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additional linting of datatypes to make it more strict

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This commit is contained in:
Bjoern Gruening
2015-07-12 21:31:12 +01:00
committed by Nicola Soranzo
parent 1dab5f9384
commit f1fa2ab316
33 changed files with 171 additions and 159 deletions
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lib/galaxy/datatypes/converters/bed_to_gff_converter.py
+2 -1
View File
@@ -71,4 +71,5 @@ def __main__():
info_msg += "Skipped %d blank/comment/invalid lines starting with line #%d." % ( skipped_lines, first_skipped_line )
print info_msg
if __name__ == "__main__": __main__()
if __name__ == "__main__":
__main__()
lib/galaxy/datatypes/converters/fasta_to_len.py
+2 -3
View File
@@ -5,8 +5,7 @@ Output: tabular
Return titles with lengths of corresponding seq
"""
import sys, os
import sys
assert sys.version_info[:2] >= ( 2, 4 )
@@ -32,7 +31,7 @@ def compute_fasta_length( fasta_file, out_file, keep_first_char, keep_first_word
if not line or line.startswith( '#' ):
continue
if line[0] == '>':
if first_entry == False:
if first_entry is False:
if keep_first_word:
fasta_title = fasta_title.split()[0]
out.write( "%s\t%d\n" % ( fasta_title[ 1:keep_first_char ], seq_len ) )
lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py
+4 -2
View File
@@ -11,7 +11,8 @@ Input: fasta
Output: tabular
"""
import sys, os
import sys
import os
seq_hash = {}
@@ -47,4 +48,5 @@ def __main__():
out.write("".join(sequence.split()) + '\n')
if __name__ == "__main__" : __main__()
if __name__ == "__main__" :
__main__()
lib/galaxy/datatypes/converters/fastq_to_fqtoc.py
+2 -2
View File
@@ -1,6 +1,6 @@
#!/usr/bin/env python
import sys, os, gzip
import sys
from galaxy.datatypes.checkers import is_gzip
@@ -30,7 +30,7 @@ def main():
in_file = open(input_fname)
out_file.write('{"sections" : [');
out_file.write('{"sections" : [')
for line in in_file:
current_line += 1
lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py
+3 -6
View File
@@ -14,9 +14,7 @@ Usage:
%python fastqsolexa_to_fasta_converter.py <your_fastqsolexa_filename> <output_seq_filename> <output_score_filename>
"""
import sys, os
from math import *
import sys
assert sys.version_info[:2] >= ( 2, 4 )
@@ -43,15 +41,14 @@ def __main__():
seq_title_startswith = line_startswith
if seq_title_startswith != line_startswith:
stop_err( 'Invalid fastqsolexa format at line %d: %s.' % ( i + 1, line ) )
read_title = line[ 1: ]
outfile.write( '>%s\n' % line[1:] )
elif fastq_block_lines == 2:
# line 2 is nucleotides
read_length = len( line )
outfile.write( '%s\n' % line )
else:
pass
outfile.close()
if __name__ == "__main__": __main__()
if __name__ == "__main__":
__main__()
lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py
+5 -5
View File
@@ -13,8 +13,7 @@ the order should be:
Usage:
%python fastqsolexa_to_qual_converter.py <your_fastqsolexa_filename> <output_seq_filename> <output_score_filename>
"""
import sys, os
from math import *
import sys
assert sys.version_info[:2] >= ( 2, 4 )
@@ -27,7 +26,7 @@ def stop_err( msg ):
def __main__():
infile_name = sys.argv[1]
outfile_score = open( sys.argv[2], 'w' )
datatype = sys.argv[3]
# datatype = sys.argv[3]
qual_title_startswith = ''
seq_title_startswith = ''
default_coding_value = 64
@@ -70,7 +69,7 @@ def __main__():
val = line.split()[0]
try:
check = int( val )
int( val )
fastq_integer = True
except:
fastq_integer = False
@@ -94,4 +93,5 @@ def __main__():
outfile_score.close()
if __name__ == "__main__": __main__()
if __name__ == "__main__":
__main__()
lib/galaxy/datatypes/converters/gff_to_bed_converter.py
+2 -1
View File
@@ -40,4 +40,5 @@ def __main__():
info_msg += "Skipped %d blank/comment/invalid lines starting with line #%d." % ( skipped_lines, first_skipped_line )
print info_msg
if __name__ == "__main__": __main__()
if __name__ == "__main__":
__main__()
lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py
+6 -4
View File
@@ -9,10 +9,12 @@ usage:
from __future__ import division
import sys, fileinput
from galaxy import eggs
import pkg_resources; pkg_resources.require( "bx-python" )
from galaxy.datatypes.util.gff_util import *
import sys
import fileinput
import pkg_resources
pkg_resources.require( "bx-python" )
from galaxy.datatypes.util.gff_util import GFFReaderWrapper, GenomicInterval, convert_gff_coords_to_bed
from bx.interval_index_file import Indexes
lib/galaxy/datatypes/converters/interval_to_bed_converter.py
+5 -4
View File
@@ -2,8 +2,8 @@
# Dan Blankenberg
import sys
from galaxy import eggs
import pkg_resources; pkg_resources.require( "bx-python" )
import pkg_resources
pkg_resources.require( "bx-python" )
import bx.intervals.io
assert sys.version_info[:2] >= ( 2, 4 )
@@ -51,7 +51,7 @@ def __main__():
name = "region_%i" % count
try:
out.write( "%s\t%i\t%i\t%s\t%i\t%s\n" % ( region.chrom, region.start, region.end, name, 0, region.strand ) )
out.write( "%s\t%i\t%i\t%s\t%i\t%s\n" % ( region.chrom, region.start, region.end, name, 0, region.strand ) )
except:
skipped_lines += 1
if not first_skipped_line:
@@ -61,4 +61,5 @@ def __main__():
if skipped_lines > 0:
print "Skipped %d blank or invalid lines starting with line # %d." % ( skipped_lines, first_skipped_line )
if __name__ == "__main__": __main__()
if __name__ == "__main__":
__main__()
lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py
+4 -3
View File
@@ -2,8 +2,8 @@
# Dan Blankenberg
import sys
from galaxy import eggs
import pkg_resources; pkg_resources.require( "bx-python" )
import pkg_resources
pkg_resources.require( "bx-python" )
import bx.intervals.io
assert sys.version_info[:2] >= ( 2, 4 )
@@ -153,4 +153,5 @@ def __main__():
if skipped_lines > 0:
print "Skipped %d blank or invalid lines starting with line # %d." % ( skipped_lines, first_skipped_line )
if __name__ == "__main__": __main__()
if __name__ == "__main__":
__main__()
lib/galaxy/datatypes/converters/interval_to_coverage.py
+4 -6
View File
@@ -6,14 +6,12 @@ usage: %prog bed_file out_file
-1, --cols1=N,N,N,N: Columns for chrom, start, end, strand in interval file
-2, --cols2=N,N,N,N: Columns for chrom, start, end, strand in coverage file
"""
import sys
from galaxy import eggs
import pkg_resources; pkg_resources.require( "bx-python" )
import pkg_resources
pkg_resources.require( "bx-python" )
from bx.intervals import io
from bx.cookbook import doc_optparse
import psyco_full
import commands
import os
from os import environ
import tempfile
from bisect import bisect
@@ -41,7 +39,6 @@ def main( interval, coverage ):
partitions = []
forward_covs = []
reverse_covs = []
offset = 0
chrom = None
lastchrom = None
for record in interval:
@@ -114,7 +111,8 @@ class CoverageWriter( object ):
self.template = "%(0)s\t%(1)s\t%(2)s\t%(3)s\n" % positions
def write(self, **kwargs ):
if self.reverseCol < 0: kwargs['forward'] += kwargs['reverse']
if self.reverseCol < 0:
kwargs['forward'] += kwargs['reverse']
posgen = kwargs['position']
for position in posgen:
kwargs['position'] = position
lib/galaxy/datatypes/converters/interval_to_fli.py
+4 -5
View File
@@ -13,10 +13,9 @@ where location is formatted as:
and symbols are sorted in lexigraphical order.
'''
import sys, optparse
from galaxy import eggs
import pkg_resources; pkg_resources.require( "bx-python" )
import optparse
import pkg_resources
pkg_resources.require( "bx-python" )
from bx.tabular.io import Comment
from galaxy.datatypes.util.gff_util import GFFReaderWrapper, read_unordered_gtf, convert_gff_coords_to_bed
@@ -83,7 +82,7 @@ def main():
name_loc_dict[ fields[3] ] = {
'contig': fields[0],
'start': int( fields[1] ),
'end': int ( fields[2] )
'end': int( fields[2] )
}
# Create sorted list of entries.
lib/galaxy/datatypes/converters/interval_to_tabix_converter.py
+6 -3
View File
@@ -7,9 +7,12 @@ Supported presets: bed, gff, vcf
usage: %prog in_file out_file
"""
from galaxy import eggs
import pkg_resources; pkg_resources.require( "pysam" )
import ctabix, subprocess, tempfile, sys, os, optparse
import pkg_resources
pkg_resources.require( "pysam" )
import ctabix
import sys
import os
import optparse
def main():
lib/galaxy/datatypes/converters/lped_to_fped_converter.py
+3 -1
View File
@@ -3,7 +3,9 @@
# much slower so best to always
# use numeric alleles internally
import sys, os, time
import sys
import os
import time
prog = os.path.split(sys.argv[0])[-1]
lib/galaxy/datatypes/converters/lped_to_pbed_converter.py
+4 -2
View File
@@ -4,8 +4,10 @@
# eg lped/eigen/fbat/snpmatrix all to pbed
# and pbed to lped/eigen/fbat/snpmatrix ?
# that's a lot of converters
import sys, os, time, subprocess
import sys
import os
import time
import subprocess
prog = os.path.split(sys.argv[0])[-1]
myversion = 'Oct 10 2009'
lib/galaxy/datatypes/converters/maf_to_fasta_converter.py
+4 -3
View File
@@ -2,8 +2,8 @@
# Dan Blankenberg
import sys
from galaxy import eggs
import pkg_resources; pkg_resources.require( "bx-python" )
import pkg_resources
pkg_resources.require( "bx-python" )
import bx.align.maf
from galaxy.tools.util import maf_utilities
@@ -30,4 +30,5 @@ def __main__():
print "%i MAF blocks converted to FASTA." % ( count )
if __name__ == "__main__": __main__()
if __name__ == "__main__":
__main__()
lib/galaxy/datatypes/converters/maf_to_interval_converter.py
+5 -4
View File
@@ -2,8 +2,8 @@
# Dan Blankenberg
import sys
from galaxy import eggs
import pkg_resources; pkg_resources.require( "bx-python" )
import pkg_resources
pkg_resources.require( "bx-python" )
import bx.align.maf
from galaxy.tools.util import maf_utilities
@@ -22,7 +22,7 @@ def __main__():
for block in bx.align.maf.Reader( open( input_name, 'r' ) ):
for c in maf_utilities.iter_components_by_src_start( block, species ):
if c is not None:
out.write( "%s\t%i\t%i\t%s\n" % ( maf_utilities.src_split( c.src )[-1], c.get_forward_strand_start(), c.get_forward_strand_end(), c.strand ) )
out.write( "%s\t%i\t%i\t%s\n" % ( maf_utilities.src_split( c.src )[-1], c.get_forward_strand_start(), c.get_forward_strand_end(), c.strand ) )
count += 1
except Exception as e:
print >> sys.stderr, "There was a problem processing your input: %s" % e
@@ -30,4 +30,5 @@ def __main__():
print "%i MAF blocks converted to Genomic Intervals for species %s." % ( count, species )
if __name__ == "__main__": __main__()
if __name__ == "__main__":
__main__()
lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py
+9 -15
View File
@@ -2,9 +2,11 @@
# used for grr and eigenstrat - shellfish if we get around to it
#
import os, sys, tempfile, subprocess, time
from galaxy import eggs
import os
import sys
import tempfile
import subprocess
import time
prog = "pbed_ldreduced_converter.py"
@@ -40,11 +42,11 @@ def pruneLD(plinktasks=[], cd='./', vclbase=[]):
vcl = vclbase + task
sto = file(plog, 'w')
x = subprocess.Popen(' '.join(vcl), shell=True, stdout=sto, stderr=sto, cwd=cd)
retval = x.wait()
x.wait()
sto.close()
try:
lplog = file(plog, 'r').readlines()
lplog = [x for x in lplog if x.find('Pruning SNP') == -1]
lplog = [elem for elem in lplog if elem.find('Pruning SNP') == -1]
alog += lplog
alog.append('\n')
os.unlink(plog) # no longer needed
@@ -57,22 +59,14 @@ def makeLDreduced(basename, infpath=None, outfpath=None, plinke='plink', forcere
winsize="60", winmove="40", r2thresh="0.1" ):
""" not there so make and leave in output dir for post job hook to copy back into input extra files path for next time
"""
ldr = basename # we store ld reduced and thinned data
ldreduced = os.path.join(outfpath, ldr) # note where this is going
outbase = os.path.join(outfpath, basename)
inbase = os.path.join(infpath)
loglines = []
ldbedname = '%s.bed' % ldreduced
bedname = '%s.bed' % basename
ldbedfn = os.path.join(infpath, ldbedname)
bedfn = os.path.join(infpath, bedname)
bmap = os.path.join(infpath, '%s.bim' % basename)
plinktasks = []
vclbase = [plinke, '--noweb']
plinktasks += [['--bfile', inbase, '--indep-pairwise %s %s %s' % (winsize, winmove, r2thresh), '--out %s' % outbase],
['--bfile', inbase, '--extract %s.prune.in --make-bed --out %s' % (outbase, outbase)]]
vclbase = [plinke, '--noweb']
loglines = pruneLD(plinktasks=plinktasks, cd=outfpath, vclbase=vclbase)
pruneLD(plinktasks=plinktasks, cd=outfpath, vclbase=vclbase)
def main():
@@ -120,4 +114,4 @@ def main():
if __name__ == "__main__":
main()
main()
lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py
+2 -4
View File
@@ -16,7 +16,6 @@ def __main__():
out = open( output_name, 'w' )
i = 0
for i, line in enumerate( open( input_name ) ):
complete_interval = False
line = line.rstrip( '\r\n' )
if line:
if line.startswith( HEADER_STARTS_WITH ):
@@ -24,8 +23,6 @@ def __main__():
else:
try:
elems = line.split( '\t' )
if len( elems ) >= 5:
complete_interval = True
out.write( '%s\t%s\t%s\t%s\t0\t%s\n' % ( elems[0], int(elems[1]) - 1, elems[2], elems[4], elems[3] ) )
except Exception as e:
print e
@@ -42,4 +39,5 @@ def __main__():
info_msg += "Skipped %d blank/comment/invalid lines starting with line #%d." % ( skipped_lines, first_skipped_line )
print info_msg
if __name__ == "__main__": __main__()
if __name__ == "__main__":
__main__()
lib/galaxy/datatypes/converters/sam_to_bam.py
+8 -3
View File
@@ -5,8 +5,12 @@
A wrapper script for converting SAM to BAM, with sorting.
%prog input_filename.sam output_filename.bam
"""
import sys, optparse, os, tempfile, subprocess, shutil
import os
import sys
import optparse
import tempfile
import subprocess
import shutil
CHUNK_SIZE = 2 ** 20 # 1mb
@@ -67,4 +71,5 @@ def __main__():
cleanup_before_exit( tmp_dir )
if __name__ == "__main__": __main__()
if __name__ == "__main__":
__main__()
lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py
+2 -2
View File
@@ -7,8 +7,8 @@ Convert from VCF file to interval index file.
from __future__ import division
import optparse
from galaxy import eggs
import pkg_resources; pkg_resources.require( "bx-python" )
import pkg_resources
pkg_resources.require( "bx-python" )
import galaxy_utils.sequence.vcf
from bx.interval_index_file import Indexes
lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py
+4 -4
View File
@@ -7,10 +7,10 @@ Original ordering, which may be specifically needed by tools or external displa
usage: %prog in_file out_file
"""
from galaxy import eggs
import pkg_resources; pkg_resources.require( "pysam" )
import ctabix, optparse
import pkg_resources
pkg_resources.require( "pysam" )
import ctabix
import optparse
def main():
lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py
+5 -4
View File
@@ -7,10 +7,10 @@ Read a wiggle track and print out a series of lines containing
and fixedStep wiggle lines.
"""
import sys
from galaxy import eggs
import pkg_resources; pkg_resources.require( "bx-python" )
import pkg_resources
pkg_resources.require( "bx-python" )
import bx.wiggle
from galaxy.tools.exception_handling import *
from galaxy.tools.exception_handling import UCSCOutWrapper, UCSCLimitException
def stop_err( msg ):
@@ -43,4 +43,5 @@ def main():
in_file.close()
out_file.close()
if __name__ == "__main__": main()
if __name__ == "__main__":
main()
lib/galaxy/datatypes/tabular.py
+21 -21
View File
@@ -929,47 +929,47 @@ class CSV( TabularData ):
dataset.metadata.column_names = header_row
dataset.metadata.delimiter = reader.dialect.delimiter
class ConnectivityTable( Tabular ):
edam_format = "format_3309"
file_ext = "ct"
header_regexp = re.compile( "^[0-9]+" + "(?:\t|[ ]+)" + ".*?" + "(?:ENERGY|energy|dG)" + "[ \t].*?=")
structure_regexp = re.compile( "^[0-9]+" + "(?:\t|[ ]+)" + "[ACGTURYKMSWBDHVN]+" + "(?:\t|[ ]+)" + "[^\t]+" + "(?:\t|[ ]+)" + "[^\t]+" + "(?:\t|[ ]+)" + "[^\t]+" + "(?:\t|[ ]+)" + "[^\t]+")
structure_regexp = re.compile( "^[0-9]+" + "(?:\t|[ ]+)" + "[ACGTURYKMSWBDHVN]+" + "(?:\t|[ ]+)" + "[^\t]+" + "(?:\t|[ ]+)" + "[^\t]+" + "(?:\t|[ ]+)" + "[^\t]+" + "(?:\t|[ ]+)" + "[^\t]+")
def __init__(self, **kwd):
Tabular.__init__( self, **kwd )
self.columns = 6
self.column_names = ['base_index', 'base', 'neighbor_left', 'neighbor_right', 'partner', 'natural_numbering']
self.column_types = ['int', 'str', 'int', 'int', 'int', 'int']
def set_meta( self, dataset, **kwd ):
data_lines = 0
for line in file( dataset.file_name ):
data_lines += 1
dataset.metadata.data_lines = data_lines
def sniff(self, filename):
"""
The ConnectivityTable (CT) is a file format used for describing
RNA 2D structures by tools including MFOLD, UNAFOLD and
the RNAStructure package. The tabular file format is defined as
follows:
5 energy = -12.3 sequence name
1 G 0 2 0 1
2 A 1 3 0 2
3 A 2 4 0 3
4 A 3 5 0 4
5 C 4 6 1 5
The links given at the edam ontology page do not indicate what
type of separator is used (space or tab) while different
implementations exist. The implementation that uses spaces as
separator (implemented in RNAStructure) is as follows:
10 ENERGY = -34.8 seqname
1 G 0 2 9 1
2 G 1 3 8 2
@@ -982,26 +982,26 @@ class ConnectivityTable( Tabular ):
9 C 8 10 1 9
10 a 9 0 0 10
"""
i = 0
j = 1
try:
with open( filename ) as handle:
for line in handle:
line = line.strip()
if len(line) > 0:
if i == 0:
if not self.header_regexp.match(line):
return False
else:
length = int(re.split('\W+', line,1)[0])
length = int(re.split('\W+', line, 1)[0])
else:
if not self.structure_regexp.match(line.upper()):
return False
else:
if j != int(re.split('\W+', line,1)[0]):
if j != int(re.split('\W+', line, 1)[0]):
return False
elif j == length: # Last line of first sequence has been recheached
return True
@@ -1011,7 +1011,7 @@ class ConnectivityTable( Tabular ):
return False
except:
return False
def get_chunk(self, trans, dataset, chunk):
ck_index = int(chunk)
f = open(dataset.file_name)
@@ -1026,12 +1026,12 @@ class ConnectivityTable( Tabular ):
while cursor and ck_data[-1] != '\n':
ck_data += cursor
cursor = f.read(1)
# The ConnectivityTable format has several derivatives of which one is delimited by (multiple) spaces.
# By converting these spaces back to tabs, chucks can still be interpreted by tab delimited file parsers
ck_data_header, ck_data_body = ck_data.split('\n', 1)
ck_data_header = re.sub('^([0-9]+)[ ]+',r'\1\t',ck_data_header)
ck_data_body = re.sub('\n[ \t]+','\n',ck_data_body)
ck_data_body = re.sub('[ ]+','\t',ck_data_body)
ck_data_header = re.sub('^([0-9]+)[ ]+', r'\1\t', ck_data_header)
ck_data_body = re.sub('\n[ \t]+', '\n', ck_data_body)
ck_data_body = re.sub('[ ]+', '\t', ck_data_body)
return dumps( { 'ck_data': util.unicodify(ck_data_header + "\n" + ck_data_body ), 'ck_index': ck_index + 1 } )
lib/galaxy/model/__init__.py
+5 -6
View File
@@ -1234,12 +1234,11 @@ class History( object, Dictifiable, UsesAnnotations, HasName ):
.filter( HistoryDatasetAssociation.table.c.history_id == self.id )
.filter( not_( HistoryDatasetAssociation.deleted ) )
.order_by( HistoryDatasetAssociation.table.c.hid.asc() )
.options(
joinedload("children"),
joinedload("dataset"),
joinedload("dataset.actions"),
joinedload("dataset.actions.role"),
))
.options( joinedload("children"),
joinedload("dataset"),
joinedload("dataset.actions"),
joinedload("dataset.actions.role"),
))
self._active_datasets_children_and_roles = query.all()
return self._active_datasets_children_and_roles
lib/galaxy/webapps/galaxy/controllers/async.py
+2 -2
View File
@@ -120,8 +120,8 @@ class ASync( BaseUIController ):
try:
key = hmac_new( trans.app.config.tool_secret, "%d:%d" % ( data.id, data.history_id ) )
galaxy_url = trans.request.base + '/async/%s/%s/%s' % ( tool_id, data.id, key )
params.update( { 'GALAXY_URL' :galaxy_url } )
params.update( { 'data_id' :data.id } )
params.update( { 'GALAXY_URL': galaxy_url } )
params.update( { 'data_id': data.id } )
# Use provided URL or fallback to tool action
url = URL or tool.action
# Does url already have query params?
lib/galaxy/webapps/galaxy/controllers/dataset.py
+1 -1
View File
@@ -62,7 +62,7 @@ class HistoryDatasetAssociationListGrid( grids.Grid ):
# Link name to dataset's history.
link=( lambda item: iff( item.history.deleted, None, dict( operation="switch", id=item.id ) ) ), filterable="advanced", attach_popup=True, inbound=True ),
HistoryColumn( "History", key="history", sortable=False, inbound=True,
link=( lambda item: iff( item.history.deleted, None, dict( operation="switch_history", id=item.id ) ) ) ),
link=( lambda item: iff( item.history.deleted, None, dict( operation="switch_history", id=item.id ) ) ) ),
grids.IndividualTagsColumn( "Tags", key="tags", model_tag_association_class=model.HistoryDatasetAssociationTagAssociation, filterable="advanced", grid_name="HistoryDatasetAssocationListGrid" ),
StatusColumn( "Status", key="deleted", attach_popup=False ),
grids.GridColumn( "Last Updated", key="update_time", format=time_ago ),
lib/galaxy/webapps/galaxy/controllers/page.py
+12 -12
View File
@@ -391,13 +391,13 @@ class PageController( BaseUIController, SharableMixin,
web.FormBuilder( web.url_for(controller='page', action='create'), "Create new page", submit_text="Submit" )
.add_text( "page_title", "Page title", value=page_title, error=page_title_err )
.add_text( "page_slug", "Page identifier", value=page_slug, error=page_slug_err,
help="""A unique identifier that will be used for
public links to this page. A default is generated
from the page title, but can be edited. This field
must contain only lowercase letters, numbers, and
the '-' character.""" )
help="""A unique identifier that will be used for
public links to this page. A default is generated
from the page title, but can be edited. This field
must contain only lowercase letters, numbers, and
the '-' character.""" )
.add_text( "page_annotation", "Page annotation", value=page_annotation, error=page_annotation_err,
help="A description of the page; annotation is shown alongside published pages."),
help="A description of the page; annotation is shown alongside published pages."),
template="page/create.mako" )
@web.expose
@@ -442,13 +442,13 @@ class PageController( BaseUIController, SharableMixin,
web.FormBuilder( web.url_for(controller='page', action='edit', id=encoded_id ), "Edit page attributes", submit_text="Submit" )
.add_text( "page_title", "Page title", value=page_title, error=page_title_err )
.add_text( "page_slug", "Page identifier", value=page_slug, error=page_slug_err,
help="""A unique identifier that will be used for
public links to this page. A default is generated
from the page title, but can be edited. This field
must contain only lowercase letters, numbers, and
the '-' character.""" )
help="""A unique identifier that will be used for
public links to this page. A default is generated
from the page title, but can be edited. This field
must contain only lowercase letters, numbers, and
the '-' character.""" )
.add_text( "page_annotation", "Page annotation", value=page_annotation, error=page_annotation_err,
help="A description of the page; annotation is shown alongside published pages."),
help="A description of the page; annotation is shown alongside published pages."),
template="page/create.mako" )
@web.expose
lib/galaxy/webapps/galaxy/controllers/visualization.py
+12 -12
View File
@@ -656,14 +656,14 @@ class VisualizationController( BaseUIController, SharableMixin, UsesVisualizatio
.add_text( "visualization_title", "Visualization title", value=visualization_title, error=visualization_title_err )
.add_select( "visualization_type", "Type", options=viz_type_options, error=None )
.add_text( "visualization_slug", "Visualization identifier", value=visualization_slug, error=visualization_slug_err,
help="""A unique identifier that will be used for
public links to this visualization. A default is generated
from the visualization title, but can be edited. This field
must contain only lowercase letters, numbers, and
the '-' character.""" )
help="""A unique identifier that will be used for
public links to this visualization. A default is generated
from the visualization title, but can be edited. This field
must contain only lowercase letters, numbers, and
the '-' character.""" )
.add_select( "visualization_dbkey", "Visualization DbKey/Build", value=visualization_dbkey, options=trans.app.genomes.get_dbkeys( trans, chrom_info=True ), error=None)
.add_text( "visualization_annotation", "Visualization annotation", value=visualization_annotation, error=visualization_annotation_err,
help="A description of the visualization; annotation is shown alongside published visualizations."),
help="A description of the visualization; annotation is shown alongside published visualizations."),
template="visualization/create.mako"
)
@@ -723,13 +723,13 @@ class VisualizationController( BaseUIController, SharableMixin, UsesVisualizatio
web.FormBuilder( web.url_for(controller='visualization', action='edit', id=id ), "Edit visualization attributes", submit_text="Submit" )
.add_text( "visualization_title", "Visualization title", value=visualization_title, error=visualization_title_err )
.add_text( "visualization_slug", "Visualization identifier", value=visualization_slug, error=visualization_slug_err,
help="""A unique identifier that will be used for
public links to this visualization. A default is generated
from the visualization title, but can be edited. This field
must contain only lowercase letters, numbers, and
the '-' character.""" )
help="""A unique identifier that will be used for
public links to this visualization. A default is generated
from the visualization title, but can be edited. This field
must contain only lowercase letters, numbers, and
the '-' character.""" )
.add_text( "visualization_annotation", "Visualization annotation", value=visualization_annotation, error=visualization_annotation_err,
help="A description of the visualization; annotation is shown alongside published visualizations."),
help="A description of the visualization; annotation is shown alongside published visualizations."),
template="visualization/create.mako" )
# ------------------------- registry.
lib/galaxy/webapps/tool_shed/api/tools.py
+1 -1
View File
@@ -52,7 +52,7 @@ class ToolsController( BaseAPIController ):
page_size = kwd.get( 'page_size', 10 )
try:
page = int( page )
page_size = int ( page_size )
page_size = int( page_size )
except ValueError:
raise RequestParameterInvalidException( 'The "page" and "page_size" have to be integers.' )
return_jsonp = util.asbool( kwd.get( 'jsonp', False ) )
lib/log_tempfile.py
+5 -1
View File
@@ -1,16 +1,19 @@
# override tempfile methods for debugging
import tempfile, traceback
import tempfile
import traceback
import logging
log = logging.getLogger( __name__ )
class TempFile( object ):
def __init__( self ):
tempfile._NamedTemporaryFile = tempfile.NamedTemporaryFile
tempfile._mkstemp = tempfile.mkstemp
tempfile.NamedTemporaryFile = self.NamedTemporaryFile
tempfile.mkstemp = self.mkstemp
def NamedTemporaryFile( self, *args, **kwargs ):
f = tempfile._NamedTemporaryFile( *args, **kwargs )
try:
@@ -18,6 +21,7 @@ class TempFile( object ):
except AttributeError:
pass
return f
def mkstemp( self, *args, **kwargs ):
f = tempfile._mkstemp( *args, **kwargs )
try:
lib/mimeparse.py
+16 -10
View File
@@ -19,6 +19,7 @@ __author__ = 'Joe Gregorio'
__email__ = "joe@bitworking.org"
__credits__ = ""
def parse_mime_type(mime_type):
"""Carves up a mime-type and returns a tuple of the
(type, subtype, params) where 'params' is a dictionary
@@ -29,15 +30,16 @@ def parse_mime_type(mime_type):
('application', 'xhtml', {'q', '0.5'})
"""
parts = mime_type.split(";")
params = dict([tuple([s.strip() for s in param.split("=")])\
for param in parts[1:] ])
params = dict( [tuple([s.strip() for s in param.split("=")]) for param in parts[1:] ] )
full_type = parts[0].strip()
# Java URLConnection class sends an Accept header that includes a single "*"
# Turn it into a legal wildcard.
if full_type == '*': full_type = '*/*'
if full_type == '*':
full_type = '*/*'
(type, subtype) = full_type.split("/")
return (type.strip(), subtype.strip(), params)
def parse_media_range(range):
r"""
Carves up a media range and returns a tuple of the
@@ -55,12 +57,13 @@ def parse_media_range(range):
in with a proper default if necessary.
"""
(type, subtype, params) = parse_mime_type(range)
if not params.has_key('q') or not params['q'] or \
if 'q' not in params or not params['q'] or \
not float(params['q']) or float(params['q']) > 1\
or float(params['q']) < 0:
params['q'] = '1'
return (type, subtype, params)
def fitness_and_quality_parsed(mime_type, parsed_ranges):
"""Find the best match for a given mime-type against
a list of media_ranges that have already been
@@ -72,13 +75,13 @@ def fitness_and_quality_parsed(mime_type, parsed_ranges):
best_fitness = -1
best_fit_q = 0
(target_type, target_subtype, target_params) =\
parse_media_range(mime_type)
parse_media_range(mime_type)
for (type, subtype, params) in parsed_ranges:
if (type == target_type or type == '*' or target_type == '*') and \
(subtype == target_subtype or subtype == '*' or target_subtype == '*'):
param_matches = reduce(lambda x, y: x+y, [1 for (key, value) in \
target_params.iteritems() if key != 'q' and \
params.has_key(key) and value == params[key]], 0)
param_matches = reduce(lambda x, y: x + y, [1 for (key, value) in
target_params.iteritems() if key != 'q' and
key in params and value == params[key]], 0)
fitness = (type == target_type) and 100 or 0
fitness += (subtype == target_subtype) and 10 or 0
fitness += param_matches
@@ -88,6 +91,7 @@ def fitness_and_quality_parsed(mime_type, parsed_ranges):
return best_fitness, float(best_fit_q)
def quality_parsed(mime_type, parsed_ranges):
"""Find the best match for a given mime-type against
a list of media_ranges that have already been
@@ -98,6 +102,7 @@ def quality_parsed(mime_type, parsed_ranges):
parsed media ranges. """
return fitness_and_quality_parsed(mime_type, parsed_ranges)[1]
def quality(mime_type, ranges):
"""Returns the quality 'q' of a mime-type when compared
against the media-ranges in ranges. For example:
@@ -109,6 +114,7 @@ def quality(mime_type, ranges):
parsed_ranges = [parse_media_range(r) for r in ranges.split(",")]
return quality_parsed(mime_type, parsed_ranges)
def best_match(supported, header):
"""Takes a list of supported mime-types and finds the best
match for all the media-ranges listed in header. The value of
@@ -120,8 +126,8 @@ def best_match(supported, header):
'text/xml'
"""
parsed_header = [parse_media_range(r) for r in header.split(",")]
weighted_matches = [(fitness_and_quality_parsed(mime_type, parsed_header), mime_type)\
for mime_type in supported]
weighted_matches = [(fitness_and_quality_parsed(mime_type, parsed_header), mime_type)
for mime_type in supported]
weighted_matches.sort()
return weighted_matches[-1][0][1] and weighted_matches[-1][1] or ''
lib/psyco_full.py
+1 -6
View File
@@ -1,10 +1,5 @@
import sys
try:
import psyco
psyco.full()
except:
pass
#print >> sys.stderr, "Psyco not found, continuing without it"
pass