October 2012 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: dan: Fix importing ordering of boto in cloudlaunch.
by Bitbucket 17 Oct '12

17 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/ba9a8b52e853/ changeset: ba9a8b52e853 user: dan date: 2012-10-17 22:14:17 summary: Fix importing ordering of boto in cloudlaunch. affected #: 1 file diff -r b9c0d2847d68269f67241f730e5f3ca8bc534ed3 -r ba9a8b52e8539693606b07811a6b2bf48b071ae2 lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py --- a/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py +++ b/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py @@ -11,10 +11,10 @@ import os import tempfile import time -import boto import pkg_resources from galaxy import eggs pkg_resources.require('boto') +import boto from galaxy import web from galaxy.web.base.controller import BaseUIController from galaxy.util.json import to_json_string Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by Bitbucket 17 Oct '12

17 Oct '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/be1853972823/ changeset: be1853972823 user: dan date: 2012-10-17 22:06:20 summary: Use simplejson for python2.5 compatibility in genome index. affected #: 1 file diff -r be7a8d4808676c7519919483f115811a1b77ec9f -r be1853972823836ffd50654900632d6cd7c74acb lib/galaxy/tools/genome_index/index_genome.py --- a/lib/galaxy/tools/genome_index/index_genome.py +++ b/lib/galaxy/tools/genome_index/index_genome.py @@ -7,7 +7,11 @@ """ from __future__ import with_statement -import optparse, sys, os, tempfile, time, subprocess, shlex, json, tarfile, shutil +import optparse, sys, os, tempfile, time, subprocess, shlex, tarfile, shutil + +import pkg_resources +pkg_resources.require("simplejson") +import simplejson class ManagedIndexer(): def __init__( self, output_file, infile, workingdir, rsync_url, tooldata ): @@ -72,7 +76,7 @@ return result def _flush_files( self ): - json.dump( self.locations, self.outfile ) + simplejson.dump( self.locations, self.outfile ) self.outfile.close() self.logfile.close() https://bitbucket.org/galaxy/galaxy-central/changeset/b9c0d2847d68/ changeset: b9c0d2847d68 user: dan date: 2012-10-17 22:06:22 summary: Fix for enumerator in python2.5 in datatype sniffer affected #: 1 file diff -r be1853972823836ffd50654900632d6cd7c74acb -r b9c0d2847d68269f67241f730e5f3ca8bc534ed3 lib/galaxy/datatypes/sniff.py --- a/lib/galaxy/datatypes/sniff.py +++ b/lib/galaxy/datatypes/sniff.py @@ -94,10 +94,14 @@ """ fd, temp_name = tempfile.mkstemp() fp = os.fdopen( fd, "wt" ) - i = 0 - for i, line in enumerate( file( fname, "U" ), 1 ): + i = None + for i, line in enumerate( file( fname, "U" ) ): fp.write( "%s\n" % line.rstrip( "\r\n" ) ) fp.close() + if i is None: + i = 0 + else: + i += 1 if in_place: shutil.move( temp_name, fname ) # Return number of lines in file. @@ -119,12 +123,16 @@ regexp = re.compile( patt ) fd, temp_name = tempfile.mkstemp() fp = os.fdopen( fd, "wt" ) - i = 0 - for i, line in enumerate( file( fname ), 1): + i = None + for i, line in enumerate( file( fname ) ): line = line.rstrip( '\r\n' ) elems = regexp.split( line ) fp.write( "%s\n" % '\t'.join( elems ) ) fp.close() + if i is None: + i = 0 + else: + i += 1 if in_place: shutil.move( temp_name, fname ) # Return number of lines in file. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 8 new changesets
by Bitbucket 17 Oct '12

17 Oct '12

8 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/73dabef59a23/ changeset: 73dabef59a23 user: dan date: 2012-10-17 21:56:11 summary: Add util.isinf function. affected #: 1 file diff -r 53c2605a8ca2fa8086c5c6da3bbbfacd37737510 -r 73dabef59a235e318973fab5a80e844ebc917cc3 lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -16,6 +16,14 @@ except ImportError: from md5 import new as md5 +try: + from math import isinf +except ImportError: + INF = float( 'inf' ) + NEG_INF = -INF + ISINF_LIST = [ INF, NEG_INF ] + isinf = lambda x: x in ISINF_LIST + from galaxy import eggs import pkg_resources https://bitbucket.org/galaxy/galaxy-central/changeset/33c475973e46/ changeset: 33c475973e46 user: dan date: 2012-10-17 21:56:11 summary: Have exit range isinf test use util.isinf for python2.5 compatibility. affected #: 1 file diff -r 73dabef59a235e318973fab5a80e844ebc917cc3 -r 33c475973e46d91ff7daef18f537357cbdaf6c06 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -1276,8 +1276,8 @@ # isn't bogus. If we have two infinite values, then # the start must be -inf and the end must be +inf. # So at least warn about this situation: - if ( math.isinf( exit_code.range_start ) and - math.isinf( exit_code.range_end ) ): + if ( util.isinf( exit_code.range_start ) and + util.isinf( exit_code.range_end ) ): log.warning( "Tool exit_code range %s will match on " + "all exit codes" % code_range ) self.stdio_exit_codes.append( exit_code ) https://bitbucket.org/galaxy/galaxy-central/changeset/1de87a3f82a2/ changeset: 1de87a3f82a2 user: dan date: 2012-10-17 21:56:12 summary: Fix file read sentinel. Use simplejson for python2.5 compatibility in genome index. affected #: 1 file diff -r 33c475973e46d91ff7daef18f537357cbdaf6c06 -r 1de87a3f82a27b89461c0964b77f647ac8619a69 lib/galaxy/tools/genome_index/__init__.py --- a/lib/galaxy/tools/genome_index/__init__.py +++ b/lib/galaxy/tools/genome_index/__init__.py @@ -1,6 +1,6 @@ from __future__ import with_statement -import os, shutil, logging, tempfile, json, tarfile +import os, shutil, logging, tempfile, tarfile from galaxy import model, util from galaxy.web.framework.helpers import to_unicode @@ -9,6 +9,10 @@ from galaxy.web.base.controller import UsesHistoryMixin from galaxy.tools.data import ToolDataTableManager +import pkg_resources +pkg_resources.require("simplejson") +import simplejson + log = logging.getLogger(__name__) def load_genome_index_tools( toolbox ): @@ -70,7 +74,7 @@ fp = open( gitd.dataset.get_file_name(), 'r' ) deferred = sa_session.query( model.DeferredJob ).filter_by( id=gitd.deferred_job_id ).first() try: - logloc = json.load( fp ) + logloc = simplejson.load( fp ) except ValueError: deferred.state = app.model.DeferredJob.states.ERROR sa_session.add( deferred ) @@ -211,7 +215,7 @@ import hashlib md5 = hashlib.md5() with open( filename, 'rb' ) as f: - for chunk in iter( lambda: f.read( 8192 ), b'' ): + for chunk in iter( lambda: f.read( 8192 ), '' ): md5.update( chunk ) return md5.digest() https://bitbucket.org/galaxy/galaxy-central/changeset/3fd0416c1062/ changeset: 3fd0416c1062 user: dan date: 2012-10-17 21:56:12 summary: Use simplejson in lib/galaxy/visualization/data_providers/phyloviz/baseparser.py for python2.5 compatibility. affected #: 1 file diff -r 1de87a3f82a27b89461c0964b77f647ac8619a69 -r 3fd0416c1062e269e813004263532d85f1ac7f9b lib/galaxy/visualization/data_providers/phyloviz/baseparser.py --- a/lib/galaxy/visualization/data_providers/phyloviz/baseparser.py +++ b/lib/galaxy/visualization/data_providers/phyloviz/baseparser.py @@ -1,4 +1,6 @@ -import json +import pkg_resources +pkg_resources.require("simplejson") +import simplejson class Node(object): """Node class of PhyloTree, which represents a CLAUDE in a phylogenetic tree""" @@ -116,7 +118,7 @@ def toJson(self, jsonDict): """Convenience method to get a json string from a python json dict""" - return json.dumps(jsonDict) + return simplejson.dumps(jsonDict) def _writeJsonToFile(self, filepath, json): """Writes the file out to the system""" https://bitbucket.org/galaxy/galaxy-central/changeset/cc3550b576f8/ changeset: cc3550b576f8 user: dan date: 2012-10-17 21:56:12 summary: Use simplejson in lib/galaxy/visualization/data_providers/phyloviz/newickparser.py for python2.5 compatibility. affected #: 1 file diff -r 3fd0416c1062e269e813004263532d85f1ac7f9b -r cc3550b576f8a1d64b81c4b209aa209d25bf73d9 lib/galaxy/visualization/data_providers/phyloviz/newickparser.py --- a/lib/galaxy/visualization/data_providers/phyloviz/newickparser.py +++ b/lib/galaxy/visualization/data_providers/phyloviz/newickparser.py @@ -1,3 +1,4 @@ +from __future__ import with_statement from baseparser import Base_Parser, PhyloTree import re https://bitbucket.org/galaxy/galaxy-central/changeset/7389ec156e62/ changeset: 7389ec156e62 user: dan date: 2012-10-17 21:56:12 summary: Use simplejson in lib/galaxy/visualization/data_providers/phyloviz/nexusparser.py for python2.5 compatibility. affected #: 1 file diff -r cc3550b576f8a1d64b81c4b209aa209d25bf73d9 -r 7389ec156e62c3ca3af24b7458396a58ed54ca68 lib/galaxy/visualization/data_providers/phyloviz/nexusparser.py --- a/lib/galaxy/visualization/data_providers/phyloviz/nexusparser.py +++ b/lib/galaxy/visualization/data_providers/phyloviz/nexusparser.py @@ -1,3 +1,4 @@ +from __future__ import with_statement from newickparser import Newick_Parser import re https://bitbucket.org/galaxy/galaxy-central/changeset/e6ab6f0524ea/ changeset: e6ab6f0524ea user: dan date: 2012-10-17 21:56:12 summary: Use simplejson in data_admin for python2.5 compatibility. affected #: 1 file diff -r 7389ec156e62c3ca3af24b7458396a58ed54ca68 -r e6ab6f0524eae90757c4aa17d24c43a2d65fabca lib/galaxy/webapps/galaxy/controllers/data_admin.py --- a/lib/galaxy/webapps/galaxy/controllers/data_admin.py +++ b/lib/galaxy/webapps/galaxy/controllers/data_admin.py @@ -1,4 +1,4 @@ -import sys, ftplib, json +import sys, ftplib from galaxy import model, util from galaxy.jobs import transfer_manager from galaxy.web.base.controller import * @@ -6,6 +6,10 @@ from galaxy.model.orm import * from library_common import get_comptypes, lucene_search, whoosh_search +import pkg_resources +pkg_resources.require("simplejson") +import simplejson + # Older py compatibility try: set() @@ -157,7 +161,7 @@ gname = deferred.params[ 'intname' ] indexers = ', '.join( deferred.params[ 'indexes' ] ) jobs = self._get_jobs( deferred, trans ) - jsonjobs = json.dumps( jobs ) + jsonjobs = simplejson.dumps( jobs ) return trans.fill_template( '/admin/data_admin/download_status.mako', name=gname, indexers=indexers, mainjob=jobid, jobs=jobs, jsonjobs=jsonjobs ) @web.expose @@ -169,7 +173,7 @@ jobid = params.get( 'jobid', '' ) job = sa_session.query( model.DeferredJob ).filter_by( id=jobid ).first() jobs = self._get_jobs( job, trans ) - return trans.fill_template( '/admin/data_admin/ajax_status.mako', json=json.dumps( jobs ) ) + return trans.fill_template( '/admin/data_admin/ajax_status.mako', json=simplejson.dumps( jobs ) ) def _get_job( self, jobid, jobtype, trans ): sa = trans.app.model.context.current https://bitbucket.org/galaxy/galaxy-central/changeset/be7a8d480867/ changeset: be7a8d480867 user: dan date: 2012-10-17 21:56:29 summary: Fix for trying to set httponly cookie attribute for python2.5 compatibility. affected #: 1 file diff -r e6ab6f0524eae90757c4aa17d24c43a2d65fabca -r be7a8d4808676c7519919483f115811a1b77ec9f lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py +++ b/lib/galaxy/web/framework/__init__.py @@ -6,6 +6,7 @@ import os, sys, time, socket, random, string import inspect +from Cookie import CookieError pkg_resources.require( "Cheetah" ) from Cheetah.Template import Template @@ -414,7 +415,10 @@ tstamp = time.localtime ( time.time() + 3600 * 24 * age ) self.response.cookies[name]['expires'] = time.strftime( '%a, %d-%b-%Y %H:%M:%S GMT', tstamp ) self.response.cookies[name]['version'] = version - self.response.cookies[name]['httponly'] = True + try: + self.response.cookies[name]['httponly'] = True + except CookieError, e: + log.warning( "Error setting httponly attribute in cookie '%s': %s" % ( name, e ) ) def _ensure_valid_session( self, session_cookie, create=True): """ Ensure that a valid Galaxy session exists and is available as Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dannon: CloudLaunch: Add password confirm field to cloudlaunch to prevent accidentally not knowing your password during presentations.
by Bitbucket 17 Oct '12

17 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/53c2605a8ca2/ changeset: 53c2605a8ca2 user: dannon date: 2012-10-17 19:25:29 summary: CloudLaunch: Add password confirm field to cloudlaunch to prevent accidentally not knowing your password during presentations. Actually display errormessage box to show issues. affected #: 2 files diff -r a70bb556b9a5458a878e8abef7a55c88e2f0e058 -r 53c2605a8ca2fa8086c5c6da3bbbfacd37737510 lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py --- a/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py +++ b/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py @@ -61,7 +61,7 @@ # We need to get persistent data, and the cluster name. for key in bucket.list(): if key.name.endswith('.clusterName'): - clusters.append({'name':key.name.split('.clusterName')[0], 'persistent_data': pd.get_contents_as_string()}) + clusters.append({'name': key.name.split('.clusterName')[0], 'persistent_data': pd.get_contents_as_string()}) account_info['clusters'] = clusters return to_json_string(account_info) @@ -76,13 +76,13 @@ except EC2ResponseError, err: ec2_error = err.error_message if ec2_error: - #return trans.fill_template("cloud/run.mako", error = ec2_error) - return {'errors':[ec2_error]} + trans.response.status = 400 + return ec2_error else: - user_provided_data={'cluster_name':cluster_name, - 'access_key':key_id, - 'secret_key':secret, - 'instance_type':instance_type} + user_provided_data = {'cluster_name': cluster_name, + 'access_key': key_id, + 'secret_key': secret, + 'instance_type': instance_type} if password: user_provided_data['password'] = password if share_string: @@ -95,15 +95,13 @@ instance = rs.instances[0] ct = 0 while not instance.public_dns_name: - # Can take a second to have public dns name registered. - # DBTODO, push this into a page update, this is not ideal. try: instance.update() except EC2ResponseError: - #This can happen when update is invoked before the instance is fully registered. Prevent - #failure, wait it out. + #This can happen when update is invoked before the instance is fully registered. + #Prevent failure, wait it out. pass - ct +=1 + ct += 1 time.sleep(1) if kp_material: #We have created a keypair. Save to tempfile for one time retrieval. @@ -123,7 +121,8 @@ 'kp_material_tag':kp_material_tag }) else: - return {'errors':["Instance failure, but no specific error was detected. Please check your AWS Console."]} + trans.response.status = 400 + return "Instance failure, but no specific error was detected. Please check your AWS Console." @web.expose def get_pkey(self, trans, kp_material_tag=None): diff -r a70bb556b9a5458a878e8abef7a55c88e2f0e058 -r 53c2605a8ca2fa8086c5c6da3bbbfacd37737510 templates/cloud/index.mako --- a/templates/cloud/index.mako +++ b/templates/cloud/index.mako @@ -113,9 +113,16 @@ type: 'POST', dataType: 'json', beforeSubmit: function(data){ - //Hide the form, show pending box with spinner. - $('#launchFormContainer').hide('fast'); - $('#responsePanel').show('fast'); + if ($('#id_password').val() != $('#id_password_confirm').val()){ + //Passwords don't match. + $('#cloudlaunch_form').prepend('<div class="errormessage">Passwords do not match</div>'); + return false; + }else{ + $('.errormessage').remove() + //Hide the form, show pending box with spinner. + $('#launchFormContainer').hide('fast'); + $('#responsePanel').show('fast'); + } }, success: function(data){ //Success Message, link to key download if required, link to server itself. @@ -144,6 +151,9 @@ $('#instance_dns').text(data.public_dns_name); $('#launchSuccess').show('fast'); } + }, + error: function(data){ + $('#cloudlaunch_form').prepend('<div class="errormessage">' + data.responseText + '</div>'); } }); }); @@ -201,6 +211,12 @@ </div><div class="form-row"> + <label for="id_password_confirm">Cluster Password - Confirmation</label> + <input type="password" size="40" name="password_confirm" id="id_password_confirm"/><br/> + </div> + + + <div class="form-row"><label for="id_keypair">Key Pair</label><select name="keypair" id="id_keypair"><option name="Create" value="cloudman_keypair">cloudman_keypair</option> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Fix for python2.5.
by Bitbucket 17 Oct '12

17 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/a70bb556b9a5/ changeset: a70bb556b9a5 user: dan date: 2012-10-17 18:32:35 summary: Fix for python2.5. affected #: 1 file diff -r d68822fb944998597f3d16944eb6e42edb8041c8 -r a70bb556b9a5458a878e8abef7a55c88e2f0e058 lib/galaxy/security/__init__.py --- a/lib/galaxy/security/__init__.py +++ b/lib/galaxy/security/__init__.py @@ -318,7 +318,7 @@ % ( item.library_dataset_id, len( base_result ), len( new_result ) ) ) log.debug( "get_actions_for_items: Test end" ) - except Exception as e: + except Exception, e: log.debug( "Exception in test code: %s" % e ) return ret_permissions Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Remove unused imports, fix exception log str(e) (which was actually `e` imported from another package, not the exception...)
by Bitbucket 16 Oct '12

16 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/d68822fb9449/ changeset: d68822fb9449 user: dannon date: 2012-10-16 22:47:31 summary: Remove unused imports, fix exception log str(e) (which was actually `e` imported from another package, not the exception...) affected #: 1 file diff -r 1e0de1ac4cd50e72926d977510b5185b9d6d5111 -r d68822fb944998597f3d16944eb6e42edb8041c8 test/base/twilltestcase.py --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -1,8 +1,7 @@ import pkg_resources pkg_resources.require( "twill==0.9" ) -import StringIO, os, sys, random, filecmp, time, unittest, urllib, logging, difflib, tarfile, zipfile, tempfile, re, shutil, subprocess -from itertools import * +import StringIO, os, filecmp, time, unittest, urllib, logging, difflib, tarfile, zipfile, tempfile, re, shutil, subprocess import twill import twill.commands as tc @@ -703,7 +702,7 @@ shutil.copy( temp_name, ofn ) except Exception, exc: error_log_msg = ( 'TwillTestCase could not save output file %s to %s: ' % ( temp_name, ofn ) ) - error_log_msg += str( e ) + error_log_msg += str( exc ) else: log.debug('## GALAXY_TEST_SAVE=%s. saved %s' % ( self.keepOutdir, ofn ) ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Fix test cases failing due to non-reflected password change. This resolves failures of:
by Bitbucket 16 Oct '12

16 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/1e0de1ac4cd5/ changeset: 1e0de1ac4cd5 user: dannon date: 2012-10-16 22:43:58 summary: Fix test cases failing due to non-reflected password change. This resolves failures of: functional.test_user_info.TestUserInfo.test_010_user_reqistration_multiple_user_info_forms functional.test_user_info.TestUserInfo.test_015_user_reqistration_single_user_info_forms functional.test_user_info.TestUserInfo.test_020_edit_user_info functional.test_user_info.TestUserInfo.test_999_reset_data_for_later_test_runs affected #: 1 file diff -r 5a9acc6d83bd4b738e56e7875b941ffbb89158ba -r 1e0de1ac4cd50e72926d977510b5185b9d6d5111 test/base/twilltestcase.py --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -878,6 +878,8 @@ if user_type_fd_id: # The user_type_fd_id SelectField requires a refresh_on_change self.refresh_form( 'user_type_fd_id', user_type_fd_id ) + tc.fv( "1", "password", password ) + tc.fv( "1", "confirm", password ) for index, ( field_name, info_value ) in enumerate( user_info_values ): tc.fv( "1", field_name, info_value ) for check_str in strings_displayed: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: smcmanus: Added folder_contents controller and enabled both folder and folder_contents controllers
by Bitbucket 16 Oct '12

16 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/5a9acc6d83bd/ changeset: 5a9acc6d83bd user: smcmanus date: 2012-10-16 22:32:01 summary: Added folder_contents controller and enabled both folder and folder_contents controllers affected #: 2 files diff -r 2a1b619a3fe6f94c764d1e2154f1b1a1195f03cc -r 5a9acc6d83bd4b738e56e7875b941ffbb89158ba lib/galaxy/webapps/galaxy/api/folder_contents.py --- /dev/null +++ b/lib/galaxy/webapps/galaxy/api/folder_contents.py @@ -0,0 +1,111 @@ +""" +API operations on the contents of a library. +""" +import logging, os, string, shutil, urllib, re, socket +from cgi import escape, FieldStorage +from galaxy import util, datatypes, jobs, web, util +from galaxy.web.base.controller import * +from galaxy.util.sanitize_html import sanitize_html +from galaxy.model.orm import * + +log = logging.getLogger( __name__ ) + +class FolderContentsController( BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems ): + + @web.expose_api + def index( self, trans, folder_id, **kwd ): + """ + GET /api/folders/{encoded_folder_id}/contents + Displays a collection (list) of a folder's contents (files and folders). + The /api/library_contents/{encoded_library_id}/contents + lists everything in a library recursively, which is not what + we want here. We could add a parameter to use the recursive + style, but this is meant to act similar to an "ls" directory listing. + """ + log.debug( "FolderContentsController.index: enter" ) + rval = [] + current_user_roles = trans.get_current_user_roles() + def traverse( folder ): + admin = trans.user_is_admin() + rval = [] + for subfolder in folder.active_folders: + log.debug( "Subfolder type: %s" % type(subfolder) ) + if not admin: + log.debug( "calling check_folder_contents" ) + can_access, folder_ids = trans.app.security_agent.check_folder_contents( trans.user, current_user_roles, subfolder ) + if (admin or can_access) and not subfolder.deleted: + subfolder.api_type = 'folder' + rval.append( subfolder ) + for ld in folder.datasets: + log.debug( "Folder type: %s" % type(folder) ) + if not admin: + can_access = trans.app.security_agent.can_access_dataset( current_user_roles, ld.library_dataset_dataset_association.dataset ) + if (admin or can_access) and not ld.deleted: + log.debug( "Folder attributes: %s" % dir(folder) ) + ld.api_type = 'file' + rval.append( ld ) + return rval + + try: + decoded_folder_id = trans.security.decode_id( folder_id[-16:] ) + except TypeError: + trans.response.status = 400 + return "Malformed folder id ( %s ) specified, unable to decode." % str( folder_id ) + + try: + folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( decoded_folder_id ) + except: + folder = None + log.error( "FolderContentsController.index: Unable to retrieve folder %s" + % folder_id ) + + # TODO: Find the API's path to this folder if necessary. + # This was needed in recursive descent, but it's not needed + # for "ls"-style content checking: + if not folder or not ( trans.user_is_admin() or trans.app.security_agent.can_access_library_item( current_user_roles, folder ) ): + trans.response.status = 400 + return "Invalid folder id ( %s ) specified." % str( folder_id ) + + for content in traverse( folder ): + encoded_id = trans.security.encode_id( content.id ) + if content.api_type == 'folder': + encoded_id = 'F' + encoded_id + rval.append( dict( id = encoded_id, + type = content.api_type, + name = content.name, + # TODO: calculate the folder's library id + # (if necessary) and add library_id=X below: + url = url_for( controller='folder_content', id=encoded_id ) ) ) + return rval + + @web.expose_api + def show( self, trans, id, library_id, **kwd ): + """ + GET /api/folders/{encoded_folder_id}/ + """ + pass + + @web.expose_api + def create( self, trans, library_id, payload, **kwd ): + """ + POST /api/folders/{encoded_folder_id}/contents + Creates a new folder. This should be superseded by the + LibraryController. + """ + pass + + @web.expose_api + def update( self, trans, id, library_id, payload, **kwd ): + """ + PUT /api/folders/{encoded_folder_id}/contents + """ + pass + + # TODO: Move to library_common. + def __decode_library_content_id( self, trans, content_id ): + if ( len( content_id ) % 16 == 0 ): + return 'LibraryDataset', content_id + elif ( content_id.startswith( 'F' ) ): + return 'LibraryFolder', content_id[1:] + else: + raise HTTPBadRequest( 'Malformed library content id ( %s ) specified, unable to decode.' % str( content_id ) ) diff -r 2a1b619a3fe6f94c764d1e2154f1b1a1195f03cc -r 5a9acc6d83bd4b738e56e7875b941ffbb89158ba lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -63,7 +63,7 @@ # The /folders section is experimental at this point: log.debug( "app.config.api_folders: %s" % app.config.api_folders ) if app.config.api_folders: - #webapp.api_mapper.resource( 'folder', 'folders', path_prefix='/api' ) + webapp.api_mapper.resource( 'folder', 'folders', path_prefix='/api' ) webapp.api_mapper.resource( 'content', 'contents', controller='folder_contents', name_prefix='folder_', Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dan: Performance enhancements for Build custom track for UCSC genome browser tool.
by Bitbucket 16 Oct '12

16 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/2a1b619a3fe6/ changeset: 2a1b619a3fe6 user: dan date: 2012-10-16 21:25:01 summary: Performance enhancements for Build custom track for UCSC genome browser tool. affected #: 1 file diff -r d5f1c28102befb1032b277b4c2fb75aa2d8cd88c -r 2a1b619a3fe6f94c764d1e2154f1b1a1195f03cc tools/visualization/build_ucsc_custom_track.py --- a/tools/visualization/build_ucsc_custom_track.py +++ b/tools/visualization/build_ucsc_custom_track.py @@ -11,6 +11,22 @@ sys.stderr.write( msg ) sys.exit() +FILE_TYPE_TO_TRACK_TYPE = { 'bed': None, 'bedstrict': None, 'bed6': None, 'bed12': None, 'bedgraph':'bedGraph', 'wig':'wiggle_0' } +CHUNK_SIZE = 2**20 #1mb + +def get_track_line_is_interval( file_type, name, description, color, visibility ): + if file_type in FILE_TYPE_TO_TRACK_TYPE: + track_type = FILE_TYPE_TO_TRACK_TYPE[ file_type ] + is_interval = False + else: + track_type = None + is_interval = True + track_line = 'track ' + if track_type: + track_line += 'type=%s ' % ( track_type ) + track_line += 'name="%s" description="%s" color=%s visibility=%s\n' % ( name, description, color, visibility ) + return track_line, is_interval + args = sys.argv[1:] out_fname = args.pop(0) @@ -22,25 +38,23 @@ while args: # Suck in one dataset worth of arguments in_fname = args.pop(0) - type = args.pop(0) + file_type = args.pop(0) colspec = args.pop(0) name = args.pop(0) description = args.pop(0) color = args.pop(0).replace( '-', ',' ) visibility = args.pop(0) + track_line, is_interval = get_track_line_is_interval( file_type, name, description, color, visibility ) # Do the work - if type == "wig": - print >> out, '''track type=wiggle_0 name="%s" description="%s" color=%s visibility=%s''' \ - % ( name, description, color, visibility ) - for i, line in enumerate( file( in_fname ) ): - print >> out, line, - print >> out - elif type == "bed": - print >> out, '''track name="%s" description="%s" color=%s visibility=%s''' \ - % ( name, description, color, visibility ) - for i, line in enumerate( file( in_fname ) ): - print >> out, line, - print >> out + in_file = open( in_fname ) + out.write( track_line ) + if not is_interval: + while True: + chunk = in_file.read( CHUNK_SIZE ) + if chunk: + out.write( chunk ) + else: + break else: # Assume type is interval (don't pass this script anything else!) try: @@ -52,29 +66,27 @@ except: stop_err( "Columns in interval file invalid for UCSC custom track." ) - print >> out, '''track name="%s" description="%s" color=%s visibility=%s''' \ - % ( name, description, color, visibility ) i = 0 - for i, line in enumerate( file( in_fname ) ): + for i, line in enumerate( in_file ): line = line.rstrip( '\r\n' ) if line and not line.startswith( '#' ): fields = line.split( "\t" ) if st > 0: #strand column is present try: - print >> out, "%s\t%s\t%s\t%d\t0\t%s" % ( fields[c], fields[s], fields[e], i, fields[st] ) + out.write( "%s\t%s\t%s\t%d\t0\t%s\n" % ( fields[c], fields[s], fields[e], i, fields[st] ) ) except: skipped_lines += 1 if not first_invalid_line: first_invalid_line = i+1 else: try: - print >> out, "%s\t%s\t%s" % ( fields[c], fields[s], fields[e] ) + out.write( "%s\t%s\t%s\n" % ( fields[c], fields[s], fields[e] ) ) except: skipped_lines += 1 if not first_invalid_line: first_invalid_line = i+1 - print >> out + out.write( "\n" ) #separating newline num_tracks += 1 out.close() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Add genomespace tools to tool_conf.xml.main.
by Bitbucket 16 Oct '12

16 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/d5f1c28102be/ changeset: d5f1c28102be user: dan date: 2012-10-16 21:04:40 summary: Add genomespace tools to tool_conf.xml.main. affected #: 1 file diff -r e1ea65232d19a053be0725a91b47a1d81e309ee6 -r d5f1c28102befb1032b277b4c2fb75aa2d8cd88c tool_conf.xml.main --- a/tool_conf.xml.main +++ b/tool_conf.xml.main @@ -18,9 +18,12 @@ <tool file="data_source/eupathdb.xml" /><tool file="data_source/encode_db.xml" /><tool file="data_source/epigraph_import.xml" /> + <tool file="genomespace/genomespace_file_browser_prod.xml" /> + <tool file="genomespace/genomespace_importer.xml" /></section><section name="Send Data" id="send"><tool file="data_destination/epigraph.xml" /> + <tool file="genomespace/genomespace_exporter.xml" /></section><section name="ENCODE Tools" id="EncodeTools"><tool file="encode/gencode_partition.xml" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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