galaxy-commits November 2014

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184 discussions

commit/galaxy-central: dannon: Remove unnecessary split on wsgi.url_scheme
by commits-noreply＠bitbucket.org 25 Nov '14

25 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/624c1f52f627/ Changeset: 624c1f52f627 User: dannon Date: 2014-11-25 16:33:26+00:00 Summary: Remove unnecessary split on wsgi.url_scheme Affected #: 1 file diff -r 25698b985bf51cbd732025d9f84444019c788ef4 -r 624c1f52f62771dda89de969eed67c94c4bfeef5 lib/galaxy/web/framework/middleware/xforwardedhost.py --- a/lib/galaxy/web/framework/middleware/xforwardedhost.py +++ b/lib/galaxy/web/framework/middleware/xforwardedhost.py @@ -5,6 +5,7 @@ """ def __init__( self, app, global_conf=None ): self.app = app + def __call__( self, environ, start_response ): x_forwarded_host = environ.get( 'HTTP_X_FORWARDED_HOST', None ) if x_forwarded_host: @@ -17,5 +18,5 @@ x_url_scheme = environ.get( 'HTTP_X_URL_SCHEME', None ) if x_url_scheme: environ[ 'original_wsgi.url_scheme' ] = environ[ 'wsgi.url_scheme' ] - environ[ 'wsgi.url_scheme' ] = x_url_scheme.split(', ', 1)[0] + environ[ 'wsgi.url_scheme' ] = x_url_scheme return self.app( environ, start_response ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Merged in JanKanis/galaxy-central (pull request #560)
by commits-noreply＠bitbucket.org 25 Nov '14

25 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/25698b985bf5/ Changeset: 25698b985bf5 User: dannon Date: 2014-11-25 16:32:20+00:00 Summary: Merged in JanKanis/galaxy-central (pull request #560) use first component of X-Forwarded-{For,Host,Scheme} Affected #: 1 file diff -r 69a6f901230540012d38f17adb1995d96f6a5dba -r 25698b985bf51cbd732025d9f84444019c788ef4 lib/galaxy/web/framework/middleware/xforwardedhost.py --- a/lib/galaxy/web/framework/middleware/xforwardedhost.py +++ b/lib/galaxy/web/framework/middleware/xforwardedhost.py @@ -9,13 +9,13 @@ x_forwarded_host = environ.get( 'HTTP_X_FORWARDED_HOST', None ) if x_forwarded_host: environ[ 'ORGINAL_HTTP_HOST' ] = environ[ 'HTTP_HOST' ] - environ[ 'HTTP_HOST' ] = x_forwarded_host + environ[ 'HTTP_HOST' ] = x_forwarded_host.split(', ', 1)[0] x_forwarded_for = environ.get( 'HTTP_X_FORWARDED_FOR', None ) if x_forwarded_for: environ[ 'ORGINAL_REMOTE_ADDR' ] = environ[ 'REMOTE_ADDR' ] - environ[ 'REMOTE_ADDR' ] = x_forwarded_for + environ[ 'REMOTE_ADDR' ] = x_forwarded_for.split(', ', 1)[0] x_url_scheme = environ.get( 'HTTP_X_URL_SCHEME', None ) if x_url_scheme: environ[ 'original_wsgi.url_scheme' ] = environ[ 'wsgi.url_scheme' ] - environ[ 'wsgi.url_scheme' ] = x_url_scheme + environ[ 'wsgi.url_scheme' ] = x_url_scheme.split(', ', 1)[0] return self.app( environ, start_response ) 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 25 Nov '14

25 Nov '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3d707aa29b5e/ Changeset: 3d707aa29b5e User: JanKanis Date: 2014-11-13 15:48:02+00:00 Summary: use first component of X-Forwarded-{For,Host,Scheme} X-Forwarded-{For,Host,Scheme} can contain multiple comma-separated components if there are multiple reverse proxies. Use the first (outer) one. See http://httpd.apache.org/docs/2.4/mod/mod_proxy.html#x-headers for apache docs. Affected #: 1 file diff -r e372aaa3b3bc1ab9f9b8053d277c678647e8007a -r 3d707aa29b5e0114827ccfc70dc93d7118e8c2e1 lib/galaxy/web/framework/middleware/xforwardedhost.py --- a/lib/galaxy/web/framework/middleware/xforwardedhost.py +++ b/lib/galaxy/web/framework/middleware/xforwardedhost.py @@ -9,13 +9,13 @@ x_forwarded_host = environ.get( 'HTTP_X_FORWARDED_HOST', None ) if x_forwarded_host: environ[ 'ORGINAL_HTTP_HOST' ] = environ[ 'HTTP_HOST' ] - environ[ 'HTTP_HOST' ] = x_forwarded_host + environ[ 'HTTP_HOST' ] = x_forwarded_host.split(', ', 1)[0] x_forwarded_for = environ.get( 'HTTP_X_FORWARDED_FOR', None ) if x_forwarded_for: environ[ 'ORGINAL_REMOTE_ADDR' ] = environ[ 'REMOTE_ADDR' ] - environ[ 'REMOTE_ADDR' ] = x_forwarded_for + environ[ 'REMOTE_ADDR' ] = x_forwarded_for.split(', ', 1)[0] x_url_scheme = environ.get( 'HTTP_X_URL_SCHEME', None ) if x_url_scheme: environ[ 'original_wsgi.url_scheme' ] = environ[ 'wsgi.url_scheme' ] - environ[ 'wsgi.url_scheme' ] = x_url_scheme + environ[ 'wsgi.url_scheme' ] = x_url_scheme.split(', ', 1)[0] return self.app( environ, start_response ) https://bitbucket.org/galaxy/galaxy-central/commits/25698b985bf5/ Changeset: 25698b985bf5 User: dannon Date: 2014-11-25 16:32:20+00:00 Summary: Merged in JanKanis/galaxy-central (pull request #560) use first component of X-Forwarded-{For,Host,Scheme} Affected #: 1 file diff -r 69a6f901230540012d38f17adb1995d96f6a5dba -r 25698b985bf51cbd732025d9f84444019c788ef4 lib/galaxy/web/framework/middleware/xforwardedhost.py --- a/lib/galaxy/web/framework/middleware/xforwardedhost.py +++ b/lib/galaxy/web/framework/middleware/xforwardedhost.py @@ -9,13 +9,13 @@ x_forwarded_host = environ.get( 'HTTP_X_FORWARDED_HOST', None ) if x_forwarded_host: environ[ 'ORGINAL_HTTP_HOST' ] = environ[ 'HTTP_HOST' ] - environ[ 'HTTP_HOST' ] = x_forwarded_host + environ[ 'HTTP_HOST' ] = x_forwarded_host.split(', ', 1)[0] x_forwarded_for = environ.get( 'HTTP_X_FORWARDED_FOR', None ) if x_forwarded_for: environ[ 'ORGINAL_REMOTE_ADDR' ] = environ[ 'REMOTE_ADDR' ] - environ[ 'REMOTE_ADDR' ] = x_forwarded_for + environ[ 'REMOTE_ADDR' ] = x_forwarded_for.split(', ', 1)[0] x_url_scheme = environ.get( 'HTTP_X_URL_SCHEME', None ) if x_url_scheme: environ[ 'original_wsgi.url_scheme' ] = environ[ 'wsgi.url_scheme' ] - environ[ 'wsgi.url_scheme' ] = x_url_scheme + environ[ 'wsgi.url_scheme' ] = x_url_scheme.split(', ', 1)[0] return self.app( environ, start_response ) 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: davebgx: Actually fix migration 23.
by commits-noreply＠bitbucket.org 25 Nov '14

25 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/69a6f9012305/ Changeset: 69a6f9012305 User: davebgx Date: 2014-11-25 15:33:01+00:00 Summary: Actually fix migration 23. Affected #: 1 file diff -r c35433664129cfcf07c39365350d2811b88c8a0f -r 69a6f901230540012d38f17adb1995d96f6a5dba lib/galaxy/webapps/tool_shed/model/migrate/versions/0023_add_repository_url_and_hompeage_url.py --- a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0023_add_repository_url_and_hompeage_url.py +++ b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0023_add_repository_url_and_hompeage_url.py @@ -7,6 +7,7 @@ from sqlalchemy.orm import * from migrate import * from migrate.changeset import * +from galaxy.model.custom_types import TrimmedString import sys, logging @@ -35,7 +36,6 @@ assert c_homepage is Repository_table.c.homepage_url except Exception, e: print "Adding remote_repository_url and homepage_url columns to the repository table failed: %s" % str( e ) - migrate_engine.execute( cmd ) def downgrade( migrate_engine ): metadata.bind = migrate_engine @@ -43,7 +43,7 @@ # Drop type column from repository table. Repository_table = Table( "repository", metadata, autoload=True ) try: - Repository_table.c.drop() + Repository_table.c.remote_repository_url.drop() Repository_table.c.homepage_url.drop() except Exception, e: print "Dropping columns remote_repository_url and homepage_url from the repository table failed: %s" % str( e ) 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: davebgx: Fix error in migration stage 23.
by commits-noreply＠bitbucket.org 25 Nov '14

25 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c35433664129/ Changeset: c35433664129 User: davebgx Date: 2014-11-25 15:14:31+00:00 Summary: Fix error in migration stage 23. Affected #: 1 file diff -r 237bf9f39e6da44f99c291154892155b8847bd97 -r c35433664129cfcf07c39365350d2811b88c8a0f lib/galaxy/webapps/tool_shed/model/migrate/versions/0023_add_repository_url_and_hompeage_url.py --- a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0023_add_repository_url_and_hompeage_url.py +++ b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0023_add_repository_url_and_hompeage_url.py @@ -43,7 +43,7 @@ # Drop type column from repository table. Repository_table = Table( "repository", metadata, autoload=True ) try: - Repository_table.c..drop() + Repository_table.c.drop() Repository_table.c.homepage_url.drop() except Exception, e: print "Dropping columns remote_repository_url and homepage_url from the repository table failed: %s" % str( e ) 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: ToolForm: Handle boolean definition without modifying shared code
by commits-noreply＠bitbucket.org 24 Nov '14

24 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/237bf9f39e6d/ Changeset: 237bf9f39e6d User: guerler Date: 2014-11-25 03:34:33+00:00 Summary: ToolForm: Handle boolean definition without modifying shared code Affected #: 1 file diff -r 622f3fd9202a009620f56fced7ff2c5461a8fdf0 -r 237bf9f39e6da44f99c291154892155b8847bd97 lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -588,6 +588,21 @@ for input in inputs.itervalues(): state[input.name] = input.get_initial_value(trans, context) + # check the current state of a value and update it if necessary + def check_state(trans, input, default_value, context): + value = default_value + error = 'State validation failed.' + try: + # resolves the inconsistent definition of boolean parameters (see base.py) without modifying shared code + if input.type == 'boolean': + value, error = [util.string_as_bool(default_value), None] + else: + value, error = check_param(trans, input, default_value, context) + except Exception: + log.error('Checking parameter %s failed.', input.name) + pass + return [value, error] + # populates state with incoming url parameters def populate_state(trans, inputs, state, incoming, prefix="", context=None ): errors = dict() @@ -620,9 +635,9 @@ group_prefix = "%s|" % ( key ) test_param_key = group_prefix + input.test_param.name default_value = incoming.get(test_param_key, group_state.get(input.test_param.name, None)) - value, test_param_error = check_param( trans, input.test_param, default_value, context) - if test_param_error: - errors[input.name] = [test_param_error] + value, error = check_state(trans, input.test_param, default_value, context) + if error: + errors[input.name] = [error] else: current_case = input.get_current_case(value, trans) group_state = state[input.name] = {} @@ -631,16 +646,13 @@ if group_errors: errors[input.name] = group_errors group_state['__current_case__'] = current_case - group_state[ input.test_param.name ] = value + group_state[input.test_param.name] = value else: - try: - value, error = check_param(trans, input, incoming.get(key, state.get(input.name, None)), context) - if error: - errors[input.name] = error - state[input.name] = value - except Exception: - log.error('Checking parameter %s failed.', input.name) - pass + default_value = incoming.get(key, state.get(input.name, None)) + value, error = check_state(trans, input, default_value, context) + if error: + errors[input.name] = error + state[input.name] = value return errors # builds tool model including all attributes 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: martenson: allow for setting page title in galaxy.panels.mako; set one for data libraries
by commits-noreply＠bitbucket.org 24 Nov '14

24 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/622f3fd9202a/ Changeset: 622f3fd9202a User: martenson Date: 2014-11-25 01:48:56+00:00 Summary: allow for setting page title in galaxy.panels.mako; set one for data libraries Affected #: 2 files diff -r f8eb167f92141c345426db259914028317767973 -r 622f3fd9202a009620f56fced7ff2c5461a8fdf0 lib/galaxy/webapps/galaxy/controllers/library.py --- a/lib/galaxy/webapps/galaxy/controllers/library.py +++ b/lib/galaxy/webapps/galaxy/controllers/library.py @@ -84,8 +84,10 @@ app = { 'jscript' : "galaxy.library" } - # fill template - return trans.fill_template('galaxy.panels.mako', config = {'app' : app}) + return trans.fill_template( 'galaxy.panels.mako', + config = { + 'title': 'Galaxy Data Libraries', + 'app': app } ) @web.expose def index( self, trans, **kwd ): diff -r f8eb167f92141c345426db259914028317767973 -r 622f3fd9202a009620f56fced7ff2c5461a8fdf0 templates/webapps/galaxy/galaxy.panels.mako --- a/templates/webapps/galaxy/galaxy.panels.mako +++ b/templates/webapps/galaxy/galaxy.panels.mako @@ -8,7 +8,7 @@ ## set defaults self.galaxy_config = { ## template options - 'title' : '', + 'title' : 'Galaxy - Data Intensive Biology for Everyone', 'master' : True, 'left_panel' : False, 'right_panel' : False, @@ -160,7 +160,11 @@ ## document <html><head> - <title></title> + <title> + %if self.galaxy_config['title']: + ${self.galaxy_config['title']} + %endif + </title><meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> ## for mobile browsers, don't scale up Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Correct usage of log.exception.
by commits-noreply＠bitbucket.org 24 Nov '14

24 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f8eb167f9214/ Changeset: f8eb167f9214 User: dannon Date: 2014-11-24 23:11:58+00:00 Summary: Correct usage of log.exception. Affected #: 1 file diff -r 6045d6e2f2da3737736cb7ec9564d49f1e7f8232 -r f8eb167f92141c345426db259914028317767973 lib/galaxy/webapps/galaxy/controllers/user.py --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -1150,7 +1150,7 @@ except Exception, e: status = 'error' message = 'Failed to reset password: %s' % str( e ) - log.exception( 'Unable to reset password: ' + str( e ) ) + log.exception( 'Unable to reset password.' ) elif email is not None: message = "The specified user does not exist." status = 'error' 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: jmchilton: Fix xml sample file - fixes broken unit tests.
by commits-noreply＠bitbucket.org 24 Nov '14

24 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6045d6e2f2da/ Changeset: 6045d6e2f2da User: jmchilton Date: 2014-11-24 20:23:02+00:00 Summary: Fix xml sample file - fixes broken unit tests. Affected #: 1 file diff -r 9c02b22ca58f3c59da8cbfd73678b9ac9b4e9216 -r 6045d6e2f2da3737736cb7ec9564d49f1e7f8232 config/job_conf.xml.sample_advanced --- a/config/job_conf.xml.sample_advanced +++ b/config/job_conf.xml.sample_advanced @@ -205,7 +205,7 @@ Docker. --> + above options. --> 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: ToolForm: More batch mode validation logic
by commits-noreply＠bitbucket.org 24 Nov '14

24 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9c02b22ca58f/ Changeset: 9c02b22ca58f User: guerler Date: 2014-11-24 19:48:09+00:00 Summary: ToolForm: More batch mode validation logic Affected #: 6 files diff -r 963fb2afb6d2876e0e9f1a2b7021dce18e6ef0d4 -r 9c02b22ca58f3c59da8cbfd73678b9ac9b4e9216 client/galaxy/scripts/mvc/tools/tools-jobs.js --- a/client/galaxy/scripts/mvc/tools/tools-jobs.js +++ b/client/galaxy/scripts/mvc/tools/tools-jobs.js @@ -145,14 +145,12 @@ } // check number of inputs - if (n > 1) { - if (batch_n === -1) { - batch_n = n; - } else { - if (batch_n !== n) { - this._foundError(input_id, 'Please make sure that you select the same number or a single input for all batch mode fields. This field contains ' + n + ' selection(s) while a previous field contains ' + batch_n + '.'); - return false; - } + if (batch_n === -1) { + batch_n = n; + } else { + if (batch_n !== n) { + this._foundError(input_id, 'Please make sure that you select the same number of inputs for all batch mode fields. This field contains ' + n + ' selection(s) while a previous field contains ' + batch_n + '.'); + return false; } } } diff -r 963fb2afb6d2876e0e9f1a2b7021dce18e6ef0d4 -r 9c02b22ca58f3c59da8cbfd73678b9ac9b4e9216 client/galaxy/scripts/mvc/tools/tools-select-content.js --- a/client/galaxy/scripts/mvc/tools/tools-select-content.js +++ b/client/galaxy/scripts/mvc/tools/tools-select-content.js @@ -190,7 +190,7 @@ // prepare result dict var result = { - batch : !this.options.multiple && (this.current == 'collection' || id_list.length > 1), + batch : !this.options.multiple && this.current != 'single', values : [] } diff -r 963fb2afb6d2876e0e9f1a2b7021dce18e6ef0d4 -r 9c02b22ca58f3c59da8cbfd73678b9ac9b4e9216 static/scripts/mvc/tools/tools-jobs.js --- a/static/scripts/mvc/tools/tools-jobs.js +++ b/static/scripts/mvc/tools/tools-jobs.js @@ -145,14 +145,12 @@ } // check number of inputs - if (n > 1) { - if (batch_n === -1) { - batch_n = n; - } else { - if (batch_n !== n) { - this._foundError(input_id, 'Please make sure that you select the same number or a single input for all batch mode fields. This field contains ' + n + ' selection(s) while a previous field contains ' + batch_n + '.'); - return false; - } + if (batch_n === -1) { + batch_n = n; + } else { + if (batch_n !== n) { + this._foundError(input_id, 'Please make sure that you select the same number of inputs for all batch mode fields. This field contains ' + n + ' selection(s) while a previous field contains ' + batch_n + '.'); + return false; } } } diff -r 963fb2afb6d2876e0e9f1a2b7021dce18e6ef0d4 -r 9c02b22ca58f3c59da8cbfd73678b9ac9b4e9216 static/scripts/mvc/tools/tools-select-content.js --- a/static/scripts/mvc/tools/tools-select-content.js +++ b/static/scripts/mvc/tools/tools-select-content.js @@ -190,7 +190,7 @@ // prepare result dict var result = { - batch : !this.options.multiple && (this.current == 'collection' || id_list.length > 1), + batch : !this.options.multiple && this.current != 'single', values : [] } diff -r 963fb2afb6d2876e0e9f1a2b7021dce18e6ef0d4 -r 9c02b22ca58f3c59da8cbfd73678b9ac9b4e9216 static/scripts/packed/mvc/tools/tools-jobs.js --- a/static/scripts/packed/mvc/tools/tools-jobs.js +++ b/static/scripts/packed/mvc/tools/tools-jobs.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/tools/tools-template"],function(b,a){return Backbone.Model.extend({initialize:function(d,c){this.app=d;this.options=b.merge(c,this.optionsDefault)},submit:function(){var c=this;var d={tool_id:this.app.options.id,inputs:this.app.tree.finalize()};this.app.reset();if(!this._validation(d)){console.debug("tools-jobs::submit - Submission canceled. Validation failed.");return}console.debug(d);this.app.modal.show({title:"Please wait...",body:"progress",closing_events:true,buttons:{Close:function(){c.app.modal.hide()}}});b.request({type:"POST",url:galaxy_config.root+"api/tools",data:d,success:function(e){c.app.modal.hide();c.app.message(a.success(e));c._refreshHdas()},error:function(e,g){c.app.modal.hide();if(e&&e.message&&e.message.data){var h=c.app.tree.matchResponse(e.message.data);for(var f in h){c._foundError(f,h[f]);break}}else{console.debug(e);c.app.modal.show({title:"Job submission failed",body:a.error(d),buttons:{Close:function(){c.app.modal.hide()}}})}}})},_foundError:function(c,d){var e=this.app.element_list[c];e.error(d||"Please verify this parameter.");$(this.app.container).animate({scrollTop:e.$el.offset().top-20},500)},_validation:function(h){var d=h.inputs;var m=-1;var i=null;for(var k in d){var f=d[k];var l=this.app.tree.match(k);var e=this.app.field_list[l];var j=this.app.input_list[l];if(!l||!j||!e){console.debug("tools-jobs::_validation - Retrieving input objects failed.");continue}if(!j.optional&&e.validate&&!e.validate()){this._foundError(l);return false}if(f&&f.batch){var g=f.values.length;var c=null;if(g>0){c=f.values[0]&&f.values[0].src}if(c){if(i===null){i=c}else{if(i!==c){this._foundError(l,"Please select either dataset or dataset list fields for all batch mode fields.");return false}}}if(g>1){if(m===-1){m=g}else{if(m!==g){this._foundError(l,"Please make sure that you select the same number or a single input for all batch mode fields. This field contains "+g+" selection(s) while a previous field contains "+m+".");return false}}}}}return true},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})}); \ No newline at end of file +define(["utils/utils","mvc/tools/tools-template"],function(b,a){return Backbone.Model.extend({initialize:function(d,c){this.app=d;this.options=b.merge(c,this.optionsDefault)},submit:function(){var c=this;var d={tool_id:this.app.options.id,inputs:this.app.tree.finalize()};this.app.reset();if(!this._validation(d)){console.debug("tools-jobs::submit - Submission canceled. Validation failed.");return}console.debug(d);this.app.modal.show({title:"Please wait...",body:"progress",closing_events:true,buttons:{Close:function(){c.app.modal.hide()}}});b.request({type:"POST",url:galaxy_config.root+"api/tools",data:d,success:function(e){c.app.modal.hide();c.app.message(a.success(e));c._refreshHdas()},error:function(e,g){c.app.modal.hide();if(e&&e.message&&e.message.data){var h=c.app.tree.matchResponse(e.message.data);for(var f in h){c._foundError(f,h[f]);break}}else{console.debug(e);c.app.modal.show({title:"Job submission failed",body:a.error(d),buttons:{Close:function(){c.app.modal.hide()}}})}}})},_foundError:function(c,d){var e=this.app.element_list[c];e.error(d||"Please verify this parameter.");$(this.app.container).animate({scrollTop:e.$el.offset().top-20},500)},_validation:function(h){var d=h.inputs;var m=-1;var i=null;for(var k in d){var f=d[k];var l=this.app.tree.match(k);var e=this.app.field_list[l];var j=this.app.input_list[l];if(!l||!j||!e){console.debug("tools-jobs::_validation - Retrieving input objects failed.");continue}if(!j.optional&&e.validate&&!e.validate()){this._foundError(l);return false}if(f&&f.batch){var g=f.values.length;var c=null;if(g>0){c=f.values[0]&&f.values[0].src}if(c){if(i===null){i=c}else{if(i!==c){this._foundError(l,"Please select either dataset or dataset list fields for all batch mode fields.");return false}}}if(m===-1){m=g}else{if(m!==g){this._foundError(l,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains "+g+" selection(s) while a previous field contains "+m+".");return false}}}}return true},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})}); \ No newline at end of file diff -r 963fb2afb6d2876e0e9f1a2b7021dce18e6ef0d4 -r 9c02b22ca58f3c59da8cbfd73678b9ac9b4e9216 static/scripts/packed/mvc/tools/tools-select-content.js --- a/static/scripts/packed/mvc/tools/tools-select-content.js +++ b/static/scripts/packed/mvc/tools/tools-select-content.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(k,g){this.app=k;this.options=g;var f=this;this.setElement("<div/>");this.list={};var j=[];if(!g.multiple){this.current="single"}else{this.current="multiple"}if(!g.multiple){j.push({icon:"fa-file-o",label:"Single dataset",value:"single"});this.select_single=new e.Select.View({onchange:function(){f.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}j.push({icon:"fa-files-o",label:"Multiple datasets",value:"multiple"});this.select_multiple=new e.Select.View({multiple:true,onchange:function(){f.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"};j.push({icon:"fa-folder-o",label:"List of datasets",value:"collection"});this.select_collection=new e.Select.View({onchange:function(){f.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"};this.button_type=new e.RadioButton.View({value:this.current,data:j,onchange:function(i){f.current=i;f.refresh();f.trigger("change")}});this.$batch=$(a.batchMode());this.$el.append(c.wrap(this.button_type.$el));for(var h in this.list){this.$el.append(this.list[h].field.$el)}this.$el.append(this.$batch);this.update(g.data);this.refresh();this.on("change",function(){if(g.onchange){g.onchange(f.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){var l=[];for(var j in g.hda){var k=g.hda[j];l.push({label:k.hid+": "+k.name,value:k.id})}var f=[];for(var j in g.hdca){var h=g.hdca[j];f.push({label:h.hid+": "+h.name,value:h.id})}this.select_single&&this.select_single.update(l);this.select_multiple.update(l);this.select_collection.update(f);this.app.content.add(g)},value:function(m){if(m&&m.values){try{var l=[];for(var h in m.values){l.push(m.values[h].id)}if(m&&m.values.length>0&&m.values[0].src=="hcda"){this.current="collection";this.select_collection.value(l[0])}else{if(l.length>1||this.options.multiple){this.current="multiple";this.select_multiple.value(l)}else{this.current="single";this.select_single.value(l[0])}}this.refresh();var g=this._select();if(!g.validate()){g.value(g.first())}}catch(k){console.debug("tools-select-content::value() - Skipped.")}}var j=this._select().value();if(!(j instanceof Array)){j=[j]}var f={batch:!this.options.multiple&&(this.current=="collection"||j.length>1),values:[]};for(var h in j){f.values.push({id:j[h],src:this.list[this.current].type})}return f},validate:function(){return this._select().validate()},refresh:function(){for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this.current!="single"&&!this.options.multiple){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field}});return{View:d}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(k,g){this.app=k;this.options=g;var f=this;this.setElement("<div/>");this.list={};var j=[];if(!g.multiple){this.current="single"}else{this.current="multiple"}if(!g.multiple){j.push({icon:"fa-file-o",label:"Single dataset",value:"single"});this.select_single=new e.Select.View({onchange:function(){f.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}j.push({icon:"fa-files-o",label:"Multiple datasets",value:"multiple"});this.select_multiple=new e.Select.View({multiple:true,onchange:function(){f.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"};j.push({icon:"fa-folder-o",label:"List of datasets",value:"collection"});this.select_collection=new e.Select.View({onchange:function(){f.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"};this.button_type=new e.RadioButton.View({value:this.current,data:j,onchange:function(i){f.current=i;f.refresh();f.trigger("change")}});this.$batch=$(a.batchMode());this.$el.append(c.wrap(this.button_type.$el));for(var h in this.list){this.$el.append(this.list[h].field.$el)}this.$el.append(this.$batch);this.update(g.data);this.refresh();this.on("change",function(){if(g.onchange){g.onchange(f.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){var l=[];for(var j in g.hda){var k=g.hda[j];l.push({label:k.hid+": "+k.name,value:k.id})}var f=[];for(var j in g.hdca){var h=g.hdca[j];f.push({label:h.hid+": "+h.name,value:h.id})}this.select_single&&this.select_single.update(l);this.select_multiple.update(l);this.select_collection.update(f);this.app.content.add(g)},value:function(m){if(m&&m.values){try{var l=[];for(var h in m.values){l.push(m.values[h].id)}if(m&&m.values.length>0&&m.values[0].src=="hcda"){this.current="collection";this.select_collection.value(l[0])}else{if(l.length>1||this.options.multiple){this.current="multiple";this.select_multiple.value(l)}else{this.current="single";this.select_single.value(l[0])}}this.refresh();var g=this._select();if(!g.validate()){g.value(g.first())}}catch(k){console.debug("tools-select-content::value() - Skipped.")}}var j=this._select().value();if(!(j instanceof Array)){j=[j]}var f={batch:!this.options.multiple&&this.current!="single",values:[]};for(var h in j){f.values.push({id:j[h],src:this.list[this.current].type})}return f},validate:function(){return this._select().validate()},refresh:function(){for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this.current!="single"&&!this.options.multiple){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field}});return{View:d}}); \ 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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galaxy-commits November 2014