May 2014 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 23 May '14

23 May '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/cbd0a239259b/ Changeset: cbd0a239259b Branch: next-stable User: davebgx Date: 2014-05-23 16:00:33 Summary: Fix server error when registering a new account. Affected #: 1 file diff -r 2b0cdcea282b2ea92b649df9a5d63f40b2bd545f -r cbd0a239259b694afadfc62bdde820eef0c30b4f lib/galaxy/webapps/galaxy/controllers/user.py --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -1144,9 +1144,9 @@ return "A public user name is required in the tool shed." if username in [ 'repos' ]: return "The term %s is a reserved word in the tool shed, so it cannot be used as a public user name." % username - message = "\n".join(validate_email( trans, email ), - validate_password( trans, password, confirm ), - validate_publicname( trans, username )) + message = "\n".join( [ validate_email( trans, email ), + validate_password( trans, password, confirm ), + validate_publicname( trans, username ) ] ).rstrip() if not message: if trans.webapp.name == 'galaxy': if self.get_all_forms( trans, https://bitbucket.org/galaxy/galaxy-central/commits/89bdb65761f6/ Changeset: 89bdb65761f6 User: davebgx Date: 2014-05-23 16:01:07 Summary: Merge with next-stable. Affected #: 1 file diff -r af76f0273d3de8ccc38f78dfb0aae9974574aa7b -r 89bdb65761f631921d3a21cfd2335103715de5bb lib/galaxy/webapps/galaxy/controllers/user.py --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -1144,9 +1144,9 @@ return "A public user name is required in the tool shed." if username in [ 'repos' ]: return "The term %s is a reserved word in the tool shed, so it cannot be used as a public user name." % username - message = "\n".join(validate_email( trans, email ), - validate_password( trans, password, confirm ), - validate_publicname( trans, username )) + message = "\n".join( [ validate_email( trans, email ), + validate_password( trans, password, confirm ), + validate_publicname( trans, username ) ] ).rstrip() if not message: if trans.webapp.name == 'galaxy': if self.get_all_forms( trans, 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: guerler: Charts: Allow chart groups to have different number of rows
by commits-noreply＠bitbucket.org 22 May '14

22 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/47810c6ec62c/ Changeset: 47810c6ec62c User: guerler Date: 2014-05-22 23:16:52 Summary: Charts: Allow chart groups to have different number of rows Affected #: 1 file diff -r e959799971fc33d0490973c6b28673049d8ece61 -r 47810c6ec62c258423ea4527cf3214326a9b417b config/plugins/visualizations/charts/static/library/datasets.js --- a/config/plugins/visualizations/charts/static/library/datasets.js +++ b/config/plugins/visualizations/charts/static/library/datasets.js @@ -142,16 +142,25 @@ // log console.debug('Datasets::_fill_from_cache() - Filling request from cache.'); - // get dataset - var dataset = this.list[request_dictionary.id]; - if (!dataset) { - console.debug('FAILED - Datasets::_fill_from_cache() - Dataset not found.'); + // identify start of request + var start = request_dictionary.start; + + // identify end of request + var limit = 0; + for (var i in request_dictionary.groups) { + var group = request_dictionary.groups[i]; + for (var key in group.columns) { + var column = group.columns[key]; + var block_id = this._block_id(request_dictionary, column.index); + var column_data = this.cache[block_id]; + if (column_data) { + limit = Math.max(limit, column_data.length); + } + } } - // identify start/end of request - var start = request_dictionary.start; - var end = Math.min(request_dictionary.end, dataset.metadata_data_lines); - if (end - start <= 0) { + // check length + if (limit == 0) { console.debug('FAILED - Datasets::_fill_from_cache() - Invalid range.'); } @@ -164,7 +173,7 @@ group.values = []; // add values - for (var j = 0; j < end - start; j++) { + for (var j = 0; j < limit; j++) { // add default x values group.values[j] = { x : parseInt(j) + start @@ -184,7 +193,7 @@ // check if auto block is requested if (column.index == 'auto') { - for (var j = start; j < end; j++) { + for (var j = 0; j < limit; j++) { // get value dictionary var value = group.values[j]; @@ -197,7 +206,7 @@ var column_data = this.cache[block_id]; // go through column - for (var j = start; j < end; j++) { + for (var j = 0; j < limit; j++) { // get value dictionary var value = group.values[j]; 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 commits-noreply＠bitbucket.org 22 May '14

22 May '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1830e34c80c0/ Changeset: 1830e34c80c0 Branch: next-stable User: davebgx Date: 2014-05-22 16:59:18 Summary: Enable running the create_users and create_categories scripts via run_tool_shed.sh Affected #: 7 files diff -r f0a5e3666e844d907e7ef3c7fc4e23a443ba65d1 -r 1830e34c80c086696f83383871b6027f3b44ea8b lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh --- /dev/null +++ b/lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh @@ -0,0 +1,100 @@ +#!/bin/bash + +stop_err() { + echo $1 + python ./scripts/paster.py serve tool_shed_wsgi.ini --pid-file=tool_shed_bootstrap.pid --log-file=tool_shed_bootstrap.log --stop-daemon + exit 1 +} + +tool_shed=`./lib/tool_shed/scripts/bootstrap_tool_shed/parse_run_sh_args.sh $@` + +if [ $? -ne 0 ] ; then + exit 0 +fi + +log_file="lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap.log" + +database_result=`python ./lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py --execute check_db --config_file tool_shed_wsgi.ini` + +if [ $? -ne 0 ] ; then + stop_err "Unable to bootstrap tool shed. $database_result" +fi + +echo "Bootstrapping from tool shed at $tool_shed." +echo -n "Creating database... " +python scripts/create_db.py tool_shed + +if [ $? -eq 0 ] ; then + echo "done." +else + stop_err "failed." +fi + +if [ $? -eq 0 ] ; then + user_auth=`python ./lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py --execute admin_user_info --config_file tool_shed_wsgi.ini` + local_shed_url=`python ./lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py --execute get_url --config_file tool_shed_wsgi.ini` +fi + +admin_user_name=`echo $user_auth | awk 'BEGIN { FS="__SEP__" } ; { print \$1 }'` +admin_user_email=`echo $user_auth | awk 'BEGIN { FS="__SEP__" } ; { print \$2 }'` +admin_user_password=`echo $user_auth | awk 'BEGIN { FS="__SEP__" } ; { print \$3 }'` + +echo -n "Creating user '$admin_user_name' with email address '$admin_user_email'..." + +python lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py tool_shed_wsgi.ini >> $log_file + +echo " done." + +sed -i "s/#admin_users = user1@example.org,user2@example.org/admin_users = $admin_user_email/" tool_shed_wsgi.ini +echo -n "Starting tool shed in order to populate users and categories... " + +if [ -f tool_shed_bootstrap.pid ] ; then + stop_err "A bootstrap process is already running." +fi + +python ./scripts/paster.py serve tool_shed_wsgi.ini --pid-file=tool_shed_bootstrap.pid --log-file=tool_shed_bootstrap.log --daemon > /dev/null + +shed_pid=`cat tool_shed_bootstrap.pid` + +while : ; do + tail -n 1 tool_shed_bootstrap.log | grep -q "Removing PID file tool_shed_webapp.pid" + if [ $? -eq 0 ] ; then + echo "failed." + echo "More information about this failure may be found in the following log snippet from tool_shed_bootstrap.log:" + echo "========================================" + tail -n 40 tool_shed_bootstrap.log + echo "========================================" + stop_err " " + fi + tail -n 2 tool_shed_bootstrap.log | grep -q "Starting server in PID $shed_pid" + if [ $? -eq 0 ] ; then + echo "done." + break + fi +done + +echo -n "Retrieving admin user's API key..." +api_key_json=`curl -s --user $admin_user_email:$admin_user_password $local_shed_url/api/authenticate/baseauth/` +api_key=`echo $api_key_json | grep api_key | awk 'BEGIN { FS="\"" } ; { print \$4 }' | sed 's/\\s\+//'` + +if [[ -z $api_key && ${api_key+x} ]] ; then + stop_err "Error getting API key for user $admin_user_email." +fi + +echo " done." + +if [ $? -eq 0 ] ; then + echo -n "Creating users... " + python lib/tool_shed/scripts/api/create_users.py -a $api_key -f $tool_shed -t $local_shed_url >> $log_file + echo "done." + echo -n "Creating categories... " + python lib/tool_shed/scripts/api/create_categories.py -a $api_key -f $tool_shed -t $local_shed_url >> $log_file + echo "done." +else + stop_err "Error getting API key from local tool shed." +fi + +echo "Bootstrap complete, shutting down temporary tool shed process. A log has been saved to tool_shed_bootstrap.log" +python ./scripts/paster.py serve tool_shed_wsgi.ini --pid-file=tool_shed_bootstrap.pid --log-file=tool_shed_bootstrap.log --stop-daemon + +exit 0 \ No newline at end of file diff -r f0a5e3666e844d907e7ef3c7fc4e23a443ba65d1 -r 1830e34c80c086696f83383871b6027f3b44ea8b lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py --- /dev/null +++ b/lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py @@ -0,0 +1,130 @@ +#!/usr/bin/python +import argparse +import ConfigParser +import os +import sys + +new_path = [ os.path.join( os.getcwd(), "lib" ) ] +new_path.extend( sys.path[1:] ) +sys.path = new_path + +from galaxy import eggs +eggs.require( "SQLAlchemy >= 0.4" ) +import galaxy.webapps.tool_shed.model.mapping as tool_shed_model +from sqlalchemy.exc import ProgrammingError +from sqlalchemy.exc import OperationalError + +from tool_shed.util import xml_util + +def check_db( config_parser ): + dburi = None + + if config_parser.has_option( 'app:main', 'database_connection' ): + dburi = config_parser.get( 'app:main', 'database_connection' ) + elif config_parser.has_option( 'app:main', 'database_file' ): + db_file = config_parser.get( 'app:main', 'database_file' ) + dburi = "sqlite:///%s?isolation_level=IMMEDIATE" % db_file + else: + print 'The database configuration setting is missing from the tool_shed_wsgi.ini file. Add this setting before attempting to bootstrap.' + exit(1) + + sa_session = None + + database_exists_message = 'The database configured for this Tool Shed is not new, so bootstrapping is not allowed. ' + database_exists_message += 'Create a new database that has not been migrated before attempting to bootstrap.' + + try: + model = tool_shed_model.init( config_parser.get( 'app:main', 'file_path' ), dburi, engine_options={}, create_tables=False ) + sa_session = model.context.current + print database_exists_message + exit(1) + except ProgrammingError, e: + pass + except OperationalError, e: + pass + + try: + if sa_session is not None: + result = sa_session.execute( 'SELECT version FROM migrate_version' ).first() + if result[0] >= 2: + print database_exists_message + exit(1) + else: + pass + except ProgrammingError, e: + pass + + if config_parser.has_option( 'app:main', 'hgweb_config_dir' ): + hgweb_config_parser = ConfigParser.ConfigParser() + hgweb_dir = config_parser.get( 'app:main', 'hgweb_config_dir' ) + hgweb_config_file = os.path.join( hgweb_dir, 'hgweb.config' ) + if not os.path.exists( hgweb_config_file ): + exit(0) + hgweb_config_parser.read( hgweb_config_file ) + configured_repos = hgweb_config_parser.items( 'paths' ) + if len( configured_repos ) >= 1: + message = "This Tool Shed's hgweb.config file contains entries, so bootstrapping is not allowed. Delete" + message += " the current hgweb.config file along with all associated repositories in the configured " + message += "location before attempting to boostrap." + print + exit(1) + else: + exit(0) + else: + exit(0) + + exit(0) + +def admin_user_info( config_parser ): + user_info_config = os.path.abspath( os.path.join( os.getcwd(), 'lib/tool_shed/scripts/bootstrap_tool_shed', 'user_info.xml' ) ) + tree, error_message = xml_util.parse_xml( user_info_config ) + if tree is None: + print "The XML file ", user_info_config, " seems to be invalid, using defaults." + email = 'admin(a)test.org' + password = 'testuser' + username = 'admin' + else: + root = tree.getroot() + for elem in root: + if elem.tag == 'email': + email = elem.text + elif elem.tag == 'password': + password = elem.text + elif elem.tag == 'username': + username = elem.text + print '%s__SEP__%s__SEP__%s' % ( username, email, password ) + return 0 + +def get_local_tool_shed_url( config_parser ): + port = '9009' + if config_parser.has_section( 'server:main' ): + if config_parser.has_option( 'server:main', 'port' ): + port = config_parser.get( 'server:main', 'port' ) + host = '127.0.0.1' + print 'http://%s:%s' % ( host, port ) + return 0 + +def main( args ): + config_parser = ConfigParser.ConfigParser() + + if os.path.exists( args.config ): + config_parser.read( args.config ) + else: + return 1 + + if args.method == 'check_db': + return check_db( config_parser ) + elif args.method == 'admin_user_info': + return admin_user_info( config_parser ) + elif args.method == 'get_url': + return get_local_tool_shed_url( config_parser ) + else: + return 1 + +parser = argparse.ArgumentParser() +parser.add_argument( '-c', '--config_file', dest='config', action='store', default='tool_shed_wsgi.ini' ) +parser.add_argument( '-e', '--execute', dest='method', action='store', default='check_db' ) +args = parser.parse_args() + +if __name__ == '__main__': + exit( main( args ) ) \ No newline at end of file diff -r f0a5e3666e844d907e7ef3c7fc4e23a443ba65d1 -r 1830e34c80c086696f83383871b6027f3b44ea8b lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py --- a/lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py +++ b/lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py @@ -125,7 +125,7 @@ return '' def validate_publicname( username ): - """""Validates the public username.""" + """Validates the public username.""" if len( username ) < 3: return "Public name must be at least 3 characters in length" if len( username ) > 255: @@ -154,5 +154,7 @@ if user is not None: api_key = create_api_key( app, user ) print "Created new user with public username '", user.username, ". An API key was also created and associated with the user." + exit(0) else: print "Problem creating a new user and an associated API key." + exit(1) diff -r f0a5e3666e844d907e7ef3c7fc4e23a443ba65d1 -r 1830e34c80c086696f83383871b6027f3b44ea8b lib/tool_shed/scripts/bootstrap_tool_shed/parse_run_sh_args.sh --- /dev/null +++ b/lib/tool_shed/scripts/bootstrap_tool_shed/parse_run_sh_args.sh @@ -0,0 +1,15 @@ +#!/bin/bash + +while (( $# )) ; do + case "$1" in + -bootstrap_from_tool_shed|--bootstrap_from_tool_shed) + bootstrap="true" + tool_shed=$2 + echo $tool_shed + exit 0 + break + ;; + esac + shift 1 +done +exit 1 \ No newline at end of file diff -r f0a5e3666e844d907e7ef3c7fc4e23a443ba65d1 -r 1830e34c80c086696f83383871b6027f3b44ea8b run.sh --- a/run.sh +++ b/run.sh @@ -5,41 +5,7 @@ python ./scripts/check_python.py [ $? -ne 0 ] && exit 1 -SAMPLES=" - community_wsgi.ini.sample - datatypes_conf.xml.sample - external_service_types_conf.xml.sample - migrated_tools_conf.xml.sample - reports_wsgi.ini.sample - shed_tool_conf.xml.sample - tool_conf.xml.sample - shed_tool_data_table_conf.xml.sample - tool_data_table_conf.xml.sample - tool_sheds_conf.xml.sample - data_manager_conf.xml.sample - shed_data_manager_conf.xml.sample - openid_conf.xml.sample - job_metrics_conf.xml.sample - universe_wsgi.ini.sample - tool-data/shared/ncbi/builds.txt.sample - tool-data/shared/ensembl/builds.txt.sample - tool-data/shared/ucsc/builds.txt.sample - tool-data/shared/ucsc/publicbuilds.txt.sample - tool-data/shared/ucsc/ucsc_build_sites.txt.sample - tool-data/shared/igv/igv_build_sites.txt.sample - tool-data/shared/rviewer/rviewer_build_sites.txt.sample - tool-data/*.sample - static/welcome.html.sample -" - -# Create any missing config/location files -for sample in $SAMPLES; do - file=`echo $sample | sed -e 's/\.sample$//'` - if [ ! -f "$file" -a -f "$sample" ]; then - echo "Initializing $file from `basename $sample`" - cp $sample $file - fi -done +./scripts/copy_sample_files.sh if [ -n "$GALAXY_UNIVERSE_CONFIG_DIR" ]; then python ./scripts/build_universe_config.py "$GALAXY_UNIVERSE_CONFIG_DIR" diff -r f0a5e3666e844d907e7ef3c7fc4e23a443ba65d1 -r 1830e34c80c086696f83383871b6027f3b44ea8b run_tool_shed.sh --- a/run_tool_shed.sh +++ b/run_tool_shed.sh @@ -2,37 +2,14 @@ cd `dirname $0` -SAMPLES=" - tool_shed_wsgi.ini.sample - datatypes_conf.xml.sample - external_service_types_conf.xml.sample - migrated_tools_conf.xml.sample - reports_wsgi.ini.sample - shed_tool_conf.xml.sample - tool_conf.xml.sample - shed_tool_data_table_conf.xml.sample - tool_data_table_conf.xml.sample - tool_sheds_conf.xml.sample - openid_conf.xml.sample - universe_wsgi.ini.sample - lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml.sample - tool-data/shared/ncbi/builds.txt.sample - tool-data/shared/ensembl/builds.txt.sample - tool-data/shared/ucsc/builds.txt.sample - tool-data/shared/ucsc/publicbuilds.txt.sample - tool-data/shared/igv/igv_build_sites.txt.sample - tool-data/shared/rviewer/rviewer_build_sites.txt.sample - tool-data/*.sample - static/welcome.html.sample -" +./scripts/copy_sample_files.sh -# Create any missing config/location files -for sample in $SAMPLES; do - file=`echo $sample | sed -e 's/\.sample$//'` - if [ ! -f "$file" -a -f "$sample" ]; then - echo "Initializing $file from `basename $sample`" - cp $sample $file - fi -done +tool_shed=`./lib/tool_shed/scripts/bootstrap_tool_shed/parse_run_sh_args.sh $@` +args=$@ -python ./scripts/paster.py serve tool_shed_wsgi.ini --pid-file=tool_shed_webapp.pid --log-file=tool_shed_webapp.log $@ +if [ $? -eq 0 ] ; then + bash ./lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh $@ + args=`echo $@ | sed "s#-\?-bootstrap_from_tool_shed $tool_shed##"` +fi + +python ./scripts/paster.py serve tool_shed_wsgi.ini --pid-file=tool_shed_webapp.pid --log-file=tool_shed_webapp.log $args diff -r f0a5e3666e844d907e7ef3c7fc4e23a443ba65d1 -r 1830e34c80c086696f83383871b6027f3b44ea8b scripts/copy_sample_files.sh --- /dev/null +++ b/scripts/copy_sample_files.sh @@ -0,0 +1,39 @@ +#!/bin/bash + +SAMPLES=" + tool_shed_wsgi.ini.sample + datatypes_conf.xml.sample + external_service_types_conf.xml.sample + migrated_tools_conf.xml.sample + reports_wsgi.ini.sample + shed_tool_conf.xml.sample + tool_conf.xml.sample + shed_tool_data_table_conf.xml.sample + tool_data_table_conf.xml.sample + tool_sheds_conf.xml.sample + data_manager_conf.xml.sample + shed_data_manager_conf.xml.sample + openid_conf.xml.sample + job_metrics_conf.xml.sample + universe_wsgi.ini.sample + lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml.sample + tool-data/shared/ncbi/builds.txt.sample + tool-data/shared/ensembl/builds.txt.sample + tool-data/shared/ucsc/builds.txt.sample + tool-data/shared/ucsc/publicbuilds.txt.sample + tool-data/shared/ucsc/ucsc_build_sites.txt.sample + tool-data/shared/igv/igv_build_sites.txt.sample + tool-data/shared/rviewer/rviewer_build_sites.txt.sample + tool-data/*.sample + static/welcome.html.sample +" + +# Create any missing config/location files +for sample in $SAMPLES; do + file=${sample%.sample} + if [ ! -f "$file" -a -f "$sample" ]; then + echo "Initializing $file from `basename $sample`" + cp $sample $file + fi +done + https://bitbucket.org/galaxy/galaxy-central/commits/e959799971fc/ Changeset: e959799971fc User: davebgx Date: 2014-05-22 18:41:13 Summary: Merge next-stable. Affected #: 0 files 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: 3 new changesets
by commits-noreply＠bitbucket.org 22 May '14

22 May '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8e0034733cf9/ Changeset: 8e0034733cf9 Branch: next-stable User: jmchilton Date: 2014-05-22 18:01:04 Summary: Fix GUI for f24bb5d. Affected #: 1 file diff -r 316db249f068ded4e541415232b480250c7cdd56 -r 8e0034733cf936643078de18f77394256e55001d static/scripts/mvc/dataset/hda-model.js --- a/static/scripts/mvc/dataset/hda-model.js +++ b/static/scripts/mvc/dataset/hda-model.js @@ -667,8 +667,8 @@ if( ids.length != 2 ){ // TODO: Do something... } - element_identifiers.push( { name: "left", src: "hda", id: ids[ 0 ] } ); - element_identifiers.push( { name: "right", src: "hda", id: ids[ 1 ] } ); + element_identifiers.push( { name: "forward", src: "hda", id: ids[ 0 ] } ); + element_identifiers.push( { name: "reverse", src: "hda", id: ids[ 1 ] } ); name = "New Dataset Pair"; } options.data = {type: "dataset_collection", https://bitbucket.org/galaxy/galaxy-central/commits/f0a5e3666e84/ Changeset: f0a5e3666e84 Branch: next-stable User: jmchilton Date: 2014-05-22 18:02:05 Summary: Pack scripts. Affected #: 1 file diff -r 8e0034733cf936643078de18f77394256e55001d -r f0a5e3666e844d907e7ef3c7fc4e23a443ba65d1 static/scripts/packed/mvc/dataset/hda-model.js --- a/static/scripts/packed/mvc/dataset/hda-model.js +++ b/static/scripts/packed/mvc/dataset/hda-model.js @@ -1,1 +1,1 @@ -define(["mvc/base-mvc","utils/localization"],function(e,c){var a=Backbone.Model.extend(e.LoggableMixin).extend({urlRoot:galaxy_config.root+"api/histories/",url:function(){return this.urlRoot+this.get("history_id")+"/contents/"+this.get("history_content_type")+"s/"+this.get("id")},hidden:function(){return !this.get("visible")},"delete":function f(m){if(this.get("deleted")){return jQuery.when()}return this.save({deleted:true},m)},undelete:function i(m){if(!this.get("deleted")||this.get("purged")){return jQuery.when()}return this.save({deleted:false},m)},hide:function d(m){if(!this.get("visible")){return jQuery.when()}return this.save({visible:false},m)},unhide:function h(m){if(this.get("visible")){return jQuery.when()}return this.save({visible:true},m)},isVisible:function(n,o){var m=true;if((!n)&&(this.get("deleted")||this.get("purged"))){m=false}if((!o)&&(!this.get("visible"))){m=false}return m},searchAttribute:function(o,m){var n=this.get(o);if(!m||(n===undefined||n===null)){return false}if(_.isArray(n)){return this._searchArrayAttribute(n,m)}return(n.toString().toLowerCase().indexOf(m.toLowerCase())!==-1)},_searchArrayAttribute:function(n,m){m=m.toLowerCase();return _.any(n,function(o){return(o.toString().toLowerCase().indexOf(m.toLowerCase())!==-1)})},search:function(m){var n=this;return _.filter(this.searchAttributes,function(o){return n.searchAttribute(o,m)})},matches:function(n){var p="=",m=n.split(p);if(m.length>=2){var o=m[0];o=this.searchAliases[o]||o;return this.searchAttribute(o,m[1])}return !!this.search(n).length},matchesAll:function(n){var m=this;n=n.match(/(".*"|\w*=".*"|\S*)/g).filter(function(o){return !!o});return _.all(n,function(o){o=o.replace(/"/g,"");return m.matches(o)})}});var l=a.extend({defaults:{history_id:null,model_class:"HistoryDatasetAssociation",history_content_type:"dataset",hid:0,id:null,name:"(unnamed dataset)",state:"new",deleted:false,visible:true,accessible:true,purged:false,data_type:"",file_size:0,file_ext:"",meta_files:[],misc_blurb:"",misc_info:"",tags:[],annotation:""},urls:function(){var n=this.get("id");if(!n){return{}}var m={purge:galaxy_config.root+"datasets/"+n+"/purge_async",display:galaxy_config.root+"datasets/"+n+"/display/?preview=True",edit:galaxy_config.root+"datasets/"+n+"/edit",download:galaxy_config.root+"datasets/"+n+"/display?to_ext="+this.get("file_ext"),report_error:galaxy_config.root+"dataset/errors?id="+n,rerun:galaxy_config.root+"tool_runner/rerun?id="+n,show_params:galaxy_config.root+"datasets/"+n+"/show_params",visualization:galaxy_config.root+"visualization",annotation:{get:galaxy_config.root+"dataset/get_annotation_async?id="+n,set:galaxy_config.root+"dataset/annotate_async?id="+n},meta_download:galaxy_config.root+"dataset/get_metadata_file?hda_id="+n+"&metadata_name="};return m},initialize:function(m){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",l.STATES.NOT_VIEWABLE)}this._setUpListeners()},_setUpListeners:function(){this.on("change:state",function(n,m){this.log(this+" has changed state:",n,m);if(this.inReadyState()){this.trigger("state:ready",n,m,this.previous("state"))}})},isDeletedOrPurged:function(){return(this.get("deleted")||this.get("purged"))},inReadyState:function(){var m=_.contains(l.READY_STATES,this.get("state"));return(this.isDeletedOrPurged()||m)},hasDetails:function(){return _.has(this.attributes,"genome_build")},hasData:function(){return(this.get("file_size")>0)},"delete":function f(m){if(this.get("deleted")){return jQuery.when()}return this.save({deleted:true},m)},undelete:function i(m){if(!this.get("deleted")||this.get("purged")){return jQuery.when()}return this.save({deleted:false},m)},hide:function d(m){if(!this.get("visible")){return jQuery.when()}return this.save({visible:false},m)},unhide:function h(m){if(this.get("visible")){return jQuery.when()}return this.save({visible:true},m)},purge:function g(m){if(this.get("purged")){return jQuery.when()}m=m||{};m.url=galaxy_config.root+"datasets/"+this.get("id")+"/purge_async";var n=this,o=jQuery.ajax(m);o.done(function(r,p,q){n.set({deleted:true,purged:true})});o.fail(function(t,p,s){var q=c("Unable to purge dataset");var r=("Removal of datasets by users is not allowed in this Galaxy instance");if(t.responseJSON&&t.responseJSON.error){q=t.responseJSON.error}else{if(t.responseText.indexOf(r)!==-1){q=r}}t.responseText=q;n.trigger("error",n,t,m,c(q),{error:q})});return o},searchAttributes:["name","file_ext","genome_build","misc_blurb","misc_info","annotation","tags"],searchAliases:{title:"name",format:"file_ext",database:"genome_build",blurb:"misc_blurb",description:"misc_blurb",info:"misc_info",tag:"tags"},toString:function(){var m=this.get("id")||"";if(this.get("name")){m=this.get("hid")+' :"'+this.get("name")+'",'+m}return"HDA("+m+")"}});l.STATES={UPLOAD:"upload",QUEUED:"queued",RUNNING:"running",SETTING_METADATA:"setting_metadata",NEW:"new",EMPTY:"empty",OK:"ok",PAUSED:"paused",FAILED_METADATA:"failed_metadata",NOT_VIEWABLE:"noPermission",DISCARDED:"discarded",ERROR:"error"};l.READY_STATES=[l.STATES.OK,l.STATES.EMPTY,l.STATES.PAUSED,l.STATES.FAILED_METADATA,l.STATES.NOT_VIEWABLE,l.STATES.DISCARDED,l.STATES.ERROR];l.NOT_READY_STATES=[l.STATES.UPLOAD,l.STATES.QUEUED,l.STATES.RUNNING,l.STATES.SETTING_METADATA,l.STATES.NEW];var b=Backbone.Collection.extend(e.LoggableMixin).extend({model:function(n,m){if(n.history_content_type=="dataset"){return new l(n,m)}else{if(n.history_content_type=="dataset_collection"){return new j(n,m)}else{}}},urlRoot:galaxy_config.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},initialize:function(n,m){m=m||{};this.historyId=m.historyId},ids:function(){return this.map(function(m){return m.id})},notReady:function(){return this.filter(function(m){return !m.inReadyState()})},running:function(){var m=[];this.each(function(n){if(!n.inReadyState()){m.push(n.get("id"))}});return m},getByHid:function(m){return _.first(this.filter(function(n){return n.get("hid")===m}))},getVisible:function(m,p,o){o=o||[];var n=new b(this.filter(function(q){return q.isVisible(m,p)}));_.each(o,function(q){if(!_.isFunction(q)){return}n=new b(n.filter(q))});return n},haveDetails:function(){return this.all(function(m){return m.hasDetails()})},fetchAllDetails:function(n){n=n||{};var m={details:"all"};n.data=(n.data)?(_.extend(n.data,m)):(m);return this.fetch(n)},ajaxQueue:function(p,o){var n=jQuery.Deferred(),m=this.length,r=[];if(!m){n.resolve([]);return n}var q=this.chain().reverse().map(function(t,s){return function(){var u=p.call(t,o);u.done(function(v){n.notify({curr:s,total:m,response:v,model:t})});u.always(function(v){r.push(v);if(q.length){q.shift()()}else{n.resolve(r)}})}}).value();q.shift()();return n},matches:function(m){return this.filter(function(n){return n.matches(m)})},set:function(o,m){var n=this;o=_.map(o,function(q){var r=n.get(q.id);if(!r){return q}var p=r.toJSON();_.extend(p,q);return p});Backbone.Collection.prototype.set.call(this,o,m)},promoteToHistoryDatasetCollection:function k(r,p,n){n=n||{};n.url=this.url();n.type="POST";var t=p;var q=[],m=null;if(p=="list"){this.chain().each(function(w){var u=w.attributes.name;var x=w.id;var v=w.attributes.history_content_type;if(v=="dataset"){if(t!="list"){console.log("Invalid collection type")}q.push({name:u,src:"hda",id:x})}else{if(t=="list"){t="list:"+w.attributes.collection_type}else{if(t!="list:"+w.attributes.collection_type){console.log("Invalid collection type")}}q.push({name:u,src:"hdca",id:x})}});m="New Dataset List"}else{if(p=="paired"){var o=this.ids();if(o.length!=2){}q.push({name:"left",src:"hda",id:o[0]});q.push({name:"right",src:"hda",id:o[1]});m="New Dataset Pair"}}n.data={type:"dataset_collection",name:m,collection_type:t,element_identifiers:JSON.stringify(q),};var s=jQuery.ajax(n);s.done(function(w,u,v){r.refresh()});s.fail(function(w,u,v){if(w.responseJSON&&w.responseJSON.error){error=w.responseJSON.error}else{error=w.responseJSON}w.responseText=error});return s},toString:function(){return(["HDACollection(",[this.historyId,this.length].join(),")"].join(""))}});var j=a.extend({defaults:{history_id:null,model_class:"HistoryDatasetCollectionAssociation",history_content_type:"dataset_collection",hid:0,id:null,name:"(unnamed dataset collection)",state:"ok",accessible:true,deleted:false,visible:true,purged:false,tags:[],annotation:""},urls:function(){},inReadyState:function(){return true},searchAttributes:["name"],searchAliases:{title:"name"},});return{HistoryDatasetAssociation:l,HDACollection:b}}); \ No newline at end of file +define(["mvc/base-mvc","utils/localization"],function(e,c){var a=Backbone.Model.extend(e.LoggableMixin).extend({urlRoot:galaxy_config.root+"api/histories/",url:function(){return this.urlRoot+this.get("history_id")+"/contents/"+this.get("history_content_type")+"s/"+this.get("id")},hidden:function(){return !this.get("visible")},"delete":function f(m){if(this.get("deleted")){return jQuery.when()}return this.save({deleted:true},m)},undelete:function i(m){if(!this.get("deleted")||this.get("purged")){return jQuery.when()}return this.save({deleted:false},m)},hide:function d(m){if(!this.get("visible")){return jQuery.when()}return this.save({visible:false},m)},unhide:function h(m){if(this.get("visible")){return jQuery.when()}return this.save({visible:true},m)},isVisible:function(n,o){var m=true;if((!n)&&(this.get("deleted")||this.get("purged"))){m=false}if((!o)&&(!this.get("visible"))){m=false}return m},searchAttribute:function(o,m){var n=this.get(o);if(!m||(n===undefined||n===null)){return false}if(_.isArray(n)){return this._searchArrayAttribute(n,m)}return(n.toString().toLowerCase().indexOf(m.toLowerCase())!==-1)},_searchArrayAttribute:function(n,m){m=m.toLowerCase();return _.any(n,function(o){return(o.toString().toLowerCase().indexOf(m.toLowerCase())!==-1)})},search:function(m){var n=this;return _.filter(this.searchAttributes,function(o){return n.searchAttribute(o,m)})},matches:function(n){var p="=",m=n.split(p);if(m.length>=2){var o=m[0];o=this.searchAliases[o]||o;return this.searchAttribute(o,m[1])}return !!this.search(n).length},matchesAll:function(n){var m=this;n=n.match(/(".*"|\w*=".*"|\S*)/g).filter(function(o){return !!o});return _.all(n,function(o){o=o.replace(/"/g,"");return m.matches(o)})}});var l=a.extend({defaults:{history_id:null,model_class:"HistoryDatasetAssociation",history_content_type:"dataset",hid:0,id:null,name:"(unnamed dataset)",state:"new",deleted:false,visible:true,accessible:true,purged:false,data_type:"",file_size:0,file_ext:"",meta_files:[],misc_blurb:"",misc_info:"",tags:[],annotation:""},urls:function(){var n=this.get("id");if(!n){return{}}var m={purge:galaxy_config.root+"datasets/"+n+"/purge_async",display:galaxy_config.root+"datasets/"+n+"/display/?preview=True",edit:galaxy_config.root+"datasets/"+n+"/edit",download:galaxy_config.root+"datasets/"+n+"/display?to_ext="+this.get("file_ext"),report_error:galaxy_config.root+"dataset/errors?id="+n,rerun:galaxy_config.root+"tool_runner/rerun?id="+n,show_params:galaxy_config.root+"datasets/"+n+"/show_params",visualization:galaxy_config.root+"visualization",annotation:{get:galaxy_config.root+"dataset/get_annotation_async?id="+n,set:galaxy_config.root+"dataset/annotate_async?id="+n},meta_download:galaxy_config.root+"dataset/get_metadata_file?hda_id="+n+"&metadata_name="};return m},initialize:function(m){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",l.STATES.NOT_VIEWABLE)}this._setUpListeners()},_setUpListeners:function(){this.on("change:state",function(n,m){this.log(this+" has changed state:",n,m);if(this.inReadyState()){this.trigger("state:ready",n,m,this.previous("state"))}})},isDeletedOrPurged:function(){return(this.get("deleted")||this.get("purged"))},inReadyState:function(){var m=_.contains(l.READY_STATES,this.get("state"));return(this.isDeletedOrPurged()||m)},hasDetails:function(){return _.has(this.attributes,"genome_build")},hasData:function(){return(this.get("file_size")>0)},"delete":function f(m){if(this.get("deleted")){return jQuery.when()}return this.save({deleted:true},m)},undelete:function i(m){if(!this.get("deleted")||this.get("purged")){return jQuery.when()}return this.save({deleted:false},m)},hide:function d(m){if(!this.get("visible")){return jQuery.when()}return this.save({visible:false},m)},unhide:function h(m){if(this.get("visible")){return jQuery.when()}return this.save({visible:true},m)},purge:function g(m){if(this.get("purged")){return jQuery.when()}m=m||{};m.url=galaxy_config.root+"datasets/"+this.get("id")+"/purge_async";var n=this,o=jQuery.ajax(m);o.done(function(r,p,q){n.set({deleted:true,purged:true})});o.fail(function(t,p,s){var q=c("Unable to purge dataset");var r=("Removal of datasets by users is not allowed in this Galaxy instance");if(t.responseJSON&&t.responseJSON.error){q=t.responseJSON.error}else{if(t.responseText.indexOf(r)!==-1){q=r}}t.responseText=q;n.trigger("error",n,t,m,c(q),{error:q})});return o},searchAttributes:["name","file_ext","genome_build","misc_blurb","misc_info","annotation","tags"],searchAliases:{title:"name",format:"file_ext",database:"genome_build",blurb:"misc_blurb",description:"misc_blurb",info:"misc_info",tag:"tags"},toString:function(){var m=this.get("id")||"";if(this.get("name")){m=this.get("hid")+' :"'+this.get("name")+'",'+m}return"HDA("+m+")"}});l.STATES={UPLOAD:"upload",QUEUED:"queued",RUNNING:"running",SETTING_METADATA:"setting_metadata",NEW:"new",EMPTY:"empty",OK:"ok",PAUSED:"paused",FAILED_METADATA:"failed_metadata",NOT_VIEWABLE:"noPermission",DISCARDED:"discarded",ERROR:"error"};l.READY_STATES=[l.STATES.OK,l.STATES.EMPTY,l.STATES.PAUSED,l.STATES.FAILED_METADATA,l.STATES.NOT_VIEWABLE,l.STATES.DISCARDED,l.STATES.ERROR];l.NOT_READY_STATES=[l.STATES.UPLOAD,l.STATES.QUEUED,l.STATES.RUNNING,l.STATES.SETTING_METADATA,l.STATES.NEW];var b=Backbone.Collection.extend(e.LoggableMixin).extend({model:function(n,m){if(n.history_content_type=="dataset"){return new l(n,m)}else{if(n.history_content_type=="dataset_collection"){return new j(n,m)}else{}}},urlRoot:galaxy_config.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},initialize:function(n,m){m=m||{};this.historyId=m.historyId},ids:function(){return this.map(function(m){return m.id})},notReady:function(){return this.filter(function(m){return !m.inReadyState()})},running:function(){var m=[];this.each(function(n){if(!n.inReadyState()){m.push(n.get("id"))}});return m},getByHid:function(m){return _.first(this.filter(function(n){return n.get("hid")===m}))},getVisible:function(m,p,o){o=o||[];var n=new b(this.filter(function(q){return q.isVisible(m,p)}));_.each(o,function(q){if(!_.isFunction(q)){return}n=new b(n.filter(q))});return n},haveDetails:function(){return this.all(function(m){return m.hasDetails()})},fetchAllDetails:function(n){n=n||{};var m={details:"all"};n.data=(n.data)?(_.extend(n.data,m)):(m);return this.fetch(n)},ajaxQueue:function(p,o){var n=jQuery.Deferred(),m=this.length,r=[];if(!m){n.resolve([]);return n}var q=this.chain().reverse().map(function(t,s){return function(){var u=p.call(t,o);u.done(function(v){n.notify({curr:s,total:m,response:v,model:t})});u.always(function(v){r.push(v);if(q.length){q.shift()()}else{n.resolve(r)}})}}).value();q.shift()();return n},matches:function(m){return this.filter(function(n){return n.matches(m)})},set:function(o,m){var n=this;o=_.map(o,function(q){var r=n.get(q.id);if(!r){return q}var p=r.toJSON();_.extend(p,q);return p});Backbone.Collection.prototype.set.call(this,o,m)},promoteToHistoryDatasetCollection:function k(r,p,n){n=n||{};n.url=this.url();n.type="POST";var t=p;var q=[],m=null;if(p=="list"){this.chain().each(function(w){var u=w.attributes.name;var x=w.id;var v=w.attributes.history_content_type;if(v=="dataset"){if(t!="list"){console.log("Invalid collection type")}q.push({name:u,src:"hda",id:x})}else{if(t=="list"){t="list:"+w.attributes.collection_type}else{if(t!="list:"+w.attributes.collection_type){console.log("Invalid collection type")}}q.push({name:u,src:"hdca",id:x})}});m="New Dataset List"}else{if(p=="paired"){var o=this.ids();if(o.length!=2){}q.push({name:"forward",src:"hda",id:o[0]});q.push({name:"reverse",src:"hda",id:o[1]});m="New Dataset Pair"}}n.data={type:"dataset_collection",name:m,collection_type:t,element_identifiers:JSON.stringify(q),};var s=jQuery.ajax(n);s.done(function(w,u,v){r.refresh()});s.fail(function(w,u,v){if(w.responseJSON&&w.responseJSON.error){error=w.responseJSON.error}else{error=w.responseJSON}w.responseText=error});return s},toString:function(){return(["HDACollection(",[this.historyId,this.length].join(),")"].join(""))}});var j=a.extend({defaults:{history_id:null,model_class:"HistoryDatasetCollectionAssociation",history_content_type:"dataset_collection",hid:0,id:null,name:"(unnamed dataset collection)",state:"ok",accessible:true,deleted:false,visible:true,purged:false,tags:[],annotation:""},urls:function(){},inReadyState:function(){return true},searchAttributes:["name"],searchAliases:{title:"name"},});return{HistoryDatasetAssociation:l,HDACollection:b}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/cc19c4caa043/ Changeset: cc19c4caa043 User: jmchilton Date: 2014-05-22 18:02:17 Summary: Merge next-stable. Affected #: 2 files diff -r 21a66ac74e37c80fe6d5a7c44988f83db5413d87 -r cc19c4caa0434bd871b390a64113ad735c4ba223 static/scripts/mvc/dataset/hda-model.js --- a/static/scripts/mvc/dataset/hda-model.js +++ b/static/scripts/mvc/dataset/hda-model.js @@ -667,8 +667,8 @@ if( ids.length != 2 ){ // TODO: Do something... } - element_identifiers.push( { name: "left", src: "hda", id: ids[ 0 ] } ); - element_identifiers.push( { name: "right", src: "hda", id: ids[ 1 ] } ); + element_identifiers.push( { name: "forward", src: "hda", id: ids[ 0 ] } ); + element_identifiers.push( { name: "reverse", src: "hda", id: ids[ 1 ] } ); name = "New Dataset Pair"; } options.data = {type: "dataset_collection", diff -r 21a66ac74e37c80fe6d5a7c44988f83db5413d87 -r cc19c4caa0434bd871b390a64113ad735c4ba223 static/scripts/packed/mvc/dataset/hda-model.js --- a/static/scripts/packed/mvc/dataset/hda-model.js +++ b/static/scripts/packed/mvc/dataset/hda-model.js @@ -1,1 +1,1 @@ -define(["mvc/base-mvc","utils/localization"],function(e,c){var a=Backbone.Model.extend(e.LoggableMixin).extend({urlRoot:galaxy_config.root+"api/histories/",url:function(){return this.urlRoot+this.get("history_id")+"/contents/"+this.get("history_content_type")+"s/"+this.get("id")},hidden:function(){return !this.get("visible")},"delete":function f(m){if(this.get("deleted")){return jQuery.when()}return this.save({deleted:true},m)},undelete:function i(m){if(!this.get("deleted")||this.get("purged")){return jQuery.when()}return this.save({deleted:false},m)},hide:function d(m){if(!this.get("visible")){return jQuery.when()}return this.save({visible:false},m)},unhide:function h(m){if(this.get("visible")){return jQuery.when()}return this.save({visible:true},m)},isVisible:function(n,o){var m=true;if((!n)&&(this.get("deleted")||this.get("purged"))){m=false}if((!o)&&(!this.get("visible"))){m=false}return m},searchAttribute:function(o,m){var n=this.get(o);if(!m||(n===undefined||n===null)){return false}if(_.isArray(n)){return this._searchArrayAttribute(n,m)}return(n.toString().toLowerCase().indexOf(m.toLowerCase())!==-1)},_searchArrayAttribute:function(n,m){m=m.toLowerCase();return _.any(n,function(o){return(o.toString().toLowerCase().indexOf(m.toLowerCase())!==-1)})},search:function(m){var n=this;return _.filter(this.searchAttributes,function(o){return n.searchAttribute(o,m)})},matches:function(n){var p="=",m=n.split(p);if(m.length>=2){var o=m[0];o=this.searchAliases[o]||o;return this.searchAttribute(o,m[1])}return !!this.search(n).length},matchesAll:function(n){var m=this;n=n.match(/(".*"|\w*=".*"|\S*)/g).filter(function(o){return !!o});return _.all(n,function(o){o=o.replace(/"/g,"");return m.matches(o)})}});var l=a.extend({defaults:{history_id:null,model_class:"HistoryDatasetAssociation",history_content_type:"dataset",hid:0,id:null,name:"(unnamed dataset)",state:"new",deleted:false,visible:true,accessible:true,purged:false,data_type:"",file_size:0,file_ext:"",meta_files:[],misc_blurb:"",misc_info:"",tags:[],annotation:""},urls:function(){var n=this.get("id");if(!n){return{}}var m={purge:galaxy_config.root+"datasets/"+n+"/purge_async",display:galaxy_config.root+"datasets/"+n+"/display/?preview=True",edit:galaxy_config.root+"datasets/"+n+"/edit",download:galaxy_config.root+"datasets/"+n+"/display?to_ext="+this.get("file_ext"),report_error:galaxy_config.root+"dataset/errors?id="+n,rerun:galaxy_config.root+"tool_runner/rerun?id="+n,show_params:galaxy_config.root+"datasets/"+n+"/show_params",visualization:galaxy_config.root+"visualization",annotation:{get:galaxy_config.root+"dataset/get_annotation_async?id="+n,set:galaxy_config.root+"dataset/annotate_async?id="+n},meta_download:galaxy_config.root+"dataset/get_metadata_file?hda_id="+n+"&metadata_name="};return m},initialize:function(m){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",l.STATES.NOT_VIEWABLE)}this._setUpListeners()},_setUpListeners:function(){this.on("change:state",function(n,m){this.log(this+" has changed state:",n,m);if(this.inReadyState()){this.trigger("state:ready",n,m,this.previous("state"))}})},isDeletedOrPurged:function(){return(this.get("deleted")||this.get("purged"))},inReadyState:function(){var m=_.contains(l.READY_STATES,this.get("state"));return(this.isDeletedOrPurged()||m)},hasDetails:function(){return _.has(this.attributes,"genome_build")},hasData:function(){return(this.get("file_size")>0)},"delete":function f(m){if(this.get("deleted")){return jQuery.when()}return this.save({deleted:true},m)},undelete:function i(m){if(!this.get("deleted")||this.get("purged")){return jQuery.when()}return this.save({deleted:false},m)},hide:function d(m){if(!this.get("visible")){return jQuery.when()}return this.save({visible:false},m)},unhide:function h(m){if(this.get("visible")){return jQuery.when()}return this.save({visible:true},m)},purge:function g(m){if(this.get("purged")){return jQuery.when()}m=m||{};m.url=galaxy_config.root+"datasets/"+this.get("id")+"/purge_async";var n=this,o=jQuery.ajax(m);o.done(function(r,p,q){n.set({deleted:true,purged:true})});o.fail(function(t,p,s){var q=c("Unable to purge dataset");var r=("Removal of datasets by users is not allowed in this Galaxy instance");if(t.responseJSON&&t.responseJSON.error){q=t.responseJSON.error}else{if(t.responseText.indexOf(r)!==-1){q=r}}t.responseText=q;n.trigger("error",n,t,m,c(q),{error:q})});return o},searchAttributes:["name","file_ext","genome_build","misc_blurb","misc_info","annotation","tags"],searchAliases:{title:"name",format:"file_ext",database:"genome_build",blurb:"misc_blurb",description:"misc_blurb",info:"misc_info",tag:"tags"},toString:function(){var m=this.get("id")||"";if(this.get("name")){m=this.get("hid")+' :"'+this.get("name")+'",'+m}return"HDA("+m+")"}});l.STATES={UPLOAD:"upload",QUEUED:"queued",RUNNING:"running",SETTING_METADATA:"setting_metadata",NEW:"new",EMPTY:"empty",OK:"ok",PAUSED:"paused",FAILED_METADATA:"failed_metadata",NOT_VIEWABLE:"noPermission",DISCARDED:"discarded",ERROR:"error"};l.READY_STATES=[l.STATES.OK,l.STATES.EMPTY,l.STATES.PAUSED,l.STATES.FAILED_METADATA,l.STATES.NOT_VIEWABLE,l.STATES.DISCARDED,l.STATES.ERROR];l.NOT_READY_STATES=[l.STATES.UPLOAD,l.STATES.QUEUED,l.STATES.RUNNING,l.STATES.SETTING_METADATA,l.STATES.NEW];var b=Backbone.Collection.extend(e.LoggableMixin).extend({model:function(n,m){if(n.history_content_type=="dataset"){return new l(n,m)}else{if(n.history_content_type=="dataset_collection"){return new j(n,m)}else{}}},urlRoot:galaxy_config.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},initialize:function(n,m){m=m||{};this.historyId=m.historyId},ids:function(){return this.map(function(m){return m.id})},notReady:function(){return this.filter(function(m){return !m.inReadyState()})},running:function(){var m=[];this.each(function(n){if(!n.inReadyState()){m.push(n.get("id"))}});return m},getByHid:function(m){return _.first(this.filter(function(n){return n.get("hid")===m}))},getVisible:function(m,p,o){o=o||[];var n=new b(this.filter(function(q){return q.isVisible(m,p)}));_.each(o,function(q){if(!_.isFunction(q)){return}n=new b(n.filter(q))});return n},haveDetails:function(){return this.all(function(m){return m.hasDetails()})},fetchAllDetails:function(n){n=n||{};var m={details:"all"};n.data=(n.data)?(_.extend(n.data,m)):(m);return this.fetch(n)},ajaxQueue:function(p,o){var n=jQuery.Deferred(),m=this.length,r=[];if(!m){n.resolve([]);return n}var q=this.chain().reverse().map(function(t,s){return function(){var u=p.call(t,o);u.done(function(v){n.notify({curr:s,total:m,response:v,model:t})});u.always(function(v){r.push(v);if(q.length){q.shift()()}else{n.resolve(r)}})}}).value();q.shift()();return n},matches:function(m){return this.filter(function(n){return n.matches(m)})},set:function(o,m){var n=this;o=_.map(o,function(q){var r=n.get(q.id);if(!r){return q}var p=r.toJSON();_.extend(p,q);return p});Backbone.Collection.prototype.set.call(this,o,m)},promoteToHistoryDatasetCollection:function k(r,p,n){n=n||{};n.url=this.url();n.type="POST";var t=p;var q=[],m=null;if(p=="list"){this.chain().each(function(w){var u=w.attributes.name;var x=w.id;var v=w.attributes.history_content_type;if(v=="dataset"){if(t!="list"){console.log("Invalid collection type")}q.push({name:u,src:"hda",id:x})}else{if(t=="list"){t="list:"+w.attributes.collection_type}else{if(t!="list:"+w.attributes.collection_type){console.log("Invalid collection type")}}q.push({name:u,src:"hdca",id:x})}});m="New Dataset List"}else{if(p=="paired"){var o=this.ids();if(o.length!=2){}q.push({name:"left",src:"hda",id:o[0]});q.push({name:"right",src:"hda",id:o[1]});m="New Dataset Pair"}}n.data={type:"dataset_collection",name:m,collection_type:t,element_identifiers:JSON.stringify(q),};var s=jQuery.ajax(n);s.done(function(w,u,v){r.refresh()});s.fail(function(w,u,v){if(w.responseJSON&&w.responseJSON.error){error=w.responseJSON.error}else{error=w.responseJSON}w.responseText=error});return s},toString:function(){return(["HDACollection(",[this.historyId,this.length].join(),")"].join(""))}});var j=a.extend({defaults:{history_id:null,model_class:"HistoryDatasetCollectionAssociation",history_content_type:"dataset_collection",hid:0,id:null,name:"(unnamed dataset collection)",state:"ok",accessible:true,deleted:false,visible:true,purged:false,tags:[],annotation:""},urls:function(){},inReadyState:function(){return true},searchAttributes:["name"],searchAliases:{title:"name"},});return{HistoryDatasetAssociation:l,HDACollection:b}}); \ No newline at end of file +define(["mvc/base-mvc","utils/localization"],function(e,c){var a=Backbone.Model.extend(e.LoggableMixin).extend({urlRoot:galaxy_config.root+"api/histories/",url:function(){return this.urlRoot+this.get("history_id")+"/contents/"+this.get("history_content_type")+"s/"+this.get("id")},hidden:function(){return !this.get("visible")},"delete":function f(m){if(this.get("deleted")){return jQuery.when()}return this.save({deleted:true},m)},undelete:function i(m){if(!this.get("deleted")||this.get("purged")){return jQuery.when()}return this.save({deleted:false},m)},hide:function d(m){if(!this.get("visible")){return jQuery.when()}return this.save({visible:false},m)},unhide:function h(m){if(this.get("visible")){return jQuery.when()}return this.save({visible:true},m)},isVisible:function(n,o){var m=true;if((!n)&&(this.get("deleted")||this.get("purged"))){m=false}if((!o)&&(!this.get("visible"))){m=false}return m},searchAttribute:function(o,m){var n=this.get(o);if(!m||(n===undefined||n===null)){return false}if(_.isArray(n)){return this._searchArrayAttribute(n,m)}return(n.toString().toLowerCase().indexOf(m.toLowerCase())!==-1)},_searchArrayAttribute:function(n,m){m=m.toLowerCase();return _.any(n,function(o){return(o.toString().toLowerCase().indexOf(m.toLowerCase())!==-1)})},search:function(m){var n=this;return _.filter(this.searchAttributes,function(o){return n.searchAttribute(o,m)})},matches:function(n){var p="=",m=n.split(p);if(m.length>=2){var o=m[0];o=this.searchAliases[o]||o;return this.searchAttribute(o,m[1])}return !!this.search(n).length},matchesAll:function(n){var m=this;n=n.match(/(".*"|\w*=".*"|\S*)/g).filter(function(o){return !!o});return _.all(n,function(o){o=o.replace(/"/g,"");return m.matches(o)})}});var l=a.extend({defaults:{history_id:null,model_class:"HistoryDatasetAssociation",history_content_type:"dataset",hid:0,id:null,name:"(unnamed dataset)",state:"new",deleted:false,visible:true,accessible:true,purged:false,data_type:"",file_size:0,file_ext:"",meta_files:[],misc_blurb:"",misc_info:"",tags:[],annotation:""},urls:function(){var n=this.get("id");if(!n){return{}}var m={purge:galaxy_config.root+"datasets/"+n+"/purge_async",display:galaxy_config.root+"datasets/"+n+"/display/?preview=True",edit:galaxy_config.root+"datasets/"+n+"/edit",download:galaxy_config.root+"datasets/"+n+"/display?to_ext="+this.get("file_ext"),report_error:galaxy_config.root+"dataset/errors?id="+n,rerun:galaxy_config.root+"tool_runner/rerun?id="+n,show_params:galaxy_config.root+"datasets/"+n+"/show_params",visualization:galaxy_config.root+"visualization",annotation:{get:galaxy_config.root+"dataset/get_annotation_async?id="+n,set:galaxy_config.root+"dataset/annotate_async?id="+n},meta_download:galaxy_config.root+"dataset/get_metadata_file?hda_id="+n+"&metadata_name="};return m},initialize:function(m){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",l.STATES.NOT_VIEWABLE)}this._setUpListeners()},_setUpListeners:function(){this.on("change:state",function(n,m){this.log(this+" has changed state:",n,m);if(this.inReadyState()){this.trigger("state:ready",n,m,this.previous("state"))}})},isDeletedOrPurged:function(){return(this.get("deleted")||this.get("purged"))},inReadyState:function(){var m=_.contains(l.READY_STATES,this.get("state"));return(this.isDeletedOrPurged()||m)},hasDetails:function(){return _.has(this.attributes,"genome_build")},hasData:function(){return(this.get("file_size")>0)},"delete":function f(m){if(this.get("deleted")){return jQuery.when()}return this.save({deleted:true},m)},undelete:function i(m){if(!this.get("deleted")||this.get("purged")){return jQuery.when()}return this.save({deleted:false},m)},hide:function d(m){if(!this.get("visible")){return jQuery.when()}return this.save({visible:false},m)},unhide:function h(m){if(this.get("visible")){return jQuery.when()}return this.save({visible:true},m)},purge:function g(m){if(this.get("purged")){return jQuery.when()}m=m||{};m.url=galaxy_config.root+"datasets/"+this.get("id")+"/purge_async";var n=this,o=jQuery.ajax(m);o.done(function(r,p,q){n.set({deleted:true,purged:true})});o.fail(function(t,p,s){var q=c("Unable to purge dataset");var r=("Removal of datasets by users is not allowed in this Galaxy instance");if(t.responseJSON&&t.responseJSON.error){q=t.responseJSON.error}else{if(t.responseText.indexOf(r)!==-1){q=r}}t.responseText=q;n.trigger("error",n,t,m,c(q),{error:q})});return o},searchAttributes:["name","file_ext","genome_build","misc_blurb","misc_info","annotation","tags"],searchAliases:{title:"name",format:"file_ext",database:"genome_build",blurb:"misc_blurb",description:"misc_blurb",info:"misc_info",tag:"tags"},toString:function(){var m=this.get("id")||"";if(this.get("name")){m=this.get("hid")+' :"'+this.get("name")+'",'+m}return"HDA("+m+")"}});l.STATES={UPLOAD:"upload",QUEUED:"queued",RUNNING:"running",SETTING_METADATA:"setting_metadata",NEW:"new",EMPTY:"empty",OK:"ok",PAUSED:"paused",FAILED_METADATA:"failed_metadata",NOT_VIEWABLE:"noPermission",DISCARDED:"discarded",ERROR:"error"};l.READY_STATES=[l.STATES.OK,l.STATES.EMPTY,l.STATES.PAUSED,l.STATES.FAILED_METADATA,l.STATES.NOT_VIEWABLE,l.STATES.DISCARDED,l.STATES.ERROR];l.NOT_READY_STATES=[l.STATES.UPLOAD,l.STATES.QUEUED,l.STATES.RUNNING,l.STATES.SETTING_METADATA,l.STATES.NEW];var b=Backbone.Collection.extend(e.LoggableMixin).extend({model:function(n,m){if(n.history_content_type=="dataset"){return new l(n,m)}else{if(n.history_content_type=="dataset_collection"){return new j(n,m)}else{}}},urlRoot:galaxy_config.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},initialize:function(n,m){m=m||{};this.historyId=m.historyId},ids:function(){return this.map(function(m){return m.id})},notReady:function(){return this.filter(function(m){return !m.inReadyState()})},running:function(){var m=[];this.each(function(n){if(!n.inReadyState()){m.push(n.get("id"))}});return m},getByHid:function(m){return _.first(this.filter(function(n){return n.get("hid")===m}))},getVisible:function(m,p,o){o=o||[];var n=new b(this.filter(function(q){return q.isVisible(m,p)}));_.each(o,function(q){if(!_.isFunction(q)){return}n=new b(n.filter(q))});return n},haveDetails:function(){return this.all(function(m){return m.hasDetails()})},fetchAllDetails:function(n){n=n||{};var m={details:"all"};n.data=(n.data)?(_.extend(n.data,m)):(m);return this.fetch(n)},ajaxQueue:function(p,o){var n=jQuery.Deferred(),m=this.length,r=[];if(!m){n.resolve([]);return n}var q=this.chain().reverse().map(function(t,s){return function(){var u=p.call(t,o);u.done(function(v){n.notify({curr:s,total:m,response:v,model:t})});u.always(function(v){r.push(v);if(q.length){q.shift()()}else{n.resolve(r)}})}}).value();q.shift()();return n},matches:function(m){return this.filter(function(n){return n.matches(m)})},set:function(o,m){var n=this;o=_.map(o,function(q){var r=n.get(q.id);if(!r){return q}var p=r.toJSON();_.extend(p,q);return p});Backbone.Collection.prototype.set.call(this,o,m)},promoteToHistoryDatasetCollection:function k(r,p,n){n=n||{};n.url=this.url();n.type="POST";var t=p;var q=[],m=null;if(p=="list"){this.chain().each(function(w){var u=w.attributes.name;var x=w.id;var v=w.attributes.history_content_type;if(v=="dataset"){if(t!="list"){console.log("Invalid collection type")}q.push({name:u,src:"hda",id:x})}else{if(t=="list"){t="list:"+w.attributes.collection_type}else{if(t!="list:"+w.attributes.collection_type){console.log("Invalid collection type")}}q.push({name:u,src:"hdca",id:x})}});m="New Dataset List"}else{if(p=="paired"){var o=this.ids();if(o.length!=2){}q.push({name:"forward",src:"hda",id:o[0]});q.push({name:"reverse",src:"hda",id:o[1]});m="New Dataset Pair"}}n.data={type:"dataset_collection",name:m,collection_type:t,element_identifiers:JSON.stringify(q),};var s=jQuery.ajax(n);s.done(function(w,u,v){r.refresh()});s.fail(function(w,u,v){if(w.responseJSON&&w.responseJSON.error){error=w.responseJSON.error}else{error=w.responseJSON}w.responseText=error});return s},toString:function(){return(["HDACollection(",[this.historyId,this.length].join(),")"].join(""))}});var j=a.extend({defaults:{history_id:null,model_class:"HistoryDatasetCollectionAssociation",history_content_type:"dataset_collection",hid:0,id:null,name:"(unnamed dataset collection)",state:"ok",accessible:true,deleted:false,visible:true,purged:false,tags:[],annotation:""},urls:function(){},inReadyState:function(){return true},searchAttributes:["name"],searchAliases:{title:"name"},});return{HistoryDatasetAssociation:l,HDACollection:b}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: davebgx: Enable running the create_users and create_categories scripts via run_tool_shed.sh
by commits-noreply＠bitbucket.org 22 May '14

22 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/21a66ac74e37/ Changeset: 21a66ac74e37 User: davebgx Date: 2014-05-22 16:59:18 Summary: Enable running the create_users and create_categories scripts via run_tool_shed.sh Affected #: 7 files diff -r 581e7c8e353e9348db75d269446651e7122f10ce -r 21a66ac74e37c80fe6d5a7c44988f83db5413d87 lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh --- /dev/null +++ b/lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh @@ -0,0 +1,100 @@ +#!/bin/bash + +stop_err() { + echo $1 + python ./scripts/paster.py serve tool_shed_wsgi.ini --pid-file=tool_shed_bootstrap.pid --log-file=tool_shed_bootstrap.log --stop-daemon + exit 1 +} + +tool_shed=`./lib/tool_shed/scripts/bootstrap_tool_shed/parse_run_sh_args.sh $@` + +if [ $? -ne 0 ] ; then + exit 0 +fi + +log_file="lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap.log" + +database_result=`python ./lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py --execute check_db --config_file tool_shed_wsgi.ini` + +if [ $? -ne 0 ] ; then + stop_err "Unable to bootstrap tool shed. $database_result" +fi + +echo "Bootstrapping from tool shed at $tool_shed." +echo -n "Creating database... " +python scripts/create_db.py tool_shed + +if [ $? -eq 0 ] ; then + echo "done." +else + stop_err "failed." +fi + +if [ $? -eq 0 ] ; then + user_auth=`python ./lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py --execute admin_user_info --config_file tool_shed_wsgi.ini` + local_shed_url=`python ./lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py --execute get_url --config_file tool_shed_wsgi.ini` +fi + +admin_user_name=`echo $user_auth | awk 'BEGIN { FS="__SEP__" } ; { print \$1 }'` +admin_user_email=`echo $user_auth | awk 'BEGIN { FS="__SEP__" } ; { print \$2 }'` +admin_user_password=`echo $user_auth | awk 'BEGIN { FS="__SEP__" } ; { print \$3 }'` + +echo -n "Creating user '$admin_user_name' with email address '$admin_user_email'..." + +python lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py tool_shed_wsgi.ini >> $log_file + +echo " done." + +sed -i "s/#admin_users = user1@example.org,user2@example.org/admin_users = $admin_user_email/" tool_shed_wsgi.ini +echo -n "Starting tool shed in order to populate users and categories... " + +if [ -f tool_shed_bootstrap.pid ] ; then + stop_err "A bootstrap process is already running." +fi + +python ./scripts/paster.py serve tool_shed_wsgi.ini --pid-file=tool_shed_bootstrap.pid --log-file=tool_shed_bootstrap.log --daemon > /dev/null + +shed_pid=`cat tool_shed_bootstrap.pid` + +while : ; do + tail -n 1 tool_shed_bootstrap.log | grep -q "Removing PID file tool_shed_webapp.pid" + if [ $? -eq 0 ] ; then + echo "failed." + echo "More information about this failure may be found in the following log snippet from tool_shed_bootstrap.log:" + echo "========================================" + tail -n 40 tool_shed_bootstrap.log + echo "========================================" + stop_err " " + fi + tail -n 2 tool_shed_bootstrap.log | grep -q "Starting server in PID $shed_pid" + if [ $? -eq 0 ] ; then + echo "done." + break + fi +done + +echo -n "Retrieving admin user's API key..." +api_key_json=`curl -s --user $admin_user_email:$admin_user_password $local_shed_url/api/authenticate/baseauth/` +api_key=`echo $api_key_json | grep api_key | awk 'BEGIN { FS="\"" } ; { print \$4 }' | sed 's/\\s\+//'` + +if [[ -z $api_key && ${api_key+x} ]] ; then + stop_err "Error getting API key for user $admin_user_email." +fi + +echo " done." + +if [ $? -eq 0 ] ; then + echo -n "Creating users... " + python lib/tool_shed/scripts/api/create_users.py -a $api_key -f $tool_shed -t $local_shed_url >> $log_file + echo "done." + echo -n "Creating categories... " + python lib/tool_shed/scripts/api/create_categories.py -a $api_key -f $tool_shed -t $local_shed_url >> $log_file + echo "done." +else + stop_err "Error getting API key from local tool shed." +fi + +echo "Bootstrap complete, shutting down temporary tool shed process. A log has been saved to tool_shed_bootstrap.log" +python ./scripts/paster.py serve tool_shed_wsgi.ini --pid-file=tool_shed_bootstrap.pid --log-file=tool_shed_bootstrap.log --stop-daemon + +exit 0 \ No newline at end of file diff -r 581e7c8e353e9348db75d269446651e7122f10ce -r 21a66ac74e37c80fe6d5a7c44988f83db5413d87 lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py --- /dev/null +++ b/lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py @@ -0,0 +1,130 @@ +#!/usr/bin/python +import argparse +import ConfigParser +import os +import sys + +new_path = [ os.path.join( os.getcwd(), "lib" ) ] +new_path.extend( sys.path[1:] ) +sys.path = new_path + +from galaxy import eggs +eggs.require( "SQLAlchemy >= 0.4" ) +import galaxy.webapps.tool_shed.model.mapping as tool_shed_model +from sqlalchemy.exc import ProgrammingError +from sqlalchemy.exc import OperationalError + +from tool_shed.util import xml_util + +def check_db( config_parser ): + dburi = None + + if config_parser.has_option( 'app:main', 'database_connection' ): + dburi = config_parser.get( 'app:main', 'database_connection' ) + elif config_parser.has_option( 'app:main', 'database_file' ): + db_file = config_parser.get( 'app:main', 'database_file' ) + dburi = "sqlite:///%s?isolation_level=IMMEDIATE" % db_file + else: + print 'The database configuration setting is missing from the tool_shed_wsgi.ini file. Add this setting before attempting to bootstrap.' + exit(1) + + sa_session = None + + database_exists_message = 'The database configured for this Tool Shed is not new, so bootstrapping is not allowed. ' + database_exists_message += 'Create a new database that has not been migrated before attempting to bootstrap.' + + try: + model = tool_shed_model.init( config_parser.get( 'app:main', 'file_path' ), dburi, engine_options={}, create_tables=False ) + sa_session = model.context.current + print database_exists_message + exit(1) + except ProgrammingError, e: + pass + except OperationalError, e: + pass + + try: + if sa_session is not None: + result = sa_session.execute( 'SELECT version FROM migrate_version' ).first() + if result[0] >= 2: + print database_exists_message + exit(1) + else: + pass + except ProgrammingError, e: + pass + + if config_parser.has_option( 'app:main', 'hgweb_config_dir' ): + hgweb_config_parser = ConfigParser.ConfigParser() + hgweb_dir = config_parser.get( 'app:main', 'hgweb_config_dir' ) + hgweb_config_file = os.path.join( hgweb_dir, 'hgweb.config' ) + if not os.path.exists( hgweb_config_file ): + exit(0) + hgweb_config_parser.read( hgweb_config_file ) + configured_repos = hgweb_config_parser.items( 'paths' ) + if len( configured_repos ) >= 1: + message = "This Tool Shed's hgweb.config file contains entries, so bootstrapping is not allowed. Delete" + message += " the current hgweb.config file along with all associated repositories in the configured " + message += "location before attempting to boostrap." + print + exit(1) + else: + exit(0) + else: + exit(0) + + exit(0) + +def admin_user_info( config_parser ): + user_info_config = os.path.abspath( os.path.join( os.getcwd(), 'lib/tool_shed/scripts/bootstrap_tool_shed', 'user_info.xml' ) ) + tree, error_message = xml_util.parse_xml( user_info_config ) + if tree is None: + print "The XML file ", user_info_config, " seems to be invalid, using defaults." + email = 'admin(a)test.org' + password = 'testuser' + username = 'admin' + else: + root = tree.getroot() + for elem in root: + if elem.tag == 'email': + email = elem.text + elif elem.tag == 'password': + password = elem.text + elif elem.tag == 'username': + username = elem.text + print '%s__SEP__%s__SEP__%s' % ( username, email, password ) + return 0 + +def get_local_tool_shed_url( config_parser ): + port = '9009' + if config_parser.has_section( 'server:main' ): + if config_parser.has_option( 'server:main', 'port' ): + port = config_parser.get( 'server:main', 'port' ) + host = '127.0.0.1' + print 'http://%s:%s' % ( host, port ) + return 0 + +def main( args ): + config_parser = ConfigParser.ConfigParser() + + if os.path.exists( args.config ): + config_parser.read( args.config ) + else: + return 1 + + if args.method == 'check_db': + return check_db( config_parser ) + elif args.method == 'admin_user_info': + return admin_user_info( config_parser ) + elif args.method == 'get_url': + return get_local_tool_shed_url( config_parser ) + else: + return 1 + +parser = argparse.ArgumentParser() +parser.add_argument( '-c', '--config_file', dest='config', action='store', default='tool_shed_wsgi.ini' ) +parser.add_argument( '-e', '--execute', dest='method', action='store', default='check_db' ) +args = parser.parse_args() + +if __name__ == '__main__': + exit( main( args ) ) \ No newline at end of file diff -r 581e7c8e353e9348db75d269446651e7122f10ce -r 21a66ac74e37c80fe6d5a7c44988f83db5413d87 lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py --- a/lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py +++ b/lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py @@ -125,7 +125,7 @@ return '' def validate_publicname( username ): - """""Validates the public username.""" + """Validates the public username.""" if len( username ) < 3: return "Public name must be at least 3 characters in length" if len( username ) > 255: @@ -154,5 +154,7 @@ if user is not None: api_key = create_api_key( app, user ) print "Created new user with public username '", user.username, ". An API key was also created and associated with the user." + exit(0) else: print "Problem creating a new user and an associated API key." + exit(1) diff -r 581e7c8e353e9348db75d269446651e7122f10ce -r 21a66ac74e37c80fe6d5a7c44988f83db5413d87 lib/tool_shed/scripts/bootstrap_tool_shed/parse_run_sh_args.sh --- /dev/null +++ b/lib/tool_shed/scripts/bootstrap_tool_shed/parse_run_sh_args.sh @@ -0,0 +1,15 @@ +#!/bin/bash + +while (( $# )) ; do + case "$1" in + -bootstrap_from_tool_shed|--bootstrap_from_tool_shed) + bootstrap="true" + tool_shed=$2 + echo $tool_shed + exit 0 + break + ;; + esac + shift 1 +done +exit 1 \ No newline at end of file diff -r 581e7c8e353e9348db75d269446651e7122f10ce -r 21a66ac74e37c80fe6d5a7c44988f83db5413d87 run.sh --- a/run.sh +++ b/run.sh @@ -5,41 +5,7 @@ python ./scripts/check_python.py [ $? -ne 0 ] && exit 1 -SAMPLES=" - community_wsgi.ini.sample - datatypes_conf.xml.sample - external_service_types_conf.xml.sample - migrated_tools_conf.xml.sample - reports_wsgi.ini.sample - shed_tool_conf.xml.sample - tool_conf.xml.sample - shed_tool_data_table_conf.xml.sample - tool_data_table_conf.xml.sample - tool_sheds_conf.xml.sample - data_manager_conf.xml.sample - shed_data_manager_conf.xml.sample - openid_conf.xml.sample - job_metrics_conf.xml.sample - universe_wsgi.ini.sample - tool-data/shared/ncbi/builds.txt.sample - tool-data/shared/ensembl/builds.txt.sample - tool-data/shared/ucsc/builds.txt.sample - tool-data/shared/ucsc/publicbuilds.txt.sample - tool-data/shared/ucsc/ucsc_build_sites.txt.sample - tool-data/shared/igv/igv_build_sites.txt.sample - tool-data/shared/rviewer/rviewer_build_sites.txt.sample - tool-data/*.sample - static/welcome.html.sample -" - -# Create any missing config/location files -for sample in $SAMPLES; do - file=`echo $sample | sed -e 's/\.sample$//'` - if [ ! -f "$file" -a -f "$sample" ]; then - echo "Initializing $file from `basename $sample`" - cp $sample $file - fi -done +./scripts/copy_sample_files.sh if [ -n "$GALAXY_UNIVERSE_CONFIG_DIR" ]; then python ./scripts/build_universe_config.py "$GALAXY_UNIVERSE_CONFIG_DIR" diff -r 581e7c8e353e9348db75d269446651e7122f10ce -r 21a66ac74e37c80fe6d5a7c44988f83db5413d87 run_tool_shed.sh --- a/run_tool_shed.sh +++ b/run_tool_shed.sh @@ -2,37 +2,14 @@ cd `dirname $0` -SAMPLES=" - tool_shed_wsgi.ini.sample - datatypes_conf.xml.sample - external_service_types_conf.xml.sample - migrated_tools_conf.xml.sample - reports_wsgi.ini.sample - shed_tool_conf.xml.sample - tool_conf.xml.sample - shed_tool_data_table_conf.xml.sample - tool_data_table_conf.xml.sample - tool_sheds_conf.xml.sample - openid_conf.xml.sample - universe_wsgi.ini.sample - lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml.sample - tool-data/shared/ncbi/builds.txt.sample - tool-data/shared/ensembl/builds.txt.sample - tool-data/shared/ucsc/builds.txt.sample - tool-data/shared/ucsc/publicbuilds.txt.sample - tool-data/shared/igv/igv_build_sites.txt.sample - tool-data/shared/rviewer/rviewer_build_sites.txt.sample - tool-data/*.sample - static/welcome.html.sample -" +./scripts/copy_sample_files.sh -# Create any missing config/location files -for sample in $SAMPLES; do - file=`echo $sample | sed -e 's/\.sample$//'` - if [ ! -f "$file" -a -f "$sample" ]; then - echo "Initializing $file from `basename $sample`" - cp $sample $file - fi -done +tool_shed=`./lib/tool_shed/scripts/bootstrap_tool_shed/parse_run_sh_args.sh $@` +args=$@ -python ./scripts/paster.py serve tool_shed_wsgi.ini --pid-file=tool_shed_webapp.pid --log-file=tool_shed_webapp.log $@ +if [ $? -eq 0 ] ; then + bash ./lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh $@ + args=`echo $@ | sed "s#-\?-bootstrap_from_tool_shed $tool_shed##"` +fi + +python ./scripts/paster.py serve tool_shed_wsgi.ini --pid-file=tool_shed_webapp.pid --log-file=tool_shed_webapp.log $args diff -r 581e7c8e353e9348db75d269446651e7122f10ce -r 21a66ac74e37c80fe6d5a7c44988f83db5413d87 scripts/copy_sample_files.sh --- /dev/null +++ b/scripts/copy_sample_files.sh @@ -0,0 +1,39 @@ +#!/bin/bash + +SAMPLES=" + tool_shed_wsgi.ini.sample + datatypes_conf.xml.sample + external_service_types_conf.xml.sample + migrated_tools_conf.xml.sample + reports_wsgi.ini.sample + shed_tool_conf.xml.sample + tool_conf.xml.sample + shed_tool_data_table_conf.xml.sample + tool_data_table_conf.xml.sample + tool_sheds_conf.xml.sample + data_manager_conf.xml.sample + shed_data_manager_conf.xml.sample + openid_conf.xml.sample + job_metrics_conf.xml.sample + universe_wsgi.ini.sample + lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml.sample + tool-data/shared/ncbi/builds.txt.sample + tool-data/shared/ensembl/builds.txt.sample + tool-data/shared/ucsc/builds.txt.sample + tool-data/shared/ucsc/publicbuilds.txt.sample + tool-data/shared/ucsc/ucsc_build_sites.txt.sample + tool-data/shared/igv/igv_build_sites.txt.sample + tool-data/shared/rviewer/rviewer_build_sites.txt.sample + tool-data/*.sample + static/welcome.html.sample +" + +# Create any missing config/location files +for sample in $SAMPLES; do + file=${sample%.sample} + if [ ! -f "$file" -a -f "$sample" ]; then + echo "Initializing $file from `basename $sample`" + cp $sample $file + fi +done + Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Add missing import to the Tool Shed's repository grids utility component.
by commits-noreply＠bitbucket.org 22 May '14

22 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/581e7c8e353e/ Changeset: 581e7c8e353e User: greg Date: 2014-05-22 14:44:18 Summary: Add missing import to the Tool Shed's repository grids utility component. Affected #: 1 file diff -r b38587cb8937d678f2edcd17659fc3ce1724794d -r 581e7c8e353e9348db75d269446651e7122f10ce lib/tool_shed/grids/util.py --- a/lib/tool_shed/grids/util.py +++ b/lib/tool_shed/grids/util.py @@ -5,6 +5,7 @@ from galaxy.web.form_builder import SelectField from tool_shed.util import hg_util +from tool_shed.util import shed_util_common as suc log = logging.getLogger( __name__ ) 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: guerler: Charts: Improve options mapping between different chart types
by commits-noreply＠bitbucket.org 22 May '14

22 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b38587cb8937/ Changeset: b38587cb8937 User: guerler Date: 2014-05-22 10:45:43 Summary: Charts: Improve options mapping between different chart types Affected #: 7 files diff -r d18b0f6cac6cb7bea6bd66900cc2d119bb733fbe -r b38587cb8937d678f2edcd17659fc3ce1724794d config/plugins/visualizations/charts/static/charts/nvd3_bar_horizontal_stacked/config.js --- a/config/plugins/visualizations/charts/static/charts/nvd3_bar_horizontal_stacked/config.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3_bar_horizontal_stacked/config.js @@ -9,11 +9,6 @@ } }, columns : { - x : { - title : 'Values for x-axis', - is_label: true, - is_auto : true - }, y : { title : 'Values for y-axis' } diff -r d18b0f6cac6cb7bea6bd66900cc2d119bb733fbe -r b38587cb8937d678f2edcd17659fc3ce1724794d config/plugins/visualizations/charts/static/charts/nvd3_bar_stacked/config.js --- a/config/plugins/visualizations/charts/static/charts/nvd3_bar_stacked/config.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3_bar_stacked/config.js @@ -4,11 +4,6 @@ title : 'Stacked', category : 'Bar diagrams', columns : { - x : { - title : 'Values for x-axis', - is_label: true, - is_auto : true - }, y : { title : 'Values for y-axis' } diff -r d18b0f6cac6cb7bea6bd66900cc2d119bb733fbe -r b38587cb8937d678f2edcd17659fc3ce1724794d config/plugins/visualizations/charts/static/charts/nvd3_histogram_discrete/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/nvd3_histogram_discrete/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3_histogram_discrete/wrapper.js @@ -40,7 +40,7 @@ // draw var nvd3 = new NVD3(this.app, this.options); nvd3.draw(process_id, nv.models.multiBarChart(), chart, tmp_dict, function(nvd3_model) { - nvd3_model.options({showControls: true}); + nvd3_model.options({showControls: false}); }); } }); diff -r d18b0f6cac6cb7bea6bd66900cc2d119bb733fbe -r b38587cb8937d678f2edcd17659fc3ce1724794d config/plugins/visualizations/charts/static/library/ui-select.js --- a/config/plugins/visualizations/charts/static/library/ui-select.js +++ b/config/plugins/visualizations/charts/static/library/ui-select.js @@ -5,7 +5,7 @@ var View = Backbone.View.extend( { // options - optionsDefault: { + optionsDefault : { id : '', cls : '', empty : 'No data available', @@ -21,6 +21,9 @@ // configure options this.options = Utils.merge(options, this.optionsDefault); + // initial value + this.selected = this.options.value; + // create new element this.setElement(this._template(this.options)); @@ -28,10 +31,7 @@ this.$select = this.$el.find('#select'); this.$icon = this.$el.find('#icon'); - // initial value - this.selected = this.options.value; - - // add change event + // add change event. fires only on user activity var self = this; this.$select.on('change', function() { self.value(self.$select.val()); @@ -67,9 +67,9 @@ // get current id/value var after = this.selected; - if(after) { + if (after) { // fire onchange - if ((after != before && this.options.onchange)) { + if (after != before && this.options.onchange) { this.options.onchange(after); } } @@ -78,6 +78,16 @@ return after; }, + // first + first: function() { + var options = this.$select.find('option'); + if (options.length > 0) { + return options.val(); + } else { + return undefined; + } + }, + // label text : function () { return this.$select.find('option:selected').text(); @@ -147,40 +157,17 @@ this.$select.append(this._templateOption(options[key])); } - // select first option if nothing else is selected - if (!this.selected && options.length > 0) { - this.value(options[0].value); - } - // refresh this._refresh(); }, - // force selection to existing value - force: function() { - if (!this._exists(this.selected)) { - // get select options - var options = this.$select.find('option'); - if (options.length > 0) { - // get value from options field - var value = options.val(); - - // log - console.debug('Ui-Select()::force() - Forcing value from "' + this.selected + '" to "' + value + '".'); - - // set value - this.value(value); - } - } - }, - // set on change event - onchange: function(callback) { + setOnChange: function(callback) { this.options.onchange = callback; }, // check if selected value exists - _exists: function(value) { + exists: function(value) { return this.$select.find('option[value=' + value + ']').length > 0; }, @@ -200,11 +187,11 @@ } else { // enable select field this.enable(); - - // update selected value - if (this.selected) { - this.$select.val(this.selected); - } + } + + // update value + if (this.selected) { + this.$select.val(this.selected); } }, diff -r d18b0f6cac6cb7bea6bd66900cc2d119bb733fbe -r b38587cb8937d678f2edcd17659fc3ce1724794d config/plugins/visualizations/charts/static/library/ui-table-form.js --- a/config/plugins/visualizations/charts/static/library/ui-table-form.js +++ b/config/plugins/visualizations/charts/static/library/ui-table-form.js @@ -40,14 +40,6 @@ for (var id in settings) { this._add(id, settings[id], model); } - - // trigger change - for (var id in this.list) { - var onchange = this.list[id].options.onchange; - if (onchange) { - onchange(); - } - } }, // add table row @@ -66,8 +58,9 @@ field = new Ui.Input({ id : id, placeholder : settings_def.placeholder, - onchange : function() { - model.set(id, field.value()); + value : model.get(id), + onchange : function(value) { + model.set(id, value); } }); break; @@ -76,13 +69,13 @@ field = new Ui.Select.View({ id : id, data : settings_def.data, - onchange : function() { + value : model.get(id), + onchange : function(value) { // set new value - var selected = field.value(); - model.set(id, selected); + model.set(id, value); // find selected dictionary - var dict = _.findWhere(settings_def.data, {value: selected}); + var dict = _.findWhere(settings_def.data, {value: value}); if (dict) { if (dict.show) { self.$el.find('#' + dict.show).fadeIn('fast'); diff -r d18b0f6cac6cb7bea6bd66900cc2d119bb733fbe -r b38587cb8937d678f2edcd17659fc3ce1724794d config/plugins/visualizations/charts/static/library/ui.js --- a/config/plugins/visualizations/charts/static/library/ui.js +++ b/config/plugins/visualizations/charts/static/library/ui.js @@ -550,13 +550,13 @@ this.$el.hide(); } - // onchange event handler + // onchange event handler. fires on user activity. var self = this; - if (this.options.onchange) { - this.$el.on('input', function() { - self.options.onchange(); - }); - } + this.$el.on('input', function() { + if (self.options.onchange) { + self.options.onchange(self.$el.val()); + } + }); }, // value diff -r d18b0f6cac6cb7bea6bd66900cc2d119bb733fbe -r b38587cb8937d678f2edcd17659fc3ce1724794d config/plugins/visualizations/charts/static/views/group.js --- a/config/plugins/visualizations/charts/static/views/group.js +++ b/config/plugins/visualizations/charts/static/views/group.js @@ -22,8 +22,8 @@ // ui elements this.group_key = new Ui.Input({ placeholder: 'Data label', - onchange: function() { - self.group.set('key', self.group_key.value()); + onchange: function(value) { + self.group.set('key', value); } }); this.table = new Table.View({content: 'No data column.'}); @@ -92,8 +92,6 @@ // create select field var select = new Ui.Select.View({ id : 'select_' + id, - gid : id, - value : this.group.get(id), wait : true }); @@ -116,48 +114,7 @@ this.app.datasets.request({id : dataset_id}, function(dataset) { // update select fields for (var id in list) { - - // select - var select = list[id]; - - // is a numeric number required - var is_label = chart_settings.columns[id].is_label; - var is_auto = chart_settings.columns[id].is_auto; - - // configure columns - var columns = []; - - // add auto selection column - if (is_auto) { - columns.push({ - 'label' : 'Column: Row Number', - 'value' : 'auto' - }); - } - - // meta data - var meta = dataset.metadata_column_types; - for (var key in meta) { - // check type - if ((!is_label && (meta[key] == 'int' || meta[key] == 'float')) || is_label) { - // add to selection - columns.push({ - 'label' : 'Column: ' + (parseInt(key) + 1) + ' [' + meta[key] + ']', - 'value' : key - }); - } - } - - // add onchange event - select.onchange(function(value) { - self.group.set(this.gid, value); - self.chart.set('modified', true); - }); - - // list - select.update(columns); - select.force(); - select.show(); + self._addRow(id, dataset, list[id], chart_settings.columns[id]) } // loading @@ -168,6 +125,62 @@ }); }, + // add row + _addRow: function(id, dataset, select, chart_setting) { + // is a numeric number required + var is_label = chart_setting.is_label; + var is_auto = chart_setting.is_auto; + + // configure columns + var columns = []; + + // add auto selection column + if (is_auto) { + columns.push({ + 'label' : 'Column: Row Number', + 'value' : 'auto' + }); + } + + // meta data + var meta = dataset.metadata_column_types; + for (var key in meta) { + // check type + if ((!is_label && (meta[key] == 'int' || meta[key] == 'float')) || is_label) { + // add to selection + columns.push({ + 'label' : 'Column: ' + (parseInt(key) + 1) + ' [' + meta[key] + ']', + 'value' : key + }); + } + } + + // update selection list + select.update(columns); + select.show(); + + // update current value + if (!select.exists(this.group.get(id))) { + // get first value + var first = select.first(); + + // log + console.debug('Group()::_addRow() - Switching model value from "' + this.group.get(id) + '" to "' + first + '".'); + + // update model value + this.group.set(id, first); + } + select.value(this.group.get(id)); + + // add onchange event + var self = this; + select.setOnChange(function(value) { + // update model value + self.group.set(id, value); + self.chart.set('modified', true); + }); + }, + // update _refreshGroup: function() { this.group.set('date', Utils.time()); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: guerler: Charts: Adds histograms for string columns/bins and generalizes column selection
by commits-noreply＠bitbucket.org 21 May '14

21 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d18b0f6cac6c/ Changeset: d18b0f6cac6c User: guerler Date: 2014-05-22 04:48:11 Summary: Charts: Adds histograms for string columns/bins and generalizes column selection Affected #: 21 files diff -r 6c3cc96d1fa7888b7af015dd73c7451df7338ad5 -r d18b0f6cac6cb7bea6bd66900cc2d119bb733fbe config/plugins/visualizations/charts/static/app.css --- a/config/plugins/visualizations/charts/static/app.css +++ b/config/plugins/visualizations/charts/static/app.css @@ -63,5 +63,6 @@ .charts-viewport .charts-viewport-canvas { display: block; width:100%; + min-height: 100px; height: inherit; } \ No newline at end of file diff -r 6c3cc96d1fa7888b7af015dd73c7451df7338ad5 -r d18b0f6cac6cb7bea6bd66900cc2d119bb733fbe config/plugins/visualizations/charts/static/charts/heatmap/heatmap-plugin.js --- a/config/plugins/visualizations/charts/static/charts/heatmap/heatmap-plugin.js +++ b/config/plugins/visualizations/charts/static/charts/heatmap/heatmap-plugin.js @@ -285,14 +285,15 @@ } // prepare indices + dataRangeFormat = d3.format('.3f'); var dataRangeMin = 0; - var dataRangeMid = parseInt((dataRange.length - 1) / 2); + var dataRangeMid = ''; var dataRangeMax = dataRange.length - 1; // add labels - dataRange[dataRangeMin] = this.min; + dataRange[dataRangeMin] = dataRangeFormat(this.min); dataRange[dataRangeMid] = this.mid; - dataRange[dataRangeMax] = this.max; + dataRange[dataRangeMax] = dataRangeFormat(this.max); // create legend var legend = this.svg.selectAll('.legend') diff -r 6c3cc96d1fa7888b7af015dd73c7451df7338ad5 -r d18b0f6cac6cb7bea6bd66900cc2d119bb733fbe config/plugins/visualizations/charts/static/charts/nvd3/config.js --- a/config/plugins/visualizations/charts/static/charts/nvd3/config.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/config.js @@ -5,12 +5,7 @@ category : '', library : 'nvd3.js', tag : 'svg', - columns : { - y : { - title : 'Values for y-axis' - } - }, - settings : { + settings : { separator_label : { title : 'X axis', type : 'separator' diff -r 6c3cc96d1fa7888b7af015dd73c7451df7338ad5 -r d18b0f6cac6cb7bea6bd66900cc2d119bb733fbe config/plugins/visualizations/charts/static/charts/nvd3/nvd3.js --- a/config/plugins/visualizations/charts/static/charts/nvd3/nvd3.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/nvd3.js @@ -34,11 +34,13 @@ nvd3_model.options({showControls: false}); // legend - var legend_visible = true; - if (chart.settings.get('show_legend') == 'false') { - legend_visible = false; + if (nvd3_model.showLegend) { + var legend_visible = true; + if (chart.settings.get('show_legend') == 'false') { + legend_visible = false; + } + nvd3_model.showLegend(legend_visible); } - nvd3_model.showLegend(legend_visible); // custom callback if (callback) { diff -r 6c3cc96d1fa7888b7af015dd73c7451df7338ad5 -r d18b0f6cac6cb7bea6bd66900cc2d119bb733fbe config/plugins/visualizations/charts/static/charts/nvd3_bar/config.js --- a/config/plugins/visualizations/charts/static/charts/nvd3_bar/config.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3_bar/config.js @@ -2,7 +2,17 @@ return $.extend(true, {}, nvd3_config, { title : 'Regular', - category : 'Bar diagrams' + category : 'Bar diagrams', + columns : { + x : { + title : 'Values for x-axis', + is_label: true, + is_auto : true + }, + y : { + title : 'Values for y-axis' + } + } }); }); \ No newline at end of file diff -r 6c3cc96d1fa7888b7af015dd73c7451df7338ad5 -r d18b0f6cac6cb7bea6bd66900cc2d119bb733fbe config/plugins/visualizations/charts/static/charts/nvd3_bar_horizontal/config.js --- a/config/plugins/visualizations/charts/static/charts/nvd3_bar_horizontal/config.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3_bar_horizontal/config.js @@ -3,6 +3,16 @@ return $.extend(true, {}, nvd3_config, { title : 'Horizontal', category : 'Bar diagrams', + columns : { + x : { + title : 'Values for x-axis', + is_label: true, + is_auto : true + }, + y : { + title : 'Values for y-axis' + } + }, settings : { x_axis_type : { init : 'hide' diff -r 6c3cc96d1fa7888b7af015dd73c7451df7338ad5 -r d18b0f6cac6cb7bea6bd66900cc2d119bb733fbe config/plugins/visualizations/charts/static/charts/nvd3_bar_horizontal_stacked/config.js --- a/config/plugins/visualizations/charts/static/charts/nvd3_bar_horizontal_stacked/config.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3_bar_horizontal_stacked/config.js @@ -7,6 +7,16 @@ x_axis_type : { init : 'hide' } + }, + columns : { + x : { + title : 'Values for x-axis', + is_label: true, + is_auto : true + }, + y : { + title : 'Values for y-axis' + } } }); diff -r 6c3cc96d1fa7888b7af015dd73c7451df7338ad5 -r d18b0f6cac6cb7bea6bd66900cc2d119bb733fbe config/plugins/visualizations/charts/static/charts/nvd3_bar_stacked/config.js --- a/config/plugins/visualizations/charts/static/charts/nvd3_bar_stacked/config.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3_bar_stacked/config.js @@ -2,7 +2,17 @@ return $.extend(true, {}, nvd3_config, { title : 'Stacked', - category : 'Bar diagrams' + category : 'Bar diagrams', + columns : { + x : { + title : 'Values for x-axis', + is_label: true, + is_auto : true + }, + y : { + title : 'Values for y-axis' + } + } }); }); \ No newline at end of file diff -r 6c3cc96d1fa7888b7af015dd73c7451df7338ad5 -r d18b0f6cac6cb7bea6bd66900cc2d119bb733fbe config/plugins/visualizations/charts/static/charts/nvd3_histogram_discrete/config.js --- a/config/plugins/visualizations/charts/static/charts/nvd3_histogram_discrete/config.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3_histogram_discrete/config.js @@ -5,7 +5,7 @@ category : 'Data processing (requires \'charts\' tool from Toolshed)', execute : 'histogramdiscrete', columns : { - y : { + x : { title : 'Observations', is_label : true } diff -r 6c3cc96d1fa7888b7af015dd73c7451df7338ad5 -r d18b0f6cac6cb7bea6bd66900cc2d119bb733fbe config/plugins/visualizations/charts/static/charts/nvd3_histogram_discrete/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/nvd3_histogram_discrete/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3_histogram_discrete/wrapper.js @@ -15,24 +15,33 @@ { // configure request var index = 1; - for (var i in request_dictionary.groups) { - var group = request_dictionary.groups[i]; - group.columns = { - x: { - index: 0 - }, - y: { - index: index++ - }, - } + var tmp_dict = { + id : request_dictionary.id, + groups : [] + }; + + // configure groups + for (var group_index in request_dictionary.groups) { + var group = request_dictionary.groups[group_index]; + tmp_dict.groups.push({ + key : group.key, + columns : { + x: { + index : 0, + is_label : true + }, + y: { + index : index++ + } + } + }); } - // link this - var self = this; - - // load nvd3 + // draw var nvd3 = new NVD3(this.app, this.options); - nvd3.draw(process_id, nv.models.multiBarChart(), chart, request_dictionary); + nvd3.draw(process_id, nv.models.multiBarChart(), chart, tmp_dict, function(nvd3_model) { + nvd3_model.options({showControls: true}); + }); } }); diff -r 6c3cc96d1fa7888b7af015dd73c7451df7338ad5 -r d18b0f6cac6cb7bea6bd66900cc2d119bb733fbe config/plugins/visualizations/charts/static/charts/nvd3_line/config.js --- a/config/plugins/visualizations/charts/static/charts/nvd3_line/config.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3_line/config.js @@ -2,7 +2,16 @@ return $.extend(true, {}, nvd3_config, { title : 'Line chart', - category : 'Others' + category : 'Others', + columns : { + x : { + title : 'Values for x-axis', + is_auto : true + }, + y : { + title : 'Values for y-axis' + } + } }); }); \ No newline at end of file diff -r 6c3cc96d1fa7888b7af015dd73c7451df7338ad5 -r d18b0f6cac6cb7bea6bd66900cc2d119bb733fbe config/plugins/visualizations/charts/static/charts/nvd3_line_focus/config.js --- a/config/plugins/visualizations/charts/static/charts/nvd3_line_focus/config.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3_line_focus/config.js @@ -2,7 +2,12 @@ return $.extend(true, {}, nvd3_config, { title : 'Line with focus', - category : 'Others' + category : 'Others', + columns : { + y : { + title : 'Values for y-axis' + } + } }); }); \ No newline at end of file diff -r 6c3cc96d1fa7888b7af015dd73c7451df7338ad5 -r d18b0f6cac6cb7bea6bd66900cc2d119bb733fbe config/plugins/visualizations/charts/static/charts/nvd3_pie/config.js --- a/config/plugins/visualizations/charts/static/charts/nvd3_pie/config.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3_pie/config.js @@ -9,7 +9,8 @@ columns : { label : { title : 'Labels', - is_label : true + is_label : true, + is_auto : true }, y : { title : 'Values' diff -r 6c3cc96d1fa7888b7af015dd73c7451df7338ad5 -r d18b0f6cac6cb7bea6bd66900cc2d119bb733fbe config/plugins/visualizations/charts/static/charts/nvd3_scatter/config.js --- a/config/plugins/visualizations/charts/static/charts/nvd3_scatter/config.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3_scatter/config.js @@ -6,6 +6,9 @@ columns : { x : { title : 'Values for x-axis' + }, + y : { + title : 'Values for y-axis' } } }); diff -r 6c3cc96d1fa7888b7af015dd73c7451df7338ad5 -r d18b0f6cac6cb7bea6bd66900cc2d119bb733fbe config/plugins/visualizations/charts/static/charts/nvd3_stackedarea/config.js --- a/config/plugins/visualizations/charts/static/charts/nvd3_stackedarea/config.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3_stackedarea/config.js @@ -2,7 +2,12 @@ return $.extend(true, {}, nvd3_config, { title : 'Regular', - category : 'Area charts' + category : 'Area charts', + columns : { + y : { + title : 'Values for y-axis' + } + } }); }); \ No newline at end of file diff -r 6c3cc96d1fa7888b7af015dd73c7451df7338ad5 -r d18b0f6cac6cb7bea6bd66900cc2d119bb733fbe config/plugins/visualizations/charts/static/charts/nvd3_stackedarea_full/config.js --- a/config/plugins/visualizations/charts/static/charts/nvd3_stackedarea_full/config.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3_stackedarea_full/config.js @@ -2,7 +2,12 @@ return $.extend(true, {}, nvd3_config, { title : 'Expanded', - category : 'Area charts' + category : 'Area charts', + columns : { + y : { + title : 'Values for y-axis' + } + } }); }); \ No newline at end of file diff -r 6c3cc96d1fa7888b7af015dd73c7451df7338ad5 -r d18b0f6cac6cb7bea6bd66900cc2d119bb733fbe config/plugins/visualizations/charts/static/charts/nvd3_stackedarea_stream/config.js --- a/config/plugins/visualizations/charts/static/charts/nvd3_stackedarea_stream/config.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3_stackedarea_stream/config.js @@ -2,7 +2,12 @@ return $.extend(true, {}, nvd3_config, { title : 'Stream', - category : 'Area charts' + category : 'Area charts', + columns : { + y : { + title : 'Values for y-axis' + } + } }); }); \ No newline at end of file diff -r 6c3cc96d1fa7888b7af015dd73c7451df7338ad5 -r d18b0f6cac6cb7bea6bd66900cc2d119bb733fbe config/plugins/visualizations/charts/static/charts/types.js --- a/config/plugins/visualizations/charts/static/charts/types.js +++ b/config/plugins/visualizations/charts/static/charts/types.js @@ -48,7 +48,7 @@ 'nvd3_scatter' : nvd3_scatter, 'nvd3_pie' : nvd3_pie, 'nvd3_histogram' : nvd3_histogram, - //'nvd3_histogram_discrete' : nvd3_histogram_discrete, + 'nvd3_histogram_discrete' : nvd3_histogram_discrete, 'highcharts_boxplot' : highcharts_boxplot, 'heatmap' : heatmap } diff -r 6c3cc96d1fa7888b7af015dd73c7451df7338ad5 -r d18b0f6cac6cb7bea6bd66900cc2d119bb733fbe config/plugins/visualizations/charts/static/library/datasets.js --- a/config/plugins/visualizations/charts/static/library/datasets.js +++ b/config/plugins/visualizations/charts/static/library/datasets.js @@ -27,29 +27,37 @@ // check if column data is requested if (request_dictionary.groups) { - this._get(request_dictionary, success); + this._get_dataset(request_dictionary.id, function() { + self._get(request_dictionary, success); + }); } else { - // check if dataset is available from cache - var dataset = this.list[request_dictionary.id]; - if (dataset) { - success(dataset); - return; + this._get_dataset(request_dictionary.id, success, error) + } + }, + + // get dataset + _get_dataset: function(id, success, error) { + // check if dataset is available from cache + var dataset = this.list[id]; + if (dataset) { + success(dataset); + return; + } + + // request dataset + var self = this; + Utils.request('GET', config.root + 'api/datasets/' + id, {}, function(dataset) { + switch (dataset.state) { + case 'error': + if (error) { + error(dataset); + } + break; + default: + self.list[id] = dataset; + success(dataset); } - - // request dataset - Utils.request('GET', config.root + 'api/datasets/' + request_dictionary.id, {}, function(dataset) { - switch (dataset.state) { - case 'error': - if (error) { - error(dataset); - } - break; - default: - self.list[request_dictionary.id] = dataset; - success(dataset); - } - }); - } + }); }, // get block id @@ -78,7 +86,7 @@ // check if column is in cache var block_id = this._block_id(request_dictionary, column); - if (this.cache[block_id]) { + if (this.cache[block_id] || column === 'auto') { continue; } @@ -134,45 +142,74 @@ // log console.debug('Datasets::_fill_from_cache() - Filling request from cache.'); + // get dataset + var dataset = this.list[request_dictionary.id]; + if (!dataset) { + console.debug('FAILED - Datasets::_fill_from_cache() - Dataset not found.'); + } + + // identify start/end of request + var start = request_dictionary.start; + var end = Math.min(request_dictionary.end, dataset.metadata_data_lines); + if (end - start <= 0) { + console.debug('FAILED - Datasets::_fill_from_cache() - Invalid range.'); + } + + // initialize group values + for (var i in request_dictionary.groups) { + // get group + var group = request_dictionary.groups[i]; + + // reset group + group.values = []; + + // add values + for (var j = 0; j < end - start; j++) { + // add default x values + group.values[j] = { + x : parseInt(j) + start + }; + } + } + // collect all data into the defined groups for (var i in request_dictionary.groups) { // get group var group = request_dictionary.groups[i]; - // create array for values - group.values = []; - // fill value for (var key in group.columns) { // get column var column = group.columns[key]; - // get block - var block_id = this._block_id(request_dictionary, column.index); - var column_data = this.cache[block_id]; - - // go through column - for (k in column_data) { - // initialize value - var value = group.values[k]; - if (value === undefined) { - // create new value field - value = { - x : parseInt(k) + request_dictionary.start + // check if auto block is requested + if (column.index == 'auto') { + for (var j = start; j < end; j++) { + // get value dictionary + var value = group.values[j]; + + // add auto value + value[key] = parseInt(j) + start; + } + } else { + // get block + var block_id = this._block_id(request_dictionary, column.index); + var column_data = this.cache[block_id]; + + // go through column + for (var j = start; j < end; j++) { + // get value dictionary + var value = group.values[j]; + + // get/fix value + var v = column_data[j]; + if (isNaN(v) && !column.is_label) { + v = 0; } - // add to group - group.values[k] = value; - }; - - // get/fix value - var v = column_data[k]; - if (isNaN(v) && !column.is_label) { - v = 0; + // add to dict + value[key] = v; } - - // add to dict - value[key] = v; } } } diff -r 6c3cc96d1fa7888b7af015dd73c7451df7338ad5 -r d18b0f6cac6cb7bea6bd66900cc2d119bb733fbe config/plugins/visualizations/charts/static/library/ui-select.js --- a/config/plugins/visualizations/charts/static/library/ui-select.js +++ b/config/plugins/visualizations/charts/static/library/ui-select.js @@ -33,11 +33,9 @@ // add change event var self = this; - if (this.options.onchange) { - this.$select.on('change', function() { - self.value(self.$select.val()); - }); - } + this.$select.on('change', function() { + self.value(self.$select.val()); + }); // refresh this._refresh(); @@ -158,6 +156,34 @@ this._refresh(); }, + // force selection to existing value + force: function() { + if (!this._exists(this.selected)) { + // get select options + var options = this.$select.find('option'); + if (options.length > 0) { + // get value from options field + var value = options.val(); + + // log + console.debug('Ui-Select()::force() - Forcing value from "' + this.selected + '" to "' + value + '".'); + + // set value + this.value(value); + } + } + }, + + // set on change event + onchange: function(callback) { + this.options.onchange = callback; + }, + + // check if selected value exists + _exists: function(value) { + return this.$select.find('option[value=' + value + ']').length > 0; + }, + // refresh _refresh: function() { // remove placeholder @@ -166,9 +192,11 @@ // count remaining entries var remaining = this.$select.find('option').length; if (remaining == 0) { + // disable select field + this.disable(); + // append placeholder this.$select.append(this._templateOption({value : 'null', label : this.options.empty})); - this.disable(); } else { // enable select field this.enable(); @@ -180,12 +208,6 @@ } }, - // exists - _exists: function(value) { - // check if selected value exists - return 0 != this.$select.find('option[value=' + value + ']').length; - }, - // option _templateOption: function(options) { return '<option value="' + options.value + '">' + options.label + '</option>'; diff -r 6c3cc96d1fa7888b7af015dd73c7451df7338ad5 -r d18b0f6cac6cb7bea6bd66900cc2d119bb733fbe config/plugins/visualizations/charts/static/views/group.js --- a/config/plugins/visualizations/charts/static/views/group.js +++ b/config/plugins/visualizations/charts/static/views/group.js @@ -82,25 +82,21 @@ // load list var list = {}; for (var id in chart_settings.columns) { - // initialize - var value = this.group.get(id); - if (!value) { - this.group.set(id, 0); + // get definition + var data_def = chart_settings.columns[id]; + if (!data_def) { + console.debug('Group::_refreshTable() - Skipping column definition.'); + continue; } + + // create select field + var select = new Ui.Select.View({ + id : 'select_' + id, + gid : id, + value : this.group.get(id), + wait : true + }); - // create select field - var data_def = chart_settings.columns[id]; - var select = new Ui.Select.View({ - id : 'select_' + id, - gid : id, - onchange : function(value) { - self.group.set(this.gid, value); - self.chart.set('modified', true); - }, - value : value, - wait : true - }); - // add row to table this.table.add(data_def.title, '25%'); this.table.add(select.$el); @@ -121,11 +117,25 @@ // update select fields for (var id in list) { + // select + var select = list[id]; + // is a numeric number required - var is_label = chart_settings.columns[id].is_label; - + var is_label = chart_settings.columns[id].is_label; + var is_auto = chart_settings.columns[id].is_auto; + // configure columns var columns = []; + + // add auto selection column + if (is_auto) { + columns.push({ + 'label' : 'Column: Row Number', + 'value' : 'auto' + }); + } + + // meta data var meta = dataset.metadata_column_types; for (var key in meta) { // check type @@ -138,9 +148,16 @@ } } + // add onchange event + select.onchange(function(value) { + self.group.set(this.gid, value); + self.chart.set('modified', true); + }); + // list - list[id].update(columns); - list[id].show(); + select.update(columns); + select.force(); + select.show(); } // loading Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 21 May '14

21 May '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/316db249f068/ Changeset: 316db249f068 Branch: next-stable User: jmchilton Date: 2014-05-21 22:09:52 Summary: Fix for running workflows with collection inptus. takadonet reported running such workflows were not behaving correctly when copying inputs to new history is enabled. Affected #: 1 file diff -r fc89661b92dcbd9684ac779171235525601d0f4a -r 316db249f068ded4e541415232b480250c7cdd56 lib/galaxy/workflow/run.py --- a/lib/galaxy/workflow/run.py +++ b/lib/galaxy/workflow/run.py @@ -203,9 +203,17 @@ # ds_map. if self.copy_inputs_to_history: for input_dataset_hda in out_data.values(): - new_hda = input_dataset_hda.copy( copy_children=True ) - self.target_history.add_dataset( new_hda ) - outputs[ step.id ][ 'input_ds_copy' ] = new_hda + content_type = input_dataset_hda.history_content_type + if content_type == "dataset": + new_hda = input_dataset_hda.copy( copy_children=True ) + self.target_history.add_dataset( new_hda ) + outputs[ step.id ][ 'input_ds_copy' ] = new_hda + elif content_type == "dataset_collection": + new_hdca = input_dataset_hda.copy() + self.target_history.add_dataset_collection( new_hdca ) + outputs[ step.id ][ 'input_ds_copy' ] = new_hdca + else: + raise Exception("Unknown history content encountered") if self.ds_map: outputs[ step.id ][ 'output' ] = self.ds_map[ str( step.id ) ][ 'hda' ] https://bitbucket.org/galaxy/galaxy-central/commits/6c3cc96d1fa7/ Changeset: 6c3cc96d1fa7 User: jmchilton Date: 2014-05-21 22:10:44 Summary: Merge next-stable. Affected #: 1 file diff -r e8f2c4f3e8c8ed63a99254a50ceb18fc33c52080 -r 6c3cc96d1fa7888b7af015dd73c7451df7338ad5 lib/galaxy/workflow/run.py --- a/lib/galaxy/workflow/run.py +++ b/lib/galaxy/workflow/run.py @@ -203,9 +203,17 @@ # ds_map. if self.copy_inputs_to_history: for input_dataset_hda in out_data.values(): - new_hda = input_dataset_hda.copy( copy_children=True ) - self.target_history.add_dataset( new_hda ) - outputs[ step.id ][ 'input_ds_copy' ] = new_hda + content_type = input_dataset_hda.history_content_type + if content_type == "dataset": + new_hda = input_dataset_hda.copy( copy_children=True ) + self.target_history.add_dataset( new_hda ) + outputs[ step.id ][ 'input_ds_copy' ] = new_hda + elif content_type == "dataset_collection": + new_hdca = input_dataset_hda.copy() + self.target_history.add_dataset_collection( new_hdca ) + outputs[ step.id ][ 'input_ds_copy' ] = new_hdca + else: + raise Exception("Unknown history content encountered") if self.ds_map: outputs[ step.id ][ 'output' ] = self.ds_map[ str( step.id ) ][ 'hda' ] 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: greg: Remove appropriate entries from the Tool Shed's new repository registry for repositories that have been marked deprecated or deleted.
by commits-noreply＠bitbucket.org 21 May '14

21 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e8f2c4f3e8c8/ Changeset: e8f2c4f3e8c8 User: greg Date: 2014-05-21 21:57:54 Summary: Remove appropriate entries from the Tool Shed's new repository registry for repositories that have been marked deprecated or deleted. Affected #: 3 files diff -r 155be7ce7910c2effb12fff904390401bdd7976b -r e8f2c4f3e8c8ed63a99254a50ceb18fc33c52080 lib/galaxy/webapps/tool_shed/controllers/admin.py --- a/lib/galaxy/webapps/tool_shed/controllers/admin.py +++ b/lib/galaxy/webapps/tool_shed/controllers/admin.py @@ -171,6 +171,8 @@ repository.deleted = True trans.sa_session.add( repository ) trans.sa_session.flush() + # Update the repository registry. + trans.app.repository_registry.remove_entry( repository ) count += 1 deleted_repositories += " %s " % repository.name if count: diff -r 155be7ce7910c2effb12fff904390401bdd7976b -r e8f2c4f3e8c8ed63a99254a50ceb18fc33c52080 lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -1051,6 +1051,8 @@ trans.sa_session.add( repository ) trans.sa_session.flush() if mark_deprecated: + # Update the repository registry. + trans.app.repository_registry.remove_entry( repository ) message = 'The repository %s has been marked as deprecated.' % repository.name else: # Update the repository registry. diff -r 155be7ce7910c2effb12fff904390401bdd7976b -r e8f2c4f3e8c8ed63a99254a50ceb18fc33c52080 lib/tool_shed/repository_registry.py --- a/lib/tool_shed/repository_registry.py +++ b/lib/tool_shed/repository_registry.py @@ -17,6 +17,7 @@ class Registry( object ): def __init__( self, app ): + log.debug( "Loading the repository registry..." ) self.app = app self.certified_level_one_clause_list = self.get_certified_level_one_clause_list() # The following lists contain tuples like ( repository.name, repository.user.username, changeset_revision ) @@ -164,9 +165,11 @@ if tip_changeset_hash != suc.INITIAL_CHANGELOG_HASH: certified_level_one_tuple = ( name, owner, tip_changeset_hash ) if repository.type == rt_util.REPOSITORY_SUITE_DEFINITION: - self.certified_level_one_suite_tuples.append( certified_level_one_tuple ) + if certified_level_one_tuple not in self.certified_level_one_suite_tuples: + self.certified_level_one_suite_tuples.append( certified_level_one_tuple ) else: - self.certified_level_one_repository_and_suite_tuples.append( certified_level_one_tuple ) + if certified_level_one_tuple not in self.certified_level_one_repository_and_suite_tuples: + self.certified_level_one_repository_and_suite_tuples.append( certified_level_one_tuple ) def load_repository_and_suite_tuple( self, repository ): name = str( repository.name ) @@ -174,9 +177,11 @@ for repository_metadata in repository.metadata_revisions: changeset_revision = str( repository_metadata.changeset_revision ) tuple = ( name, owner, changeset_revision ) - self.repository_and_suite_tuples.append( tuple ) + if tuple not in self.repository_and_suite_tuples: + self.repository_and_suite_tuples.append( tuple ) if repository.type == rt_util.REPOSITORY_SUITE_DEFINITION: - self.suite_tuples.append( tuple ) + if tuple not in self.suite_tuples: + self.suite_tuples.append( tuple ) def load_repository_and_suite_tuples( self ): # Load self.certified_level_one_repository_and_suite_tuples and self.certified_level_one_suite_tuples. @@ -237,6 +242,55 @@ if repository.type in [ rt_util.REPOSITORY_SUITE_DEFINITION ]: self.certified_level_one_viewable_suites_by_category[ category_name ] += 1 + def remove_entry( self, repository ): + if repository: + is_valid = self.is_valid( repository ) + for rca in repository.categories: + category = rca.category + category_name = str( category.name ) + self.viewable_repositories_and_suites_by_category[ category_name ] -= 1 + if is_valid: + self.viewable_valid_repositories_and_suites_by_category[ category_name ] -= 1 + if repository.type == rt_util.REPOSITORY_SUITE_DEFINITION: + self.viewable_suites_by_category[ category_name ] -= 1 + if is_valid: + self.viewable_valid_suites_by_category[ category_name ] -= 1 + certified_level_one_tuple = self.get_certified_level_one_tuple( repository ) + latest_installable_changeset_revision, is_level_one_certified = certified_level_one_tuple + if is_level_one_certified: + self.certified_level_one_viewable_repositories_and_suites_by_category[ category_name ] -= 1 + if repository.type == rt_util.REPOSITORY_SUITE_DEFINITION: + self.certified_level_one_viewable_suites_by_category[ category_name ] -= 1 + self.unload_repository_and_suite_tuple( repository ) + if is_level_one_certified: + self.unload_certified_level_one_repository_and_suite_tuple( repository ) + @property def sa_session( self ): return self.app.model.context.current + + def unload_certified_level_one_repository_and_suite_tuple( self, repository ): + # The received repository has been determined to be level one certified. + name = str( repository.name ) + owner = str( repository.user.username ) + tip_changeset_hash = repository.tip( self.app ) + if tip_changeset_hash != suc.INITIAL_CHANGELOG_HASH: + certified_level_one_tuple = ( name, owner, tip_changeset_hash ) + if repository.type == rt_util.REPOSITORY_SUITE_DEFINITION: + if certified_level_one_tuple in self.certified_level_one_suite_tuples: + self.certified_level_one_suite_tuples.remove( certified_level_one_tuple ) + else: + if certified_level_one_tuple in self.certified_level_one_repository_and_suite_tuples: + self.certified_level_one_repository_and_suite_tuples.remove( certified_level_one_tuple ) + + def unload_repository_and_suite_tuple( self, repository ): + name = str( repository.name ) + owner = str( repository.user.username ) + for repository_metadata in repository.metadata_revisions: + changeset_revision = str( repository_metadata.changeset_revision ) + tuple = ( name, owner, changeset_revision ) + if tuple in self.repository_and_suite_tuples: + self.repository_and_suite_tuples.remove( tuple ) + if repository.type == rt_util.REPOSITORY_SUITE_DEFINITION: + if tuple in self.suite_tuples: + self.suite_tuples.remove( tuple ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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