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commit/galaxy-central: dan: Allow importing one's own history.
by Bitbucket 22 Mar '11

22 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/dc9efb540f61/ changeset: r5248:dc9efb540f61 user: dan date: 2011-03-23 00:43:32 summary: Allow importing one's own history. affected #: 1 file (49 bytes) --- a/lib/galaxy/web/controllers/history.py Tue Mar 22 17:49:09 2011 -0400 +++ b/lib/galaxy/web/controllers/history.py Tue Mar 22 19:43:32 2011 -0400 @@ -669,8 +669,9 @@ if not trans.user_is_admin() and not self.security_check( user, import_history, check_ownership=False, check_accessible=True ): return trans.show_error_message( "You cannot access this history.<br>You can %s." % referer_message, use_panels=True ) if user: - if import_history.user_id == user.id: - return trans.show_error_message( "You cannot import your own history.<br>You can %s." % referer_message, use_panels=True ) + #dan: I can import my own history. + #if import_history.user_id == user.id: + # return trans.show_error_message( "You cannot import your own history.<br>You can %s." % referer_message, use_panels=True ) new_history = import_history.copy( target_user=user ) new_history.name = "imported: " + new_history.name new_history.user_id = user.id 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: Refactor Grouping tool and fix bug where data after a blank value in the group_by column returns the wrong data.
by Bitbucket 22 Mar '11

22 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/4d521da04318/ changeset: r5247:4d521da04318 user: kanwei date: 2011-03-22 22:49:09 summary: Refactor Grouping tool and fix bug where data after a blank value in the group_by column returns the wrong data. affected #: 2 files (5.1 KB) --- a/tools/stats/grouping.py Tue Mar 22 14:08:32 2011 -0400 +++ b/tools/stats/grouping.py Tue Mar 22 17:49:09 2011 -0400 @@ -1,10 +1,12 @@ #!/usr/bin/env python -#Guruprasad Ananda +# Guruprasad Ananda +# Refactored 2011, Kanwei Li """ This tool provides the SQL "group by" functionality. """ import sys, string, re, commands, tempfile, random from rpy import * +from itertools import groupby def stop_err(msg): sys.stderr.write(msg) @@ -53,10 +55,10 @@ stop_err( "Group column not specified." ) str_ops = ['c', 'length', 'unique', 'random', 'cuniq', 'Mode'] #ops that can handle string/non-numeric inputs - for k,col in enumerate(cols): + for k, col in enumerate(cols): col = int(col)-1 if ops[k] not in str_ops: - # We'll get here only if the user didn't choose 'Concatenate' or 'Count' or 'Count Distinct' or 'pick randmly', which are the + # We'll get here only if the user didn't choose 'Concatenate' or 'Count' or 'Count Distinct' or 'pick randomly', which are the # only aggregation functions that can be used on columns containing strings. try: float( elems[col] ) @@ -90,191 +92,94 @@ if error_code != 0: stop_err( "Sorting input dataset resulted in error: %s: %s" %( error_code, stdout )) - prev_item = "" - prev_vals = [] + prev_item = None skipped_lines = 0 - first_invalid_line = 0 - invalid_line = '' + first_invalid_line = None invalid_value = '' invalid_column = 0 fout = open(sys.argv[1], "w") - for ii, line in enumerate( file( tmpfile.name )): - if line and not line.startswith( '#' ): - line = line.rstrip( '\r\n' ) - try: - fields = line.split("\t") - item = fields[group_col] - if ignorecase == 1: - item = item.lower() - if prev_item != "": - # At this level, we're grouping on values (item and prev_item) in group_col - if item == prev_item: - # Keep iterating and storing values until a new value is encountered. - for i, col in enumerate(cols): - col = int(col)-1 - valid = True - # Before appending the current value, make sure it is numeric if the - # operation for the column requires it. - if ops[i] not in str_ops: - try: - float( fields[col].strip()) - except: - valid = False - skipped_lines += 1 - if not first_invalid_line: - first_invalid_line = ii+1 - invalid_value = fields[col] - invalid_column = col+1 - if valid: - prev_vals[i].append(fields[col].strip()) - else: - """ - When a new value is encountered, write the previous value and the - corresponding aggregate values into the output file. This works - due to the sort on group_col we've applied to the data above. - """ - out_str = prev_item - multiple_modes = False - mode_index = None - for i, op in enumerate( ops ): - if op == 'cuniq': - rfunc = "r.c" - else: - rfunc = "r." + op - if op not in str_ops: - for j, elem in enumerate( prev_vals[i] ): - prev_vals[i][j] = float( elem ) - rout = eval( rfunc )( prev_vals[i] ) - if rounds[i] == 'yes': - rout = int(round(float(rout))) - else: - rout = '%g' %(float(rout)) - else: - if op != 'random': - rout = eval( rfunc )( prev_vals[i] ) - else: - try: - rand_index = random.randint(0,len(prev_vals[i])-1) #if the two inputs to randint are equal, it seems to throw a ValueError. This can't be reproduced with the python interpreter in its interactive mode. - except Exception, ValueError: - rand_index = 0 - rout = prev_vals[i][rand_index] - - if op == 'Mode' and rout == '>1 mode': - multiple_modes = True - mode_index = i - if op == 'unique': - rfunc = "r.length" - rout = eval( rfunc )( rout ) - if op in ['c', 'cuniq']: - if op == 'c': - if type(rout) == type([]): - out_str += "\t" + ','.join(rout) - else: - out_str += "\t" + str(rout) - else: - if type(rout) == type([]): - out_str += "\t" + ','.join(list(set(rout))) - else: - out_str += "\t" + str(rout) - else: - out_str += "\t" + str(rout) - if multiple_modes and mode_index != None: - out_str_list = out_str.split('\t') - for val in prev_vals[mode_index]: - out_str = '\t'.join(out_str_list[:mode_index+1]) + '\t' + str(val) + '\t' + '\t'.join(out_str_list[mode_index+2:]) - print >>fout, out_str.rstrip('\t') - else: - print >>fout, out_str - - prev_item = item - prev_vals = [] - for col in cols: - col = int(col)-1 - val_list = [] - val_list.append(fields[col].strip()) - prev_vals.append(val_list) - else: - # This only occurs once, right at the start of the iteration. - prev_item = item - for col in cols: - col = int(col)-1 - val_list = [] - val_list.append(fields[col].strip()) - prev_vals.append(val_list) - - except Exception, exc: - skipped_lines += 1 - if not first_invalid_line: - first_invalid_line = ii+1 - else: - skipped_lines += 1 - if not first_invalid_line: - first_invalid_line = ii+1 - - # Handle the last grouped value - out_str = prev_item - multiple_modes = False - mode_index = None - for i, op in enumerate(ops): - if op == 'cuniq': - rfunc = "r.c" - else: - rfunc = "r." + op - try: + def is_new_item(line): + item = line.strip().split("\t")[group_col] + if ignorecase == 1: + item = item.lower() + return item + + for key, line_list in groupby(tmpfile, key=is_new_item): + op_vals = [ [] for op in cols ] + out_str = key + multiple_modes = False + mode_index = None + + for line in line_list: + fields = line.strip().split("\t") + for i, col in enumerate(cols): + col = int(col)-1 # cXX from galaxy is 1-based + val = fields[col].strip() + # Before appending the current value, make sure it is numeric if the + # operation for the column requires it. + if ops[i] not in str_ops: + try: + float(val) + except ValueError: + skipped_lines += 1 + if first_invalid_line is None: + first_invalid_line = i+1 + invalid_value = fields[col] + invalid_column = col+1 + break + + op_vals[i].append(val) + + for i, op in enumerate( ops ): + if op == 'cuniq': + rfunc = "r.c" + else: + rfunc = "r." + op if op not in str_ops: - for j, elem in enumerate( prev_vals[i] ): - prev_vals[i][j] = float( elem ) - rout = eval( rfunc )( prev_vals[i] ) + for j, elem in enumerate( op_vals[i] ): + op_vals[i][j] = float( elem ) + rout = eval( rfunc )( op_vals[i] ) if rounds[i] == 'yes': - rout = int(round(float(rout))) + rout = round(float(rout)) else: rout = '%g' %(float(rout)) else: if op != 'random': - rout = eval( rfunc )( prev_vals[i] ) + rout = eval( rfunc )( op_vals[i] ) else: try: - rand_index = random.randint(0,len(prev_vals[i])-1) #if the two inputs to randint are equal, it seems to throw a ValueError. This can't be reproduced with the python interpreter in its interactive mode. - except Exception, ValueError: + rand_index = random.randint(0,len(op_vals[i])-1) #if the two inputs to randint are equal, it seems to throw a ValueError. This can't be reproduced with the python interpreter in its interactive mode. + except: rand_index = 0 - rout = prev_vals[i][rand_index] + rout = op_vals[i][rand_index] if op == 'Mode' and rout == '>1 mode': multiple_modes = True - mode_index = i + mode_index = i if op == 'unique': rfunc = "r.length" - rout = eval( rfunc )( rout ) - if op in ['c','cuniq']: - if op == 'c': - if type(rout) == type([]): - out_str += "\t" + ','.join(rout) - else: - out_str += "\t" + str(rout) + rout = eval( rfunc )( rout ) + if op in ['c', 'cuniq']: + if isinstance(rout, list): + if op == 'cuniq': + rout = set(rout) + out_str += "\t" + ','.join(rout) else: - if type(rout) == type([]): - out_str += "\t" + ','.join(list(set(rout))) - else: - out_str += "\t" + str(rout) + out_str += "\t" + str(rout) else: - out_str += "\t" + str( rout ) - except: - skipped_lines += 1 - if not first_invalid_line: - first_invalid_line = ii+1 - - if multiple_modes and mode_index != None: - out_str_list = out_str.split('\t') - for val in prev_vals[mode_index]: - out_str = '\t'.join(out_str_list[:mode_index+1]) + '\t' + str(val) + '\t' + '\t'.join(out_str_list[mode_index+2:]) - print >>fout, out_str.rstrip('\t') - else: - print >>fout, out_str + out_str += "\t" + str(rout) + if multiple_modes and mode_index != None: + out_str_list = out_str.split('\t') + for val in op_vals[mode_index]: + out_str = '\t'.join(out_str_list[:mode_index+1]) + '\t' + str(val) + '\t' + '\t'.join(out_str_list[mode_index+2:]) + fout.write(out_str.rstrip('\t') + "\n") + else: + fout.write(out_str + "\n") # Generate a useful info message. msg = "--Group by c%d: " %(group_col+1) - for i,op in enumerate(ops): + for i, op in enumerate(ops): if op == 'c': op = 'concat' elif op == 'length': --- a/tools/stats/grouping.xml Tue Mar 22 14:08:32 2011 -0400 +++ b/tools/stats/grouping.xml Tue Mar 22 17:49:09 2011 -0400 @@ -1,4 +1,4 @@ -<tool id="Grouping1" name="Group" version="1.9.3"> +<tool id="Grouping1" name="Group" version="1.9.4"><description>data by a column and perform aggregate operation on other columns.</description><command interpreter="python"> grouping.py Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: fubar: Adding two new tool wrappers and tests - clustalw (http://www.clustal.org) for multiple alignments and a sequence motif generator based on weblogo3 (http://weblogo.berkeley.edu) which works on fasta files such as alignments from clustalw
by Bitbucket 22 Mar '11

22 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/0319becf5e76/ changeset: r5246:0319becf5e76 user: fubar date: 2011-03-22 19:08:32 summary: Adding two new tool wrappers and tests - clustalw (http://www.clustal.org) for multiple alignments and a sequence motif generator based on weblogo3 (http://weblogo.berkeley.edu) which works on fasta files such as alignments from clustalw affected #: 8 files (155 bytes) --- a/tool_conf.xml.sample Tue Mar 22 13:45:31 2011 -0400 +++ b/tool_conf.xml.sample Tue Mar 22 14:08:32 2011 -0400 @@ -204,6 +204,10 @@ </section><section name="Motif Tools" id="motifs"><tool file="meme/meme.xml"/> + <tool file="rgenetics/rgWebLogo3.xml" /> + </section> + <section name="Multiple Alignments" id="clustal"> + <tool file="rgenetics/rgClustalw.xml" /></section><section name="Metagenomic analyses" id="tax_manipulation"><tool file="taxonomy/gi2taxonomy.xml" /> 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: richard_burhans: fixed comment bug and added additional error messages for SIFT tool
by Bitbucket 22 Mar '11

22 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/1113dcc5aaa7/ changeset: r5245:1113dcc5aaa7 user: richard_burhans date: 2011-03-22 18:45:31 summary: fixed comment bug and added additional error messages for SIFT tool affected #: 1 file (2.0 KB) --- a/tools/human_genome_variation/sift_variants_wrapper.sh Tue Mar 22 10:50:27 2011 -0400 +++ b/tools/human_genome_variation/sift_variants_wrapper.sh Tue Mar 22 13:45:31 2011 -0400 @@ -16,10 +16,48 @@ sift_input="$working_dir/sift_input.txt" sift_output="$working_dir/sift_output.txt" +################################################################################ +## make sure input file column selections are mutually exclusive ## +################################################################################ +ERROR=0 +declare -a col_use -## -## get/check the db directory from the argument org,db_loc -## +function check_col () { + local col=$1 + local use=$2 + local int=$3 + + if [ -n "${col//[0-9]}" ]; then + if [ $int -eq 1 ]; then + echo "ERROR: invalid value for $use column: $col" 1>&2 + ERROR=1 + fi + return + fi + + local cur=${col_use[$col]} + if [ -n "$cur" ]; then + echo "ERROR: $use column is the same as $cur column" 1>&2 + col_use[$col]="${cur},$use" + ERROR=1 + else + col_use[$col]=$use + fi +} + +check_col $chrom_col 'chromosome' 1 +check_col $pos_col 'position' 1 +check_col $allele_col 'allele' 1 +check_col $strand_col 'strand' 0 +check_col $comment_col 'comment' 0 + +if [ $ERROR -ne 0 ]; then + exit 1 +fi + +################################################################################ +## get/check the db directory from the argument org,db_loc ## +################################################################################ db_dir=$( awk '$1 == org { print $2 }' org=$org $db_loc ) if [ -z "$db_dir" ]; then @@ -32,9 +70,9 @@ exit 1 fi -## -## create input file for SIFT_exome_nssnvs.pl -## +################################################################################ +## create input file for SIFT_exome_nssnvs.pl ## +################################################################################ if [ ! -r "$input_file" ]; then echo "Can't read input file \"$input_file\"" 1>&2 exit 1 @@ -57,32 +95,26 @@ strand='"-1"' else strand="\$$strand_col" - strand_cvt='if ( '"${strand}"' == "+") { '"${strand}"' = "1" } else if ( '"${strand}"' == "-") { '"${strand}"' = "-1"}' + strand_cvt='if ('"${strand}"' == "+") {'"${strand}"' = "1"} else if ('"${strand}"' == "-") {'"${strand}"' = "-1"}' fi -if [ "$comment_col" = "-" ]; then - is_comment=0 -else - is_comment=1 +print_row='print $'"${chrom_col}"', $'"${beg_col}"', $'"${end_col}"', '"${strand}"', $'"${allele_col}"'' +if [ "$comment_col" != "-" ]; then + print_row=''"${print_row}"', $'"${comment_col}"'' fi awk ' BEGIN {FS="\t";OFS=","} +$'"${chrom_col}"' ~ /^[cC][hH][rR]/ {$'"${chrom_col}"' = substr($'"${chrom_col}"',4)} { - $'"${chrom_col}"' = tolower($'"${chrom_col}"') - sub(/^chr/, "", $'"${chrom_col}"') '"${strand_cvt}"' - if ('"${is_comment}"') { - print $'"${chrom_col}"', $'"${beg_col}"', $'"${end_col}"', '"${strand}"', $'"${allele_col}"', $'"${comment_col}"' - } else { - print $'"${chrom_col}"', $'"${beg_col}"', $'"${end_col}"', '"${strand}"', $'"${allele_col}"' - } + '"${print_row}"' } ' "$input_file" > "$sift_input" -## -## run SIFT variants command line program -## +################################################################################ +## run SIFT_exome_nssnvs.pl command line program ## +################################################################################ if [ "$output_opts" = "None" ]; then output_opts="" else @@ -92,18 +124,18 @@ SIFT_exome_nssnvs.pl -i "$sift_input" -d "$db_dir" -o "$working_dir" $output_opts &> "$sift_output" if [ $? -ne 0 ]; then - echo "failed: SIFT_exome_nssnvs.pl -i \"$sift_input\" -d \"$db_dir\" -o \"$working_dir\" $output_opts" - exit 1 + echo "failed: SIFT_exome_nssnvs.pl -i \"$sift_input\" -d \"$db_dir\" -o \"$working_dir\" $output_opts" + exit 1 fi -## -## locate the output file -## +################################################################################ +## locate the SIFT_exome_nssnvs.pl output file ## +################################################################################ sift_pid=$( sed -n -e 's/^.*Your job id is $[0-9][0-9]*$ and is currently running.*$/\1/p' "$sift_output" ) if [ -z "$sift_pid" ]; then - echo "Can't find SIFT pid in \"$sift_output\"" 1>&2 - exit 1 + echo "Can't find SIFT pid in \"$sift_output\"" 1>&2 + exit 1 fi sift_outdir="$working_dir/$sift_pid" @@ -118,9 +150,9 @@ exit 1 fi -## -## create output file -## +################################################################################ +## create galaxy output file ## +################################################################################ awk ' BEGIN {FS="\t";OFS="\t"} NR == 1 { @@ -139,14 +171,14 @@ print "#" $0 } NR != 1 { - if ($3 == "1") { $3 = "+" } else if ($3 == "-1") { $3 = "-" } + if ($3 == "1") {$3 = "+"} else if ($3 == "-1") {$3 = "-"} '"${pos_adj}"' print } ' > "$output_file" -## -## cleanup -## +################################################################################ +## cleanup ## +################################################################################ rm -rf "$sift_outdir" "$sift_input" "$sift_output" 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 bug introduced in change set 5243:45b772580403.
by Bitbucket 22 Mar '11

22 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/47f813d8cd6a/ changeset: r5244:47f813d8cd6a user: greg date: 2011-03-22 15:50:27 summary: Fix for bug introduced in change set 5243:45b772580403. affected #: 1 file (0 bytes) --- a/lib/galaxy/web/controllers/user.py Tue Mar 22 10:33:42 2011 -0400 +++ b/lib/galaxy/web/controllers/user.py Tue Mar 22 10:50:27 2011 -0400 @@ -494,7 +494,7 @@ else: status = 'error' if webapp == 'galaxy': - user_type_form_definition = self.__get_user_type_form_definition( trans, user=user, **kwd ) + user_type_form_definition = self.__get_user_type_form_definition( trans, user=None, **kwd ) user_type_fd_id = params.get( 'user_type_fd_id', 'none' ) if user_type_fd_id == 'none' and user_type_form_definition is not None: user_type_fd_id = trans.security.encode_id( user_type_form_definition.id ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by Bitbucket 21 Mar '11

21 Mar '11

2 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/ca9a43ca12f5/ changeset: r5241:ca9a43ca12f5 user: jgoecks date: 2011-03-21 18:01:24 summary: Add count GFF features tool and tests. Tool counts the number of features in a GFF file; this is different than the number of lines b/c GFF features are often multiline. affected #: 5 files (1.5 KB) --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count_gff_features_out1.txt Mon Mar 21 13:01:24 2011 -0400 @@ -0,0 +1,1 @@ +3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count_gff_features_out2.txt Mon Mar 21 13:01:24 2011 -0400 @@ -0,0 +1,1 @@ +14 --- a/tool_conf.xml.sample Mon Mar 21 11:08:32 2011 -0400 +++ b/tool_conf.xml.sample Mon Mar 21 13:01:24 2011 -0400 @@ -142,6 +142,8 @@ <tool file="stats/plot_from_lda.xml" /><tool file="regVariation/t_test_two_samples.xml" /><tool file="regVariation/compute_q_values.xml" /> + <label text="GFF" id="gff" /> + <tool file="stats/count_gff_features.xml" /></section><section name="Wavelet Analysis" id="dwt"><tool file="discreteWavelet/execute_dwt_IvC_all.xml" /> --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/stats/count_gff_features.py Mon Mar 21 13:01:24 2011 -0400 @@ -0,0 +1,18 @@ +#!/usr/bin/env python +# This tool takes a gff file as input and counts the number of features in it. + +import sys, fileinput +from galaxy import eggs +from galaxy.datatypes.util.gff_util import GFFReaderWrapper +from bx.intervals.io import GenomicInterval + +# Get args. +input_file = sys.argv[1:] + +# Count features. +count = 0 +for feature in GFFReaderWrapper( fileinput.FileInput( input_file ), fix_strand=True ): + if isinstance( feature, GenomicInterval ): + count += 1 + +print count \ No newline at end of file --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/stats/count_gff_features.xml Mon Mar 21 13:01:24 2011 -0400 @@ -0,0 +1,26 @@ +<tool id="count_gff_features" name="Count GFF Features" version="0.1"> + <description></description> + <command interpreter="python"> + count_gff_features.py $input > $output + </command> + <inputs> + <param format="gff" name="input" type="data" label="GFF Dataset to Filter"/> + </inputs> + <outputs> + <data format="txt" name="output"/> + </outputs> + <tests> + <test> + <param name="input" value="gff2bed_in2.gff"/> + <output name="output" file="count_gff_features_out1.txt"/> + </test> + <test> + <param name="input" value="gff_filter_by_feature_count_out1.gff"/> + <output name="output" file="count_gff_features_out2.txt"/> + </test> + </tests> + <help> + Counts the number of features in a GFF dataset. GFF features are often spread across multiple lines; this tool counts the number of + features in dataset rather than the number of lines. + </help> +</tool> http://bitbucket.org/galaxy/galaxy-central/changeset/8d476956222e/ changeset: r5242:8d476956222e user: jgoecks date: 2011-03-21 20:24:05 summary: Merge. affected #: 0 files (0 bytes) --- a/tools/filters/trimmer.xml Mon Mar 21 13:01:24 2011 -0400 +++ b/tools/filters/trimmer.xml Mon Mar 21 15:24:05 2011 -0400 @@ -1,11 +1,11 @@ -<tool id="trimmer" name="Trim" version="0.0.1"> - <description>leading or trailing characters</description> +<tool id="trimmer" name="Trim" version="0.0.1"> + <description>leading or trailing characters</description><command interpreter="python"> - trimmer.py -a -f $input1 -c $col -s $start -e $end -i $ignore $fastq > $out_file1 - </command> - <inputs> + trimmer.py -a -f $input1 -c $col -s $start -e $end -i $ignore $fastq > $out_file1 + </command> + <inputs><param format="tabular,txt" name="input1" type="data" label="this dataset"/> - <param name="col" type="integer" value="0" label="Trim this column only" help="0 = process entire line" /> + <param name="col" type="integer" value="0" label="Trim this column only" help="0 = process entire line" /><param name="start" type="integer" size="10" value="1" label="Trim from the beginning to this position" help="1 = do not trim the beginning"/><param name="end" type="integer" size="10" value="0" label="Remove everything from this position to the end" help="0 = do not trim the end"/><param name="fastq" type="select" label="Is input dataset in fastq format?" help="If set to YES, the tool will not trim evenly numbered lines (0, 2, 4, etc...)"> @@ -30,9 +30,9 @@ <option value="94">^</option><option value="35">#</option></param> - </inputs> - <outputs> - <data name="out_file1" format="input" metadata_source="input1"/> + </inputs> + <outputs> + <data name="out_file1" format="input" metadata_source="input1"/></outputs><tests><test> @@ -55,42 +55,42 @@ </test></tests> - - <help> - - -**What it does** - -Trims specified number of characters from a dataset or its field (if dataset is tab-delimited). - ------ - -**Example 1** - -Trimming this dataset:: + + <help> + + +**What it does** + +Trims specified number of characters from a dataset or its field (if dataset is tab-delimited). + +----- + +**Example 1** + +Trimming this dataset:: 1234567890 - abcdefghijk - + abcdefghijk + by setting **Trim from the beginning to this position** to *2* and **Remove everything from this position to the end** to *6* will produce:: 23456 - bcdef + bcdef ----- -**Eaxmple 2** +**Example 2** Trimming column 2 of this dataset:: - bcde 12345 fghij 67890 - fghij 67890 abcde 12345 + abcde 12345 fghij 67890 + fghij 67890 abcde 12345 -by setting **Trim content of this column only** to *2*, **Trim from the beginning to this position** to *2*, and **Remove everything from this position to the end** to *4* will produce:: +by setting **Trim content of this column only** to *2*, **Trim from the beginning to this position** to *2*, and **Remove everything from this position to the end** to *4* will produce:: - abcde 234 fghij 67890 - fghij 789 abcde 12345 - + abcde 234 fghij 67890 + fghij 789 abcde 12345 + ----- **Trimming FASTQ datasets** @@ -111,10 +111,10 @@ **Note** that headers are skipped. -.. class:: warningmark - -**WARNING:** This tool will only work on properly formatted fastq datasets where (1) each read and quality string occupy one line and (2) '@' (read header) and "+" (quality header) lines are evenly numbered like in the above example. +.. class:: warningmark - - </help> -</tool> +**WARNING:** This tool will only work on properly formatted fastq datasets where (1) each read and quality string occupy one line and (2) '@' (read header) and "+" (quality header) lines are evenly numbered like in the above example. + + + </help> +</tool> --- a/tools/new_operations/join.xml Mon Mar 21 13:01:24 2011 -0400 +++ b/tools/new_operations/join.xml Mon Mar 21 15:24:05 2011 -0400 @@ -11,12 +11,12 @@ <param name="min" size="4" type="integer" value="1" help="(bp)"><label>with min overlap</label></param> - <param name="fill" type="select" label="Return"> - <option value="none">Only records that are joined (INNER JOIN)</option> - <option value="right">All records of first dataset (fill null with ".")</option> - <option value="left">All records of second dataset (fill null with ".")</option> - <option value="both">All records of both datasets (fill nulls with ".")</option> - </param> + <param name="fill" type="select" label="Return"> + <option value="none">Only records that are joined (INNER JOIN)</option> + <option value="right">All records of first dataset (fill null with ".")</option> + <option value="left">All records of second dataset (fill null with ".")</option> + <option value="both">All records of both datasets (fill nulls with ".")</option> + </param></inputs><outputs><data format="interval" name="output" metadata_source="input1" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: kanwei: Typos in tool confs
by Bitbucket 21 Mar '11

21 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/5541018c4738/ changeset: r5240:5541018c4738 user: kanwei date: 2011-03-21 18:48:28 summary: Typos in tool confs affected #: 2 files (38 bytes) --- a/tools/filters/trimmer.xml Mon Mar 21 11:08:32 2011 -0400 +++ b/tools/filters/trimmer.xml Mon Mar 21 13:48:28 2011 -0400 @@ -1,11 +1,11 @@ -<tool id="trimmer" name="Trim" version="0.0.1"> - <description>leading or trailing characters</description> +<tool id="trimmer" name="Trim" version="0.0.1"> + <description>leading or trailing characters</description><command interpreter="python"> - trimmer.py -a -f $input1 -c $col -s $start -e $end -i $ignore $fastq > $out_file1 - </command> - <inputs> + trimmer.py -a -f $input1 -c $col -s $start -e $end -i $ignore $fastq > $out_file1 + </command> + <inputs><param format="tabular,txt" name="input1" type="data" label="this dataset"/> - <param name="col" type="integer" value="0" label="Trim this column only" help="0 = process entire line" /> + <param name="col" type="integer" value="0" label="Trim this column only" help="0 = process entire line" /><param name="start" type="integer" size="10" value="1" label="Trim from the beginning to this position" help="1 = do not trim the beginning"/><param name="end" type="integer" size="10" value="0" label="Remove everything from this position to the end" help="0 = do not trim the end"/><param name="fastq" type="select" label="Is input dataset in fastq format?" help="If set to YES, the tool will not trim evenly numbered lines (0, 2, 4, etc...)"> @@ -30,9 +30,9 @@ <option value="94">^</option><option value="35">#</option></param> - </inputs> - <outputs> - <data name="out_file1" format="input" metadata_source="input1"/> + </inputs> + <outputs> + <data name="out_file1" format="input" metadata_source="input1"/></outputs><tests><test> @@ -55,42 +55,42 @@ </test></tests> - - <help> - - -**What it does** - -Trims specified number of characters from a dataset or its field (if dataset is tab-delimited). - ------ - -**Example 1** - -Trimming this dataset:: + + <help> + + +**What it does** + +Trims specified number of characters from a dataset or its field (if dataset is tab-delimited). + +----- + +**Example 1** + +Trimming this dataset:: 1234567890 - abcdefghijk - + abcdefghijk + by setting **Trim from the beginning to this position** to *2* and **Remove everything from this position to the end** to *6* will produce:: 23456 - bcdef + bcdef ----- -**Eaxmple 2** +**Example 2** Trimming column 2 of this dataset:: - bcde 12345 fghij 67890 - fghij 67890 abcde 12345 + abcde 12345 fghij 67890 + fghij 67890 abcde 12345 -by setting **Trim content of this column only** to *2*, **Trim from the beginning to this position** to *2*, and **Remove everything from this position to the end** to *4* will produce:: +by setting **Trim content of this column only** to *2*, **Trim from the beginning to this position** to *2*, and **Remove everything from this position to the end** to *4* will produce:: - abcde 234 fghij 67890 - fghij 789 abcde 12345 - + abcde 234 fghij 67890 + fghij 789 abcde 12345 + ----- **Trimming FASTQ datasets** @@ -111,10 +111,10 @@ **Note** that headers are skipped. -.. class:: warningmark - -**WARNING:** This tool will only work on properly formatted fastq datasets where (1) each read and quality string occupy one line and (2) '@' (read header) and "+" (quality header) lines are evenly numbered like in the above example. +.. class:: warningmark - - </help> -</tool> +**WARNING:** This tool will only work on properly formatted fastq datasets where (1) each read and quality string occupy one line and (2) '@' (read header) and "+" (quality header) lines are evenly numbered like in the above example. + + + </help> +</tool> --- a/tools/new_operations/join.xml Mon Mar 21 11:08:32 2011 -0400 +++ b/tools/new_operations/join.xml Mon Mar 21 13:48:28 2011 -0400 @@ -11,12 +11,12 @@ <param name="min" size="4" type="integer" value="1" help="(bp)"><label>with min overlap</label></param> - <param name="fill" type="select" label="Return"> - <option value="none">Only records that are joined (INNER JOIN)</option> - <option value="right">All records of first dataset (fill null with ".")</option> - <option value="left">All records of second dataset (fill null with ".")</option> - <option value="both">All records of both datasets (fill nulls with ".")</option> - </param> + <param name="fill" type="select" label="Return"> + <option value="none">Only records that are joined (INNER JOIN)</option> + <option value="right">All records of first dataset (fill null with ".")</option> + <option value="left">All records of second dataset (fill null with ".")</option> + <option value="both">All records of both datasets (fill nulls with ".")</option> + </param></inputs><outputs><data format="interval" name="output" metadata_source="input1" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dannon: Added row id print and pre/post value prints to the migration script addressing form value errors.
by Bitbucket 21 Mar '11

21 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/6ffd5bca9d84/ changeset: r5239:6ffd5bca9d84 user: dannon date: 2011-03-21 16:08:32 summary: Added row id print and pre/post value prints to the migration script addressing form value errors. affected #: 1 file (348 bytes) --- a/lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py Fri Mar 18 15:23:27 2011 -0400 +++ b/lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py Mon Mar 21 11:08:32 2011 -0400 @@ -20,7 +20,6 @@ def _sniffnfix_pg9_hex(value): """ Sniff for and fix postgres 9 hex decoding issue - """ try: if value[0] == 'x': @@ -33,7 +32,6 @@ def upgrade(): print __doc__ metadata.reflect() - cmd = "SELECT form_values.id as id, form_values.content as field_values, form_definition.fields as fields " \ + " FROM form_definition, form_values " \ + " WHERE form_values.form_definition_id=form_definition.id " \ @@ -50,6 +48,12 @@ # content field is corrupted fields_list = from_json_string( _sniffnfix_pg9_hex( str( row['fields'] ) ) ) field_values_str = _sniffnfix_pg9_hex( str( row['field_values'] ) ) + try: + #Encoding errors? Just to be safe. + print "Attempting to fix row %s" % row['id'] + print "Prior to replacement: %s" % field_values_str + except: + pass field_values_dict = {} # look for each field name in the values and extract its value (string) for index in range( len(fields_list) ): @@ -84,10 +88,15 @@ json_values = to_json_string(field_values_dict) cmd = "UPDATE form_values SET content='%s' WHERE id=%i" %( json_values, int( row['id'] ) ) db_session.execute( cmd ) + try: + print "Post replacement: %s" % json_values + except: + pass if corrupted_rows: print 'Fixed %i corrupted rows.' % corrupted_rows else: print 'No corrupted rows found.' def downgrade(): - pass \ No newline at end of file + pass + 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 recently used tool submenu that was caused by changeset 4967:d6559b2d69fc
by Bitbucket 18 Mar '11

18 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/4c5bf02bb0e8/ changeset: r5238:4c5bf02bb0e8 user: jgoecks date: 2011-03-18 20:23:27 summary: Fix bug in recently used tool submenu that was caused by changeset 4967:d6559b2d69fc affected #: 1 file (48 bytes) --- a/templates/root/tool_menu.mako Fri Mar 18 14:42:08 2011 -0400 +++ b/templates/root/tool_menu.mako Fri Mar 18 15:23:27 2011 -0400 @@ -199,10 +199,10 @@ var found_in_list = false; // Look for new tool in current list. If found, rearrange list to move tool to top. + var new_tool_info_id = new_tool_info.id.toLowerCase().replace(/[^a-z0-9_]/, "_") recently_used_elts.each( function(index) { var anchor = $(this).find("a"); - var tool_id = anchor.attr("id").split("-")[1]; - if (tool_id === new_tool_info.id) { + if (anchor.hasClass("link-" + new_tool_info_id)) { found_in_list = true; // If tool is first, do nothing. @@ -219,7 +219,7 @@ // If tool not in list, create new element, remove last element, and put new element first in list. if (!found_in_list) { new_tool_elt = $("<div class='toolTitle'> \ - <a id='link-" + new_tool_info.id + "' href='" + new_tool_info.link + "' target='" + + <a class='link-" + new_tool_info.id + "' href='" + new_tool_info.link + "' target='" + new_tool_info.target + "' minsizehint='" + new_tool_info.minsizehint + "'>" + new_tool_info.name + "</a> " + new_tool_info.description + " \ </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.

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commit/galaxy-central: jgoecks: Trackster: fix feature track bugs so that intervals are correctly drawn as half-open.
by Bitbucket 18 Mar '11

18 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/622acea0a86b/ changeset: r5237:622acea0a86b user: jgoecks date: 2011-03-18 19:42:08 summary: Trackster: fix feature track bugs so that intervals are correctly drawn as half-open. affected #: 1 file (30 bytes) --- a/static/scripts/trackster.js Fri Mar 18 14:12:10 2011 -0400 +++ b/static/scripts/trackster.js Fri Mar 18 14:42:08 2011 -0400 @@ -2348,7 +2348,8 @@ var feature_uid = feature[0], feature_start = feature[1], - feature_end = feature[2], + // -1 b/c intervals are half-open. + feature_end = feature[2] - 1, feature_name = feature[3], f_start = Math.floor( Math.max(0, (feature_start - tile_low) * w_scale) ), f_end = Math.ceil( Math.min(width, Math.max(0, (feature_end - tile_low) * w_scale)) ), @@ -2440,8 +2441,9 @@ for (var k = 0, k_len = feature_blocks.length; k < k_len; k++) { var block = feature_blocks[k], block_start = Math.floor( Math.max(0, (block[0] - tile_low) * w_scale) ), - block_end = Math.ceil( Math.min(width, Math.max((block[1] - tile_low) * w_scale)) ); - + // -1 b/c intervals are half-open. + block_end = Math.ceil( Math.min(width, Math.max((block[1] - 1 - tile_low) * w_scale)) ); + // Skip drawing if block not on tile. if (block_start > block_end) { continue; } @@ -2453,8 +2455,7 @@ // If block intersects with thick region, draw block as thick. if (thick_start !== undefined && !(block_start > thick_end || block_end < thick_start) ) { var block_thick_start = Math.max(block_start, thick_start), - // -1 b/c intervals are half-open. - block_thick_end = Math.min(block_end, thick_end-1); + block_thick_end = Math.min(block_end, thick_end); ctx.fillRect(block_thick_start + left_offset, y_center + 1, block_thick_end - block_thick_start, thick_height); } 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: set_peek should check for None, not false
by Bitbucket 18 Mar '11

18 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/3070455afbdd/ changeset: r5236:3070455afbdd user: kanwei date: 2011-03-18 19:12:10 summary: set_peek should check for None, not false affected #: 3 files (36 bytes) --- a/lib/galaxy/datatypes/data.py Fri Mar 18 13:51:51 2011 -0400 +++ b/lib/galaxy/datatypes/data.py Fri Mar 18 14:12:10 2011 -0400 @@ -422,7 +422,7 @@ dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte ) if line_count is None: # See if line_count is stored in the metadata - if dataset.metadata.data_lines: + if dataset.metadata.data_lines is not None: dataset.blurb = "%s %s" % ( util.commaify( str(dataset.metadata.data_lines) ), inflector.cond_plural(dataset.metadata.data_lines, "line") ) else: # Number of lines is not known ( this should not happen ), and auto-detect is --- a/lib/galaxy/datatypes/interval.py Fri Mar 18 13:51:51 2011 -0400 +++ b/lib/galaxy/datatypes/interval.py Fri Mar 18 14:12:10 2011 -0400 @@ -66,7 +66,7 @@ dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte ) if line_count is None: # See if line_count is stored in the metadata - if dataset.metadata.data_lines: + if dataset.metadata.data_lines is not None: dataset.blurb = "%s regions" % util.commaify( str( dataset.metadata.data_lines ) ) else: # Number of lines is not known ( this should not happen ), and auto-detect is --- a/lib/galaxy/datatypes/tabular.py Fri Mar 18 13:51:51 2011 -0400 +++ b/lib/galaxy/datatypes/tabular.py Fri Mar 18 14:12:10 2011 -0400 @@ -398,7 +398,7 @@ dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte ) if line_count is None: # See if line_count is stored in the metadata - if dataset.metadata.data_lines: + if dataset.metadata.data_lines is not None: dataset.blurb = "%s genomic coordinates" % util.commaify( str( dataset.metadata.data_lines ) ) else: # Number of lines is not known ( this should not happen ), and auto-detect is 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: Trackster: fix issues with navigation input: (a) arrow keys no longer perform navigation and (b) invalid chromosome names are handled well.
by Bitbucket 18 Mar '11

18 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/dc9b64810fde/ changeset: r5235:dc9b64810fde user: jgoecks date: 2011-03-18 18:51:51 summary: Trackster: fix issues with navigation input: (a) arrow keys no longer perform navigation and (b) invalid chromosome names are handled well. affected #: 2 files (530 bytes) --- a/static/scripts/trackster.js Fri Mar 18 13:40:58 2011 -0400 +++ b/static/scripts/trackster.js Fri Mar 18 13:51:51 2011 -0400 @@ -367,9 +367,9 @@ view.go_to( $(this).val() ); } $(this).hide(); + $(this).val(''); view.location_span.show(); view.chrom_select.show(); - return false; } }; this.nav_input = $("<input/>").addClass("nav-input").hide().bind("keyup focusout", submit_nav).appendTo(this.nav_controls); @@ -377,6 +377,7 @@ this.location_span.bind("click", function() { view.location_span.hide(); view.chrom_select.hide(); + view.nav_input.val(view.chrom + ":" + view.low + "-" + view.high); view.nav_input.css("display", "inline-block"); view.nav_input.select(); view.nav_input.focus(); @@ -520,7 +521,14 @@ url: chrom_url, data: url_parms, dataType: "json", - success: function ( result ) { + success: function (result) { + // Show error if could not load chroms. + if (result.chrom_info.length === 0) { + alert("Invalid chromosome: " + url_parms.chrom); + return; + } + + // Load chroms. if (result.reference) { view.add_label_track( new ReferenceTrack(view) ); } @@ -543,13 +551,12 @@ view.chrom_start_index = result.start_index; }, error: function() { - alert( "Could not load chroms for this dbkey:", view.dbkey ); + alert("Could not load chroms for this dbkey:", view.dbkey); } }); }, change_chrom: function(chrom, low, high) { - // Don't do anything if chrom is "None" (hackish but some browsers already have this set), or null/blank if (!chrom || chrom === "None") { return; --- a/templates/tracks/browser.mako Fri Mar 18 13:40:58 2011 -0400 +++ b/templates/tracks/browser.mako Fri Mar 18 13:51:51 2011 -0400 @@ -256,6 +256,11 @@ // Keyboard navigation. Scroll ~7% of height when scrolling up/down. // $(document).keydown(function(e) { + // Do not navigate if arrow keys used in input element. + if ($(e.srcElement).is(':input')) { + return; + } + // Key codes: left == 37, up == 38, right == 39, down == 40 switch(e.which) { case 37: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Fix minor typo in 5233:b5f4df8c3956
by Bitbucket 18 Mar '11

18 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/ad11762fe328/ changeset: r5234:ad11762fe328 user: dan date: 2011-03-18 18:40:58 summary: Fix minor typo in 5233:b5f4df8c3956 affected #: 1 file (3 bytes) --- a/scripts/tools/maf/check_loc_file.py Fri Mar 18 13:39:19 2011 -0400 +++ b/scripts/tools/maf/check_loc_file.py Fri Mar 18 13:40:58 2011 -0400 @@ -45,7 +45,7 @@ #existing species for spec in species_exist: if spec not in species_found_in_maf: - print "Line %i, %s claims to be have blocks for %s, but was not found in MAF files." % ( i, uid, spec ) + print "Line %i, %s claims to have blocks for %s, but was not found in MAF files." % ( i, uid, spec ) for spec in species_found_in_maf: if spec not in species_exist: print "Line %i, %s contains %s, but is not listed in loc file." % ( i, uid, spec ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Add a script that will check a maf_index.loc file for inconsistencies between listed information and content of MAF indexes and files.
by Bitbucket 18 Mar '11

18 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/b5f4df8c3956/ changeset: r5233:b5f4df8c3956 user: dan date: 2011-03-18 18:39:19 summary: Add a script that will check a maf_index.loc file for inconsistencies between listed information and content of MAF indexes and files. affected #: 1 file (0 bytes) 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 typo in 5093:1dfad17e81a8 that broke page editor.
by Bitbucket 17 Mar '11

17 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/642f1f9e5e3a/ changeset: r5231:642f1f9e5e3a user: jgoecks date: 2011-03-17 22:39:16 summary: Fix typo in 5093:1dfad17e81a8 that broke page editor. affected #: 1 file (1 byte) --- a/templates/page/editor.mako Thu Mar 17 15:44:05 2011 -0400 +++ b/templates/page/editor.mako Thu Mar 17 17:39:16 2011 -0400 @@ -21,7 +21,7 @@ <%def name="javascripts()"> ${parent.javascripts()} - ${h.js( "jquery.event.drag", "jquery.event.drop", "jquery.event.hover", "jquery.form", "json2", "jstorage" + ${h.js( "jquery.event.drag", "jquery.event.drop", "jquery.event.hover", "jquery.form", "json2", "jstorage", "galaxy.base", "jquery.wymeditor", "jquery.autocomplete", "autocomplete_tagging")} <script type="text/javascript"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: And 1em margin to the top and bottom of tables in Pages.
by Bitbucket 17 Mar '11

17 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/4f14387d3178/ changeset: r5230:4f14387d3178 user: dan date: 2011-03-17 20:44:05 summary: And 1em margin to the top and bottom of tables in Pages. affected #: 1 file (61 bytes) --- a/templates/page/display.mako Thu Mar 17 09:57:25 2011 -0400 +++ b/templates/page/display.mako Thu Mar 17 15:44:05 2011 -0400 @@ -98,6 +98,8 @@ padding: 8px 5px 5px; min-width: 500px; border: none; + margin-top: 1em; + margin-bottom: 1em; } .page-body caption { text-align: left; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Fix check for displaying old-style display applications when line count approximation is used. Additional cleaner link display for display applications which was started in 4886:f820c9d2c285.
by Bitbucket 17 Mar '11

17 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/0861dc121b0f/ changeset: r5229:0861dc121b0f user: dan date: 2011-03-17 14:57:25 summary: Fix check for displaying old-style display applications when line count approximation is used. Additional cleaner link display for display applications which was started in 4886:f820c9d2c285. affected #: 3 files (37 bytes) --- a/lib/galaxy/datatypes/interval.py Wed Mar 16 22:27:15 2011 -0400 +++ b/lib/galaxy/datatypes/interval.py Thu Mar 17 09:57:25 2011 -0400 @@ -144,7 +144,7 @@ return dataset.has_data() \ and dataset.state == dataset.states.OK \ and dataset.metadata.columns > 0 \ - and dataset.metadata.data_lines > 0 \ + and dataset.metadata.data_lines != 0 \ and dataset.metadata.chromCol \ and dataset.metadata.startCol \ and dataset.metadata.endCol --- a/lib/galaxy/datatypes/tabular.py Wed Mar 16 22:27:15 2011 -0400 +++ b/lib/galaxy/datatypes/tabular.py Thu Mar 17 09:57:25 2011 -0400 @@ -235,7 +235,7 @@ return dataset.has_data() \ and dataset.state == dataset.states.OK \ and dataset.metadata.columns > 0 \ - and dataset.metadata.data_lines > 0 + and dataset.metadata.data_lines != 0 except: return False def as_gbrowse_display_file( self, dataset, **kwd ): --- a/templates/root/history_common.mako Wed Mar 16 22:27:15 2011 -0400 +++ b/templates/root/history_common.mako Thu Mar 17 09:57:25 2011 -0400 @@ -179,6 +179,7 @@ %for display_name, display_link in display_links: <a target="${target_frame}" href="${display_link}">${_(display_name)}</a> %endfor + <br /> %endif %endfor %for display_app in data.get_display_applications( trans ).itervalues(): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: When using re_match comparison method in functional tests and line counts do not match, print out first 40 lines of the history file.
by Bitbucket 16 Mar '11

16 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/b32617347a63/ changeset: r5228:b32617347a63 user: dan date: 2011-03-17 03:27:15 summary: When using re_match comparison method in functional tests and line counts do not match, print out first 40 lines of the history file. affected #: 1 file (66 bytes) --- a/test/base/twilltestcase.py Wed Mar 16 18:36:27 2011 -0400 +++ b/test/base/twilltestcase.py Wed Mar 16 22:27:15 2011 -0400 @@ -109,7 +109,7 @@ """Checks the contents of 2 files for differences using re.match""" local_file = open( file1, 'U' ).readlines() #regex file history_data = open( file2, 'U' ).readlines() - assert len( local_file ) == len( history_data ), 'Data File and Regular Expression File contain a different number of lines (%s != %s)' % ( len( local_file ), len( history_data ) ) + assert len( local_file ) == len( history_data ), 'Data File and Regular Expression File contain a different number of lines (%s != %s)\nHistory Data (first 40 lines):\n%s' % ( len( local_file ), len( history_data ), ''.join( history_data[:40] ) ) if attributes is None: attributes = {} if attributes.get( 'sort', False ): 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: Description text for viz metadata column
by Bitbucket 16 Mar '11

16 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/f889ddcd4a8a/ changeset: r5227:f889ddcd4a8a user: kanwei date: 2011-03-16 23:36:27 summary: Description text for viz metadata column affected #: 2 files (78 bytes) --- a/lib/galaxy/datatypes/interval.py Wed Mar 16 10:41:38 2011 -0400 +++ b/lib/galaxy/datatypes/interval.py Wed Mar 16 18:36:27 2011 -0400 @@ -400,7 +400,7 @@ MetadataElement( name="endCol", default=3, desc="End column", param=metadata.ColumnParameter ) MetadataElement( name="strandCol", desc="Strand column (click box & select)", param=metadata.ColumnParameter, optional=True, no_value=0 ) MetadataElement( name="columns", default=3, desc="Number of columns", readonly=True, visible=False ) - MetadataElement( name="viz_filter_cols", default=[4], param=metadata.ColumnParameter, multiple=True ) + MetadataElement( name="viz_filter_cols", desc="Score column for visualization", default=[4], param=metadata.ColumnParameter, multiple=True ) ###do we need to repeat these? they are the same as should be inherited from interval type def set_meta( self, dataset, overwrite = True, **kwd ): --- a/lib/galaxy/datatypes/tabular.py Wed Mar 16 10:41:38 2011 -0400 +++ b/lib/galaxy/datatypes/tabular.py Wed Mar 16 18:36:27 2011 -0400 @@ -493,7 +493,7 @@ MetadataElement( name="columns", default=10, desc="Number of columns", readonly=True, visible=False ) MetadataElement( name="column_types", default=['str','int','str','str','str','int','str','list','str','str'], param=metadata.ColumnTypesParameter, desc="Column types", readonly=True, visible=False ) - MetadataElement( name="viz_filter_cols", default=[5], param=metadata.ColumnParameter, multiple=True ) + MetadataElement( name="viz_filter_cols", desc="Score column for visualization", default=[5], param=metadata.ColumnParameter, multiple=True ) def sniff( self, filename ): try: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Update CCAT to version 3.0.
by Bitbucket 16 Mar '11

16 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/3b8dec50ea26/ changeset: r5226:3b8dec50ea26 user: dan date: 2011-03-16 15:41:38 summary: Update CCAT to version 3.0. affected #: 14 files (177 bytes) Diff too large to display. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: kanwei: Small tweaks to custom builds
by Bitbucket 16 Mar '11

16 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/6ae06d89fec7/ changeset: r5225:6ae06d89fec7 user: kanwei date: 2011-03-16 14:01:57 summary: Small tweaks to custom builds affected #: 1 file (70 bytes) --- a/templates/user/dbkeys.mako Tue Mar 15 23:40:53 2011 -0400 +++ b/templates/user/dbkeys.mako Wed Mar 16 09:01:57 2011 -0400 @@ -116,22 +116,20 @@ <form action="dbkeys" method="post" enctype="multipart/form-data"><div class="toolForm" style="float: left;"><div class="toolFormTitle">Add a Custom Build</div> - - <div class="toolFormBody"><div class="form-row"> - <label for="name">Build Name (eg: Human Chromosome):</label> + <label for="name">Build Name (eg: Mouse):</label><input type="text" id="name" name="name" /></div><div class="form-row"> - <label for="key">Build Key (eg: hg18):</label> + <label for="key">Build Key (eg: mm9):</label><input type="text" id="key" name="key" /></div><div class="form-row"> - <label for="len_file">Chromosome Length file upload (.len file):</label> + <label for="len_file">Upload .len file:</label><input type="file" id="len_file" name="len_file" /><br /><label for="len_text">Or paste length info below:</label> - <textarea id="len_text" name="len_text" cols="40" rows="10"></textarea> + <textarea id="len_text" name="len_text" cols="30" rows="10"></textarea></div><div class="form-row"><input type="submit" name="add" value="Submit"/></div> @@ -157,8 +155,7 @@ <p>Trackster uses this information to populate the select box for chrom/contig, and to set the maximum basepair of the track browser. You may either upload a .len file - of this format, or directly enter the information in the box. - </p> + of this format, or directly enter the information into the box.</p></div></%def> \ No newline at end of file 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: Improved custom builds UI. Better help text explaining len file format. Now split on last whitespace instead of tab only so that len info can be typed into the box directly.
by Bitbucket 15 Mar '11

15 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/9e327e97acba/ changeset: r5224:9e327e97acba user: kanwei date: 2011-03-16 04:40:53 summary: Improved custom builds UI. Better help text explaining len file format. Now split on last whitespace instead of tab only so that len info can be typed into the box directly. affected #: 2 files (1.7 KB) --- a/lib/galaxy/web/controllers/user.py Tue Mar 15 15:39:35 2011 -0400 +++ b/lib/galaxy/web/controllers/user.py Tue Mar 15 23:40:53 2011 -0400 @@ -5,7 +5,7 @@ from galaxy.web.base.controller import * from galaxy.model.orm import * from galaxy import util, model -import logging, os, string, re, smtplib, socket +import logging, os, string, re, smtplib, socket, glob from random import choice from email.MIMEText import MIMEText from galaxy.web.form_builder import * @@ -53,6 +53,8 @@ class User( BaseController, UsesFormDefinitions ): user_openid_grid = UserOpenIDGrid() + installed_len_files = None + @web.expose def index( self, trans, webapp='galaxy', **kwd ): return trans.fill_template( '/user/index.mako', webapp=webapp ) @@ -1237,12 +1239,21 @@ """ Log a user action asynchronously. If user is not logged in, do nothing. """ if trans.user: trans.log_action( trans.get_user(), action, context, params ) + @web.expose @web.require_login() def dbkeys( self, trans, **kwds ): user = trans.get_user() message = None lines_skipped = 0 + if self.installed_len_files is None: + installed_builds = [] + for build in glob.glob( os.path.join(trans.app.config.len_file_path, "*.len") ): + installed_builds.append( os.path.basename(build).split(".len")[0] ) + + self.installed_len_files = ", ".join(installed_builds) + + if 'dbkeys' not in user.preferences: dbkeys = {} else: @@ -1263,6 +1274,8 @@ len_text = kwds.get('len_text', '') if not name or not key or not len_text: message = "You must specify values for all the fields." + elif key in dbkeys: + message = "There is already a custom build with that key. Delete it first if you want to replace it." else: # Create new len file new_len = trans.app.model.HistoryDatasetAssociation( extension="len", create_dataset=True, sa_session=trans.sa_session ) @@ -1278,7 +1291,7 @@ # LEN files have format: # <chrom_name><tab><chrom_length> for line in len_text.split("\n"): - lst = line.strip().split("\t") + lst = line.strip().rsplit(None, 1) # Splits at the last whitespace in the line if not lst or len(lst) < 2: lines_skipped += 1 continue @@ -1300,6 +1313,7 @@ user=user, dbkeys=dbkeys, message=message, + installed_len_files=self.installed_len_files, lines_skipped=lines_skipped, use_panels=kwds.get( 'use_panels', None ) ) @web.expose --- a/templates/user/dbkeys.mako Tue Mar 15 15:39:35 2011 -0400 +++ b/templates/user/dbkeys.mako Tue Mar 15 23:40:53 2011 -0400 @@ -61,27 +61,28 @@ </script></%def> -% if message: - <div class="errormessagelarge">${message}</div> -% elif lines_skipped > 0: - <div class="warningmessagelarge">Skipped ${lines_skipped} lines that could not be parsed</div> -% endif - <%def name="center_panel()"> ${self.body()} </%def><%def name="body()"> + + % if message: + <div class="errormessagelarge">${message}</div> + % elif lines_skipped > 0: + <div class="warningmessagelarge">Skipped ${lines_skipped} lines that could not be parsed. (Line was either blank or not 2-column, with 2nd column being an integer)</div> + % endif + <h2>Custom Database/Builds</h2> - <p>You may specify your own database/builds here.</p> + <p>Current custom builds:</p> % if dbkeys: <table id="custom_dbkeys" class="colored" cellspacing="0" cellpadding="0"><tr class="header"><th>Name</th><th>Key</th> - <th>Number of Chroms</th> + <th>Number of chroms/contigs</th><th></th></tr> % for key, dct in dbkeys.iteritems(): @@ -109,23 +110,27 @@ % else: <p>You currently have no custom builds.</p> % endif + <p>Builds with system-installed len files: <em>${installed_len_files}</em></p><br /> + <form action="dbkeys" method="post" enctype="multipart/form-data"> - <div class="toolForm"> - <div class="toolFormTitle">Add a Build</div> + <div class="toolForm" style="float: left;"> + <div class="toolFormTitle">Add a Custom Build</div> + + <div class="toolFormBody"><div class="form-row"> - <label for="name">Name (eg: Human Chromosome):</label> + <label for="name">Build Name (eg: Human Chromosome):</label><input type="text" id="name" name="name" /></div><div class="form-row"> - <label for="key">Key (eg: hg18):</label> + <label for="key">Build Key (eg: hg18):</label><input type="text" id="key" name="key" /></div><div class="form-row"><label for="len_file">Chromosome Length file upload (.len file):</label><input type="file" id="len_file" name="len_file" /><br /> - <label for="len_text">Alternatively, paste length info:</label> + <label for="len_text">Or paste length info below:</label><textarea id="len_text" name="len_text" cols="40" rows="10"></textarea></div> @@ -133,4 +138,27 @@ </div></div></form> + <div class="infomessagesmall" style="float: left; margin-left: 10px; width: 40%;"> + <h3>Length Format</h3> + <p> + The length format is two-column, separated by whitespace, of the form: + <pre>chrom/contig length of chrom/contig</pre> + </p> + <p> + For example, the first few entries of <em>mm9.len</em> are as follows: + <pre> +chr1 197195432 +chr2 181748087 +chr3 159599783 +chr4 155630120 +chr5 152537259 + </pre> + </p> + + <p>Trackster uses this information to populate the select box for chrom/contig, and + to set the maximum basepair of the track browser. You may either upload a .len file + of this format, or directly enter the information in the box. + </p> + + </div></%def> \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Fix for example workflow api script failing when the requested library doesn't exist and an attempt is made to create it.
by Bitbucket 15 Mar '11

15 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/82f9422864ff/ changeset: r5223:82f9422864ff user: dannon date: 2011-03-15 20:39:35 summary: Fix for example workflow api script failing when the requested library doesn't exist and an attempt is made to create it. affected #: 1 file (3 bytes) --- a/scripts/api/example_watch_folder.py Tue Mar 15 14:43:06 2011 -0400 +++ b/scripts/api/example_watch_folder.py Tue Mar 15 15:39:35 2011 -0400 @@ -27,7 +27,7 @@ if not library_id: lib_create_data = {'name':data_library} library = submit(api_key, api_url + 'libraries', lib_create_data, return_formatted=False) - library_id = library['id'] + library_id = library[0]['id'] folders = display(api_key, api_url + "libraries/%s/contents" % library_id, return_formatted = False) for f in folders: if f['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: greg: Allow Importing items from a history to replace a library dataset with a new version.
by Bitbucket 15 Mar '11

15 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/e1d024f26f53/ changeset: r5222:e1d024f26f53 user: greg date: 2011-03-15 19:43:06 summary: Allow Importing items from a history to replace a library dataset with a new version. affected #: 2 files (938 bytes) --- a/lib/galaxy/web/controllers/library_common.py Tue Mar 15 09:38:29 2011 -0400 +++ b/lib/galaxy/web/controllers/library_common.py Tue Mar 15 14:43:06 2011 -0400 @@ -726,11 +726,8 @@ roles = params.get( 'roles', '' ) is_admin = trans.user_is_admin() and cntrller in ( 'library_admin', 'api' ) current_user_roles = trans.get_current_user_roles() - if replace_id not in [ None, 'None' ]: - try: - replace_dataset = trans.sa_session.query( trans.app.model.LibraryDataset ).get( trans.security.decode_id( replace_id ) ) - except: - replace_dataset = None + if replace_id not in [ '', None, 'None' ]: + replace_dataset = trans.sa_session.query( trans.app.model.LibraryDataset ).get( trans.security.decode_id( replace_id ) ) self._check_access( trans, cntrller, is_admin, replace_dataset, current_user_roles, use_panels, library_id, show_deleted ) self._check_modify( trans, cntrller, is_admin, replace_dataset, current_user_roles, use_panels, library_id, show_deleted ) library = replace_dataset.folder.parent_library @@ -740,8 +737,6 @@ replace_dataset_name = replace_dataset.name if not last_used_build: last_used_build = replace_dataset.library_dataset_dataset_association.dbkey - # Don't allow multiple datasets to be uploaded when replacing a dataset with a new version - upload_option = 'upload_file' else: folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( trans.security.decode_id( folder_id ) ) self._check_access( trans, cntrller, is_admin, folder, current_user_roles, use_panels, library_id, show_deleted ) @@ -776,7 +771,6 @@ show_deleted=show_deleted, message=util.sanitize_text( message ), status='error' ) ) - else: # See if we have any inherited templates. info_association, inherited = folder.get_info_association( inherited=True ) @@ -919,7 +913,11 @@ action = trans.app.config.nginx_upload_path + '?nginx_redir=' + web.url_for( controller='library_common', action='upload_library_dataset' ) else: action = web.url_for( controller='library_common', action='upload_library_dataset' ) - upload_option_select_list = self._build_upload_option_select_list( trans, upload_option, is_admin ) + do_not_display_options = [] + if replace_dataset: + # TODO: Not sure why, but 'upload_paths' is not allowed if replacing a dataset. See self.make_library_uploaded_dataset(). + do_not_display_options = [ 'upload_directory', 'upload_paths' ] + upload_option_select_list = self._build_upload_option_select_list( trans, upload_option, is_admin, do_not_display_options ) roles_select_list = self._build_roles_select_list( trans, cntrller, library, util.listify( roles ) ) return trans.fill_template( '/library/common/upload.mako', cntrller=cntrller, @@ -1302,29 +1300,35 @@ return roles_select_list else: return None - def _build_upload_option_select_list( self, trans, upload_option, is_admin ): - # Build the upload_option select list - upload_refresh_on_change_values = [ option_value for option_value, option_label in trans.model.LibraryDataset.upload_options ] + def _build_upload_option_select_list( self, trans, upload_option, is_admin, do_not_include_values=[] ): + # Build the upload_option select list. The do_not_include_values param can contain options that + # should not be included in the list. For example, the 'upload_directory' option should not be + # included if uploading a new version of a librar dataset. + upload_refresh_on_change_values = [] + for option_value, option_label in trans.model.LibraryDataset.upload_options: + if option_value not in do_not_include_values: + upload_refresh_on_change_values.append( option_value ) upload_option_select_list = SelectField( 'upload_option', refresh_on_change=True, refresh_on_change_values=upload_refresh_on_change_values ) for option_value, option_label in trans.model.LibraryDataset.upload_options: - if option_value == 'upload_directory': - if is_admin and not trans.app.config.library_import_dir: - continue - elif not is_admin: - if not trans.app.config.user_library_import_dir: + if option_value not in do_not_include_values: + if option_value == 'upload_directory': + if is_admin and not trans.app.config.library_import_dir: continue - path = os.path.join( trans.app.config.user_library_import_dir, trans.user.email ) - if not os.path.isdir( path ): - try: - os.makedirs( path ) - except: + elif not is_admin: + if not trans.app.config.user_library_import_dir: continue - elif option_value == 'upload_paths': - if not is_admin or not trans.app.config.allow_library_path_paste: - continue - upload_option_select_list.add_option( option_label, option_value, selected=option_value==upload_option ) + path = os.path.join( trans.app.config.user_library_import_dir, trans.user.email ) + if not os.path.isdir( path ): + try: + os.makedirs( path ) + except: + continue + elif option_value == 'upload_paths': + if not is_admin or not trans.app.config.allow_library_path_paste: + continue + upload_option_select_list.add_option( option_label, option_value, selected=option_value==upload_option ) return upload_option_select_list def _get_populated_widgets( self, folder ): # See if we have any inherited templates. --- a/templates/library/common/common.mako Tue Mar 15 09:38:29 2011 -0400 +++ b/templates/library/common/common.mako Tue Mar 15 14:43:06 2011 -0400 @@ -104,21 +104,16 @@ <div style="clear: both"></div></div> %endif - %if replace_dataset in [ None, 'None' ]: - ## Don't allow multiple datasets to be uploaded when replacing a dataset with a new version - <div class="form-row"> - <label>Upload option:</label> - <div class="form-row-input"> - ${upload_option_select_list.get_html()} - </div> - <div class="toolParamHelp" style="clear: both;"> - Choose upload option (file, directory, filesystem paths, current history). - </div> - <div style="clear: both"></div> + <div class="form-row"> + <label>Upload option:</label> + <div class="form-row-input"> + ${upload_option_select_list.get_html()} </div> - %else: - <input type="hidden" name="upload_option" value="upload_file"/> - %endif + <div class="toolParamHelp" style="clear: both;"> + Choose upload option (file, directory, filesystem paths, current history). + </div> + <div style="clear: both"></div> + </div><div class="form-row"><label>File Format:</label><div class="form-row-input"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Don't alter the contents of a file while uploading to a data library if using the filesystem_paths option. This partially resolves the issue where a supposedly sorted BAM file was being resorted upon upload to a data library when using this option. A better imlementation of determining whether a BAM file has been sorted (so that it does not get resorted) remains to be done.
by Bitbucket 15 Mar '11

15 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/b5ecb8f4839d/ changeset: r5221:b5ecb8f4839d user: greg date: 2011-03-15 14:38:29 summary: Don't alter the contents of a file while uploading to a data library if using the filesystem_paths option. This partially resolves the issue where a supposedly sorted BAM file was being resorted upon upload to a data library when using this option. A better imlementation of determining whether a BAM file has been sorted (so that it does not get resorted) remains to be done. affected #: 4 files (832 bytes) --- a/lib/galaxy/datatypes/binary.py Mon Mar 14 23:01:11 2011 -0400 +++ b/lib/galaxy/datatypes/binary.py Tue Mar 15 09:38:29 2011 -0400 @@ -59,7 +59,8 @@ output = subprocess.Popen(params, stderr=subprocess.PIPE, stdout=subprocess.PIPE).communicate()[0] # find returns -1 if string is not found return output.find("SO:coordinate") != -1 or output.find("SO:sorted") != -1 - + def dataset_content_needs_grooming( self, file_name ): + return not self._is_coordinate_sorted( file_name ) def groom_dataset_content( self, file_name ): """ Ensures that the Bam file contents are sorted. This function is called @@ -72,11 +73,9 @@ ## This command may also create temporary files <out.prefix>.%d.bam when the ## whole alignment cannot be fitted into memory ( controlled by option -m ). #do this in a unique temp directory, because of possible <out.prefix>.%d.bam temp files - - if self._is_coordinate_sorted(file_name): + if not self.dataset_content_needs_grooming( file_name ): # Don't re-sort if already sorted return - tmp_dir = tempfile.mkdtemp() tmp_sorted_dataset_file_name_prefix = os.path.join( tmp_dir, 'sorted' ) stderr_name = tempfile.NamedTemporaryFile( dir = tmp_dir, prefix = "bam_sort_stderr" ).name @@ -84,7 +83,6 @@ command = "samtools sort %s %s" % ( file_name, tmp_sorted_dataset_file_name_prefix ) proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=open( stderr_name, 'wb' ) ) exit_code = proc.wait() - #Did sort succeed? stderr = open( stderr_name ).read().strip() if stderr: @@ -93,10 +91,8 @@ raise Exception, "Error Grooming BAM file contents: %s" % stderr else: print stderr - # Move samtools_created_sorted_file_name to our output dataset location shutil.move( samtools_created_sorted_file_name, file_name ) - # Remove temp file and empty temporary directory os.unlink( stderr_name ) os.rmdir( tmp_dir ) @@ -124,9 +120,7 @@ raise Exception, "Error Setting BAM Metadata: %s" % stderr else: print stderr - dataset.metadata.bam_index = index_file - # Remove temp file os.unlink( stderr_name ) def sniff( self, filename ): --- a/lib/galaxy/datatypes/data.py Mon Mar 14 23:01:11 2011 -0400 +++ b/lib/galaxy/datatypes/data.py Tue Mar 15 09:38:29 2011 -0400 @@ -88,8 +88,11 @@ except OSError, e: log.exception('%s reading a file that does not exist %s' % (self.__class__.__name__, dataset.file_name)) return '' + def dataset_content_needs_grooming( self, file_name ): + """This function is called on an output dataset file after the content is initially generated.""" + return False def groom_dataset_content( self, file_name ): - """This function is called on an output dataset file after the content is initially generated.""" + """This function is called on an output dataset file if dataset_content_needs_grooming returns True.""" pass def init_meta( self, dataset, copy_from=None ): # Metadata should be left mostly uninitialized. Dataset will --- a/test/base/twilltestcase.py Mon Mar 14 23:01:11 2011 -0400 +++ b/test/base/twilltestcase.py Tue Mar 15 09:38:29 2011 -0400 @@ -637,10 +637,10 @@ try: if attributes is None: attributes = {} + compare = attributes.get( 'compare', 'diff' ) if attributes.get( 'ftype', None ) == 'bam': local_fh, temp_name = self._bam_to_sam( local_name, temp_name ) local_name = local_fh.name - compare = attributes.get( 'compare', 'diff' ) extra_files = attributes.get( 'extra_files', None ) if compare == 'diff': self.files_diff( local_name, temp_name, attributes=attributes ) --- a/tools/data_source/upload.py Mon Mar 14 23:01:11 2011 -0400 +++ b/tools/data_source/upload.py Tue Mar 15 09:38:29 2011 -0400 @@ -334,8 +334,7 @@ file_err( 'The uploaded file contains inappropriate HTML content', dataset, json_file ) return if data_type != 'binary': - # don't convert newlines on data we're only going to symlink - if link_data_only == 'link_to_files': + if link_data_only == 'copy_files': in_place = True if dataset.type in ( 'server_dir', 'path_paste' ): in_place = False @@ -353,8 +352,16 @@ ext = dataset.ext if ext == 'auto': ext = 'data' - # Move the dataset to its "real" path + datatype = registry.get_datatype_by_extension( ext ) + if dataset.type in ( 'server_dir', 'path_paste' ) and link_data_only == 'link_to_files': + # Never alter a file that will not be copied to Galaxy's local file store. + if datatype.dataset_content_needs_grooming( output_path ): + err_msg = 'The uploaded files need grooming, so change your <b>Copy data into Galaxy?</b> selection to be ' + \ + '<b>Copy files into Galaxy</b> instead of <b>Link to files without copying into Galaxy</b> so grooming can be performed.' + file_err( err_msg, dataset, json_file ) + return if link_data_only == 'copy_files' and dataset.type in ( 'server_dir', 'path_paste' ): + # Move the dataset to its "real" path if converted_path is not None: shutil.copy( converted_path, output_path ) try: @@ -362,7 +369,7 @@ except: pass else: - # this should not happen, but it's here just in case + # This should not happen, but it's here just in case shutil.copy( dataset.path, output_path ) elif link_data_only == 'copy_files': shutil.move( dataset.path, output_path ) @@ -375,9 +382,9 @@ name = dataset.name, line_count = line_count ) json_file.write( to_json_string( info ) + "\n" ) - # Groom the dataset content if necessary - datatype = registry.get_datatype_by_extension( ext ) - datatype.groom_dataset_content( output_path ) + if datatype.dataset_content_needs_grooming( output_path ): + # Groom the dataset content if necessary + datatype.groom_dataset_content( output_path ) def add_composite_file( dataset, registry, json_file, output_path, files_path ): if dataset.composite_files: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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