1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/61036b55f4e4/
changeset: r5285:61036b55f4e4
user: dannon
date: 2011-03-30 16:38:45
summary: Removing a debug print from previous commit.
affected #: 1 file (25 bytes)
--- a/lib/galaxy/datatypes/tabular.py Wed Mar 30 10:34:21 2011 -0400
+++ b/lib/galaxy/datatypes/tabular.py Wed Mar 30 10:38:45 2011 -0400
@@ -224,7 +224,6 @@
out.append( '%s</td></tr>' % escape( comments.pop(0) ) )
return "".join( out )
def set_peek( self, dataset, line_count=None, is_multi_byte=False):
- print line_count
super(Tabular, self).set_peek( dataset, line_count=line_count, is_multi_byte=is_multi_byte)
if dataset.metadata.comment_lines:
dataset.blurb = "%s, %s comments" % ( dataset.blurb, util.commaify( str( dataset.metadata.comment_lines ) ) )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/41a416e61021/
changeset: r5283:41a416e61021
user: dannon
date: 2011-03-30 13:14:20
summary: Refactor set_peek to a single method in class Text. Should also fix bug introduced in 5236 that prevented setting of some metadata.
affected #: 3 files (2.1 KB)
--- a/lib/galaxy/datatypes/data.py Tue Mar 29 16:27:35 2011 -0400
+++ b/lib/galaxy/datatypes/data.py Wed Mar 30 07:14:20 2011 -0400
@@ -354,6 +354,7 @@
class Text( Data ):
file_ext = 'txt'
+ line_class = 'line'
"""Add metadata elements"""
MetadataElement( name="data_lines", default=0, desc="Number of data lines", readonly=True, optional=True, visible=False, no_value=0 )
@@ -417,26 +418,30 @@
data_lines += 1
return data_lines
def set_peek( self, dataset, line_count=None, is_multi_byte=False ):
+ """
+ Set the peek. This method is used by various subclasses of Text.
+ """
if not dataset.dataset.purged:
# The file must exist on disk for the get_file_peek() method
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 is not None:
- dataset.blurb = "%s %s" % ( util.commaify( str(dataset.metadata.data_lines) ), inflector.cond_plural(dataset.metadata.data_lines, "line") )
+ if dataset.metadata.data_lines:
+ dataset.blurb = "%s %s" % ( util.commaify( str(dataset.metadata.data_lines) ), inflector.cond_plural(dataset.metadata.data_lines, self.line_class) )
else:
# Number of lines is not known ( this should not happen ), and auto-detect is
# needed to set metadata
# This can happen when the file is larger than max_optional_metadata_filesize.
if int(dataset.get_size()) <= 1048576:
#Small dataset, recount all lines and reset peek afterward.
- dataset.metadata.data_lines = self.count_data_lines(dataset)
- self.set_peek(dataset)
+ lc = self.count_data_lines(dataset)
+ dataset.metadata.data_lines = lc
+ dataset.blurb = "%s %s" % util.commaify( str(lc) ), inflector.cond_plural(lc, self.line_class)
else:
est_lines = self.estimate_file_lines(dataset)
- dataset.blurb = "~%s %s" % ( util.commaify(util.roundify(str(est_lines))), inflector.cond_plural(est_lines, "line") )
+ dataset.blurb = "~%s %s" % ( util.commaify(util.roundify(str(est_lines))), inflector.cond_plural(est_lines, self.line_class) )
else:
- dataset.blurb = "%s %s" % util.commaify( str(line_count) ), inflector.cond_plural(line_count, "line")
+ dataset.blurb = "%s %s" % util.commaify( str(line_count) ), inflector.cond_plural(line_count, self.line_class)
else:
dataset.peek = 'file does not exist'
dataset.blurb = 'file purged from disk'
--- a/lib/galaxy/datatypes/interval.py Tue Mar 29 16:27:35 2011 -0400
+++ b/lib/galaxy/datatypes/interval.py Wed Mar 30 07:14:20 2011 -0400
@@ -45,6 +45,7 @@
class Interval( Tabular ):
"""Tab delimited data containing interval information"""
file_ext = "interval"
+ line_class = "region"
"""Add metadata elements"""
MetadataElement( name="chromCol", default=1, desc="Chrom column", param=metadata.ColumnParameter )
@@ -60,23 +61,6 @@
self.add_display_app ( 'ucsc', 'display at UCSC', 'as_ucsc_display_file', 'ucsc_links' )
def init_meta( self, dataset, copy_from=None ):
Tabular.init_meta( self, dataset, copy_from=copy_from )
- def set_peek( self, dataset, line_count=None, is_multi_byte=False ):
- """Set the peek and blurb text"""
- if not dataset.dataset.purged:
- 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 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
- # needed to set metadata
- dataset.blurb = "~%s regions" % util.commaify(util.roundify(str(self.estimate_file_lines(dataset))))
- else:
- dataset.blurb = "%s regions" % util.commaify( str( line_count ) )
- else:
- dataset.peek = 'file does not exist'
- dataset.blurb = 'file purged from disk'
def set_meta( self, dataset, overwrite = True, first_line_is_header = False, **kwd ):
"""Tries to guess from the line the location number of the column for the chromosome, region start-end and strand"""
Tabular.set_meta( self, dataset, overwrite = overwrite, skip = 0 )
--- a/lib/galaxy/datatypes/tabular.py Tue Mar 29 16:27:35 2011 -0400
+++ b/lib/galaxy/datatypes/tabular.py Wed Mar 30 07:14:20 2011 -0400
@@ -223,8 +223,9 @@
out.append( '<tr><td>' )
out.append( '%s</td></tr>' % escape( comments.pop(0) ) )
return "".join( out )
- def set_peek( self, dataset, line_count=None, is_multi_byte=False ):
- data.Text.set_peek( self, dataset, line_count=line_count, is_multi_byte=is_multi_byte )
+ def set_peek( self, dataset, line_count=None, is_multi_byte=False):
+ print line_count
+ super(Tabular, self).set_peek( dataset, line_count=line_count, is_multi_byte=is_multi_byte)
if dataset.metadata.comment_lines:
dataset.blurb = "%s, %s comments" % ( dataset.blurb, util.commaify( str( dataset.metadata.comment_lines ) ) )
def display_peek( self, dataset ):
@@ -383,6 +384,7 @@
class Pileup( Tabular ):
"""Tab delimited data in pileup (6- or 10-column) format"""
file_ext = "pileup"
+ line_class = "genomic coordinate"
"""Add metadata elements"""
MetadataElement( name="chromCol", default=1, desc="Chrom column", param=metadata.ColumnParameter )
@@ -392,24 +394,6 @@
def init_meta( self, dataset, copy_from=None ):
Tabular.init_meta( self, dataset, copy_from=copy_from )
- def set_peek( self, dataset, line_count=None, is_multi_byte=False ):
- """Set the peek and blurb text"""
- if not dataset.dataset.purged:
- 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 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
- # needed to set metadata
- dataset.blurb = "? genomic coordinates"
- else:
- dataset.blurb = "%s genomic coordinates" % util.commaify( str( line_count ) )
- else:
- dataset.peek = 'file does not exist'
- dataset.blurb = 'file purged from disk'
-
def make_html_table( self, dataset, skipchars=[] ):
"""Create HTML table, used for displaying peek"""
out = ['<table cellspacing="0" cellpadding="3">']
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/4a63c840c6ab/
changeset: r5281:4a63c840c6ab
user: jgoecks
date: 2011-03-29 20:28:17
summary: Fix read id bug in Trackster BAM data provider.
affected #: 1 file (6 bytes)
--- a/lib/galaxy/visualization/tracks/data_providers.py Tue Mar 29 13:59:07 2011 -0400
+++ b/lib/galaxy/visualization/tracks/data_providers.py Tue Mar 29 14:28:17 2011 -0400
@@ -306,12 +306,12 @@
if read.is_proper_pair:
if qname in paired_pending: # one in dict is always first
pair = paired_pending[qname]
- results.append( [ "%i_%s" % ( read.pos, qname ),
+ results.append( [ "%i_%s" % ( pair['start'], qname ),
pair['start'],
read.pos + read_len,
qname,
[ pair['start'], pair['end'], pair['cigar'], pair['seq'] ],
- [ read.pos, read.pos + read_len, read.cigar, seq]
+ [ read.pos, read.pos + read_len, read.cigar, seq ]
] )
del paired_pending[qname]
else:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/c761ea39e3c9/
changeset: r5280:c761ea39e3c9
user: kellyv
date: 2011-03-29 19:59:07
summary: Modified add_manual_builds script so that it will include the build in parentheses after the name even if there are no chromosome lengths listed (previously would not because of line break after name); also added a couple of new manual builds
affected #: 2 files (454 bytes)
--- a/cron/add_manual_builds.py Tue Mar 29 13:43:24 2011 -0400
+++ b/cron/add_manual_builds.py Tue Mar 29 13:59:07 2011 -0400
@@ -21,12 +21,12 @@
build_file_out = open(build_file,'a')
for line in open(input_file):
try:
- fields = line.split("\t")
+ fields = line.replace("\n","").replace("\r","").split("\t")
build = fields.pop(0)
if build in existing_builds: continue # if build exists, leave alone
name = fields.pop(0)
try: # get chrom lens if included in file, otherwise still add build
- chrs = fields.pop(0).replace("\n","").replace("\r","").split(",")
+ chrs = fields.pop(0).split(",")
except:
chrs = []
print>>build_file_out, build+"\t"+name+" ("+build+")"
--- a/tool-data/shared/ucsc/manual_builds.txt Tue Mar 29 13:43:24 2011 -0400
+++ b/tool-data/shared/ucsc/manual_builds.txt Tue Mar 29 13:59:07 2011 -0400
@@ -698,3 +698,5 @@
Hydra_JCVI Hydra magnipapillata str. 105
Araly1 Arabidopsis lyrata
Zea_mays_B73_RefGen_v2 Maize (Zea mays) chr1=301354135,chr2=237068928,chr3=232140222,chr4=241473566,chr5=217872898,chr6=169174371,chr7=176764813,chr8=175793772,chr9=156750718,chr10=150189513,chr11=7140224
+Homo_sapiens_AK1 Korean Man chrM=16571,chr1=247249719,chr2=242951149,chr3=199501827,chr4=191273063,chr5=180857866,chr6=170899992,chr7=158821424,chr8=146274826,chr9=140273252,chr10=135374737,chr11=134452384,chr12=132349534,chr13=114142980,chr14=106368585,chr15=100338915,chr16=88827254,chr17=78774742,chr18=76117153,chr19=63811651,chr20=62435964,chr21=46944323,chr22=49691432,chrX=154913754,chrY=57772954
+Tcas_3.0 Red Flour Beetle (Tribolium castaneum)
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/2be2b8e0e916/
changeset: r5278:2be2b8e0e916
user: natefoo
date: 2011-03-29 14:18:49
summary: Use new_file_path as tempfile's tempdir, obviates the need for $TEMP in the environment.
affected #: 1 file (56 bytes)
--- a/lib/galaxy/config.py Mon Mar 28 15:27:14 2011 -0400
+++ b/lib/galaxy/config.py Tue Mar 29 08:18:49 2011 -0400
@@ -2,7 +2,7 @@
Universe configuration builder.
"""
-import sys, os
+import sys, os, tempfile
import logging, logging.config
import ConfigParser
from galaxy.util import string_as_bool
@@ -39,6 +39,7 @@
# Where dataset files are stored
self.file_path = resolve_path( kwargs.get( "file_path", "database/files" ), self.root )
self.new_file_path = resolve_path( kwargs.get( "new_file_path", "database/tmp" ), self.root )
+ tempfile.tempdir = self.new_file_path
self.openid_consumer_cache_path = resolve_path( kwargs.get( "openid_consumer_cache_path", "database/openid_consumer_cache" ), self.root )
self.cookie_path = kwargs.get( "cookie_path", "/" )
# web API
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/9d6a34b0a4fa/
changeset: r5276:9d6a34b0a4fa
user: fubar
date: 2011-03-25 18:26:40
summary: Remove bogus makeGFF from rgutils
affected #: 1 file (1 byte)
--- a/tools/rgenetics/rgutils.py Fri Mar 25 13:21:13 2011 -0400
+++ b/tools/rgenetics/rgutils.py Fri Mar 25 13:26:40 2011 -0400
@@ -62,6 +62,7 @@
chr1 67065090 67065317 - CCDS635.1_cds_2_0_chr1_67065091_r
chr1 67066082 67066181 - CCDS635.1_cds_3_0_chr1_67066083_r
+
see http://genome.ucsc.edu/FAQ/FAQtracks.html#tracks1
we need to add 1 to start coordinates on the way through - but length calculations are easier
"""
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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