[hg] galaxy 2636: Merge
by Greg Von Kuster
details: http://www.bx.psu.edu/hg/galaxy/rev/b7a3a82b71ce
changeset: 2636:b7a3a82b71ce
user: James Taylor <james(a)jamestaylor.org>
date: Fri Aug 28 15:07:48 2009 -0400
description:
Merge
0 file(s) affected in this change:
diffs (44 lines):
diff -r 3df00582ca44 -r b7a3a82b71ce lib/galaxy/datatypes/images.py
--- a/lib/galaxy/datatypes/images.py Fri Aug 28 15:06:41 2009 -0400
+++ b/lib/galaxy/datatypes/images.py Fri Aug 28 15:07:48 2009 -0400
@@ -9,6 +9,7 @@
from galaxy.datatypes.sniff import *
from urllib import urlencode, quote_plus
import zipfile
+import os, subprocess, tempfile
log = logging.getLogger(__name__)
@@ -240,6 +241,26 @@
"""Class describing a BAM binary file"""
file_ext = "bam"
MetadataElement( name="bam_index", desc="BAM Index File", param=metadata.FileParameter, readonly=True, no_value=None, visible=False, optional=True )
+ def init_meta( self, dataset, copy_from=None ):
+ data.Binary.init_meta( self, dataset, copy_from=copy_from )
+ def set_meta( self, dataset, overwrite = True, **kwd ):
+ """
+ Sets index for BAM file.
+ """
+ index_file = dataset.metadata.bam_index
+ if not index_file:
+ index_file = dataset.metadata.spec['bam_index'].param.new_file( dataset = dataset )
+ tmp_dir = tempfile.gettempdir()
+ tmpf1 = tempfile.NamedTemporaryFile(dir=tmp_dir)
+ try:
+ subprocess.check_call(['cd', tmp_dir], shell=True)
+ subprocess.check_call('cp %s %s' % (dataset.file_name, tmpf1.name), shell=True)
+ subprocess.check_call('samtools index %s' % tmpf1.name, shell=True)
+ subprocess.check_call('cp %s.bai %s' % (tmpf1.name, index_file.file_name), shell=True)
+ except subprocess.CalledProcessError:
+ sys.stderr.write('There was a problem creating the index for the BAM file\n')
+ tmpf1.close()
+ dataset.metadata.bam_index = index_file
def set_peek( self, dataset ):
if not dataset.dataset.purged:
export_url = "/history_add_to?" + urlencode({'history_id':dataset.history_id,'ext':'bam','name':'bam alignments','info':'Alignments file','dbkey':dataset.dbkey})
@@ -256,4 +277,3 @@
def get_mime(self):
"""Returns the mime type of the datatype"""
return 'application/octet-stream'
-
\ No newline at end of file
12 years, 8 months
[hg] galaxy 2638: One more flup reference
by Greg Von Kuster
details: http://www.bx.psu.edu/hg/galaxy/rev/d261f41a2a03
changeset: 2638:d261f41a2a03
user: James Taylor <james(a)jamestaylor.org>
date: Fri Aug 28 15:29:53 2009 -0400
description:
One more flup reference
1 file(s) affected in this change:
lib/galaxy/web/framework/base.py
diffs (11 lines):
diff -r 0fd76a02c2b2 -r d261f41a2a03 lib/galaxy/web/framework/base.py
--- a/lib/galaxy/web/framework/base.py Fri Aug 28 15:12:55 2009 -0400
+++ b/lib/galaxy/web/framework/base.py Fri Aug 28 15:29:53 2009 -0400
@@ -13,7 +13,6 @@
import pkg_resources;
pkg_resources.require( "Paste" )
pkg_resources.require( "Routes" )
-pkg_resources.require( "flup" )
pkg_resources.require( "WebOb" )
import routes
12 years, 8 months
[hg] galaxy 2637: Purge references to Beaker and flup from buildapp
by Greg Von Kuster
details: http://www.bx.psu.edu/hg/galaxy/rev/0fd76a02c2b2
changeset: 2637:0fd76a02c2b2
user: James Taylor <james(a)jamestaylor.org>
date: Fri Aug 28 15:12:55 2009 -0400
description:
Purge references to Beaker and flup from buildapp
2 file(s) affected in this change:
eggs.ini
lib/galaxy/web/buildapp.py
diffs (48 lines):
diff -r b7a3a82b71ce -r 0fd76a02c2b2 eggs.ini
--- a/eggs.ini Fri Aug 28 15:07:48 2009 -0400
+++ b/eggs.ini Fri Aug 28 15:12:55 2009 -0400
@@ -29,7 +29,6 @@
Beaker = 1.4
docutils = 0.4
elementtree = 1.2.6_20050316
-flup = 0.5
lrucache = 0.2
;lsprof - james
Mako = 0.2.4
@@ -79,7 +78,6 @@
Beaker = http://cheeseshop.python.org/packages/source/B/Beaker/Beaker-1.4.tar.gz
docutils = http://downloads.sourceforge.net/docutils/docutils-0.4.tar.gz
elementtree = http://effbot.org/downloads/elementtree-1.2.6-20050316.tar.gz
-flup = http://www.saddi.com/software/flup/dist/archive/flup-r2311.tar.gz
lrucache = http://evan.prodromou.name/lrucache/lrucache-0.2.tar.gz
Mako = http://www.makotemplates.org/downloads/Mako-0.2.4.tar.gz
MyghtyUtils = http://cheeseshop.python.org/packages/source/M/MyghtyUtils/MyghtyUtils-0....
diff -r b7a3a82b71ce -r 0fd76a02c2b2 lib/galaxy/web/buildapp.py
--- a/lib/galaxy/web/buildapp.py Fri Aug 28 15:07:48 2009 -0400
+++ b/lib/galaxy/web/buildapp.py Fri Aug 28 15:12:55 2009 -0400
@@ -11,7 +11,6 @@
from paste.util import import_string
from paste import httpexceptions
from paste.deploy.converters import asbool
-import flup.middleware.session as flup_session
import pkg_resources
log = logging.getLogger( __name__ )
@@ -116,17 +115,6 @@
from paste import recursive
app = recursive.RecursiveMiddleware( app, conf )
log.debug( "Enabling 'recursive' middleware" )
- ## # Session middleware puts a session factory into the environment
- ## if asbool( conf.get( 'use_session', True ) ):
- ## store = flup_session.MemorySessionStore()
- ## app = flup_session.SessionMiddleware( store, app )
- ## log.debug( "Enabling 'flup session' middleware" )
- # Beaker session middleware
- if asbool( conf.get( 'use_beaker_session', False ) ):
- pkg_resources.require( "Beaker" )
- import beaker.session
- app = beaker.session.SessionMiddleware( app, conf )
- log.debug( "Enabling 'beaker session' middleware" )
# Various debug middleware that can only be turned on if the debug
# flag is set, either because they are insecure or greatly hurt
# performance
12 years, 8 months
[hg] galaxy 2629: Updated the Bam datatype so that the file is i...
by Greg Von Kuster
details: http://www.bx.psu.edu/hg/galaxy/rev/d8240234bd10
changeset: 2629:d8240234bd10
user: Kelly Vincent <kpvincent(a)bx.psu.edu>
date: Thu Aug 27 10:04:01 2009 -0400
description:
Updated the Bam datatype so that the file is indexed and the index is stored as metadata
1 file(s) affected in this change:
lib/galaxy/datatypes/images.py
diffs (44 lines):
diff -r d99cee3a4efd -r d8240234bd10 lib/galaxy/datatypes/images.py
--- a/lib/galaxy/datatypes/images.py Wed Aug 26 07:12:04 2009 -0400
+++ b/lib/galaxy/datatypes/images.py Thu Aug 27 10:04:01 2009 -0400
@@ -9,6 +9,7 @@
from galaxy.datatypes.sniff import *
from urllib import urlencode, quote_plus
import zipfile
+import os, subprocess, tempfile
log = logging.getLogger(__name__)
@@ -240,6 +241,26 @@
"""Class describing a BAM binary file"""
file_ext = "bam"
MetadataElement( name="bam_index", desc="BAM Index File", param=metadata.FileParameter, readonly=True, no_value=None, visible=False, optional=True )
+ def init_meta( self, dataset, copy_from=None ):
+ data.Binary.init_meta( self, dataset, copy_from=copy_from )
+ def set_meta( self, dataset, overwrite = True, **kwd ):
+ """
+ Sets index for BAM file.
+ """
+ index_file = dataset.metadata.bam_index
+ if not index_file:
+ index_file = dataset.metadata.spec['bam_index'].param.new_file( dataset = dataset )
+ tmp_dir = tempfile.gettempdir()
+ tmpf1 = tempfile.NamedTemporaryFile(dir=tmp_dir)
+ try:
+ subprocess.check_call(['cd', tmp_dir], shell=True)
+ subprocess.check_call('cp %s %s' % (dataset.file_name, tmpf1.name), shell=True)
+ subprocess.check_call('samtools index %s' % tmpf1.name, shell=True)
+ subprocess.check_call('cp %s.bai %s' % (tmpf1.name, index_file.file_name), shell=True)
+ except subprocess.CalledProcessError:
+ sys.stderr.write('There was a problem creating the index for the BAM file\n')
+ tmpf1.close()
+ dataset.metadata.bam_index = index_file
def set_peek( self, dataset ):
if not dataset.dataset.purged:
export_url = "/history_add_to?" + urlencode({'history_id':dataset.history_id,'ext':'bam','name':'bam alignments','info':'Alignments file','dbkey':dataset.dbkey})
@@ -256,4 +277,3 @@
def get_mime(self):
"""Returns the mime type of the datatype"""
return 'application/octet-stream'
-
\ No newline at end of file
12 years, 8 months
[hg] galaxy 2631: Image files for tagging UI
by Greg Von Kuster
details: http://www.bx.psu.edu/hg/galaxy/rev/4b4bac1f66bd
changeset: 2631:4b4bac1f66bd
user: jeremy goecks <jeremy.goecks at emory.edu>
date: Thu Aug 27 16:27:10 2009 -0400
description:
Image files for tagging UI
4 file(s) affected in this change:
static/images/add_icon.png
static/images/add_icon_dark.png
static/images/delete_tag_icon_gray.png
static/images/delete_tag_icon_white.png
diffs (8 lines):
diff -r 3c48856d80eb -r 4b4bac1f66bd static/images/add_icon.png
Binary file static/images/add_icon.png has changed
diff -r 3c48856d80eb -r 4b4bac1f66bd static/images/add_icon_dark.png
Binary file static/images/add_icon_dark.png has changed
diff -r 3c48856d80eb -r 4b4bac1f66bd static/images/delete_tag_icon_gray.png
Binary file static/images/delete_tag_icon_gray.png has changed
diff -r 3c48856d80eb -r 4b4bac1f66bd static/images/delete_tag_icon_white.png
Binary file static/images/delete_tag_icon_white.png has changed
12 years, 8 months
[hg] galaxy 2630: Add tables to support tagging of histories, da...
by Greg Von Kuster
details: http://www.bx.psu.edu/hg/galaxy/rev/3c48856d80eb
changeset: 2630:3c48856d80eb
user: jeremy goecks <jeremy.goecks at emory.edu>
date: Thu Aug 27 16:10:51 2009 -0400
description:
Add tables to support tagging of histories, datasets, ands HDAs.
1 file(s) affected in this change:
lib/galaxy/model/migrate/versions/0015_tagging.py
diffs (61 lines):
diff -r d99cee3a4efd -r 3c48856d80eb lib/galaxy/model/migrate/versions/0015_tagging.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/lib/galaxy/model/migrate/versions/0015_tagging.py Thu Aug 27 16:10:51 2009 -0400
@@ -0,0 +1,56 @@
+from sqlalchemy import *
+from migrate import *
+
+import datetime
+now = datetime.datetime.utcnow
+
+# Need our custom types, but don't import anything else from model
+from galaxy.model.custom_types import *
+
+import logging
+log = logging.getLogger( __name__ )
+
+metadata = MetaData( migrate_engine )
+
+# New tables to support tagging of histories, datasets, and history-dataset associations.
+Tag_table = Table( "tag", metadata,
+ Column( "id", Integer, primary_key=True ),
+ Column( "type", Integer ),
+ Column( "parent_id", Integer, ForeignKey( "tag.id" ) ),
+ Column( "name", TrimmedString(255) ),
+ UniqueConstraint( "name" ) )
+
+HistoryTagAssociation_table = Table( "history_tag_association", metadata,
+ Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ),
+ Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ),
+ Column( "user_tname", TrimmedString(255), index=True),
+ Column( "value", TrimmedString(255), index=True),
+ Column( "user_value", TrimmedString(255), index=True) )
+
+DatasetTagAssociation_table = Table( "dataset_tag_association", metadata,
+ Column( "dataset_id", Integer, ForeignKey( "dataset.id" ), index=True ),
+ Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ),
+ Column( "user_tname", TrimmedString(255), index=True),
+ Column( "value", TrimmedString(255), index=True),
+ Column( "user_value", TrimmedString(255), index=True) )
+
+HistoryDatasetAssociationTagAssociation_table = Table( "history_dataset_association_tag_association", metadata,
+ Column( "history_dataset_association_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True ),
+ Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ),
+ Column( "user_tname", TrimmedString(255), index=True),
+ Column( "value", TrimmedString(255), index=True),
+ Column( "user_value", TrimmedString(255), index=True) )
+
+def upgrade():
+ metadata.reflect()
+ Tag_table.create()
+ HistoryTagAssociation_table.create()
+ DatasetTagAssociation_table.create()
+ HistoryDatasetAssociationTagAssociation_table.create()
+
+def downgrade():
+ metadata.reflect()
+ Tag_table.drop()
+ HistoryTagAssociation_table.drop()
+ DatasetTagAssociation_table.drop()
+ HistoryDatasetAssociationTagAssociation_table.drop()
\ No newline at end of file
12 years, 8 months
[hg] galaxy 2632: Added documentation and exception handling for...
by Greg Von Kuster
details: http://www.bx.psu.edu/hg/galaxy/rev/31150f0b216d
changeset: 2632:31150f0b216d
user: jeremy goecks <jeremy.goecks(a)emory.edu>
date: Fri Aug 28 12:52:43 2009 -0400
description:
Added documentation and exception handling for mysql index error.
1 file(s) affected in this change:
lib/galaxy/model/migrate/versions/0015_tagging.py
diffs (98 lines):
diff -r 4b4bac1f66bd -r 31150f0b216d lib/galaxy/model/migrate/versions/0015_tagging.py
--- a/lib/galaxy/model/migrate/versions/0015_tagging.py Thu Aug 27 16:27:10 2009 -0400
+++ b/lib/galaxy/model/migrate/versions/0015_tagging.py Fri Aug 28 12:52:43 2009 -0400
@@ -1,3 +1,15 @@
+"""
+This migration script adds the tables necessary to support tagging of histories,
+datasets, and history-dataset associations (user views of datasets).
+
+If using mysql, this script will display the following error, which is corrected in the next
+migration script:
+
+history_dataset_association_tag_association table failed: (OperationalError)
+(1059, "Identifier name 'ix_history_dataset_association_tag_association_history_dataset_association_id'
+is too long)
+"""
+
from sqlalchemy import *
from migrate import *
@@ -11,6 +23,19 @@
log = logging.getLogger( __name__ )
metadata = MetaData( migrate_engine )
+
+def display_migration_details():
+ print ""
+ print "This migration script adds the tables necessary to support tagging of histories,"
+ print "datasets, and history-dataset associations (user views of datasets)."
+ print ""
+ print "If using mysql, this script will display the following error, which is "
+ print "corrected in the next migration script:"
+ print "history_dataset_association_tag_association table failed: "
+ print "(OperationalError) (1059, 'Identifier name "
+ print "'ix_history_dataset_association_tag_association_history_dataset_association_id'"
+ print "is too long)"
+
# New tables to support tagging of histories, datasets, and history-dataset associations.
Tag_table = Table( "tag", metadata,
@@ -42,15 +67,48 @@
Column( "user_value", TrimmedString(255), index=True) )
def upgrade():
+ display_migration_details()
metadata.reflect()
- Tag_table.create()
- HistoryTagAssociation_table.create()
- DatasetTagAssociation_table.create()
- HistoryDatasetAssociationTagAssociation_table.create()
+ try:
+ Tag_table.create()
+ except Exception, e:
+ print str(e)
+ log.debug( "Creating tag table failed: %s" % str( e ) )
+ try:
+ HistoryTagAssociation_table.create()
+ except Exception, e:
+ print str(e)
+ log.debug( "Creating history_tag_association table failed: %s" % str( e ) )
+ try:
+ DatasetTagAssociation_table.create()
+ except Exception, e:
+ print str(e)
+ log.debug( "Creating dataset_tag_association table failed: %s" % str( e ) )
+ try:
+ HistoryDatasetAssociationTagAssociation_table.create()
+ except Exception, e:
+ print str(e)
+ log.debug( "Creating history_dataset_association_tag_association table failed: %s" % str( e ) )
def downgrade():
metadata.reflect()
- Tag_table.drop()
- HistoryTagAssociation_table.drop()
- DatasetTagAssociation_table.drop()
- HistoryDatasetAssociationTagAssociation_table.drop()
\ No newline at end of file
+ try:
+ Tag_table.drop()
+ except Exception, e:
+ print str(e)
+ log.debug( "Dropping tag table failed: %s" % str( e ) )
+ try:
+ HistoryTagAssociation_table.drop()
+ except Exception, e:
+ print str(e)
+ log.debug( "Dropping history_tag_association table failed: %s" % str( e ) )
+ try:
+ DatasetTagAssociation_table.drop()
+ except Exception, e:
+ print str(e)
+ log.debug( "Dropping dataset_tag_association table failed: %s" % str( e ) )
+ try:
+ HistoryDatasetAssociationTagAssociation_table.drop()
+ except Exception, e:
+ print str(e)
+ log.debug( "Dropping history_dataset_association_tag_association table failed: %s" % str( e ) )
\ No newline at end of file
12 years, 8 months
<param> multiple formats
by Dominic Tolle
Hi,
is it possible for a input parameter to accept multiple format types
(e.g csfasta and fast), or do I need to write two separate tool
configs? For example if I have a format conversion tool which accepts
a number of input formats and converts them to a specific output
format do I need to write a tool config for each conversion? One way
around this would be to include a conditional in the tool config and
let the user specify the input type, but is there another way
(preferably not involving writing large conditionals)?
Cheers
Dominic
12 years, 8 months
[hg] galaxy 2628: Fix for importing a shared history via a link ...
by Greg Von Kuster
details: http://www.bx.psu.edu/hg/galaxy/rev/d99cee3a4efd
changeset: 2628:d99cee3a4efd
user: Greg Von Kuster <greg(a)bx.psu.edu>
date: Wed Aug 26 07:12:04 2009 -0400
description:
Fix for importing a shared history via a link for an anonymous user with no existing Galaxy cookies.
1 file(s) affected in this change:
lib/galaxy/web/controllers/history.py
diffs (12 lines):
diff -r 03accd13066e -r d99cee3a4efd lib/galaxy/web/controllers/history.py
--- a/lib/galaxy/web/controllers/history.py Tue Aug 25 16:59:28 2009 -0400
+++ b/lib/galaxy/web/controllers/history.py Wed Aug 26 07:12:04 2009 -0400
@@ -322,7 +322,7 @@
return trans.show_ok_message( """
History "%s" has been imported. Click <a href="%s">here</a>
to begin.""" % ( new_history.name, web.url_for( '/' ) ) )
- elif not user_history.datasets or confirm:
+ elif not user_history or not user_history.datasets or confirm:
new_history = import_history.copy()
new_history.name = "imported: " + new_history.name
new_history.user_id = None
12 years, 8 months
