +1,6 @@ -<tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="0.0.10"> +<tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="0.0.11"><description>Search protein database with translated nucleotide query sequence(s)</description> + <version_string>blastx -version</version_string><command interpreter="python">hide_stderr.py ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces --- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Tue Jul 12 15:02:37 2011 -0400 +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Thu Jul 07 11:19:33 2011 +0100 @@ -1,5 +1,6 @@ -<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.10"> +<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.11"><description>Search translated nucleotide database with protein query sequence(s)</description> + <version_string>tblastn -version</version_string><command interpreter="python">hide_stderr.py ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces --- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Tue Jul 12 15:02:37 2011 -0400 +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Thu Jul 07 11:19:33 2011 +0100 @@ -1,5 +1,6 @@ -<tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="0.0.10"> +<tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="0.0.11"><description>Search translated nucleotide database with translated nucleotide query sequence(s)</description> + <version_string>tblastx -version</version_string><command interpreter="python">hide_stderr.py ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fix for displaying tools.
by Bitbucket 12 Jul '11

12 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/661aca672402/ changeset: 661aca672402 user: greg date: 2011-07-12 21:02:37 summary: Fix for displaying tools. affected #: 1 file (14 bytes) --- a/templates/webapps/community/repository/tool_form.mako Tue Jul 12 13:51:28 2011 -0400 +++ b/templates/webapps/community/repository/tool_form.mako Tue Jul 12 15:02:37 2011 -0400 @@ -84,7 +84,7 @@ field = SelectField( param.name ) field.add_option( param.name, param.name ) field_html = field.get_html() - elif isinstance( param, SelectToolParameter ) and param.data_ref: + elif isinstance( param, SelectToolParameter ) and hasattr( param, 'data_ref' ): field = SelectField( param.name, display=param.display ) field.add_option( param.data_ref, param.data_ref ) field_html = field.get_html( prefix ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Make a backup copy of the tool shed's hgweb.config file just before changes are made to it. Add the ability for a repository owner to change categories associated with their repository.
by Bitbucket 12 Jul '11

12 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/af9b19b57969/ changeset: af9b19b57969 user: greg date: 2011-07-12 19:51:28 summary: Make a backup copy of the tool shed's hgweb.config file just before changes are made to it. Add the ability for a repository owner to change categories associated with their repository. affected #: 4 files (3.8 KB) --- a/lib/galaxy/webapps/community/controllers/repository.py Tue Jul 12 10:07:15 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/repository.py Tue Jul 12 13:51:28 2011 -0400 @@ -356,11 +356,19 @@ if not( VALID_REPOSITORYNAME_RE.match( name ) ): return "Repository names must contain only lower-case letters, numbers and underscore '_'." return '' + def __make_hgweb_config_copy( self, trans, hgweb_config ): + # Make a backup of the hgweb.config file + today = date.today() + backup_date = today.strftime( "%Y_%m_%d" ) + hgweb_config_copy = '%s/hgweb.config_%s_backup' % ( trans.app.config.root, backup_date ) + shutil.copy( os.path.abspath( hgweb_config ), os.path.abspath( hgweb_config_copy ) ) def __add_hgweb_config_entry( self, trans, repository, repository_path ): # Add an entry in the hgweb.config file for a new repository. # An entry looks something like: # repos/test/mira_assembler = database/community_files/000/repo_123. hgweb_config = "%s/hgweb.config" % trans.app.config.root + # Make a backup of the hgweb.config file since we're going to be changing it. + self.__make_hgweb_config_copy( trans, hgweb_config ) entry = "repos/%s/%s = %s" % ( repository.user.username, repository.name, repository_path.lstrip( './' ) ) if os.path.exists( hgweb_config ): output = open( hgweb_config, 'a' ) @@ -374,6 +382,8 @@ # the owner changes the name of the repository. An entry looks something like: # repos/test/mira_assembler = database/community_files/000/repo_123. hgweb_config = "%s/hgweb.config" % trans.app.config.root + # Make a backup of the hgweb.config file since we're going to be changing it. + self.__make_hgweb_config_copy( trans, hgweb_config ) repo_dir = repository.repo_path old_lhs = "repos/%s/%s" % ( repository.user.username, old_repository_name ) old_entry = "%s = %s" % ( old_lhs, repo_dir ) @@ -537,6 +547,7 @@ display_reviews = util.string_as_bool( params.get( 'display_reviews', False ) ) alerts = params.get( 'alerts', '' ) alerts_checked = CheckboxField.is_checked( alerts ) + category_ids = util.listify( params.get( 'category_id', '' ) ) if repository.email_alerts: email_alerts = from_json_string( repository.email_alerts ) else: @@ -572,7 +583,21 @@ if flush_needed: trans.sa_session.add( repository ) trans.sa_session.flush() - message = "The repository information has been updated." + message = "The repository information has been updated." + elif params.get( 'manage_categories_button', False ): + flush_needed = False + # Delete all currently existing categories. + for rca in repository.categories: + trans.sa_session.delete( rca ) + trans.sa_session.flush() + if category_ids: + # Create category associations + for category_id in category_ids: + category = trans.app.model.Category.get( trans.security.decode_id( category_id ) ) + rca = trans.app.model.RepositoryCategoryAssociation( repository, category ) + trans.sa_session.add( rca ) + trans.sa_session.flush() + message = "The repository information has been updated." elif params.get( 'user_access_button', False ): if allow_push not in [ 'none' ]: remove_auth = params.get( 'remove_auth', '' ) @@ -586,6 +611,7 @@ usernames.append( user.username ) usernames = ','.join( usernames ) repository.set_allow_push( usernames, remove_auth=remove_auth ) + message = "The repository information has been updated." elif params.get( 'receive_email_alerts_button', False ): flush_needed = False if alerts_checked: @@ -601,6 +627,7 @@ if flush_needed: trans.sa_session.add( repository ) trans.sa_session.flush() + message = "The repository information has been updated." if error: status = 'error' if repository.allow_push: @@ -615,6 +642,8 @@ metadata = repository_metadata.metadata else: metadata = None + categories = get_categories( trans ) + selected_categories = [ rca.category_id for rca in repository.categories ] return trans.fill_template( '/webapps/community/repository/manage_repository.mako', repo_name=repo_name, description=description, @@ -623,6 +652,8 @@ allow_push_select_field=allow_push_select_field, repo=repo, repository=repository, + selected_categories=selected_categories, + categories=categories, metadata=metadata, avg_rating=avg_rating, display_reviews=display_reviews, --- a/templates/webapps/community/repository/create_repository.mako Tue Jul 12 10:07:15 2011 -0400 +++ b/templates/webapps/community/repository/create_repository.mako Tue Jul 12 13:51:28 2011 -0400 @@ -38,7 +38,7 @@ <div style="clear: both"></div></div><div class="form-row"> - <label>Category</label> + <label>Categories</label><div class="form-row"><select name="category_id" multiple> %for category in categories: @@ -50,6 +50,9 @@ %endfor </select></div> + <div class="toolParamHelp" style="clear: both;"> + Multi-select list - hold the appropriate key while clicking to select multiple categories. + </div><div style="clear: both"></div></div><div class="form-row"> --- a/templates/webapps/community/repository/manage_repository.mako Tue Jul 12 10:07:15 2011 -0400 +++ b/templates/webapps/community/repository/manage_repository.mako Tue Jul 12 13:51:28 2011 -0400 @@ -151,6 +151,34 @@ </form></div></div> +<p/> +<div class="toolForm"> + <div class="toolFormTitle">Manage categories</div> + <div class="toolFormBody"> + <form name="categories" id="categories" action="${h.url_for( controller='repository', action='manage_repository', id=trans.security.encode_id( repository.id ) )}" method="post" > + <div class="form-row"> + <label>Categories</label> + <select name="category_id" multiple> + %for category in categories: + %if category.id in selected_categories: + <option value="${trans.security.encode_id( category.id )}" selected>${category.name}</option> + %else: + <option value="${trans.security.encode_id( category.id )}">${category.name}</option> + %endif + %endfor + </select> + <div class="toolParamHelp" style="clear: both;"> + Multi-select list - hold the appropriate key while clicking to select multiple categories. + </div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <input type="submit" name="manage_categories_button" value="Save"/> + </div> + </form> + </div> +</div> +<p/> %if can_set_metadata: <p/><div class="toolForm"> @@ -215,7 +243,7 @@ %if trans.app.config.smtp_server: <p/><div class="toolForm"> - <div class="toolFormTitle">${repository.name}</div> + <div class="toolFormTitle">Notification on update</div><div class="toolFormBody"><form name="receive_email_alerts" id="receive_email_alerts" action="${h.url_for( controller='repository', action='manage_repository', id=trans.security.encode_id( repository.id ) )}" method="post" ><div class="form-row"> --- a/templates/webapps/community/repository/view_repository.mako Tue Jul 12 10:07:15 2011 -0400 +++ b/templates/webapps/community/repository/view_repository.mako Tue Jul 12 13:51:28 2011 -0400 @@ -145,6 +145,20 @@ %endif </div></div> +%if repository.categories: + <p/> + <div class="toolForm"> + <div class="toolFormTitle">Categories</div> + <div class="toolFormBody"> + %for rca in repository.categories: + <div class="form-row"> + ${rca.category.name} + </div> + %endfor + <div style="clear: both"></div> + </div> + </div> +%endif %if metadata: <p/><div class="toolForm"> @@ -197,7 +211,7 @@ %if trans.user and trans.app.config.smtp_server: <p/><div class="toolForm"> - <div class="toolFormTitle">${repository.name}</div> + <div class="toolFormTitle">Notification on update</div><div class="toolFormBody"><form name="receive_email_alerts" id="receive_email_alerts" action="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ) )}" method="post" ><div class="form-row"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Fix for renaming a tool shed repository, and aother fix for displaying a tool that includes a SelectToolParameter with a data_ref.
by Bitbucket 12 Jul '11

12 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/7c7d01c511d0/ changeset: 7c7d01c511d0 user: greg date: 2011-07-12 16:07:15 summary: Fix for renaming a tool shed repository, and aother fix for displaying a tool that includes a SelectToolParameter with a data_ref. affected #: 5 files (2.0 KB) --- a/lib/galaxy/webapps/community/controllers/repository.py Mon Jul 11 14:48:12 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/repository.py Tue Jul 12 10:07:15 2011 -0400 @@ -369,6 +369,23 @@ output.write( '[paths]\n' ) output.write( "%s\n" % entry ) output.close() + def __change_hgweb_config_entry( self, trans, repository, old_repository_name, new_repository_name ): + # Change an entry in the hgweb.config file for a repository. This only happens when + # the owner changes the name of the repository. An entry looks something like: + # repos/test/mira_assembler = database/community_files/000/repo_123. + hgweb_config = "%s/hgweb.config" % trans.app.config.root + repo_dir = repository.repo_path + old_lhs = "repos/%s/%s" % ( repository.user.username, old_repository_name ) + old_entry = "%s = %s" % ( old_lhs, repo_dir ) + new_entry = "repos/%s/%s = %s\n" % ( repository.user.username, new_repository_name, repo_dir ) + tmp_fd, tmp_fname = tempfile.mkstemp() + new_hgweb_config = open( tmp_fname, 'wb' ) + for i, line in enumerate( open( hgweb_config ) ): + if line.startswith( old_lhs ): + new_hgweb_config.write( new_entry ) + else: + new_hgweb_config.write( line ) + shutil.move( tmp_fname, os.path.abspath( hgweb_config ) ) def __create_hgrc_file( self, repository ): # At this point, an entry for the repository is required to be in the hgweb.config # file so we can call repository.repo_path. @@ -511,7 +528,8 @@ message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) repository = get_repository( trans, id ) - repo = hg.repository( ui.ui(), repository.repo_path ) + repo_dir = repository.repo_path + repo = hg.repository( ui.ui(), repo_dir ) repo_name = util.restore_text( params.get( 'repo_name', repository.name ) ) description = util.restore_text( params.get( 'description', repository.description ) ) long_description = util.restore_text( params.get( 'long_description', repository.long_description ) ) @@ -528,6 +546,7 @@ user = trans.user if params.get( 'edit_repository_button', False ): flush_needed = False + # TODO: add a can_manage in the security agent. if user != repository.user: message = "You are not the owner of this repository, so you cannot manage it." status = error @@ -541,6 +560,7 @@ if message: error = True else: + self.__change_hgweb_config_entry( trans, repository, repository.name, repo_name ) repository.name = repo_name flush_needed = True if description != repository.description: @@ -552,6 +572,7 @@ if flush_needed: trans.sa_session.add( repository ) trans.sa_session.flush() + message = "The repository information has been updated." elif params.get( 'user_access_button', False ): if allow_push not in [ 'none' ]: remove_auth = params.get( 'remove_auth', '' ) --- a/lib/galaxy/webapps/community/model/__init__.py Mon Jul 11 14:48:12 2011 -0400 +++ b/lib/galaxy/webapps/community/model/__init__.py Tue Jul 12 10:07:15 2011 -0400 @@ -4,7 +4,7 @@ Naming: try to use class names that have a distinct plural form so that the relationship cardinalities are obvious (e.g. prefer Dataset to Data) """ -import os.path, os, errno, sys, codecs, operator, tempfile, logging, tarfile, mimetypes, ConfigParser +import os.path, os, errno, sys, codecs, operator, logging, tarfile, mimetypes, ConfigParser from galaxy import util from galaxy.util.bunch import Bunch from galaxy.util.hash_util import * --- a/templates/webapps/community/repository/manage_repository.mako Mon Jul 11 14:48:12 2011 -0400 +++ b/templates/webapps/community/repository/manage_repository.mako Tue Jul 12 10:07:15 2011 -0400 @@ -9,6 +9,7 @@ can_push = trans.app.security_agent.can_push( trans.user, repository ) can_upload = can_push can_browse_contents = not is_new + can_set_metadata = not is_new can_rate = not is_new and trans.user and repository.user != trans.user can_view_change_log = not is_new if can_push: @@ -79,10 +80,10 @@ %endif %if can_browse_contents: <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='zip' )}">Download as a zip file</a> %endif - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='zip' )}">Download as a zip file</a></div> %endif </ul> @@ -150,65 +151,67 @@ </form></div></div> -<p/> -<div class="toolForm"> - <div class="toolFormTitle">Repository metadata</div> - <div class="toolFormBody"> - %if metadata: - %if 'tools' in metadata: +%if can_set_metadata: + <p/> + <div class="toolForm"> + <div class="toolFormTitle">Repository metadata</div> + <div class="toolFormBody"> + %if metadata: + %if 'tools' in metadata: + <div class="form-row"> + <label>Tools:</label> + <% tool_dicts = metadata[ 'tools' ] %> + <table class="grid"> + <tr> + <td><b>name</b></td> + <td><b>description</b></td> + <td><b>version</b></td> + <td><b>requirements</b></td> + </tr> + %for tool_dict in tool_dicts: + <tr> + <td><a href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=tool_dict[ 'tool_config' ] )}">${tool_dict[ 'name' ]}</a></td> + <td>${tool_dict[ 'description' ]}</td> + <td>${tool_dict[ 'version' ]}</td> + <td> + <% + if 'requirements' in tool_dict: + requirements = tool_dict[ 'requirements' ] + else: + requirements = None + %> + %if requirements: + <% + requirements_str = '' + for requirement_dict in tool_dict[ 'requirements' ]: + requirements_str += '%s (%s), ' % ( requirement_dict[ 'name' ], requirement_dict[ 'type' ] ) + requirements_str = requirements_str.rstrip( ', ' ) + %> + ${requirements_str} + %else: + none + %endif + </td> + </tr> + %endfor + </table> + </div> + <div style="clear: both"></div> + %endif + %endif + <form name="set_metadata" action="${h.url_for( controller='repository', action='set_metadata', id=trans.security.encode_id( repository.id ), ctx_str=repository.tip )}" method="post"><div class="form-row"> - <label>Tools:</label> - <% tool_dicts = metadata[ 'tools' ] %> - <table class="grid"> - <tr> - <td><b>name</b></td> - <td><b>description</b></td> - <td><b>version</b></td> - <td><b>requirements</b></td> - </tr> - %for tool_dict in tool_dicts: - <tr> - <td><a href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=tool_dict[ 'tool_config' ] )}">${tool_dict[ 'name' ]}</a></td> - <td>${tool_dict[ 'description' ]}</td> - <td>${tool_dict[ 'version' ]}</td> - <td> - <% - if 'requirements' in tool_dict: - requirements = tool_dict[ 'requirements' ] - else: - requirements = None - %> - %if requirements: - <% - requirements_str = '' - for requirement_dict in tool_dict[ 'requirements' ]: - requirements_str += '%s (%s), ' % ( requirement_dict[ 'name' ], requirement_dict[ 'type' ] ) - requirements_str = requirements_str.rstrip( ', ' ) - %> - ${requirements_str} - %else: - none - %endif - </td> - </tr> - %endfor - </table> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input type="submit" name="set_metadata_button" value="Reset metadata"/> + </div> + <div class="toolParamHelp" style="clear: both;"> + Inspect the repository and reset the above attributes for the repository tip. + </div></div> - <div style="clear: both"></div> - %endif - %endif - <form name="set_metadata" action="${h.url_for( controller='repository', action='set_metadata', id=trans.security.encode_id( repository.id ), ctx_str=repository.tip )}" method="post"> - <div class="form-row"> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="submit" name="set_metadata_button" value="Reset metadata"/> - </div> - <div class="toolParamHelp" style="clear: both;"> - Inspect the repository and reset the above attributes for the repository tip. - </div> - </div> - </form> + </form> + </div></div> -</div> +%endif %if trans.app.config.smtp_server: <p/><div class="toolForm"> --- a/templates/webapps/community/repository/tool_form.mako Mon Jul 11 14:48:12 2011 -0400 +++ b/templates/webapps/community/repository/tool_form.mako Tue Jul 12 10:07:15 2011 -0400 @@ -4,7 +4,7 @@ <% from galaxy.util.expressions import ExpressionContext from galaxy import util - from galaxy.tools.parameters.basic import DataToolParameter, ColumnListParameter + from galaxy.tools.parameters.basic import DataToolParameter, ColumnListParameter, SelectToolParameter from galaxy.web.form_builder import SelectField is_admin = trans.user_is_admin() @@ -84,6 +84,10 @@ field = SelectField( param.name ) field.add_option( param.name, param.name ) field_html = field.get_html() + elif isinstance( param, SelectToolParameter ) and param.data_ref: + field = SelectField( param.name, display=param.display ) + field.add_option( param.data_ref, param.data_ref ) + field_html = field.get_html( prefix ) else: field = param.get_html_field( trans, None, other_values ) field_html = field.get_html( prefix ) --- a/templates/webapps/community/repository/view_repository.mako Mon Jul 11 14:48:12 2011 -0400 +++ b/templates/webapps/community/repository/view_repository.mako Tue Jul 12 10:07:15 2011 -0400 @@ -79,10 +79,10 @@ %endif %if can_browse_contents: <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='zip' )}">Download as a zip file</a> %endif - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='zip' )}">Download as a zip file</a></div> %endif </ul> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fix for setting tool shed repository etadata multiple times when nothing in the repository has changed.
by Bitbucket 11 Jul '11

11 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/38899d79629b/ changeset: 38899d79629b user: greg date: 2011-07-11 20:48:12 summary: Fix for setting tool shed repository etadata multiple times when nothing in the repository has changed. affected #: 1 file (178 bytes) --- a/lib/galaxy/webapps/community/controllers/common.py Mon Jul 11 14:10:56 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/common.py Mon Jul 11 14:48:12 2011 -0400 @@ -146,10 +146,13 @@ metadata_dict[ 'tools' ] = [ tool_dict ] except Exception, e: invalid_tool_configs.append( ( name, str( e ) ) ) - repository_metadata = trans.model.RepositoryMetadata( repository.id, repository.tip, metadata_dict ) - trans.sa_session.add( repository_metadata ) - if not flush_needed: - flush_needed = True + if metadata_dict: + # The metadata_dict dictionary will contain items only + # if the repository did not already have metadata set. + repository_metadata = trans.model.RepositoryMetadata( repository.id, repository.tip, metadata_dict ) + trans.sa_session.add( repository_metadata ) + if not flush_needed: + flush_needed = True else: message = "Repository does not include changeset revision '%s'." % str( ctx_str ) status = 'error' Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Bug fix for setting tool shed repository metadata on repositories containing more than 1 tool.
by Bitbucket 11 Jul '11

11 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/6e9fca39e3f4/ changeset: 6e9fca39e3f4 user: greg date: 2011-07-11 20:10:56 summary: Bug fix for setting tool shed repository metadata on repositories containing more than 1 tool. affected #: 1 file (106 bytes) --- a/lib/galaxy/webapps/community/controllers/common.py Mon Jul 11 13:45:57 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/common.py Mon Jul 11 14:10:56 2011 -0400 @@ -86,6 +86,7 @@ invalid_tool_configs = [] flush_needed = False if change_set is not None: + metadata_dict = {} for root, dirs, files in os.walk( repo_dir ): if not root.find( '.hg' ) >= 0 and not root.find( 'hgrc' ) >= 0: if '.hg' in dirs: @@ -139,13 +140,16 @@ if not flush_needed: flush_needed = True else: - metadata_dict = dict( tools = [ tool_dict ] ) - repository_metadata = trans.model.RepositoryMetadata( repository.id, repository.tip, metadata_dict ) - trans.sa_session.add( repository_metadata ) - if not flush_needed: - flush_needed = True + if 'tools' in metadata_dict: + metadata_dict[ 'tools' ].append( tool_dict ) + else: + metadata_dict[ 'tools' ] = [ tool_dict ] except Exception, e: invalid_tool_configs.append( ( name, str( e ) ) ) + repository_metadata = trans.model.RepositoryMetadata( repository.id, repository.tip, metadata_dict ) + trans.sa_session.add( repository_metadata ) + if not flush_needed: + flush_needed = True else: message = "Repository does not include changeset revision '%s'." % str( ctx_str ) status = 'error' Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Allow an admin user to manage repositories they do not own.
by Bitbucket 11 Jul '11

11 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/0007cf69d1dc/ changeset: 0007cf69d1dc user: greg date: 2011-07-11 19:45:57 summary: Allow an admin user to manage repositories they do not own. affected #: 1 file (61 bytes) --- a/lib/galaxy/webapps/community/controllers/repository.py Mon Jul 11 13:34:23 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/repository.py Mon Jul 11 13:45:57 2011 -0400 @@ -214,7 +214,8 @@ if operation == "view_or_manage_repository": repository_id = kwd.get( 'id', None ) repository = get_repository( trans, repository_id ) - if repository.user == trans.user: + is_admin = trans.user_is_admin() + if is_admin or repository.user == trans.user: return trans.response.send_redirect( web.url_for( controller='repository', action='manage_repository', **kwd ) ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Do not set tool shed repository metadata if tool does not load. Add tool config <requirements> settings to tool shed repository metadata.
by Bitbucket 11 Jul '11

11 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/34c190323b36/ changeset: 34c190323b36 user: greg date: 2011-07-11 19:34:23 summary: Do not set tool shed repository metadata if tool does not load. Add tool config <requirements> settings to tool shed repository metadata. affected #: 5 files (4.3 KB) --- a/lib/galaxy/webapps/community/controllers/common.py Fri Jul 08 16:11:28 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/common.py Mon Jul 11 13:34:23 2011 -0400 @@ -75,9 +75,100 @@ .filter( and_( trans.model.RepositoryMetadata.table.c.repository_id == trans.security.decode_id( id ), trans.model.RepositoryMetadata.table.c.changeset_revision == changeset_revision ) ) \ .first() +def set_repository_metadata( trans, id, ctx_str, **kwd ): + """Set repository metadata""" + message = '' + status = 'done' + repository = get_repository( trans, id ) + repo_dir = repository.repo_path + repo = hg.repository( ui.ui(), repo_dir ) + change_set = get_change_set( trans, repo, ctx_str ) + invalid_tool_configs = [] + flush_needed = False + if change_set is not None: + for root, dirs, files in os.walk( repo_dir ): + if not root.find( '.hg' ) >= 0 and not root.find( 'hgrc' ) >= 0: + if '.hg' in dirs: + # Don't visit .hg directories - should be impossible since we don't + # allow uploaded archives that contain .hg dirs, but just in case... + dirs.remove( '.hg' ) + if 'hgrc' in files: + # Don't include hgrc files in commit. + files.remove( 'hgrc' ) + for name in files: + # Find all tool configs. + if name.endswith( '.xml' ): + try: + full_path = os.path.abspath( os.path.join( root, name ) ) + tool = load_tool( trans, full_path ) + if tool is not None: + repository_metadata = get_repository_metadata( trans, id, repository.tip ) + tool_requirements = [] + for tr in tool.requirements: + requirement_dict = dict( name=tr.name, + type=tr.type, + version=tr.version ) + tool_requirements.append( requirement_dict ) + tool_dict = dict( id = tool.id, + name = tool.name, + version = tool.version, + description = tool.description, + tool_config = os.path.join( root, name ), + requirements = tool_requirements ) + if repository_metadata: + metadata = repository_metadata.metadata + if metadata and 'tools' in metadata: + metadata_tools = metadata[ 'tools' ] + found = False + for tool_metadata_dict in metadata_tools: + if 'id' in tool_metadata_dict and tool_metadata_dict[ 'id' ] == tool.id and \ + 'version' in tool_metadata_dict and tool_metadata_dict[ 'version' ] == tool.version: + found = True + tool_metadata_dict[ 'name' ] = tool.name + tool_metadata_dict[ 'description' ] = tool.description + tool_metadata_dict[ 'tool_config' ] = os.path.join( root, name ) + tool_metadata_dict[ 'requirements' ] = tool_requirements + flush_needed = True + if not found: + metadata_tools.append( tool_dict ) + else: + if metadata is None: + repository_metadata.metadata = {} + repository_metadata.metadata[ 'tools' ] = [ tool_dict ] + trans.sa_session.add( repository_metadata ) + if not flush_needed: + flush_needed = True + else: + metadata_dict = dict( tools = [ tool_dict ] ) + repository_metadata = trans.model.RepositoryMetadata( repository.id, repository.tip, metadata_dict ) + trans.sa_session.add( repository_metadata ) + if not flush_needed: + flush_needed = True + except Exception, e: + invalid_tool_configs.append( ( name, str( e ) ) ) + else: + message = "Repository does not include changeset revision '%s'." % str( ctx_str ) + status = 'error' + if invalid_tool_configs: + message = "Metadata cannot be defined for change set revision '%s'. Correct the following problems and reset metadata.<br/>" % str( ctx_str ) + for itc_tup in invalid_tool_configs: + message += "<b>%s</b> - %s<br/>" % ( itc_tup[0], itc_tup[1] ) + status = 'error' + elif flush_needed: + # We only flush if there are no tool config errors, so change sets will only have metadata + # if everything in them is valid. + trans.sa_session.flush() + return message, status def get_repository_by_name( trans, name ): """Get a repository from the database via name""" return trans.sa_session.query( app.model.Repository ).filter_by( name=name ).one() +def get_change_set( trans, repo, ctx_str, **kwd ): + """Retrieve a specified change set from a repository""" + for changeset in repo.changelog: + ctx = repo.changectx( changeset ) + if str( ctx ) == ctx_str: + return ctx + return None def get_user( trans, id ): """Get a user from the database""" return trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( id ) ) @@ -184,77 +275,3 @@ ToolClass = Tool return ToolClass( config_file, root, trans.app ) return None -def set_repository_metadata( trans, id, ctx_str, **kwd ): - """Set repository metadata""" - message = '' - status = 'done' - repository = get_repository( trans, id ) - repo_dir = repository.repo_path - repo = hg.repository( ui.ui(), repo_dir ) - found = False - invalid_tool_configs = [] - for changeset in repo.changelog: - ctx = repo.changectx( changeset ) - if str( ctx ) == ctx_str: - found = True - break - if found: - for root, dirs, files in os.walk( repo_dir ): - if not root.find( '.hg' ) >= 0 and not root.find( 'hgrc' ) >= 0: - if '.hg' in dirs: - # Don't visit .hg directories - should be impossible since we don't - # allow uploaded archives that contain .hg dirs, but just in case... - dirs.remove( '.hg' ) - if 'hgrc' in files: - # Don't include hgrc files in commit. - files.remove( 'hgrc' ) - for name in files: - # Find all tool configs. - if name.endswith( '.xml' ): - try: - full_path = os.path.abspath( os.path.join( root, name ) ) - tool = load_tool( trans, full_path ) - if tool is not None: - repository_metadata = get_repository_metadata( trans, id, repository.tip ) - # TODO: add more stuff, like requirements - tool_dict = dict( id = tool.id, - name = tool.name, - version = tool.version, - description = tool.description, - tool_config = full_path ) - if repository_metadata: - metadata = repository_metadata.metadata - if metadata and 'tools' in metadata: - metadata_tools = metadata[ 'tools' ] - found = False - for tool_metadata_dict in metadata_tools: - if 'id' in tool_metadata_dict and tool_metadata_dict[ 'id' ] == tool.id and \ - 'version' in tool_metadata_dict and tool_metadata_dict[ 'version' ] == tool.version: - found = True - tool_metadata_dict[ 'name' ] = tool.name - tool_metadata_dict[ 'description' ] = tool.description - tool_metadata_dict[ 'tool_config' ] = os.path.join( root, name ) - # TODO: add more stuff, like tool requirements, code files, etc - if not found: - metadata_tools.append( tool_dict ) - else: - if metadata is None: - repository_metadata.metadata = {} - repository_metadata.metadata[ 'tools' ] = [ tool_dict ] - trans.sa_session.add( repository_metadata ) - else: - metadata_dict = dict( tools = [ tool_dict ] ) - repository_metadata = trans.model.RepositoryMetadata( repository.id, repository.tip, metadata_dict ) - trans.sa_session.add( repository_metadata ) - trans.sa_session.flush() - except Exception, e: - invalid_tool_configs.append( ( name, str( e ) ) ) - else: - message = "Repository does not include changeset revision '%s'." % str( ctx_str ) - status = 'error' - if invalid_tool_configs: - message = "The following tool configs are invalid and were not added to the repository metadata:<br/>" - for itc_tup in invalid_tool_configs: - message += "<b>%s</b> - %s<br/>" % ( itc_tup[0], itc_tup[1] ) - status = 'error' - return message, status --- a/lib/galaxy/webapps/community/controllers/repository.py Fri Jul 08 16:11:28 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/repository.py Mon Jul 11 13:34:23 2011 -0400 @@ -643,13 +643,8 @@ status = params.get( 'status', 'done' ) repository = get_repository( trans, id ) repo = hg.repository( ui.ui(), repository.repo_path ) - found = False - for changeset in repo.changelog: - ctx = repo.changectx( changeset ) - if str( ctx ) == ctx_str: - found = True - break - if not found: + ctx = get_change_set( trans, repo, ctx_str ) + if ctx is None: message = "Repository does not include changeset revision '%s'." % str( ctx_str ) status = 'error' return trans.response.send_redirect( web.url_for( controller='repository', @@ -753,6 +748,8 @@ @web.require_login( "set repository metadata" ) def set_metadata( self, trans, id, ctx_str, **kwd ): message, status = set_repository_metadata( trans, id, ctx_str, **kwd ) + if not message: + message = "Metadata for change set revision '%s' has been reset." % str( ctx_str ) return trans.response.send_redirect( web.url_for( controller='repository', action='manage_repository', id=id, --- a/templates/webapps/community/repository/manage_repository.mako Fri Jul 08 16:11:28 2011 -0400 +++ b/templates/webapps/community/repository/manage_repository.mako Mon Jul 11 13:34:23 2011 -0400 @@ -160,11 +160,36 @@ <label>Tools:</label><% tool_dicts = metadata[ 'tools' ] %><table class="grid"> + <tr> + <td><b>name</b></td> + <td><b>description</b></td> + <td><b>version</b></td> + <td><b>requirements</b></td> + </tr> %for tool_dict in tool_dicts: <tr><td><a href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=tool_dict[ 'tool_config' ] )}">${tool_dict[ 'name' ]}</a></td><td>${tool_dict[ 'description' ]}</td> - <td>version: ${tool_dict[ 'version' ]}</td> + <td>${tool_dict[ 'version' ]}</td> + <td> + <% + if 'requirements' in tool_dict: + requirements = tool_dict[ 'requirements' ] + else: + requirements = None + %> + %if requirements: + <% + requirements_str = '' + for requirement_dict in tool_dict[ 'requirements' ]: + requirements_str += '%s (%s), ' % ( requirement_dict[ 'name' ], requirement_dict[ 'type' ] ) + requirements_str = requirements_str.rstrip( ', ' ) + %> + ${requirements_str} + %else: + none + %endif + </td></tr> %endfor </table> --- a/templates/webapps/community/repository/tool_form.mako Fri Jul 08 16:11:28 2011 -0400 +++ b/templates/webapps/community/repository/tool_form.mako Mon Jul 11 13:34:23 2011 -0400 @@ -15,6 +15,10 @@ can_rate = trans.user and repository.user != trans.user can_manage = is_admin or repository.user == trans.user can_view_change_log = not is_new + if can_push: + browse_label = 'Browse or delete repository files' + else: + browse_label = 'Browse repository files' %><html> @@ -116,6 +120,9 @@ %if can_view_change_log: <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> %endif + %if can_browse_contents: + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> + %endif %if can_rate: <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a> %endif --- a/templates/webapps/community/repository/view_repository.mako Fri Jul 08 16:11:28 2011 -0400 +++ b/templates/webapps/community/repository/view_repository.mako Mon Jul 11 13:34:23 2011 -0400 @@ -155,11 +155,36 @@ <label>Tools:</label><% tool_dicts = metadata[ 'tools' ] %><table class="grid"> + <tr> + <td><b>name</b></td> + <td><b>description</b></td> + <td><b>version</b></td> + <td><b>requirements</b></td> + </tr> %for tool_dict in tool_dicts: <tr><td><a href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=tool_dict[ 'tool_config' ] )}">${tool_dict[ 'name' ]}</a></td><td>${tool_dict[ 'description' ]}</td><td>version: ${tool_dict[ 'version' ]}</td> + <td> + <% + if 'requirements' in tool_dict: + requirements = tool_dict[ 'requirements' ] + else: + requirements = None + %> + %if requirements: + <% + requirements_str = '' + for requirement_dict in tool_dict[ 'requirements' ]: + requirements_str += '%s (%s), ' % ( requirement_dict[ 'name' ], requirement_dict[ 'type' ] ) + requirements_str = requirements_str.rstrip( ', ' ) + %> + ${requirements_str} + %else: + none + %endif + </td></tr> %endfor </table> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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