diff --git a/datatypes_conf.xml.sample b/datatypes_conf.xml.sample
index 645cb00c2ee..13543cab296 100644
--- a/datatypes_conf.xml.sample
+++ b/datatypes_conf.xml.sample
@@ -8,6 +8,9 @@
+
+
+
@@ -31,7 +34,7 @@
-
+
diff --git a/lib/galaxy/datatypes/data.py b/lib/galaxy/datatypes/data.py
index 9934eb40df3..ef407cfca13 100644
--- a/lib/galaxy/datatypes/data.py
+++ b/lib/galaxy/datatypes/data.py
@@ -40,7 +40,7 @@ class Data( object ):
__metaclass__ = DataMeta
"""Add metadata elements"""
- MetadataElement( name="dbkey", desc="Database/Build", default="?", param=metadata.SelectParameter, multiple=False, values=util.dbnames, no_value="?" )
+ MetadataElement( name="dbkey", desc="Database/Build", default="?", param=metadata.DBKeyParameter, multiple=False, no_value="?" )
"""Stores the set of display applications, and viewing methods, supported by this datatype """
supported_display_apps = {}
@@ -242,7 +242,7 @@ class Data( object ):
def after_edit( self, dataset ):
"""This function is called on the dataset after metadata is edited."""
dataset.clear_associated_files( metadata_safe = True )
-
+
@property
def has_resolution(self):
return False
diff --git a/lib/galaxy/datatypes/indexers/coverage.py b/lib/galaxy/datatypes/indexers/coverage.py
index 1cb94955b0a..2bfec91c25f 100644
--- a/lib/galaxy/datatypes/indexers/coverage.py
+++ b/lib/galaxy/datatypes/indexers/coverage.py
@@ -37,7 +37,7 @@ def write_chrom(max, out_base, instream):
os.rename( fname+".npy", fname )
# Write average
- for window in 10, 100, 1000, 10000:
+ for window in 10, 100, 1000, 10000, 100000:
input = scores.copy()
size = len( input )
input.resize( ( ( size / window ), window ) )
diff --git a/lib/galaxy/datatypes/indexers/interval.awk b/lib/galaxy/datatypes/indexers/interval.awk
new file mode 100644
index 00000000000..fa84d6a0593
--- /dev/null
+++ b/lib/galaxy/datatypes/indexers/interval.awk
@@ -0,0 +1,43 @@
+BEGIN {
+ # from galaxy.utils
+ mapped_chars[">"] = "__gt__"
+ mapped_chars["<"] = "__lt__"
+ mapped_chars["'"] = "__sq__"
+ mapped_chars["\""] = "__dq__"
+ mapped_chars["\\["] = "__ob__"
+ mapped_chars["\\]"] = "__cb__"
+ mapped_chars["\\{"] = "__oc__"
+ mapped_chars["\\}"] = "__cc__"
+ mapped_chars["@"] = "__at__"
+ # additional, not in galaxy.utils
+ mapped_chars["/"] = "__fs__"
+ mapped_chars["^manifest\.tab$"] = "__manifest.tab__"
+}
+function escape_filename( name )
+{
+ for( char in mapped_chars ) {
+ gsub( char, mapped_chars[char], name )
+ }
+ return name
+}
+!_[$chrom]++ {
+ # close files only when we switch to a new one.
+ fn && close(fn)
+ fn = storepath "/" escape_filename($1) }
+{
+ print $0 >> fn;
+ # the || part is needed to catch 0 length chromosomes, which
+ # should never happen but...
+ if ($end > chroms[$chrom] || !chroms[$chrom])
+ chroms[$chrom] = $end }
+END {
+ fn = storepath "/manifest.tab"
+ for( x in chroms ) {
+ # add line to manifest
+ print x "\t" chroms[x] >> fn
+ chromfile = storepath "/" escape_filename(x)
+ # sort in-place
+ system( "sort -f -n -k " chrom " -k " start " -k " end " -o " chromfile " " chromfile )
+ close(chromfile)
+ }
+}
\ No newline at end of file
diff --git a/lib/galaxy/datatypes/indexers/interval.py b/lib/galaxy/datatypes/indexers/interval.py
index ca044c931a1..43693cfe567 100644
--- a/lib/galaxy/datatypes/indexers/interval.py
+++ b/lib/galaxy/datatypes/indexers/interval.py
@@ -29,13 +29,11 @@ def divide( intervals, out_path ):
manifest[chrom] = max(manifest.get(chrom,0),line.end)
if not lastchrom == chrom:
if current_file:
- current_file.flush()
current_file.close()
current_file = open( os.path.join( out_path, "%s" % chrom), "a" )
print >> current_file, "\t".join(line)
lastchrom = chrom
if current_file:
- current_file.flush()
current_file.close()
return manifest
diff --git a/lib/galaxy/datatypes/indexers/interval_awk.xml b/lib/galaxy/datatypes/indexers/interval_awk.xml
new file mode 100644
index 00000000000..965a9434b0f
--- /dev/null
+++ b/lib/galaxy/datatypes/indexers/interval_awk.xml
@@ -0,0 +1,16 @@
+
+
+ interval.awk
+ chrom=${input_dataset.metadata.chromCol} start=${input_dataset.metadata.startCol}
+ end=${input_dataset.metadata.endCol} strand=${input_dataset.metadata.strandCol}
+ storepath=${store_path}
+ $input_dataset 2>&1
+
+
+
+
+
+
+
+
+
diff --git a/lib/galaxy/datatypes/indexers/wiggle.py b/lib/galaxy/datatypes/indexers/wiggle.py
index ec4dd15c816..5ba1380aaa1 100644
--- a/lib/galaxy/datatypes/indexers/wiggle.py
+++ b/lib/galaxy/datatypes/indexers/wiggle.py
@@ -18,6 +18,8 @@ pkg_resources.require("numpy>=1.2.1")
from numpy import *
import tempfile
import os
+from galaxy.tracks.store import sanitize_name
+
def write_chrom(max, out_base, instream):
@@ -35,7 +37,7 @@ def write_chrom(max, out_base, instream):
os.rename( fname+".npy", fname )
# Write average
- for window in 10, 100, 1000, 10000:
+ for window in 10, 100, 1000, 10000, 100000:
input = scores.copy()
size = len( input )
input.resize( ( ( size / window ), window ) )
@@ -60,7 +62,7 @@ def main():
LEN[chrom] = max2( LEN.get(chrom,0), pos+1 )
for chrom, stream in chroms.items():
stream.seek(0)
- prefix = os.path.join(sys.argv[2], chrom)
+ prefix = os.path.join(sys.argv[2], sanitize_name(chrom))
write_chrom( LEN[chrom], prefix, stream )
manifest_file = open( os.path.join( sys.argv[2], "manifest.tab" ),"w" )
diff --git a/lib/galaxy/datatypes/interval.py b/lib/galaxy/datatypes/interval.py
index f6b18414a25..be0c07ed258 100644
--- a/lib/galaxy/datatypes/interval.py
+++ b/lib/galaxy/datatypes/interval.py
@@ -792,7 +792,7 @@ class Wiggle( Tabular ):
# Determine appropriate resolution to plot ~1000 points
resolution = ( 10 ** math.ceil( math.log10( range / 1000 ) ) )
# Restrict to valid range
- resolution = min( resolution, 10000 )
+ resolution = min( resolution, 100000 )
resolution = max( resolution, 1 )
# Memory map the array (don't load all the data)
data = numpy.load( data )
@@ -809,7 +809,7 @@ class Wiggle( Tabular ):
# Determine appropriate resolution to plot ~1000 points
resolution = math.ceil( 10 ** math.ceil( math.log10( range / 1000 ) ) )
# Restrict to valid range
- resolution = min( resolution, 10000 )
+ resolution = min( resolution, 100000 )
resolution = max( resolution, 1 )
return resolution
diff --git a/lib/galaxy/datatypes/metadata.py b/lib/galaxy/datatypes/metadata.py
index 233f59a9a38..07e2c7ad93d 100644
--- a/lib/galaxy/datatypes/metadata.py
+++ b/lib/galaxy/datatypes/metadata.py
@@ -289,7 +289,22 @@ class SelectParameter( MetadataParameter ):
if value is None: return []
if not isinstance( value, list ): return [value]
return value
-
+
+
+class DBKeyParameter( SelectParameter ):
+ def get_html_field( self, value=None, context={}, other_values={}, values=None, **kwd):
+ try:
+ values = kwd['trans'].db_builds
+ except AttributeError: pass
+ return super(DBKeyParameter, self).get_html_field( value, context, other_values, values, **kwd)
+
+ def get_html( self, value=None, context={}, other_values={}, values=None, **kwd):
+ try:
+ values = kwd['trans'].db_builds
+ except AttributeError: pass
+ return super(DBKeyParameter, self).get_html( value, context, other_values, values, **kwd)
+
+
class RangeParameter( SelectParameter ):
def __init__( self, spec ):
SelectParameter.__init__( self, spec )
diff --git a/lib/galaxy/datatypes/registry.py b/lib/galaxy/datatypes/registry.py
index 77c74d52832..1cf0adc0871 100644
--- a/lib/galaxy/datatypes/registry.py
+++ b/lib/galaxy/datatypes/registry.py
@@ -3,7 +3,7 @@ Provides mapping between extensions and datatypes, mime-types, etc.
"""
import os
import logging
-import data, tabular, interval, images, sequence, qualityscore, genetics, xml, coverage, tracks
+import data, tabular, interval, images, sequence, qualityscore, genetics, xml, coverage, tracks, chrominfo
import galaxy.util
from galaxy.util.odict import odict
diff --git a/lib/galaxy/tools/actions/__init__.py b/lib/galaxy/tools/actions/__init__.py
index 6b8e42bd24b..4d62e1f4bc8 100644
--- a/lib/galaxy/tools/actions/__init__.py
+++ b/lib/galaxy/tools/actions/__init__.py
@@ -107,6 +107,7 @@ class DefaultToolAction( object ):
out_data = {}
# Collect any input datasets from the incoming parameters
inp_data = self.collect_input_datasets( tool, incoming, trans )
+
# Deal with input dataset names, 'dbkey' and types
input_names = []
input_ext = 'data'
@@ -119,6 +120,16 @@ class DefaultToolAction( object ):
data = NoneDataset( datatypes_registry = trans.app.datatypes_registry )
if data.dbkey not in [None, '?']:
input_dbkey = data.dbkey
+
+ # Collect chromInfo dataset and add as parameters to incoming
+ db_datasets = {}
+ db_dataset = trans.db_dataset_for( input_dbkey )
+ if db_dataset:
+ db_datasets[ "chromInfo" ] = db_dataset
+ incoming[ "chromInfo" ] = db_dataset.file_name
+ else:
+ incoming[ "chromInfo" ] = os.path.join( trans.app.config.tool_data_path, 'shared','ucsc','chrom', "%s.len" % input_dbkey )
+ inp_data.update( db_datasets )
# Determine output dataset permission/roles list
existing_datasets = [ inp for inp in inp_data.values() if inp ]
diff --git a/lib/galaxy/tools/actions/upload.py b/lib/galaxy/tools/actions/upload.py
index d286b815dae..82a51b7e071 100644
--- a/lib/galaxy/tools/actions/upload.py
+++ b/lib/galaxy/tools/actions/upload.py
@@ -21,7 +21,7 @@ class UploadToolAction( object ):
def execute( self, tool, trans, incoming={}, set_output_hid = True ):
data_file = incoming['file_data']
file_type = incoming['file_type']
- dbkey = incoming['dbkey']
+ dbkey = incoming['other_dbkey'] or incoming['dbkey']
url_paste = incoming['url_paste']
is_multi_byte = False
space_to_tab = False
diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index 14f33f51026..cf00b587e59 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -657,7 +657,7 @@ class GenomeBuildParameter( SelectToolParameter ):
>>> # Create a mock transcation with 'hg17' as the current build
>>> from galaxy.util.bunch import Bunch
- >>> trans = Bunch( history=Bunch( genome_build='hg17' ) )
+ >>> trans = Bunch( history=Bunch( genome_build='hg17' ), db_builds=util.dbnames )
>>> p = GenomeBuildParameter( None, XML(
... '''
@@ -692,10 +692,10 @@ class GenomeBuildParameter( SelectToolParameter ):
"""
def get_options( self, trans, other_values ):
last_used_build = trans.history.genome_build
- for dbkey, build_name in util.dbnames:
+ for dbkey, build_name in trans.db_builds:
yield build_name, dbkey, ( dbkey == last_used_build )
def get_legal_values( self, trans, other_values ):
- return set( dbkey for dbkey, _ in util.dbnames )
+ return set( dbkey for dbkey, _ in trans.db_builds )
class ColumnListParameter( SelectToolParameter ):
"""
diff --git a/lib/galaxy/tracks/store.py b/lib/galaxy/tracks/store.py
index 3009bd1c60f..07523a7ed56 100644
--- a/lib/galaxy/tracks/store.py
+++ b/lib/galaxy/tracks/store.py
@@ -1,5 +1,17 @@
import os
+import re
from string import Template
+from galaxy.util import sanitize_text
+
+# extra mappings/escape to keep users from traversing around the
+# filesystem and wreaking havoc
+extra_mappings = { r"/": "__fs__", r"^manifest.tab$": "__manifest.tab__" }
+
+def sanitize_name( name ):
+ name = sanitize_text( name )
+ for key, value in extra_mappings.items():
+ name = re.sub( key, value, name )
+ return name
class TemplateSubber( object ):
def __init__(self, obj):
@@ -56,7 +68,7 @@ class TrackStore( object ):
fd.close()
def _get_object_path( self, chrom, resolution ):
- object_name = chrom
+ object_name = sanitize_name(chrom)
if resolution: object_name += "_%d" % resolution
return os.path.join( self.path, object_name )
diff --git a/lib/galaxy/web/controllers/root.py b/lib/galaxy/web/controllers/root.py
index 823bc29d6f0..972a50c6eb7 100644
--- a/lib/galaxy/web/controllers/root.py
+++ b/lib/galaxy/web/controllers/root.py
@@ -234,11 +234,15 @@ class RootController( BaseController ):
if spec.get("readonly"):
continue
optional = params.get("is_"+name, None)
+ other = params.get("or_"+name, None)
if optional and optional == 'true':
# optional element... == 'true' actually means it is NOT checked (and therefore omitted)
setattr(data.metadata, name, None)
else:
- setattr( data.metadata, name, spec.unwrap( params.get (name, None) ) )
+ if other:
+ setattr( data.metadata, name, other )
+ else:
+ setattr( data.metadata, name, spec.unwrap( params.get (name, None) ) )
data.datatype.after_edit( data )
trans.app.model.flush()
diff --git a/lib/galaxy/web/controllers/tracks.py b/lib/galaxy/web/controllers/tracks.py
index 479568055ce..0e840667a54 100644
--- a/lib/galaxy/web/controllers/tracks.py
+++ b/lib/galaxy/web/controllers/tracks.py
@@ -1,13 +1,11 @@
-from mako import exceptions
-from mako.template import Template
-from mako.lookup import TemplateLookup
+import math
+
+import mimeparse
+from galaxy.tracks import messages
+from galaxy.util.json import to_json_string
from galaxy.web.base.controller import *
from galaxy.web.framework import simplejson
-from galaxy import web
-from galaxy.tracks import messages
-import mimeparse
-from galaxy.util.json import to_json_string
-import math
+
class MultiResponse(object):
"""
@@ -82,18 +80,19 @@ class WebRoot( BaseController ):
def build( self, trans, **kwargs ):
trans.session["track_sets"] = list(kwargs.keys())
trans.session.save()
- waiting = False
- for id, value in kwargs.items():
- status = self.data_handler( trans, id )
- if status == messages.PENDING:
- waiting = True
- if not waiting:
- return trans.response.send_redirect( web.url_for( controller='tracks', action='chroms', dbkey=trans.session["track_dbkey"]) )
- return trans.fill_template( 'tracks/build.mako' )
+ #waiting = False
+ #for id, value in kwargs.items():
+ # status = self.data_handler( trans, id )
+ # if status == messages.PENDING:
+ # waiting = True
+ #if not waiting:
+ return trans.response.send_redirect( web.url_for( controller='tracks/', action='index', chrom="" ) )
+ #return trans.fill_template( 'tracks/build.mako' )
@web.expose
def index(self, trans, **kwargs):
tracks = []
+ dbkey = ""
for track in trans.session["track_sets"]:
dataset = trans.app.model.HistoryDatasetAssociation.get( track )
tracks.append({
@@ -101,17 +100,23 @@ class WebRoot( BaseController ):
"name": dataset.name,
"id": dataset.id
})
+ dbkey = dataset.dbkey
chrom = kwargs.get("chrom","")
LEN = self.chroms_handler(trans, trans.session["track_dbkey"]).get(chrom,0)
return trans.fill_template( 'tracks/index.mako',
- tracks=tracks, chrom=chrom,
+ tracks=tracks, chrom=chrom, dbkey=dbkey,
LEN=LEN )
def chroms_handler(self, trans, dbkey ):
- db_manifest = os.path.join( trans.app.config.tool_data_path, 'shared','ucsc','chrom', "%s.len" % dbkey )
+ db_manifest = trans.db_dataset_for( dbkey )
+ if not db_manifest:
+ db_manifest = os.path.join( trans.app.config.tool_data_path, 'shared','ucsc','chrom', "%s.len" % dbkey )
+ else:
+ db_manifest = db_manifest.file_name
manifest = {}
if os.path.exists( db_manifest ):
for line in open( db_manifest ):
+ if line.startswith("#"): continue
line = line.rstrip("\r\n")
fields = line.split("\t")
manifest[fields[0]] = int(fields[1])
diff --git a/lib/galaxy/web/framework/__init__.py b/lib/galaxy/web/framework/__init__.py
index 9d8457713e5..d99d15e1573 100644
--- a/lib/galaxy/web/framework/__init__.py
+++ b/lib/galaxy/web/framework/__init__.py
@@ -547,6 +547,31 @@ class UniverseWebTransaction( base.DefaultWebTransaction ):
template = Template( source=template_string,
searchList=[context or kwargs, dict(caller=self)] )
return str(template)
+
+ @property
+ def db_builds( self ):
+ """
+ Returns the builds defined by galaxy and the builds defined by
+ the user (chromInfo in history).
+ """
+ dbnames = list()
+ datasets = self.app.model.HistoryDatasetAssociation.filter_by(deleted=False, history_id=self.history.id, extension="len").all()
+ if len(datasets) > 0:
+ dbnames.append( (util.dbnames.default_value, '--------- User Defined Builds ----------') )
+ for dataset in datasets:
+ dbnames.append( (dataset.dbkey, dataset.name) )
+ dbnames.extend( util.dbnames )
+ return dbnames
+
+ def db_dataset_for( self, dbkey ):
+ """
+ Returns the db_file dataset associated/needed by `dataset`, or `None`.
+ """
+ datasets = self.app.model.HistoryDatasetAssociation.filter_by(deleted=False, history_id=self.history.id, extension="len").all()
+ for ds in datasets:
+ if dbkey == ds.dbkey:
+ return ds
+ return None
class FormBuilder( object ):
"""
diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index 83036c67e47..e349a19fa42 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -85,7 +85,7 @@ $.extend( TiledTrack.prototype, Track.prototype, {
var resolution = Math.pow( 10, Math.ceil( Math.log( range / DENSITY ) / Math.log( 10 ) ) );
resolution = Math.max( resolution, 1 );
- resolution = Math.min( resolution, 10000 );
+ resolution = Math.min( resolution, 100000 );
var parent_element = $("");
this.content_div.children( ":first" ).remove();
@@ -152,10 +152,20 @@ $.extend( DataCache.prototype, {
var low = position * DENSITY * resolution;
var high = ( position + 1 ) * DENSITY * resolution;
cache[resolution][position] = { state: "loading" };
- $.getJSON( "data" + this.type, { chr: this.view.chr, low: low, high: high, dataset_id: this.track.dataset_id }, function ( data ) {
- cache[resolution][position] = { state: "loaded", values: data };
- $(document).trigger( "redraw" );
- });
+ // use closure to preserve this and parameters for getJSON
+ var fetcher = function (ref) {
+ return function () {
+ $.getJSON( "data" + ref.type, { chr: ref.view.chr, low: low, high: high, dataset_id: ref.track.dataset_id }, function ( data ) {
+ if( data == "pending" ) {
+ setTimeout( fetcher, 5000 );
+ } else {
+ cache[resolution][position] = { state: "loaded", values: data };
+ }
+ $(document).trigger( "redraw" );
+ });
+ };
+ }(this);
+ fetcher();
}
return cache[resolution][position];
}
@@ -288,8 +298,11 @@ $.extend( FeatureTrack.prototype, TiledTrack.prototype, {
var chunk = this.cache.get( resolution, tile_index );
if ( chunk.state == "loading" ) {
- return null;
- }
+ parent_element.addClass("loading");
+ return null;
+ } else {
+ parent_element.removeClass("loading");
+ }
var values = chunk.values;
for ( var index in values ) {
diff --git a/static/trackster.css b/static/trackster.css
index d90ec9b0eb3..b160fea3b71 100644
--- a/static/trackster.css
+++ b/static/trackster.css
@@ -85,7 +85,10 @@ body {
}
.loading {
- background: #DDDDDD;
+ background-image: url("/static/images/loading_large_white_bg.gif");
+ background-position: center center;
+ background-repeat: no-repeat;
+ min-height: 100px;
}
.label-track .label {
diff --git a/templates/dataset/edit_attributes.mako b/templates/dataset/edit_attributes.mako
index f60f47b30de..930d201b68e 100644
--- a/templates/dataset/edit_attributes.mako
+++ b/templates/dataset/edit_attributes.mako
@@ -46,7 +46,7 @@
${spec.desc}:
- ${data.metadata.get_html_by_name( name )}
+ ${data.metadata.get_html_by_name( name, trans=trans )}
diff --git a/templates/tracks/index.mako b/templates/tracks/index.mako
index e7794140576..3df253c5d52 100644
--- a/templates/tracks/index.mako
+++ b/templates/tracks/index.mako
@@ -17,18 +17,19 @@ ${parent.stylesheets()}
${parent.late_javascripts()}
-
@@ -79,11 +114,14 @@ ${parent.late_javascripts()}
diff --git a/tools/data_source/upload.xml b/tools/data_source/upload.xml
index 4d12af2624e..a55c11fe1bb 100644
--- a/tools/data_source/upload.xml
+++ b/tools/data_source/upload.xml
@@ -21,6 +21,7 @@
+
diff --git a/tools/new_operations/complement.xml b/tools/new_operations/complement.xml
index be661ee6f4a..4b318fb9787 100644
--- a/tools/new_operations/complement.xml
+++ b/tools/new_operations/complement.xml
@@ -1,6 +1,6 @@
intervals of a query
- gops_complement.py $input1 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} -l ${GALAXY_DATA_INDEX_DIR}/shared/ucsc/chrom/${dbkey}.len $allchroms
+ gops_complement.py $input1 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} -l ${chromInfo} $allchroms
@@ -58,4 +58,4 @@ See Galaxy Interval Operation Screencasts_ (right click to open this link in ano
.. image:: ../static/operation_icons/gops_complement.gif
-
\ No newline at end of file
+