opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-24 16:30:27 +08:00
Code Issues Packages Projects Releases Wiki Activity

Merge pull request #446 from jgoecks/trackster-close-files

Browse Source 
Trackster fixes: (a) close data provider files after reading from the…
This commit is contained in:
carlfeberhard
2015-07-13 11:36:02 -04:00
parent 2bf2844b21 75ab206ca5
commit 4792825924
5 changed files with 79 additions and 68 deletions
Download Patch File Download Diff File Expand all files Collapse all files
client/galaxy/scripts/viz/trackster/tracks.js
+4 -5
View File
@@ -2209,15 +2209,14 @@ extend(Track.prototype, Drawable.prototype, {
title: "Tool parameter space visualization",
css_class: "arrow-split",
on_click_fn: function(track) {
var template =
'<strong>Tool</strong>: <%= track.tool.get("name") %><br/>' +
'<strong>Dataset</strong>: <%= track.config.get_value("name") %><br/>' +
var html =
'<strong>Tool</strong>:' + track.tool.get("name") + '<br/>' +
'<strong>Dataset</strong>:' + track.config.get_value("name") + '<br/>' +
'<strong>Region(s)</strong>: <select name="regions">' +
'<option value="cur">current viewing area</option>' +
'<option value="bookmarks">bookmarks</option>' +
'<option value="both">current viewing area and bookmarks</option>' +
'</select>',
html = _.template(template, { track: track });
'</select>';
var cancel_fn = function() { Galaxy.modal.hide(); $(window).unbind("keypress.check_enter_esc"); },
ok_fn = function() {
var regions_to_use = $('select[name="regions"] option:selected').val(),
lib/galaxy/visualization/data_providers/genome.py
+71 -58
View File
@@ -143,11 +143,6 @@ class GenomeDataProvider( BaseDataProvider ):
dependencies=dependencies,
error_max_vals=error_max_vals )
# File/pointer where data is obtained from. It is useful to set this for repeated
# queries, such as is necessary for genome-wide data.
# TODO: add functions to (a) create data_file and (b) clean up data_file.
self.data_file = None
def write_data_to_file( self, regions, filename ):
"""
Write data in region defined by chrom, start, and end to a file.
@@ -167,7 +162,13 @@ class GenomeDataProvider( BaseDataProvider ):
"""
raise Exception( "Unimplemented Function" )
def get_iterator( self, chrom, start, end, **kwargs ):
def open_data_file( self ):
"""
Open data file for reading data.
"""
raise Exception( "Unimplemented Function" )
def get_iterator( self, data_file, chrom, start, end, **kwargs ):
"""
Returns an iterator that provides data in the region chrom:start-end
"""
@@ -189,8 +190,19 @@ class GenomeDataProvider( BaseDataProvider ):
dataset_type, data
"""
start, end = int( low ), int( high )
iterator = self.get_iterator( chrom, start, end, **kwargs )
return self.process_data( iterator, start_val, max_vals, start=start, end=end, **kwargs )
data_file = self.open_data_file()
iterator = self.get_iterator( data_file, chrom, start, end, **kwargs )
data = self.process_data( iterator, start_val, max_vals, start=start, end=end, **kwargs )
try:
data_file.close()
except AttributeError:
# FIXME: some data providers do not have a close function implemented.
# Providers without a close function include:
# pysam Tabixfile
# bx IntervalIndex
pass
return data
def get_genome_data( self, chroms_info, **kwargs ):
"""
@@ -335,40 +347,40 @@ class TabixDataProvider( FilterableMixin, GenomeDataProvider ):
col_name_data_attr_mapping = { 4 : { 'index': 4 , 'name' : 'Score' } }
def get_iterator( self, chrom, start, end, **kwargs ):
def open_data_file( self ):
return ctabix.Tabixfile(self.dependencies['bgzip'].file_name,
index_filename=self.converted_dataset.file_name)
def get_iterator( self, data_file, chrom, start, end, **kwargs ):
start, end = int(start), int(end)
if end >= (2 << 29):
end = (2 << 29 - 1) # Tabix-enforced maximum
bgzip_fname = self.dependencies['bgzip'].file_name
if not self.data_file:
self.data_file = ctabix.Tabixfile(bgzip_fname, index_filename=self.converted_dataset.file_name)
# Get iterator using either naming scheme.
iterator = iter( [] )
if chrom in self.data_file.contigs:
iterator = self.data_file.fetch(reference=chrom, start=start, end=end)
if chrom in data_file.contigs:
iterator = data_file.fetch(reference=chrom, start=start, end=end)
else:
# Try alternative naming scheme.
chrom = _convert_between_ucsc_and_ensemble_naming( chrom )
if chrom in self.data_file.contigs:
iterator = self.data_file.fetch(reference=chrom, start=start, end=end)
if chrom in data_file.contigs:
iterator = data_file.fetch(reference=chrom, start=start, end=end)
return iterator
def write_data_to_file( self, regions, filename ):
out = open( filename, "w" )
data_file = self.open_data_file()
for region in regions:
# Write data in region.
chrom = region.chrom
start = region.start
end = region.end
iterator = self.get_iterator( chrom, start, end )
iterator = self.get_iterator( data_file, region.chrom, region.start, region.end )
for line in iterator:
out.write( "%s\n" % line )
# TODO: once Pysam is updated and Tabixfile has a close() method,
# data_file.close()
out.close()
#
@@ -385,7 +397,7 @@ class IntervalDataProvider( GenomeDataProvider ):
Payload format: [ uid (offset), start, end, name, strand, thick_start, thick_end, blocks ]
"""
def get_iterator( self, chrom, start, end, **kwargs ):
def get_iterator( self, data_file, chrom, start, end, **kwargs ):
raise Exception( "Unimplemented Function" )
def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ):
@@ -470,7 +482,7 @@ class BedDataProvider( GenomeDataProvider ):
dataset_type = 'interval_index'
def get_iterator( self, chrom, start, end, **kwargs ):
def get_iterator( self, data_file, chrom, start, end, **kwargs ):
raise Exception( "Unimplemented Method" )
def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ):
@@ -545,9 +557,11 @@ class BedDataProvider( GenomeDataProvider ):
chrom = region.chrom
start = region.start
end = region.end
iterator = self.get_iterator( chrom, start, end )
data_file = self.open_data_file()
iterator = self.get_iterator( data_file, chrom, start, end )
for line in iterator:
out.write( "%s\n" % line )
data_file.close()
out.close()
@@ -567,14 +581,14 @@ class RawBedDataProvider( BedDataProvider ):
for large datasets.
"""
def get_iterator( self, source, chrom=None, start=None, end=None, **kwargs ):
def get_iterator( self, data_file, chrom=None, start=None, end=None, **kwargs ):
# Read first line in order to match chrom naming format.
line = source.readline()
line = data_file.readline()
dataset_chrom = line.split()[0]
if not _chrom_naming_matches( chrom, dataset_chrom ):
chrom = _convert_between_ucsc_and_ensemble_naming( chrom )
# Undo read.
source.seek( 0 )
data_file.seek( 0 )
def line_filter_iter():
for line in open( self.original_dataset.file_name ):
@@ -741,13 +755,11 @@ class VcfDataProvider( GenomeDataProvider ):
def write_data_to_file( self, regions, filename ):
out = open( filename, "w" )
data_file = self.open_data_file()
for region in regions:
# Write data in region.
chrom = region.chrom
start = region.start
end = region.end
iterator = self.get_iterator( chrom, start, end )
iterator = self.get_iterator( data_file, region.chrom, region.start, region.end )
for line in iterator:
out.write( "%s\n" % line )
out.close()
@@ -769,12 +781,13 @@ class RawVcfDataProvider( VcfDataProvider ):
for large datasets.
"""
def get_iterator( self, chrom, start, end, **kwargs ):
source = open( self.original_dataset.file_name )
def open_data_file( self ):
return open( self.original_dataset.file_name )
def get_iterator( self, data_file, chrom, start, end, **kwargs ):
# Skip comments.
line = None
for line in source:
for line in data_file:
if not line.startswith("#"):
break
@@ -796,13 +809,13 @@ class RawVcfDataProvider( VcfDataProvider ):
return variant_chrom == chrom and variant_start >= start and variant_start <= end
def line_filter_iter():
""" Yields lines in source that are in region chrom:start-end """
""" Yields lines in data that are in region chrom:start-end """
# Yield data line read above.
if line_in_region( line, chrom, start, end ):
yield line
# Search for and yield other data lines.
for data_line in source:
for data_line in data_file:
if line_in_region( data_line, chrom, start, end ):
yield data_line
@@ -866,23 +879,24 @@ class BamDataProvider( GenomeDataProvider, FilterableMixin ):
new_bamfile.close()
bamfile.close()
def get_iterator( self, chrom, start, end, **kwargs ):
def open_data_file( self ):
# Attempt to open the BAM file with index
return csamtools.Samfile( filename=self.original_dataset.file_name, mode='rb',
index_filename=self.converted_dataset.file_name )
def get_iterator( self, data_file, chrom, start, end, **kwargs ):
"""
Returns an iterator that provides data in the region chrom:start-end
"""
start, end = int( start ), int( end )
orig_data_filename = self.original_dataset.file_name
index_filename = self.converted_dataset.file_name
# Attempt to open the BAM file with index
bamfile = csamtools.Samfile( filename=orig_data_filename, mode='rb', index_filename=index_filename )
# Fetch and return data.
try:
data = bamfile.fetch( start=start, end=end, reference=chrom )
data = data_file.fetch( start=start, end=end, reference=chrom )
except ValueError:
# Try alternative chrom naming.
chrom = _convert_between_ucsc_and_ensemble_naming( chrom )
try:
data = bamfile.fetch( start=start, end=end, reference=chrom )
data = data_file.fetch( start=start, end=end, reference=chrom )
except ValueError:
return None
return data
@@ -1299,19 +1313,18 @@ class IntervalIndexDataProvider( FilterableMixin, GenomeDataProvider ):
source.close()
out.close()
def get_iterator( self, chrom, start, end, **kwargs ):
"""
Returns an array with values: (a) source file and (b) an iterator that
provides data in the region chrom:start-end
"""
start, end = int(start), int(end)
index = Indexes( self.converted_dataset.file_name )
def open_data_file( self ):
return Indexes( self.converted_dataset.file_name )
if chrom not in index.indexes:
def get_iterator( self, data_file, chrom, start, end, **kwargs ):
"""
Returns an iterator for data in data_file in chrom:start-end
"""
if chrom not in data_file.indexes:
# Try alternative naming.
chrom = _convert_between_ucsc_and_ensemble_naming( chrom )
return index.find(chrom, start, end)
return data_file.find(chrom, start, end)
def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ):
results = []
@@ -1358,7 +1371,7 @@ class RawGFFDataProvider( GenomeDataProvider ):
dataset_type = 'interval_index'
def get_iterator( self, chrom, start, end, **kwargs ):
def get_iterator( self, data_file, chrom, start, end, **kwargs ):
"""
Returns an iterator that provides data in the region chrom:start-end as well as
a file offset.
@@ -1467,7 +1480,7 @@ class ENCODEPeakDataProvider( GenomeDataProvider ):
Payload format: [ uid (offset), start, end, name, strand, thick_start, thick_end, blocks ]
"""
def get_iterator( self, chrom, start, end, **kwargs ):
def get_iterator( self, data_file, chrom, start, end, **kwargs ):
raise "Unimplemented Method"
def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ):
@@ -1615,7 +1628,7 @@ class ChromatinInteractionsDataProvider( GenomeDataProvider ):
class ChromatinInteractionsTabixDataProvider( TabixDataProvider, ChromatinInteractionsDataProvider ):
def get_iterator( self, chrom, start=0, end=sys.maxint, interchromosomal=False, **kwargs ):
def get_iterator( self, data_file, chrom, start=0, end=sys.maxint, interchromosomal=False, **kwargs ):
"""
"""
# Modify start as needed to get earlier interactions with start region.
@@ -1636,7 +1649,7 @@ class ChromatinInteractionsTabixDataProvider( TabixDataProvider, ChromatinIntera
# Check for interchromosal interactions.
if interchromosomal and c != chrom:
yield line
return filter( TabixDataProvider.get_iterator( self, chrom, filter_start, end ) )
return filter( TabixDataProvider.get_iterator( self, data_file, chrom, filter_start, end ) )
#
# -- Helper methods. --
lib/galaxy/webapps/galaxy/api/tools.py
+1 -1
View File
@@ -387,7 +387,7 @@ class ToolsController( BaseAPIController, UsesVisualizationMixin ):
# job's previous parameters and incoming parameters. Incoming parameters
# have priority.
#
original_job = self.hda_manager.creating_job( trans, original_dataset )
original_job = self.hda_manager.creating_job( original_dataset )
tool = trans.app.toolbox.get_tool( original_job.tool_id )
if not tool or not tool.allow_user_access( trans.user ):
return trans.app.model.Dataset.conversion_messages.NO_TOOL
static/maps/viz/trackster/tracks.js.map
+1 -1
View File
File diff suppressed because one or more lines are too long
static/scripts/viz/trackster/tracks.js
+2 -3
View File
File diff suppressed because one or more lines are too long