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Prevent make_html_table() datatype methods from raising Exceptions

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This was preventing the browse of a data library which contained a
purged dataset of gg datatype.

Also fix import order and Python3 compatibility.
This commit is contained in:
Nicola Soranzo
2017-02-10 11:53:21 +00:00
parent 884cff33fa
commit a7d05a47da
6 changed files with 68 additions and 62 deletions
Download Patch File Download Diff File Expand all files Collapse all files
.ci/flake8_lint_include_list.txt
+2
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@@ -53,8 +53,10 @@ lib/galaxy/datatypes/dataproviders/__init__.py
lib/galaxy/datatypes/data.py
lib/galaxy/datatypes/display_applications/__init__.py
lib/galaxy/datatypes/display_applications/util.py
lib/galaxy/datatypes/genetics.py
lib/galaxy/datatypes/images.py
lib/galaxy/datatypes/__init__.py
lib/galaxy/datatypes/interval.py
lib/galaxy/datatypes/metadata.py
lib/galaxy/datatypes/msa.py
lib/galaxy/datatypes/ngsindex.py
.ci/py3_sources.txt
+2
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@@ -13,7 +13,9 @@ lib/galaxy/datatypes/constructive_solid_geometry.py
lib/galaxy/datatypes/converters/
lib/galaxy/datatypes/dataproviders/
lib/galaxy/datatypes/data.py
lib/galaxy/datatypes/genetics.py
lib/galaxy/datatypes/images.py
lib/galaxy/datatypes/interval.py
lib/galaxy/datatypes/msa.py
lib/galaxy/datatypes/ngsindex.py
lib/galaxy/datatypes/proteomics.py
lib/galaxy/datatypes/genetics.py
+32 -32
View File
@@ -11,18 +11,18 @@ subsequent row values are all numeric ! Will fail if any non numeric (eg '+' or
ross lazarus for rgenetics
august 20 2007
"""
import logging
import os
import re
import sys
import urllib
from cgi import escape
from six.moves.urllib.parse import quote_plus
from galaxy.datatypes import metadata
from galaxy.datatypes.text import Html
from galaxy.datatypes.metadata import MetadataElement
from galaxy.datatypes.tabular import Tabular
from galaxy.datatypes.text import Html
from galaxy.util import nice_size
from galaxy.web import url_for
@@ -95,9 +95,9 @@ class GenomeGraphs( Tabular ):
action='display_at',
filename='ucsc_' + site_name )
display_url = "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" % (base_url, url_for( controller='root' ), dataset.id, type)
display_url = urllib.quote_plus( display_url )
# was display_url = urllib.quote_plus( "%s/display_as?id=%i&display_app=%s" % (base_url, dataset.id, type) )
# redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % (site_url, dataset.dbkey, chrom, start, stop) )
display_url = quote_plus( display_url )
# was display_url = quote_plus( "%s/display_as?id=%i&display_app=%s" % (base_url, dataset.id, type) )
# redirect_url = quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % (site_url, dataset.dbkey, chrom, start, stop) )
sl = ["%sdb=%s" % (site_url, dataset.dbkey ), ]
# sl.append("&hgt.customText=%s")
sl.append("&hgGenome_dataSetName=%s&hgGenome_dataSetDescription=%s" % (dataset.name, 'GalaxyGG_data'))
@@ -106,7 +106,7 @@ class GenomeGraphs( Tabular ):
sl.append("&hgGenome_doSubmitUpload=submit")
sl.append("&hgGenome_maxGapToFill=25000000&hgGenome_uploadFile=%s" % display_url)
s = ''.join(sl)
s = urllib.quote_plus(s)
s = quote_plus(s)
redirect_url = s
link = '%s?redirect_url=%s&display_url=%s' % ( internal_url, redirect_url, display_url )
ret_val.append( (site_name, link) )
@@ -117,17 +117,17 @@ class GenomeGraphs( Tabular ):
Create HTML table, used for displaying peek
"""
out = ['<table cellspacing="0" cellpadding="3">']
f = open(dataset.file_name, 'r')
d = f.readlines()[:5]
if len(d) == 0:
out = "Cannot find anything to parse in %s" % dataset.name
return out
hasheader = 0
try:
['%f' % x for x in d[0][1:]] # first is name - see if starts all numerics
except:
hasheader = 1
try:
with open(dataset.file_name, 'r') as f:
d = f.readlines()[:5]
if len(d) == 0:
out = "Cannot find anything to parse in %s" % dataset.name
return out
hasheader = 0
try:
['%f' % x for x in d[0][1:]] # first is name - see if starts all numerics
except:
hasheader = 1
# Generate column header
out.append( '<tr>' )
if hasheader:
@@ -150,16 +150,16 @@ class GenomeGraphs( Tabular ):
Validate a gg file - all numeric after header row
"""
errors = list()
infile = open(dataset.file_name, "r")
infile.next() # header
for i, row in enumerate(infile):
ll = row.strip().split('\t')[1:] # first is alpha feature identifier
badvals = []
for j, x in enumerate(ll):
try:
x = float(x)
except:
badvals.append('col%d:%s' % (j + 1, x))
with open(dataset.file_name, "r") as infile:
next(infile) # header
for i, row in enumerate(infile):
ll = row.strip().split('\t')[1:] # first is alpha feature identifier
badvals = []
for j, x in enumerate(ll):
try:
x = float(x)
except:
badvals.append('col%d:%s' % (j + 1, x))
if len(badvals) > 0:
errors.append('row %d, %s' % (' '.join(badvals)))
return errors
@@ -219,7 +219,7 @@ class rgTabList(Tabular):
def display_peek( self, dataset ):
"""Returns formated html of peek"""
return Tabular.make_html_table( self, dataset, column_names=self.column_names )
return self.make_html_table( dataset, column_names=self.column_names )
def get_mime(self):
"""Returns the mime type of the datatype"""
@@ -246,8 +246,8 @@ class rgSampleList(rgTabList):
# this is what Plink wants as at 2009
def sniff(self, filename):
infile = open(filename, "r")
header = infile.next() # header
with open(filename, "r") as infile:
header = next(infile) # header
if header[0] == 'FID' and header[1] == 'IID':
return True
else:
@@ -287,7 +287,7 @@ class Rgenetics(Html):
def generate_primary_file( self, dataset=None ):
rval = ['<html><head><title>Rgenetics Galaxy Composite Dataset </title></head><p/>']
rval.append('<div>This composite dataset is composed of the following files:<p/><ul>')
for composite_name, composite_file in self.get_composite_files( dataset=dataset ).iteritems():
for composite_name, composite_file in self.get_composite_files( dataset=dataset ).items():
fn = composite_name
opt_text = ''
if composite_file.optional:
@@ -617,7 +617,7 @@ class RexpBase( Html ):
del useConc[i] # get rid of concordance
del useCols[i] # and usecols entry
for i, conc in enumerate(useConc): # these are all unique columns for the design matrix
ccounts = sorted([(conc.get(code, 0), code) for code in conc.keys()]) # decorate
ccounts = sorted((conc.get(code, 0), code) for code in conc.keys()) # decorate
cc = [(x[1], x[0]) for x in ccounts] # list of code count tuples
codeDetails = (head[useCols[i]], cc) # ('foo',[('a',3),('b',11),..])
listCol.append(codeDetails)
lib/galaxy/datatypes/interval.py
+24 -22
View File
@@ -6,10 +6,10 @@ import math
import os
import sys
import tempfile
import urllib
import numpy
from bx.intervals.io import GenomicIntervalReader, ParseError
from six.moves.urllib.parse import quote_plus
from galaxy import util
from galaxy.datatypes import metadata
@@ -19,8 +19,10 @@ from galaxy.datatypes.tabular import Tabular
from galaxy.datatypes.util.gff_util import parse_gff_attributes
from galaxy.web import url_for
import data
import dataproviders
from . import (
data,
dataproviders
)
log = logging.getLogger(__name__)
@@ -86,7 +88,7 @@ class Interval( Tabular ):
self.init_meta( dataset )
line = line.strip( '#' )
elems = line.split( '\t' )
for meta_name, header_list in alias_spec.iteritems():
for meta_name, header_list in alias_spec.items():
for header_val in header_list:
if header_val in elems:
# found highest priority header to meta_name
@@ -239,7 +241,7 @@ class Interval( Tabular ):
def display_peek( self, dataset ):
"""Returns formated html of peek"""
return Tabular.make_html_table( self, dataset, column_parameter_alias={'chromCol': 'Chrom', 'startCol': 'Start', 'endCol': 'End', 'strandCol': 'Strand', 'nameCol': 'Name'} )
return self.make_html_table( dataset, column_parameter_alias={'chromCol': 'Chrom', 'startCol': 'Start', 'endCol': 'End', 'strandCol': 'Strand', 'nameCol': 'Name'} )
def ucsc_links( self, dataset, type, app, base_url ):
"""
@@ -263,10 +265,10 @@ class Interval( Tabular ):
for site_name, site_url in valid_sites:
internal_url = url_for( controller='dataset', dataset_id=dataset.id,
action='display_at', filename='ucsc_' + site_name )
display_url = urllib.quote_plus( "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at"
% (base_url, url_for( controller='root' ), dataset.id, type) )
redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s"
% (site_url, dataset.dbkey, chrom, start, stop ) )
display_url = quote_plus( "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" %
(base_url, url_for( controller='root' ), dataset.id, type) )
redirect_url = quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" %
(site_url, dataset.dbkey, chrom, start, stop ) )
link = '%s?redirect_url=%s&display_url=%s' % ( internal_url, redirect_url, display_url )
ret_val.append( ( site_name, link ) )
return ret_val
@@ -286,7 +288,7 @@ class Interval( Tabular ):
while True:
try:
reader.next()
next(reader)
except ParseError as e:
errors.append(e)
except StopIteration:
@@ -635,8 +637,8 @@ class _RemoteCallMixin:
"""
internal_url = "%s" % url_for( controller='dataset', dataset_id=dataset.id, action='display_at', filename='%s_%s' % ( type, site_name ) )
base_url = app.config.get( "display_at_callback", base_url )
display_url = urllib.quote_plus( "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" %
( base_url, url_for( controller='root' ), dataset.id, type ) )
display_url = quote_plus( "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" %
( base_url, url_for( controller='root' ), dataset.id, type ) )
link = '%s?redirect_url=%s&display_url=%s' % ( internal_url, redirect_url, display_url )
return link
@@ -723,7 +725,7 @@ class Gff( Tabular, _RemoteCallMixin ):
def display_peek( self, dataset ):
"""Returns formated html of peek"""
return Tabular.make_html_table( self, dataset, column_names=self.column_names )
return self.make_html_table( dataset, column_names=self.column_names )
def get_estimated_display_viewport( self, dataset ):
"""
@@ -808,7 +810,7 @@ class Gff( Tabular, _RemoteCallMixin ):
if seqid is not None:
for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('ucsc', dataset.dbkey ):
if site_name in app.datatypes_registry.get_display_sites('ucsc'):
redirect_url = urllib.quote_plus(
redirect_url = quote_plus(
"%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" %
( site_url, dataset.dbkey, seqid, start, stop ) )
link = self._get_remote_call_url( redirect_url, site_name, dataset, type, app, base_url )
@@ -823,7 +825,7 @@ class Gff( Tabular, _RemoteCallMixin ):
if site_name in app.datatypes_registry.get_display_sites('gbrowse'):
if seqid.startswith( 'chr' ) and len( seqid ) > 3:
seqid = seqid[3:]
redirect_url = urllib.quote_plus( "%s/?q=%s:%s..%s&eurl=%%s" % ( site_url, seqid, start, stop ) )
redirect_url = quote_plus( "%s/?q=%s:%s..%s&eurl=%%s" % ( site_url, seqid, start, stop ) )
link = self._get_remote_call_url( redirect_url, site_name, dataset, type, app, base_url )
ret_val.append( ( site_name, link ) )
return ret_val
@@ -1170,7 +1172,7 @@ class Wiggle( Tabular, _RemoteCallMixin ):
if site_name in app.datatypes_registry.get_display_sites('gbrowse'):
if chrom.startswith( 'chr' ) and len( chrom ) > 3:
chrom = chrom[3:]
redirect_url = urllib.quote_plus( "%s/?q=%s:%s..%s&eurl=%%s" % ( site_url, chrom, start, stop ) )
redirect_url = quote_plus( "%s/?q=%s:%s..%s&eurl=%%s" % ( site_url, chrom, start, stop ) )
link = self._get_remote_call_url( redirect_url, site_name, dataset, type, app, base_url )
ret_val.append( ( site_name, link ) )
return ret_val
@@ -1181,14 +1183,14 @@ class Wiggle( Tabular, _RemoteCallMixin ):
if chrom is not None:
for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('ucsc', dataset.dbkey ):
if site_name in app.datatypes_registry.get_display_sites('ucsc'):
redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % ( site_url, dataset.dbkey, chrom, start, stop ) )
redirect_url = quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % ( site_url, dataset.dbkey, chrom, start, stop ) )
link = self._get_remote_call_url( redirect_url, site_name, dataset, type, app, base_url )
ret_val.append( ( site_name, link ) )
return ret_val
def display_peek( self, dataset ):
"""Returns formated html of peek"""
return Tabular.make_html_table( self, dataset, skipchars=['track', '#'] )
return self.make_html_table( dataset, skipchars=['track', '#'] )
def set_meta( self, dataset, overwrite=True, **kwd ):
max_data_lines = None
@@ -1266,7 +1268,7 @@ class Wiggle( Tabular, _RemoteCallMixin ):
x = numpy.arange( t_start, t_end ) * resolution
y = data[ t_start : t_end ]
return zip(x.tolist(), y.tolist())
return list(zip(x.tolist(), y.tolist()))
def get_track_resolution( self, dataset, start, end):
range = end - start
@@ -1305,7 +1307,7 @@ class CustomTrack ( Tabular ):
def display_peek( self, dataset ):
"""Returns formated html of peek"""
return Tabular.make_html_table( self, dataset, skipchars=['track', '#'] )
return self.make_html_table( dataset, skipchars=['track', '#'] )
def get_estimated_display_viewport( self, dataset, chrom_col=None, start_col=None, end_col=None ):
"""Return a chrom, start, stop tuple for viewing a file."""
@@ -1372,8 +1374,8 @@ class CustomTrack ( Tabular ):
for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('ucsc', dataset.dbkey):
if site_name in app.datatypes_registry.get_display_sites('ucsc'):
internal_url = "%s" % url_for( controller='dataset', dataset_id=dataset.id, action='display_at', filename='ucsc_' + site_name )
display_url = urllib.quote_plus( "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" % (base_url, url_for( controller='root' ), dataset.id, type) )
redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % (site_url, dataset.dbkey, chrom, start, stop ) )
display_url = quote_plus( "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" % (base_url, url_for( controller='root' ), dataset.id, type) )
redirect_url = quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % (site_url, dataset.dbkey, chrom, start, stop ) )
link = '%s?redirect_url=%s&display_url=%s' % ( internal_url, redirect_url, display_url )
ret_val.append( (site_name, link) )
return ret_val
lib/galaxy/datatypes/proteomics.py
+4 -4
View File
@@ -61,12 +61,12 @@ class PepXmlReport(Tabular):
file_ext = "pepxml.tsv"
def __init__(self, **kwd):
Tabular.__init__(self, **kwd)
super(PepXmlReport, self).__init__(**kwd)
self.column_names = ['Protein', 'Peptide', 'Assumed Charge', 'Neutral Pep Mass (calculated)', 'Neutral Mass', 'Retention Time', 'Start Scan', 'End Scan', 'Search Engine', 'PeptideProphet Probability', 'Interprophet Probabaility']
def display_peek(self, dataset):
"""Returns formated html of peek"""
return Tabular.make_html_table(self, dataset, column_names=self.column_names)
return self.make_html_table(dataset, column_names=self.column_names)
class ProtXmlReport(Tabular):
@@ -76,7 +76,7 @@ class ProtXmlReport(Tabular):
comment_lines = 1
def __init__(self, **kwd):
Tabular.__init__(self, **kwd)
super(ProtXmlReport, self).__init__(**kwd)
self.column_names = [
"Entry Number", "Group Probability",
"Protein", "Protein Link", "Protein Probability",
@@ -91,7 +91,7 @@ class ProtXmlReport(Tabular):
def display_peek(self, dataset):
"""Returns formated html of peek"""
return Tabular.make_html_table(self, dataset, column_names=self.column_names)
return self.make_html_table(dataset, column_names=self.column_names)
class ProteomicsXml(GenericXml):
lib/galaxy/datatypes/tabular.py
+4 -4
View File
@@ -408,7 +408,7 @@ class Taxonomy( Tabular ):
def display_peek( self, dataset ):
"""Returns formated html of peek"""
return super(Taxonomy, self).make_html_table( dataset, column_names=self.column_names )
return self.make_html_table( dataset, column_names=self.column_names )
@dataproviders.decorators.has_dataproviders
@@ -428,7 +428,7 @@ class Sam( Tabular ):
def display_peek( self, dataset ):
"""Returns formated html of peek"""
return super( Sam, self ).make_html_table( dataset, column_names=self.column_names )
return self.make_html_table( dataset, column_names=self.column_names )
def sniff( self, filename ):
"""
@@ -614,7 +614,7 @@ class Pileup( Tabular ):
def display_peek( self, dataset ):
"""Returns formated html of peek"""
return super( Pileup, self ).make_html_table( dataset, column_parameter_alias={'chromCol': 'Chrom', 'startCol': 'Start', 'baseCol': 'Base'} )
return self.make_html_table( dataset, column_parameter_alias={'chromCol': 'Chrom', 'startCol': 'Start', 'baseCol': 'Base'} )
def repair_methods( self, dataset ):
"""Return options for removing errors along with a description"""
@@ -691,7 +691,7 @@ class Vcf( Tabular ):
def display_peek( self, dataset ):
"""Returns formated html of peek"""
return super( Vcf, self ).make_html_table( dataset, column_names=self.column_names )
return self.make_html_table( dataset, column_names=self.column_names )
def set_meta( self, dataset, **kwd ):
super( Vcf, self ).set_meta( dataset, **kwd )